diff --git a/.gitignore b/.gitignore
index c6fdfc4d387f8be1bb3a4f51a73230aabcc9b02b..943855c51e4610211c89b47d4642d127f5acb330 100644
--- a/.gitignore
+++ b/.gitignore
@@ -47,4 +47,4 @@ src/doc/development/api/xml/*.jar
# data directories
-CaosDBFileSystem
+LinkAheadFileSystem
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 885b791421f5ddef4014692409e9358d7e6c507d..17beba26576e4ac430e41b3beb1e47812ba14b6e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,5 +1,5 @@
#
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -23,7 +23,9 @@
#
variables:
- DEPLOY_REF: dev
+ # TODO Reset to "dev"
+ DEPLOY_REF: f-linkahead-rename
+ # TODO Rename to linkahead
CI_REGISTRY_IMAGE: $CI_REGISTRY/caosdb/src/caosdb-server/caosdb-server-testenv:latest
GIT_SUBMODULE_STRATEGY: normal
@@ -134,6 +136,7 @@ trigger_inttest:
CPPINT: $TMP_CPPINT
MYSQLBACKEND: $TMP_MYSQLBACKEND
trigger:
+ # TODO Rename to linkahead
project: caosdb/src/caosdb-deploy
branch: $DEPLOY_REF
strategy: depend
diff --git a/.gitlab/merge_request_templates/Default.md b/.gitlab/merge_request_templates/Default.md
index 3629e0ca3695000863d8c254516f64bf59a7bf60..0d4d8e2391da91f15f09f37e91f1cf931b972e24 100644
--- a/.gitlab/merge_request_templates/Default.md
+++ b/.gitlab/merge_request_templates/Default.md
@@ -21,7 +21,7 @@ specs, finding more corner cases, concrete questions)?*
Please, prepare your MR for a review. Be sure to write a summary and a focus and create gitlab
comments for the reviewer. They should guide the reviewer through the changes, explain your changes
and also point out open questions. For further good practices have a look at [our review
-guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md)
+guidelines](https://gitlab.com/linkahead/linkahead/-/blob/dev/REVIEW_GUIDELINES.md)
- [ ] All automated tests pass
- [ ] Reference related issues
@@ -49,7 +49,7 @@ guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md)
- [ ] In-code documentation and comments are up-to-date.
- [ ] Check: Are there specifications? Are they satisfied?
-For further good practices have a look at [our review guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md).
+For further good practices have a look at [our review guidelines](https://gitlab.com/linkahead/linkahead/-/blob/dev/REVIEW_GUIDELINES.md).
/assign me
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a4d71f73495699c50b38ba204b3a8275e57a9546..943b0ef2a43d71e9dd56003e543fb1522e424059 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,6 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed ###
+* Renamed CaosDB to LinkAhead.
* The default behavior of the query `FIND SomeName [...]` (as well as COUNT and SELECT) is being
made configurable and changes:
* `FIND SomeName` will be interpreted as `FIND <FIND_QUERY_DEFAULT_ROLE>
@@ -246,7 +247,7 @@ process. It is identical to v0.7.1
### Added
-* Endpoint for CaosDB GRPC API 0.1 (see https://gitlab.com/caosdb-proto.git for
+* Endpoint for LinkAhead GRPC API 0.1 (see https://gitlab.com/caosdb-proto.git for
more).
Authentication is supported via a Basic scheme, using the well-known
"authentication" header.
@@ -369,7 +370,7 @@ process. It is identical to v0.7.1
* New query functionality: `ANY VERSION OF` modifier. E.g. `FIND ANY VERSION OF
RECORD WITH pname=val` returns all current and old versions of records where
`pname=val`. For further information, examples and limitations see the wiki
- page on [CQL](https://gitlab.com/caosdb/caosdb/-/wikis/manuals/CQL/CaosDB%20Query%20Language)
+ page on [CQL](https://gitlab.com/caosdb/caosdb/-/wikis/manuals/CQL/LinkAhead%20Query%20Language)
* New server property `SERVER_SIDE_SCRIPTING_BIN_DIRS` which accepts a comma or
space separated list as values. The server looks for scripts in all
directories in the order or the list and uses the first matching file.
diff --git a/CITATION.cff b/CITATION.cff
index a45e422c288822d0c34e1f5df2bcb83ceedd8e23..1fdb5ba825be628e3fe25458918e99b65f974d19 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -22,7 +22,7 @@ authors:
- family-names: Luther
given-names: Stefan
orcid: https://orcid.org/0000-0001-7214-8125
-title: "CaosDB - Server"
+title: "LinkAhead - Server"
version: 0.10.0
doi: 10.3390/data4020083
date-released: 2023-06-02
diff --git a/DEPENDENCIES.md b/DEPENDENCIES.md
index fbcb186e45ff5bff20ca7ff20fa321f547048527..7e062cb5db7f918ab86ceeca7c91d44200549622 100644
--- a/DEPENDENCIES.md
+++ b/DEPENDENCIES.md
@@ -2,8 +2,8 @@
## For Building and Running the Server
-* `>=caosdb-proto 0.3.0`
-* `>=caosdb-mysqlbackend 5.0.0`
+* `>=linkahead-proto 0.3.0`
+* `>=linkahead-mysqlbackend 5.0.0`
* `>=Java 11`
* `>=Apache Maven 3.6.0`
* `>=Make 4.2`
@@ -13,7 +13,7 @@
## For Deploying a Web User Interface (optional)
-* `>=caosdb-webui 0.8.0`
+* `>=linkahead-webui 0.8.0`
## For Building the Documentation (optional)
diff --git a/Doxyfile b/Doxyfile
index 9d12b22c58d370bfe365f87112bcd54561c42c99..83cafd69eadfdad5c4785de9b8dd524d24222f54 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -32,7 +32,7 @@ DOXYFILE_ENCODING = UTF-8
# title of most generated pages and in a few other places.
# The default value is: My Project.
-PROJECT_NAME = "CaosDB Server"
+PROJECT_NAME = "LinkAhead Server"
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
diff --git a/FEATURES.md b/FEATURES.md
index 2c046daee0518eb12e4de807a7ffe165c74d8664..f4af2923f853532130603f5784d64402f54e39e6 100644
--- a/FEATURES.md
+++ b/FEATURES.md
@@ -1,21 +1,21 @@
# Features
-* The CaosDB Server implements a CaosDB GRPC API Endpoint (v0.3.0)
+* The LinkAhead Server implements a LinkAhead GRPC API Endpoint (v0.3.0)
Authentication is supported via a Basic scheme, using the well-known
"authentication" header.
Notable limitations of the current implementation of the API:
* It is currently not possible to mix retrievals
- (caosdb.entity.v1.RetrieveRequest) with any other transaction type - so
+ (linkahead.entity.v1.RetrieveRequest) with any other transaction type - so
transaction are either read-only or write-only. The server throws an error
if it finds mixed read/write transactions.
* It is currently not possible to have more that one query
- (caosdb.entity.v1.Query) in a single transaction. The server throws an
+ (linkahead.entity.v1.Query) in a single transaction. The server throws an
error if it finds more than one query.
* Legacy XML/HTTP API (Deprecated)
-* Deployment of caosdb-webui (>=0.8.0)
+* Deployment of linkahead-webui (>=0.8.0)
* Server-side Scripting API (v0.1)
-* CaosDB Query Language Processor
-* CaosDB FileSystem
+* LinkAhead Query Language Processor
+* LinkAhead FileSystem
* User Management, Authentication and Authorization
* Internal authentication service
* Authentication via an external service (PAM, LDAP)
diff --git a/Makefile b/Makefile
index 29b7d5a51cb110e35f999da0a7c6b366b5bd0d05..9f629c33f60c80d345d34b5119d4379709349938 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -23,8 +23,8 @@
# ** end header
#
-CAOSDB_SERVER_VERSION ?= $(shell mvn org.apache.maven.plugins:maven-help-plugin:3.1.0:evaluate -Dexpression=project.version -q -DforceStdout)
-CAOSDB_COMMAND_LINE_OPTIONS ?=
+LINKAHEAD_SERVER_VERSION ?= $(shell mvn org.apache.maven.plugins:maven-help-plugin:3.1.0:evaluate -Dexpression=project.version -q -DforceStdout)
+LINKAHEAD_COMMAND_LINE_OPTIONS ?=
SHELL:=/bin/bash
JPDA_PORT ?= 9000
JMX_PORT ?= 9090
@@ -33,7 +33,7 @@ compile: print-version easy-units
mvn compile
print-version:
- @echo "This is CaosDB $(CAOSDB_SERVER_VERSION)"
+ @echo "This is LinkAhead $(LINKAHEAD_SERVER_VERSION)"
runserver: print-version
mvn exec:java@run
@@ -42,14 +42,14 @@ run: compile
mvn exec:java@run
run-debug: jar
- java -Xrunjdwp:transport=dt_socket,address=0.0.0.0:$(JPDA_PORT),server=y,suspend=n -Dcaosdb.debug=true -jar target/caosdb-server.jar $(CAOSDB_COMMAND_LINE_OPTIONS)
+ java -Xrunjdwp:transport=dt_socket,address=0.0.0.0:$(JPDA_PORT),server=y,suspend=n -Dlinkahead.debug=true -jar target/linkahead-server.jar $(LINKAHEAD_COMMAND_LINE_OPTIONS)
run-debug-single:
- java -Dcom.sun.management.jmxremote -Dcom.sun.management.jmxremote.port=$(JMX_PORT) -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false -Xrunjdwp:transport=dt_socket,address=0.0.0.0:$(JPDA_PORT),server=y,suspend=n -Dcaosdb.debug=true -jar target/caosdb-server.jar $(CAOSDB_COMMAND_LINE_OPTIONS)
+ java -Dcom.sun.management.jmxremote -Dcom.sun.management.jmxremote.port=$(JMX_PORT) -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false -Xrunjdwp:transport=dt_socket,address=0.0.0.0:$(JPDA_PORT),server=y,suspend=n -Dlinkahead.debug=true -jar target/linkahead-server.jar $(LINKAHEAD_COMMAND_LINE_OPTIONS)
run-single:
- java -jar target/caosdb-server.jar $(CAOSDB_COMMAND_LINE_OPTIONS)
+ java -jar target/linkahead-server.jar $(LINKAHEAD_COMMAND_LINE_OPTIONS)
formatting:
mvn fmt:format
@@ -59,14 +59,14 @@ formatting:
jar: print-version easy-units
mvn -e package -DskipTests
@pushd target ; \
- ln -s caosdb-server-$(CAOSDB_SERVER_VERSION)-jar-with-dependencies.jar caosdb-server.jar; \
+ ln -s linkahead-server-$(LINKAHEAD_SERVER_VERSION)-jar-with-dependencies.jar linkahead-server.jar; \
popd
antlr:
mvn antlr4:antlr4
test: print-version easy-units
- MAVEN_DEBUG_OPTS="-Xdebug -Xnoagent -Djava.compiler=NONE -Dcaosdb.debug=true -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=0.0.0.0:$(JPDA_PORT)"
+ MAVEN_DEBUG_OPTS="-Xdebug -Xnoagent -Djava.compiler=NONE -Dlinkahead.debug=true -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=0.0.0.0:$(JPDA_PORT)"
mvn test -X
test_misc:
@@ -84,15 +84,15 @@ clean-antlr:
.PHONY: run-server-screen
run-server-screen:
- @if test "$$(screen -ls | grep -c 'caosdb-screen')" -eq "1"; then \
+ @if test "$$(screen -ls | grep -c 'linkahead-screen')" -eq "1"; then \
echo "server is probably running. try 'screen -ls'"; \
exit 1 ; \
fi
# start and wait for server
- @screen -L -S caosdb-screen -t server -d -m -A make run
+ @screen -L -S linkahead-screen -t server -d -m -A make run
@sleep 2
@while [ 1 -eq 1 ] ; do \
- screen -S caosdb-screen -X hardcopy .screen.log || break ; \
+ screen -S linkahead-screen -X hardcopy .screen.log || break ; \
[ $$(grep -c "org.restlet.ext.jetty.JettyServerHelper start" .screen.log) -eq 0 ] || break ; \
done; \
@@ -100,20 +100,20 @@ run-server-screen:
.PHONY: stop-server-screen
stop-server-screen:
# stop screen session with server
- @screen -S caosdb-screen -X hardcopy screen.log || true
- @screen -S caosdb-screen -p server -X stuff "^C"
+ @screen -S linkahead-screen -X hardcopy screen.log || true
+ @screen -S linkahead-screen -p server -X stuff "^C"
.PHONY: run-debug-screen
run-debug-screen:
- @if test "$$(screen -ls | grep -c 'caosdb-debug-screen')" -eq "1"; then \
+ @if test "$$(screen -ls | grep -c 'linkahead-debug-screen')" -eq "1"; then \
echo "server is probably running. try 'screen -ls'"; \
exit 1 ; \
fi
# start and wait for server
- @screen -L -S caosdb-debug-screen -t server -d -m -A make run-debug
+ @screen -L -S linkahead-debug-screen -t server -d -m -A make run-debug
@sleep 2
@while [ 1 -eq 1 ] ; do \
- screen -S caosdb-debug-screen -X hardcopy .screen.log || break ; \
+ screen -S linkahead-debug-screen -X hardcopy .screen.log || break ; \
[ $$(grep -c "org.restlet.ext.jetty.JettyServerHelper start" .screen.log) -eq 0 ] || break ; \
done; \
@@ -121,8 +121,8 @@ run-debug-screen:
.PHONY: stop-debug-screen
stop-debug-screen:
# stop screen session with debug server
- @screen -S caosdb-debug-screen -X hardcopy screen.log || true
- @screen -S caosdb-debug-screen -p server -X stuff "^C"
+ @screen -S linkahead-debug-screen -X hardcopy screen.log || true
+ @screen -S linkahead-debug-screen -p server -X stuff "^C"
.m2-local:
mkdir .m2-local
diff --git a/README.md b/README.md
index 3aac5df2153281a9ef67a203956114aad1641b18..c98bdc63be8214c9ca7223dcd22d64e9d52fb74d 100644
--- a/README.md
+++ b/README.md
@@ -3,8 +3,8 @@
## Welcome
-This is the **CaosDB Java Server** repository and a part of the
-CaosDB project.
+This is the **LinkAhead Java Server** repository and a part of the
+LinkAhead project.
## Setup
@@ -14,30 +14,30 @@ setup this code.
## Further Reading
-Please refer to the [official documentation](https://docs.indiscale.com/caosdb-server/) for more information.
+Please refer to the [official documentation](https://docs.linkahead.org/linkahead-server/) for more information.
## Contributing
-Thank you very much to all contributers—[past, present](https://gitlab.com/caosdb/caosdb/-/blob/dev/HUMANS.md), and prospective ones.
+Thank you very much to all contributers—[past, present](https://gitlab.com/linkahead/linkahead/-/blob/dev/HUMANS.md), and prospective ones.
### Code of Conduct
-By participating, you are expected to uphold our [Code of Conduct](https://gitlab.com/caosdb/caosdb/-/blob/dev/CODE_OF_CONDUCT.md).
+By participating, you are expected to uphold our [Code of Conduct](https://gitlab.com/linkahead/linkahead/-/blob/dev/CODE_OF_CONDUCT.md).
### How to Contribute
* You found a bug, have a question, or want to request a feature? Please
-[create an issue](https://gitlab.com/caosdb/caosdb-server/-/issues).
+[create an issue](https://gitlab.com/linkahead/linkahead-server/-/issues).
* You want to contribute code? Please fork the repository and create a merge
request in GitLab and choose this repository as target. Make sure to select
"Allow commits from members who can merge the target branch" under Contribution
when creating the merge request. This allows our team to work with you on your request.
-- If you have a suggestion for the [documentation](https://docs.indiscale.com/caosdb-server/),
+- If you have a suggestion for the [documentation](https://docs.linkahead.org/linkahead-server/),
the preferred way is also a merge request as describe above (the documentation resides in `src/doc`).
However, you can also create an issue for it.
-- You can also contact us at **info (AT) caosdb.org** and join the
- CaosDB community on
- [#caosdb:matrix.org](https://matrix.to/#/!unwwlTfOznjEnMMXxf:matrix.org).
+- You can also contact us at **info (AT) linkahead.org** and join the
+ LinkAhead community on
+ [#linkahead:matrix.org](https://matrix.to/#/!unwwlTfOznjEnMMXxf:matrix.org).
## License
diff --git a/README_CONFIGURATION.md b/README_CONFIGURATION.md
index 27045eea4523c5009e246fe506ec6319965d8e9f..06b36ebd7dc6a5d9d6faba0a13328e3190659f2e 100644
--- a/README_CONFIGURATION.md
+++ b/README_CONFIGURATION.md
@@ -9,7 +9,7 @@ The default configuration can be overriden by
1. the file ./conf/ext/server.conf
2. any file in ./conf/ext/server.conf.d/ in (approximately?) alphabetical order
-3. environment variables with the prefix `CAOSDB_CONFIG_`
+3. environment variables with the prefix `LINKAHEAD_CONFIG_`
in this order.
diff --git a/README_SETUP.md b/README_SETUP.md
index acb3a79ad256fbba6a0d0a69887bb7c7ba7b28b9..b52c64edd970a23c307df499da508dd91e0189e3 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -1,11 +1,11 @@
-# Getting Started with the CaosDB Server
+# Getting Started with the LinkAhead Server
Here, you find information on requirements, the installation, configuration and
-more. Note, that building the CaosDB Server from the sources and maintaining
+more. Note, that building the LinkAhead Server from the sources and maintaining
the server requires the knowledge/skill of an experienced Linux administrator.
**Note:** If you are looking for a quick and easy way to get startet, check
-out [the docker deployment](https://gitlab.indiscale.com/caosdb/src/caosdb-docker).
+out [the docker deployment](https://gitlab.com/linkahead/linkahead-docker).
## Requirements
@@ -37,9 +37,9 @@ On Fedora, the required packages can be installed with:
#### Web UI ###
- If the WebUI shall run, check out the respective submodule: `git submodule
- update --init caosdb-webui`
+ update --init linkahead-webui`
- Then configure and compile it according to its
- [documentation](https://docs.indiscale.com/caosdb-webui/getting_started.html).
+ [documentation](https://docs.linkahead.org/linkahead-webui/getting_started.html).
#### PAM ###
Authentication via PAM is possible, for this the PAM development library must be
@@ -50,11 +50,11 @@ installed and the pam user tool must be compiled:
- If you want, you can run a test now: `./pam_authentication.sh asdf` asks for a password for user
`asdf`. If no such user exists or the wrong passowrd is entered, it print `[FAILED]` and return
with a non-zero exit code.
-- If you want to run the CaosDB server without root privilege, you need to use
- the setuid bit for the binary. For example, if the user `caosdb` runs the
+- If you want to run the LinkAhead server without root privilege, you need to use
+ the setuid bit for the binary. For example, if the user `linkahead` runs the
server process the permissions of `bin/pam_authentication` should be the
following:
- `-rwsr-x--- 1 root caosdb pam_authentication`
+ `-rwsr-x--- 1 root linkahead pam_authentication`
##### Troubleshooting ####
If `make` fails with `pam_authentication.c:4:31: fatal error:
@@ -69,7 +69,7 @@ After a fresh clone of the repository, this is what you need to setup the
server:
1. Install the `proto` submodule (and submodules for those extensions you want, see above):
- `git submodule update --init caosdb-proto`
+ `git submodule update --init linkahead-proto`
2. Compile the server with `make compile`. This may take a while and there
needs to be an internet connection as packages are downloaded to be
integrated in the java file.
@@ -78,19 +78,19 @@ server:
3. Create an SSL certificate somewhere with a `Java Key Store` file. For
self-signed certificates (not recommended for production use) you can do:
- `mkdir certificates; cd certificates`
- - `keytool -genkey -keyalg RSA -alias selfsigned -keystore caosdb.jks -validity 375 -keysize 2048 -ext san=dns:localhost`
+ - `keytool -genkey -keyalg RSA -alias selfsigned -keystore linkahead.jks -validity 375 -keysize 2048 -ext san=dns:localhost`
Replace `localhost` by your host name, if you want.
- - `keytool -importkeystore -srckeystore caosdb.jks -destkeystore caosdb.p12 -deststoretype PKCS12 -srcalias selfsigned`
- - Export the public part only: `openssl pkcs12 -in caosdb.p12 -nokeys -out cert.pem`.
+ - `keytool -importkeystore -srckeystore linkahead.jks -destkeystore linkahead.p12 -deststoretype PKCS12 -srcalias selfsigned`
+ - Export the public part only: `openssl pkcs12 -in linkahead.p12 -nokeys -out cert.pem`.
The resulting `cert.pem` can safely be given to users to allow ssl
verification.
- You can check the content of the certificate with `openssl x509 -in cert.pem -text`
Alternatively, you can create a keystore from certificate files that you already have:
- `openssl pkcs12 -export -inkey privkey.pem -in fullchain.pem -out all-certs.pkcs12`
- - `keytool -importkeystore -srckeystore all-certs.pkcs12 -srcstoretype PKCS12 -deststoretype pkcs12 -destkeystore caosdb.jks`
+ - `keytool -importkeystore -srckeystore all-certs.pkcs12 -srcstoretype PKCS12 -deststoretype pkcs12 -destkeystore linkahead.jks`
4. Install/configure the MySQL back-end: see the `README_SETUP.md` of the
- `caosdb-mysqlbackend` repository
+ `linkahead-mysqlbackend` repository
5. Create an authtoken config (e.g. copy `conf/core/authtoken.example.yaml` to
`conf/ext/authtoken.yml` and change it)
6. If any of the settings in `conf/core/server.conf` do not fit your needs, create
@@ -98,7 +98,7 @@ server:
* Setup for MySQL back-end:
specify the fields `MYSQL_USER_NAME`, `MYSQL_USER_PASSWORD`,
`MYSQL_DATABASE_NAME`, and `MYSQL_HOST`.
- * Choose the host and ports under which CaosDB will be accessible. The host
+ * Choose the host and ports under which LinkAhead will be accessible. The host
is the IP address the server should listen on. Blank (the default) means
all interfaces, and `127.0.0.1` means only localhost.
* Setup the SSL certificate: Assuming that there is an appropriate `Java Key
@@ -108,8 +108,8 @@ server:
certificate passwords are stored in plaintext.
* Set the path to the authtoken config (see step 4)
* Set the file system paths:
- - `FILE_SYSTEM_ROOT`: The root for all the files managed by CaosDB.
- - `DROP_OFF_BOX`: Files can be put here for insertion into CaosDB.
+ - `FILE_SYSTEM_ROOT`: The root for all the files managed by LinkAhead.
+ - `DROP_OFF_BOX`: Files can be put here for insertion into LinkAhead.
- `TMP_FILES`: Temporary files go here, for example during script
execution or when uploading or moving files.
- `SHARED_FOLDER`: Folder for sharing files via cryptographic tokens,
@@ -118,23 +118,23 @@ server:
of directories (relative or absolute) where the server will be looking
for executables which are then callable as server-side scripts. By
default this list only contains `./scripting/bin`. If you want to
- include e.g. scripts which are maintained as part of the caosdb-webui
+ include e.g. scripts which are maintained as part of the linkahead-webui
repository (because they are intended for usage by the webui), you
- should add `./caosdb-webui/sss_bin/` as well.
+ should add `./linkahead-webui/sss_bin/` as well.
- `INSERT_FILES_IN_DIR_ALLOWED_DIRS`: add mounted filesystems here that
- shall be accessible by CaosDB
+ shall be accessible by LinkAhead
* Maybe set another `SESSION_TIMEOUT_MS`.
* See also [CONFIGURATION.rst](src/doc/administration/configuration.rst)
7. Copy `conf/core/usersources.ini.template` to `conf/ext/usersources.ini`.
* You can skip this if you do not want to use an external authentication.
- Local users (CaosDB realm) are always available.
+ Local users (`CaosDB` realm) are always available.
* Define the users/groups who you want to include/exclude.
* Assign at least one user the `administration` role.
- * For example, if the admin user is called `caosdb`, there should be the
+ * For example, if the admin user is called `linkahead`, there should be the
following lines:
```
- include.user = caosdb
- user.caosdb.roles = administration
+ include.user = linkahead
+ user.linkahead.roles = administration
```
* It is important that the file complies with the ini file specification.
Especially that there are no `properties` (aka `keys`) without a
@@ -149,7 +149,7 @@ Done!
`$ make run`
-This can take a while. Once you see `Starting org.caosdb.server.CaosDBServer
+This can take a while. Once you see `Starting org.linkahead.server.LinkAheadServer
application` the server is ready and you can try it out by connecting with a
client, e.g. the web client, if you installed it. Typically, you just need to
type `https://localhost:10443` in your Browser, assuming you used 10443 as port.
@@ -212,6 +212,21 @@ Done!
## Migration
+### From 0.9 to 0.10
+
+CaosDB is now LinkAhead! This name changes leads to a few necessary changes on the administrator
+side:
+
+* All configuration environment variables should change from `CAOSDB_CONFIG_...` to
+ `LINKAHEAD_CONFIG_...`. The old environment variables will remain deprecated but valid for some
+ time, but mixing old and new variables is forbidden: If you rename one, you have to rename all.
+* If you install LinkAhead from git, the submodules have changed their names, and most probably also
+ the remotes have different URLs now.
+* The default paths for the file system have changed. Make sure that your paths match your
+ configuration (see `server.conf` for the new default paths).
+* The Java class structure was renamed from `org.caosdb.server....` to `org.linkahead.server....`.
+ This may be relevant for you if you customized the `usersources.ini` or the logging configuration.
+
### From 0.1 to 0.2
A major change in the code is the renaming of the java packages (from
@@ -254,21 +269,21 @@ pip3 install .
### Installation without or with restricted internet connection on the host system
-It is of course possible to install CaosDB on servers which do not have an
+It is of course possible to install LinkAhead on servers which do not have an
internet connection or only have limited access to the internet.
-However, maven, which is used to build the CaosDB server, typically accesses
+However, maven, which is used to build the LinkAhead server, typically accesses
the internet very often, and some reconfiguration might be necessary to prevent
timeout issues and similar headache.
A recommendation to proceed is:
-- Clone the repositories (caosdb-server, caosdb-mysqlbackend and subrepository
- caosdb-webui) on a second machine that has internet connection.
-- Run `make install` and `make run` in the caosdb-server repository. This will
+- Clone the repositories (linkahead-server, linkahead-mysqlbackend and subrepository
+ linkahead-webui) on a second machine that has internet connection.
+- Run `make install` and `make run` in the linkahead-server repository. This will
download all required dependencies and setup all maven-related artifacts in
a folder called `.m2` typically located in the home directory.
- In addition to copying over the repositories for the server, mysqlbackend and
webui to the target host machine, also copy the complete `.m2` folder to the
- **home directory of the user that is running the CaosDB server**.
+ **home directory of the user that is running the LinkAhead server**.
- On the host machine, open the file `pom.xml` in the server repository.
- Look for the section `<repositories>`. There should be a `<respository>` with
`<id>local-maven-repo</id>`. It should be moved on top of the list of
@@ -285,7 +300,7 @@ Make sure that you:
- Installed the WebUI according to the section [Web UI]
- Run `make install` in the webui sub folder
-### How can I run the CaosDB server using ports 443 and 80?
+### How can I run the LinkAhead server using ports 443 and 80?
On standard linux setups, ports 443 and 80 cannot be opened by non-root processes.
@@ -303,6 +318,6 @@ Using authbind is a simple solution that is briefly described here:
- Install the package authbind
- Create (empty) files `/etc/authbind/byport/80` (and `.../443`), e.g. using `touch`
- Grant execution permissions for the user who runs the server to the new files.
-- Run the CaosDB server using authbind with the `--deep` option:
+- Run the LinkAhead server using authbind with the `--deep` option:
`authbind --deep make run`. The `--deep` option is necessary because the
server starts a subprocess which actually opens the ports.
diff --git a/RELEASE_GUIDELINES.md b/RELEASE_GUIDELINES.md
index 1b5ae48906d4e8328064ecaf7e7c4f7a4a2bd20f..60a32fd8cd611a8dd25cc875011143542726f1d1 100644
--- a/RELEASE_GUIDELINES.md
+++ b/RELEASE_GUIDELINES.md
@@ -1,8 +1,8 @@
-# Release Guidelines for the CaosDB Server
+# Release Guidelines for the LinkAhead Server
This document specifies release guidelines in addition to the general release
-guidelines of the CaosDB Project
-([RELEASE_GUIDELINES.md](https://gitlab.com/caosdb/caosdb/blob/dev/RELEASE_GUIDELINES.md))
+guidelines of the LinkAhead Project
+([RELEASE_GUIDELINES.md](https://gitlab.com/linkahead/linkahead/blob/dev/RELEASE_GUIDELINES.md))
## General Prerequisites
@@ -38,11 +38,11 @@ guidelines of the CaosDB Project
* `CHANGELOG.md`: Re-add the `[Unreleased]` section.
10. Add a gitlab release in the respective repository:
- https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/releases
+ https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/releases
Add a description, which can be a copy&paste from the CHANGELOG, possibly prepended by:
```md
# Changelog
-[See full changelog](https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/${TAG}/CHANGELOG.md)
+[See full changelog](https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/${TAG}/CHANGELOG.md)
```
diff --git a/conf/core/authtoken.example.yaml b/conf/core/authtoken.example.yaml
index 4d57c919ef122a7786850f4feddf2ac5d98e7e67..04211fa4aae1bcb2edfa580a4f0b94cb0fd4f039 100644
--- a/conf/core/authtoken.example.yaml
+++ b/conf/core/authtoken.example.yaml
@@ -7,7 +7,7 @@
# Authentication Tokens.
#
# This yaml file contains an array of configuration objects which may have the
-# properties that are defined by the org.caosdb.server.accessControl.Config class.
+# properties that are defined by the org.linkahead.server.accessControl.Config class.
#
# These properties are:
#
diff --git a/conf/core/jobs.csv b/conf/core/jobs.csv
index 84795bee8657288473188cd9e7a6af81f6295221..72dd0423fbb48d43f173d9068cc298bd27678836 100644
--- a/conf/core/jobs.csv
+++ b/conf/core/jobs.csv
@@ -1,5 +1,5 @@
#
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2021 Timm Fitsche <t.fitschen@indiscale.com>
# Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
diff --git a/conf/core/log4j2-debug.properties b/conf/core/log4j2-debug.properties
index 3ae3ed266ef865fcffde45c21458650dc5ccc0c1..cab0fc945273288af19490ae0efed254e8c04b17 100644
--- a/conf/core/log4j2-debug.properties
+++ b/conf/core/log4j2-debug.properties
@@ -4,8 +4,8 @@
property.LOG_DIR = testlog
# for unit testing
-logger.caosdb_server_logging.name = org.caosdb.server.logging
-logger.caosdb_server_logging.level = TRACE
+logger.linkahead_server_logging.name = org.linkahead.server.logging
+logger.linkahead_server_logging.level = TRACE
# ${LOG_DIR}/debug.log
appender.debug.type = RandomAccessFile
diff --git a/conf/core/server.conf b/conf/core/server.conf
index 5df6c40ca04a9c6f22d03f61c937ab5fbeab565f..ef5df36c0805866ea4945f10042772e05d61a241 100644
--- a/conf/core/server.conf
+++ b/conf/core/server.conf
@@ -5,8 +5,8 @@ TIMEZONE=
# Set the name of the server owner
# e.g: SERVER_OWNER=XY Department
SERVER_OWNER=
-# Name of this CaosDB Server
-SERVER_NAME=CaosDB Server
+# Name of this LinkAhead Server
+SERVER_NAME=LinkAhead Server
# --------------------------------------------------
# The following paths are relative to the working directory of the server.
@@ -26,26 +26,26 @@ SERVER_SIDE_SCRIPTING_WORKING_DIR=./scripting/working/
# can go into a specific home directory for the respective script within this folder.
SERVER_SIDE_SCRIPTING_HOME_DIR=./scripting/home/
-# The CaosDB file system root.
-# The file hierarchy of CaosDB's internal file system starts at this folder.
-# An absolute file path of File objects within CaosDB is relative to this folder.
-FILE_SYSTEM_ROOT=./CaosDBFileSystem/FileSystemRoot/
+# The LinkAhead file system root.
+# The file hierarchy of LinkAhead's internal file system starts at this folder.
+# An absolute file path of File objects within LinkAhead is relative to this folder.
+FILE_SYSTEM_ROOT=./LinkAheadFileSystem/FileSystemRoot/
# Path to the drop off box.
-# This is were users can place files that should be picked up by the CaosDB drop off box program.
-DROP_OFF_BOX=./CaosDBFileSystem/DropOffBox/
+# This is were users can place files that should be picked up by the LinkAhead drop off box program.
+DROP_OFF_BOX=./LinkAheadFileSystem/DropOffBox/
# Location of temporary files
# All temporary files with the exception of files created by the scripting API will go into this folder.
-TMP_FILES=./CaosDBFileSystem/TMP/
+TMP_FILES=./LinkAheadFileSystem/TMP/
# Shared folder
# Additional folder for longer term storage of scripting API output.
# In contrast to the script's working directory, these subdirectories are publicly accessible.
-SHARED_FOLDER=./CaosDBFileSystem/Shared/
+SHARED_FOLDER=./LinkAheadFileSystem/Shared/
# Path to the chown script which is needed by the drop off box in order to change permissions of files.
-CHOWN_SCRIPT=./misc/chown_script/caosdb_chown_dropoffbox
+CHOWN_SCRIPT=./misc/chown_script/linkahead_chown_dropoffbox
# This file is responsible for setting individual user and group permissions.
USER_SOURCES_INI_FILE=./conf/ext/usersources.ini
@@ -58,7 +58,7 @@ AUTH_OPTIONAL=FALSE
# --------------------------------------------------
# MySQL settings
# --------------------------------------------------
-# Hostname of the mysql instance used by CaosDB
+# Hostname of the mysql instance used by LinkAhead
MYSQL_HOST=localhost
# Port of the mysql instance
MYSQL_PORT=3306
@@ -68,17 +68,17 @@ MYSQL_DATABASE_NAME=caosdb
MYSQL_USER_NAME=caosdb
# Password for the user
MYSQL_USER_PASSWORD=random1234
-# Schema of mysql procedures and tables which is required by this CaosDB instance
+# Schema of mysql procedures and tables which is required by this LinkAhead instance
MYSQL_SCHEMA_VERSION=v5.0
# --------------------------------------------------
# Server options
# --------------------------------------------------
-# The context root is a prefix which allows running multiple instances of CaosDB using the same
+# The context root is a prefix which allows running multiple instances of LinkAhead using the same
# hostname and port. Must start with "/".
CONTEXT_ROOT=
-#CONTEXT_ROOT=/caosdb
+#CONTEXT_ROOT=/linkahead
# Server bind/host address, which is the address to listen to. Set to blank, or
# 0.0.0.0 in IPv4, to listen to all. Set to 127.0.0.1 to make it available to
@@ -169,7 +169,7 @@ WEBUI_HTTP_HEADER_CACHE_MAX_AGE=28800
# --------------------------------------------------
# The handler that treats sent mails.
# The default handler pipes mails to a file.
-MAIL_HANDLER_CLASS=org.caosdb.server.utils.mail.ToFileHandler
+MAIL_HANDLER_CLASS=org.linkahead.server.utils.mail.ToFileHandler
# The file were the ToFileHanlder pipes messages to.
MAIL_TO_FILE_HANDLER_LOC=./
@@ -177,7 +177,7 @@ MAIL_TO_FILE_HANDLER_LOC=./
# Admin settings
# --------------------------------------------------
# Name of the administrator of this instance
-ADMIN_NAME=CaosDB Admin
+ADMIN_NAME=LinkAhead Admin
# Email of the administrator of this instance
ADMIN_EMAIL=
# An URL to the bugtracker for managing instance related bugs.
@@ -186,14 +186,14 @@ BUGTRACKER_URI=
# If set to true MySQL stores transaction benchmarks for all SQL queries. Used for benchmarking and debugging.
TRANSACTION_BENCHMARK_ENABLED=FALSE
#TRANSACTION_BENCHMARK_ENABLED=TRUE
-# Location of the configuration file for the CaosDB cache.
+# Location of the configuration file for the LinkAhead cache.
CACHE_CONF_LOC=./conf/core/cache.ccf
# Set this option to true to lobally disable caching. Used for debugging.
CACHE_DISABLE=false
# The server is allowed to create symlinks to files and folders within this whitelist of directories.
INSERT_FILES_IN_DIR_ALLOWED_DIRS=
-#INSERT_FILES_IN_DIR_ALLOWED_DIRS=/data/caosdb,/fileserver01/caosdb
+#INSERT_FILES_IN_DIR_ALLOWED_DIRS=/data/linkahead,/fileserver01/linkahead
# Sudo password of the system.
# Needed by the drop off box to set file permissions.
@@ -205,7 +205,7 @@ QUERY_FILTER_ENTITIES_WITHOUT_RETRIEVE_PERMISSIONS=TRUE
# When checking the ACL of an entity roles which are unknown to the server
# raise an error (when set to MUST) or a warning (when set to SHOULD).
# Unknown roles occur when a user or group is removed or when entities are
-# loaded from other instances of the CaosDB Server where different users are
+# loaded from other instances of the LinkAhead Server where different users are
# present.
# CHECK_ENTITY_ACL_ROLES_MODE=[MUST,SHOULD]
CHECK_ENTITY_ACL_ROLES_MODE=MUST
diff --git a/conf/core/usersources.ini.template b/conf/core/usersources.ini.template
index fb3285723f0721da3280e5ef33461ff4b684e89f..b0a72a2ddab5f7c444278bf410eab8c0bc094620 100644
--- a/conf/core/usersources.ini.template
+++ b/conf/core/usersources.ini.template
@@ -1,7 +1,7 @@
# -*- mode:conf; -*-
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -37,11 +37,11 @@ defaultRealm = PAM
# realm can be looked up in that realm's documentation.
#
# Hint: Realms are implemented by classes which are typically in the
-# org.caosdb.server.accessControl.Pam package and implement the UserSource interface.
+# org.linkahead.server.accessControl.Pam package and implement the UserSource interface.
# Options for authentication against Linux' PAM.
[PAM]
-class = org.caosdb.server.accessControl.Pam
+class = org.linkahead.server.accessControl.Pam
# The script which does the actual checking. It is possible to put custom
# scripts or the misc/pam_authentication/ldap_authentication.sh script here.
; pam_script = ./misc/pam_authentication/pam_authentication.sh
diff --git a/misc/bend_symlinks/README.md b/misc/bend_symlinks/README.md
index a1fa833e262b47e619237bf79db77c1d4b2421a5..f9eefec475073d9fcfdeae1bb78a27d67f3779b3 100644
--- a/misc/bend_symlinks/README.md
+++ b/misc/bend_symlinks/README.md
@@ -54,7 +54,7 @@
storage.
All symlinks below this directory are being process by
this script.
- E.g. '/mnt/caosdb_fs/ExperimentalData/'
+ E.g. '/mnt/linkahead_fs/ExperimentalData/'
TARGET_PATTERN A (extended sed-style) regular expression for matching
broken symlink targets.
TARGET_REPLACEMENT A (sed-style) replacement string for the new (fixed)
@@ -78,14 +78,14 @@
1. Files have been moved from '/mnt/data/current/experiments/' to
/mnt/data/archive/experiments/2019/'. Execute the script in the root
- directory of the caosdb server's internal file system:
+ directory of the LinkAhead server's internal file system:
$ ./bend_symlinks.sh -d ./ /mnt/data/current/experiments /mnt/data/archive/experiments/2019
2. A File was renamed from '/mnt/data/procotol.pdf' to
'/mnt/data/protocol.pdf'. The symlink is located at
- '/mnt/caosdb_fs/procotol.pdf'. Execute the script in the root directory
- of the caosdb server's internal file system:
+ '/mnt/linkahead_fs/procotol.pdf'. Execute the script in the root directory
+ of the linkahead server's internal file system:
$ ./bend_symlinks.sh ./ procotol\.pdf$ protocol.pdf
diff --git a/misc/bend_symlinks/bend_symlinks.sh b/misc/bend_symlinks/bend_symlinks.sh
index 5a296fcdf7c447619751b958b6dc411273e9c951..427d5c9f5eda5603757dab032b928f8f36cc3b68 100755
--- a/misc/bend_symlinks/bend_symlinks.sh
+++ b/misc/bend_symlinks/bend_symlinks.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019 Timm Fitschen (t.fitschen@indiscale.com)
# Copyright (C) 2019 IndiScale (info@indiscale.com)
@@ -74,7 +74,7 @@ USAGE="# Usage
storage.
All symlinks below this directory are being process by
this script.
- E.g. '/mnt/caosdb_fs/ExperimentalData/'
+ E.g. '/mnt/linkahead_fs/ExperimentalData/'
TARGET_PATTERN A (extended sed-style) regular expression for matching
broken symlink targets.
TARGET_REPLACEMENT A (sed-style) replacement string for the new (fixed)
@@ -98,14 +98,14 @@ USAGE="# Usage
1. Files have been moved from '/mnt/data/current/experiments/' to
/mnt/data/archive/experiments/2019/'. Execute the script in the root
- directory of the caosdb server's internal file system:
+ directory of the LinkAhead server's internal file system:
$ $0 -d ./ /mnt/data/current/experiments /mnt/data/archive/experiments/2019
2. A File was renamed from '/mnt/data/procotol.pdf' to
'/mnt/data/protocol.pdf'. The symlink is located at
- '/mnt/caosdb_fs/procotol.pdf'. Execute the script in the root directory
- of the caosdb server's internal file system:
+ '/mnt/linkahead_fs/procotol.pdf'. Execute the script in the root directory
+ of the LinkAhead server's internal file system:
$ $0 ./ procotol\\.pdf$ protocol.pdf
diff --git a/misc/bend_symlinks/src/main.sh b/misc/bend_symlinks/src/main.sh
index 1d148df30533529855f65141ba5705d76b0cb687..98a9e29a3b93f3d5f93e2b5919775b18482a4381 100644
--- a/misc/bend_symlinks/src/main.sh
+++ b/misc/bend_symlinks/src/main.sh
@@ -1,5 +1,5 @@
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019 Timm Fitschen (t.fitschen@indiscale.com)
# Copyright (C) 2019 IndiScale (info@indiscale.com)
diff --git a/misc/bend_symlinks/src/utils.sh b/misc/bend_symlinks/src/utils.sh
index 2ddda289639a9a38e13540da2caad32dc439aa4a..0d9b7d6f4b3cb464538593d1ae4a6d8004ad00ec 100644
--- a/misc/bend_symlinks/src/utils.sh
+++ b/misc/bend_symlinks/src/utils.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019-2020 Timm Fitschen (t.fitschen@indiscale.com)
# Copyright (C) 2019-2020 IndiScale GmbH (info@indiscale.com)
diff --git a/misc/check_symlinks/check_symlinks b/misc/check_symlinks/check_symlinks
index 0f6eb0d1d3626ed32fa99aa6a31891c6ddf90635..a2a4f41576410f06b9299575d7557a7cc8e14f69 100755
--- a/misc/check_symlinks/check_symlinks
+++ b/misc/check_symlinks/check_symlinks
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/chown_script/README b/misc/chown_script/README
index 03f24071f16c2837074a91bc736c22099a1643b4..421b877d850aee5e7f1a54b1ad296a4db16ca349 100644
--- a/misc/chown_script/README
+++ b/misc/chown_script/README
@@ -1,4 +1,4 @@
-* The chown_script for the caosdb DropOffBox.
+* The chown_script for the LinkAhead DropOffBox.
* @author: Timm Fitschen (timm.fitschen@ds.mpg.de)
* @date: 2015-10-12
@@ -21,8 +21,8 @@ COPY this into a file called "CONFIG" (upper case) and edit it to your own needs
--- copy below this line ---
#This config file defines the parameters needed for the installation as a KEY/VALUE list. A line beginning with `#` will be ignored.
-#DB_USER is the unix user who runs the caosdb server
-DB_USER=caosdb
+#DB_USER is the unix user who runs the LinkAhead server
+DB_USER=linkahead
#LOC_DROPOFFBOX is the directory of the DropOffBox. ATTENTION: The path must not end with `/`!
LOC_DROPOFFBOX=/path/to/dropOffBox
@@ -30,7 +30,7 @@ LOC_DROPOFFBOX=/path/to/dropOffBox
#LOC_SUDOERS is a directory which files are included by the sudoers file. ATTENTION: The path must not end with `/`!
LOC_SUDOERS=/etc/sudoers.d
-#LOC_PREFIX is the folder which the caosdb_chown_script is stored to. ATTENTION: The path must not end with `/`!
+#LOC_PREFIX is the folder which the linkahead_chown_script is stored to. ATTENTION: The path must not end with `/`!
LOC_PREFIX=/usr/local/sbin
--- copy above this line ---
diff --git a/misc/chown_script/chown_script_template b/misc/chown_script/chown_script_template
index bd006f7ec22826e67937c347a50de75dea03685c..b4a6e8e2005b66bcd5d0ef3bc64b9619cf7b7226 100755
--- a/misc/chown_script/chown_script_template
+++ b/misc/chown_script/chown_script_template
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/chown_script/install b/misc/chown_script/install
index 55ab1fa2c719d97dc4eb3016fc305a441b0b0084..01efaffbc9398bf0ee7093cc78a2f987e50cf846 100755
--- a/misc/chown_script/install
+++ b/misc/chown_script/install
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -137,7 +137,7 @@ fi
# promt for dbuser
# default: caosdb
-prompt "the unix user which who runs the caosdb server" DB_USER
+prompt "the unix user which who runs the LinkAhead server" DB_USER
# TODO
DB_GROUP=$DB_USER
@@ -146,13 +146,13 @@ DB_GROUP=$DB_USER
# default: /etc/sudoers.d/
prompt "the location of sudoers.d" LOC_SUDOERS -f
LOC_SUDOERS=$(get_abs_filename $LOC_SUDOERS)
-LOC_SUDO_SCRIPT="${LOC_SUDOERS}/caosdb_chown_script"
+LOC_SUDO_SCRIPT="${LOC_SUDOERS}/linkahead_chown_script"
# promt for prefix
# default: /usr/local/sbin/
prompt "the location of the script which is to be generated" LOC_PREFIX -f
LOC_PREFIX=$(get_abs_filename $LOC_PREFIX)
-LOC_SCRIPT="${LOC_PREFIX}/caosdb_chown_dropoffbox"
+LOC_SCRIPT="${LOC_PREFIX}/linkahead_chown_dropoffbox"
check_parameters
@@ -202,7 +202,7 @@ $CMD_CHOWN root:root $LOC_SCRIPT
chmod 500 $LOC_SCRIPT
## configure sudo
-echo -en "# Generated by caosdb install script. Do not edit!
+echo -en "# Generated by LinkAhead install script. Do not edit!
# CONTACT: Timm Fitschen (timm.fitschen@ds.mpg.de)
# DATE: 2015-10-09
$DB_USER ALL = (root) NOPASSWD: $LOC_SCRIPT
diff --git a/misc/chown_script/test_functions b/misc/chown_script/test_functions
index 303f612f6c98d6ce360790e1a5a4707a950b1e58..614cae74f201baeb10bb112bc29c7f242283df07 100644
--- a/misc/chown_script/test_functions
+++ b/misc/chown_script/test_functions
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/move_files/README.md b/misc/move_files/README.md
index df67f2025b8627a09e6886038646db4ec4436941..8bd8ef33d34f1fa4bfa3aee5bbb2760f7b480c15 100644
--- a/misc/move_files/README.md
+++ b/misc/move_files/README.md
@@ -4,9 +4,9 @@ Version: 0.1
Usage: `./move_files.py [-h] changes`
-This script moves files in the internal file system of the CaosDB server. It
+This script moves files in the internal file system of the LinkAhead server. It
reads file paths form a tsv file with columns from and to. For each line it
-creates an update of a caosdb file object where the path that equals "from" is
+creates an update of a LinkAhead file object where the path that equals "from" is
changed to "to".
positional arguments:
@@ -17,8 +17,10 @@ optional arguments:
# Tests
-The tests a integration tests which require a running test database and a sufficiently configured caosdb-pylib.
+The tests a integration tests which require a running test database and a sufficiently configured
+linkahead-pylib.
-Run `pytest test_move_files.py` to insert a bunch of test files, rename and subsequently delete them.
+Run `pytest test_move_files.py` to insert a bunch of test files, rename and subsequently delete
+them.
diff --git a/misc/move_files/move_files.py b/misc/move_files/move_files.py
index 7498feef96e3a6e2aee465518b34ebd64e4561e4..e2eb67d78a78470976188fee1d83c47ddfb69719 100755
--- a/misc/move_files/move_files.py
+++ b/misc/move_files/move_files.py
@@ -2,7 +2,7 @@
# encoding: utf-8
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019 Henrik tom Wörden
#
@@ -23,9 +23,9 @@
#
"""
-This script moves files in the internal file system of the CaosDB server. It
+This script moves files in the internal file system of the LinkAhead server. It
reads file paths form a tsv file with columns from and to. For each line it
-creates an update of a caosdb file object where the path that equals "from" is
+creates an update of a LinkAhead file object where the path that equals "from" is
changed to "to".
Version: 0.1
@@ -39,7 +39,7 @@ from argparse import ArgumentParser
import pandas as pd
from tqdm import tqdm
-import caosdb as db
+import linkahead as db
def rename(changes, chunksize=10):
diff --git a/misc/move_files/test_move_files.py b/misc/move_files/test_move_files.py
index 2edb76509dc6a350057997cc6f894abd4a4bb163..632f0a1048f412fa3c413d2c2277826cc0df8e2e 100644
--- a/misc/move_files/test_move_files.py
+++ b/misc/move_files/test_move_files.py
@@ -1,6 +1,6 @@
# encoding: utf-8
#
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019 Henrik tom Wörden
#
@@ -24,7 +24,7 @@ import unittest
import pandas as pd
-import caosdb as db
+import linkahead as db
from move_files import rename
diff --git a/misc/pam_authentication/ldap_authentication.sh b/misc/pam_authentication/ldap_authentication.sh
index e58b5caa3e518a386169b37d1723b76418570162..cf15210dd3e5533461ac0ac616eff67213a7d97e 100755
--- a/misc/pam_authentication/ldap_authentication.sh
+++ b/misc/pam_authentication/ldap_authentication.sh
@@ -1,7 +1,7 @@
#!/bin/bash
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (c) 2020 IndiScale GmbH
# Copyright (c) 2020 Daniel Hornung <d.hornung@indiscale.com>
diff --git a/misc/pam_authentication/makefile b/misc/pam_authentication/makefile
index 0cd1b7d250358a116a32a45ba18875d5f72d887a..4b78674178735a099687d1d679daae99ef428c7b 100644
--- a/misc/pam_authentication/makefile
+++ b/misc/pam_authentication/makefile
@@ -1,6 +1,6 @@
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/pam_authentication/pam_authentication.c b/misc/pam_authentication/pam_authentication.c
index 4abef5bddb2a6c11ecefdcc8a1bf9179835bca84..d2fd5d113f6f6320c4b04cc20ef791b334601852 100644
--- a/misc/pam_authentication/pam_authentication.c
+++ b/misc/pam_authentication/pam_authentication.c
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/pam_authentication/pam_authentication.sh b/misc/pam_authentication/pam_authentication.sh
index 972e48f1ccc9c65ca0c56773f7e20a5da0977ebb..d5214f5ed80764d66258ef35fd2ac50bb62db7eb 100755
--- a/misc/pam_authentication/pam_authentication.sh
+++ b/misc/pam_authentication/pam_authentication.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/pam_authentication/test_authentication.sh b/misc/pam_authentication/test_authentication.sh
index ffaedd1381641f21f689c89634bb83ba345edbbe..baebf02e802511ea217b18eea1c0a6b52a51d263 100755
--- a/misc/pam_authentication/test_authentication.sh
+++ b/misc/pam_authentication/test_authentication.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/mvn_install_jar.sh b/mvn_install_jar.sh
index b7bdb6cf820e05327caa8aed5e68c4f6b3f2e86b..d1ea465cc52a9ec4e9dfa7c1052a1d453787ef8e 100755
--- a/mvn_install_jar.sh
+++ b/mvn_install_jar.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -25,5 +25,5 @@
# Alexander Schlemmer, 01/2013
# Installiert die jar-Datei des Servers in das lokale mvn-Repository.
-mvn install:install-file -DgroupId=ds.mpg.de -DartifactId=caosdb-server \
- -Dversion=1.0 -Dpackaging=jar -Dfile=dist/CaosDBServer.jar
+mvn install:install-file -DgroupId=ds.mpg.de -DartifactId=linkahead-server \
+ -Dversion=1.0 -Dpackaging=jar -Dfile=dist/LinkAheadServer.jar
diff --git a/pom.xml b/pom.xml
index 76c2cd85ad9ae0e918f3c5770311ed017308e02a..3cc7ee6e5b2c7a4eb965ba7572fec9e173845567 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,10 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<!--
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2023 Indiscale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Daniel Hornung <d.hornung@indiscale.com>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -23,13 +25,13 @@
-->
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
- <groupId>org.caosdb</groupId>
- <artifactId>caosdb-server</artifactId>
+ <groupId>org.linkahead</groupId>
+ <artifactId>linkahead-server</artifactId>
<version>0.10.1-SNAPSHOT</version>
<packaging>jar</packaging>
- <name>CaosDB Server</name>
+ <name>LinkAhead Server</name>
<scm>
- <connection>scm:git:https://gitlab.indiscale.com/caosdb/src/caosdb-server.git</connection>
+ <connection>scm:git:https://gitlab.indiscale.com/caosdb/src/linkahead-server.git</connection>
</scm>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -265,7 +267,7 @@
<transformers>
<transformer implementation="com.github.edwgiz.mavenShadePlugin.log4j2CacheTransformer.PluginsCacheFileTransformer"></transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
- <mainClass>org.caosdb.server.CaosDBServer</mainClass>
+ <mainClass>org.linkahead.server.LinkAheadServer</mainClass>
</transformer>
</transformers>
</configuration>
@@ -312,7 +314,7 @@
<include>**/*.java</include>
</includes>
<systemPropertyVariables>
- <caosdb.debug>true</caosdb.debug>
+ <linkahead.debug>true</linkahead.debug>
<log4j2.debug>true</log4j2.debug>
</systemPropertyVariables>
<reuseForks>false</reuseForks>
@@ -339,7 +341,7 @@
<revisionPropertyName>project.revision</revisionPropertyName>
<versionPropertyName>project.version</versionPropertyName>
<timestampPropertyName>build.timestamp</timestampPropertyName>
- <outputDirectory>${basedir}/target/classes/org/caosdb/server/</outputDirectory>
+ <outputDirectory>${basedir}/target/classes/org/linkahead/server/</outputDirectory>
<outputName>build.properties</outputName>
</configuration>
</plugin>
@@ -354,7 +356,7 @@
<goal>java</goal>
</goals>
<configuration>
- <mainClass>org.caosdb.server.CaosDBServer</mainClass>
+ <mainClass>org.linkahead.server.LinkAheadServer</mainClass>
<arguments>
<argument>silent</argument>
</arguments>
@@ -366,13 +368,13 @@
<goal>java</goal>
</goals>
<configuration>
- <mainClass>org.caosdb.server.CaosDBServer</mainClass>
+ <mainClass>org.linkahead.server.LinkAheadServer</mainClass>
<arguments>
<argument>silent</argument>
</arguments>
<systemProperties>
<systemProperty>
- <key>caosdb.debug</key>
+ <key>linkahead.debug</key>
<value>true</value>
</systemProperty>
</systemProperties>
@@ -426,7 +428,7 @@
<artifactId>protobuf-maven-plugin</artifactId>
<version>0.6.1</version>
<configuration>
- <protoSourceRoot>${basedir}/caosdb-proto/proto/</protoSourceRoot>
+ <protoSourceRoot>${basedir}/linkahead-proto/proto/</protoSourceRoot>
<protocArtifact>com.google.protobuf:protoc:${protobuf.version}:exe:${os.detected.classifier}</protocArtifact>
<pluginId>grpc-java</pluginId>
<pluginArtifact>io.grpc:protoc-gen-grpc-java:${grpc.version}:exe:${os.detected.classifier}</pluginArtifact>
@@ -442,5 +444,5 @@
</plugin>
</plugins>
</build>
- <url>caosdb.org</url>
+ <url>linkahead.org</url>
</project>
diff --git a/scripting/bin/administration/diagnostics.py b/scripting/bin/administration/diagnostics.py
index ccecbd583ffdaf5f941a2df873ac10982560af31..79a227fc73e18d16f44a06680d7745ad170ff45a 100755
--- a/scripting/bin/administration/diagnostics.py
+++ b/scripting/bin/administration/diagnostics.py
@@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -34,7 +34,7 @@ should not be executable for non-admin users.
import sys
TEST_MODULES = [
- "caosdb",
+ "linkahead",
"numpy",
"pandas",
"validate_email"
@@ -73,8 +73,8 @@ def get_query():
return get_option("query")
-def get_caosdb_info(auth_token):
- import caosdb as db
+def get_linkahead_info(auth_token):
+ import linkahead as db
result = dict()
result["version"] = db.version.version
@@ -136,8 +136,8 @@ def main():
auth_token = get_auth_token()
diagnostics["auth_token"] = auth_token
- if diagnostics["import"]["caosdb"][0] is True:
- diagnostics["caosdb"] = get_caosdb_info(auth_token)
+ if diagnostics["import"]["linkahead"][0] is True:
+ diagnostics["linkahead"] = get_linkahead_info(auth_token)
finally:
json.dump(diagnostics, sys.stdout)
diff --git a/scripting/bin/xls_from_csv.py b/scripting/bin/xls_from_csv.py
index 73bb6b0ac23fc2df093bd6797e864aad1f2d5592..df05f7e5282ced2ece81e39b43c2ddb0440737a0 100755
--- a/scripting/bin/xls_from_csv.py
+++ b/scripting/bin/xls_from_csv.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python3
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019 IndiScale GmbH
#
diff --git a/src/doc/CaosDB-Query-Language.md b/src/doc/CaosDB-Query-Language.md
index 6cbe64f1582b53f9e5c6dc60e21d988fd193d476..0b8cd5a236cdd6a1c5a39aa1d269ee8b77a1c9bd 100644
--- a/src/doc/CaosDB-Query-Language.md
+++ b/src/doc/CaosDB-Query-Language.md
@@ -1,8 +1,8 @@
-# CaosDB Query Language Examples
+# LinkAhead Query Language Examples
-See syntax specification in [CaosDB Query Language Syntax](query-syntax).
+See syntax specification in [LinkAhead Query Language Syntax](query-syntax).
-In this chapter, the CaosDB Query Language (CQL) is presented as a means of
+In this chapter, the LinkAhead Query Language (CQL) is presented as a means of
formulating search commands, commonly referred to as queries. It is highly
recommended that you experiment with the examples provided, such as those found
on https://demo.indiscale.com. An interactive tour is also available on this
@@ -55,7 +55,7 @@ with some external tool.
`SELECT` queries offer to represent the query result in a tabular form.
If you replace the `FIND` keyword of a query with `SELECT x, y, z FROM`, then
-CaosDB will return the result as tabular data.
+LinkAhead will return the result as tabular data.
For example, instead of `FIND Guitar`, try out
`SELECT name, electric FROM Guitar`
@@ -75,7 +75,7 @@ like the creation time of a Record to restrict the query result set.
We already learned, that we can provide the name of a RecordType after the `FIND`
keyword. Let's call this part of the query "entity expression". In general, we
-need to identify with the entity expression one or more entities via their name, CaosDB ID
+need to identify with the entity expression one or more entities via their name, LinkAhead ID
or a pattern.
- `FIND Guitar`
- `FIND Guit*` ('*' represents none, one or more characters)
@@ -86,7 +86,7 @@ The result set will contain Entities that are either identified by the entity ex
directly (i.e. they have the name or the given ID) or the have such an Entity as
parent.
-As you know, CaosDB distincts among different Entity roles:
+As you know, LinkAhead distincts among different Entity roles:
- Entity
- Record
- RecordType
@@ -500,7 +500,7 @@ Note: When a property `responsible` with data type `Person` exists, the above `S
## Versioning
-Since Caosdb 0.2 entities are optionally version controlled. The query language will be extended to include versioning in the future. A current minimal implementation introduces the `ANY VERSION OF` modifier which can be used to return all matching versions in the results of `COUNT`, `FIND`, and `SELECT` queries.
+Since LinkAhead 0.2 entities are optionally version controlled. The query language will be extended to include versioning in the future. A current minimal implementation introduces the `ANY VERSION OF` modifier which can be used to return all matching versions in the results of `COUNT`, `FIND`, and `SELECT` queries.
### Example
@@ -513,7 +513,7 @@ Since Caosdb 0.2 entities are optionally version controlled. The query language
## Configuration
-In CaosDB Server implementations before version 0.9.0, the `FIND ename` query
+In LinkAhead Server implementations before version 0.9.0, the `FIND ename` query
would return any entity with that name and all children, regardless of the
entity's role. Basically, `FIND ename` *was* equivalent to `FIND ENTITY ename`.
Since 0.9.0 the default behavior has changed and now `FIND ename` is equivalent
diff --git a/src/doc/Data-Model.md b/src/doc/Data-Model.md
index b471b8241301644b7484376a6e87f72c7f04d3bb..2c33e7da57ec8a93e4eaa4b929e8a41154fd3f38 100644
--- a/src/doc/Data-Model.md
+++ b/src/doc/Data-Model.md
@@ -1,5 +1,5 @@
-# CaosDB Data Model
+# LinkAhead Data Model
The data structure is built from some basic building blocks which are
shown in the following picture:
@@ -9,7 +9,7 @@ shown in the following picture:
It has a base object called **Entity**. Entities are either **Record
Types**, **Records**, or **Abstract Properties** (and Record like
objects for files). What *kind of data* is stored is defined by the
-Record Types. Actual data is then stored in CaosDB as Records which
+Record Types. Actual data is then stored in LinkAhead as Records which
are of some Record Type. Those Records can have Properties that
contain information about the Record. The following is a more detailed
explanation (also see this
diff --git a/src/doc/FAQ.rst b/src/doc/FAQ.rst
index 54bfb296fa96e645034504e94368b34e76448b75..2caabbadff6a1b82b078639613f8ddc078403d00 100644
--- a/src/doc/FAQ.rst
+++ b/src/doc/FAQ.rst
@@ -3,7 +3,7 @@ FAQs
====
These FAQs (frequently asked questions) can be extended, if *you* help us. Please `submit an issue
-<https://gitlab.com/caosdb/caosdb-server/issues/new>`__ if you have a question that should be
+<https://gitlab.com/linkahead/linkahead-server/issues/new>`__ if you have a question that should be
answered here.
.. contents:: Select your question:
@@ -18,12 +18,12 @@ with the ``add_property`` method and the ``LIST`` function.
.. code:: python
# with constructor
- p = caosdb.Property(name="ListOfDoubles", datatype=caosdb.LIST(caosdb.DOUBLE))
+ p = linkahead.Property(name="ListOfDoubles", datatype=linkahead.LIST(linkahead.DOUBLE))
# with add_property method
- my_entity.add_property(name="ListOfIntegers", datatype=caosdb.LIST(caosdb.INTEGER))
- my_entity.add_property(name="ListOfThings", datatype=caosdb.LIST("Thing"))
- my_entity.add_property(name="ListOfThings", datatype=caosdb.LIST(caosdb.RecordType('Thing'))
+ my_entity.add_property(name="ListOfIntegers", datatype=linkahead.LIST(linkahead.INTEGER))
+ my_entity.add_property(name="ListOfThings", datatype=linkahead.LIST("Thing"))
+ my_entity.add_property(name="ListOfThings", datatype=linkahead.LIST(linkahead.RecordType('Thing'))
Which data types are there?
===========================
@@ -49,7 +49,7 @@ And furthermore,…
.. code:: python
- p = caosdb.Property(name="Conductor", datatype="Person")
+ p = linkahead.Property(name="Conductor", datatype="Person")
will only accept those Entities as value which have a “Person”
RecordType as a direct or indirect parent.
diff --git a/src/doc/Makefile b/src/doc/Makefile
index 1f0af46e75a27dc9ff8d124782fca27400e4a240..73f5a4cf5bc8c9302ad58c29750b072df9d4d49f 100644
--- a/src/doc/Makefile
+++ b/src/doc/Makefile
@@ -1,4 +1,4 @@
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
@@ -47,7 +47,7 @@ doc-help:
# sphinx-build -M html . ../../build/doc
apidoc:
- $(SPHINXAPIDOC) -o _apidoc --update --title="CaosDB Server" ../main/
+ $(SPHINXAPIDOC) -o _apidoc --update --title="LinkAhead Server" ../main/
apixml:
$(MAKE) -C $(APIXMLDIR) doc
diff --git a/src/doc/administration/configuration.rst b/src/doc/administration/configuration.rst
index c91ac16b1068b9261638aa697f3d11fd42a0d5cc..778c93741b3f33c8d7090230da922b54c900ba55 100644
--- a/src/doc/administration/configuration.rst
+++ b/src/doc/administration/configuration.rst
@@ -16,7 +16,7 @@ with a hash (`#`). Key-value lines must have the format `KEY_NAME=VALUE` or
The server default configuration is located at `./conf/core/server.conf`.
Upstream defaults are stored here. The possible configuration options are
documented inside the
-`default file <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/server.conf>`__.
+`default file <https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/dev/conf/core/server.conf>`__.
User specific configuration should be in `./conf/ext/` and override settings
in `./conf/core/`.
@@ -27,7 +27,7 @@ The default configuration can be overriden by
2. any file in ./conf/ext/server.conf.d/ in (approximately?) alphabetical order
- 3. environment variables with the prefix `CAOSDB_CONFIG_`
+ 3. environment variables with the prefix `LINKAHEAD_CONFIG_`
in this order.
@@ -39,7 +39,7 @@ Further settings are to be set in files which are by default stored in `./conf/c
``global_entity_permissions.xml``
:doc:`Permissions<../permissions>` which are automatically set, based on user roles. See the
`default file
- <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/global_entity_permissions.xml>`__.
+ <https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/dev/conf/core/global_entity_permissions.xml>`__.
``usersources.ini``
This file defines possible sources which are checked when a user tries to authenticate. Each
@@ -47,23 +47,23 @@ Further settings are to be set in files which are by default stored in `./conf/c
source. At the moment the best place to look for this specific documentation is at the API
documentation of :java:type:`UserSource` and its implementing classes. The provided `template
file
- <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/usersources.ini.template>`__
+ <https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/dev/conf/core/usersources.ini.template>`__
also has some information. The general concept about authentication realms is described in
:java:type:`UserSources`.
``authtoken.yaml``
- Configuration for dispensed authentication tokens, which can be used to authenticate to CaosDB
+ Configuration for dispensed authentication tokens, which can be used to authenticate to LinkAhead
without the need of a user/password combination. One-time Authentication Tokens can be configure
to be issued for special purposes (e.g. a call of a server-side script or initial setup after the server start)
or to be written to a file on a regular basis. An example of a configuration is located at `./conf/core/authtoken.example.yaml`.
There is more documentation inside the `template file
- <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/authtoken.example.yaml>`__.
+ <https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/dev/conf/core/authtoken.example.yaml>`__.
``cache.ccf``
Configuration for the Java Caching System (JCS) which can be used by the server. More
documentation is `upstream
<http://commons.apache.org/proper/commons-jcs/getting_started/intro.html>`_ and inside `the file
- <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/cache.ccf>`_.
+ <https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/dev/conf/core/cache.ccf>`_.
``log4j2-default.properties``, ``log4j2-debug.properties``
Configuration for logging, following the standard described by the `log4j library
@@ -82,4 +82,4 @@ Remark:
In the debug case, the server provides the ``_server_properties`` resource which allows the ``GET``
and ``POST`` methods to access the server's properties. The Python client library conveniently
-wraps this in the :any:`caosdb-pylib:caosdb.common.administration` module.
+wraps this in the :any:`linkahead-pylib:linkahead.common.administration` module.
diff --git a/src/doc/administration/curl-access.rst b/src/doc/administration/curl-access.rst
index 79b10a712056959bf03a5ee6a41671b9cb3c3119..88d473a8567f8f25c771076842c88ef9977f7233 100644
--- a/src/doc/administration/curl-access.rst
+++ b/src/doc/administration/curl-access.rst
@@ -1,15 +1,15 @@
-Curl Access for CaosDB
+Curl Access for LinkAhead
======================
-As the API that is used to communicate with the CaosDB server is XML
+As the API that is used to communicate with the LinkAhead server is XML
over HTTP also simple HTTP clients, such as
`cURL <https://curl.haxx.se/>`__ can be used. cURL is an old and
established command line program for transferring files over networks
that implements various protocols including HTTP/HTTPS. It is installed
by default on many Linux distributions and can therefore be very useful
-for testing and debugging of CaosDB.
+for testing and debugging of LinkAhead.
-This small manual also gives some practical insights about the CaosDB
+This small manual also gives some practical insights about the LinkAhead
protocol itself.
Doing a simple retrieve
@@ -24,7 +24,7 @@ Let’s do a query on our demo instance:
curl "https://demo.indiscale.com/Entity/?query=FIND%20Experiment"
By default cURL sends an HTTP GET request which is needed for doing
-queries for CaosDB. CaosDB requires sending them to ``/Entity``. The
+queries for LinkAhead. LinkAhead requires sending them to ``/Entity``. The
query itself is specified after the HTTP query string ``?query=``.
``%20`` is specific to URL encoding and corresponds to a space (see
https://en.wikipedia.org/wiki/Percent-encoding for details). So the
@@ -36,7 +36,7 @@ The response should look like:
.. code:: xml
<?xml version="1.0" encoding="UTF-8"?>
- <?xml-stylesheet type="text/xsl" href="https://demo.indiscale.com/webinterface/webcaosdb.xsl" ?>
+ <?xml-stylesheet type="text/xsl" href="https://demo.indiscale.com/webinterface/weblinkahead.xsl" ?>
<Response srid="b56e3d1a442460c46dde924a54e8afba" timestamp="1561453363382" baseuri="https://demo.indiscale.com" count="3">
<UserInfo>
<Roles>
@@ -101,7 +101,7 @@ returned. Furthermore the response contains some additional information:
timestamp <https://en.wikipedia.org/wiki/Unix_time>`__ for this
request.
- ``baseuri="https://demo.indiscale.com"`` The base URI of the
- instance of CaosDB that performed the request.
+ instance of LinkAhead that performed the request.
- ``count="3"`` The number of results (2 ``RecordTypes`` and 1
``Record``)
@@ -155,7 +155,7 @@ Logging in
----------
You might have asked yourself, what we need the cookie for. The simple
-answer is: authentication. For many operations done on the CaosDB server
+answer is: authentication. For many operations done on the LinkAhead server
we have to log in first. The demo instance is configured to allow for
anonymous read access by default. But depending on the instance you are
accessing, even this might be disallowed.
@@ -192,7 +192,7 @@ password in the variable ``$PW``:
Custom Certificates
-------------------
-If you are running your own CaosDB instance it might be necessary to use
+If you are running your own LinkAhead instance it might be necessary to use
a custom SSL certificate.
You can specify this using the option ``--cacert``, e.g.:
@@ -238,7 +238,7 @@ The attributes have the following meaning: - ``upload=testfile.bla`` The
filename given here is actually no filename, but an identifier to find
the multipart data chunk that contains the file. I called it
``testfile.bla`` for simplicity here. -
-``destination="/test/testfile.bla"`` The destination path on the CaosDB
+``destination="/test/testfile.bla"`` The destination path on the LinkAhead
server file system.
Before looking at the other attributes let’s have a look at the file
diff --git a/src/doc/administration/maintenance.rst b/src/doc/administration/maintenance.rst
index 5b9faeb1c5da3e68def79acae2d6901efa2e78de..245a8b1bdb5c778d356f09bcbd6793feb638fa7b 100644
--- a/src/doc/administration/maintenance.rst
+++ b/src/doc/administration/maintenance.rst
@@ -1,42 +1,42 @@
-Maintenance of the CaosDB Server
+Maintenance of the LinkAhead Server
================================
Creating a Backup
-----------------
-In order to create a full backup of CaosDB, the state of the SQL-Backend (MySQL, MariaDB)
-has to be saved and the internal file system of CaosDB (symbolic links to
+In order to create a full backup of LinkAhead, the state of the SQL-Backend (MySQL, MariaDB)
+has to be saved and the internal file system of LinkAhead (symbolic links to
file systems that are mounted and uploaded files) has to be saved.
-You find the documentation on how to backup the SQL-Backend :any:`caosdb-mysqlbackend:Maintenance`
+You find the documentation on how to backup the SQL-Backend :any:`linkahead-mysqlbackend:Maintenance`
In order to save the file backend we recommend to tar the file system. However,
you could use other backup methods that allow to restore the file system.
-The CaosDB internal file system is located at the path defined by the
+The LinkAhead internal file system is located at the path defined by the
``FILE_SYSTEM_ROOT`` configuration variable (see :any:`configuration`).
The command could look like::
- tar czvf /path/to/new/backup /path/to/caosdb/filesystem.tar.gz
+ tar czvf /path/to/new/backup /path/to/linkahead/filesystem.tar.gz
-You can also save the content of CaosDB using XML. This is **not recommended** since it produces
+You can also save the content of LinkAhead using XML. This is **not recommended** since it produces
less reproducible results than a plain SQL backup. However there may be cases in which an XML backup
-is necessary, e.g., when transferring entities between two different CaosDB instances.
+is necessary, e.g., when transferring entities between two different LinkAhead instances.
Collect the entities that you want to export in a
-:any:`Container<caosdb-pylib:caosdb.common.models.Container>`, named ``cont`` here. Then you can
+:any:`Container<linkahead-pylib:linkahead.common.models.Container>`, named ``cont`` here. Then you can
export the XML with::
- from caosadvancedtools.export_related import invert_ids
+ from linkaheadadvancedtools.export_related import invert_ids
from lxml import etree
invert_ids(cont)
xml = etree.tounicode(cont.to_xml(
local_serialization=True), pretty_print=True)
- with open("caosdb_data.xml"), "w") as fi:
+ with open("linkahead_data.xml"), "w") as fi:
fi.write(xml)
@@ -44,21 +44,21 @@ Restoring a Backup
------------------
.. warning::
- CaosDB should be offline before restoring data.
+ LinkAhead should be offline before restoring data.
If you want to restore the internal file system, simply replace it. E.g. if your
backup is a tarball::
- tar xvf /path/to/caosroot.tar.gz
+ tar xvf /path/to/linkaheadroot.tar.gz
-You find the documentation on how to restore the data in the SQL-Backend :any:`caosdb-mysqlbackend:Maintenance`
+You find the documentation on how to restore the data in the SQL-Backend :any:`linkahead-mysqlbackend:Maintenance`
If you want to restore the entities exported to XML, you can do::
cont = db.Container()
- with open("caosdb_data.xml") as fi:
+ with open("linkahead_data.xml") as fi:
cont = cont.from_xml(fi.read())
cont.insert()
@@ -68,6 +68,6 @@ User Management
The configuration of authentication mechanisms is done via the ``usersources.ini`` file (see
:any:`configuration`).
-We recommend the Python tools (:any:`caosdb-pylib:administration`) for further administrative tasks
+We recommend the Python tools (:any:`linkahead-pylib:administration`) for further administrative tasks
(e.g. setting user passwords).
diff --git a/src/doc/administration/server_side_scripting.rst b/src/doc/administration/server_side_scripting.rst
index 6dc08999f38e1912e72440c609b8cde1ea7ce0bb..f23e2ba8a2cc9256de41309c6d4e13d1425d8439 100644
--- a/src/doc/administration/server_side_scripting.rst
+++ b/src/doc/administration/server_side_scripting.rst
@@ -4,7 +4,7 @@ Server-Side Scripting
Introduction
------------
-Small computation task, like some visualization, might be easily implemented in Python or some other language, but cumbersome to integrate into the server. Furthermore, the CaosDB server should stay a general tool without burden from specific projects. Also, one might want to trigger some standardized processing task from the web interface for convenience. For these situations the "server side scripting" is intended.
+Small computation task, like some visualization, might be easily implemented in Python or some other language, but cumbersome to integrate into the server. Furthermore, the LinkAhead server should stay a general tool without burden from specific projects. Also, one might want to trigger some standardized processing task from the web interface for convenience. For these situations the "server side scripting" is intended.
Concepts
------------
@@ -49,8 +49,8 @@ script invocation from a skeleton directory, located in the server directory, in
- `readme.md` :: A small text file describing the purpose of the directory.
-Users of CaosDB are invited to populate the directory with whatever their
-scripts need (for example a `.pycaosdb.ini` file).
+Users of LinkAhead are invited to populate the directory with whatever their
+scripts need (for example a `.pylinkahead.ini` file).
Invocation
------------
diff --git a/src/doc/concepts.rst b/src/doc/concepts.rst
index 4403c95810f9b2edaa67e8561306b80031ac803e..0eef6b6a693440784689c2be9ea2c5031b125dc0 100644
--- a/src/doc/concepts.rst
+++ b/src/doc/concepts.rst
@@ -1,5 +1,5 @@
-Basic concepts of the CaosDB server
+Basic concepts of the LinkAhead server
===================================
.. toctree::
@@ -10,6 +10,6 @@ Basic concepts of the CaosDB server
permissions
roles
-The CaosDB server provides the HTTP API resources to users and client libraries. It uses a plain
+The LinkAhead server provides the HTTP API resources to users and client libraries. It uses a plain
MariaDB/MySQL database as backend for data storage, raw files are stored separately on the file
system.
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 6b9b1f56157812db20cc7d7ebcb8525687956208..cd2020806caaae16e90f1a31e93da0cc513b60b0 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -14,14 +14,14 @@
#
# import os
# import sys
-# sys.path.insert(0, os.path.abspath('../caosdb'))
+# sys.path.insert(0, os.path.abspath('../linkahead'))
import sphinx_rtd_theme
from os.path import dirname, abspath
# -- Project information -----------------------------------------------------
-project = 'caosdb-server'
+project = 'linkahead-server'
copyright = '2023, IndiScale GmbH'
author = 'Daniel Hornung, Timm Fitschen'
@@ -69,7 +69,7 @@ master_doc = 'index'
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
@@ -118,7 +118,7 @@ html_css_files = [
# -- Options for HTMLHelp output ---------------------------------------------
# Output file base name for HTML help builder.
-htmlhelp_basename = 'caosdb-serverdoc'
+htmlhelp_basename = 'linkahead-serverdoc'
# -- Options for LaTeX output ------------------------------------------------
@@ -145,7 +145,7 @@ latex_elements = {
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
- (master_doc, 'caosdb-server.tex', 'caosdb-server Documentation',
+ (master_doc, 'linkahead-server.tex', 'linkahead-server Documentation',
'IndiScale GmbH', 'manual'),
]
@@ -155,7 +155,7 @@ latex_documents = [
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
- (master_doc, 'caosdb-server', 'caosdb-server Documentation',
+ (master_doc, 'linkahead-server', 'linkahead-server Documentation',
[author], 1)
]
@@ -166,8 +166,8 @@ man_pages = [
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
- (master_doc, 'caosdb-server', 'caosdb-server Documentation',
- author, 'caosdb-server', 'One line description of project.',
+ (master_doc, 'linkahead-server', 'linkahead-server Documentation',
+ author, 'linkahead-server', 'One line description of project.',
'Miscellaneous'),
]
@@ -209,8 +209,8 @@ javadoc_url_map = {
# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_mapping
intersphinx_mapping = {
"python": ("https://docs.python.org/", None),
- "caosdb-pylib": ("https://docs.indiscale.com/caosdb-pylib/", None),
- "caosdb-mysqlbackend": ("https://docs.indiscale.com/caosdb-mysqlbackend/", None),
+ "linkahead-pylib": ("https://docs.linkahead.org/linkahead-pylib/", None),
+ "linkahead-mysqlbackend": ("https://docs.linkahead.org/linkahead-mysqlbackend/", None),
}
@@ -228,4 +228,4 @@ autosectionlabel_prefix_document = True
# -- Options for sphinx_a4doc ------------------------------------------------
-a4_base_path = abspath(dirname(__file__) + '/../main/java/org/caosdb/server/query')
+a4_base_path = abspath(dirname(__file__) + '/../main/java/org/linkahead/server/query')
diff --git a/src/doc/development/api/xml/Makefile b/src/doc/development/api/xml/Makefile
index b2314adb191575895a89770332261b505543e0f3..1eaf731ea1bcfb2f30ebdc8957755601542d57eb 100644
--- a/src/doc/development/api/xml/Makefile
+++ b/src/doc/development/api/xml/Makefile
@@ -1,4 +1,4 @@
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2021 Daniel Hornung <d.hornung@indiscale.com>
@@ -25,11 +25,11 @@ BUILDDIR ?= ../../../_static/api/xml/
doc:
mkdir -p $(BUILDDIR)
[ -e openapi-generator-cli.jar ] || wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/5.2.0/openapi-generator-cli-5.2.0.jar -O openapi-generator-cli.jar
- java -jar openapi-generator-cli.jar generate -i caosdb_openapi.yaml --config openapi_config.json -g html2 -o $(BUILDDIR)
+ java -jar openapi-generator-cli.jar generate -i linkahead_openapi.yaml --config openapi_config.json -g html2 -o $(BUILDDIR)
## Not needed (the same code anyway?)
# [ -e swagger-codegen-cli.jar ] || wget https://repo1.maven.org/maven2/io/swagger/codegen/v3/swagger-codegen-cli/3.0.27/swagger-codegen-cli-3.0.27.jar -O swagger-codegen-cli.jar
-# java -jar swagger-codegen-cli.jar generate -i caosdb_openapi.yaml -l html2 -o $(BUILDDIR)
+# java -jar swagger-codegen-cli.jar generate -i linkahead_openapi.yaml -l html2 -o $(BUILDDIR)
diff --git a/src/doc/development/api/xml/caosdb_openapi.yaml b/src/doc/development/api/xml/caosdb_openapi.yaml
index b2e0b7449d0ab9c4bc147692862aa69107828bac..f60a0a72599bcf4cb93eb271d75e3434a67eb984 100644
--- a/src/doc/development/api/xml/caosdb_openapi.yaml
+++ b/src/doc/development/api/xml/caosdb_openapi.yaml
@@ -1,7 +1,7 @@
openapi: "3.0.3"
info:
- title: CaosDB XML REST API
- description: The XML API of CaosDB, see also https://docs.indiscale.com/caosdb-server
+ title: LinkAhead XML REST API
+ description: The XML API of LinkAhead, see also https://docs.linkahead.org/linkahead-server
version: 0.0-poc.1
servers:
- url: https://demo.indiscale.com
@@ -83,7 +83,7 @@ paths:
get:
operationId: executeQuery
summary: Return the entities matching the given query
- description: Use arbitrary CaosDB queries to retrieve all matching entities
+ description: Use arbitrary LinkAhead queries to retrieve all matching entities
parameters:
- name: query
in: query
@@ -400,7 +400,7 @@ components:
properties:
datatype:
type: string
- description: The CaosDB datatype of this property
+ description: The LinkAhead datatype of this property
example: BOOLEAN
xml:
attribute: true
diff --git a/src/doc/development/api/xml/openapi_config.json b/src/doc/development/api/xml/openapi_config.json
index f27abea7e89a96ba0b39aa0f1ee5f3fdc836c854..3f861b15997053179de88cc9cfef48efdbbc0e7e 100644
--- a/src/doc/development/api/xml/openapi_config.json
+++ b/src/doc/development/api/xml/openapi_config.json
@@ -1,8 +1,8 @@
{
- "appName": "CaosDB",
- "appDescription": "CaosDB, the open data management toolkit",
- "infoUrl": "https://docs.indiscale.com/caosdb-server",
+ "appName": "LinkAhead",
+ "appDescription": "LinkAhead, the open data management toolkit",
+ "infoUrl": "https://docs.linkahead.org/linkahead-server",
"infoEmail": "info@indiscale.com",
"licenseInfo": "License: AGPLv3",
- "licenseUrl": "https://gitlab.com/caosdb/caosdb-server/-/blob/dev/LICENSE.md"
+ "licenseUrl": "https://gitlab.com/linkahead/linkahead-server/-/blob/dev/LICENSE.md"
}
diff --git a/src/doc/development/benchmarking.rst b/src/doc/development/benchmarking.rst
index 60d36d125b3749cff3538f837c8bd4f299233602..577bb522152b4fc957a207f1c049d3c5dddfafac 100644
--- a/src/doc/development/benchmarking.rst
+++ b/src/doc/development/benchmarking.rst
@@ -1,7 +1,7 @@
-Benchmarking CaosDB
+Benchmarking LinkAhead
===================
-Benchmarking CaosDB may encompass several distinct areas: How much time
+Benchmarking LinkAhead may encompass several distinct areas: How much time
is spent in the server’s Java code, how much time is spent inside the
SQL backend, are the same costly methods called more than once? This
documentation tries to answer some questions connected with these
@@ -32,8 +32,8 @@ Tools for the benchmarking
For averaging over many runs of comparable requests and for putting the
database into a representative state, Python scripts are used. The
-scripts can be found in the ``caosdb-dev-tools`` repository, located at
-https://gitlab.indiscale.com/caosdb/src/caosdb-dev-tools in the folder
+scripts can be found in the ``linkahead-dev-tools`` repository, located at
+https://gitlab.indiscale.com/caosdb/src/linkahead-dev-tools in the folder
``benchmarking``:
Python Script ``fill_database.py``
@@ -47,7 +47,7 @@ The script inserts predefined amounts of randomized Entities into the
database, RecordTypes, Properties and Records. Each Record has a random
(but with defined average) number of Properties, some of which may be
references to other Records which have been inserted before. Actual
-insertion of the Entities into CaosDB is done in chunks of a defined
+insertion of the Entities into LinkAhead is done in chunks of a defined
size.
Users can tell the script to store times needed for the insertion of
@@ -70,7 +70,7 @@ An sql file is automatically executed which enables the correct
mariadb needs to be enabled. Add ``performance_schema=ON`` to the
configuration file of mariadb as it needs to be enabled on start up.
This script expects the MariaDB server to be accessible on 127.0.0.1
-with the default caosdb user and password (caosdb;random1234).
+with the default linkahead user and password (caosdb; random1234).
You might consider to increase
``performance_schema_events_transactions_history_long_size``.
@@ -194,7 +194,7 @@ following for the mariadb service:
networks:
# available on port 3306, host name 'sqldb'
- - caosnet
+ - linkaheadnet
ports:
- 3306:3306
@@ -207,7 +207,7 @@ Manual Java-side benchmarking
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Benchmarking can be done using the ``TransactionBenchmark`` class (in
-package ``org.caosdb.server.database.misc``).
+package ``org.linkahead.server.database.misc``).
- Single timings can be added to instances of that class via the
``addBenchmark(object, time)`` method. Multiple benchmarks for the
@@ -288,7 +288,7 @@ In the sampler settings, you may want to add these expressions to the
blocked packages: ``org.restlet.**, com.mysql.**``. Branches on the call
tree which are entirely inside the blacklist, will become leaves.
Alternatively, specify a whitelist, for example with
-``org.caosdb.server.database.backend.implementation.**``, if you only
+``org.linkahead.server.database.backend.implementation.**``, if you only
want to see the time spent for certain MySQL calls.
How to set up a representative database
@@ -318,7 +318,7 @@ requests to the server are started.
When doing performance tests which are used for detailed analysis, it is
important that
-1. CaosDB is in a reproducible state, which should be documented
+1. LinkAhead is in a reproducible state, which should be documented
2. all measurements are repeated several times to account for inevitable
variance in access (for example file system caching, network
variablity etc.)
diff --git a/src/doc/development/devel.rst b/src/doc/development/devel.rst
index cf0ba37e75c967b755bc2951e803110b15f23baf..8c552a314b23ae82b744ab6ec84212cb44356367 100644
--- a/src/doc/development/devel.rst
+++ b/src/doc/development/devel.rst
@@ -1,5 +1,5 @@
-Developing CaosDB
-=================
+Developing LinkAhead
+====================
.. toctree::
:glob:
@@ -8,20 +8,20 @@ Developing CaosDB
Structure of the Java code <structure>
Testing the server code <testing>
Logging server output <logging>
- Benchmarking CaosDB <benchmarking>
+ Benchmarking LinkAhead <benchmarking>
-CaosDB is an Open-Source project, so anyone may modify the source as they like. These pages aim to
-provide some help for all CaosDB developers.
+LinkAhead is an Open-Source project, so anyone may modify the source as they like. These pages aim
+to provide some help for all LinkAhead developers.
-More generally, these are the most common ways to contribute to CaosDB:
+More generally, these are the most common ways to contribute to LinkAhead:
- You found a bug, have a question, or want to request a feature? Please `create an issue
- <https://gitlab.com/caosdb/caosdb-server/-/issues>`_.
+ <https://gitlab.com/linkahead/linkahead-server/-/issues>`_.
- You want to contribute code? Please fork the repository and create a merge request in GitLab and
choose this repository as target. Make sure to select "Allow commits from members who can merge
the target branch" under Contribution when creating the merge request. This allows our team to
work with you on your request.
-- If you have a suggestion for this `documentation <https://docs.indiscale.com/caosdb-server/>`_,
+- If you have a suggestion for this `documentation <https://docs.linkahead.org/linkahead-server/>`_,
the preferred way is also a merge request as describe above (the documentation resides in
``src/doc``). However, you can also create an issue for it.
-- You can also contact the developers at *info (AT) caosdb.de*.
+- You can also contact the developers at *info (AT) linkahead.org*.
diff --git a/src/doc/development/structure.rst b/src/doc/development/structure.rst
index 3848e983fca5d05871212e0985b98d539c04b7fe..8c2d03345a14cf5736d9bb80f498947aa30caa6a 100644
--- a/src/doc/development/structure.rst
+++ b/src/doc/development/structure.rst
@@ -1,7 +1,7 @@
-CaosDB's Internal Structure
+LinkAhead's Internal Structure
===========================
-The CaosDB server
+The LinkAhead server
- builds upon the `Restlet <https://restlet.talend.com/>`_ framework to provide a REST interface to
the network. See the :ref:`HTTP Resources` section for more information.
@@ -16,28 +16,28 @@ The CaosDB server
HTTP Resources
--------------
-HTTP resources are implemented in the :java:ref:`resource<org.caosdb.server.resource>` package, in
-classes inheriting from :java:ref:`AbstractCaosDBServerResource` (which inherits Restlet's
-:java:ref:`Resource<org.restlet.resource.Resource>` class). The main :java:ref:`CaosDBServer` class
+HTTP resources are implemented in the :java:ref:`resource<org.linkahead.server.resource>` package, in
+classes inheriting from :java:ref:`AbstractLinkAheadServerResource` (which inherits Restlet's
+:java:ref:`Resource<org.restlet.resource.Resource>` class). The main :java:ref:`LinkAheadServer` class
defines which HTTP resource (for example ``/Entity/{specifier}``) will be handled by which class
(:java:ref:`EntityResource` in this case).
Implementing classes need to overwrite for example the ``httpGetInChildClass()`` method (or methods
corresponding to other HTTP request methods such as POST, PUT, ...). Typically, they might call the
-``execute()`` method of a :java:ref:`Transaction<org.caosdb.server.transaction.Transaction>` object.
+``execute()`` method of a :java:ref:`Transaction<org.linkahead.server.transaction.Transaction>` object.
Transactions are explained in detail in the :ref:`Transactions and Schedules<transactions>` section.
.. uml::
@startuml
- abstract AbstractCaosDBServerResource {
+ abstract AbstractLinkAheadServerResource {
{abstract} httpGetInChildClass()
{abstract} httpPostInChildClass()
{abstract} ...InChildClass()
}
abstract RetrieveEntityResource
class EntityResource
- AbstractCaosDBServerResource <|-- RetrieveEntityResource
+ AbstractLinkAheadServerResource <|-- RetrieveEntityResource
RetrieveEntityResource <|-- EntityResource
@enduml
@@ -46,7 +46,7 @@ Transactions are explained in detail in the :ref:`Transactions and Schedules<tra
MySQL Backend
-------------
-The MySQL backend in CaosDB may be substituted by other backends, but at the time of writing this
+The MySQL backend in LinkAhead may be substituted by other backends, but at the time of writing this
documentation, only MySQL (MariaDB is used for testing) is implemented. There are the following
main packages which handle the backend:
@@ -108,7 +108,7 @@ For example, the structure when getting an Entity ID by name looks like this:
Transactions and Schedules
--------------------------
-In CaosDB, several client requests may be handled concurrently. This poses no problem as long as
+In LinkAhead, several client requests may be handled concurrently. This poses no problem as long as
only read-only requests are processed, but writing transactions need to block other requests.
Therefore all transactions (between their first and last access) block write transactions other than
themselves from writing to the backend, while read transactions may happen at any time, except when
@@ -116,13 +116,13 @@ a write transaction actually writes to the backend.
.. note::
- There is a fine distinction between write transactions on the CaosDB server and actually writing
+ There is a fine distinction between write transactions on the LinkAhead server and actually writing
to the backend, since even transactions which need only very short write access to the backend may
require extensive read access before, for example to check for permissions or to check if the
intended write action makes sense (linked entities must exist, they may need to be of the correct
RecordType, etc.).
-The request handling in CaosDB is organized in the following way:
+The request handling in LinkAhead is organized in the following way:
- HTTP resources usually create a :java:ref:`Transaction` object and call its
:java:ref:`Transaction.execute()` method. Entities are passed to and from the transaction via
diff --git a/src/doc/development/testing.rst b/src/doc/development/testing.rst
index 2587695d67684d132e942b8eb4f25cd1038c9907..aa8cfd410f4094765e07b5185d7409643d4ad9b9 100644
--- a/src/doc/development/testing.rst
+++ b/src/doc/development/testing.rst
@@ -8,7 +8,7 @@ and incorrect input.
Writing tests
~~~~~~~~~~~~~
-Tests go into ``src/test/java/caosdb/``, the files there can serve as examples for
+Tests go into ``src/test/java/linkahead/``, the files there can serve as examples for
writing tests.
Running tests with Maven
diff --git a/src/doc/entity-permission-table.rst b/src/doc/entity-permission-table.rst
index 1ff75f2138d7ae5382a00ee6fc9a60317fbbed28..efcb1c4f0e47dbf6b5d047b5e82fc2f2ce33274b 100644
--- a/src/doc/entity-permission-table.rst
+++ b/src/doc/entity-permission-table.rst
@@ -3,7 +3,7 @@
Entity Permissions
==================
-Permission to the following actions can be granted or denied in CaosDB:
+Permission to the following actions can be granted or denied in LinkAhead:
.. list-table:: Entity permission actions
:header-rows: 1
diff --git a/src/doc/index.rst b/src/doc/index.rst
index e34afd382f0c4a1a5520b94a4fc00e1c0a67427b..ed19ceb2a9437ae5eb9c99b5d38379d842bf10de 100644
--- a/src/doc/index.rst
+++ b/src/doc/index.rst
@@ -1,6 +1,6 @@
-Welcome to caosdb-server's documentation!
-=========================================
+Welcome to the documentation of the LinkAhead server!
+=====================================================
.. toctree::
:maxdepth: 2
@@ -12,7 +12,7 @@ Welcome to caosdb-server's documentation!
Concepts <concepts>
tutorials
FAQ
- Query Language <CaosDB-Query-Language>
+ Query Language <LinkAhead-Query-Language>
administration
Development <development/devel>
Dependencies <DEPENDENCIES>
@@ -21,11 +21,14 @@ Welcome to caosdb-server's documentation!
Glossary
Server Internals<_apidoc/packages>
-Welcome to the CaosDB, the flexible semantic data management toolkit!
+Welcome to the LinkAhead, the flexible semantic data management toolkit!
+
+.. note::
+ LinkAhead was formerly known as CaosDB, the name was changed in 2023.
This documentation helps you to :doc:`get started<README_SETUP>`,
explains the most important :doc:`concepts<concepts>` and has
-information if you want to :doc:`develop<development/devel>` CaosDB
+information if you want to :doc:`develop<development/devel>` LinkAhead
yourself.
diff --git a/src/doc/permissions.rst b/src/doc/permissions.rst
index 3d9c5ed7c26349ca0a20dec4e89b8889d4e10bf1..109b26e84f4e1b09d4f6f2a879698b1cbef1cee1 100644
--- a/src/doc/permissions.rst
+++ b/src/doc/permissions.rst
@@ -1,7 +1,7 @@
Permissions
===========
-CaosDB has a fine grained role-based permission system. Each interaction with
+LinkAhead has a fine grained role-based permission system. Each interaction with
the server is governed by the current role(s) of the user, by default this is
the ``anonymous`` role. The permissions for an action which involves one or more
objects are set either manually or via default permissions which can be
@@ -126,15 +126,15 @@ How to set permissions
There are multiple ways to set role and entity permissions. The most
common and best tested way currently is to set global default *entity* permissions
in the ``global_entity_permissions.xml`` config file, and role-based *role*
-permissions with the ``caosdb_admin.py`` `utility script
-<https://gitlab.com/caosdb/caosdb-pylib/-/blob/main/src/caosdb/utils/caosdb_admin.py>`__
-of CaosDB's Python library which is also used to `manage users and
-roles <https://docs.indiscale.com/caosdb-pylib/administration.html>`__. Below you
+permissions with the ``linkahead_admin.py`` `utility script
+<https://gitlab.com/linkahead/linkahead-pylib/-/blob/main/src/linkahead/utils/linkahead_admin.py>`__
+of LinkAhead's Python library which is also used to `manage users and
+roles <https://docs.linkahead.org/linkahead-pylib/administration.html>`__. Below you
find a more detailed description of the possible ways of setting permissions.
- **Config file:** Some default permissions are typically set in the
``global_entity_permissions.xml`` file, see also the `default file
- <https://gitlab.com/caosdb/caosdb-server/-/blob/main/conf/core/global_entity_permissions.xml>`__. Here,
+ <https://gitlab.com/linkahead/linkahead-server/-/blob/main/conf/core/global_entity_permissions.xml>`__. Here,
you can set the default permissions that every entity on the server has. The
global default permissions can **only** be set in this file; all other ways
below can only change the permissions of individual entities. Note that you
@@ -147,22 +147,22 @@ find a more detailed description of the possible ways of setting permissions.
set with one of the other ways explained below.
- **API:** Both REST and GRPC API allow to set the permissions. This hasn't been
documented properly yet, but for the GRPC API, `the specification
- <https://gitlab.com/caosdb/caosdb-proto/-/blob/main/proto/caosdb/acm/v1alpha1/main.proto>`__
+ <https://gitlab.com/linkahead/linkahead-proto/-/blob/main/proto/linkahead/acm/v1alpha1/main.proto>`__
may give some insight.
- **The Python library:** The permissions can also conveniently be set via the
Python library. Currently the best documentation is inside various files
which use the permission API:
- The `example file
- <https://gitlab.com/caosdb/caosdb-pylib/-/blob/main/examples/set_permissions.py>`__
- - The ``caosdb_admin.py`` `utility script
- <https://gitlab.com/caosdb/caosdb-pylib/-/blob/main/src/caosdb/utils/caosdb_admin.py>`__
- - There is a comprehensive `example <https://docs.indiscale.com/caosdb-pylib/gallery/curator-permissions.html>`_
- in PyCaosDB's gode gallery.
+ <https://gitlab.com/linkahead/linkahead-pylib/-/blob/main/examples/set_permissions.py>`__
+ - The ``linkahead_admin.py`` `utility script
+ <https://gitlab.com/linkahead/linkahead-pylib/-/blob/main/src/linkahead/utils/linkahead_admin.py>`__
+ - There is a comprehensive `example <https://docs.linkahead.org/linkahead-pylib/gallery/curator-permissions.html>`_
+ in PyLinkAhead's gode gallery.
- The `integration tests
- <https://gitlab.com/caosdb/caosdb-pyinttest/-/blob/main/tests/test_permissions.py>`__
+ <https://gitlab.com/linkahead/linkahead-pyinttest/-/blob/main/tests/test_permissions.py>`__
also cover quite a bit of the permission API.
- **WebUI:** This is currently work in progress. A WebUI ACM module which uses the
GRPC interface is under `active development
- <https://gitlab.indiscale.com/caosdb/src/caosdb-webui2>`__.
+ <https://gitlab.indiscale.com/caosdb/src/linkahead-webui2>`__.
diff --git a/src/doc/query-syntax.rst b/src/doc/query-syntax.rst
index 00df440fb9cf2a175e371c3038b164643d89a84a..3e15427c5a30ff808e0d8e1f53a187d50349527d 100644
--- a/src/doc/query-syntax.rst
+++ b/src/doc/query-syntax.rst
@@ -1,14 +1,14 @@
-CaosDB Query Language Syntax
+LinkAhead Query Language Syntax
============================
-This is the documentation of the CaosDB Query Language Syntax. The
+This is the documentation of the LinkAhead Query Language Syntax. The
authoritative specification of the syntax is the ANTLR4 grammar you can find in
the source code:
-`CQLParser.g4 <https://gitlab.com/caosdb/caosdb-server/-/blob/main/src/main/java/org/caosdb/server/query/CQLParser.g4>`__
+`CQLParser.g4 <https://gitlab.com/linkahead/linkahead-server/-/blob/main/src/main/java/org/linkahead/server/query/CQLParser.g4>`__
and
-`CQLLexer.g4 <https://https://gitlab.com/caosdb/caosdb-server/-/blob/main/src/main/java/org/caosdb/server/query/CQLLexer.g4>`__
+`CQLLexer.g4 <https://https://gitlab.com/linkahead/linkahead-server/-/blob/main/src/main/java/org/linkahead/server/query/CQLLexer.g4>`__
-See examples in :doc:`Query Language<CaosDB-Query-Language>`.
+See examples in :doc:`Query Language<LinkAhead-Query-Language>`.
.. a4:autogrammar:: CQLParser.g4
diff --git a/src/doc/role-permission-table.rst b/src/doc/role-permission-table.rst
index 2860407fad11d53e7ddefc8adff06c8ae0fde420..ce46dc53595aa8ac145fe542d95ac8aebc45eb63 100644
--- a/src/doc/role-permission-table.rst
+++ b/src/doc/role-permission-table.rst
@@ -3,7 +3,7 @@
Role Permissions
================
-Roles in CaosDB can have the following permissions
+Roles in LinkAhead can have the following permissions
.. list-table:: Role permissions
:header-rows: 1
diff --git a/src/doc/roles.md b/src/doc/roles.md
index 838b3d9ec92626676c2ca16535496620bedd5842..b83cb200813e16b17a4695070973ea77149fb044 100644
--- a/src/doc/roles.md
+++ b/src/doc/roles.md
@@ -2,8 +2,8 @@
## Users and roles ##
-Interaction with CaosDB happens either as an authenticated *user* or without
-authentication. In CaosDB, users can have zero, one or more *roles*, several
+Interaction with LinkAhead happens either as an authenticated *user* or without
+authentication. In LinkAhead, users can have zero, one or more *roles*, several
users may have the same role, and there may be roles without any users.
## What are users and roles good for? ##
diff --git a/src/doc/specification/AbstractProperty.md b/src/doc/specification/AbstractProperty.md
index 062ef205e048aef4142c683c9c4c1820fd89fe36..fd65d9b27ca00d6b245c03d847ad24ec6e42d800 100644
--- a/src/doc/specification/AbstractProperty.md
+++ b/src/doc/specification/AbstractProperty.md
@@ -6,10 +6,10 @@ up-to-date description of the `Property` entity.
## Note ##
> This document has not been updated for a long time. Although it is concerned with the mostly
-> stable API, its content may no longer reflect the actual CaosDB behavior.
+> stable API, its content may no longer reflect the actual LinkAhead behavior.
## Introduction
-An `AbstractProperty` is one of the basal objects of CaosDB.
+An `AbstractProperty` is one of the basal objects of LinkAhead.
An `AbstractProperty` MUST have the following _qualities_ (shortcut in brackets):
* a persistent id (`id`)
* an unique name (`name`)
@@ -42,7 +42,7 @@ An `AbstractProperty` is represented in xml by a `<Property/>` tag. It's _qualit
Depending on the purpose of the xml document (shall it represent an object in the database or an object _to be posted _to the database?) the `<Property/>` tag may actually have just a few of the mentioned "quality-attributes".
### GET AbstractProperty
-Any xml representation of an `AbstractProperty` that is retrieved from the CaosDB Server MUST have exactly ONE of the following forms, depending on the `AbstractProperty's` type:
+Any xml representation of an `AbstractProperty` that is retrieved from the LinkAhead Server MUST have exactly ONE of the following forms, depending on the `AbstractProperty's` type:
#### text
<Property id="$id" name="$name" description="$description" generator="$generator" creator="$creator" created="$created" type="text" />
@@ -62,10 +62,10 @@ Any xml representation of an `AbstractProperty` that is retrieved from the CaosD
<Property id="$id" name="$name" description="$description" generator="$generator" creator="$creator" created="$created" type="file" />
'''General Notes:
-* If the called Property does not exist or if the Property called without permission, the CaosDB Server will return an Error.
+* If the called Property does not exist or if the Property called without permission, the LinkAhead Server will return an Error.
### POST AbstractProperty
-Any xml representation of an `AbstractProperty` that is to be posted to the CaosDB server MUST have exactly ONE of the following forms, depending on the `AbstractProperty's` type:
+Any xml representation of an `AbstractProperty` that is to be posted to the LinkAhead server MUST have exactly ONE of the following forms, depending on the `AbstractProperty's` type:
#### text
<Property name="$name" description="$description" generator="$generator" type="text" />
@@ -85,10 +85,10 @@ Any xml representation of an `AbstractProperty` that is to be posted to the Caos
<Property name="$name" description="$description" generator="$generator" type="file" />
*General Notes:*
-* The `AbstractProperty's` `id` and timestamp (`created`) will be generated by the CaosDB Server.
-* The `AbstractProperty's` creator will be determined by the CaosDB Server depending on it's policy configuration.
+* The `AbstractProperty's` `id` and timestamp (`created`) will be generated by the LinkAhead Server.
+* The `AbstractProperty's` creator will be determined by the LinkAhead Server depending on it's policy configuration.
* Any given attribute beyond these will be *ignored*.
-* If the `<Property/>` tag isn't compliant with these the CaosDB Server will return an Error.
+* If the `<Property/>` tag isn't compliant with these the LinkAhead Server will return an Error.
----
## Examples
diff --git a/src/doc/specification/Authentication.rst b/src/doc/specification/Authentication.rst
index 3fcd25dad0d7fb9e591e1d4a2d845b3d353fff8b..a8d4d33a44a7364ce98d289f538fe3b1b0efbbf6 100644
--- a/src/doc/specification/Authentication.rst
+++ b/src/doc/specification/Authentication.rst
@@ -2,7 +2,7 @@
Authentication
==============
-Some features of CaosDB are available to registered users only. Making any changes to the data stock
+Some features of LinkAhead are available to registered users only. Making any changes to the data stock
via HTTP requires authentication.
Sessions
@@ -18,7 +18,7 @@ username:
The user name, for example ``admin`` (on demo.indiscale.com).
password:
- The password, for example ``caosdb`` (on demo.indiscale.com).
+ The password, for example ``linkahead`` (on demo.indiscale.com).
Logout
------
diff --git a/src/doc/specification/Datatype.md b/src/doc/specification/Datatype.md
index 6354d6f2cfdb5215d94836bfe263e2d013bd71a8..795e2408d50af5ef4384bbb5efba425a1081ceaa 100644
--- a/src/doc/specification/Datatype.md
+++ b/src/doc/specification/Datatype.md
@@ -55,7 +55,7 @@ The DateTime data type exists in (currently) three flavors which are dynamically
* It is allowed to ommit the nanosecond part of a UTCDateTime (`2016-01-01T13:23:00CEST`). This indicates a precision of seconds for a UTCDateTime value.
### Date
- Description:: This DATETIME flavor stores values which represent a single date, month or year according to the [gregorian calendar](https://en.wikipedia.org/wiki/Gregorian_Calendar). A month/year is conceived as a single date with the presion of a month/year. This concept is useful if you try to understand the query semantics which are explained [elsewhere](../CaosDB-Query-Language.html#pov-property-operator-value).
+ Description:: This DATETIME flavor stores values which represent a single date, month or year according to the [gregorian calendar](https://en.wikipedia.org/wiki/Gregorian_Calendar). A month/year is conceived as a single date with the presion of a month/year. This concept is useful if you try to understand the query semantics which are explained [elsewhere](../LinkAhead-Query-Language.html#pov-property-operator-value).
Format:: `Y[YYY][-MM[-dd]]` (where square brackets mean that the expression is optional).
Range:: Any valid date according to the gregorian calendar from `-9999-01-01` to `9999-12-31` (and respective dates with lower precision. E.g. the year `-9999`). There is no year `0`.
* Note: Date is a specialization of [#SemiCompleteDateTime].
diff --git a/src/doc/specification/Entity_Overview.md b/src/doc/specification/Entity_Overview.md
index ca197e50050d9ba2c593973148627c4d56708a67..7c60b8b4bd78ecaca62031deeb84b69952b26ed5 100644
--- a/src/doc/specification/Entity_Overview.md
+++ b/src/doc/specification/Entity_Overview.md
@@ -1,4 +1,4 @@
-# Overview of the CaosDB Entities' structure
+# Overview of the LinkAhead Entities' structure
**Warning:** This overview may be outdated.
@@ -12,7 +12,7 @@ Date: 2017-12-17
## Introduction
-CaosDB is a database management system that stores it's data into `Entities`. An `Entity` can be thought of as the equivalent to tables, rows, columns and the tuples that fill the tables of a traditional RDBMS. Entities are not only used to store the data they also define the structure of the data.
+LinkAhead is a database management system that stores it's data into `Entities`. An `Entity` can be thought of as the equivalent to tables, rows, columns and the tuples that fill the tables of a traditional RDBMS. Entities are not only used to store the data they also define the structure of the data.
## Formal Definition
diff --git a/src/doc/specification/Fileserver.md b/src/doc/specification/Fileserver.md
index dd3e0f37f4da98aef413c3a4aed15da2e8230b66..4701ea6f6f0bb8c10c0ee61863e9184110c68c76 100644
--- a/src/doc/specification/Fileserver.md
+++ b/src/doc/specification/Fileserver.md
@@ -1,12 +1,12 @@
# Fileserver
## Info
-There are several ways to utilize the file server component of CaosDB. It is possible to upload a file or a whole folder including subfolders via HTTP and the _drop off box_. It is possible to download a file via HTTP identified by its ID or by its path in the internal file system. Furthermore, it is possible to get the files metadata via HTTP as an xml.
+There are several ways to utilize the file server component of LinkAhead. It is possible to upload a file or a whole folder including subfolders via HTTP and the _drop off box_. It is possible to download a file via HTTP identified by its ID or by its path in the internal file system. Furthermore, it is possible to get the files metadata via HTTP as an xml.
## File upload
### Drop off box
-The drop off box is a directory on the CaosDB server's local file system, specified in the `server.conf` file in the server's basepath (something like `~/CaosDB/server/server.conf`). The key in the `server.conf` is called `dropoffbox`. Since the drop off box directory is writable for all, users can push their files or complete folders via a `mv` or a `cp` (recommended!) in that folder. The server deletes files older than their maximum lifetime (24 hours by default, specified `in server.conf`). But within their lifetime a user can prompt the server to pick up the file (or folder) from the drop off box in order to transfer it to the internal file system.
+The drop off box is a directory on the LinkAhead server's local file system, specified in the `server.conf` file in the server's basepath (something like `~/LinkAhead/server/server.conf`). The key in the `server.conf` is called `dropoffbox`. Since the drop off box directory is writable for all, users can push their files or complete folders via a `mv` or a `cp` (recommended!) in that folder. The server deletes files older than their maximum lifetime (24 hours by default, specified `in server.conf`). But within their lifetime a user can prompt the server to pick up the file (or folder) from the drop off box in order to transfer it to the internal file system.
Now, the user may send a pick up request to `POST http://host:port/mpidsserver/FilesDropOff` with a similar body:
@@ -38,9 +38,9 @@ where
There is an example on file upload using cURL described in detail in [the curl section of this
documentation](../administration/curl-access.md).
-File upload via HTTP is implemented in a [rfc1867](http://www.ietf.org/rfc/rfc1867.txt) consistent way. This is a de-facto standard that defines a file upload as a part of an HTML form submission. This concept shall not be amplified here. But it has to be noticed that this protocol is not designed for uploads of complete structured folders. Therefore the CaosDB file components have to impose that structure on the upload protocol.
+File upload via HTTP is implemented in a [rfc1867](http://www.ietf.org/rfc/rfc1867.txt) consistent way. This is a de-facto standard that defines a file upload as a part of an HTML form submission. This concept shall not be amplified here. But it has to be noticed that this protocol is not designed for uploads of complete structured folders. Therefore the LinkAhead file components have to impose that structure on the upload protocol.
-CaosDB's file upload resource does exclusively accept POST requests of MIME media type `multipart/form-data`. The first part of each POST body is expected to be a form-data text field, containing information about the files to be uploaded. It has to meet the following requirements:
+LinkAhead's file upload resource does exclusively accept POST requests of MIME media type `multipart/form-data`. The first part of each POST body is expected to be a form-data text field, containing information about the files to be uploaded. It has to meet the following requirements:
* `Content-type: text/plain; charset=UTF-8`
* `Content-disposition: form-data; name="FileRepresentation"`
diff --git a/src/doc/specification/RecordType.rst b/src/doc/specification/RecordType.rst
index 53e8e1613dddeea901e1b8404f186d67ebc2be23..16a9d4a54a3993ceca6bc2cc7f7c7b6471cdf02a 100644
--- a/src/doc/specification/RecordType.rst
+++ b/src/doc/specification/RecordType.rst
@@ -103,7 +103,7 @@ Examples
The following examples have not been updated in a while and may
serve as a starting point, but are not guaranteed to be fully
- applicable to the most recent versions of CaosDB.
+ applicable to the most recent versions of LinkAhead.
GET Requests
~~~~~~~~~~~~
diff --git a/src/doc/specification/Server-side-scripting.md b/src/doc/specification/Server-side-scripting.md
index 18dfe9eab0201fdd322bb2f61cbc87370ced99d5..5da939fed77f01cd9e7e340d0e907d379211e2c1 100644
--- a/src/doc/specification/Server-side-scripting.md
+++ b/src/doc/specification/Server-side-scripting.md
@@ -1,13 +1,13 @@
# Server-Side Scripting API (v0.1)
-The CaosDB Server can execute scripts (bash/python/perl) and
+The LinkAhead Server can execute scripts (bash/python/perl) and
compiled executables. The scripts can be invoked by a remote-procedure-call
(RPC) protocol. Both, the requirements for the scripts and the
RPC are described in this document.
## Configuration of the Server
-The CaosDB Server has two relevant properties:
+The LinkAhead Server has two relevant properties:
### `SERVER_SIDE_SCRIPTING_BIN_DIR`
is the directory where executable scripts are to be placed. The server will not execute scripts which are out side of this directory. This directory must be readable and executable for the server. But it should not be readable or executable for anyone else.
@@ -50,7 +50,7 @@ is the directory under which the server creates temporary working directories. T
3. Zero or more parameter form fields with a unique name which starts with the string `-p` (positional command line arguments).
4. Zero or more file form fields which have a unique field name and a unique file name (upload files). If the field names or file names are not unique, the behavior is not defined.
5. A parameter form field with name="timeout" (the request timeout)
- 6. A parameter form field with name="auth-token" and a valid CaosDB AuthToken string or "generate" as value.
+ 6. A parameter form field with name="auth-token" and a valid LinkAhead AuthToken string or "generate" as value.
## How Does the Server Call the Script?
* The server executes the script in a temporary working directory, called *PWD* (which will be deleted afterwards).
@@ -81,9 +81,9 @@ where the user uploads `my.conf` as `-Oconfig-file` and `my.input.tsv` as `-p1`,
$SERVER_SIDE_SCRIPTING_BIN_DIR/my/script.py --config-file=.upload_files/my.conf --algorithm=fast analyze .upload_files/my.input.tsv
```
-## CaosDB Server Response
+## LinkAhead Server Response
-The CaosDB Server responds with an xml document. The root element is the usual `/Response`. If no errors occurred (which would be represented with `/Response/Error` elements) the result of the script execution is represented as a `/Response/script/` element.
+The LinkAhead Server responds with an xml document. The root element is the usual `/Response`. If no errors occurred (which would be represented with `/Response/Error` elements) the result of the script execution is represented as a `/Response/script/` element.
* It has a `code` attribute which contains the exit code value of the execution.
* It has `stdout` and `stderr` children which contain the dump of the stdout and stderr file of the execution environment.
@@ -100,13 +100,13 @@ The CaosDB Server responds with an xml document. The root element is the usual `
</Response>
```
-## CaosDB Clients and Authentication Token
+## LinkAhead Clients and Authentication Token
-A special use case for server side scripting is the automated execution of CaosDB clients. These clients need to connect to the CaosDB Server and thus need a way to authenticate themselves.
+A special use case for server side scripting is the automated execution of LinkAhead clients. These clients need to connect to the LinkAhead Server and thus need a way to authenticate themselves.
For this special case the server can pass an Authentication Token which can be used by the script to authenticate itself. If the invocation request send a particulare AuthToken in the form, this AuthToken will be passed to the script with the `--auth-token` option. Otherwise, if the `auth-token` field has "generate" as value, a fresh AuthToken is generated which belongs to the user who requested the script execution.
Thus the script is executed (and connects back to the server) as the user who called the script in the first place.
-A CaosDB client might use the python client library to connect to the server with that AuthToken.
+A LinkAhead client might use the python client library to connect to the server with that AuthToken.
### Example Script
@@ -115,7 +115,7 @@ A CaosDB client might use the python client library to connect to the server wit
# -*- coding: utf-8 -*-
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -150,7 +150,7 @@ specified with the commandline option --exit
import sys
from os import listdir
-from caosdb import configure_connection, execute_query
+from linkahead import configure_connection, execute_query
# parse --auth-token option and configure connection
diff --git a/src/doc/specification/entity_api.rst b/src/doc/specification/entity_api.rst
index 3f6bdbcf700aaeebbe7d49fe79ac47c4ad4303ad..997105373f3fae7f07d87bea60352e3829370da7 100644
--- a/src/doc/specification/entity_api.rst
+++ b/src/doc/specification/entity_api.rst
@@ -6,7 +6,7 @@ The Entity API
:caption: Contents:
:hidden:
- Overview of the CaosDB Entities' structure<Entity_Overview>
+ Overview of the LinkAhead Entities' structure<Entity_Overview>
.. note::
@@ -16,7 +16,7 @@ The Entity API
The details of the specification, including interactive examples, can
be found `here
-<https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/tree/dev/src/doc/development/api/xml/caosdb_openapi.yaml>`_.
+<https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/tree/dev/src/doc/development/api/xml/linkahead_openapi.yaml>`_.
Note that some commands may require authentication, which can be done with
an authentication cookie as described in the :doc:`api
documentation<Authentication>`. Specialities of the :doc:`scripting
diff --git a/src/doc/tutorials/data_model_tutorial.rst b/src/doc/tutorials/data_model_tutorial.rst
index c1de9b08a38623751ec3d50a38ee001fbe8619d9..f510266c26b80845e49d096aeba28b9f584cf345 100644
--- a/src/doc/tutorials/data_model_tutorial.rst
+++ b/src/doc/tutorials/data_model_tutorial.rst
@@ -3,7 +3,7 @@ Data model tutorial
Data models are a central concept of research data management. The
open-source framework LinkAhead makes it easy to create an `agile
-data model <https://docs.indiscale.com/caosdb-server/Data-Model.html>`__
+data model <https://docs.linkahead.org/linkahead-server/Data-Model.html>`__
which suits your needs, so you can profit from your collected data fast.
.. contents::
@@ -15,7 +15,7 @@ Frequently asked questions about data models
What is a data model?
~~~~~~~~~~~~~~~~~~~~~
-In LinkAhead, the `data model <https://docs.indiscale.com/caosdb-server/Data-Model.html>`__
+In LinkAhead, the `data model <https://docs.linkahead.org/linkahead-server/Data-Model.html>`__
describes in a generic way how the data is structured. This document will help you understand this
concept and how you can adjust the data model to your needs.
@@ -44,9 +44,9 @@ will be available to all cell culture experiments.
A simple data model, with four RecordTypes
In LinkAhead, the data model consists of *RecordTypes* and *Properties*. Each `*RecordType*
-<https://docs.indiscale.com/caosdb-server/Data-Model.html#record-types>`__ corresponds to one type
+<https://docs.linkahead.org/linkahead-server/Data-Model.html#record-types>`__ corresponds to one type
of data set, for example an experiment, a cell culture experiment or a cell line. And each data set
-can have `*Properties* <https://docs.indiscale.com/caosdb-server/Data-Model.html#properties>`__
+can have `*Properties* <https://docs.linkahead.org/linkahead-server/Data-Model.html#properties>`__
which define it further: for example
the number of dishes in a cell culture experiment, a publication
describing a cell line or the cell line which was used for an
@@ -102,17 +102,17 @@ Modifying the data model in LinkAhead
The easiest way to change the data model is to `use the LinkAhead
web
-application <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html>`__.
+application <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html>`__.
But the first step is to look at the current data model (*RecordTypes*
and *Properties*) and your current situation, to find out what you need
changed. It may help to ask yourself these questions:
- Do you want to describe data of existing types in more detail? -> :ref:`Create
*Properties*<new_property>` if necessary, then `add
- <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#add-properties-to-an-existing-recordtype>`__
+ <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html#add-properties-to-an-existing-recordtype>`__
these *Properties* to the existing *RecordTypes*.
- Do you need to add a property more than once? -> Make that property `a list property
- <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#make-a-property-into-a-list>`__\
+ <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html#make-a-property-into-a-list>`__\
.
- Are there completely new types of data? -> :ref:`Create a new
*RecordType* <new_recordtype>` .
@@ -127,11 +127,11 @@ changed. It may help to ask yourself these questions:
*RecordType* <new_recordtype>` .
- Are there *Properties* or *RecordTypes* which were created in the past, but will never be used? ->
`Delete them
- <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#delete-an-entity>`__.
+ <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html#delete-an-entity>`__.
Once you know what you want to do, open the LinkAhead web application, log in and click on the “Edit
Mode” button in the menu. Then follow one of the instructions in the next sections or the general `Edit
-Mode documentation <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html>`__..
+Mode documentation <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html>`__..
.. figure:: img/edit_mode_button.png
:alt: The Edit Mode button appears when a user is logged in.
@@ -162,7 +162,7 @@ the data model.
3. Click on the “Create Property” button in the toolbox. A dialog for
the new Property shows up.
4. Follow the `WebUI documentation
- <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#new-property>`__ for Property
+ <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html#new-property>`__ for Property
creation.
.. _new_recordtype:
@@ -187,7 +187,7 @@ Create a new RecordType
the new Property shows up.
4. Follow the `WebUI documentation
- <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#new-recordtype>`__ for
+ <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html#new-recordtype>`__ for
RecordType creation.
What about letting users only choose from a fixed set of values (a.k.a. enums)?
diff --git a/src/doc/tutorials/setup_state_model.py b/src/doc/tutorials/setup_state_model.py
index 0a1a7daa3b14d7c3e7a5b8eac093857bddfad330..27cc528cf7d7c7dc5c8c1470dbc02e197f51482b 100755
--- a/src/doc/tutorials/setup_state_model.py
+++ b/src/doc/tutorials/setup_state_model.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python3
# encoding: utf-8
#
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2021 Indiscale GmbH <info@indiscale.com>
# Copyright (C) 2021 Henrik tom Wörden <h.tomwoerden@indiscale.com>
@@ -33,8 +33,8 @@ order:
"""
from argparse import ArgumentParser, RawDescriptionHelpFormatter
-import caosdb as db
-from caosdb.common.administration import generate_password
+import linkahead as db
+from linkahead.common.administration import generate_password
def teardown(args):
diff --git a/src/doc/tutorials/statemachine.rst b/src/doc/tutorials/statemachine.rst
index dc46885a39548042314e77c76b1578e1a8ac2a74..693d95bd1ae6f48b36eb44821d75f793a1a74d4f 100644
--- a/src/doc/tutorials/statemachine.rst
+++ b/src/doc/tutorials/statemachine.rst
@@ -9,7 +9,7 @@ In order to use the state machine functionality you have to set the
corresponding server setting: ``EXT_ENTITY_STATE=ENABLED``.
Also, a few RecordTypes and Properties are required. You can use the
-script `setup_state_model.py <https://gitlab.com/caosdb/caosdb-server/-/blob/dev/src/doc/tutorials/setup_state_model.py>`_
+script `setup_state_model.py <https://gitlab.com/linkahead/linkahead-server/-/blob/dev/src/doc/tutorials/setup_state_model.py>`_
to create those or you may have a look at it to see what is needed (``setup_state_data_model`` function).
Defining the State Machine
diff --git a/src/main/java/org/caosdb/datetime/Date.java b/src/main/java/org/caosdb/datetime/Date.java
index 2b7aa522272f48b468dd8c4945360dee14f52d6e..e6e40d131aaabda4f9ddb786dbed70a5b3f9dae3 100644
--- a/src/main/java/org/caosdb/datetime/Date.java
+++ b/src/main/java/org/caosdb/datetime/Date.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.Calendar;
import java.util.GregorianCalendar;
import java.util.TimeZone;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
public class Date extends SemiCompleteDateTime {
diff --git a/src/main/java/org/caosdb/datetime/DateTimeFactory2.java b/src/main/java/org/caosdb/datetime/DateTimeFactory2.java
index 14088ea5d1033771d8835352b61e5bf430c4ff5f..93773a28a581ae0955a4d5359e889368a59b551d 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeFactory2.java
+++ b/src/main/java/org/caosdb/datetime/DateTimeFactory2.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.Arrays;
import java.util.Calendar;
import java.util.TimeZone;
import org.antlr.v4.runtime.CharStreams;
import org.antlr.v4.runtime.CommonTokenStream;
-import org.caosdb.server.query.CQLParsingErrorListener;
-import org.caosdb.server.query.CQLParsingErrorListener.ParsingError;
+import org.linkahead.server.query.CQLParsingErrorListener;
+import org.linkahead.server.query.CQLParsingErrorListener.ParsingError;
/**
- * Factory which parses string into CaosDB's DATETIME values.
+ * Factory which parses string into LinkAhead's DATETIME values.
*
* @author tf
*/
diff --git a/src/main/java/org/caosdb/datetime/DateTimeFactoryInterface.java b/src/main/java/org/caosdb/datetime/DateTimeFactoryInterface.java
index c81018f939747344b6991e291d3439f164dad283..08065bbcc62efb53a2553fedbeb74c1713252c5f 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeFactoryInterface.java
+++ b/src/main/java/org/caosdb/datetime/DateTimeFactoryInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.Date;
diff --git a/src/main/java/org/caosdb/datetime/DateTimeInterface.java b/src/main/java/org/caosdb/datetime/DateTimeInterface.java
index e6f1b93382da7deaf1ec1226d193fe1db4b3735d..acd5ef694e9c9e66d915e820dd2c8da238a25b0f 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeInterface.java
+++ b/src/main/java/org/caosdb/datetime/DateTimeInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.TimeZone;
-import org.caosdb.server.datatype.SingleValue;
+import org.linkahead.server.datatype.SingleValue;
public interface DateTimeInterface extends SingleValue {
diff --git a/src/main/java/org/caosdb/datetime/DateTimeLexer.g4 b/src/main/java/org/caosdb/datetime/DateTimeLexer.g4
index 1be8e2853b1c39c761489b686dfdad36d832a42f..9e814d972e863f4568a8c0b06ebf158d7685a9ff 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeLexer.g4
+++ b/src/main/java/org/caosdb/datetime/DateTimeLexer.g4
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/src/main/java/org/caosdb/datetime/DateTimeParser.g4 b/src/main/java/org/caosdb/datetime/DateTimeParser.g4
index 3923e9c36a4d0c72b4d0aa831c9a4db7e1618a39..2dd15720dc5732419d20754d5faf8df5e2358b39 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeParser.g4
+++ b/src/main/java/org/caosdb/datetime/DateTimeParser.g4
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/src/main/java/org/caosdb/datetime/DateTimeStringStrategy.java b/src/main/java/org/caosdb/datetime/DateTimeStringStrategy.java
index 635b2cfa0569e62847e8f4f2af0684c5919e8f8d..a95b9e26a6bb46621c286d8fc7d7a471990366d6 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeStringStrategy.java
+++ b/src/main/java/org/caosdb/datetime/DateTimeStringStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.TimeZone;
diff --git a/src/main/java/org/caosdb/datetime/FragmentDateTime.java b/src/main/java/org/caosdb/datetime/FragmentDateTime.java
index 38c16a988a0103a121767b99078c0ca41c6263d5..6f5f23b1fcd2e2b742747539cf6cdc27579d9bb5 100644
--- a/src/main/java/org/caosdb/datetime/FragmentDateTime.java
+++ b/src/main/java/org/caosdb/datetime/FragmentDateTime.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,11 +22,11 @@
*/
/** @review Daniel Hornung 2022-03-04 */
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.Objects;
import java.util.TimeZone;
-import org.caosdb.server.datatype.Value;
+import org.linkahead.server.datatype.Value;
public abstract class FragmentDateTime implements DateTimeInterface {
diff --git a/src/main/java/org/caosdb/datetime/GregorianCalendarDateTimeStringStrategy.java b/src/main/java/org/caosdb/datetime/GregorianCalendarDateTimeStringStrategy.java
index 459f1d592beca6b62704e9592c6afe39c1104f57..8983694e8bd247a832591d05e10a55c0e60c8eeb 100644
--- a/src/main/java/org/caosdb/datetime/GregorianCalendarDateTimeStringStrategy.java
+++ b/src/main/java/org/caosdb/datetime/GregorianCalendarDateTimeStringStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.text.SimpleDateFormat;
import java.util.Calendar;
diff --git a/src/main/java/org/caosdb/datetime/Interval.java b/src/main/java/org/caosdb/datetime/Interval.java
index 9890fb4c0643c498dc5e7d5108b9c9c4a13cc9b8..f4e6f1c2fe98300d1b481402da0092da42e663d7 100644
--- a/src/main/java/org/caosdb/datetime/Interval.java
+++ b/src/main/java/org/caosdb/datetime/Interval.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
public interface Interval extends DateTimeInterface {
diff --git a/src/main/java/org/caosdb/datetime/LeapSecondDateTimeStringStrategy.java b/src/main/java/org/caosdb/datetime/LeapSecondDateTimeStringStrategy.java
index 5aff2dce7979e32f595c4ec8bae12378239cc3dc..b2ef6edd7413c1b7555554661b4e4516b77819dd 100644
--- a/src/main/java/org/caosdb/datetime/LeapSecondDateTimeStringStrategy.java
+++ b/src/main/java/org/caosdb/datetime/LeapSecondDateTimeStringStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.text.SimpleDateFormat;
import java.util.Calendar;
diff --git a/src/main/java/org/caosdb/datetime/SemiCompleteDateTime.java b/src/main/java/org/caosdb/datetime/SemiCompleteDateTime.java
index 5bd4daca00dae6c70473b76147736e65dcc2da68..71786ca6dcf5d02a3d1bb15f31744668e878c1fb 100644
--- a/src/main/java/org/caosdb/datetime/SemiCompleteDateTime.java
+++ b/src/main/java/org/caosdb/datetime/SemiCompleteDateTime.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.TimeZone;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
public class SemiCompleteDateTime extends FragmentDateTime implements Interval {
diff --git a/src/main/java/org/caosdb/datetime/UTCDateTime.java b/src/main/java/org/caosdb/datetime/UTCDateTime.java
index 1dd86cc975d4b92066f2cf44fff51493ade5babe..af1aec2fde2c9f51b07b8e416642c7b084c68e68 100644
--- a/src/main/java/org/caosdb/datetime/UTCDateTime.java
+++ b/src/main/java/org/caosdb/datetime/UTCDateTime.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,16 +22,16 @@
*/
/** @review Daniel Hornung 2022-03-04 */
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.GregorianCalendar;
import java.util.Objects;
import java.util.TimeZone;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
-import org.caosdb.server.datatype.Value;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
+import org.linkahead.server.datatype.Value;
public class UTCDateTime implements Interval {
diff --git a/src/main/java/org/caosdb/datetime/UTCTimeZoneShift.java b/src/main/java/org/caosdb/datetime/UTCTimeZoneShift.java
index 5cd9de48a183f18dd0ca39adaae0c7671cf8efdb..16505f2432cf9f0404ed9b3c0561c252e1e0ef3b 100644
--- a/src/main/java/org/caosdb/datetime/UTCTimeZoneShift.java
+++ b/src/main/java/org/caosdb/datetime/UTCTimeZoneShift.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.Date;
import java.util.TimeZone;
diff --git a/src/main/java/org/caosdb/server/CaosAuthenticator.java b/src/main/java/org/caosdb/server/CaosAuthenticator.java
index b26e50008e47fbf471e8721423aff9b583ce571a..c7a727aefb6921c80cc7af488eba11c9b463d6f3 100644
--- a/src/main/java/org/caosdb/server/CaosAuthenticator.java
+++ b/src/main/java/org/caosdb/server/CaosAuthenticator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authc.AuthenticationToken;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.resource.DefaultResource;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.resource.DefaultResource;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.Context;
import org.restlet.Request;
import org.restlet.Response;
@@ -37,11 +37,12 @@ import org.restlet.security.Authenticator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-public class CaosAuthenticator extends Authenticator {
+public class LinkAheadAuthenticator extends Authenticator {
- private static final Logger logger = LoggerFactory.getLogger(CaosAuthenticator.class.getName());
+ private static final Logger logger =
+ LoggerFactory.getLogger(LinkAheadAuthenticator.class.getName());
- public CaosAuthenticator(final Context context) {
+ public LinkAheadAuthenticator(final Context context) {
super(context);
}
@@ -64,7 +65,7 @@ public class CaosAuthenticator extends Authenticator {
// anonymous users
if (!subject.isAuthenticated()
- && CaosDBServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
+ && LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
.equalsIgnoreCase("TRUE")) {
subject.login(AnonymousAuthenticationToken.getInstance());
}
diff --git a/src/main/java/org/caosdb/server/CaosAuthorizer.java b/src/main/java/org/caosdb/server/CaosAuthorizer.java
index 58e814a374ae2d7c5018d041b23eb4fdafa39ef0..f73bf1ea33685061ca37971b0a03f45dc04635a3 100644
--- a/src/main/java/org/caosdb/server/CaosAuthorizer.java
+++ b/src/main/java/org/caosdb/server/CaosAuthorizer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
-import org.caosdb.server.resource.DefaultResource;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.resource.DefaultResource;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.Request;
import org.restlet.Response;
import org.restlet.security.Authorizer;
-public class CaosAuthorizer extends Authorizer {
+public class LinkAheadAuthorizer extends Authorizer {
@Override
protected boolean authorize(final Request request, final Response response) {
diff --git a/src/main/java/org/caosdb/server/CaosDBException.java b/src/main/java/org/caosdb/server/CaosDBException.java
index 617dfdff95d17ffc15d24bdec2497902eab495a7..da51b02dcddc7ac6ed12540f2dee8c4f3d89775d 100644
--- a/src/main/java/org/caosdb/server/CaosDBException.java
+++ b/src/main/java/org/caosdb/server/CaosDBException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
-public class CaosDBException extends RuntimeException {
+public class LinkAheadException extends RuntimeException {
private static final long serialVersionUID = -6679522664294087311L;
- public CaosDBException(final String string) {
+ public LinkAheadException(final String string) {
super(string);
}
- public CaosDBException(final Throwable t) {
+ public LinkAheadException(final Throwable t) {
super(t);
}
}
diff --git a/src/main/java/org/caosdb/server/CaosDBServer.java b/src/main/java/org/caosdb/server/CaosDBServer.java
index 2a115c5cfa06ed0e3db85847c27fb4c8424eadaf..c22581e0fece277244fca013ed5a30077a1c565d 100644
--- a/src/main/java/org/caosdb/server/CaosDBServer.java
+++ b/src/main/java/org/caosdb/server/CaosDBServer.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server;
+package org.linkahead.server;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
@@ -42,53 +42,53 @@ import org.apache.shiro.env.BasicIniEnvironment;
import org.apache.shiro.mgt.SecurityManager;
import org.apache.shiro.subject.Subject;
import org.apache.shiro.util.ThreadContext;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AnonymousRealm;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.CaosDBAuthorizingRealm;
-import org.caosdb.server.accessControl.CaosDBDefaultRealm;
-import org.caosdb.server.accessControl.ConsumedInfoCleanupJob;
-import org.caosdb.server.accessControl.OneTimeAuthenticationToken;
-import org.caosdb.server.accessControl.SessionToken;
-import org.caosdb.server.accessControl.SessionTokenRealm;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.RetrieveDatatypes;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.container.Container;
-import org.caosdb.server.grpc.GRPCServer;
-import org.caosdb.server.jobs.core.AccessControl;
-import org.caosdb.server.jobs.core.CheckStateTransition;
-import org.caosdb.server.logging.RequestErrorLogMessage;
-import org.caosdb.server.resource.AuthenticationResource;
-import org.caosdb.server.resource.DefaultResource;
-import org.caosdb.server.resource.EntityOwnerResource;
-import org.caosdb.server.resource.EntityPermissionsResource;
-import org.caosdb.server.resource.FileSystemResource;
-import org.caosdb.server.resource.InfoResource;
-import org.caosdb.server.resource.LogoutResource;
-import org.caosdb.server.resource.PermissionRulesResource;
-import org.caosdb.server.resource.RolesResource;
-import org.caosdb.server.resource.ScriptingResource;
-import org.caosdb.server.resource.ServerLogsResource;
-import org.caosdb.server.resource.ServerPropertiesResource;
-import org.caosdb.server.resource.SharedFileResource;
-import org.caosdb.server.resource.ThumbnailsResource;
-import org.caosdb.server.resource.UserResource;
-import org.caosdb.server.resource.UserRolesResource;
-import org.caosdb.server.resource.Webinterface;
-import org.caosdb.server.resource.WebinterfaceBuildNumber;
-import org.caosdb.server.resource.transaction.EntityNamesResource;
-import org.caosdb.server.resource.transaction.EntityResource;
-import org.caosdb.server.scripting.ScriptingPermissions;
-import org.caosdb.server.transaction.ChecksumUpdater;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.Initialization;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AnonymousRealm;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.ConsumedInfoCleanupJob;
+import org.linkahead.server.accessControl.LinkAheadAuthorizingRealm;
+import org.linkahead.server.accessControl.LinkAheadDefaultRealm;
+import org.linkahead.server.accessControl.OneTimeAuthenticationToken;
+import org.linkahead.server.accessControl.SessionToken;
+import org.linkahead.server.accessControl.SessionTokenRealm;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.RetrieveDatatypes;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.container.Container;
+import org.linkahead.server.grpc.GRPCServer;
+import org.linkahead.server.jobs.core.AccessControl;
+import org.linkahead.server.jobs.core.CheckStateTransition;
+import org.linkahead.server.logging.RequestErrorLogMessage;
+import org.linkahead.server.resource.AuthenticationResource;
+import org.linkahead.server.resource.DefaultResource;
+import org.linkahead.server.resource.EntityOwnerResource;
+import org.linkahead.server.resource.EntityPermissionsResource;
+import org.linkahead.server.resource.FileSystemResource;
+import org.linkahead.server.resource.InfoResource;
+import org.linkahead.server.resource.LogoutResource;
+import org.linkahead.server.resource.PermissionRulesResource;
+import org.linkahead.server.resource.RolesResource;
+import org.linkahead.server.resource.ScriptingResource;
+import org.linkahead.server.resource.ServerLogsResource;
+import org.linkahead.server.resource.ServerPropertiesResource;
+import org.linkahead.server.resource.SharedFileResource;
+import org.linkahead.server.resource.ThumbnailsResource;
+import org.linkahead.server.resource.UserResource;
+import org.linkahead.server.resource.UserRolesResource;
+import org.linkahead.server.resource.Webinterface;
+import org.linkahead.server.resource.WebinterfaceBuildNumber;
+import org.linkahead.server.resource.transaction.EntityNamesResource;
+import org.linkahead.server.resource.transaction.EntityResource;
+import org.linkahead.server.scripting.ScriptingPermissions;
+import org.linkahead.server.transaction.ChecksumUpdater;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.Initialization;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
import org.quartz.JobDetail;
import org.quartz.Scheduler;
import org.quartz.SchedulerException;
@@ -118,9 +118,9 @@ import org.restlet.util.Series;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-public class CaosDBServer extends Application {
+public class LinkAheadServer extends Application {
- private static Logger logger = LoggerFactory.getLogger(CaosDBServer.class);
+ private static Logger logger = LoggerFactory.getLogger(LinkAheadServer.class);
private static ServerProperties SERVER_PROPERTIES = null;
private static Component component = null;
private static ArrayList<Runnable> postShutdownHooks = new ArrayList<Runnable>();
@@ -169,12 +169,12 @@ public class CaosDBServer extends Application {
* Parse the command line arguments.
*
* <ul>
- * <li>"--no-backend": flag to run caosdb without any backend (for testing purposes)
+ * <li>"--no-backend": flag to run linkahead without any backend (for testing purposes)
* <li>"--no-tls": flag to start only a http server (no https server)
* </ul>
*
* <p>The --no-backend flag is only available in the debug mode which is controlled by the
- * `caosdb.debug` JVM Property.
+ * `linkahead.debug` JVM Property.
*
* @param args
*/
@@ -321,13 +321,13 @@ public class CaosDBServer extends Application {
public static Ini getShiroConfig() {
final Ini config = new Ini();
final Section mainSec = config.addSection("main");
- mainSec.put("CaosDB", CaosDBDefaultRealm.class.getCanonicalName());
+ mainSec.put("CaosDB", LinkAheadDefaultRealm.class.getCanonicalName());
mainSec.put("SessionTokenValidator", SessionTokenRealm.class.getCanonicalName());
- mainSec.put("CaosDBAuthorizingRealm", CaosDBAuthorizingRealm.class.getCanonicalName());
+ mainSec.put("LinkAheadAuthorizingRealm", LinkAheadAuthorizingRealm.class.getCanonicalName());
mainSec.put("AnonymousRealm", AnonymousRealm.class.getCanonicalName());
mainSec.put(
"securityManager.realms",
- "$CaosDB, $SessionTokenValidator, $CaosDBAuthorizingRealm, $AnonymousRealm");
+ "$CaosDB, $SessionTokenValidator, $LinkAheadAuthorizingRealm, $AnonymousRealm");
// disable shiro's default session management. We have quasi-stateless
// sessions
@@ -432,7 +432,7 @@ public class CaosDBServer extends Application {
.add(new org.restlet.ext.jetty.HttpServerHelper(null));
// Create a component.
- component = new CaosDBComponent();
+ component = new LinkAheadComponent();
final Server httpServer =
new Server(
@@ -450,7 +450,7 @@ public class CaosDBServer extends Application {
parameters.add("maxTotalConnections", Integer.toString(maxTotalConnections));
// Create an application (this class).
- final Application application = new CaosDBServer();
+ final Application application = new LinkAheadServer();
application
.getStatusService()
.setContactEmail(getServerProperty(ServerProperties.KEY_ADMIN_EMAIL));
@@ -491,10 +491,10 @@ public class CaosDBServer extends Application {
final int maxTotalConnections)
throws Exception {
- Engine.getInstance().getRegisteredServers().add(new CaosDBServerConnectorHelper(null));
+ Engine.getInstance().getRegisteredServers().add(new LinkAheadServerConnectorHelper(null));
// Create a component.
- component = new CaosDBComponent();
+ component = new LinkAheadComponent();
final Server httpsServer =
new Server(
@@ -503,7 +503,7 @@ public class CaosDBServer extends Application {
server_bind_address,
port_https,
(Restlet) null,
- "org.caosdb.server.CaosDBServerConnectorHelper");
+ "org.linkahead.server.LinkAheadServerConnectorHelper");
component.getServers().add(httpsServer);
// redirector http to https
@@ -540,7 +540,7 @@ public class CaosDBServer extends Application {
parameters.add("certAlias", "1");
// Create an application (this class).
- final Application application = new CaosDBServer();
+ final Application application = new LinkAheadServer();
application
.getStatusService()
.setContactEmail(
@@ -572,7 +572,7 @@ public class CaosDBServer extends Application {
@Override
public Restlet createInboundRoot() {
/** Authenticator. Protects the protectedRouter. */
- final CaosAuthenticator authenticator = new CaosAuthenticator(getContext());
+ final LinkAheadAuthenticator authenticator = new LinkAheadAuthenticator(getContext());
/** ProtectedRouter. Is protected by the authenticator. */
final Router protectedRouter =
@@ -676,7 +676,7 @@ public class CaosDBServer extends Application {
});
// baseRouter.attachDefault(authenticator);
- final CaosAuthorizer authorizer = new CaosAuthorizer();
+ final LinkAheadAuthorizer authorizer = new LinkAheadAuthorizer();
// The protectedRouter handles the request if the authorization
// succeeds.
@@ -800,7 +800,7 @@ public class CaosDBServer extends Application {
public static ServerInfo getServerInfo() {
if (serverInfo == null) {
serverInfo = new ServerInfo();
- serverInfo.setAgent("CaosDB Server");
+ serverInfo.setAgent("LinkAhead Server");
}
return serverInfo;
}
@@ -864,7 +864,7 @@ public class CaosDBServer extends Application {
}
public static boolean isDebugMode() {
- return Boolean.getBoolean("caosdb.debug");
+ return Boolean.getBoolean("linkahead.debug");
}
/**
@@ -888,24 +888,24 @@ public class CaosDBServer extends Application {
}
}
-class CaosDBComponent extends Component {
+class LinkAheadComponent extends Component {
private static Logger request_error_logger =
- LoggerFactory.getLogger(CaosDBServer.REQUEST_ERRORS_LOGGER);
+ LoggerFactory.getLogger(LinkAheadServer.REQUEST_ERRORS_LOGGER);
private static Logger request_time_logger =
- LoggerFactory.getLogger(CaosDBServer.REQUEST_TIME_LOGGER);
+ LoggerFactory.getLogger(LinkAheadServer.REQUEST_TIME_LOGGER);
- public CaosDBComponent() {
+ public LinkAheadComponent() {
super();
String responseLogFormat =
- CaosDBServer.getServerProperty(ServerProperties.KEY_REST_RESPONSE_LOG_FORMAT);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_REST_RESPONSE_LOG_FORMAT);
if ("OFF".equalsIgnoreCase(responseLogFormat)) {
getLogService().setEnabled(false);
} else if (responseLogFormat != null && !responseLogFormat.isEmpty()) {
getLogService().setResponseLogFormat(responseLogFormat);
}
- setName(CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_NAME));
- setOwner(CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_OWNER));
+ setName(LinkAheadServer.getServerProperty(ServerProperties.KEY_SERVER_NAME));
+ setOwner(LinkAheadServer.getServerProperty(ServerProperties.KEY_SERVER_OWNER));
}
/**
@@ -923,7 +923,7 @@ class CaosDBComponent extends Component {
final long t1 = System.currentTimeMillis();
// The server request ID is just a long random number
request.getAttributes().put("SRID", UUID.randomUUID().toString());
- response.setServerInfo(CaosDBServer.getServerInfo());
+ response.setServerInfo(LinkAheadServer.getServerInfo());
super.handle(request, response);
log(request, response, t1);
}
diff --git a/src/main/java/org/caosdb/server/CaosDBServerConnectorHelper.java b/src/main/java/org/caosdb/server/CaosDBServerConnectorHelper.java
index 8a9749bc2225d71b87ea338a88db3f9aa9596bba..4a7ea3f0128abf44ae4f13aafc61460418800298 100644
--- a/src/main/java/org/caosdb/server/CaosDBServerConnectorHelper.java
+++ b/src/main/java/org/caosdb/server/CaosDBServerConnectorHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,21 +20,21 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
import java.util.LinkedList;
import org.restlet.Server;
-public class CaosDBServerConnectorHelper extends org.restlet.ext.jetty.HttpsServerHelper {
+public class LinkAheadServerConnectorHelper extends org.restlet.ext.jetty.HttpsServerHelper {
- private static LinkedList<CaosDBServerConnectorHelper> instances =
- new LinkedList<CaosDBServerConnectorHelper>();
+ private static LinkedList<LinkAheadServerConnectorHelper> instances =
+ new LinkedList<LinkAheadServerConnectorHelper>();
- public CaosDBServerConnectorHelper(final Server server) {
+ public LinkAheadServerConnectorHelper(final Server server) {
super(server);
}
- public static LinkedList<CaosDBServerConnectorHelper> getInstances() {
+ public static LinkedList<LinkAheadServerConnectorHelper> getInstances() {
return instances;
}
diff --git a/src/main/java/org/caosdb/server/FileSystem.java b/src/main/java/org/caosdb/server/FileSystem.java
index c05314655b8e1112e60576cc8c96b9f6b30ce2fa..d53e0ddbd2424d61e2c06bb80883d43854542124 100644
--- a/src/main/java/org/caosdb/server/FileSystem.java
+++ b/src/main/java/org/caosdb/server/FileSystem.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
import com.google.common.io.Files;
import java.io.File;
@@ -35,17 +35,17 @@ import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.regex.Pattern;
import org.apache.commons.fileupload.FileItemStream;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.GetFileRecordByPath;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.GetFileRecordByPath;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
public class FileSystem {
private static String filesystem = null;
@@ -108,10 +108,10 @@ public class FileSystem {
}
public static void init() {
- filesystem = CaosDBServer.getServerProperty(ServerProperties.KEY_FILE_SYSTEM_ROOT);
- dropOffBox = CaosDBServer.getServerProperty(ServerProperties.KEY_DROP_OFF_BOX);
- tmpdir = CaosDBServer.getServerProperty(ServerProperties.KEY_TMP_FILES);
- sharedDir = CaosDBServer.getServerProperty(ServerProperties.KEY_SHARED_FOLDER);
+ filesystem = LinkAheadServer.getServerProperty(ServerProperties.KEY_FILE_SYSTEM_ROOT);
+ dropOffBox = LinkAheadServer.getServerProperty(ServerProperties.KEY_DROP_OFF_BOX);
+ tmpdir = LinkAheadServer.getServerProperty(ServerProperties.KEY_TMP_FILES);
+ sharedDir = LinkAheadServer.getServerProperty(ServerProperties.KEY_SHARED_FOLDER);
check();
}
@@ -152,10 +152,10 @@ public class FileSystem {
* @return FileProperties of the uploaded File.
* @throws NoSuchAlgorithmException
* @throws IOException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
public static final FileProperties upload(final FileItemStream item, final String session)
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
String checksum = null;
// Name of the temporary FILE object.
@@ -209,7 +209,7 @@ public class FileSystem {
* @throws NoSuchAlgorithmException
* @throws IOException
* @throws Message
- * @throws CaosDBException
+ * @throws LinkAheadException
* @throws InterruptedException
*/
public static final FileProperties pickUp(final String path, final String session)
diff --git a/src/main/java/org/caosdb/server/HttpToHttpsRedirector.java b/src/main/java/org/caosdb/server/HttpToHttpsRedirector.java
index 5f15406faa837d311a8e5bf62b5e8dd28209d094..ffe2fd74b0cd1a24012db231aeca703fe2322dc2 100644
--- a/src/main/java/org/caosdb/server/HttpToHttpsRedirector.java
+++ b/src/main/java/org/caosdb/server/HttpToHttpsRedirector.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
import org.restlet.Request;
import org.restlet.Response;
diff --git a/src/main/java/org/caosdb/server/ServerProperties.java b/src/main/java/org/caosdb/server/ServerProperties.java
index 93a0c7473be1c31565e4b159ba55e01d557687e7..acffb8a2756b621d567efe1745e01b1acc0aa961 100644
--- a/src/main/java/org/caosdb/server/ServerProperties.java
+++ b/src/main/java/org/caosdb/server/ServerProperties.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server;
+package org.linkahead.server;
import java.io.BufferedInputStream;
import java.io.File;
@@ -31,10 +31,10 @@ import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.Properties;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.utils.AbstractObservable;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.utils.AbstractObservable;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -44,6 +44,9 @@ public class ServerProperties extends Properties implements Observable {
private static final long serialVersionUID = -6178774548807398071L;
private static Logger logger = LoggerFactory.getLogger(ServerProperties.class.getName());
+ public static final String prefix = "LINKAHEAD_CONFIG_";
+ public static final String prefix_old = "CAOSDB_CONFIG_";
+
public static final String KEY_FILE_SYSTEM_ROOT = "FILE_SYSTEM_ROOT";
public static final String KEY_DROP_OFF_BOX = "DROP_OFF_BOX";
public static final String KEY_TMP_FILES = "TMP_FILES";
@@ -162,7 +165,7 @@ public class ServerProperties extends Properties implements Observable {
final ServerProperties serverProperties = new ServerProperties();
final String basepath = System.getProperty("user.dir");
- final URL url = CaosDBServer.class.getResource("/build.properties");
+ final URL url = LinkAheadServer.class.getResource("/build.properties");
serverProperties.load(url.openStream());
// load standard config
@@ -185,9 +188,21 @@ public class ServerProperties extends Properties implements Observable {
}
// load env vars
+ final ArrayList<String> vars_set = new ArrayList<>();
for (final java.util.Map.Entry<String, String> envvar : System.getenv().entrySet()) {
- if (envvar.getKey().startsWith("CAOSDB_CONFIG_") && envvar.getKey().length() > 14) {
- serverProperties.setProperty(envvar.getKey().substring(14), envvar.getValue());
+ if (envvar.getKey().startsWith(prefix) && envvar.getKey().length() > prefix.length()) {
+ serverProperties.setProperty(envvar.getKey().substring(prefix.length()), envvar.getValue());
+ vars_set.append(envvar.getKey().substring(prefix.length()));
+ }
+ }
+ for (final java.util.Map.Entry<String, String> envvar : System.getenv().entrySet()) {
+ if (envvar.getKey().startsWith(prefix_old) && envvar.getKey().length() > prefix.length()) {
+ serverProperties.setProperty(envvar.getKey().substring(prefix.length()), envvar.getValue());
+ if (vars_set.contains(envvar.getKey().substring(prefix.length()))){
+ throw new IOException("You must not set server variables using environment variables"
+ +" with keys with both prefixes: the old, deprecated 'CAOSDB_' and the new"
+ +"'LINKAHEAD' one.");
+ }
}
}
diff --git a/src/main/java/org/caosdb/server/ServerPropertiesSerializer.java b/src/main/java/org/caosdb/server/ServerPropertiesSerializer.java
index f68538a3aa8bb15ec6f53944dfb072e20dfbc557..5e478c8376cf4dcaeafaa25bdb8c917a480bfdac 100644
--- a/src/main/java/org/caosdb/server/ServerPropertiesSerializer.java
+++ b/src/main/java/org/caosdb/server/ServerPropertiesSerializer.java
@@ -1,11 +1,11 @@
-package org.caosdb.server;
+package org.linkahead.server;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Properties;
-import org.caosdb.server.utils.Serializer;
import org.jdom2.Element;
+import org.linkahead.server.utils.Serializer;
public class ServerPropertiesSerializer implements Serializer<Properties, Element> {
diff --git a/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java b/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
index 075036921aba51acc05ff1b76df01763485c53c2..5495f9336ca93252b4442351dbab51d4a06f9bad 100644
--- a/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
+++ b/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Collections;
import java.util.HashSet;
diff --git a/src/main/java/org/caosdb/server/accessControl/AnonymousAuthenticationToken.java b/src/main/java/org/caosdb/server/accessControl/AnonymousAuthenticationToken.java
index 97b6f9ee669b673f969e6856a5e23172327fb33e..1302d18c0cf4c703ec1c4754034f2c647f71304e 100644
--- a/src/main/java/org/caosdb/server/accessControl/AnonymousAuthenticationToken.java
+++ b/src/main/java/org/caosdb/server/accessControl/AnonymousAuthenticationToken.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.authc.AuthenticationToken;
diff --git a/src/main/java/org/caosdb/server/accessControl/AnonymousRealm.java b/src/main/java/org/caosdb/server/accessControl/AnonymousRealm.java
index 92b37c0ec15b110670a55ea46b6efa1a418bb597..bf52611e35f5f2abe213f391d9fd7ccefdb79c08 100644
--- a/src/main/java/org/caosdb/server/accessControl/AnonymousRealm.java
+++ b/src/main/java/org/caosdb/server/accessControl/AnonymousRealm.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,22 +20,22 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.authc.AuthenticationInfo;
import org.apache.shiro.authc.AuthenticationToken;
import org.apache.shiro.authc.SimpleAuthenticationInfo;
import org.apache.shiro.authc.credential.AllowAllCredentialsMatcher;
import org.apache.shiro.realm.AuthenticatingRealm;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
public class AnonymousRealm extends AuthenticatingRealm {
@Override
protected AuthenticationInfo doGetAuthenticationInfo(AuthenticationToken token) {
- if (CaosDBServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
+ if (LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
.equalsIgnoreCase("true")) {
return new SimpleAuthenticationInfo(token.getPrincipal(), null, getName());
}
diff --git a/src/main/java/org/caosdb/server/accessControl/AuthenticationUtils.java b/src/main/java/org/caosdb/server/accessControl/AuthenticationUtils.java
index dc40e72e44ffdd6fca21824c6f3dd036f0b6f9ed..b2af88a2d2a71f2ded730dee17496e496e7f7f01 100644
--- a/src/main/java/org/caosdb/server/accessControl/AuthenticationUtils.java
+++ b/src/main/java/org/caosdb/server/accessControl/AuthenticationUtils.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,20 +22,20 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
-import static org.caosdb.server.utils.Utils.URLDecodeWithUTF8;
+import static org.linkahead.server.utils.Utils.URLDecodeWithUTF8;
import java.sql.Timestamp;
import java.util.Collection;
import java.util.LinkedList;
import org.apache.shiro.authz.AuthorizationInfo;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.permissions.ResponsibleAgent;
-import org.caosdb.server.permissions.Role;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.permissions.ResponsibleAgent;
+import org.linkahead.server.permissions.Role;
+import org.linkahead.server.utils.Utils;
import org.restlet.data.Cookie;
import org.restlet.data.CookieSetting;
@@ -76,7 +76,7 @@ public class AuthenticationUtils {
0,
cookieName,
Utils.URLEncodeWithUTF8(token.toString()),
- CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
null,
null,
exp_in_sec,
@@ -132,7 +132,7 @@ public class AuthenticationUtils {
0,
AuthenticationUtils.SESSION_TIMEOUT_COOKIE,
Utils.URLEncodeWithUTF8(t),
- CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
null,
null,
exp_in_sec,
@@ -163,7 +163,7 @@ public class AuthenticationUtils {
0,
AuthenticationUtils.SESSION_TOKEN_COOKIE,
"invalid",
- CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
null,
null,
0,
@@ -183,7 +183,7 @@ public class AuthenticationUtils {
0,
AuthenticationUtils.SESSION_TIMEOUT_COOKIE,
"invalid",
- CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
null,
null,
0,
@@ -192,7 +192,7 @@ public class AuthenticationUtils {
}
public static Collection<String> getRoles(Subject user) {
- return new CaosDBAuthorizingRealm().doGetAuthorizationInfo(user.getPrincipals()).getRoles();
+ return new LinkAheadAuthorizingRealm().doGetAuthorizationInfo(user.getPrincipals()).getRoles();
}
public static boolean isFromOneTimeTokenRealm(Subject subject) {
@@ -202,6 +202,6 @@ public class AuthenticationUtils {
}
public static AuthorizationInfo getAuthorizationInfo(Subject user) {
- return new CaosDBAuthorizingRealm().doGetAuthorizationInfo(user.getPrincipals());
+ return new LinkAheadAuthorizingRealm().doGetAuthorizationInfo(user.getPrincipals());
}
}
diff --git a/src/main/java/org/caosdb/server/accessControl/CaosDBAuthorizingRealm.java b/src/main/java/org/caosdb/server/accessControl/CaosDBAuthorizingRealm.java
index 52f8d3db87f9748a254f7a6f60fc00100a1bef0e..a8c803c390d52737cae12905703a217658448737 100644
--- a/src/main/java/org/caosdb/server/accessControl/CaosDBAuthorizingRealm.java
+++ b/src/main/java/org/caosdb/server/accessControl/CaosDBAuthorizingRealm.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Collection;
import java.util.Set;
@@ -32,10 +32,10 @@ import org.apache.shiro.authz.SimpleAuthorizationInfo;
import org.apache.shiro.realm.AuthorizingRealm;
import org.apache.shiro.subject.PrincipalCollection;
-public class CaosDBAuthorizingRealm extends AuthorizingRealm {
+public class LinkAheadAuthorizingRealm extends AuthorizingRealm {
- private static final CaosDBRolePermissionResolver role_permission_resolver =
- new CaosDBRolePermissionResolver();
+ private static final LinkAheadRolePermissionResolver role_permission_resolver =
+ new LinkAheadRolePermissionResolver();
public Collection<String> getSessionRoles(SelfValidatingAuthenticationToken token) {
return token.getRoles();
@@ -77,7 +77,7 @@ public class CaosDBAuthorizingRealm extends AuthorizingRealm {
return authzInfo;
}
- public CaosDBAuthorizingRealm() {
+ public LinkAheadAuthorizingRealm() {
setCachingEnabled(false);
setAuthorizationCachingEnabled(false);
}
diff --git a/src/main/java/org/caosdb/server/accessControl/CaosDBDefaultRealm.java b/src/main/java/org/caosdb/server/accessControl/CaosDBDefaultRealm.java
index 47fe71fd9dc3407c736998e79524f034933936a9..9be19663c5ee5c731ca6e2ac52dbd023ae90e7a8 100644
--- a/src/main/java/org/caosdb/server/accessControl/CaosDBDefaultRealm.java
+++ b/src/main/java/org/caosdb/server/accessControl/CaosDBDefaultRealm.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.authc.AuthenticationInfo;
import org.apache.shiro.authc.AuthenticationToken;
@@ -28,7 +28,7 @@ import org.apache.shiro.authc.SimpleAuthenticationInfo;
import org.apache.shiro.authc.credential.AllowAllCredentialsMatcher;
import org.apache.shiro.realm.AuthenticatingRealm;
-public class CaosDBDefaultRealm extends AuthenticatingRealm {
+public class LinkAheadDefaultRealm extends AuthenticatingRealm {
@Override
protected AuthenticationInfo doGetAuthenticationInfo(final AuthenticationToken token) {
@@ -43,7 +43,7 @@ public class CaosDBDefaultRealm extends AuthenticatingRealm {
}
}
- public CaosDBDefaultRealm() {
+ public LinkAheadDefaultRealm() {
setCredentialsMatcher(new AllowAllCredentialsMatcher());
setCachingEnabled(false);
diff --git a/src/main/java/org/caosdb/server/accessControl/CaosDBRolePermissionResolver.java b/src/main/java/org/caosdb/server/accessControl/CaosDBRolePermissionResolver.java
index 5bc711e17b60309f851e55bf249a22beeec56d61..53878fa47ec3978b630a43527a4a97ade9f22112 100644
--- a/src/main/java/org/caosdb/server/accessControl/CaosDBRolePermissionResolver.java
+++ b/src/main/java/org/caosdb/server/accessControl/CaosDBRolePermissionResolver.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,21 +20,21 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.HashSet;
import java.util.Set;
import org.apache.shiro.authc.AuthenticationException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.permissions.CaosPermission;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.transaction.RetrievePermissionRulesTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.permissions.LinkAheadPermission;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.transaction.RetrievePermissionRulesTransaction;
+import org.linkahead.server.utils.ServerMessages;
-public class CaosDBRolePermissionResolver {
+public class LinkAheadRolePermissionResolver {
- /** Return CaosPermission with the rules which are associated with the roles. */
- public CaosPermission resolvePermissionsInRole(final Set<String> roles) {
+ /** Return LinkAheadPermission with the rules which are associated with the roles. */
+ public LinkAheadPermission resolvePermissionsInRole(final Set<String> roles) {
final HashSet<PermissionRule> rules = new HashSet<PermissionRule>();
for (final String role : roles) {
final RetrievePermissionRulesTransaction t = new RetrievePermissionRulesTransaction(role);
@@ -50,6 +50,6 @@ public class CaosDBRolePermissionResolver {
}
}
- return new CaosPermission(rules);
+ return new LinkAheadPermission(rules);
}
}
diff --git a/src/main/java/org/caosdb/server/accessControl/Config.java b/src/main/java/org/caosdb/server/accessControl/Config.java
index 4c50b445127c089dd1be7151dc6d35825877a2ae..9350897d7a8c4e607cfd7a769d0f1fdfd80263f0 100644
--- a/src/main/java/org/caosdb/server/accessControl/Config.java
+++ b/src/main/java/org/caosdb/server/accessControl/Config.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
public class Config {
private String[] permissions = {};
diff --git a/src/main/java/org/caosdb/server/accessControl/ConsumedInfoCleanupJob.java b/src/main/java/org/caosdb/server/accessControl/ConsumedInfoCleanupJob.java
index b5945c5cd2dbec86a7de6ffa265c65706342f86e..8167f72f46b1dc2426763551a28a85be1b8feb4e 100644
--- a/src/main/java/org/caosdb/server/accessControl/ConsumedInfoCleanupJob.java
+++ b/src/main/java/org/caosdb/server/accessControl/ConsumedInfoCleanupJob.java
@@ -1,6 +1,6 @@
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
-import org.caosdb.server.CaosDBServer;
+import org.linkahead.server.LinkAheadServer;
import org.quartz.CronScheduleBuilder;
import org.quartz.Job;
import org.quartz.JobBuilder;
@@ -19,7 +19,7 @@ public class ConsumedInfoCleanupJob implements Job {
TriggerBuilder.newTrigger()
.withSchedule(CronScheduleBuilder.dailyAtHourAndMinute(0, 0))
.build();
- CaosDBServer.scheduleJob(job, trigger);
+ LinkAheadServer.scheduleJob(job, trigger);
}
@Override
diff --git a/src/main/java/org/caosdb/server/accessControl/CredentialsValidator.java b/src/main/java/org/caosdb/server/accessControl/CredentialsValidator.java
index dfcbe8dfe5a2c840b2674c0fa419df185fe638ad..52c52d95009dabb3ecb4e9889b4d8e9ba7095b41 100644
--- a/src/main/java/org/caosdb/server/accessControl/CredentialsValidator.java
+++ b/src/main/java/org/caosdb/server/accessControl/CredentialsValidator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
public interface CredentialsValidator<T> {
diff --git a/src/main/java/org/caosdb/server/accessControl/HashPasswordValidator.java b/src/main/java/org/caosdb/server/accessControl/HashPasswordValidator.java
index dcf1e3feabbb1e6855844169f03961d5ad71532a..47432ce757b8192757824d16d38e97ee4c9253b6 100644
--- a/src/main/java/org/caosdb/server/accessControl/HashPasswordValidator.java
+++ b/src/main/java/org/caosdb/server/accessControl/HashPasswordValidator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.utils.Utils;
public class HashPasswordValidator implements CredentialsValidator<String> {
diff --git a/src/main/java/org/caosdb/server/accessControl/InternalUserSource.java b/src/main/java/org/caosdb/server/accessControl/InternalUserSource.java
index 23f772dfbd24aef21a6335ce4bc6df392e082078..0e1fb296d8f22c9c7b150b326f706be97fa2d3b0 100644
--- a/src/main/java/org/caosdb/server/accessControl/InternalUserSource.java
+++ b/src/main/java/org/caosdb/server/accessControl/InternalUserSource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Map;
import java.util.Set;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.transaction.RetrievePasswordValidatorTransaction;
-import org.caosdb.server.transaction.RetrieveUserTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.transaction.RetrievePasswordValidatorTransaction;
+import org.linkahead.server.transaction.RetrieveUserTransaction;
+import org.linkahead.server.utils.ServerMessages;
public class InternalUserSource implements UserSource {
diff --git a/src/main/java/org/caosdb/server/accessControl/Mode.java b/src/main/java/org/caosdb/server/accessControl/Mode.java
index 8f91a9ba6eb6fc8c35a0cb519e0e7820e3628f57..d8afc538a6e1e37041b297c3134f7f45aef444fd 100644
--- a/src/main/java/org/caosdb/server/accessControl/Mode.java
+++ b/src/main/java/org/caosdb/server/accessControl/Mode.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
public enum Mode {
ONETIME,
diff --git a/src/main/java/org/caosdb/server/accessControl/OneTimeAuthenticationToken.java b/src/main/java/org/caosdb/server/accessControl/OneTimeAuthenticationToken.java
index f87dd0da71b5478c636476dac3041ced82035e27..9f7627c49083f4f1175efe83a508088569c47130 100644
--- a/src/main/java/org/caosdb/server/accessControl/OneTimeAuthenticationToken.java
+++ b/src/main/java/org/caosdb/server/accessControl/OneTimeAuthenticationToken.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectReader;
@@ -36,9 +36,9 @@ import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.quartz.SchedulerException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -48,10 +48,11 @@ public class OneTimeAuthenticationToken extends SelfValidatingAuthenticationToke
public static final long DEFAULT_MAX_REPLAYS = 1L;
public static final int DEFAULT_REPLAYS_TIMEOUT_MS =
Integer.parseInt(
- CaosDBServer.getServerProperty(ServerProperties.KEY_ONE_TIME_TOKEN_REPLAYS_TIMEOUT_MS));
+ LinkAheadServer.getServerProperty(
+ ServerProperties.KEY_ONE_TIME_TOKEN_REPLAYS_TIMEOUT_MS));
public static final int DEFAULT_TIMEOUT_MS =
Integer.parseInt(
- CaosDBServer.getServerProperty(ServerProperties.KEY_ONE_TIME_TOKEN_EXPIRES_MS));
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_ONE_TIME_TOKEN_EXPIRES_MS));
public static final String REALM_NAME = "OneTimeAuthenticationToken"; // TODO move to UserSources
public static final Logger LOGGER = LoggerFactory.getLogger(OneTimeAuthenticationToken.class);
@@ -204,7 +205,7 @@ public class OneTimeAuthenticationToken extends SelfValidatingAuthenticationToke
resetConfig();
try (FileInputStream f =
new FileInputStream(
- CaosDBServer.getServerProperty(ServerProperties.KEY_AUTHTOKEN_CONFIG))) {
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTHTOKEN_CONFIG))) {
initConfig(f);
} catch (IOException e) {
LOGGER.error("Could not load the auth token configuration", e);
diff --git a/src/main/java/org/caosdb/server/accessControl/OneTimeTokenConsumedInfo.java b/src/main/java/org/caosdb/server/accessControl/OneTimeTokenConsumedInfo.java
index 20c648b2d6b4aa2a492de6bc4bb6d1f5465eea27..1f55d822a01f2b701f49ad3cd3d5bf052b7ac692 100644
--- a/src/main/java/org/caosdb/server/accessControl/OneTimeTokenConsumedInfo.java
+++ b/src/main/java/org/caosdb/server/accessControl/OneTimeTokenConsumedInfo.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.HashMap;
import java.util.Iterator;
diff --git a/src/main/java/org/caosdb/server/accessControl/OneTimeTokenToFile.java b/src/main/java/org/caosdb/server/accessControl/OneTimeTokenToFile.java
index 46017701069f9f184bf50b8bab285014cd8a47ad..409395ba53dff58d1f7ee587ad681c82f0d4193e 100644
--- a/src/main/java/org/caosdb/server/accessControl/OneTimeTokenToFile.java
+++ b/src/main/java/org/caosdb/server/accessControl/OneTimeTokenToFile.java
@@ -1,10 +1,10 @@
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import com.google.common.io.Files;
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
-import org.caosdb.server.CaosDBServer;
+import org.linkahead.server.LinkAheadServer;
import org.quartz.CronScheduleBuilder;
import org.quartz.Job;
import org.quartz.JobBuilder;
@@ -63,7 +63,7 @@ public class OneTimeTokenToFile implements Job {
.withIdentity(config.toString())
.withSchedule(CronScheduleBuilder.cronSchedule(this.schedule))
.build();
- CaosDBServer.scheduleJob(outputJob, trigger);
+ LinkAheadServer.scheduleJob(outputJob, trigger);
} else {
output(OneTimeAuthenticationToken.generate(config), file);
}
diff --git a/src/main/java/org/caosdb/server/accessControl/Pam.java b/src/main/java/org/caosdb/server/accessControl/Pam.java
index 992665c1db3ef42d3770c71e89fa5444f43f9d95..a4d1f99a21641927e076bc770af1b22bfa4141f6 100644
--- a/src/main/java/org/caosdb/server/accessControl/Pam.java
+++ b/src/main/java/org/caosdb/server/accessControl/Pam.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -23,7 +23,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.io.File;
import java.io.IOException;
@@ -35,9 +35,9 @@ import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.caching.Cache;
import org.jvnet.libpam.PAMException;
import org.jvnet.libpam.UnixUser;
+import org.linkahead.server.caching.Cache;
/**
* PAM UserSource for authenticating users via the Host's pam module.
diff --git a/src/main/java/org/caosdb/server/accessControl/PamScriptCaller.java b/src/main/java/org/caosdb/server/accessControl/PamScriptCaller.java
index dc9137e0192cb73d35ae6579b760a8d4f56685b7..e906a9aaf50b111ec588822b88794841b1ef958e 100644
--- a/src/main/java/org/caosdb/server/accessControl/PamScriptCaller.java
+++ b/src/main/java/org/caosdb/server/accessControl/PamScriptCaller.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
public interface PamScriptCaller {
public boolean isValid(String username, String password);
diff --git a/src/main/java/org/caosdb/server/accessControl/Principal.java b/src/main/java/org/caosdb/server/accessControl/Principal.java
index 7d4144557d89ddf90ec99edb190abb66ec0119aa..b0b6e7bbaa938191f72808232e77bcde1bb3c66d 100644
--- a/src/main/java/org/caosdb/server/accessControl/Principal.java
+++ b/src/main/java/org/caosdb/server/accessControl/Principal.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.HashMap;
-import org.caosdb.server.permissions.ResponsibleAgent;
import org.jdom2.Element;
+import org.linkahead.server.permissions.ResponsibleAgent;
public class Principal implements ResponsibleAgent {
diff --git a/src/main/java/org/caosdb/server/accessControl/RealmUsernamePasswordToken.java b/src/main/java/org/caosdb/server/accessControl/RealmUsernamePasswordToken.java
index 1d9343104a5ffea8f3d0db4eb0498ae210381f0a..1b6e4cbddbb12c6e765be79b2862c235be86c4f2 100644
--- a/src/main/java/org/caosdb/server/accessControl/RealmUsernamePasswordToken.java
+++ b/src/main/java/org/caosdb/server/accessControl/RealmUsernamePasswordToken.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.authc.AuthenticationToken;
diff --git a/src/main/java/org/caosdb/server/accessControl/Role.java b/src/main/java/org/caosdb/server/accessControl/Role.java
index d1b04918e76ecbe6c94db8b00c6bb50f1c9a351c..5a4035e52c2f2ced8a900270c80d4c244f494249 100644
--- a/src/main/java/org/caosdb/server/accessControl/Role.java
+++ b/src/main/java/org/caosdb/server/accessControl/Role.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,13 +21,13 @@
*
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.io.Serializable;
import java.util.LinkedList;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.permissions.PermissionRule;
import org.jdom2.Element;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.permissions.PermissionRule;
public class Role implements Serializable {
diff --git a/src/main/java/org/caosdb/server/accessControl/SelfValidatingAuthenticationToken.java b/src/main/java/org/caosdb/server/accessControl/SelfValidatingAuthenticationToken.java
index 1832563fb981b52da8c90168e7dae97d6dfbc487..842514fdf0d01a348d4eb3305835b36a46555560 100644
--- a/src/main/java/org/caosdb/server/accessControl/SelfValidatingAuthenticationToken.java
+++ b/src/main/java/org/caosdb/server/accessControl/SelfValidatingAuthenticationToken.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,14 +22,14 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Arrays;
import java.util.Collection;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authc.AuthenticationToken;
-import org.caosdb.server.utils.Utils;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.utils.Utils;
/**
* These AuthenticationTokens are characterized by the following properties:
diff --git a/src/main/java/org/caosdb/server/accessControl/SessionToken.java b/src/main/java/org/caosdb/server/accessControl/SessionToken.java
index 760f119541918a153cf8d4ca452fa0f9b7adced0..aa02c5c8b54ce13b082f4abe90abae85e880ec64 100644
--- a/src/main/java/org/caosdb/server/accessControl/SessionToken.java
+++ b/src/main/java/org/caosdb/server/accessControl/SessionToken.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -23,12 +23,12 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
/**
* Session tokens are formatted as JSON arrays with the following elements:
@@ -82,7 +82,8 @@ public class SessionToken extends SelfValidatingAuthenticationToken {
private static SessionToken generate(
final Principal principal, final String[] permissions, final String[] roles) {
int timeout =
- Integer.parseInt(CaosDBServer.getServerProperty(ServerProperties.KEY_SESSION_TIMEOUT_MS));
+ Integer.parseInt(
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_SESSION_TIMEOUT_MS));
return new SessionToken(principal, timeout, permissions, roles);
}
diff --git a/src/main/java/org/caosdb/server/accessControl/SessionTokenRealm.java b/src/main/java/org/caosdb/server/accessControl/SessionTokenRealm.java
index 270565be3dd8fc25408a1d7992638ef24bcfaa1c..afe01b918c5676fac4602b7f555efbeeb5319a90 100644
--- a/src/main/java/org/caosdb/server/accessControl/SessionTokenRealm.java
+++ b/src/main/java/org/caosdb/server/accessControl/SessionTokenRealm.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.authc.AuthenticationInfo;
import org.apache.shiro.authc.AuthenticationToken;
diff --git a/src/main/java/org/caosdb/server/accessControl/SinglePermissionSubject.java b/src/main/java/org/caosdb/server/accessControl/SinglePermissionSubject.java
index 2c3a3479420c5f0642e0d42bf53b717ab0219571..9d8936dd916646e6378e35fa03b118fd36aed1f2 100644
--- a/src/main/java/org/caosdb/server/accessControl/SinglePermissionSubject.java
+++ b/src/main/java/org/caosdb/server/accessControl/SinglePermissionSubject.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Collection;
import java.util.Iterator;
diff --git a/src/main/java/org/caosdb/server/accessControl/UserSource.java b/src/main/java/org/caosdb/server/accessControl/UserSource.java
index ff9882bfbf581e3633d99c3a20c5113e1d329e55..204fecb75775c1faf9d041ab485c59d9f04d23f2 100644
--- a/src/main/java/org/caosdb/server/accessControl/UserSource.java
+++ b/src/main/java/org/caosdb/server/accessControl/UserSource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Map;
import java.util.Set;
@@ -37,8 +37,8 @@ import java.util.Set;
* <li>get the default {@link UserStatus} - {@link #getDefaultUserStatus(String)}
* <li>get the default email address - {@link #getDefaultUserEmail(String)}
* <li>retrieve a users roles - {@link #resolveRolesForUsername(String)} The default email and
- * default {@link UserStatus} might be overridden by other settings in CaosDB - that's why they
- * are called "default".
+ * default {@link UserStatus} might be overridden by other settings in LinkAhead - that's why
+ * they are called "default".
*
* <p>Also, the user's roles might be overridden by the internal user source {@link
* InternalUserSource}.
@@ -50,7 +50,7 @@ import java.util.Set;
public interface UserSource {
/**
- * Every UserSource has a unique name, e.g. PAM, CaosDB (which is default name of the internal
+ * Every UserSource has a unique name, e.g. PAM, LinkAhead (which is default name of the internal
* user source {@link InternalUserSource}).
*
* @return name
diff --git a/src/main/java/org/caosdb/server/accessControl/UserSources.java b/src/main/java/org/caosdb/server/accessControl/UserSources.java
index 04c2ecab9fee23c62b042657c69911e2d69846a0..7eb945f92ea0c01a7fc79c9c804d648422e99385 100644
--- a/src/main/java/org/caosdb/server/accessControl/UserSources.java
+++ b/src/main/java/org/caosdb/server/accessControl/UserSources.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.io.FileInputStream;
import java.io.IOException;
@@ -34,14 +34,14 @@ import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.config.Ini;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.permissions.Role;
-import org.caosdb.server.transaction.LogUserVisitTransaction;
-import org.caosdb.server.transaction.RetrieveRoleTransaction;
-import org.caosdb.server.transaction.RetrieveUserTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.permissions.Role;
+import org.linkahead.server.transaction.LogUserVisitTransaction;
+import org.linkahead.server.transaction.RetrieveRoleTransaction;
+import org.linkahead.server.transaction.RetrieveUserTransaction;
+import org.linkahead.server.utils.ServerMessages;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -53,7 +53,7 @@ import org.slf4j.LoggerFactory;
*
* <ul>
* <li>User name: A string which identifies a user uniquely across one realm. Why is this so?
- * Because it is possible, that two different people from collaborating work groups with
+ * Because it is possible that two different people from collaborating work groups with
* similar names have the same user name in their group e.g. "mueller@uni1.de" and
* "mueller@uni2.de" or two people from different user groups use the name "admin". In the
* "mueller" example the domain name of the email is the realm of authentication.
@@ -95,7 +95,7 @@ public class UserSources extends HashMap<String, UserSource> {
return true;
}
if (principal.toString().equals(AnonymousAuthenticationToken.PRINCIPAL.toString())
- && CaosDBServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
+ && LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
.equalsIgnoreCase("true")) {
return true;
}
@@ -162,7 +162,7 @@ public class UserSources extends HashMap<String, UserSource> {
this.map = new Ini();
try (final FileInputStream f =
new FileInputStream(
- CaosDBServer.getServerProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE))) {
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE))) {
this.map.load(f);
} catch (final IOException e) {
logger.debug("could not load usersources.ini", e);
@@ -196,6 +196,11 @@ public class UserSources extends HashMap<String, UserSource> {
return null;
}
+ /**
+ * Guess the realm for a user name.
+ *
+ * <p>Returns null if the name can not be found in any UserSource.
+ */
public static String guessRealm(final String username) {
String found = null;
for (final UserSource u : instance.values()) {
@@ -324,7 +329,7 @@ public class UserSources extends HashMap<String, UserSource> {
}
if (principal.getUsername().equals(AnonymousAuthenticationToken.PRINCIPAL.getUsername())
&& principal.getRealm().equals(AnonymousAuthenticationToken.PRINCIPAL.getRealm())
- && CaosDBServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
+ && LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
.equalsIgnoreCase("true")) {
return true;
}
diff --git a/src/main/java/org/caosdb/server/accessControl/UserStatus.java b/src/main/java/org/caosdb/server/accessControl/UserStatus.java
index 6091d3e146eb5eb835044f97d1dcbafd8d042135..73859071623057c452fcb3ca49a033ce3033c064 100644
--- a/src/main/java/org/caosdb/server/accessControl/UserStatus.java
+++ b/src/main/java/org/caosdb/server/accessControl/UserStatus.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
public enum UserStatus {
ACTIVE,
diff --git a/src/main/java/org/caosdb/server/caching/Cache.java b/src/main/java/org/caosdb/server/caching/Cache.java
index fe5e12c5ec1e7a6acd83dbfb8f64ead676600840..9600071d6a884013301696a58293b0d0016baca3 100644
--- a/src/main/java/org/caosdb/server/caching/Cache.java
+++ b/src/main/java/org/caosdb/server/caching/Cache.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,13 +22,13 @@
*
* ** end header
*/
-package org.caosdb.server.caching;
+package org.linkahead.server.caching;
import java.io.Serializable;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
/**
- * Caching Helper Class used for all caches in the CaosDB Server.
+ * Caching Helper Class used for all caches in the LinkAhead Server.
*
* <p>The actual work is delegated to an instance of {@link JCSCacheHelper}. However, the delegate
* {@link #DELEGATE} can be be overridden for testing purposes with {@link #setDelegate(Cache)}.
diff --git a/src/main/java/org/caosdb/server/caching/CacheHelper.java b/src/main/java/org/caosdb/server/caching/CacheHelper.java
index 0dfd32da5bc125b242622384fcae54eee722e4ef..bd21dfc523ee8e156449ec1aa9ce9d64aacef603 100644
--- a/src/main/java/org/caosdb/server/caching/CacheHelper.java
+++ b/src/main/java/org/caosdb/server/caching/CacheHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2019 IndiScale GmbH
* Copyright (C) 2019 Timm Fitschen (t.fitschen@indiscale.com)
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.caching;
+package org.linkahead.server.caching;
import java.io.Serializable;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
diff --git a/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java b/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java
index 1613b8be8194425ab14e5e68b9215a0ba92be8d3..176c89096b91e78f4ba79d73acb4d0bae50351a0 100644
--- a/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java
+++ b/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.caching;
+package org.linkahead.server.caching;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
@@ -34,8 +34,8 @@ import org.apache.commons.jcs.JCS;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
/**
* A CacheHelper implementation which is configured statically via the {@link
@@ -63,8 +63,8 @@ public class JCSCacheHelper implements CacheHelper {
public static void init() {
final boolean disabled =
- Boolean.parseBoolean(CaosDBServer.getServerProperty(ServerProperties.KEY_CACHE_DISABLE));
- init(CaosDBServer.getServerProperty(ServerProperties.KEY_CACHE_CONF_LOC), disabled);
+ Boolean.parseBoolean(LinkAheadServer.getServerProperty(ServerProperties.KEY_CACHE_DISABLE));
+ init(LinkAheadServer.getServerProperty(ServerProperties.KEY_CACHE_CONF_LOC), disabled);
}
public static void init(String configFileLocation, boolean disabled) {
diff --git a/src/main/java/org/caosdb/server/database/BackendTransaction.java b/src/main/java/org/caosdb/server/database/BackendTransaction.java
index 05ea26c255ae5b2bd1e75df7f3fdc4d94fca5e5a..16b0912f0d58920588d4f5c81c6c2347478deb2d 100644
--- a/src/main/java/org/caosdb/server/database/BackendTransaction.java
+++ b/src/main/java/org/caosdb/server/database/BackendTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,119 +19,119 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
import java.util.HashMap;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeleteEntityProperties;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeletePassword;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeleteRole;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeleteSparseEntity;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeleteUser;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetAllNames;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetChildren;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetDependentEntities;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetFileRecordByPath;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetIDByName;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetInfo;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetUpdateableChecksums;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertEntityDatatype;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertEntityProperties;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertLinCon;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertLogRecord;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertParents;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertRole;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertSparseEntity;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertTransactionHistory;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLIsSubType;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLListRoles;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLListUsers;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLLogUserVisit;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveAll;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveAllUncheckedFiles;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveDatatypes;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveEntityACL;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveLogRecord;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveParents;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrievePasswordValidator;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrievePermissionRules;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveProperties;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveQueryTemplateDefinition;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveRole;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveSparseEntity;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveUser;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveVersionHistory;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSetFileCheckedTimestampImpl;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSetFileChecksum;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSetPassword;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSetPermissionRules;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSetQueryTemplateDefinition;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSyncStats;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLUpdateSparseEntity;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLUpdateUser;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLUpdateUserRoles;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckHash;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckSize;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileExists;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileWasModifiedAfter;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator;
-import org.caosdb.server.database.backend.interfaces.BackendTransactionImpl;
-import org.caosdb.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
-import org.caosdb.server.database.backend.interfaces.DeletePasswordImpl;
-import org.caosdb.server.database.backend.interfaces.DeleteRoleImpl;
-import org.caosdb.server.database.backend.interfaces.DeleteSparseEntityImpl;
-import org.caosdb.server.database.backend.interfaces.DeleteUserImpl;
-import org.caosdb.server.database.backend.interfaces.FileCheckHash;
-import org.caosdb.server.database.backend.interfaces.FileCheckSize;
-import org.caosdb.server.database.backend.interfaces.FileExists;
-import org.caosdb.server.database.backend.interfaces.FileWasModifiedAfter;
-import org.caosdb.server.database.backend.interfaces.GetAllNamesImpl;
-import org.caosdb.server.database.backend.interfaces.GetChildrenImpl;
-import org.caosdb.server.database.backend.interfaces.GetDependentEntitiesImpl;
-import org.caosdb.server.database.backend.interfaces.GetFileIteratorImpl;
-import org.caosdb.server.database.backend.interfaces.GetFileRecordByPathImpl;
-import org.caosdb.server.database.backend.interfaces.GetIDByNameImpl;
-import org.caosdb.server.database.backend.interfaces.GetInfoImpl;
-import org.caosdb.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
-import org.caosdb.server.database.backend.interfaces.InsertEntityDatatypeImpl;
-import org.caosdb.server.database.backend.interfaces.InsertEntityPropertiesImpl;
-import org.caosdb.server.database.backend.interfaces.InsertLinConImpl;
-import org.caosdb.server.database.backend.interfaces.InsertLogRecordImpl;
-import org.caosdb.server.database.backend.interfaces.InsertParentsImpl;
-import org.caosdb.server.database.backend.interfaces.InsertRoleImpl;
-import org.caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
-import org.caosdb.server.database.backend.interfaces.InsertTransactionHistoryImpl;
-import org.caosdb.server.database.backend.interfaces.IsSubTypeImpl;
-import org.caosdb.server.database.backend.interfaces.ListRolesImpl;
-import org.caosdb.server.database.backend.interfaces.ListUsersImpl;
-import org.caosdb.server.database.backend.interfaces.LogUserVisitImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveEntityACLImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveLogRecordImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
-import org.caosdb.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
-import org.caosdb.server.database.backend.interfaces.SetFileChecksumImpl;
-import org.caosdb.server.database.backend.interfaces.SetPasswordImpl;
-import org.caosdb.server.database.backend.interfaces.SetPermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.backend.interfaces.SyncStatsImpl;
-import org.caosdb.server.database.backend.interfaces.UpdateSparseEntityImpl;
-import org.caosdb.server.database.backend.interfaces.UpdateUserImpl;
-import org.caosdb.server.database.backend.interfaces.UpdateUserRolesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.utils.UndoHandler;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLDeleteEntityProperties;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLDeletePassword;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLDeleteRole;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLDeleteSparseEntity;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLDeleteUser;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetAllNames;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetChildren;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetDependentEntities;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetFileRecordByPath;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetIDByName;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetInfo;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetUpdateableChecksums;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertEntityDatatype;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertEntityProperties;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertLinCon;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertLogRecord;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertParents;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertRole;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertSparseEntity;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertTransactionHistory;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLIsSubType;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLListRoles;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLListUsers;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLLogUserVisit;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveAll;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveAllUncheckedFiles;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveDatatypes;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveEntityACL;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveLogRecord;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveParents;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrievePasswordValidator;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrievePermissionRules;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveProperties;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveQueryTemplateDefinition;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveRole;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveSparseEntity;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveUser;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveVersionHistory;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSetFileCheckedTimestampImpl;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSetFileChecksum;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSetPassword;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSetPermissionRules;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSetQueryTemplateDefinition;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSyncStats;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLUpdateSparseEntity;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLUpdateUser;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLUpdateUserRoles;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckHash;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckSize;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileExists;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileWasModifiedAfter;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator;
+import org.linkahead.server.database.backend.interfaces.BackendTransactionImpl;
+import org.linkahead.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
+import org.linkahead.server.database.backend.interfaces.DeletePasswordImpl;
+import org.linkahead.server.database.backend.interfaces.DeleteRoleImpl;
+import org.linkahead.server.database.backend.interfaces.DeleteSparseEntityImpl;
+import org.linkahead.server.database.backend.interfaces.DeleteUserImpl;
+import org.linkahead.server.database.backend.interfaces.FileCheckHash;
+import org.linkahead.server.database.backend.interfaces.FileCheckSize;
+import org.linkahead.server.database.backend.interfaces.FileExists;
+import org.linkahead.server.database.backend.interfaces.FileWasModifiedAfter;
+import org.linkahead.server.database.backend.interfaces.GetAllNamesImpl;
+import org.linkahead.server.database.backend.interfaces.GetChildrenImpl;
+import org.linkahead.server.database.backend.interfaces.GetDependentEntitiesImpl;
+import org.linkahead.server.database.backend.interfaces.GetFileIteratorImpl;
+import org.linkahead.server.database.backend.interfaces.GetFileRecordByPathImpl;
+import org.linkahead.server.database.backend.interfaces.GetIDByNameImpl;
+import org.linkahead.server.database.backend.interfaces.GetInfoImpl;
+import org.linkahead.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
+import org.linkahead.server.database.backend.interfaces.InsertEntityDatatypeImpl;
+import org.linkahead.server.database.backend.interfaces.InsertEntityPropertiesImpl;
+import org.linkahead.server.database.backend.interfaces.InsertLinConImpl;
+import org.linkahead.server.database.backend.interfaces.InsertLogRecordImpl;
+import org.linkahead.server.database.backend.interfaces.InsertParentsImpl;
+import org.linkahead.server.database.backend.interfaces.InsertRoleImpl;
+import org.linkahead.server.database.backend.interfaces.InsertSparseEntityImpl;
+import org.linkahead.server.database.backend.interfaces.InsertTransactionHistoryImpl;
+import org.linkahead.server.database.backend.interfaces.IsSubTypeImpl;
+import org.linkahead.server.database.backend.interfaces.ListRolesImpl;
+import org.linkahead.server.database.backend.interfaces.ListUsersImpl;
+import org.linkahead.server.database.backend.interfaces.LogUserVisitImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveDatatypesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveEntityACLImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveLogRecordImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveParentsImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePropertiesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveSparseEntityImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
+import org.linkahead.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
+import org.linkahead.server.database.backend.interfaces.SetFileChecksumImpl;
+import org.linkahead.server.database.backend.interfaces.SetPasswordImpl;
+import org.linkahead.server.database.backend.interfaces.SetPermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.backend.interfaces.SyncStatsImpl;
+import org.linkahead.server.database.backend.interfaces.UpdateSparseEntityImpl;
+import org.linkahead.server.database.backend.interfaces.UpdateUserImpl;
+import org.linkahead.server.database.backend.interfaces.UpdateUserRolesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.utils.UndoHandler;
+import org.linkahead.server.utils.Undoable;
public abstract class BackendTransaction implements Undoable {
diff --git a/src/main/java/org/caosdb/server/database/CacheableBackendTransaction.java b/src/main/java/org/caosdb/server/database/CacheableBackendTransaction.java
index 621fa31cd1603633fdb259591d29abf00c6312a4..8fad626cd07104069fe64275f37dc63f816a7791 100644
--- a/src/main/java/org/caosdb/server/database/CacheableBackendTransaction.java
+++ b/src/main/java/org/caosdb/server/database/CacheableBackendTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,11 +22,11 @@
*
* ** end header
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
import java.io.Serializable;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public abstract class CacheableBackendTransaction<K, V extends Serializable>
extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/ChainTransaction.java b/src/main/java/org/caosdb/server/database/ChainTransaction.java
index 6adee64ade2b4633f33f4b0a5397628d63e05e7c..472ffa7e9b9c5a9fcc53ef33da9bc20408e21a26 100644
--- a/src/main/java/org/caosdb/server/database/ChainTransaction.java
+++ b/src/main/java/org/caosdb/server/database/ChainTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
import java.util.LinkedList;
-import org.caosdb.server.database.backend.interfaces.BackendTransactionImpl;
+import org.linkahead.server.database.backend.interfaces.BackendTransactionImpl;
public class ChainTransaction<T extends BackendTransactionImpl> {
private final LinkedList<T> chain = new LinkedList<T>();
diff --git a/src/main/java/org/caosdb/server/database/Database.java b/src/main/java/org/caosdb/server/database/Database.java
index 797aadcced181febbc0539975ba1f46d8ee2d9de..808b49378a5fd2b19e6ed76fde4ec501eac9e0fb 100644
--- a/src/main/java/org/caosdb/server/database/Database.java
+++ b/src/main/java/org/caosdb/server/database/Database.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
public class Database {
diff --git a/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java b/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java
index f12c78e31bf28799b8c8ead1c9ff311a65bb01ef..002670c9d98195fbff86cc16d543d806fe642d27 100644
--- a/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java
+++ b/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -23,22 +23,22 @@
*
* ** end header
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
import java.util.concurrent.Semaphore;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.locks.ReentrantLock;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.access.AccessControlAccess;
-import org.caosdb.server.database.access.InfoAccess;
-import org.caosdb.server.database.access.InitAccess;
-import org.caosdb.server.database.access.TransactionAccess;
-import org.caosdb.server.transaction.AccessControlTransaction;
-import org.caosdb.server.transaction.TransactionInterface;
-import org.caosdb.server.transaction.WriteTransactionInterface;
-import org.caosdb.server.utils.Info;
-import org.caosdb.server.utils.Initialization;
-import org.caosdb.server.utils.Releasable;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.access.AccessControlAccess;
+import org.linkahead.server.database.access.InfoAccess;
+import org.linkahead.server.database.access.InitAccess;
+import org.linkahead.server.database.access.TransactionAccess;
+import org.linkahead.server.transaction.AccessControlTransaction;
+import org.linkahead.server.transaction.TransactionInterface;
+import org.linkahead.server.transaction.WriteTransactionInterface;
+import org.linkahead.server.utils.Info;
+import org.linkahead.server.utils.Initialization;
+import org.linkahead.server.utils.Releasable;
/**
* Acquire and release read access. {@link DatabaseAccessManager} uses this class for managing
@@ -307,7 +307,7 @@ public class DatabaseAccessManager {
}
/**
- * Special access to be used during the {@link Initialization} of the caosdb server.
+ * Special access to be used during the {@link Initialization} of the LinkAhead server.
*
* @param initialization
* @return
diff --git a/src/main/java/org/caosdb/server/database/access/AbstractAccess.java b/src/main/java/org/caosdb/server/database/access/AbstractAccess.java
index 1d30bd3fee7187b9c44378e5b94c1c6d97287f00..4e97117ddd11426a94f307b1280c3cc13f22b183 100644
--- a/src/main/java/org/caosdb/server/database/access/AbstractAccess.java
+++ b/src/main/java/org/caosdb/server/database/access/AbstractAccess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
import java.util.HashMap;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.database.misc.RollBackHandler;
-import org.caosdb.server.transaction.TransactionInterface;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.database.misc.RollBackHandler;
+import org.linkahead.server.transaction.TransactionInterface;
public abstract class AbstractAccess<T extends TransactionInterface> implements Access {
diff --git a/src/main/java/org/caosdb/server/database/access/Access.java b/src/main/java/org/caosdb/server/database/access/Access.java
index 228e8e004aea7454a287bccd898794c2bb4f1b9c..b6fc8a8e5a75641baff2fbeba2e619037145c924 100644
--- a/src/main/java/org/caosdb/server/database/access/Access.java
+++ b/src/main/java/org/caosdb/server/database/access/Access.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
-import org.caosdb.server.database.misc.DBHelper;
+import org.linkahead.server.database.misc.DBHelper;
public interface Access {
diff --git a/src/main/java/org/caosdb/server/database/access/AccessControlAccess.java b/src/main/java/org/caosdb/server/database/access/AccessControlAccess.java
index 450f0c61310e5706c450ad793c7485073393d4c9..bc2231663d47454a46ceeafa10c9c6fac969174d 100644
--- a/src/main/java/org/caosdb/server/database/access/AccessControlAccess.java
+++ b/src/main/java/org/caosdb/server/database/access/AccessControlAccess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
-import org.caosdb.server.transaction.AccessControlTransaction;
+import org.linkahead.server.transaction.AccessControlTransaction;
public class AccessControlAccess extends AbstractAccess<AccessControlTransaction> {
diff --git a/src/main/java/org/caosdb/server/database/access/InfoAccess.java b/src/main/java/org/caosdb/server/database/access/InfoAccess.java
index 3d66e67a2d243d753c98e6934688eb34e1e94c0e..78b7c63effdbdc8bdbeb809e6ec495ab34bc157e 100644
--- a/src/main/java/org/caosdb/server/database/access/InfoAccess.java
+++ b/src/main/java/org/caosdb/server/database/access/InfoAccess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
import java.sql.SQLException;
-import org.caosdb.server.utils.Info;
+import org.linkahead.server.utils.Info;
public class InfoAccess extends AbstractAccess<Info> {
diff --git a/src/main/java/org/caosdb/server/database/access/InitAccess.java b/src/main/java/org/caosdb/server/database/access/InitAccess.java
index 1a6108cc62d4dd421d40128a5346ee2d216f6b9c..0de69202d5e3ebe12a7f08b30914935ef0c5d7d2 100644
--- a/src/main/java/org/caosdb/server/database/access/InitAccess.java
+++ b/src/main/java/org/caosdb/server/database/access/InitAccess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
import java.sql.SQLException;
-import org.caosdb.server.utils.Initialization;
+import org.linkahead.server.utils.Initialization;
public class InitAccess extends AbstractAccess<Initialization> {
diff --git a/src/main/java/org/caosdb/server/database/access/TransactionAccess.java b/src/main/java/org/caosdb/server/database/access/TransactionAccess.java
index 406d0fb6577f89c6d1c49627802e39a4514f6cfd..2a71659ec7dca07ab4c02a25ed83c3bace2c82fb 100644
--- a/src/main/java/org/caosdb/server/database/access/TransactionAccess.java
+++ b/src/main/java/org/caosdb/server/database/access/TransactionAccess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
-import org.caosdb.server.transaction.TransactionInterface;
-import org.caosdb.server.utils.Releasable;
+import org.linkahead.server.transaction.TransactionInterface;
+import org.linkahead.server.utils.Releasable;
public class TransactionAccess extends AbstractAccess<TransactionInterface> {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/ConnectionException.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/ConnectionException.java
index 83c334ac21fb929606144f84960966acde59df42..164101e7dfe587a6ef68ae9edb142994cbc71d63 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/ConnectionException.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/ConnectionException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
public class ConnectionException extends Exception {
private static final long serialVersionUID = 6119424337789255870L;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
index 997de3141db6fd49ac510fa61150a2d16e7d5416..647b0b06387fe7ab6ba07abb09c052185a06aa4a 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import com.google.common.base.Objects;
import java.sql.CallableStatement;
@@ -29,9 +29,9 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import snaq.db.ConnectionPool;
@@ -76,21 +76,21 @@ class DatabaseConnectionPool {
private static synchronized ConnectionPool createConnectionPool()
throws ClassNotFoundException, InstantiationException, IllegalAccessException, SQLException,
- ConnectionException, CaosDBException {
+ ConnectionException, LinkAheadException {
final String url =
"jdbc:mysql://"
- + CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_HOST)
+ + LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_HOST)
+ ":"
- + CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_PORT)
+ + LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_PORT)
+ "/"
- + CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_DATABASE_NAME)
+ + LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_DATABASE_NAME)
+ "?noAccessToProcedureBodies=true&autoReconnect=true&serverTimezone=UTC&characterEncoding=UTF-8";
- final String user = CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_USER_NAME);
- final String pwd = CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_USER_PASSWORD);
+ final String user = LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_USER_NAME);
+ final String pwd = LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_USER_PASSWORD);
final ConnectionPool pool = new ConnectionPool("MySQL Pool", 2, 5, 0, 0, url, user, pwd);
pool.removeShutdownHook();
- CaosDBServer.addPostShutdownHook(
+ LinkAheadServer.addPostShutdownHook(
new Thread("SHUTDOWN_MYSQL_CONNECTION_POOL") {
@Override
public void run() {
@@ -185,10 +185,10 @@ class DatabaseConnectionPool {
* <p>@todo Patch versions are not handled yet.
*/
private static void checkVersion(final Connection con)
- throws SQLException, ConnectionException, CaosDBException {
+ throws SQLException, ConnectionException, LinkAheadException {
try {
final String[] expected_version =
- CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_SCHEMA_VERSION)
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_SCHEMA_VERSION)
.toLowerCase()
.split("\\.");
final String expected_major = expected_version[0];
@@ -215,7 +215,7 @@ class DatabaseConnectionPool {
actual_version);
} else {
logger.error(
- "Version of the MySQL/MariaDB schema is incompatible.\n\tExpected: {}.{}\n\tActual: {}\nPlease upgrade the CaosDB server.\n\n",
+ "Version of the MySQL/MariaDB schema is incompatible.\n\tExpected: {}.{}\n\tActual: {}\nPlease upgrade the LinkAhead server.\n\n",
expected_major,
expected_minor,
actual_version);
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
index f7d364ae6376524ef892de3353d699547417717e..ae8d77dd0db1eac32d0587fea353eac9fcae8b17 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import com.google.common.base.Objects;
import java.sql.ResultSet;
@@ -34,19 +34,19 @@ import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.stream.Collectors;
-import org.caosdb.server.database.proto.FlatProperty;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Property;
+import org.linkahead.server.database.proto.FlatProperty;
+import org.linkahead.server.database.proto.ProtoProperty;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.wrapper.Property;
public class DatabaseUtils {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java
index f8cba7d4c9734c1e6e12b72498ceaa6c57ed1a17..91f9527fcc441a6cb4750460f7f556ea887c5b7f 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLIntegrityConstraintViolationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLDeleteEntityProperties extends MySQLTransaction
implements DeleteEntityPropertiesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeletePassword.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeletePassword.java
index 2569226e271b55a1785da7b548eeae93fbd4c262..fa9228f92062dd13a4ab16bd2a6d5b3499da77e1 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeletePassword.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeletePassword.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.SQLIntegrityConstraintViolationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.DeletePasswordImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.DeletePasswordImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLDeletePassword extends MySQLTransaction implements DeletePasswordImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteRole.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteRole.java
index b0faa45f96e04e6957ff1d288d034ca9e96cb6d7..770b6832422a471874a43d41380e5522f9f1593b 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteRole.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,15 +21,15 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.SQLIntegrityConstraintViolationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.DeleteRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.DeleteRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.ServerMessages;
public class MySQLDeleteRole extends MySQLTransaction implements DeleteRoleImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java
index 7fe8ac303b53ec26dc947c1e4a84e648d7b6517d..f1e5cabaf46b6a4f3f6df001c6cf6dd903c55ae1 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLIntegrityConstraintViolationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.DeleteSparseEntityImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.DeleteSparseEntityImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLDeleteSparseEntity extends MySQLTransaction implements DeleteSparseEntityImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteUser.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteUser.java
index 88b20e4a0186844cecce2cc2f5fd14423f5bf4c1..2424c468ab65552ad045fb0776d84f8350f55d38 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.DeleteUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.DeleteUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLDeleteUser extends MySQLTransaction implements DeleteUserImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
index 474048f1a72331c3a2e35b38c5cb4c9b3e4d6543..c544f2c5fce0fff92a124ac5b71f0838f24131b0 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
@@ -1,14 +1,14 @@
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetAllNamesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetAllNamesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
/** Retrieve name, role and acl of all entities from the MySQL backend. */
public class MySQLGetAllNames extends MySQLTransaction implements GetAllNamesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetChildren.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetChildren.java
index 3c1cebf1e20a720a5f726e378bb22b1ad61c850a..c16f5ed33c0f10b6da150b847f3fc7844fac9eba 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetChildren.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetChildren.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetChildrenImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetChildrenImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLGetChildren extends MySQLTransaction implements GetChildrenImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java
index 9384c8a04861a01f1e56236b0ab42433d87990f5..6145b7f5b334339e79fee4565f5071995bda69f9 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetDependentEntitiesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetDependentEntitiesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLGetDependentEntities extends MySQLTransaction
implements GetDependentEntitiesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java
index 9b147d289b337f63dd359ce604719d9e00a149be..80dc7aa484567e3eeb94d51d431e66c66baaabaa 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetFileRecordByPathImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetFileRecordByPathImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class MySQLGetFileRecordByPath extends MySQLTransaction implements GetFileRecordByPathImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java
index c2e28cd39929f71e874fb4a69c38261ed290b18a..e3eb38c2cf91806c0b9f6635a42d55e85d5a6734 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetIDByNameImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetIDByNameImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLGetIDByName extends MySQLTransaction implements GetIDByNameImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetInfo.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetInfo.java
index 2e7a110c6f42ffe2b489525509d742810119e187..62b1e425255004b3d2b2e73758db7bbe05f370e0 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetInfo.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetInfo.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetInfoImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoInfo;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetInfoImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoInfo;
public class MySQLGetInfo extends MySQLTransaction implements GetInfoImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java
index 28c55032e0ae6b6c2fcfb779339a72b96c703ba0..1b270d16734f4e0e309e72cfad02846558350a6d 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLGetUpdateableChecksums extends MySQLTransaction
implements GetUpdateableChecksumsImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java
index 568e0e53a7b80a76c533229e13c6700c4c4ff47f..503ea244eb4630de3961d9cb2af021131e59d091 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.io.UnsupportedEncodingException;
import java.sql.CallableStatement;
@@ -31,11 +31,11 @@ import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.HashMap;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.transaction.ChecksumUpdater;
-import org.caosdb.server.transaction.TransactionInterface;
-import org.caosdb.server.transaction.WriteTransactionInterface;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.transaction.ChecksumUpdater;
+import org.linkahead.server.transaction.TransactionInterface;
+import org.linkahead.server.transaction.WriteTransactionInterface;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java
index c4cb7cf98e5da51f98d71b4c5f6fc91e6961892e..a19490ebb7b343d997d92fa3d1e7877a3f9cc00e 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java
@@ -1,12 +1,12 @@
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLIntegrityConstraintViolationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertEntityDatatypeImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertEntityDatatypeImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class MySQLInsertEntityDatatype extends MySQLTransaction
implements InsertEntityDatatypeImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
index becb56a2397fffa323f005507463a586bdecc0cf..60dc5d3c31f0acfc0e932b97b0bf3ba1aea71e53 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import static java.sql.Types.BIGINT;
@@ -33,20 +33,20 @@ import java.util.Deque;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertEntityPropertiesImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.FlatProperty;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.SingleValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.wrapper.Property;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertEntityPropertiesImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.FlatProperty;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.datatype.SingleValue;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.wrapper.Property;
public class MySQLInsertEntityProperties extends MySQLTransaction
implements InsertEntityPropertiesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLinCon.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLinCon.java
index b8ea787292e375fcda8b99caa4464bfdf32c3fd7..479c6d9e737dc2695131dd4014d596003f9cef15 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLinCon.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLinCon.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertLinConImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.LinCon;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertLinConImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.LinCon;
public class MySQLInsertLinCon extends MySQLTransaction implements InsertLinConImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLogRecord.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLogRecord.java
index 6807808d18fb6ba9ce0a4ed9287ea21612cc2d2c..5ebfb4304cba9350c4109a7f606ad981b3c61223 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLogRecord.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLogRecord.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.util.List;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertLogRecordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertLogRecordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLInsertLogRecord extends MySQLTransaction implements InsertLogRecordImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java
index 61a5e8c48cdc85098e1b0a2f5531c358d6c6058d..56821b0ef12cc52c44f488e804962f8a191ccc95 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertParentsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertParentsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLInsertParents extends MySQLTransaction implements InsertParentsImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertRole.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertRole.java
index 66f5a888dd8aa7f429dbd1698ff8245e3efb021a..1700c7ae21e443b3810f25a056a449897973e4fc 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertRole.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLInsertRole extends MySQLTransaction implements InsertRoleImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
index 27227926156fc9b35ab75473e1efa2cce55f152e..62bde118b4c1656376c146e4a278cda5bf6e5978 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLIntegrityConstraintViolationException;
import java.sql.Types;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertSparseEntityImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class MySQLInsertSparseEntity extends MySQLTransaction implements InsertSparseEntityImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java
index 0832790a0b56446570fbd7b9c3a4383390c443a7..d0e48e3ddc60599b6d3d97bf3e170a96cae815e5 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertTransactionHistoryImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertTransactionHistoryImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLInsertTransactionHistory extends MySQLTransaction
implements InsertTransactionHistoryImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java
index f6c2daf8d4a0bf4defcaa550cf715032d57cd9cd..6304b0f059149f531c40e334ad673fa8c2a610b9 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.IsSubTypeImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.IsSubTypeImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLIsSubType extends MySQLTransaction implements IsSubTypeImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListRoles.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListRoles.java
index 69ac524eae823d06fdbd4346056979ea15307437..dce046a9df43d6ac4169abdb0edbc5fce4b959a2 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListRoles.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListRoles.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,17 +19,17 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.ListRolesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.ListRolesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLListRoles extends MySQLTransaction implements ListRolesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java
index 83ebffe679e6625da720fd2933a5d8defb7264c3..b9658ae50efb1beabd2374ddaf5bf52b2e832f43 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,18 +19,18 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.accessControl.UserStatus;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.ListUsersImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.UserStatus;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.ListUsersImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class MySQLListUsers extends MySQLTransaction implements ListUsersImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java
index 23050da87e324026be1eefa02690959d0a0590cc..9b866dddc9ac27b2e43182cc7d24ca3303a33d86 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,14 +19,14 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.LogUserVisitImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.LogUserVisitImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLLogUserVisit extends MySQLTransaction implements LogUserVisitImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
index 9a2ea81629853e3baf9de7757e1abe6c8f01fe28..f82082d6460c0ee201b48d71a92b3d8392805f23 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
@@ -27,13 +27,13 @@ import java.sql.SQLException;
import java.util.LinkedList;
import java.util.List;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.permissions.EntityPermission;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.permissions.EntityPermission;
public class MySQLRetrieveAll extends MySQLTransaction implements RetrieveAllImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java
index 09a4e7c2edabea49617224fdb9159116f2cd742b..1a5f151bee16ad254f440c8faa030fc1d7408697 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Iterator;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class MySQLRetrieveAllUncheckedFiles extends MySQLTransaction
implements RetrieveAllUncheckedFilesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
index 685249417ca9c1664cc1a30af3fc3a597788c29f..d3f41cc8f20b7c17f52e7faa890a3029f450a857 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveDatatypesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
public class MySQLRetrieveDatatypes extends MySQLTransaction implements RetrieveDatatypesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java
index 5db8ed7597b1c0d357273848fb7c36febdcfed13..8a8947ea646e672625d85bd375361183e5742995 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,15 +19,15 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveEntityACLImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveEntityACLImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
public class MySQLRetrieveEntityACL extends MySQLTransaction implements RetrieveEntityACLImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveLogRecord.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveLogRecord.java
index bba36d2eb9de29fee40f023b9b97602d5b94b8a3..bec4c24545909358fee7a6cc98ae92fd30356664 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveLogRecord.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveLogRecord.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.io.ByteArrayInputStream;
import java.io.IOException;
@@ -32,9 +32,9 @@ import java.util.LinkedList;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveLogRecordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveLogRecordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLRetrieveLogRecord extends MySQLTransaction implements RetrieveLogRecordImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
index 1e2a6621d2fb85a5a5260b1a607670e970f54701..5fdb944a345fc50ae2f4f73e87015c8c27ec8875 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Types;
import java.util.LinkedList;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveParentsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.entity.EntityID;
public class MySQLRetrieveParents extends MySQLTransaction implements RetrieveParentsImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
index 9fd7e0a8e441b3ede2a3447ec364c24e16898fb5..144fb524dca11673f817ce8804d15eedf71920c6 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,19 +20,19 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.security.NoSuchAlgorithmException;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.accessControl.HashPasswordValidator;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.accessControl.HashPasswordValidator;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLRetrievePasswordValidator extends MySQLTransaction
implements RetrievePasswordValidatorImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePermissionRules.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePermissionRules.java
index 40767db34c2ba318637c87ebc7b21ba278c2c574..21e407f9ac619aa6261a30852412b239c24e4b3e 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePermissionRules.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePermissionRules.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.Map;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public class MySQLRetrievePermissionRules extends MySQLTransaction
implements RetrievePermissionRulesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
index 100df4ce72ebae75d3022866b345bacc9752ad91..d9ebb771c1cde96cabf9783ecdcbee0692d58790 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
@@ -28,11 +28,11 @@ import java.sql.SQLException;
import java.sql.Types;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrievePropertiesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoProperty;
+import org.linkahead.server.entity.EntityID;
public class MySQLRetrieveProperties extends MySQLTransaction implements RetrievePropertiesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
index 1ab95ae7afc756742475ff2f3c79eddfd632aae9..7db88b138cb747174e6ed714e3b8a98e3198acbf 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Types;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLRetrieveQueryTemplateDefinition extends MySQLTransaction
implements RetrieveQueryTemplateDefinitionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveRole.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveRole.java
index e9ee37c9a55bc07c79abc8b73d8f9bef2a5cde8c..f5e56c6bfdcc36eece7e1e87009cbfd16e318b11 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveRole.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,20 +21,20 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.LinkedList;
import java.util.Map;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.permissions.PermissionRule;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.permissions.PermissionRule;
public class MySQLRetrieveRole extends MySQLTransaction implements RetrieveRoleImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
index 48cd84b3869262ba7f1d8129fdde2335bed6cd8e..0ff92298117aefa247e2a450e56fbd03c2e3cd98 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Types;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveSparseEntityImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
/**
* Retrieve a single SparseEntity by id.
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
index 40f036f1d63753c0be9e6153f741db7d4f9d04ad..85d9ac262a9f68976e21457df609902ec5b4a7f0 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.HashSet;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserStatus;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserStatus;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class MySQLRetrieveUser extends MySQLTransaction implements RetrieveUserImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
index 6c4c2629a5effee25128f478bef20f5558a027ba..d7c3b9f66213d557a83cd586de566781d990560b 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.HashMap;
import java.util.LinkedList;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VersionHistoryItem;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VersionHistoryItem;
+import org.linkahead.server.entity.EntityID;
/**
* Transaction to retrieve all versions of an entity.
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java
index 18d7d9b7f510f5cb24e1fe844ac4caac86ff4913..448c1f81cd30638eda7db9fb000e91c5eb23f877 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLSetFileCheckedTimestampImpl extends MySQLTransaction
implements SetFileCheckedTimestampImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java
index fb6d4188c835fbc895ed4d5e427bb1b2bbc0bb4c..bcec7504b1ce7efa09498e355bf365896ec225ca 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java
@@ -1,11 +1,11 @@
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SetFileChecksumImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SetFileChecksumImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
/**
* Implements {@link SetFileChecksumImpl} for a MySQL/MariaDB back-end.
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPassword.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPassword.java
index 9972c3af019f092087158a9f85659af9cdd2b6dc..47dc173da66227505ac232b2fb16ed0110ff4ffb 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPassword.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPassword.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.math.BigInteger;
import java.security.MessageDigest;
@@ -28,10 +28,10 @@ import java.security.NoSuchAlgorithmException;
import java.security.SecureRandom;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SetPasswordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SetPasswordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.Utils;
public class MySQLSetPassword extends MySQLTransaction implements SetPasswordImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPermissionRules.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPermissionRules.java
index 1569cd494c44eed6ebc083b8e5046ea6649f7ad1..0cbc11ee4348ba02ed98d31eed626353410e0491 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPermissionRules.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPermissionRules.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SetPermissionRulesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SetPermissionRulesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public class MySQLSetPermissionRules extends MySQLTransaction implements SetPermissionRulesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java
index f3ded949383c7d250d4ad58e6ae964aa9f96324c..226bd41060a11cfebd8b5be02c6a28f436c5cd0f 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLSetQueryTemplateDefinition extends MySQLTransaction
implements SetQueryTemplateDefinitionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSyncStats.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSyncStats.java
index c874f21b14e15889cb0345303318ecf3504b7c05..077c0aefc7df64b5b3027593dc809511cf95eb1b 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSyncStats.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSyncStats.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
@@ -32,10 +32,10 @@ import java.io.ObjectOutputStream;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SyncStatsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.ServerStat;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SyncStatsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.ServerStat;
public class MySQLSyncStats extends MySQLTransaction implements SyncStatsImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLTransaction.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLTransaction.java
index 5b46579efeac34078fa176f03eb94206dc72f0e0..f86001b5529e5419c7125c6da8d6babbb0e52972 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.BackendTransactionImpl;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.BackendTransactionImpl;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.database.misc.TransactionBenchmark;
public class MySQLTransaction implements BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
index b2d0fb9e3b7615e7e95243a2a7bde2fa99e98ca2..492ab7cbc3fe860685369f22937cfffcc282f734 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.SQLIntegrityConstraintViolationException;
import java.sql.Types;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.UpdateSparseEntityImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.UpdateSparseEntityImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class MySQLUpdateSparseEntity extends MySQLTransaction implements UpdateSparseEntityImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java
index bd368698956163a8473ead7507aac0ba2b83d552..e9ab293c24275c8584ee6323286266e14767920e 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.Types;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.UpdateUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.UpdateUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class MySQLUpdateUser extends MySQLTransaction implements UpdateUserImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUserRoles.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUserRoles.java
index 6a52ab9d0e7d606d5f92038239be0ccacd03bda6..590ec57a14e0215b226f35ecdce936214d3d0579 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUserRoles.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUserRoles.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.util.Set;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.UpdateUserRolesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.UpdateUserRolesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLUpdateUserRoles extends MySQLTransaction implements UpdateUserRolesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
index 61e431bab60b9973f6aa1f0b824ffc3e3b60744e..e604d3b935f0a2d66a7293a623e14398cc605759 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,13 +17,13 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.StatementStatusInterface;
-import org.caosdb.server.entity.wrapper.Property;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.StatementStatusInterface;
+import org.linkahead.server.entity.wrapper.Property;
enum ReplacementStatus implements StatementStatusInterface {
REPLACEMENT
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckHash.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckHash.java
index e6b95a9925bbd560b9ccf80cdb6883efc2098f49..ab7ddbb0a0e7bae71d77837291488f1c4ff93182 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckHash.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckHash.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.FileCheckHash;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.Hasher;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.FileCheckHash;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.Hasher;
public class UnixFileSystemCheckHash extends UnixFileSystemTransaction implements FileCheckHash {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckSize.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckSize.java
index c695ff58ec9ca0b41f7aaa1ce5513a5ec657d9a6..4b7d46c510b79dcdaec98b1ecced80bdd6f91e58 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckSize.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckSize.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.FileCheckSize;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.FileCheckSize;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
public class UnixFileSystemCheckSize extends UnixFileSystemTransaction implements FileCheckSize {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileExists.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileExists.java
index 908d917c1b858eb7d6da77bfe90fae7e4f6c6289..cd508e17c759068d2eb8d9970554813f70c10bec 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileExists.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileExists.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.FileExists;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.FileExists;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
public class UnixFileSystemFileExists extends UnixFileSystemTransaction implements FileExists {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileWasModifiedAfter.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileWasModifiedAfter.java
index 70c97fecd67af94aa153fa6e0c6b0c8154cc936d..145df87486a079c2318f343bf0099def893e92aa 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileWasModifiedAfter.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileWasModifiedAfter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.FileWasModifiedAfter;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.FileWasModifiedAfter;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
public class UnixFileSystemFileWasModifiedAfter extends UnixFileSystemTransaction
implements FileWasModifiedAfter {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemGetFileIterator.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemGetFileIterator.java
index 89c275dd6d1fdd324f86f6cce6de179f795c7915..a98c7f0bae0418a21ff1c960b3e00b73c326dc4b 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemGetFileIterator.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemGetFileIterator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.util.Arrays;
import java.util.Iterator;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetFileIteratorImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetFileIteratorImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
public class UnixFileSystemGetFileIterator extends UnixFileSystemTransaction
implements GetFileIteratorImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemHelper.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemHelper.java
index 260a401fa6609dbfae363023a3ceb8b717bb87c7..4d2ba2aa89c55f095dd00074b824f558813d81a1 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemHelper.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.transaction.TransactionInterface;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.transaction.TransactionInterface;
public class UnixFileSystemHelper implements DBHelper {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemTransaction.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemTransaction.java
index ccf137448ee445f86594017ffc28a09d24158bcb..b1a03f07b7cf5b86187403a2f0b25f67a5a3d53e 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.BackendTransactionImpl;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.BackendTransactionImpl;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.Message;
public abstract class UnixFileSystemTransaction implements BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/BackendTransactionImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/BackendTransactionImpl.java
index 8a2dbb0cc67776e68cf6dd9a437754f233ae6190..b63a221600eb600dc59ec990c0d2fc857e638194 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/BackendTransactionImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/BackendTransactionImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.database.misc.TransactionBenchmark;
public interface BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteEntityPropertiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteEntityPropertiesImpl.java
index 1c271bcc4fec7ada01980c51c16e7c5b884fb79d..911e015a79d34acda0a55e71aae3ec95113172f4 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteEntityPropertiesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteEntityPropertiesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.utils.Undoable;
public interface DeleteEntityPropertiesImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/DeletePasswordImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/DeletePasswordImpl.java
index 32c485a97776b0b24efaf32b8719f85b2a770cab..3f0866aa654cee556224e72149236172c1450c88 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/DeletePasswordImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/DeletePasswordImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface DeletePasswordImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteRoleImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteRoleImpl.java
index 0bd6c5c71921961032fa33741c35210ffb455915..bb8b09df8e9f4b34d238ce58cf7f470feda99b68 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteRoleImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteRoleImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface DeleteRoleImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteSparseEntityImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteSparseEntityImpl.java
index 5f1d2ec2364aaead626182e13777af8c7e809a20..fd7c234b7b35c84f11f199af3862e712cceedd60 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteSparseEntityImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteSparseEntityImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.utils.Undoable;
public interface DeleteSparseEntityImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteUserImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteUserImpl.java
index 3ee0a1e4f7cea5ee00810149b2da589217e8dfe7..05b76cc48b86cfdb793b12348bc61de78c1a0893 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteUserImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteUserImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface DeleteUserImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckHash.java b/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckHash.java
index edd0718c41d17f045009c1c84f1fe31260ac225f..6b5f85c5b441d70edbc382e6e6efff0ee181b544 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckHash.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckHash.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.Hasher;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.Hasher;
public interface FileCheckHash extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckSize.java b/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckSize.java
index bce3249865e8c9373ee26e59496a568a494b2021..9de1c9c3436a13c8624e460794efe5e337273913 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckSize.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckSize.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface FileCheckSize extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/FileExists.java b/src/main/java/org/caosdb/server/database/backend/interfaces/FileExists.java
index 9a5ab664547113477a1f3ae0175d7a6f37311d10..df0029cef685b5b2f898641d22deced940ea175c 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/FileExists.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/FileExists.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface FileExists extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/FileWasModifiedAfter.java b/src/main/java/org/caosdb/server/database/backend/interfaces/FileWasModifiedAfter.java
index 08fccc584e1ae653b478abf22a34d4b57b6c4c89..dad501ed6f72f2f3b48d1e03ebe04a386349cee0 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/FileWasModifiedAfter.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/FileWasModifiedAfter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface FileWasModifiedAfter extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetAllNamesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetAllNamesImpl.java
index 9ca7a04052eef00c3202fa5b3375b3abe6d7fb54..67961f0541e8d7c52628d2ad11c1904085a03b0d 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetAllNamesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetAllNamesImpl.java
@@ -1,7 +1,7 @@
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.proto.SparseEntity;
/**
* Interface for the retrieval of all known names from the backend.
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetChildrenImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetChildrenImpl.java
index 8b0211a0b56bec22e4823058dfa72c355e59d19d..2d388a516d20c1c4b6f8b001c6f6aaa8a3f863b3 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetChildrenImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetChildrenImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface GetChildrenImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetDependentEntitiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetDependentEntitiesImpl.java
index 00c533dffb3ad067666f11d43f8469d9a7550e0a..8a7797dc3ef2f827d460678f4444eab461f9f4fe 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetDependentEntitiesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetDependentEntitiesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface GetDependentEntitiesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileIteratorImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileIteratorImpl.java
index 0b7e45707d66c945380a6398dea8f5f1a36cc604..32ad37ae1471a0b3354666fcaffca2e757a01998 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileIteratorImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileIteratorImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.Iterator;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface GetFileIteratorImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileRecordByPathImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileRecordByPathImpl.java
index e7f6966709cf34518e37ec42143f1dc8794ed5ff..17ad3cdb4f9e012329cb3a5287e9dc943e31de22 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileRecordByPathImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileRecordByPathImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public interface GetFileRecordByPathImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetIDByNameImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetIDByNameImpl.java
index 02cbc80731d1cc0d061f5aa9f080bea1364cdb7f..8902224fbb2156f2f1b3d057b0cc4bc563241430 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetIDByNameImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetIDByNameImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface GetIDByNameImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetInfoImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetInfoImpl.java
index d2bb1326e591d912a0562664ec2d26c0008827f9..134fecf15e42546e6311abdfd780803c97689234 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetInfoImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetInfoImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoInfo;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoInfo;
public interface GetInfoImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetUpdateableChecksumsImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetUpdateableChecksumsImpl.java
index 762fa2d39ccad6a96f46246962de8746087b64a8..2cd5dadde8217e1f34645d426e1b4519bf8d99fa 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetUpdateableChecksumsImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetUpdateableChecksumsImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface GetUpdateableChecksumsImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityDatatypeImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityDatatypeImpl.java
index 6da8d5cf9a7534e58cfbe634ad4594da2b2b466c..b9f98c5e204c7c390e274d1d7314f7ce20ea7f9b 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityDatatypeImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityDatatypeImpl.java
@@ -1,7 +1,7 @@
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.utils.Undoable;
public interface InsertEntityDatatypeImpl extends BackendTransactionImpl, Undoable {
public abstract void execute(SparseEntity entity);
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java
index f17643fd6ff0e980aef122a318fd9fc2668e2b79..a7f0888b79f9e84cc300a93c5b0343c30ca191e0 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.utils.Undoable;
public interface InsertEntityPropertiesImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLinConImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLinConImpl.java
index 98ba022ecf7fb061a6d95190bc3b6f1007cf51ac..651ab863e814a26a7c87f80e76d7fa8ae6b3b8d9 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLinConImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLinConImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.LinCon;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.LinCon;
+import org.linkahead.server.utils.Undoable;
public interface InsertLinConImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLogRecordImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLogRecordImpl.java
index 78bab8e251ff6e151963f1be8caf5e73211cc8e3..5382f9ea501cb8ac45e3291bd05030e3b7a752b7 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLogRecordImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLogRecordImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface InsertLogRecordImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertParentsImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertParentsImpl.java
index 890ed6422aa7e39293dc6b64fbad710089e1cf83..4eae2db1079bb5458e63b68f5a1aae343cc25df0 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertParentsImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertParentsImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.utils.Undoable;
public interface InsertParentsImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertRoleImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertRoleImpl.java
index ff305cab73f58928774cfdbdba95dbc61dad3077..59252dda7ed1d56f248c128b2ba22bc0a0403f49 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertRoleImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertRoleImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface InsertRoleImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertSparseEntityImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertSparseEntityImpl.java
index 33f46e97872bcd6a519d6980234b201639aa5e1e..c87f846360fe95909d7fce7a28adc6383f385a00 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertSparseEntityImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertSparseEntityImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.utils.Undoable;
public interface InsertSparseEntityImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertTransactionHistoryImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertTransactionHistoryImpl.java
index 927238e6cf4b311886840695e9de13cc6f86c87c..c15bbc1676927cbee0b0cd0ee56bbe18db6e108a 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertTransactionHistoryImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertTransactionHistoryImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.utils.Undoable;
public interface InsertTransactionHistoryImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/IsSubTypeImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/IsSubTypeImpl.java
index 10c18e43f07c927f049067a2767fe79f45f4990b..d1c312dc350f61203f684d71f138769b596616fe 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/IsSubTypeImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/IsSubTypeImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface IsSubTypeImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/ListRolesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/ListRolesImpl.java
index aab9041ae0f4e02d4b601e97d042dff591fbbf85..b5f63d0b55c1bcb5737ec1fe628b954324c0cff2 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/ListRolesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/ListRolesImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,10 +19,10 @@
*
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.accessControl.Role;
+import org.linkahead.server.accessControl.Role;
public interface ListRolesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/ListUsersImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/ListUsersImpl.java
index 6bdfda92f2b5a78b8b2dfc8b6f20aac3b68c08a9..a72d5721f33ef57d52feb23db327938543d02d29 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/ListUsersImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/ListUsersImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,10 +19,10 @@
*
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.database.proto.ProtoUser;
public interface ListUsersImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/LogUserVisitImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/LogUserVisitImpl.java
index 38c253e2e76075c83a7874d581f8b97d25a382f5..253a6e83cf6ea2514e5eb9df525f2ba8e7f5f300 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/LogUserVisitImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/LogUserVisitImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,7 +17,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
public interface LogUserVisitImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllImpl.java
index 8e5a55943176a557867925200230559609cf76c2..869b6089e67adf56a6993563aa7493a668ff9acc 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface RetrieveAllImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllUncheckedFilesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllUncheckedFilesImpl.java
index dc247bf6b2975f96185245813647662e8e9217f3..e9a4d3a27c1f53b8443305303bb9940ab87751a5 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllUncheckedFilesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllUncheckedFilesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.Iterator;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
/**
* Retrieve an iterator which iterates over all File entities which need to be consistency-checked.
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
index 0886ff4374e846acfd14e37b8d2414be912d6e3d..c3d94ce99cf206223fc4b7174ff66b02d7fc43c4 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
public interface RetrieveDatatypesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java
index 230d4d34103603d5499532a7dc1a941cf82068e7..3717f5a89a8ce87a5b8a0723053af6921c81bc70 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,9 +19,9 @@
*
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.proto.VerySparseEntity;
+import org.linkahead.server.database.proto.VerySparseEntity;
public interface RetrieveEntityACLImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveLogRecordImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveLogRecordImpl.java
index b6646d269123d70a3b6d06a381c7a83792e1b659..e1d0996306a663bc2d17b20a2b2531cfef13c980 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveLogRecordImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveLogRecordImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface RetrieveLogRecordImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
index 9f7eba821e8038befa47f35b31e017aa042bb28f..6007efb36c61796f51e4e827dd53e13bb808072c 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.LinkedList;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.entity.EntityID;
public interface RetrieveParentsImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePasswordValidatorImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePasswordValidatorImpl.java
index 3b3c285181416b484e3d0636828f6ef422f921c3..5c0054af7722d836e6a1f1ca99fb2f3e0ba4519e 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePasswordValidatorImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePasswordValidatorImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface RetrievePasswordValidatorImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePermissionRulesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePermissionRulesImpl.java
index cdbb5eb994cba45762c64244b9a4c1a4b2f40c33..40f44c688657cde4cc1a74b5e9b3d7717e8dd373 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePermissionRulesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePermissionRulesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.HashSet;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public interface RetrievePermissionRulesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
index 6bf2051ab1ada80bd09ca074b4b50b6af3abf574..f65ff2d9e218f80ecab149d37a2f861434fa2119 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.LinkedList;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoProperty;
+import org.linkahead.server.entity.EntityID;
public interface RetrievePropertiesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java
index 485b62899ecd1cd2c025b5928ed179a61e409fea..6f6be810a58ed9165effeea7816282e770302c39 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.entity.EntityID;
public interface RetrieveQueryTemplateDefinitionImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveRoleImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveRoleImpl.java
index 92fde36b07d205b59cbf5000da403d936f03fe35..3ba60e18b305014ca23a3e4f136ebd39909b3109 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveRoleImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveRoleImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface RetrieveRoleImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java
index 8b5c516b0d486a9bc6f7745c15eb999dffbe6182..e1c26acf325bd69dc3a444ef2b4a660ec05176c4 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
public interface RetrieveSparseEntityImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveUserImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveUserImpl.java
index 2ff8286331add6143d76d18562935d795ba85cff..3dfa0cc5d4c659fa6a4941722cc2e20d99005da5 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveUserImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveUserImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public interface RetrieveUserImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveVersionHistoryImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveVersionHistoryImpl.java
index 1dbcbfb07e53cae2cd3289a87f5fedd7997cb1a9..aaff748d1ea37ecd36626000e3ec6b62224f9179 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveVersionHistoryImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveVersionHistoryImpl.java
@@ -1,8 +1,8 @@
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.HashMap;
-import org.caosdb.server.database.proto.VersionHistoryItem;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.proto.VersionHistoryItem;
+import org.linkahead.server.entity.EntityID;
public interface RetrieveVersionHistoryImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileCheckedTimestampImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileCheckedTimestampImpl.java
index 8e6a6f2b039400c7fd74c0dbbdc6d91d61bf0210..989d2dfffeb9fd0915f9ccd134f2f3f4f2ad5517 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileCheckedTimestampImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileCheckedTimestampImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface SetFileCheckedTimestampImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java
index 26cb7ce19ce6d946c34c784a9849c29d4f8f4888..5d1a317b6858a1d379730f6251d87e6ebf23bf7b 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java
@@ -1,6 +1,6 @@
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.entity.EntityID;
/**
* Store the checksum and timestamp of the checksum for a File entity.
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SetPasswordImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SetPasswordImpl.java
index e60f578879ae1dde60c257e7b7dadd523319daa1..8ef9407f01e2a47da35940c2bbacaab1b1236eb6 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SetPasswordImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SetPasswordImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface SetPasswordImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SetPermissionRulesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SetPermissionRulesImpl.java
index 89ab9bd13acfc67e8d500b3645ffc1770b183c55..cf756c2eb3bc4a5b8dc74a16d30ee38755a49bfb 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SetPermissionRulesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SetPermissionRulesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.Set;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public interface SetPermissionRulesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SetQueryTemplateDefinitionImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SetQueryTemplateDefinitionImpl.java
index 53a0032fcab3b57d0f83a4843347a903c9078450..9b18dadbd20665802361e2101cc3e4fdf7f6bf40 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SetQueryTemplateDefinitionImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SetQueryTemplateDefinitionImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.entity.EntityID;
public interface SetQueryTemplateDefinitionImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SyncStatsImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SyncStatsImpl.java
index d5a15f0e88cdc4be6e3b726a559f766e053bda2e..0192f3a76c710b9f16b8701b0c96246f37f46d7a 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SyncStatsImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SyncStatsImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.ServerStat;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.ServerStat;
public interface SyncStatsImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateSparseEntityImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateSparseEntityImpl.java
index e7cb2612d1f90c826004fc168b355c1537574e00..9310d97e271ff3a419e1535cc0476071a58d6505 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateSparseEntityImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateSparseEntityImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.utils.Undoable;
public interface UpdateSparseEntityImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserImpl.java
index eb26002c1163295d9dd00c32bd8d092ad26b2b55..2f36361c87beb5269673987ddcb7b5a675f36d13 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public interface UpdateUserImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserRolesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserRolesImpl.java
index 891df301e992f42c38f7c52d867353a65cddd1b2..9e04d176ba7fcfd66b4730c545022d554a1befc0 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserRolesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserRolesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.Set;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface UpdateUserRolesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
index 4072c1b2877cd9231424a98948fad32747870537..628c4c629740604ea3bd18240e8b4dde04d0670a 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
-
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+package org.linkahead.server.database.backend.transaction;
+
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class DeleteEntityProperties extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityTransaction.java
index f8ebcd2af6ff73dd11f1b845d7e5aef58ff925f3..122c14a5c0d62b59282e0e40c10343ee6e90a42b 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.TransactionContainer;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.TransactionContainer;
public class DeleteEntityTransaction extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteFile.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteFile.java
index 254e4e70d27518d676ada2d73d28a750148c8871..5226c498dc6db6a67279ff2093c00d715038ee7f 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteFile.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteFile.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.io.IOException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
public class DeleteFile extends BackendTransaction {
@@ -43,7 +43,7 @@ public class DeleteFile extends BackendTransaction {
getUndoHandler().append(this.entity.getFileProperties().deleteFile());
} catch (final IOException e) {
throw new TransactionException(e);
- } catch (final CaosDBException e) {
+ } catch (final LinkAheadException e) {
throw new TransactionException(e);
} catch (final InterruptedException e) {
throw new TransactionException(e);
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeletePassword.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeletePassword.java
index 402726a945d606091cd83505c69631f28d3ec455..ba6f32920598bd5e7699e27268ae2b2b31ae970a 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeletePassword.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeletePassword.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.DeletePasswordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.DeletePasswordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class DeletePassword extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteRole.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteRole.java
index eab8f6f3d5a8bf8153d1855de653f840a41bb302..117e852ab76ea918a6737b1e1e640c69e3b13f8b 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteRole.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.DeleteRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.DeleteRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class DeleteRole extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
index e371cfe1f9caf3d4438e8801d4a6cee1119322f8..697fcc0e2e7a20321fea1b49b356c52b7fa548cb 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,14 +22,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.DeleteSparseEntityImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.DeleteSparseEntityImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class DeleteSparseEntity extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteUser.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteUser.java
index 13ea87446a8d8e786629ec6d7d9ffd032c0f58d0..4c64c2d3fa262ae84f68351b0c03ea9e35826be4 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.DeleteUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.DeleteUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class DeleteUser extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/FileConsistencyCheck.java b/src/main/java/org/caosdb/server/database/backend/transaction/FileConsistencyCheck.java
index 5cece246538219266537613aec31da24962e1910..1b3436d80b44ce2ea7135aed5f61503c2075f9cb 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/FileConsistencyCheck.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/FileConsistencyCheck.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.FileCheckHash;
-import org.caosdb.server.database.backend.interfaces.FileCheckSize;
-import org.caosdb.server.database.backend.interfaces.FileExists;
-import org.caosdb.server.database.backend.interfaces.FileWasModifiedAfter;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.Hasher;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.FileCheckHash;
+import org.linkahead.server.database.backend.interfaces.FileCheckSize;
+import org.linkahead.server.database.backend.interfaces.FileExists;
+import org.linkahead.server.database.backend.interfaces.FileWasModifiedAfter;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.Hasher;
public class FileConsistencyCheck extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetAllNames.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetAllNames.java
index 5db82a5e3b71a2fbb6280277bc57f7ace951043f..603dd344a19626ff5d59dc82605ca17aa8de3543 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetAllNames.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetAllNames.java
@@ -1,12 +1,12 @@
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetAllNamesImpl;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetAllNamesImpl;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
public class GetAllNames extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetChildren.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetChildren.java
index d0e2a809547ad2be4621ccab3f79d793dde70006..26d9885baea50309d445f7b7ffb44da42d13fe26 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetChildren.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetChildren.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetChildrenImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetChildrenImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class GetChildren extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetDependentEntities.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetDependentEntities.java
index 421fcaaed7c07e3bbbf0abb745e086260aad41d7..f5608e9f44f4ca7fd7bcdf2bb8f82f75dd23b6f2 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetDependentEntities.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetDependentEntities.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetDependentEntitiesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetDependentEntitiesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class GetDependentEntities extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetFileIterator.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetFileIterator.java
index c5db6bef59ddf18c95218f442556b6ee6b27ad8a..9a391891e5a24bbfd38fa5b8db21b4f0e2c4093e 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetFileIterator.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetFileIterator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.Iterator;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetFileIteratorImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetFileIteratorImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class GetFileIterator extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetFileRecordByPath.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetFileRecordByPath.java
index 8ce0e0e2e2e5c84116fe1eb8df1c3bdf322de022..1564b35d865a4db15e677cb808658920b7b6bf79 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetFileRecordByPath.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetFileRecordByPath.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,16 +22,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetFileRecordByPathImpl;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetFileRecordByPathImpl;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
public class GetFileRecordByPath extends CacheableBackendTransaction<String, SparseEntity> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetIDByName.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetIDByName.java
index 7855af4af3a7145bd5066875ffddc46585e599fd..057b16e15b958bb836f0d4064329849ec0f6ee89 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetIDByName.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetIDByName.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetIDByNameImpl;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetIDByNameImpl;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class GetIDByName extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetInfo.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetInfo.java
index a1662ec03f8f5dc2fe424ba10f26e9ba4803b72c..337504d33cf1539866074aaac8340117626b5280 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetInfo.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetInfo.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetInfoImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoInfo;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetInfoImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoInfo;
public class GetInfo extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetUpdateableChecksums.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetUpdateableChecksums.java
index a9a8d280586c7f749a73940c14b178fd3c10ce64..7018628e60319fb81b488822e38157e724908499 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetUpdateableChecksums.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetUpdateableChecksums.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class GetUpdateableChecksums extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
index 382dde551c3e8ec53e51d0668bdd45f3b7e12184..466414555e27c7fbb994271f5274e5fd941c2d51 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
@@ -1,12 +1,12 @@
-package org.caosdb.server.database.backend.transaction;
-
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertEntityDatatypeImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.utils.ServerMessages;
+package org.linkahead.server.database.backend.transaction;
+
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertEntityDatatypeImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.utils.ServerMessages;
public class InsertEntityDatatype extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java
index 8de8afc084ae16dea370a519a4fde3524fa8c7c9..c0cbcc7e875101b43936f2628ce25803f529b001 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertEntityPropertiesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertEntityPropertiesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
public class InsertEntityProperties extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java
index 2846fa64d56ea696d4ecb0412a88de449d0483a1..1c16626fd52f9309ba5c6b3a1f39dc2c0680b1ea 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,12 +19,12 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.utils.EntityStatus;
public class InsertEntityTransaction extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertFile.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertFile.java
index f92dc62bb131fcfe6af2cf51c1c6abeaee7c4dda..558458de10ef59b66636d640c3973a628512a01e 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertFile.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertFile.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.io.IOException;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.EntityStatus;
public class InsertFile extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertLinCon.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertLinCon.java
index 68555010031cc8f8bfe48afcf2c4d5e310bed3d8..58844b3063694b0e9ae97a0d61e1f13109dc6679 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertLinCon.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertLinCon.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertLinConImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.LinCon;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertLinConImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.LinCon;
public class InsertLinCon extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertLogRecord.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertLogRecord.java
index 3ce27add49761737c0a8365410c979665a3f16a9..fc54582cf1d36fe867258d7a63a8d48b7a2234e7 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertLogRecord.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertLogRecord.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertLogRecordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertLogRecordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class InsertLogRecord extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertParents.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertParents.java
index d71fec922477d664c8c8eff98800164b3a691513..949981b143da69a8c45d0155d95102e26cf68526 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertParents.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertParentsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertParentsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.utils.EntityStatus;
public class InsertParents extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertRole.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertRole.java
index 4ffa7d68f6ff8b2e328a22978803941b310c58a7..179f34905381729d49a6c17ce3f318e7cea9a262 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertRole.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class InsertRole extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java
index 9c9c1902019077735445295a61dfed70ce98f9fa..4ece81f8363aa00c0148ffd772a6aeb23412c4e7 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
-
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Version;
-import org.caosdb.server.utils.ServerMessages;
+package org.linkahead.server.database.backend.transaction;
+
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertSparseEntityImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Version;
+import org.linkahead.server.utils.ServerMessages;
public class InsertSparseEntity extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertTransactionHistory.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertTransactionHistory.java
index 32f628459b4a8e3a23b9ac3d047e723d7a837c28..866d85c47bd64b9b44e970aad10294306d9ae9cd 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertTransactionHistory.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertTransactionHistory.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,17 +19,17 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertTransactionHistoryImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertTransactionHistoryImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.utils.EntityStatus;
/**
* Record the current transaction in the entities transaction history.
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/IsSubType.java b/src/main/java/org/caosdb/server/database/backend/transaction/IsSubType.java
index 7404572162ec5c85f3f940a723599e7bd200667f..be3fad99e654ce39ebe52c560756d79569909651 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/IsSubType.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/IsSubType.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.IsSubTypeImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.IsSubTypeImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class IsSubType extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/ListRoles.java b/src/main/java/org/caosdb/server/database/backend/transaction/ListRoles.java
index 75792475c4c5a6ae9091f89c8de1b4ef157aa11f..83187edd129b32f4d75c8fddbde6fd0860b6aa9c 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/ListRoles.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/ListRoles.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,12 +19,12 @@
*
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.ListRolesImpl;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.ListRolesImpl;
public class ListRoles extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/ListUsers.java b/src/main/java/org/caosdb/server/database/backend/transaction/ListUsers.java
index 9f29a3c5888104140eb6e2c29b83370fc1c56401..51f46eb0395f6759d236b3fa37737e81eb01bfa7 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/ListUsers.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/ListUsers.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,12 +19,12 @@
*
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.ListUsersImpl;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.ListUsersImpl;
+import org.linkahead.server.database.proto.ProtoUser;
public class ListUsers extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/LogUserVisit.java b/src/main/java/org/caosdb/server/database/backend/transaction/LogUserVisit.java
index 43fd87495c4e7489e7f15ec8674ce01cb674dd90..1a73dfd1f295741f9f95be0f23e730d437b6d4b8 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/LogUserVisit.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/LogUserVisit.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,16 +19,16 @@
*
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.HashSet;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.LogUserVisitImpl;
-import org.caosdb.server.database.backend.interfaces.UpdateUserImpl;
-import org.caosdb.server.database.backend.interfaces.UpdateUserRolesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.LogUserVisitImpl;
+import org.linkahead.server.database.backend.interfaces.UpdateUserImpl;
+import org.linkahead.server.database.backend.interfaces.UpdateUserRolesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class LogUserVisit extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAll.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAll.java
index e7f27afccec15a324a1247dc220cea79b62b7daf..443579730f175ca46e73b9787b5f150dc65fe124 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAll.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAll.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
public class RetrieveAll extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java
index 655e47b8312c3a9772ae3e9055bc73494236a0ec..e261dd417532525c9ddb94f86259deff3d255f75 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.Iterator;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class RetrieveAllUncheckedFiles extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
index 1ca9f60e964f1e18ca49b749dde21f8e8785aaa6..82698207825f8db4200b81a7a173d938836ed34e 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.Container;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveDatatypesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.Container;
public class RetrieveDatatypes extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java
index 8ef143b44e292e5b100ff30ca023e91c0adb190e..3f97dc4165c49d839a66145e61a39bf41442d23c 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,14 +19,14 @@
*
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveEntityACLImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.permissions.EntityACL;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveEntityACLImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.permissions.EntityACL;
public class RetrieveEntityACLTransaction
extends CacheableBackendTransaction<EntityID, VerySparseEntity> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java
index eee73735a07cc2e152e0099bf5d027d1413631b4..4bd29d4ed280ccd4c5762a8c36948e27b01a6d1c 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,25 +22,25 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.container.Container;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.Selection;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.container.Container;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.Selection;
+import org.linkahead.server.utils.EntityStatus;
/**
* Retrieve the full entity from the backend - with all parents, properties, file properties and so
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveLogRecord.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveLogRecord.java
index eae8a96589aab3558a1978890c85bdd18bc161dc..9de77339fa32bf76038eb110a66a1d8e8ea08d3c 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveLogRecord.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveLogRecord.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveLogRecordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveLogRecordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class RetrieveLogRecord extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
index 262ee271acf5b6d3652a0177b0818cbf1e9f74ee..49aa672ac69e8439a7de470b36a3474934512971 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,20 +22,20 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.LinkedList;
import java.util.List;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.wrapper.Parent;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveParentsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.wrapper.Parent;
// TODO Problem with the caching.
// When an old entity version has a parent which is deleted, the name is
@@ -47,7 +47,7 @@ import org.caosdb.server.entity.wrapper.Parent;
// Changes are necessary in the backend-api, i.e. mysqlbackend and the
// interfaces as well.
//
-// See also a failing test in caosdb-pyinttest:
+// See also a failing test in linkahead-pyinttest:
// tests/test_version.py::test_bug_cached_parent_name_in_old_version
public class RetrieveParents
extends CacheableBackendTransaction<String, LinkedList<VerySparseEntity>> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePasswordValidator.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePasswordValidator.java
index d8ea908dbfb0a7f4ae83830b050f976ac383aa6f..396bbdeb1abd3bbefbfd46bfb07b1dcf6aacdec0 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePasswordValidator.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePasswordValidator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class RetrievePasswordValidator extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePermissionRules.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
index 0ec6756194342341b64f9dc131b7b912f112a1dc..4cd626f5f4512b1de780f2b04f2a6c447a3a72e3 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,15 +22,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.HashSet;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public class RetrievePermissionRules
extends CacheableBackendTransaction<String, HashSet<PermissionRule>> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
index f9c11303b31ac81696873876b532f9db95f3dbac..c1b2ae94138b9573a37912e0387547c271e190a6 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,20 +22,20 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.LinkedList;
import java.util.List;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils;
-import org.caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.wrapper.Property;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils;
+import org.linkahead.server.database.backend.interfaces.RetrievePropertiesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoProperty;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.wrapper.Property;
public class RetrieveProperties
extends CacheableBackendTransaction<String, LinkedList<ProtoProperty>> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java
index 90a8ac27d264731b5d714fdc0ada116795fd0ee2..47907de317371b585198397012254feef3f096b7 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
public class RetrieveQueryTemplateDefinition extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveRole.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveRole.java
index f4059832095acc38d3c65b828412c09cc58b3194..c44f1852db0faababdd5a7e862cbe50bf41e6ed0 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveRole.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,15 +22,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.Set;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class RetrieveRole extends CacheableBackendTransaction<String, Role> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
index f1ba8354f98fb0f6716fcfe0a742a597b69dd0a3..a6fbfdf22925d90376960a14b9363886762a62d2 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,18 +22,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveSparseEntityImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.utils.EntityStatus;
public class RetrieveSparseEntity extends CacheableBackendTransaction<String, SparseEntity> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveUser.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveUser.java
index 3ffdee13fe2eac0b2078e44ecfdb1f1101fe137a..8f30b9f12b05d661b05a4d31c9193bf42d4f42fe 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,15 +22,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class RetrieveUser extends CacheableBackendTransaction<Principal, ProtoUser> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java
index a5079c4e033882c4b1068615551b5132e4ee0cba..b1010ee0e31aef1e7270511a6e35bc1aa3d09799 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.HashMap;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VersionHistoryItem;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Version;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VersionHistoryItem;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Version;
public class RetrieveVersionHistory extends VersionTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java
index 8d0e54c95d17d0eb83af541b9fee2fb605b17ec9..aec177ea1f56605d09fec9b47478abc696490137 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.HashMap;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VersionHistoryItem;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Version;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VersionHistoryItem;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Version;
public class RetrieveVersionInfo extends VersionTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SetFileCheckedTimestamp.java b/src/main/java/org/caosdb/server/database/backend/transaction/SetFileCheckedTimestamp.java
index a96c028614baaaabe445e44cd0c4f5088db9ca42..e78193050e28f44ee8342f80956c9e0e82b72c32 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SetFileCheckedTimestamp.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SetFileCheckedTimestamp.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class SetFileCheckedTimestamp extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SetFileChecksum.java b/src/main/java/org/caosdb/server/database/backend/transaction/SetFileChecksum.java
index afca8be4afa72ac755be595ae4345bfe134ca0ca..233b6b940e34c4bd1049a94f6ed0a975047fdcd0 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SetFileChecksum.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SetFileChecksum.java
@@ -1,8 +1,8 @@
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SetFileChecksumImpl;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SetFileChecksumImpl;
+import org.linkahead.server.entity.EntityInterface;
public class SetFileChecksum extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SetPassword.java b/src/main/java/org/caosdb/server/database/backend/transaction/SetPassword.java
index a22815ab9ddb09080c34a519454db53c18aeda92..0929960e5522ed9b4ae0a31667f187f5f0e531aa 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SetPassword.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SetPassword.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SetPasswordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SetPasswordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class SetPassword extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SetPermissionRules.java b/src/main/java/org/caosdb/server/database/backend/transaction/SetPermissionRules.java
index 30986303b11eba2fb63b00d17029b81855277791..fbc6d61ab458f903a43d930ff6c445f70481dd7f 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SetPermissionRules.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SetPermissionRules.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.Set;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SetPermissionRulesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SetPermissionRulesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public class SetPermissionRules extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SetQueryTemplateDefinition.java b/src/main/java/org/caosdb/server/database/backend/transaction/SetQueryTemplateDefinition.java
index b697b04fa2be50c52c7cc565e31a58c3b2a4a3c2..d1ba53da9d134b1003aa0bd1e7bf6cd8656aca5c 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SetQueryTemplateDefinition.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SetQueryTemplateDefinition.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
public class SetQueryTemplateDefinition extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SyncStats.java b/src/main/java/org/caosdb/server/database/backend/transaction/SyncStats.java
index d2650affcc956b82b8aed76b716221a6d43d5dc8..3b3c4dff4adeca401cd770e6e6e8823ab580f101 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SyncStats.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SyncStats.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SyncStatsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.ServerStat;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SyncStatsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.ServerStat;
public class SyncStats extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntityTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntityTransaction.java
index 39d1c76ba89d486388ef085b5cf38a25f0a15d15..28fa575bf6210d87cc42b7e2183adf6ed576ccc2 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntityTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntityTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,13 +19,13 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.utils.EntityStatus;
public class UpdateEntityTransaction extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
index 837f64b32ca4cd6f035b74d13ee116205c7e82bc..c854c2bc3982535f4524d0388b772de2cbf39e4d 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,14 +22,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
-
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.UpdateSparseEntityImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Version;
+package org.linkahead.server.database.backend.transaction;
+
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.UpdateSparseEntityImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Version;
public class UpdateSparseEntity extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUser.java b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUser.java
index 07740f88f3fe7f301ffd24ec85a330c8b0afdce7..9ded2834250b7e18314c24132b49a53997d586a3 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.UpdateUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.UpdateUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class UpdateUser extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUserRoles.java b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUserRoles.java
index bbd23aa95d3eb1bed4f2bafc78fa12d112a02169..c90ca02780568412f134a77e7d540173f8dbe74e 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUserRoles.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUserRoles.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,13 +21,13 @@
*
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.Set;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.UpdateUserRolesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.UpdateUserRolesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class UpdateUserRoles extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java
index 568528f8e779c578c5c45436d71ae016cf7611b8..edfde326ca560b0e01d8938cfeed71a088044a4a 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VersionHistoryItem;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Version;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VersionHistoryItem;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Version;
/**
* Abstract base class which retrieves and caches the full, but flat version history. The
diff --git a/src/main/java/org/caosdb/server/database/exceptions/EntityDoesNotExistException.java b/src/main/java/org/caosdb/server/database/exceptions/EntityDoesNotExistException.java
index f282a355d64b583482512e550c7b4de6e6ed84ec..a373e3ecfb398f1efc5f2061def17c343dc1af5a 100644
--- a/src/main/java/org/caosdb/server/database/exceptions/EntityDoesNotExistException.java
+++ b/src/main/java/org/caosdb/server/database/exceptions/EntityDoesNotExistException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.exceptions;
+package org.linkahead.server.database.exceptions;
public class EntityDoesNotExistException extends TransactionException {
diff --git a/src/main/java/org/caosdb/server/database/exceptions/EntityWasNotUniqueException.java b/src/main/java/org/caosdb/server/database/exceptions/EntityWasNotUniqueException.java
index b792cd45905133ff6a21c744b83781248a818b7f..bb84a9941e6d7fba72aae4211d79c4bb8787e185 100644
--- a/src/main/java/org/caosdb/server/database/exceptions/EntityWasNotUniqueException.java
+++ b/src/main/java/org/caosdb/server/database/exceptions/EntityWasNotUniqueException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.exceptions;
+package org.linkahead.server.database.exceptions;
public class EntityWasNotUniqueException extends TransactionException {
private static final long serialVersionUID = 5181653214330392866L;
diff --git a/src/main/java/org/caosdb/server/database/exceptions/IntegrityException.java b/src/main/java/org/caosdb/server/database/exceptions/IntegrityException.java
index 440c1e574289285313416ba39f4fbe403d9febfe..2bb55f8e6ebfb230229fd30cef542e02209c7b56 100644
--- a/src/main/java/org/caosdb/server/database/exceptions/IntegrityException.java
+++ b/src/main/java/org/caosdb/server/database/exceptions/IntegrityException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.exceptions;
+package org.linkahead.server.database.exceptions;
public class IntegrityException extends TransactionException {
diff --git a/src/main/java/org/caosdb/server/database/exceptions/RolledBackException.java b/src/main/java/org/caosdb/server/database/exceptions/RolledBackException.java
index c99fcbbdd9b1043bf3477b552365943e0aae1a5c..45fb8871a452369b461949e75a08815bc30f53db 100644
--- a/src/main/java/org/caosdb/server/database/exceptions/RolledBackException.java
+++ b/src/main/java/org/caosdb/server/database/exceptions/RolledBackException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.exceptions;
+package org.linkahead.server.database.exceptions;
public class RolledBackException extends TransactionException {
diff --git a/src/main/java/org/caosdb/server/database/exceptions/TransactionException.java b/src/main/java/org/caosdb/server/database/exceptions/TransactionException.java
index 6564ed49914d2080b15bf08f74c8361cfaa34db7..7ef4c561222b561f2e424348a0448a8660077881 100644
--- a/src/main/java/org/caosdb/server/database/exceptions/TransactionException.java
+++ b/src/main/java/org/caosdb/server/database/exceptions/TransactionException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.exceptions;
+package org.linkahead.server.database.exceptions;
public class TransactionException extends RuntimeException {
diff --git a/src/main/java/org/caosdb/server/database/misc/DBHelper.java b/src/main/java/org/caosdb/server/database/misc/DBHelper.java
index 27bd1d089543d905416a471b6103f9b3be6e3c5b..31304d7e980df39be171607d0e966eca8b7eb0fb 100644
--- a/src/main/java/org/caosdb/server/database/misc/DBHelper.java
+++ b/src/main/java/org/caosdb/server/database/misc/DBHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.misc;
+package org.linkahead.server.database.misc;
-import org.caosdb.server.transaction.TransactionInterface;
+import org.linkahead.server.transaction.TransactionInterface;
public interface DBHelper {
diff --git a/src/main/java/org/caosdb/server/database/misc/RollBackHandler.java b/src/main/java/org/caosdb/server/database/misc/RollBackHandler.java
index 1591d858aaf9a35ca4851e4627ef6f0b6fc5bb41..164d674cca32cd57d24715b28cb61973fd41ad77 100644
--- a/src/main/java/org/caosdb/server/database/misc/RollBackHandler.java
+++ b/src/main/java/org/caosdb/server/database/misc/RollBackHandler.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.misc;
+package org.linkahead.server.database.misc;
-import org.caosdb.server.transaction.TransactionInterface;
-import org.caosdb.server.utils.UndoHandler;
+import org.linkahead.server.transaction.TransactionInterface;
+import org.linkahead.server.utils.UndoHandler;
public class RollBackHandler extends UndoHandler implements DBHelper {
diff --git a/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java b/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java
index 397a1f52201727d17b057dc92567893798b63cf5..ae3f9c13e94c1f84c4eb4785536464b067d1ac28 100644
--- a/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java
+++ b/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.misc;
+package org.linkahead.server.database.misc;
import java.io.Serializable;
import java.util.ArrayList;
@@ -33,15 +33,15 @@ import java.util.Map;
import java.util.Map.Entry;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.utils.CronJob;
-import org.caosdb.server.utils.Info;
-import org.caosdb.server.utils.ServerStat;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.utils.CronJob;
+import org.linkahead.server.utils.Info;
+import org.linkahead.server.utils.ServerStat;
class Counter implements Serializable {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private int c;
public Counter(int initial) {
@@ -58,7 +58,7 @@ class Counter implements Serializable {
}
class Timer implements Serializable {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private long c;
public Timer(long initial) {
@@ -80,7 +80,7 @@ class Timer implements Serializable {
* Measurement object knows nothing about other Measurement objects.
*/
class Measurement implements Serializable {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private final Timer timer;
private final Counter counter;
private final String name;
@@ -130,7 +130,7 @@ class Measurement implements Serializable {
class RootBenchmark extends TransactionBenchmark implements ServerStat {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private transient boolean synced = false;
/**
* Fetch old data (from before last shutdown) and fill it into this instance.
@@ -208,7 +208,7 @@ class RootBenchmark extends TransactionBenchmark implements ServerStat {
class SubBenchmark extends TransactionBenchmark {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private final String name;
public SubBenchmark(String name) {
@@ -270,12 +270,12 @@ class JdomConverter {
*/
public abstract class TransactionBenchmark implements Serializable {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private static final TransactionBenchmark rootService = new RootBenchmark().init();
public final transient Logger logger = LogManager.getLogger(getClass());
protected static final transient boolean isActive =
Boolean.valueOf(
- CaosDBServer.getServerProperty(ServerProperties.KEY_TRANSACTION_BENCHMARK_ENABLED)
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_TRANSACTION_BENCHMARK_ENABLED)
.toLowerCase());
protected StackTraceElement[] stackTraceElements;
@@ -459,11 +459,11 @@ public abstract class TransactionBenchmark implements Serializable {
/**
* Return a nice String for the StackTraceElement.
*
- * <p>The String is composed like this: CLASS::METHOD [LINE_NUMBER], with "org.caosdb.server."
+ * <p>The String is composed like this: CLASS::METHOD [LINE_NUMBER], with "org.linkahead.server."
* removed from the class name.
*/
private static String prettifyStackTraceElement(final StackTraceElement ste) {
- return ste.getClassName().replaceFirst("caosdb\\.server\\.", "")
+ return ste.getClassName().replaceFirst("linkahead\\.server\\.", "")
+ "::"
+ ste.getMethodName().replaceAll("[<>]", "")
+ " ["
diff --git a/src/main/java/org/caosdb/server/database/proto/FlatProperty.java b/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
index b92d3def38d26f0f5f6cd6a0455d472b8f4f3ccb..3acee6d453c48d2f64552b099a2f1f266fc52475 100644
--- a/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
diff --git a/src/main/java/org/caosdb/server/database/proto/LinCon.java b/src/main/java/org/caosdb/server/database/proto/LinCon.java
index 719e760215cd8ec5b45bc30c5b154dca64e3b740..041fc420f96fa31c6a9cde28947ad9d13e7a3958 100644
--- a/src/main/java/org/caosdb/server/database/proto/LinCon.java
+++ b/src/main/java/org/caosdb/server/database/proto/LinCon.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
public class LinCon {
public final long signature_from;
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoGroup.java b/src/main/java/org/caosdb/server/database/proto/ProtoGroup.java
index 31d589862cfd353a176880ea33e76327ec32ba6e..e3a2da8e546fb16f37a0e437b4d83a36e8d33fbb 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoGroup.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoGroup.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
import java.util.HashSet;
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoInfo.java b/src/main/java/org/caosdb/server/database/proto/ProtoInfo.java
index e8486e2f0ec7e1d92818bea2793f37dc34405da3..c05211704010d1225061e087a9fbe73f61849c06 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoInfo.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoInfo.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
public class ProtoInfo {
public Integer recordsCount = null;
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java b/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
index 7a11cd4daf6369649a0205a5637d3e86fbafbffe..d0dae166736a992f4aaacac9bd273c7e00854a35 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
import java.util.List;
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoUser.java b/src/main/java/org/caosdb/server/database/proto/ProtoUser.java
index 643f4250216c7829c8218113a8842ff139b313ec..67f7306d1f4e36de32a6a607ee59d22abd217cf9 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoUser.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoUser.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,11 +21,11 @@
*
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
import java.util.HashSet;
-import org.caosdb.server.accessControl.UserStatus;
+import org.linkahead.server.accessControl.UserStatus;
public class ProtoUser implements Serializable {
diff --git a/src/main/java/org/caosdb/server/database/proto/SparseEntity.java b/src/main/java/org/caosdb/server/database/proto/SparseEntity.java
index d2292c58825ac6807e24f3ad3d086b29dd8a6e7e..82e3905a9c1a35ddea76ff706d6a9887ffa56916 100644
--- a/src/main/java/org/caosdb/server/database/proto/SparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/proto/SparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
/**
* Rather abstract representation of a sparse Entity used by the data base abstraction layer.
diff --git a/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java b/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java
index 4c0a60ce57cce03cfaa7a2c4d41af7039c463838..37db0947c81e43324b37d856183d0e93b5c74b81 100644
--- a/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java
+++ b/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
import java.util.List;
diff --git a/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java b/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java
index 8f32bf52038a00275568688b016b830b19fba5f0..e39f52117b09aea6a32229c60fe30a1a1520fd34 100644
--- a/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
diff --git a/src/main/java/org/caosdb/server/datatype/AbstractCollectionDatatype.java b/src/main/java/org/caosdb/server/datatype/AbstractCollectionDatatype.java
index cbd822ee10a24127483fae9adff440404a243771..1546949598d4836b781c181d87a14a39574cf9e4 100644
--- a/src/main/java/org/caosdb/server/datatype/AbstractCollectionDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/AbstractCollectionDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.util.HashMap;
import java.util.regex.Matcher;
diff --git a/src/main/java/org/caosdb/server/datatype/AbstractDatatype.java b/src/main/java/org/caosdb/server/datatype/AbstractDatatype.java
index 583145fb19361adf08ae81bf8c9e338d53ad908f..15c2a1c0787d84f79421f666ebe305f8fd0000df 100644
--- a/src/main/java/org/caosdb/server/datatype/AbstractDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/AbstractDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.util.HashMap;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.container.Container;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.container.Container;
import org.reflections.Reflections;
public abstract class AbstractDatatype {
@@ -87,7 +87,7 @@ public abstract class AbstractDatatype {
}
private static void loadClasses() throws Exception {
- final Reflections datatypePackage = new Reflections("org.caosdb.server.datatype");
+ final Reflections datatypePackage = new Reflections("org.linkahead.server.datatype");
for (final Class<? extends AbstractDatatype> c :
datatypePackage.getSubTypesOf(AbstractDatatype.class)) {
if (c.isAnnotationPresent(DatatypeDefinition.class)) {
diff --git a/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java b/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java
index be88002543155771d2937e216c64d52931051c25..16b3721ea580413b2cc8a65b705a38def8512e5f 100644
--- a/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java
+++ b/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*/
/** @review Daniel Hornung 2022-03-04 */
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import com.google.common.base.Objects;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
public abstract class AbstractEnumValue implements SingleValue {
diff --git a/src/main/java/org/caosdb/server/datatype/BooleanDatatype.java b/src/main/java/org/caosdb/server/datatype/BooleanDatatype.java
index 366b77937d3dcf020d98c035821bed0aedaadf8d..a1fcac3c3b384cd7d99fe36a1cf8625f6dbcd3d4 100644
--- a/src/main/java/org/caosdb/server/datatype/BooleanDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/BooleanDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
@DatatypeDefinition(name = "Boolean")
public class BooleanDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/BooleanValue.java b/src/main/java/org/caosdb/server/datatype/BooleanValue.java
index 2bcbb48bcaf52ec0ef9a83a6d81d51190d1249ef..eb312f5853c8a71032709887bb3ccd3852be800d 100644
--- a/src/main/java/org/caosdb/server/datatype/BooleanValue.java
+++ b/src/main/java/org/caosdb/server/datatype/BooleanValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
public class BooleanValue extends AbstractEnumValue {
- private static CaosEnum caosEnum = new CaosEnum("TRUE", "FALSE");
+ private static LinkAheadEnum linkAheadEnum = new LinkAheadEnum("TRUE", "FALSE");
private BooleanValue(final EnumElement e) {
super(e);
}
public static BooleanValue valueOf(final String s) {
- return new BooleanValue(caosEnum.valueOf(s));
+ return new BooleanValue(linkAheadEnum.valueOf(s));
}
public static BooleanValue valueOf(final boolean b) {
diff --git a/src/main/java/org/caosdb/server/datatype/CaosEnum.java b/src/main/java/org/caosdb/server/datatype/CaosEnum.java
index 00d8cb167a158a40417e7fddcb9fbe1cf21e7cdb..03f4afd98f4a3cc12c8e8700a3b48bf4428d36ad 100644
--- a/src/main/java/org/caosdb/server/datatype/CaosEnum.java
+++ b/src/main/java/org/caosdb/server/datatype/CaosEnum.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import com.google.common.base.Objects;
import java.util.TreeSet;
@@ -59,15 +59,15 @@ class EnumElement implements Comparable<EnumElement> {
}
}
-public class CaosEnum {
+public class LinkAheadEnum {
final boolean case_sensitive; // for string operations
- public CaosEnum(final String... values) {
+ public LinkAheadEnum(final String... values) {
this(false, values);
}
- public CaosEnum(final boolean case_sensitive, final String... values) {
+ public LinkAheadEnum(final boolean case_sensitive, final String... values) {
this.case_sensitive = case_sensitive;
int index = 0;
for (String v : values) {
diff --git a/src/main/java/org/caosdb/server/datatype/CollectionDatatypeFactory.java b/src/main/java/org/caosdb/server/datatype/CollectionDatatypeFactory.java
index 1f80d937a8730891ace6a561d32f0a5bd3ce9a56..21a946ab6c8b9a48fecec34023d0f8b455d2a3c1 100644
--- a/src/main/java/org/caosdb/server/datatype/CollectionDatatypeFactory.java
+++ b/src/main/java/org/caosdb/server/datatype/CollectionDatatypeFactory.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
public interface CollectionDatatypeFactory {
diff --git a/src/main/java/org/caosdb/server/datatype/CollectionValue.java b/src/main/java/org/caosdb/server/datatype/CollectionValue.java
index fc94f660490284e560a34d1c407e2d74c51f6358..f81e0af5e66dddb7277d21889bb2444e895a2be5 100644
--- a/src/main/java/org/caosdb/server/datatype/CollectionValue.java
+++ b/src/main/java/org/caosdb/server/datatype/CollectionValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*/
/** @review Daniel Hornung 2022-03-04 */
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.util.ArrayList;
import java.util.Collections;
diff --git a/src/main/java/org/caosdb/server/datatype/DatatypeDefinition.java b/src/main/java/org/caosdb/server/datatype/DatatypeDefinition.java
index b28ce312d6c5e4252efcdfdd0476d8307b09f021..81d27fa3f5f373d5505ad8186e7bc79263f018bf 100644
--- a/src/main/java/org/caosdb/server/datatype/DatatypeDefinition.java
+++ b/src/main/java/org/caosdb/server/datatype/DatatypeDefinition.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
diff --git a/src/main/java/org/caosdb/server/datatype/DateTimeDatatype.java b/src/main/java/org/caosdb/server/datatype/DateTimeDatatype.java
index 9c66f425ef0b867a3932b5b6fa85e5d88bf8f4a7..2b55ad06966f811f97ff1d9bb10c6eba9d794c33 100644
--- a/src/main/java/org/caosdb/server/datatype/DateTimeDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/DateTimeDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.datetime.Date;
-import org.caosdb.datetime.DateTimeFactory2;
-import org.caosdb.datetime.DateTimeInterface;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.datetime.Date;
+import org.linkahead.datetime.DateTimeFactory2;
+import org.linkahead.datetime.DateTimeInterface;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
@DatatypeDefinition(name = "DateTime")
public class DateTimeDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/DoubleDatatype.java b/src/main/java/org/caosdb/server/datatype/DoubleDatatype.java
index f3f17ace28802cdb045a4cd66a7ca2a78cde2d1c..f20a56f7c59e5b20f17a9bed0ddcb7db4aebb324 100644
--- a/src/main/java/org/caosdb/server/datatype/DoubleDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/DoubleDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,10 +21,10 @@
* ** end header
*/
// Copyright (c) 2019 Daniel Hornung
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
@DatatypeDefinition(name = "Double")
public class DoubleDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/FileDatatype.java b/src/main/java/org/caosdb/server/datatype/FileDatatype.java
index febc317dbd430181784b2312ff6d6162193f4100..30d2c9ae42d19b6555870bd6387e600da7b44047 100644
--- a/src/main/java/org/caosdb/server/datatype/FileDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/FileDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
@DatatypeDefinition(name = "File")
public class FileDatatype extends ReferenceDatatype {}
diff --git a/src/main/java/org/caosdb/server/datatype/GenericValue.java b/src/main/java/org/caosdb/server/datatype/GenericValue.java
index a4b1b0b1508b9debde1f34f1dd58786bdae840c8..c9962c9081ffb217fdd645475be423c039041221 100644
--- a/src/main/java/org/caosdb/server/datatype/GenericValue.java
+++ b/src/main/java/org/caosdb/server/datatype/GenericValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import com.google.common.base.Objects;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
public class GenericValue implements SingleValue {
Object value;
diff --git a/src/main/java/org/caosdb/server/datatype/IndexedSingleValue.java b/src/main/java/org/caosdb/server/datatype/IndexedSingleValue.java
index ec9280c3ab0cbdf6e577feec4d40a01f6402dbfe..e69bca17afe94376a5cfd1905c54294640cfc495 100644
--- a/src/main/java/org/caosdb/server/datatype/IndexedSingleValue.java
+++ b/src/main/java/org/caosdb/server/datatype/IndexedSingleValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.util.Objects;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
public class IndexedSingleValue implements SingleValue, Comparable<IndexedSingleValue> {
diff --git a/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java b/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java
index f3a58a4a52b888e00ec80f71793cd452c4b98910..90bc4c7c945a640516652242cce5faf6edae458e 100644
--- a/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
@DatatypeDefinition(name = "Integer")
public class IntegerDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/ListDatatype.java b/src/main/java/org/caosdb/server/datatype/ListDatatype.java
index bdf148e66638757ba5ccc315a7eac557774d8f63..8ee15b8fa1418e9639d7b78410ca9e09f2c45139 100644
--- a/src/main/java/org/caosdb/server/datatype/ListDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/ListDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.entity.Message;
public class ListDatatype extends AbstractCollectionDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/ListDatatypeFactory.java b/src/main/java/org/caosdb/server/datatype/ListDatatypeFactory.java
index d1999f13c794a496657139dfeef78b0584784082..15dc3218b16e5d6cadcda964d09006ed5004421b 100644
--- a/src/main/java/org/caosdb/server/datatype/ListDatatypeFactory.java
+++ b/src/main/java/org/caosdb/server/datatype/ListDatatypeFactory.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
public class ListDatatypeFactory implements CollectionDatatypeFactory {
diff --git a/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java b/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java
index 769d3ebdd109e22dcbc41f2ae7bd478b709f0482..1ab0ab00b6de77fdcf149f79325bf17f04e334c5 100644
--- a/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.entity.Message;
@DatatypeDefinition(name = "Reference")
public class ReferenceDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/ReferenceDatatype2.java b/src/main/java/org/caosdb/server/datatype/ReferenceDatatype2.java
index 503e4679335381da6c08b746af8ed14665bd409b..1711ccb09154e9785347abb357f2c9ea1f9f1282 100644
--- a/src/main/java/org/caosdb/server/datatype/ReferenceDatatype2.java
+++ b/src/main/java/org/caosdb/server/datatype/ReferenceDatatype2.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
public class ReferenceDatatype2 extends ReferenceDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/ReferenceValue.java b/src/main/java/org/caosdb/server/datatype/ReferenceValue.java
index a24e2ddfda7faf333fd7d7f64420d4a6c7fdc290..3655af9cf0df0f4c0f6991e0edeea3b88e98b296 100644
--- a/src/main/java/org/caosdb/server/datatype/ReferenceValue.java
+++ b/src/main/java/org/caosdb/server/datatype/ReferenceValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -25,15 +25,15 @@
*/
/** @review Daniel Hornung 2022-03-04 */
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.util.Objects;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
/**
* A ReferenceValue represents the value of a reference property to another entity.
diff --git a/src/main/java/org/caosdb/server/datatype/SingleValue.java b/src/main/java/org/caosdb/server/datatype/SingleValue.java
index cfe2b6404119265c9cccc74349553557467cff56..7d96d6fc5c8ace17fb741e1a5b25272e7c1f1779 100644
--- a/src/main/java/org/caosdb/server/datatype/SingleValue.java
+++ b/src/main/java/org/caosdb/server/datatype/SingleValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
public interface SingleValue extends Value {
diff --git a/src/main/java/org/caosdb/server/datatype/TextDatatype.java b/src/main/java/org/caosdb/server/datatype/TextDatatype.java
index 3b32fadcb3467528ac377e67db1081295f85c7ec..49b226e41a176fd554e0eb7b82f1556900b8afc6 100644
--- a/src/main/java/org/caosdb/server/datatype/TextDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/TextDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
@DatatypeDefinition(name = "Text")
public class TextDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/Value.java b/src/main/java/org/caosdb/server/datatype/Value.java
index a2612fb37dae11953b6083f3be8132b2dd61f77f..d7e7c64a4f3cb6df1be84207efd7f6bfa8f41b8d 100644
--- a/src/main/java/org/caosdb/server/datatype/Value.java
+++ b/src/main/java/org/caosdb/server/datatype/Value.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/entity/Affiliation.java b/src/main/java/org/caosdb/server/entity/Affiliation.java
index f3e5ec73561760b889657ba20134d16aabf3e35a..4bd145bbbc5729394b6eccc51bdc8cadd645235a 100644
--- a/src/main/java/org/caosdb/server/entity/Affiliation.java
+++ b/src/main/java/org/caosdb/server/entity/Affiliation.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
public enum Affiliation {
INSTANTIATION, // RECORD is-a RECORD TYPE
diff --git a/src/main/java/org/caosdb/server/entity/ClientMessage.java b/src/main/java/org/caosdb/server/entity/ClientMessage.java
index f6b996770b1d1d88992a56551acc0d5aaa5db1f0..41780d519a81ec12387e45a558dea5362cce9e2b 100644
--- a/src/main/java/org/caosdb/server/entity/ClientMessage.java
+++ b/src/main/java/org/caosdb/server/entity/ClientMessage.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -21,7 +21,7 @@
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.HashMap;
import java.util.Map;
diff --git a/src/main/java/org/caosdb/server/entity/DeleteEntity.java b/src/main/java/org/caosdb/server/entity/DeleteEntity.java
index 38e8385ac88146809254ba0e0b39c8b4be55db85..05e5eba300c0e73fc912438428e0495b759fc9f5 100644
--- a/src/main/java/org/caosdb/server/entity/DeleteEntity.java
+++ b/src/main/java/org/caosdb/server/entity/DeleteEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
public class DeleteEntity extends Entity {
diff --git a/src/main/java/org/caosdb/server/entity/Entity.java b/src/main/java/org/caosdb/server/entity/Entity.java
index 614397c50526606176fc50b06e2f07e76cbfb9ff..dee98676ff704ebde37f045070e9d2d7848f1c52 100644
--- a/src/main/java/org/caosdb/server/entity/Entity.java
+++ b/src/main/java/org/caosdb/server/entity/Entity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.ArrayList;
import java.util.HashMap;
@@ -34,33 +34,33 @@ import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceDatatype;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.container.ParentContainer;
-import org.caosdb.server.entity.container.PropertyContainer;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.EntityToElementStrategy;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.query.Query.Selection;
-import org.caosdb.server.utils.AbstractObservable;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.TransactionLogMessage;
-import org.caosdb.unit.Unit;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceDatatype;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.container.ParentContainer;
+import org.linkahead.server.entity.container.PropertyContainer;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.EntityToElementStrategy;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.query.Query.Selection;
+import org.linkahead.server.utils.AbstractObservable;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.TransactionLogMessage;
+import org.linkahead.unit.Unit;
public abstract class Entity extends AbstractObservable implements EntityInterface {
@@ -290,7 +290,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
return;
}
if (this.entityStatus == EntityStatus.UNQUALIFIED) {
- throw new CaosDBException(
+ throw new LinkAheadException(
"It is not allowed to change the state again, once an UNQUALIFIED state has been reached.");
}
this.entityStatus = entityStatus;
@@ -488,7 +488,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
* cuid setter.
*
* @param cuid
- * @throws CaosDBException if one tried to set it once again.
+ * @throws LinkAheadException if one tried to set it once again.
*/
@Override
public final void setCuid(final String cuid) {
diff --git a/src/main/java/org/caosdb/server/entity/EntityID.java b/src/main/java/org/caosdb/server/entity/EntityID.java
index 6a2d2ca368088e54c2f3c77ae669c6feda07bb4e..2c3aa1868b4570805c43e8dd2924001d1502f7a2 100644
--- a/src/main/java/org/caosdb/server/entity/EntityID.java
+++ b/src/main/java/org/caosdb/server/entity/EntityID.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.io.Serializable;
import java.util.Objects;
diff --git a/src/main/java/org/caosdb/server/entity/EntityInterface.java b/src/main/java/org/caosdb/server/entity/EntityInterface.java
index ba77b5c4ac8b5c833d2046dec506655531ff62cb..85d24734e51900203cea7fafe5a0ff4e6aee0708 100644
--- a/src/main/java/org/caosdb/server/entity/EntityInterface.java
+++ b/src/main/java/org/caosdb/server/entity/EntityInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,27 +20,27 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.List;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.container.ParentContainer;
-import org.caosdb.server.entity.container.PropertyContainer;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.jobs.JobTarget;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.TransactionLogMessage;
-import org.caosdb.unit.Unit;
import org.jdom2.Element;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.container.ParentContainer;
+import org.linkahead.server.entity.container.PropertyContainer;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.jobs.JobTarget;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.TransactionLogMessage;
+import org.linkahead.unit.Unit;
public interface EntityInterface
extends JobTarget, Observable, ToElementable, WriteEntity, TransactionEntity {
diff --git a/src/main/java/org/caosdb/server/entity/FileProperties.java b/src/main/java/org/caosdb/server/entity/FileProperties.java
index eaf4246f6c16a0f7cb38964e0ffb12757a4f0373..b985e6ec8f2e1d4de4a126d1e13c0f6bcdd44f94 100644
--- a/src/main/java/org/caosdb/server/entity/FileProperties.java
+++ b/src/main/java/org/caosdb/server/entity/FileProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.io.File;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.UndoHandler;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.UndoHandler;
+import org.linkahead.server.utils.Undoable;
public class FileProperties {
private File thumbnail = null;
@@ -176,7 +176,8 @@ public class FileProperties {
return ret;
}
- public Undoable deleteFile() throws Message, IOException, InterruptedException, CaosDBException {
+ public Undoable deleteFile()
+ throws Message, IOException, InterruptedException, LinkAheadException {
final File file = new File(FileSystem.getPath(this.path));
final File thumbnail = new File(getThumbnailPath(file));
@@ -210,7 +211,7 @@ public class FileProperties {
} else if (file.getCanonicalPath().startsWith(FileSystem.getBasepath())) {
d = FileUtils.delete(file, file.isDirectory());
} else {
- throw new CaosDBException(
+ throw new LinkAheadException(
"File is in Filesystem, but it is neither a normal file nor a symlink.");
}
if (parent != null && parent.listFiles() != null && parent.listFiles().length == 0) {
@@ -226,14 +227,14 @@ public class FileProperties {
}
public File retrieveFromFileSystem()
- throws IOException, CaosDBException, NoSuchAlgorithmException {
+ throws IOException, LinkAheadException, NoSuchAlgorithmException {
if (this.file != null) {
return this.file;
}
if (hasPath()) {
final File f = FileSystem.getFromFileSystem(getPath());
if (f == null) {
- throw new CaosDBException(
+ throw new LinkAheadException(
"File not in file system. File system is not consistent with the data base!!! "
+ getPath());
}
diff --git a/src/main/java/org/caosdb/server/entity/InsertEntity.java b/src/main/java/org/caosdb/server/entity/InsertEntity.java
index b88b319fc956d9d0ee4f34d99d9abef94819ea86..57cd43eb6a15adb850f0da56cb742b5d4566d22b 100644
--- a/src/main/java/org/caosdb/server/entity/InsertEntity.java
+++ b/src/main/java/org/caosdb/server/entity/InsertEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/entity/MagicTypes.java b/src/main/java/org/caosdb/server/entity/MagicTypes.java
index 39556385235e6b72736bed8dff67a178cfe60aff..fcc4d251ed4aa71ccc2bb51810a464422f2ca655 100644
--- a/src/main/java/org/caosdb/server/entity/MagicTypes.java
+++ b/src/main/java/org/caosdb/server/entity/MagicTypes.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.HashMap;
import java.util.Objects;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.transaction.Retrieve;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.transaction.Retrieve;
/** Some types correspond to entities in the database with magic IDs. */
public enum MagicTypes {
diff --git a/src/main/java/org/caosdb/server/entity/Message.java b/src/main/java/org/caosdb/server/entity/Message.java
index fca6024561ede97c1b5520bc6a07f08f30f7a76a..e85d874bf4e146a00fb89ee8b17f5c98cc9a7718 100644
--- a/src/main/java/org/caosdb/server/entity/Message.java
+++ b/src/main/java/org/caosdb/server/entity/Message.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.HashMap;
import java.util.Map;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.utils.ServerMessages;
public class Message extends Exception implements Comparable<Message>, ToElementable {
diff --git a/src/main/java/org/caosdb/server/entity/NoSuchRoleException.java b/src/main/java/org/caosdb/server/entity/NoSuchRoleException.java
index 31d79a6de6e9932b680b89b133363134cbdef4ef..ad2738b0f55692aa273700eb7d4ad713a45eefa8 100644
--- a/src/main/java/org/caosdb/server/entity/NoSuchRoleException.java
+++ b/src/main/java/org/caosdb/server/entity/NoSuchRoleException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
public class NoSuchRoleException extends IllegalArgumentException {
diff --git a/src/main/java/org/caosdb/server/entity/RetrieveEntity.java b/src/main/java/org/caosdb/server/entity/RetrieveEntity.java
index 2d1ca6f2175ca2377b7f1a73f847a48377cc4694..a61b87bacb0118d810741684403c073b534d7090 100644
--- a/src/main/java/org/caosdb/server/entity/RetrieveEntity.java
+++ b/src/main/java/org/caosdb/server/entity/RetrieveEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
public class RetrieveEntity extends Entity {
diff --git a/src/main/java/org/caosdb/server/entity/Role.java b/src/main/java/org/caosdb/server/entity/Role.java
index f86158a99be307867c17f136a26e1097e6e7bc5f..1e2cc28ab95faf11105ceff9707f2bece9a3ff92 100644
--- a/src/main/java/org/caosdb/server/entity/Role.java
+++ b/src/main/java/org/caosdb/server/entity/Role.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.HashMap;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.GetIDByName;
-import org.caosdb.server.entity.xml.EntityToElementStrategy;
-import org.caosdb.server.entity.xml.FileToElementStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.GetIDByName;
+import org.linkahead.server.entity.xml.EntityToElementStrategy;
+import org.linkahead.server.entity.xml.FileToElementStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
public enum Role {
RecordType,
diff --git a/src/main/java/org/caosdb/server/entity/StatementStatus.java b/src/main/java/org/caosdb/server/entity/StatementStatus.java
index 83d0c57e4ece787e53efa2e149ff0910e1850ed5..92840787fe140524bd2a05f01a7f019b3452fe2b 100644
--- a/src/main/java/org/caosdb/server/entity/StatementStatus.java
+++ b/src/main/java/org/caosdb/server/entity/StatementStatus.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
/**
* The statement status has two purposes:
diff --git a/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java b/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
index d1596afda95a4836dcd84fc79b67cf2e0b4f12a4..102802fc27217b581fcfb0304acb2ac82457b039 100644
--- a/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
+++ b/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,12 +17,12 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
/**
* Interface for the StatementStatus. This may be used by back-end implementations to use back-end
* specific implementations (e.g.
- * org.caosdb.server.database.backend.implementation.MySQL.ReplacementStatus).
+ * org.linkahead.server.database.backend.implementation.MySQL.ReplacementStatus).
*/
public interface StatementStatusInterface {
public String name();
diff --git a/src/main/java/org/caosdb/server/entity/TransactionEntity.java b/src/main/java/org/caosdb/server/entity/TransactionEntity.java
index 976106223800802cd3e885baaad5d0113d9726da..8e450f19d8357115cfb221721e88bcd95d82895e 100644
--- a/src/main/java/org/caosdb/server/entity/TransactionEntity.java
+++ b/src/main/java/org/caosdb/server/entity/TransactionEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.query.Query.Selection;
-import org.caosdb.server.utils.EntityStatus;
import org.jdom2.Element;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.query.Query.Selection;
+import org.linkahead.server.utils.EntityStatus;
public interface TransactionEntity {
diff --git a/src/main/java/org/caosdb/server/entity/UpdateEntity.java b/src/main/java/org/caosdb/server/entity/UpdateEntity.java
index 45df0abac4d742cb024deb7f2327820cb71ebe8a..17fe68c0ae56605ad093b37ed45441d31aa00c43 100644
--- a/src/main/java/org/caosdb/server/entity/UpdateEntity.java
+++ b/src/main/java/org/caosdb/server/entity/UpdateEntity.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,11 +19,11 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.EntityStatus;
import org.jdom2.Element;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.EntityStatus;
/**
* UpdateEntity class represents entities which are to be updated. The previous version is appeded
diff --git a/src/main/java/org/caosdb/server/entity/Version.java b/src/main/java/org/caosdb/server/entity/Version.java
index 5529c7c5f5e8c83d95ad5afae7c1ae786806df89..e1005828a73e7974fb5d7318d6970c17f768c35a 100644
--- a/src/main/java/org/caosdb/server/entity/Version.java
+++ b/src/main/java/org/caosdb/server/entity/Version.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,10 +18,10 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.List;
-import org.caosdb.datetime.UTCDateTime;
+import org.linkahead.datetime.UTCDateTime;
/**
* Plain old java object (POJO) for an entity's version.
diff --git a/src/main/java/org/caosdb/server/entity/WritableEntity.java b/src/main/java/org/caosdb/server/entity/WritableEntity.java
index 6c967cc4e3404c7940066dc123bf805785a6e4c3..42e5e72ca27f5920be4cd8d610efacc11fe5a9bf 100644
--- a/src/main/java/org/caosdb/server/entity/WritableEntity.java
+++ b/src/main/java/org/caosdb/server/entity/WritableEntity.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/entity/WriteEntity.java b/src/main/java/org/caosdb/server/entity/WriteEntity.java
index 64cbbee8658148e81e09a623c3e235ea18555e5e..6aea615f061e65e7ae822375fbca4a162b5162c3 100644
--- a/src/main/java/org/caosdb/server/entity/WriteEntity.java
+++ b/src/main/java/org/caosdb/server/entity/WriteEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/entity/container/Container.java b/src/main/java/org/caosdb/server/entity/container/Container.java
index 1618fbed6a1594891ea3ddc615f48869227f2c92..0231f149aa2b899d94fdcd89ec8ca43cc6180891 100644
--- a/src/main/java/org/caosdb/server/entity/container/Container.java
+++ b/src/main/java/org/caosdb/server/entity/container/Container.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,11 +22,11 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.ArrayList;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
public class Container<T extends EntityInterface> extends ArrayList<T> {
diff --git a/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java b/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java
index a8c3e6a832848903884edda270e003a0c0dd6feb..c6b84e1ada0d94861019e362708752ffdc5e01a3 100644
--- a/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.HashMap;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.entity.EntityID;
public abstract class EntityByIdContainer extends TransactionContainer {
private static final long serialVersionUID = 7997517210502207523L;
diff --git a/src/main/java/org/caosdb/server/entity/container/ParentContainer.java b/src/main/java/org/caosdb/server/entity/container/ParentContainer.java
index 896a355c5f2df67a542ec17b0710777c543313ef..6a6b36f503d8a9b285755187ba6119ba9db4cb0e 100644
--- a/src/main/java/org/caosdb/server/entity/container/ParentContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/ParentContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,19 +20,19 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.xml.ParentToElementStrategy;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.xml.ParentToElementStrategy;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.ServerMessages;
public class ParentContainer extends Container<Parent> {
diff --git a/src/main/java/org/caosdb/server/entity/container/PropertyContainer.java b/src/main/java/org/caosdb/server/entity/container/PropertyContainer.java
index 2a6593d1e801cdd795756d58cc38e66b8f3b919b..67d779bc9aec3eddfe3d88e2f1b11e017c3cc81f 100644
--- a/src/main/java/org/caosdb/server/entity/container/PropertyContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/PropertyContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,22 +22,22 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.PropertyToElementStrategy;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.PropertyToElementStrategy;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.ServerMessages;
public class PropertyContainer extends Container<Property> {
diff --git a/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java b/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java
index bc0da7c1de2bb876551d29ad7daffb50494f9720..0016820cdbc4d1ddac57d6b50624a5653eada1f9 100644
--- a/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.HashMap;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.RetrieveEntity;
public class RetrieveContainer extends EntityByIdContainer {
diff --git a/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java b/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
index d396345508a028700db6fd8e973390fd634e54d9..be259468799748868fd4e042fecfe6202b352ee4 100644
--- a/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,23 +20,23 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.jobs.JobTarget;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.utils.EntityStatus;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.jobs.JobTarget;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.utils.EntityStatus;
public class TransactionContainer extends Container<EntityInterface>
implements ToElementable, JobTarget {
@@ -106,7 +106,7 @@ public class TransactionContainer extends Container<EntityInterface>
@Override
public void addToElement(final Element element) {
element.setAttribute("count", Integer.toString(size()));
- if (this.benchmark != null && CaosDBServer.isDebugMode()) {
+ if (this.benchmark != null && LinkAheadServer.isDebugMode()) {
element.addContent(this.benchmark.toElement());
}
for (final ToElementable m : this.messages) {
diff --git a/src/main/java/org/caosdb/server/entity/container/WritableContainer.java b/src/main/java/org/caosdb/server/entity/container/WritableContainer.java
index fcc8de4e7a44ddcfff1e85b282c4f70311c80f34..a8c43f990c4f0ca0e053fabfe2ce180d1c1525e3 100644
--- a/src/main/java/org/caosdb/server/entity/container/WritableContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/WritableContainer.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,12 +19,12 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.HashMap;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.server.entity.FileProperties;
public class WritableContainer extends TransactionContainer {
private static final long serialVersionUID = -4097777313518959519L;
diff --git a/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java b/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
index b294a17e5ea68ee02e529735ec39a748bc4f2c83..ec8b5a85cd1a949c2ba89892647f8bad4b569679 100644
--- a/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
+++ b/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,36 +22,36 @@
*
* ** end header
*/
-package org.caosdb.server.entity.wrapper;
+package org.linkahead.server.entity.wrapper;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatusInterface;
-import org.caosdb.server.entity.Version;
-import org.caosdb.server.entity.container.ParentContainer;
-import org.caosdb.server.entity.container.PropertyContainer;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.query.Query.Selection;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.TransactionLogMessage;
-import org.caosdb.unit.Unit;
import org.jdom2.Element;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.StatementStatusInterface;
+import org.linkahead.server.entity.Version;
+import org.linkahead.server.entity.container.ParentContainer;
+import org.linkahead.server.entity.container.PropertyContainer;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.query.Query.Selection;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.TransactionLogMessage;
+import org.linkahead.unit.Unit;
public abstract class EntityWrapper implements EntityInterface {
diff --git a/src/main/java/org/caosdb/server/entity/wrapper/Parent.java b/src/main/java/org/caosdb/server/entity/wrapper/Parent.java
index a2116ac3d0492e8c12487a5e9d6ddafc82b91df8..4cec7739c682a24ba3b45c3a5726319d3efe0524 100644
--- a/src/main/java/org/caosdb/server/entity/wrapper/Parent.java
+++ b/src/main/java/org/caosdb/server/entity/wrapper/Parent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.entity.wrapper;
+package org.linkahead.server.entity.wrapper;
-import org.caosdb.server.entity.Affiliation;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.xml.ParentToElementStrategy;
+import org.linkahead.server.entity.Affiliation;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.xml.ParentToElementStrategy;
public class Parent extends EntityWrapper {
diff --git a/src/main/java/org/caosdb/server/entity/wrapper/Property.java b/src/main/java/org/caosdb/server/entity/wrapper/Property.java
index 9268d7f3cb327a70a4cca872657d72e2779fc344..0755928ab621aff80404e7b3b13015f54ffcd897 100644
--- a/src/main/java/org/caosdb/server/entity/wrapper/Property.java
+++ b/src/main/java/org/caosdb/server/entity/wrapper/Property.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,19 +20,19 @@
*
* ** end header
*/
-package org.caosdb.server.entity.wrapper;
+package org.linkahead.server.entity.wrapper;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.xml.PropertyToElementStrategy;
+import org.linkahead.server.database.proto.ProtoProperty;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.xml.PropertyToElementStrategy;
public class Property extends EntityWrapper {
diff --git a/src/main/java/org/caosdb/server/entity/xml/DomainToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/DomainToElementStrategy.java
index 9480119221aec4fa31c44b812539928327d97ccd..d6a223a742ae48988c1a6d6691a6bb850976fb3b 100644
--- a/src/main/java/org/caosdb/server/entity/xml/DomainToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/DomainToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,10 +22,10 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
-import org.caosdb.server.entity.EntityInterface;
import org.jdom2.Element;
+import org.linkahead.server.entity.EntityInterface;
/**
* Generates a JDOM (XML) representation of an entity with role "Domain".
diff --git a/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java
index 35d94aa79fd62a04f8b0dae1a17829a1106c2d97..a98969a463f77b16e5d8a11b2f69bfbd173e19fd 100644
--- a/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,18 +22,18 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.TransactionLogMessage;
import org.jdom2.Attribute;
import org.jdom2.Element;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.TransactionLogMessage;
/**
* Base class for the generation of a JDOM (XML) representation for entities.
diff --git a/src/main/java/org/caosdb/server/entity/xml/FileToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/FileToElementStrategy.java
index 288159809057d08f57c71dc7cd6decf8adc3be73..fca711d2a19a0325af1a63b0e7ce35d0477014d2 100644
--- a/src/main/java/org/caosdb/server/entity/xml/FileToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/FileToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
-import org.caosdb.server.entity.EntityInterface;
import org.jdom2.Attribute;
import org.jdom2.Element;
+import org.linkahead.server.entity.EntityInterface;
public class FileToElementStrategy extends EntityToElementStrategy {
diff --git a/src/main/java/org/caosdb/server/entity/xml/IdAndServerMessagesOnlyStrategy.java b/src/main/java/org/caosdb/server/entity/xml/IdAndServerMessagesOnlyStrategy.java
index 42f7eef9536ae9525875064e7eb60ec855a3952d..fa2ec298a71cee214508ee1210b2a9d8ccde8ece 100644
--- a/src/main/java/org/caosdb/server/entity/xml/IdAndServerMessagesOnlyStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/IdAndServerMessagesOnlyStrategy.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
/**
* Special purpose subclass of {@link SerializeFieldStrategy} which only serializes the id and the
diff --git a/src/main/java/org/caosdb/server/entity/xml/ParentToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/ParentToElementStrategy.java
index 2556fdb21bbb55252144a4200f75a265a562af74..a61597f46cd14e31321dd0cfcebd359c07b1eeca 100644
--- a/src/main/java/org/caosdb/server/entity/xml/ParentToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/ParentToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,11 +22,11 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.wrapper.Parent;
import org.jdom2.Element;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.wrapper.Parent;
/**
* Generates a JDOM (XML) representation of an entity's parent.
diff --git a/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java
index 7109a0d8d5312dcb7cbdecc587dc28fe0a4146ba..ab5b60b8b7313622cc936bbb3c2349954e1c86a6 100644
--- a/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
-import org.caosdb.server.datatype.SingleValue;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.MagicTypes;
import org.jdom2.Attribute;
import org.jdom2.Element;
+import org.linkahead.server.datatype.SingleValue;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.MagicTypes;
public class PropertyToElementStrategy extends EntityToElementStrategy {
diff --git a/src/main/java/org/caosdb/server/entity/xml/SerializeFieldStrategy.java b/src/main/java/org/caosdb/server/entity/xml/SerializeFieldStrategy.java
index 30210118c0fe8c7b88f0f56532560c49c3782cc0..fcca353d489a07ca7ee0a68dde16d1ffce8ba0ce 100644
--- a/src/main/java/org/caosdb/server/entity/xml/SerializeFieldStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/SerializeFieldStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,14 +22,14 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.Selection;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.Selection;
/**
* A class which decides whether the properties, parents, name, etc. of an entity are to be included
diff --git a/src/main/java/org/caosdb/server/entity/xml/ToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/ToElementStrategy.java
index 01e114a25253865e164ca02d6cf42690c57cca0b..79359cbf976fcc15d024d18b8fe94e77fb187bac 100644
--- a/src/main/java/org/caosdb/server/entity/xml/ToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/ToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
-import org.caosdb.server.entity.EntityInterface;
import org.jdom2.Element;
+import org.linkahead.server.entity.EntityInterface;
public interface ToElementStrategy {
diff --git a/src/main/java/org/caosdb/server/entity/xml/ToElementable.java b/src/main/java/org/caosdb/server/entity/xml/ToElementable.java
index 4202111b89c91e38659f34bd6c4f89af80efd957..82b110b25a6dfd5f503c90c5cc965c02b80be561 100644
--- a/src/main/java/org/caosdb/server/entity/xml/ToElementable.java
+++ b/src/main/java/org/caosdb/server/entity/xml/ToElementable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java b/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java
index 40d19a5f3a0ef6d9448ed8567840e610be712391..8184b6c66eff2d748d94fc5790a61a88ea6d21a1 100644
--- a/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java
+++ b/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,11 +18,11 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
import java.util.TimeZone;
-import org.caosdb.server.entity.Version;
import org.jdom2.Element;
+import org.linkahead.server.entity.Version;
/**
* Creates a JDOM Element for a Version instance.
diff --git a/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java b/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java
index 88429828f27ac843903cfcfc801847c35eedb607..417dc2cd7c2e82eaa4f498362a11928b8a832eb4 100644
--- a/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java
+++ b/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,7 +19,7 @@
*
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.Status;
import io.grpc.StatusException;
@@ -30,56 +30,56 @@ import java.util.List;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.UnauthorizedException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.api.acm.v1alpha1.AccessControlManagementServiceGrpc.AccessControlManagementServiceImplBase;
-import org.caosdb.api.acm.v1alpha1.CreateSingleRoleRequest;
-import org.caosdb.api.acm.v1alpha1.CreateSingleRoleResponse;
-import org.caosdb.api.acm.v1alpha1.CreateSingleUserRequest;
-import org.caosdb.api.acm.v1alpha1.CreateSingleUserResponse;
-import org.caosdb.api.acm.v1alpha1.DeleteSingleRoleRequest;
-import org.caosdb.api.acm.v1alpha1.DeleteSingleRoleResponse;
-import org.caosdb.api.acm.v1alpha1.DeleteSingleUserRequest;
-import org.caosdb.api.acm.v1alpha1.DeleteSingleUserResponse;
-import org.caosdb.api.acm.v1alpha1.EmailSetting;
-import org.caosdb.api.acm.v1alpha1.EntitySetting;
-import org.caosdb.api.acm.v1alpha1.ListKnownPermissionsRequest;
-import org.caosdb.api.acm.v1alpha1.ListKnownPermissionsResponse;
-import org.caosdb.api.acm.v1alpha1.ListRoleItem;
-import org.caosdb.api.acm.v1alpha1.ListRolesRequest;
-import org.caosdb.api.acm.v1alpha1.ListRolesResponse;
-import org.caosdb.api.acm.v1alpha1.ListUsersRequest;
-import org.caosdb.api.acm.v1alpha1.ListUsersResponse;
-import org.caosdb.api.acm.v1alpha1.PermissionDescription;
-import org.caosdb.api.acm.v1alpha1.PermissionRule;
-import org.caosdb.api.acm.v1alpha1.RetrieveSingleRoleRequest;
-import org.caosdb.api.acm.v1alpha1.RetrieveSingleRoleResponse;
-import org.caosdb.api.acm.v1alpha1.RetrieveSingleUserRequest;
-import org.caosdb.api.acm.v1alpha1.RetrieveSingleUserResponse;
-import org.caosdb.api.acm.v1alpha1.RoleCapabilities;
-import org.caosdb.api.acm.v1alpha1.RolePermissions;
-import org.caosdb.api.acm.v1alpha1.UpdateSingleRoleRequest;
-import org.caosdb.api.acm.v1alpha1.UpdateSingleRoleResponse;
-import org.caosdb.api.acm.v1alpha1.UpdateSingleUserRequest;
-import org.caosdb.api.acm.v1alpha1.UpdateSingleUserResponse;
-import org.caosdb.api.acm.v1alpha1.User;
-import org.caosdb.api.acm.v1alpha1.UserCapabilities;
-import org.caosdb.api.acm.v1alpha1.UserPermissions;
-import org.caosdb.api.acm.v1alpha1.UserStatus;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.transaction.DeleteRoleTransaction;
-import org.caosdb.server.transaction.DeleteUserTransaction;
-import org.caosdb.server.transaction.InsertRoleTransaction;
-import org.caosdb.server.transaction.InsertUserTransaction;
-import org.caosdb.server.transaction.ListRolesTransaction;
-import org.caosdb.server.transaction.ListUsersTransaction;
-import org.caosdb.server.transaction.RetrieveRoleTransaction;
-import org.caosdb.server.transaction.RetrieveUserTransaction;
-import org.caosdb.server.transaction.UpdateRoleTransaction;
-import org.caosdb.server.transaction.UpdateUserTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.api.acm.v1alpha1.AccessControlManagementServiceGrpc.AccessControlManagementServiceImplBase;
+import org.linkahead.api.acm.v1alpha1.CreateSingleRoleRequest;
+import org.linkahead.api.acm.v1alpha1.CreateSingleRoleResponse;
+import org.linkahead.api.acm.v1alpha1.CreateSingleUserRequest;
+import org.linkahead.api.acm.v1alpha1.CreateSingleUserResponse;
+import org.linkahead.api.acm.v1alpha1.DeleteSingleRoleRequest;
+import org.linkahead.api.acm.v1alpha1.DeleteSingleRoleResponse;
+import org.linkahead.api.acm.v1alpha1.DeleteSingleUserRequest;
+import org.linkahead.api.acm.v1alpha1.DeleteSingleUserResponse;
+import org.linkahead.api.acm.v1alpha1.EmailSetting;
+import org.linkahead.api.acm.v1alpha1.EntitySetting;
+import org.linkahead.api.acm.v1alpha1.ListKnownPermissionsRequest;
+import org.linkahead.api.acm.v1alpha1.ListKnownPermissionsResponse;
+import org.linkahead.api.acm.v1alpha1.ListRoleItem;
+import org.linkahead.api.acm.v1alpha1.ListRolesRequest;
+import org.linkahead.api.acm.v1alpha1.ListRolesResponse;
+import org.linkahead.api.acm.v1alpha1.ListUsersRequest;
+import org.linkahead.api.acm.v1alpha1.ListUsersResponse;
+import org.linkahead.api.acm.v1alpha1.PermissionDescription;
+import org.linkahead.api.acm.v1alpha1.PermissionRule;
+import org.linkahead.api.acm.v1alpha1.RetrieveSingleRoleRequest;
+import org.linkahead.api.acm.v1alpha1.RetrieveSingleRoleResponse;
+import org.linkahead.api.acm.v1alpha1.RetrieveSingleUserRequest;
+import org.linkahead.api.acm.v1alpha1.RetrieveSingleUserResponse;
+import org.linkahead.api.acm.v1alpha1.RoleCapabilities;
+import org.linkahead.api.acm.v1alpha1.RolePermissions;
+import org.linkahead.api.acm.v1alpha1.UpdateSingleRoleRequest;
+import org.linkahead.api.acm.v1alpha1.UpdateSingleRoleResponse;
+import org.linkahead.api.acm.v1alpha1.UpdateSingleUserRequest;
+import org.linkahead.api.acm.v1alpha1.UpdateSingleUserResponse;
+import org.linkahead.api.acm.v1alpha1.User;
+import org.linkahead.api.acm.v1alpha1.UserCapabilities;
+import org.linkahead.api.acm.v1alpha1.UserPermissions;
+import org.linkahead.api.acm.v1alpha1.UserStatus;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.transaction.DeleteRoleTransaction;
+import org.linkahead.server.transaction.DeleteUserTransaction;
+import org.linkahead.server.transaction.InsertRoleTransaction;
+import org.linkahead.server.transaction.InsertUserTransaction;
+import org.linkahead.server.transaction.ListRolesTransaction;
+import org.linkahead.server.transaction.ListUsersTransaction;
+import org.linkahead.server.transaction.RetrieveRoleTransaction;
+import org.linkahead.server.transaction.RetrieveUserTransaction;
+import org.linkahead.server.transaction.UpdateRoleTransaction;
+import org.linkahead.server.transaction.UpdateUserTransaction;
+import org.linkahead.server.utils.ServerMessages;
public class AccessControlManagementServiceImpl extends AccessControlManagementServiceImplBase {
@@ -98,16 +98,16 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
return result;
}
- private org.caosdb.server.accessControl.UserStatus convert(UserStatus status) {
+ private org.linkahead.server.accessControl.UserStatus convert(UserStatus status) {
switch (status) {
case USER_STATUS_ACTIVE:
- return org.caosdb.server.accessControl.UserStatus.ACTIVE;
+ return org.linkahead.server.accessControl.UserStatus.ACTIVE;
case USER_STATUS_INACTIVE:
- return org.caosdb.server.accessControl.UserStatus.INACTIVE;
+ return org.linkahead.server.accessControl.UserStatus.INACTIVE;
default:
break;
}
- return org.caosdb.server.accessControl.UserStatus.INACTIVE;
+ return org.linkahead.server.accessControl.UserStatus.INACTIVE;
}
private ListUsersResponse convertUsers(List<ProtoUser> users) {
@@ -138,7 +138,7 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
return result;
}
- private UserStatus convert(org.caosdb.server.accessControl.UserStatus status) {
+ private UserStatus convert(org.linkahead.server.accessControl.UserStatus status) {
switch (status) {
case ACTIVE:
return UserStatus.USER_STATUS_ACTIVE;
@@ -149,7 +149,7 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
}
}
- private Role convert(org.caosdb.api.acm.v1alpha1.Role role) {
+ private Role convert(org.linkahead.api.acm.v1alpha1.Role role) {
Role result = new Role();
result.name = role.getName();
@@ -158,18 +158,18 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
return result;
}
- private LinkedList<org.caosdb.server.permissions.PermissionRule> convertPermissionRules(
+ private LinkedList<org.linkahead.server.permissions.PermissionRule> convertPermissionRules(
List<PermissionRule> permissionRulesList) {
- LinkedList<org.caosdb.server.permissions.PermissionRule> result = new LinkedList<>();
+ LinkedList<org.linkahead.server.permissions.PermissionRule> result = new LinkedList<>();
permissionRulesList.forEach((r) -> result.add(convert(r)));
return result;
}
- private org.caosdb.server.permissions.PermissionRule convert(PermissionRule r) {
+ private org.linkahead.server.permissions.PermissionRule convert(PermissionRule r) {
boolean grant = r.getGrant();
boolean priority = r.getPriority();
String permission = r.getPermission();
- return new org.caosdb.server.permissions.PermissionRule(grant, priority, permission);
+ return new org.linkahead.server.permissions.PermissionRule(grant, priority, permission);
}
private ListRolesResponse convert(List<Role> roles) {
@@ -193,15 +193,16 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
.build();
}
- private org.caosdb.api.acm.v1alpha1.Role.Builder convert(Role role) {
- org.caosdb.api.acm.v1alpha1.Role.Builder result = org.caosdb.api.acm.v1alpha1.Role.newBuilder();
+ private org.linkahead.api.acm.v1alpha1.Role.Builder convert(Role role) {
+ org.linkahead.api.acm.v1alpha1.Role.Builder result =
+ org.linkahead.api.acm.v1alpha1.Role.newBuilder();
result.setDescription(role.description);
result.setName(role.name);
if (role.permission_rules != null) result.addAllPermissionRules(convert(role.permission_rules));
return result;
}
- private PermissionRule convert(org.caosdb.server.permissions.PermissionRule rule) {
+ private PermissionRule convert(org.linkahead.server.permissions.PermissionRule rule) {
PermissionRule.Builder result = PermissionRule.newBuilder();
result.setGrant(rule.isGrant());
result.setPriority(rule.isPriority());
@@ -210,7 +211,7 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
}
private Iterable<PermissionRule> convert(
- LinkedList<org.caosdb.server.permissions.PermissionRule> permission_rules) {
+ LinkedList<org.linkahead.server.permissions.PermissionRule> permission_rules) {
List<PermissionRule> result = new LinkedList<>();
permission_rules.forEach(
@@ -281,10 +282,10 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
/** What can be done with this role. */
private Iterable<? extends RoleCapabilities> getRoleCapabilities(Role role) {
List<RoleCapabilities> result = new LinkedList<>();
- if (org.caosdb.server.permissions.Role.ADMINISTRATION.toString().equals(role.name)) {
+ if (org.linkahead.server.permissions.Role.ADMINISTRATION.toString().equals(role.name)) {
// administration cannot be deleted and the permissions cannot be changed (from *)
result.add(RoleCapabilities.ROLE_CAPABILITIES_ASSIGN);
- } else if (org.caosdb.server.permissions.Role.ANONYMOUS_ROLE.toString().equals(role.name)) {
+ } else if (org.linkahead.server.permissions.Role.ANONYMOUS_ROLE.toString().equals(role.name)) {
// anonymous cannot be deleted or assigned to any user
result.add(RoleCapabilities.ROLE_CAPABILITIES_UPDATE_PERMISSION_RULES);
} else {
diff --git a/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java b/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java
index ce8a62210d3c8e849397600fc112cd3103f15df4..90a83ce957d7f3405fc427a137dc18f53ea3f996 100644
--- a/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java
+++ b/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,9 +19,9 @@
*
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
-import static org.caosdb.server.utils.Utils.URLDecodeWithUTF8;
+import static org.linkahead.server.utils.Utils.URLDecodeWithUTF8;
import io.grpc.Context;
import io.grpc.Contexts;
@@ -40,15 +40,15 @@ import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.subject.Subject;
import org.apache.shiro.util.ThreadContext;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.RealmUsernamePasswordToken;
-import org.caosdb.server.accessControl.SelfValidatingAuthenticationToken;
-import org.caosdb.server.accessControl.SessionToken;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.RealmUsernamePasswordToken;
+import org.linkahead.server.accessControl.SelfValidatingAuthenticationToken;
+import org.linkahead.server.accessControl.SessionToken;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.utils.Utils;
import org.restlet.data.CookieSetting;
/**
@@ -97,7 +97,7 @@ public class AuthInterceptor implements ServerInterceptor {
/** Whether the anonymous login is possible or not. */
private final boolean isAuthOptional() {
- return CaosDBServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
+ return LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
.equalsIgnoreCase("true");
}
@@ -272,7 +272,8 @@ final class CookieSetter<ReqT, RespT>
String getSessionTimeoutSeconds() {
int ms =
- Integer.parseInt(CaosDBServer.getServerProperty(ServerProperties.KEY_SESSION_TIMEOUT_MS));
+ Integer.parseInt(
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_SESSION_TIMEOUT_MS));
int seconds = (int) Math.floor(ms / 1000);
return Integer.toString(seconds);
}
diff --git a/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java b/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
index 8ab8b0579bd6d0a32976ac6e2e28e776f00d4850..b83226687f8f2a183ab29e4b7e85b44b51338840 100644
--- a/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
+++ b/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,7 +19,7 @@
*
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.util.Iterator;
import java.util.LinkedList;
@@ -27,69 +27,69 @@ import java.util.List;
import java.util.NoSuchElementException;
import java.util.Objects;
import java.util.TimeZone;
-import org.caosdb.api.entity.v1.AtomicDataType;
-import org.caosdb.api.entity.v1.CollectionValues;
-import org.caosdb.api.entity.v1.DataType;
-import org.caosdb.api.entity.v1.Entity;
-import org.caosdb.api.entity.v1.Entity.Builder;
-import org.caosdb.api.entity.v1.EntityACL;
-import org.caosdb.api.entity.v1.EntityAclPermission;
-import org.caosdb.api.entity.v1.EntityPermissionRule;
-import org.caosdb.api.entity.v1.EntityPermissionRuleCapability;
-import org.caosdb.api.entity.v1.EntityResponse;
-import org.caosdb.api.entity.v1.EntityRole;
-import org.caosdb.api.entity.v1.FileDescriptor;
-import org.caosdb.api.entity.v1.Importance;
-import org.caosdb.api.entity.v1.ListDataType;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.api.entity.v1.Parent;
-import org.caosdb.api.entity.v1.ReferenceDataType;
-import org.caosdb.api.entity.v1.ScalarValue;
-import org.caosdb.api.entity.v1.SelectQueryColumn;
-import org.caosdb.api.entity.v1.SelectQueryHeader;
-import org.caosdb.api.entity.v1.SelectQueryResult;
-import org.caosdb.api.entity.v1.SelectQueryRow;
-import org.caosdb.api.entity.v1.SpecialValue;
-import org.caosdb.api.entity.v1.Version;
-import org.caosdb.datetime.DateTimeInterface;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.BooleanDatatype;
-import org.caosdb.server.datatype.BooleanValue;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.DateTimeDatatype;
-import org.caosdb.server.datatype.DoubleDatatype;
-import org.caosdb.server.datatype.FileDatatype;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.IntegerDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.TextDatatype;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.MagicTypes;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.StatementStatusInterface;
-import org.caosdb.server.entity.container.ParentContainer;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.permissions.EntityACI;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.Selection;
-
-public class CaosDBToGrpcConverters {
+import org.linkahead.api.entity.v1.AtomicDataType;
+import org.linkahead.api.entity.v1.CollectionValues;
+import org.linkahead.api.entity.v1.DataType;
+import org.linkahead.api.entity.v1.Entity;
+import org.linkahead.api.entity.v1.Entity.Builder;
+import org.linkahead.api.entity.v1.EntityACL;
+import org.linkahead.api.entity.v1.EntityAclPermission;
+import org.linkahead.api.entity.v1.EntityPermissionRule;
+import org.linkahead.api.entity.v1.EntityPermissionRuleCapability;
+import org.linkahead.api.entity.v1.EntityResponse;
+import org.linkahead.api.entity.v1.EntityRole;
+import org.linkahead.api.entity.v1.FileDescriptor;
+import org.linkahead.api.entity.v1.Importance;
+import org.linkahead.api.entity.v1.ListDataType;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.api.entity.v1.Parent;
+import org.linkahead.api.entity.v1.ReferenceDataType;
+import org.linkahead.api.entity.v1.ScalarValue;
+import org.linkahead.api.entity.v1.SelectQueryColumn;
+import org.linkahead.api.entity.v1.SelectQueryHeader;
+import org.linkahead.api.entity.v1.SelectQueryResult;
+import org.linkahead.api.entity.v1.SelectQueryRow;
+import org.linkahead.api.entity.v1.SpecialValue;
+import org.linkahead.api.entity.v1.Version;
+import org.linkahead.datetime.DateTimeInterface;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.BooleanDatatype;
+import org.linkahead.server.datatype.BooleanValue;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.DateTimeDatatype;
+import org.linkahead.server.datatype.DoubleDatatype;
+import org.linkahead.server.datatype.FileDatatype;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.IntegerDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.datatype.TextDatatype;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.MagicTypes;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.StatementStatusInterface;
+import org.linkahead.server.entity.container.ParentContainer;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.permissions.EntityACI;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.Selection;
+
+public class LinkAheadToGrpcConverters {
private TimeZone timeZone;
- public CaosDBToGrpcConverters(TimeZone timeZone) {
+ public LinkAheadToGrpcConverters(TimeZone timeZone) {
this.timeZone = timeZone;
}
@@ -194,18 +194,18 @@ public class CaosDBToGrpcConverters {
}
}
- public Iterable<? extends org.caosdb.api.entity.v1.Message> convert(
+ public Iterable<? extends org.linkahead.api.entity.v1.Message> convert(
final List<Message> messages) {
- final List<org.caosdb.api.entity.v1.Message> result = new LinkedList<>();
+ final List<org.linkahead.api.entity.v1.Message> result = new LinkedList<>();
for (final Message m : messages) {
result.add(convert(m));
}
return result;
}
- public org.caosdb.api.entity.v1.Message convert(final Message m) {
- final org.caosdb.api.entity.v1.Message.Builder builder =
- org.caosdb.api.entity.v1.Message.newBuilder();
+ public org.linkahead.api.entity.v1.Message convert(final Message m) {
+ final org.linkahead.api.entity.v1.Message.Builder builder =
+ org.linkahead.api.entity.v1.Message.newBuilder();
final MessageCode code = getMessageCode(m);
builder.setCode(code.getNumber());
builder.setDescription(m.getDescription());
@@ -216,15 +216,15 @@ public class CaosDBToGrpcConverters {
return m.getCode();
}
- public Version convert(final org.caosdb.server.entity.Version from) {
- final org.caosdb.api.entity.v1.Version.Builder builder = Version.newBuilder();
+ public Version convert(final org.linkahead.server.entity.Version from) {
+ final org.linkahead.api.entity.v1.Version.Builder builder = Version.newBuilder();
builder.setId(from.getId());
return builder.build();
}
- public Parent convert(final org.caosdb.server.entity.wrapper.Parent from) {
- final org.caosdb.api.entity.v1.Parent.Builder builder = Parent.newBuilder();
+ public Parent convert(final org.linkahead.server.entity.wrapper.Parent from) {
+ final org.linkahead.api.entity.v1.Parent.Builder builder = Parent.newBuilder();
if (from.hasId()) {
builder.setId(from.getId().toString());
}
@@ -238,10 +238,10 @@ public class CaosDBToGrpcConverters {
return builder.build();
}
- public org.caosdb.api.entity.v1.Property convert(final Property from) {
+ public org.linkahead.api.entity.v1.Property convert(final Property from) {
// @review Florian Spreckelsen 2022-03-22
- final org.caosdb.api.entity.v1.Property.Builder builder =
- org.caosdb.api.entity.v1.Property.newBuilder();
+ final org.linkahead.api.entity.v1.Property.Builder builder =
+ org.linkahead.api.entity.v1.Property.newBuilder();
SerializeFieldStrategy s = from.getSerializeFieldStrategy();
if (from.hasId() && s.isToBeSet("id")) {
@@ -276,12 +276,12 @@ public class CaosDBToGrpcConverters {
return builder.build();
}
- private org.caosdb.api.entity.v1.Value.Builder convert(final Value value) {
+ private org.linkahead.api.entity.v1.Value.Builder convert(final Value value) {
if (value instanceof CollectionValue) {
return convertCollectionValue((CollectionValue) value);
}
- final org.caosdb.api.entity.v1.Value.Builder builder =
- org.caosdb.api.entity.v1.Value.newBuilder();
+ final org.linkahead.api.entity.v1.Value.Builder builder =
+ org.linkahead.api.entity.v1.Value.newBuilder();
builder.setScalarValue(convertScalarValue(value));
return builder;
}
@@ -316,19 +316,19 @@ public class CaosDBToGrpcConverters {
}
}
- private org.caosdb.api.entity.v1.ScalarValue.Builder convertStringValue(final String value) {
+ private org.linkahead.api.entity.v1.ScalarValue.Builder convertStringValue(final String value) {
if (value.isEmpty()) {
return ScalarValue.newBuilder().setSpecialValue(SpecialValue.SPECIAL_VALUE_EMPTY_STRING);
}
return ScalarValue.newBuilder().setStringValue(value);
}
- private org.caosdb.api.entity.v1.ScalarValue.Builder convertDateTimeInterface(
+ private org.linkahead.api.entity.v1.ScalarValue.Builder convertDateTimeInterface(
final DateTimeInterface value) {
return convertStringValue(value.toDateTimeString(timeZone));
}
- private org.caosdb.api.entity.v1.ScalarValue.Builder convertBooleanValue(
+ private org.linkahead.api.entity.v1.ScalarValue.Builder convertBooleanValue(
final BooleanValue value) {
return ScalarValue.newBuilder().setBooleanValue(value.getValue());
}
@@ -337,11 +337,11 @@ public class CaosDBToGrpcConverters {
return convertStringValue(value.toString());
}
- private org.caosdb.api.entity.v1.Value.Builder convertCollectionValue(
+ private org.linkahead.api.entity.v1.Value.Builder convertCollectionValue(
final CollectionValue value) {
- final org.caosdb.api.entity.v1.Value.Builder builder =
- org.caosdb.api.entity.v1.Value.newBuilder();
+ final org.linkahead.api.entity.v1.Value.Builder builder =
+ org.linkahead.api.entity.v1.Value.newBuilder();
final List<ScalarValue> values = new LinkedList<>();
value.forEach(
(v) -> {
@@ -375,7 +375,7 @@ public class CaosDBToGrpcConverters {
}
}
- private org.caosdb.api.entity.v1.DataType.Builder convert(final AbstractDatatype datatype) {
+ private org.linkahead.api.entity.v1.DataType.Builder convert(final AbstractDatatype datatype) {
if (datatype instanceof ReferenceDatatype2) {
return DataType.newBuilder()
.setReferenceDataType(convertReferenceDatatype((ReferenceDatatype2) datatype));
@@ -431,10 +431,10 @@ public class CaosDBToGrpcConverters {
return AtomicDataType.ATOMIC_DATA_TYPE_BOOLEAN;
}
- private org.caosdb.api.entity.v1.ListDataType.Builder convertAbstractCollectionDatatype(
+ private org.linkahead.api.entity.v1.ListDataType.Builder convertAbstractCollectionDatatype(
final AbstractCollectionDatatype collectionDatatype) {
- final org.caosdb.api.entity.v1.ListDataType.Builder listBuilder = ListDataType.newBuilder();
+ final org.linkahead.api.entity.v1.ListDataType.Builder listBuilder = ListDataType.newBuilder();
final AbstractDatatype datatype = collectionDatatype.getDatatype();
if (datatype instanceof ReferenceDatatype) {
listBuilder.setReferenceDataType(convertReferenceDatatype((ReferenceDatatype) datatype));
@@ -456,15 +456,15 @@ public class CaosDBToGrpcConverters {
return listBuilder;
}
- private org.caosdb.api.entity.v1.ReferenceDataType.Builder convertReferenceDatatype(
+ private org.linkahead.api.entity.v1.ReferenceDataType.Builder convertReferenceDatatype(
final ReferenceDatatype datatype) {
return ReferenceDataType.newBuilder().setName(datatype.getName());
}
- public Iterable<? extends org.caosdb.api.entity.v1.Property> convertProperties(
+ public Iterable<? extends org.linkahead.api.entity.v1.Property> convertProperties(
final EntityInterface from) {
// @review Florian Spreckelsen 2022-03-22
- final Iterator<org.caosdb.server.entity.wrapper.Property> iterator =
+ final Iterator<org.linkahead.server.entity.wrapper.Property> iterator =
from.getProperties().iterator();
return () ->
new Iterator<>() {
@@ -485,7 +485,7 @@ public class CaosDBToGrpcConverters {
}
@Override
- public org.caosdb.api.entity.v1.Property next() {
+ public org.linkahead.api.entity.v1.Property next() {
if (this.property == null) {
// trigger this.property to be non-null
if (!hasNext()) {
@@ -502,7 +502,7 @@ public class CaosDBToGrpcConverters {
}
public Iterable<? extends Parent> convert(final ParentContainer from) {
- final Iterator<org.caosdb.server.entity.wrapper.Parent> iterator = from.iterator();
+ final Iterator<org.linkahead.server.entity.wrapper.Parent> iterator = from.iterator();
return () ->
new Iterator<>() {
@@ -519,7 +519,8 @@ public class CaosDBToGrpcConverters {
}
public void appendMessages(
- final EntityInterface from, final org.caosdb.api.entity.v1.EntityResponse.Builder builder) {
+ final EntityInterface from,
+ final org.linkahead.api.entity.v1.EntityResponse.Builder builder) {
// @review Florian Spreckelsen 2022-03-22
SerializeFieldStrategy s = from.getSerializeFieldStrategy();
if (from.hasMessage(Message.MessageType.Error.toString()) && s.isToBeSet("error")) {
@@ -534,7 +535,7 @@ public class CaosDBToGrpcConverters {
}
public void appendMessages(
- final EntityInterface from, final org.caosdb.api.entity.v1.IdResponse.Builder builder) {
+ final EntityInterface from, final org.linkahead.api.entity.v1.IdResponse.Builder builder) {
// @review Florian Spreckelsen 2022-03-22
SerializeFieldStrategy s = from.getSerializeFieldStrategy();
if (from.hasMessage(Message.MessageType.Error.toString()) && s.isToBeSet("error")) {
@@ -554,7 +555,8 @@ public class CaosDBToGrpcConverters {
if (e.hasEntityACL()) {
builder.addAllRules(convert(e.getEntityACL(), true));
}
- builder.addAllRules(convert(org.caosdb.server.permissions.EntityACL.GLOBAL_PERMISSIONS, false));
+ builder.addAllRules(
+ convert(org.linkahead.server.permissions.EntityACL.GLOBAL_PERMISSIONS, false));
EntityAclPermission entityAclPermission = getCurrentACLPermission(e);
if (entityAclPermission != null) {
builder.setPermission(entityAclPermission);
@@ -562,7 +564,8 @@ public class CaosDBToGrpcConverters {
return builder.build();
}
- private org.caosdb.api.entity.v1.EntityAclPermission getCurrentACLPermission(EntityInterface e) {
+ private org.linkahead.api.entity.v1.EntityAclPermission getCurrentACLPermission(
+ EntityInterface e) {
if (e.hasPermission(EntityPermission.EDIT_PRIORITY_ACL)) {
return EntityAclPermission.ENTITY_ACL_PERMISSION_EDIT_PRIORITY_ACL;
}
@@ -573,7 +576,7 @@ public class CaosDBToGrpcConverters {
}
private Iterable<? extends EntityPermissionRule> convert(
- org.caosdb.server.permissions.EntityACL entityACL, boolean deletable) {
+ org.linkahead.server.permissions.EntityACL entityACL, boolean deletable) {
List<EntityPermissionRule> result = new LinkedList<>();
for (EntityACI aci : entityACL.getRules()) {
EntityPermissionRule.Builder builder =
@@ -591,8 +594,8 @@ public class CaosDBToGrpcConverters {
return result;
}
- private Iterable<org.caosdb.api.entity.v1.EntityPermission> convert(EntityACI aci) {
- List<org.caosdb.api.entity.v1.EntityPermission> result = new LinkedList<>();
+ private Iterable<org.linkahead.api.entity.v1.EntityPermission> convert(EntityACI aci) {
+ List<org.linkahead.api.entity.v1.EntityPermission> result = new LinkedList<>();
for (EntityPermission p : aci.getPermission()) {
result.add(p.getMapping());
@@ -600,7 +603,7 @@ public class CaosDBToGrpcConverters {
return result;
}
- public org.caosdb.api.entity.v1.SelectQueryResult.Builder convertSelectResult(
+ public org.linkahead.api.entity.v1.SelectQueryResult.Builder convertSelectResult(
RetrieveContainer container) {
SelectQueryResult.Builder result = SelectQueryResult.newBuilder();
result.setHeader(convertSelectQueryHeader(container));
@@ -614,7 +617,7 @@ public class CaosDBToGrpcConverters {
SelectQueryRow.Builder result = SelectQueryRow.newBuilder();
for (Selection s : selections) {
- org.caosdb.api.entity.v1.Value.Builder value = getSelectedValue(s, e);
+ org.linkahead.api.entity.v1.Value.Builder value = getSelectedValue(s, e);
result.addCells(value);
}
return result;
@@ -623,12 +626,12 @@ public class CaosDBToGrpcConverters {
/**
* Handle special selectors like "id", "name", "value", "parent",...
*
- * @return a {@link org.caosdb.api.entity.v1.Value.Builder}, if the selector has been handled.
+ * @return a {@link org.linkahead.api.entity.v1.Value.Builder}, if the selector has been handled.
* Return null when the caller must handle the selector otherwise.
*/
- private org.caosdb.api.entity.v1.Value.Builder handleSpecialSelectors(
+ private org.linkahead.api.entity.v1.Value.Builder handleSpecialSelectors(
String selector, EntityInterface e) {
- org.caosdb.api.entity.v1.Value.Builder result = null;
+ org.linkahead.api.entity.v1.Value.Builder result = null;
switch (selector) {
case "value":
try {
@@ -642,27 +645,27 @@ public class CaosDBToGrpcConverters {
break;
case "version":
if (e.hasVersion()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getVersion().getId()));
return result;
}
break;
case "name":
if (e.hasName()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getName()));
return result;
}
break;
case "id":
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getId().toString()));
return result;
case "description":
if (e.hasDescription()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getDescription()));
return result;
}
@@ -671,30 +674,30 @@ public class CaosDBToGrpcConverters {
case "unit":
final String unit = getStringUnit(e);
if (unit != null) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(unit));
return result;
}
break;
case "datatype":
if (e.hasDatatype()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getDatatype().toString()));
return result;
}
break;
case "path":
if (e.hasFileProperties() && e.getFileProperties().hasPath()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getFileProperties().getPath()));
return result;
}
break;
case "parent":
if (e.hasParents()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
CollectionValues.Builder parents = CollectionValues.newBuilder();
- for (org.caosdb.server.entity.wrapper.Parent p : e.getParents()) {
+ for (org.linkahead.server.entity.wrapper.Parent p : e.getParents()) {
parents.addValues(ScalarValue.newBuilder().setStringValue(p.getName()));
}
result.setListValues(parents);
@@ -707,13 +710,13 @@ public class CaosDBToGrpcConverters {
return null;
}
- org.caosdb.api.entity.v1.Value.Builder getSelectedValue(Selection s, EntityInterface e) {
- org.caosdb.api.entity.v1.Value.Builder result = null;
+ org.linkahead.api.entity.v1.Value.Builder getSelectedValue(Selection s, EntityInterface e) {
+ org.linkahead.api.entity.v1.Value.Builder result = null;
String selector = s.getSelector();
result = handleSpecialSelectors(selector, e);
if (result == null) {
// selector for a normal property
- List<org.caosdb.api.entity.v1.Value.Builder> results = new LinkedList<>();
+ List<org.linkahead.api.entity.v1.Value.Builder> results = new LinkedList<>();
for (Property p : e.getProperties()) {
if (p.getName() != null && p.getName().equals(selector)) {
if (s.getSubselection() == null) {
@@ -765,7 +768,7 @@ public class CaosDBToGrpcConverters {
if (results.size() > 1) {
// There have been multiple matching properties
CollectionValues.Builder values = CollectionValues.newBuilder();
- for (org.caosdb.api.entity.v1.Value.Builder v : results) {
+ for (org.linkahead.api.entity.v1.Value.Builder v : results) {
// Concatenate all found values to a list
if (v.hasScalarValue()) {
values.addValues(v.getScalarValueBuilder());
@@ -773,7 +776,7 @@ public class CaosDBToGrpcConverters {
values.addAllValues(v.getListValuesBuilder().getValuesList());
}
}
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setListValues(values);
} else if (results.size() == 1) {
// There has been exactly one matching property
@@ -783,7 +786,7 @@ public class CaosDBToGrpcConverters {
if (result == null) {
// no matching property found
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
}
return result;
}
diff --git a/src/main/java/org/caosdb/server/grpc/DownloadBuffer.java b/src/main/java/org/caosdb/server/grpc/DownloadBuffer.java
index 06c387624c887f5ceeb73efb3ee7b042519a1a6f..a502682e79f38d623a8762ab7b4e539e679fb262 100644
--- a/src/main/java/org/caosdb/server/grpc/DownloadBuffer.java
+++ b/src/main/java/org/caosdb/server/grpc/DownloadBuffer.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import com.google.protobuf.ByteString;
import java.io.FileInputStream;
@@ -7,10 +7,10 @@ import java.io.IOException;
import java.nio.MappedByteBuffer;
import java.nio.channels.FileChannel;
import java.nio.channels.FileChannel.MapMode;
-import org.caosdb.api.entity.v1.FileChunk;
-import org.caosdb.api.entity.v1.FileDownloadResponse;
-import org.caosdb.api.entity.v1.TransmissionStatus;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.api.entity.v1.FileChunk;
+import org.linkahead.api.entity.v1.FileDownloadResponse;
+import org.linkahead.api.entity.v1.TransmissionStatus;
+import org.linkahead.server.entity.FileProperties;
public class DownloadBuffer {
diff --git a/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java b/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java
index 030b52544fec858ef3c62c531e9627baf5500551..f72f0e7a9251e8c920335366ed19c4a4e3e3bb5f 100644
--- a/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java
+++ b/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,7 +19,7 @@
*
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.stub.StreamObserver;
import java.util.HashMap;
@@ -27,53 +27,53 @@ import java.util.TimeZone;
import java.util.UUID;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authc.AuthenticationException;
-import org.caosdb.api.entity.v1.DeleteRequest;
-import org.caosdb.api.entity.v1.DeleteResponse;
-import org.caosdb.api.entity.v1.Entity;
-import org.caosdb.api.entity.v1.EntityRequest;
-import org.caosdb.api.entity.v1.EntityResponse;
-import org.caosdb.api.entity.v1.EntityTransactionServiceGrpc.EntityTransactionServiceImplBase;
-import org.caosdb.api.entity.v1.FindQueryResult;
-import org.caosdb.api.entity.v1.IdResponse;
-import org.caosdb.api.entity.v1.InsertRequest;
-import org.caosdb.api.entity.v1.InsertResponse;
-import org.caosdb.api.entity.v1.MultiRetrieveEntityACLRequest;
-import org.caosdb.api.entity.v1.MultiRetrieveEntityACLResponse;
-import org.caosdb.api.entity.v1.MultiTransactionRequest;
-import org.caosdb.api.entity.v1.MultiTransactionResponse;
-import org.caosdb.api.entity.v1.MultiUpdateEntityACLRequest;
-import org.caosdb.api.entity.v1.MultiUpdateEntityACLResponse;
-import org.caosdb.api.entity.v1.RetrieveResponse;
-import org.caosdb.api.entity.v1.SelectQueryResult;
-import org.caosdb.api.entity.v1.TransactionRequest;
-import org.caosdb.api.entity.v1.TransactionRequest.WrappedRequestsCase;
-import org.caosdb.api.entity.v1.TransactionResponse;
-import org.caosdb.api.entity.v1.UpdateRequest;
-import org.caosdb.api.entity.v1.UpdateResponse;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.entity.container.WritableContainer;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.transaction.RetrieveACL;
-import org.caosdb.server.transaction.UpdateACL;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.api.entity.v1.DeleteRequest;
+import org.linkahead.api.entity.v1.DeleteResponse;
+import org.linkahead.api.entity.v1.Entity;
+import org.linkahead.api.entity.v1.EntityRequest;
+import org.linkahead.api.entity.v1.EntityResponse;
+import org.linkahead.api.entity.v1.EntityTransactionServiceGrpc.EntityTransactionServiceImplBase;
+import org.linkahead.api.entity.v1.FindQueryResult;
+import org.linkahead.api.entity.v1.IdResponse;
+import org.linkahead.api.entity.v1.InsertRequest;
+import org.linkahead.api.entity.v1.InsertResponse;
+import org.linkahead.api.entity.v1.MultiRetrieveEntityACLRequest;
+import org.linkahead.api.entity.v1.MultiRetrieveEntityACLResponse;
+import org.linkahead.api.entity.v1.MultiTransactionRequest;
+import org.linkahead.api.entity.v1.MultiTransactionResponse;
+import org.linkahead.api.entity.v1.MultiUpdateEntityACLRequest;
+import org.linkahead.api.entity.v1.MultiUpdateEntityACLResponse;
+import org.linkahead.api.entity.v1.RetrieveResponse;
+import org.linkahead.api.entity.v1.SelectQueryResult;
+import org.linkahead.api.entity.v1.TransactionRequest;
+import org.linkahead.api.entity.v1.TransactionRequest.WrappedRequestsCase;
+import org.linkahead.api.entity.v1.TransactionResponse;
+import org.linkahead.api.entity.v1.UpdateRequest;
+import org.linkahead.api.entity.v1.UpdateResponse;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.entity.container.WritableContainer;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.transaction.RetrieveACL;
+import org.linkahead.server.transaction.UpdateACL;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.ServerMessages;
public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBase {
// TODO(tf) let the clients define the time zone of the date time values which are being returned.
- private final CaosDBToGrpcConverters caosdbToGrpc =
- new CaosDBToGrpcConverters(TimeZone.getDefault());
- private final GrpcToCaosDBConverters grpcToCaosdb = new GrpcToCaosDBConverters();
+ private final LinkAheadToGrpcConverters linkaheadToGrpc =
+ new LinkAheadToGrpcConverters(TimeZone.getDefault());
+ private final GrpcToLinkAheadConverters grpcToLinkAhead = new GrpcToLinkAheadConverters();
private final FileTransmissionServiceImpl fileTransmissionService;
public EntityTransactionServiceImpl(final FileTransmissionServiceImpl fileTransmissionService) {
@@ -93,8 +93,8 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
fileTransmissionService.registerFileDownload(
fileDownload.getId(), entity.getFileProperties()));
} catch (AuthenticationException exc) {
- entityResponse.addErrors(caosdbToGrpc.convert(ServerMessages.AUTHORIZATION_ERROR));
- entityResponse.addInfos(caosdbToGrpc.convert(new Message(exc.getMessage())));
+ entityResponse.addErrors(linkaheadToGrpc.convert(ServerMessages.AUTHORIZATION_ERROR));
+ entityResponse.addInfos(linkaheadToGrpc.convert(new Message(exc.getMessage())));
}
}
@@ -116,7 +116,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
for (final TransactionRequest sub_request : request.getRequestsList()) {
if (sub_request.getWrappedRequestsCase() != WrappedRequestsCase.RETRIEVE_REQUEST) {
- throw new CaosDBException(
+ throw new LinkAheadException(
"Cannot process a "
+ sub_request.getWrappedRequestsCase().name()
+ " in a read-only request.");
@@ -126,7 +126,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
&& !sub_request.getRetrieveRequest().getQuery().getQuery().isBlank()) {
final String query = sub_request.getRetrieveRequest().getQuery().getQuery();
if (container.getFlags().containsKey("query")) { // Check for more than one query request.
- throw new CaosDBException("Cannot process more than one query request.");
+ throw new LinkAheadException("Cannot process more than one query request.");
}
container.getFlags().put("query", query);
if (isFileDownload) {
@@ -136,7 +136,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
final String id = sub_request.getRetrieveRequest().getId();
if (!id.isBlank()) {
try {
- final RetrieveEntity entity = new RetrieveEntity(grpcToCaosdb.getId(id));
+ final RetrieveEntity entity = new RetrieveEntity(grpcToLinkAhead.getId(id));
if (isFileDownload) {
entity.setFlag("download_files", "true");
}
@@ -159,7 +159,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
} else if (container.getQuery() != null
&& container.getQuery().getType() == Query.Type.SELECT) {
// this was a select query
- SelectQueryResult.Builder selectResult = caosdbToGrpc.convertSelectResult(container);
+ SelectQueryResult.Builder selectResult = linkaheadToGrpc.convertSelectResult(container);
builder
.addResponsesBuilder()
.setRetrieveResponse(RetrieveResponse.newBuilder().setSelectResult(selectResult));
@@ -168,7 +168,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
final boolean download_files_container = container.getFlags().containsKey("download_files");
FindQueryResult.Builder findResult = FindQueryResult.newBuilder();
for (final EntityInterface entity : container) {
- final EntityResponse.Builder entityResponse = caosdbToGrpc.convert(entity);
+ final EntityResponse.Builder entityResponse = linkaheadToGrpc.convert(entity);
if ((download_files_container || entity.getFlags().containsKey("download_files"))
&& entity.hasFileProperties()) {
prepareDownload(entityResponse, entity, fileDownload);
@@ -182,7 +182,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
// normal retrieval via id
final boolean download_files_container = container.getFlags().containsKey("download_files");
for (final EntityInterface entity : container) {
- final EntityResponse.Builder entityResponse = caosdbToGrpc.convert(entity);
+ final EntityResponse.Builder entityResponse = linkaheadToGrpc.convert(entity);
if ((download_files_container || entity.getFlags().containsKey("download_files"))
&& entity.hasFileProperties()) {
prepareDownload(entityResponse, entity, fileDownload);
@@ -198,7 +198,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
final String id = sub_request.getRetrieveRequest().getId();
if (!id.isBlank()) {
try {
- grpcToCaosdb.getId(id);
+ grpcToLinkAhead.getId(id);
} catch (final NumberFormatException e) {
// ID wasn't an integer - the server doesn't support string ids yet, so that entity
// cannot exist.
@@ -214,7 +214,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
private EntityResponse entityDoesNotExist(final String id) {
return EntityResponse.newBuilder()
- .addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST))
+ .addErrors(linkaheadToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST))
.setEntity(Entity.newBuilder().setId(id))
.build();
}
@@ -285,8 +285,8 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
final InsertEntity entity =
new InsertEntity(
insertEntity.getName().isEmpty() ? null : insertEntity.getName(),
- grpcToCaosdb.convert(insertEntity.getRole()));
- grpcToCaosdb.convert(insertEntity, entity);
+ grpcToLinkAhead.convert(insertEntity.getRole()));
+ grpcToLinkAhead.convert(insertEntity, entity);
addFileUpload(container, entity, insertRequest.getEntityRequest());
container.add(entity);
}
@@ -298,9 +298,10 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
try {
final UpdateEntity entity =
new UpdateEntity(
- grpcToCaosdb.getId(updateEntity.getId()), // ID is not handled by grpc convert
- grpcToCaosdb.convert(updateEntity.getRole()));
- grpcToCaosdb.convert(updateEntity, entity);
+ grpcToLinkAhead.getId(
+ updateEntity.getId()), // ID is not handled by grpc convert
+ grpcToLinkAhead.convert(updateEntity.getRole()));
+ grpcToLinkAhead.convert(updateEntity, entity);
addFileUpload(container, entity, updateRequest.getEntityRequest());
container.add(entity);
} catch (final NumberFormatException e) {
@@ -311,7 +312,8 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
case DELETE_REQUEST:
final DeleteRequest deleteRequest = subRequest.getDeleteRequest();
try {
- final DeleteEntity entity = new DeleteEntity(grpcToCaosdb.getId(deleteRequest.getId()));
+ final DeleteEntity entity =
+ new DeleteEntity(grpcToLinkAhead.getId(deleteRequest.getId()));
container.add(entity);
} catch (final NumberFormatException e) {
@@ -320,7 +322,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
}
break;
default:
- throw new CaosDBException(
+ throw new LinkAheadException(
"Cannot process a "
+ subRequest.getWrappedRequestsCase().name()
+ " in a write request.");
@@ -338,7 +340,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
if (entity.hasId()) {
idResponse.setId(entity.getId().toString());
}
- caosdbToGrpc.appendMessages(entity, idResponse);
+ linkaheadToGrpc.appendMessages(entity, idResponse);
if (entity instanceof InsertEntity) {
builder
@@ -367,7 +369,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
* @return
*/
private MultiTransactionResponse failedWriteDueToStringId(final MultiTransactionRequest request) {
- final org.caosdb.api.entity.v1.MultiTransactionResponse.Builder builder =
+ final org.linkahead.api.entity.v1.MultiTransactionResponse.Builder builder =
MultiTransactionResponse.newBuilder();
for (final TransactionRequest subRequest : request.getRequestsList()) {
final IdResponse.Builder idResponse = IdResponse.newBuilder();
@@ -384,10 +386,10 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
idResponse.setId(updateEntity.getId());
try {
- grpcToCaosdb.getId(updateEntity.getId());
+ grpcToLinkAhead.getId(updateEntity.getId());
} catch (final NumberFormatException e) {
// ID wasn't an integer
- idResponse.addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
+ idResponse.addErrors(linkaheadToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
}
builder
.addResponsesBuilder()
@@ -397,17 +399,17 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
final DeleteRequest deleteRequest = subRequest.getDeleteRequest();
idResponse.setId(deleteRequest.getId());
try {
- grpcToCaosdb.getId(deleteRequest.getId());
+ grpcToLinkAhead.getId(deleteRequest.getId());
} catch (final NumberFormatException e) {
// ID wasn't an integer
- idResponse.addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
+ idResponse.addErrors(linkaheadToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
}
builder
.addResponsesBuilder()
.setDeleteResponse(DeleteResponse.newBuilder().setIdResponse(idResponse));
break;
default:
- throw new CaosDBException(
+ throw new LinkAheadException(
"Cannot process a "
+ subRequest.getWrappedRequestsCase().name()
+ " in a write request.");
@@ -438,7 +440,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
RetrieveACL transaction = new RetrieveACL(request.getIdList());
transaction.execute();
for (EntityInterface e : transaction.getContainer()) {
- builder.addAcls(caosdbToGrpc.convertACL(e));
+ builder.addAcls(linkaheadToGrpc.convertACL(e));
}
return builder.build();
}
@@ -446,7 +448,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
private MultiUpdateEntityACLResponse multiUpdateEntityACL(MultiUpdateEntityACLRequest request)
throws Exception {
MultiUpdateEntityACLResponse.Builder builder = MultiUpdateEntityACLResponse.newBuilder();
- UpdateACL transaction = new UpdateACL(grpcToCaosdb.convertAcls(request.getAclsList()));
+ UpdateACL transaction = new UpdateACL(grpcToLinkAhead.convertAcls(request.getAclsList()));
transaction.execute();
return builder.build();
}
diff --git a/src/main/java/org/caosdb/server/grpc/FileDownload.java b/src/main/java/org/caosdb/server/grpc/FileDownload.java
index 2f3c79899dac73174c65b14e01dbc08c71f1a243..fb0b5b581658404f51503dfea0358785e1b071e3 100644
--- a/src/main/java/org/caosdb/server/grpc/FileDownload.java
+++ b/src/main/java/org/caosdb/server/grpc/FileDownload.java
@@ -1,13 +1,13 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
-import org.caosdb.api.entity.v1.FileDownloadResponse;
-import org.caosdb.api.entity.v1.FileTransmissionSettings;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.api.entity.v1.FileDownloadResponse;
+import org.linkahead.api.entity.v1.FileTransmissionSettings;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.utils.Utils;
public class FileDownload extends FileTransmission {
diff --git a/src/main/java/org/caosdb/server/grpc/FileDownloadRegistration.java b/src/main/java/org/caosdb/server/grpc/FileDownloadRegistration.java
index 5130404024e52ec0ac36745452a609b01764dc0d..e0da93ce5cab5b6ca6ffa5842c9bc89ad1c6969a 100644
--- a/src/main/java/org/caosdb/server/grpc/FileDownloadRegistration.java
+++ b/src/main/java/org/caosdb/server/grpc/FileDownloadRegistration.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.io.FileNotFoundException;
import java.io.IOException;
@@ -7,11 +7,11 @@ import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
-import org.caosdb.api.entity.v1.FileDownloadResponse;
-import org.caosdb.api.entity.v1.FileTransmissionId;
-import org.caosdb.api.entity.v1.FileTransmissionSettings;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.api.entity.v1.FileDownloadResponse;
+import org.linkahead.api.entity.v1.FileTransmissionId;
+import org.linkahead.api.entity.v1.FileTransmissionSettings;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.utils.Utils;
public class FileDownloadRegistration {
diff --git a/src/main/java/org/caosdb/server/grpc/FileTransmission.java b/src/main/java/org/caosdb/server/grpc/FileTransmission.java
index 67eca23a8f3deb557e0d773e6de7ff0ee38821a2..7e65faab46ba584a9b94693da11b7ea90ba86b9b 100644
--- a/src/main/java/org/caosdb/server/grpc/FileTransmission.java
+++ b/src/main/java/org/caosdb/server/grpc/FileTransmission.java
@@ -1,9 +1,9 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.util.concurrent.locks.ReentrantLock;
-import org.caosdb.api.entity.v1.FileTransmissionSettings;
-import org.caosdb.api.entity.v1.RegistrationStatus;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.api.entity.v1.FileTransmissionSettings;
+import org.linkahead.api.entity.v1.RegistrationStatus;
+import org.linkahead.server.entity.FileProperties;
public abstract class FileTransmission {
diff --git a/src/main/java/org/caosdb/server/grpc/FileTransmissionServiceImpl.java b/src/main/java/org/caosdb/server/grpc/FileTransmissionServiceImpl.java
index 1f549b37a33f26c2f4ecdc5efc1258a3bb602d50..57fd49b88ae15ce84e725d6a383c1f20a9f6d74a 100644
--- a/src/main/java/org/caosdb/server/grpc/FileTransmissionServiceImpl.java
+++ b/src/main/java/org/caosdb/server/grpc/FileTransmissionServiceImpl.java
@@ -1,24 +1,24 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.stub.StreamObserver;
import java.io.IOException;
-import org.caosdb.api.entity.v1.FileChunk;
-import org.caosdb.api.entity.v1.FileDownloadRequest;
-import org.caosdb.api.entity.v1.FileDownloadResponse;
-import org.caosdb.api.entity.v1.FileTransmissionId;
-import org.caosdb.api.entity.v1.FileTransmissionServiceGrpc.FileTransmissionServiceImplBase;
-import org.caosdb.api.entity.v1.FileTransmissionSettings;
-import org.caosdb.api.entity.v1.FileUploadRequest;
-import org.caosdb.api.entity.v1.FileUploadResponse;
-import org.caosdb.api.entity.v1.RegisterFileUploadRequest;
-import org.caosdb.api.entity.v1.RegisterFileUploadResponse;
-import org.caosdb.api.entity.v1.RegisterFileUploadResponse.Builder;
-import org.caosdb.api.entity.v1.RegistrationStatus;
-import org.caosdb.api.entity.v1.TransmissionStatus;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.utils.CronJob;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.api.entity.v1.FileChunk;
+import org.linkahead.api.entity.v1.FileDownloadRequest;
+import org.linkahead.api.entity.v1.FileDownloadResponse;
+import org.linkahead.api.entity.v1.FileTransmissionId;
+import org.linkahead.api.entity.v1.FileTransmissionServiceGrpc.FileTransmissionServiceImplBase;
+import org.linkahead.api.entity.v1.FileTransmissionSettings;
+import org.linkahead.api.entity.v1.FileUploadRequest;
+import org.linkahead.api.entity.v1.FileUploadResponse;
+import org.linkahead.api.entity.v1.RegisterFileUploadRequest;
+import org.linkahead.api.entity.v1.RegisterFileUploadResponse;
+import org.linkahead.api.entity.v1.RegisterFileUploadResponse.Builder;
+import org.linkahead.api.entity.v1.RegistrationStatus;
+import org.linkahead.api.entity.v1.TransmissionStatus;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.utils.CronJob;
+import org.linkahead.server.utils.Utils;
public class FileTransmissionServiceImpl extends FileTransmissionServiceImplBase {
@@ -68,7 +68,7 @@ public class FileTransmissionServiceImpl extends FileTransmissionServiceImplBase
}
public FileTransmissionServiceImpl() {
- CaosDBServer.addPreShutdownHook(
+ LinkAheadServer.addPreShutdownHook(
() -> {
fileDownloadRegistration.cleanUp(true);
fileUploadRegistration.cleanUp(true);
diff --git a/src/main/java/org/caosdb/server/grpc/FileUpload.java b/src/main/java/org/caosdb/server/grpc/FileUpload.java
index 2ec4ca3de3d5d7ad5b9c44ec16deade8725d9145..5100f06f8b933e874adafbdfcc28579b8df27424 100644
--- a/src/main/java/org/caosdb/server/grpc/FileUpload.java
+++ b/src/main/java/org/caosdb/server/grpc/FileUpload.java
@@ -1,16 +1,16 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import com.google.protobuf.ByteString;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
-import org.caosdb.api.entity.v1.FileChunk;
-import org.caosdb.api.entity.v1.FileTransmissionSettings;
-import org.caosdb.api.entity.v1.FileTransmissionSettings.Builder;
-import org.caosdb.api.entity.v1.TransmissionStatus;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.api.entity.v1.FileChunk;
+import org.linkahead.api.entity.v1.FileTransmissionSettings;
+import org.linkahead.api.entity.v1.FileTransmissionSettings.Builder;
+import org.linkahead.api.entity.v1.TransmissionStatus;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.entity.FileProperties;
public class FileUpload extends FileTransmission {
diff --git a/src/main/java/org/caosdb/server/grpc/FileUploadRegistration.java b/src/main/java/org/caosdb/server/grpc/FileUploadRegistration.java
index bfb25be2ec91cda450be282b89f08ace26a16409..dbb782e15fb5bd36d50973771ee91256b03f68c3 100644
--- a/src/main/java/org/caosdb/server/grpc/FileUploadRegistration.java
+++ b/src/main/java/org/caosdb/server/grpc/FileUploadRegistration.java
@@ -1,13 +1,13 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
-import org.caosdb.api.entity.v1.FileTransmissionId;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.api.entity.v1.FileTransmissionId;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.utils.Utils;
public class FileUploadRegistration {
diff --git a/src/main/java/org/caosdb/server/grpc/GRPCServer.java b/src/main/java/org/caosdb/server/grpc/GRPCServer.java
index 73356140b85fb09af93bdca034a69685ce8cd4eb..096d46fa0a8edd8f369fb61b0fc1c0ec073ec943 100644
--- a/src/main/java/org/caosdb/server/grpc/GRPCServer.java
+++ b/src/main/java/org/caosdb/server/grpc/GRPCServer.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,7 +18,7 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.Server;
import io.grpc.ServerInterceptors;
@@ -43,8 +43,8 @@ import java.util.LinkedList;
import java.util.List;
import java.util.concurrent.TimeUnit;
import javax.net.ssl.KeyManagerFactory;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -59,7 +59,7 @@ public class GRPCServer {
private static GRPCServer instance = new GRPCServer();
private static String getServerProperty(final String key) {
- return CaosDBServer.getServerProperty(key);
+ return LinkAheadServer.getServerProperty(key);
}
private static final Logger logger = LoggerFactory.getLogger(GRPCServer.class.getName());
@@ -190,7 +190,7 @@ public class GRPCServer {
if (port_https_str != null && !port_https_str.isEmpty()) {
final Integer port_https = Integer.parseInt(port_https_str);
final Server server = instance.buildServer(port_https, true);
- CaosDBServer.addPreShutdownHook(new ServerStopper(server));
+ LinkAheadServer.addPreShutdownHook(new ServerStopper(server));
server.start();
started = true;
logger.info("Started GRPC (HTTPS) on port {}", port_https);
@@ -201,7 +201,7 @@ public class GRPCServer {
final Integer port_http = Integer.parseInt(port_http_str);
final Server server = instance.buildServer(port_http, false);
- CaosDBServer.addPreShutdownHook(new ServerStopper(server));
+ LinkAheadServer.addPreShutdownHook(new ServerStopper(server));
server.start();
logger.info("Started GRPC (HTTP) on port {}", port_http);
diff --git a/src/main/java/org/caosdb/server/grpc/GeneralInfoServiceImpl.java b/src/main/java/org/caosdb/server/grpc/GeneralInfoServiceImpl.java
index e47bda9c1783fd9a82703626ad8017c26dbea1fe..8393c01485f1f0e70889d9f45fe205aebc6f78d3 100644
--- a/src/main/java/org/caosdb/server/grpc/GeneralInfoServiceImpl.java
+++ b/src/main/java/org/caosdb/server/grpc/GeneralInfoServiceImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,7 +18,7 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.stub.StreamObserver;
import java.util.Collection;
@@ -27,17 +27,17 @@ import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationInfo;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.api.info.v1.GeneralInfoServiceGrpc.GeneralInfoServiceImplBase;
-import org.caosdb.api.info.v1.GetSessionInfoRequest;
-import org.caosdb.api.info.v1.GetSessionInfoResponse;
-import org.caosdb.api.info.v1.GetVersionInfoRequest;
-import org.caosdb.api.info.v1.GetVersionInfoResponse;
-import org.caosdb.api.info.v1.VersionInfo;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.permissions.CaosPermission;
+import org.linkahead.api.info.v1.GeneralInfoServiceGrpc.GeneralInfoServiceImplBase;
+import org.linkahead.api.info.v1.GetSessionInfoRequest;
+import org.linkahead.api.info.v1.GetSessionInfoResponse;
+import org.linkahead.api.info.v1.GetVersionInfoRequest;
+import org.linkahead.api.info.v1.GetVersionInfoResponse;
+import org.linkahead.api.info.v1.VersionInfo;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.permissions.LinkAheadPermission;
/**
* Implementation of the GeneralInfoService.
@@ -53,12 +53,12 @@ public class GeneralInfoServiceImpl extends GeneralInfoServiceImplBase {
private GetVersionInfoResponse getVersionInfo(GetVersionInfoRequest request) {
final String version[] =
- CaosDBServer.getServerProperty(ServerProperties.KEY_PROJECT_VERSION).split("[\\.-]", 4);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_PROJECT_VERSION).split("[\\.-]", 4);
final Integer major = Integer.parseInt(version[0]);
final Integer minor = Integer.parseInt(version[1]);
final Integer patch = Integer.parseInt(version[2]);
final String pre_release = version.length > 3 ? version[3] : "";
- final String build = CaosDBServer.getServerProperty(ServerProperties.KEY_PROJECT_REVISTION);
+ final String build = LinkAheadServer.getServerProperty(ServerProperties.KEY_PROJECT_REVISTION);
final VersionInfo versionInfo =
VersionInfo.newBuilder()
@@ -110,8 +110,8 @@ public class GeneralInfoServiceImpl extends GeneralInfoServiceImplBase {
}
for (Permission p : authorizationInfo.getObjectPermissions()) {
- if (p instanceof CaosPermission) {
- permissions.addAll(((CaosPermission) p).getStringPermissions(subject));
+ if (p instanceof LinkAheadPermission) {
+ permissions.addAll(((LinkAheadPermission) p).getStringPermissions(subject));
} else {
permissions.add(p.toString());
}
diff --git a/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java b/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java
index 0430a795457152141473c2819997ebd1597028fd..09b3fc3c2bfd40f90892332ef56ee04f4bb2af0f 100644
--- a/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java
+++ b/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,7 +19,7 @@
*
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.util.ArrayList;
import java.util.Collection;
@@ -27,44 +27,44 @@ import java.util.LinkedList;
import java.util.List;
import java.util.UUID;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.api.entity.v1.AtomicDataType;
-import org.caosdb.api.entity.v1.CollectionValues;
-import org.caosdb.api.entity.v1.DataType;
-import org.caosdb.api.entity.v1.Entity;
-import org.caosdb.api.entity.v1.EntityACL;
-import org.caosdb.api.entity.v1.EntityPermission;
-import org.caosdb.api.entity.v1.EntityPermissionRule;
-import org.caosdb.api.entity.v1.EntityRole;
-import org.caosdb.api.entity.v1.FileDescriptor;
-import org.caosdb.api.entity.v1.Importance;
-import org.caosdb.api.entity.v1.ListDataType;
-import org.caosdb.api.entity.v1.Parent;
-import org.caosdb.api.entity.v1.ReferenceDataType;
-import org.caosdb.api.entity.v1.SpecialValue;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.BooleanValue;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.FileDatatype;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ListDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.MagicTypes;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.permissions.EntityACLFactory;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.api.entity.v1.AtomicDataType;
+import org.linkahead.api.entity.v1.CollectionValues;
+import org.linkahead.api.entity.v1.DataType;
+import org.linkahead.api.entity.v1.Entity;
+import org.linkahead.api.entity.v1.EntityACL;
+import org.linkahead.api.entity.v1.EntityPermission;
+import org.linkahead.api.entity.v1.EntityPermissionRule;
+import org.linkahead.api.entity.v1.EntityRole;
+import org.linkahead.api.entity.v1.FileDescriptor;
+import org.linkahead.api.entity.v1.Importance;
+import org.linkahead.api.entity.v1.ListDataType;
+import org.linkahead.api.entity.v1.Parent;
+import org.linkahead.api.entity.v1.ReferenceDataType;
+import org.linkahead.api.entity.v1.SpecialValue;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.BooleanValue;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.FileDatatype;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ListDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.MagicTypes;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.permissions.EntityACLFactory;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
-public class GrpcToCaosDBConverters {
+public class GrpcToLinkAheadConverters {
public EntityID getId(final String id) {
return new EntityID(Integer.parseInt(id));
@@ -133,7 +133,7 @@ public class GrpcToCaosDBConverters {
return entity;
}
- private Value convert(final org.caosdb.api.entity.v1.Value value) {
+ private Value convert(final org.linkahead.api.entity.v1.Value value) {
switch (value.getValueCase()) {
case LIST_VALUES:
return convertListValue(value.getListValues());
@@ -156,7 +156,7 @@ public class GrpcToCaosDBConverters {
return result;
}
- private Value convertScalarValue(final org.caosdb.api.entity.v1.ScalarValue value) {
+ private Value convertScalarValue(final org.linkahead.api.entity.v1.ScalarValue value) {
switch (value.getScalarValueCase()) {
case BOOLEAN_VALUE:
return BooleanValue.valueOf(value.getBooleanValue());
@@ -241,7 +241,7 @@ public class GrpcToCaosDBConverters {
}
private Collection<Property> convertProperties(
- final List<org.caosdb.api.entity.v1.Property> propertiesList,
+ final List<org.linkahead.api.entity.v1.Property> propertiesList,
final StatementStatus defaultImportance) {
final Collection<Property> result = new LinkedList<>();
propertiesList.forEach(
@@ -252,7 +252,7 @@ public class GrpcToCaosDBConverters {
}
private Property convert(
- final org.caosdb.api.entity.v1.Property e, final StatementStatus defaultImportance) {
+ final org.linkahead.api.entity.v1.Property e, final StatementStatus defaultImportance) {
final Property result = new Property(new RetrieveEntity());
try {
@@ -299,9 +299,9 @@ public class GrpcToCaosDBConverters {
}
}
- private Collection<org.caosdb.server.entity.wrapper.Parent> convertParents(
+ private Collection<org.linkahead.server.entity.wrapper.Parent> convertParents(
final List<Parent> parentsList) {
- final Collection<org.caosdb.server.entity.wrapper.Parent> result = new LinkedList<>();
+ final Collection<org.linkahead.server.entity.wrapper.Parent> result = new LinkedList<>();
parentsList.forEach(
e -> {
result.add(convert(e));
@@ -309,9 +309,9 @@ public class GrpcToCaosDBConverters {
return result;
}
- private org.caosdb.server.entity.wrapper.Parent convert(final Parent e) {
- final org.caosdb.server.entity.wrapper.Parent result =
- new org.caosdb.server.entity.wrapper.Parent(new RetrieveEntity());
+ private org.linkahead.server.entity.wrapper.Parent convert(final Parent e) {
+ final org.linkahead.server.entity.wrapper.Parent result =
+ new org.linkahead.server.entity.wrapper.Parent(new RetrieveEntity());
try {
result.setId(e.getId().isBlank() ? null : getId(e.getId()));
@@ -347,32 +347,32 @@ public class GrpcToCaosDBConverters {
}
}
- private org.caosdb.server.permissions.EntityACL convertAcl(EntityACL acl) {
+ private org.linkahead.server.permissions.EntityACL convertAcl(EntityACL acl) {
EntityACLFactory fac = new EntityACLFactory();
for (EntityPermissionRule rule : acl.getRulesList()) {
if (rule.getGrant()) {
fac.grant(
- org.caosdb.server.permissions.Role.create(rule.getRole()),
+ org.linkahead.server.permissions.Role.create(rule.getRole()),
rule.getPriority(),
convert(rule.getPermissionsList()));
} else {
fac.deny(
- org.caosdb.server.permissions.Role.create(rule.getRole()),
+ org.linkahead.server.permissions.Role.create(rule.getRole()),
rule.getPriority(),
convert(rule.getPermissionsList()));
}
}
- return fac.remove(org.caosdb.server.permissions.EntityACL.GLOBAL_PERMISSIONS).create();
+ return fac.remove(org.linkahead.server.permissions.EntityACL.GLOBAL_PERMISSIONS).create();
}
- private org.caosdb.server.permissions.EntityPermission[] convert(
+ private org.linkahead.server.permissions.EntityPermission[] convert(
List<EntityPermission> permissionsList) {
- ArrayList<org.caosdb.server.permissions.EntityPermission> result =
+ ArrayList<org.linkahead.server.permissions.EntityPermission> result =
new ArrayList<>(permissionsList.size());
permissionsList.forEach(
(p) -> {
- result.add(org.caosdb.server.permissions.EntityPermission.getEntityPermission(p));
+ result.add(org.linkahead.server.permissions.EntityPermission.getEntityPermission(p));
});
- return result.toArray(new org.caosdb.server.permissions.EntityPermission[0]);
+ return result.toArray(new org.linkahead.server.permissions.EntityPermission[0]);
}
}
diff --git a/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java b/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java
index 4e52485d4af4357b90a560baee6095c3b14683ae..a0efc8b7bee0c0bed38b8122c988ac677af26353 100644
--- a/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java
+++ b/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.Attributes.Key;
import io.grpc.Context;
@@ -9,8 +9,8 @@ import io.grpc.ServerCall.Listener;
import io.grpc.ServerCallHandler;
import io.grpc.ServerInterceptor;
import java.net.SocketAddress;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.restlet.routing.Template;
import org.restlet.util.Resolver;
import org.slf4j.Logger;
@@ -56,7 +56,8 @@ public class LoggingInterceptor implements ServerInterceptor {
private Template template;
public LoggingInterceptor() {
- String format = CaosDBServer.getServerProperty(ServerProperties.KEY_GRPC_RESPONSE_LOG_FORMAT);
+ String format =
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_GRPC_RESPONSE_LOG_FORMAT);
if ("OFF".equalsIgnoreCase(format)) {
this.template = null;
} else if (format != null) {
diff --git a/src/main/java/org/caosdb/server/grpc/UploadBuffer.java b/src/main/java/org/caosdb/server/grpc/UploadBuffer.java
index b341c33cbe9e0ca911c35aad144492cc2631da63..a3dbc07464793c132e780d719dda8f997c21247d 100644
--- a/src/main/java/org/caosdb/server/grpc/UploadBuffer.java
+++ b/src/main/java/org/caosdb/server/grpc/UploadBuffer.java
@@ -1,11 +1,11 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import com.google.protobuf.ByteString;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
-import org.caosdb.api.entity.v1.TransmissionStatus;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.api.entity.v1.TransmissionStatus;
+import org.linkahead.server.entity.FileProperties;
public class UploadBuffer {
diff --git a/src/main/java/org/caosdb/server/jobs/ContainerJob.java b/src/main/java/org/caosdb/server/jobs/ContainerJob.java
index 205b28f6338434fc9edf636aaca2ae82ddd8a896..e35828dc9290176a3a74e5c2b850b977db49f8b5 100644
--- a/src/main/java/org/caosdb/server/jobs/ContainerJob.java
+++ b/src/main/java/org/caosdb/server/jobs/ContainerJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.utils.EntityStatus;
public abstract class ContainerJob extends Job {
diff --git a/src/main/java/org/caosdb/server/jobs/EntityJob.java b/src/main/java/org/caosdb/server/jobs/EntityJob.java
index b0dd8ecc9b2eadf6342e29b7c1d82adce57fc767..18cf983ed761d271c5d594272ddb68aa3b6f17e5 100644
--- a/src/main/java/org/caosdb/server/jobs/EntityJob.java
+++ b/src/main/java/org/caosdb/server/jobs/EntityJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.entity.EntityInterface;
public abstract class EntityJob extends Job {
diff --git a/src/main/java/org/caosdb/server/jobs/FilesJob.java b/src/main/java/org/caosdb/server/jobs/FilesJob.java
index 43c89be9e8c6d35d124314050f332f7a43792496..05936afc41378ad616a5ee251f8015ca851a9089 100644
--- a/src/main/java/org/caosdb/server/jobs/FilesJob.java
+++ b/src/main/java/org/caosdb/server/jobs/FilesJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.server.entity.FileProperties;
public abstract class FilesJob extends EntityJob {
diff --git a/src/main/java/org/caosdb/server/jobs/FlagJob.java b/src/main/java/org/caosdb/server/jobs/FlagJob.java
index 5c039bb3601e078d6f5ebcb3a48d4c35b6c90229..f10de84448b6112475ec22213e30c1fc222170eb 100644
--- a/src/main/java/org/caosdb/server/jobs/FlagJob.java
+++ b/src/main/java/org/caosdb/server/jobs/FlagJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
public abstract class FlagJob extends ContainerJob {
diff --git a/src/main/java/org/caosdb/server/jobs/Job.java b/src/main/java/org/caosdb/server/jobs/Job.java
index 9da74edd0db86f6d81a8636020afcdaf3faa9e09..5ddcd4b45fe889875b8862a610e4bb789f13d031 100644
--- a/src/main/java/org/caosdb/server/jobs/Job.java
+++ b/src/main/java/org/caosdb/server/jobs/Job.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
@@ -29,28 +29,28 @@ import java.util.List;
import java.util.Objects;
import java.util.Set;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.transaction.GetIDByName;
-import org.caosdb.server.database.backend.transaction.IsSubType;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.database.backend.transaction.RetrieveParents;
-import org.caosdb.server.database.backend.transaction.RetrieveSparseEntity;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.container.ParentContainer;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.jobs.core.JobFailureSeverity;
-import org.caosdb.server.transaction.Transaction;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.transaction.GetIDByName;
+import org.linkahead.server.database.backend.transaction.IsSubType;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.database.backend.transaction.RetrieveParents;
+import org.linkahead.server.database.backend.transaction.RetrieveSparseEntity;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.container.ParentContainer;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.jobs.core.JobFailureSeverity;
+import org.linkahead.server.transaction.Transaction;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
import org.reflections.Reflections;
/**
@@ -104,7 +104,7 @@ public abstract class Job {
| InvocationTargetException
| NoSuchMethodException
| SecurityException e) {
- throw new CaosDBException(e);
+ throw new LinkAheadException(e);
}
}
@@ -335,7 +335,7 @@ public abstract class Job {
if (allClasses == null || loadAlways == null) {
allClasses = new HashMap<>();
loadAlways = new ArrayList<>();
- Reflections jobPackage = new Reflections("org.caosdb.server.jobs.core");
+ Reflections jobPackage = new Reflections("org.linkahead.server.jobs.core");
Set<Class<? extends Job>> allClassesSet = jobPackage.getSubTypesOf(Job.class);
allClassesSet.addAll(jobPackage.getSubTypesOf(FlagJob.class));
for (final Class<? extends Job> c : allClassesSet) {
@@ -351,7 +351,7 @@ public abstract class Job {
}
}
// TODO merge these two parts of this function. Its the same!
- jobPackage = new Reflections("org.caosdb.server.jobs.extension");
+ jobPackage = new Reflections("org.linkahead.server.jobs.extension");
allClassesSet = jobPackage.getSubTypesOf(Job.class);
for (final Class<? extends Job> c : allClassesSet) {
allClasses.put(c.getSimpleName().toLowerCase(), c);
diff --git a/src/main/java/org/caosdb/server/jobs/JobAnnotation.java b/src/main/java/org/caosdb/server/jobs/JobAnnotation.java
index bebebd75ed386c19f8abfb7c09e802dda5ec2941..19dd0337a2cc2e82ecb83c0d72150b586c54f5cc 100644
--- a/src/main/java/org/caosdb/server/jobs/JobAnnotation.java
+++ b/src/main/java/org/caosdb/server/jobs/JobAnnotation.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
-import org.caosdb.server.transaction.TransactionInterface;
+import org.linkahead.server.transaction.TransactionInterface;
/**
* Jobs may be annotated with @JobAnnotation(...).
*
* <p>Without a JobAnnotation, the Job will run at the default {@link
- * org.caosdb.server.transaction.Transaction#check() CHECK} stage.
+ * org.linkahead.server.transaction.Transaction#check() CHECK} stage.
*
* @see {@link TransactionStage}
*/
diff --git a/src/main/java/org/caosdb/server/jobs/JobConfig.java b/src/main/java/org/caosdb/server/jobs/JobConfig.java
index 40917b36714ee95ef491a266580068a06f51703a..6b6db3eb894deb1da0b1ffc599d65a310595919e 100644
--- a/src/main/java/org/caosdb/server/jobs/JobConfig.java
+++ b/src/main/java/org/caosdb/server/jobs/JobConfig.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,7 +18,7 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import java.io.BufferedReader;
import java.io.File;
@@ -30,16 +30,16 @@ import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.core.JobFailureSeverity;
-import org.caosdb.server.transaction.Transaction;
-import org.caosdb.server.utils.ConfigurationException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.core.JobFailureSeverity;
+import org.linkahead.server.transaction.Transaction;
+import org.linkahead.server.utils.ConfigurationException;
/**
* Configuration of the jobs which have to run during all entity transactions with "job rules".
@@ -68,7 +68,7 @@ public class JobConfig {
instance = new JobConfig();
} catch (final Exception e) {
e.printStackTrace();
- // CaosDB Server cannot work without a proper job configuration.
+ // LinkAhead Server cannot work without a proper job configuration.
System.exit(1);
}
}
@@ -80,7 +80,7 @@ public class JobConfig {
private final Map<String, List<Object[]>> rules;
public JobConfig() throws FileNotFoundException, IOException {
- this(new File(CaosDBServer.getServerProperty(ServerProperties.KEY_JOB_RULES_CONFIG)));
+ this(new File(LinkAheadServer.getServerProperty(ServerProperties.KEY_JOB_RULES_CONFIG)));
}
public JobConfig(final File config) throws FileNotFoundException, IOException {
diff --git a/src/main/java/org/caosdb/server/jobs/JobTarget.java b/src/main/java/org/caosdb/server/jobs/JobTarget.java
index 27aa0d9184575d87283989f18f144683668c4b45..c9e1754af2d3c20d3344f818323c82f942561d82 100644
--- a/src/main/java/org/caosdb/server/jobs/JobTarget.java
+++ b/src/main/java/org/caosdb/server/jobs/JobTarget.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.entity.Message;
public interface JobTarget {
diff --git a/src/main/java/org/caosdb/server/jobs/Schedule.java b/src/main/java/org/caosdb/server/jobs/Schedule.java
index 57474da515418745ed0457962596dfce233bff48..dd8dccc92213b40b2193897fbb85481aa7401dcb 100644
--- a/src/main/java/org/caosdb/server/jobs/Schedule.java
+++ b/src/main/java/org/caosdb/server/jobs/Schedule.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import java.util.ArrayList;
import java.util.Collection;
@@ -27,7 +27,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.CopyOnWriteArrayList;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.entity.EntityInterface;
/**
* Keeps track of Jobs.
diff --git a/src/main/java/org/caosdb/server/jobs/ScheduledJob.java b/src/main/java/org/caosdb/server/jobs/ScheduledJob.java
index 2122b34de5f0b60db4c2b6d4c1c2358d3df02851..40ad96ad9221ad9de1def6e276496808ee50f2df 100644
--- a/src/main/java/org/caosdb/server/jobs/ScheduledJob.java
+++ b/src/main/java/org/caosdb/server/jobs/ScheduledJob.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,9 +18,9 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.entity.Message;
/**
* ScheduledJob is a wrapper class for jobs held by the Scheduler.
diff --git a/src/main/java/org/caosdb/server/jobs/TransactionStage.java b/src/main/java/org/caosdb/server/jobs/TransactionStage.java
index 9e15b4e556269def79d58e532bbe3c9e6cbb9bbd..edf6233cffde599b1434aca890e7d6e384a84831 100644
--- a/src/main/java/org/caosdb/server/jobs/TransactionStage.java
+++ b/src/main/java/org/caosdb/server/jobs/TransactionStage.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,11 +19,11 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.jobs.core.Strict;
-import org.caosdb.server.transaction.Transaction;
-import org.caosdb.server.utils.UndoHandler;
+import org.linkahead.server.jobs.core.Strict;
+import org.linkahead.server.transaction.Transaction;
+import org.linkahead.server.utils.UndoHandler;
/**
* Any {@link Transaction} of an Entity consists of sequence of stages. Jobs which have a {@link
diff --git a/src/main/java/org/caosdb/server/jobs/core/AccessControl.java b/src/main/java/org/caosdb/server/jobs/core/AccessControl.java
index ede7658580811671f19f955f36faa59db4df922f..a3ea105054c38bd3b1ace0caf5d4c875f7fe322c 100644
--- a/src/main/java/org/caosdb/server/jobs/core/AccessControl.java
+++ b/src/main/java/org/caosdb/server/jobs/core/AccessControl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,22 +19,22 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Checks the TRANSACTION:* permissions before a transaction begins.
diff --git a/src/main/java/org/caosdb/server/jobs/core/Atomic.java b/src/main/java/org/caosdb/server/jobs/core/Atomic.java
index 8639615ee6ac4ddd648a19d15262a1c526ef10c6..df79df64f03ff49b0439d2417575d3f99fe68529 100644
--- a/src/main/java/org/caosdb/server/jobs/core/Atomic.java
+++ b/src/main/java/org/caosdb/server/jobs/core/Atomic.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(
stage = TransactionStage.PRE_TRANSACTION,
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckChildDependencyExistent.java b/src/main/java/org/caosdb/server/jobs/core/CheckChildDependencyExistent.java
index d60db5a3ea2f58caefe240894920318e01efc8a6..32e7179cbdae452aa1bb01db1dbef904dfc1ad03 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckChildDependencyExistent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckChildDependencyExistent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
import java.util.Objects;
-import org.caosdb.server.database.backend.transaction.GetChildren;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.backend.transaction.GetChildren;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether any children of this entity do exist. There must not be any children left when an
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
index 40e01d2636509774555f1514c75bb0bf16870539..3d4a245238cd617daac2eceb14b8e6ef752f427a 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,25 +20,25 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.ScheduledJob;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.ScheduledJob;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether the entity has a data type. Assign the data type of the abstract property if
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckDescPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckDescPresent.java
index e430a0817e9083013330bc4d59d8f7377d10d62a..352b75ac48264d826585b53ca6faa07f7fe1f856 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckDescPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckDescPresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether an entity has a description.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckEntityACLRoles.java b/src/main/java/org/caosdb/server/jobs/core/CheckEntityACLRoles.java
index 037b38b90c94827265d47876e722686d5d030cc0..d75f0f560b23cf61cb9ba10c84515da47f2713d2 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckEntityACLRoles.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckEntityACLRoles.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.permissions.EntityACI;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.permissions.EntityACI;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class CheckEntityACLRoles extends ContainerJob {
@@ -42,7 +42,7 @@ public class CheckEntityACLRoles extends ContainerJob {
&& entity.getEntityACL() != null) {
for (final EntityACI aci : entity.getEntityACL().getRules()) {
if (!AuthenticationUtils.isResponsibleAgentExistent(aci.getResponsibleAgent())) {
- if (CaosDBServer.getServerProperty(ServerProperties.KEY_CHECK_ENTITY_ACL_ROLES_MODE)
+ if (LinkAheadServer.getServerProperty(ServerProperties.KEY_CHECK_ENTITY_ACL_ROLES_MODE)
.equalsIgnoreCase("MUST")) {
entity.addError(ServerMessages.ROLE_DOES_NOT_EXIST);
entity.setEntityStatus(EntityStatus.UNQUALIFIED);
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java b/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java
index e425649bb1bc43a9745120ed078c653f55af2e38..01ab9e2ffccfd881b1bb2414e0b5329abe53d658 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.io.File;
import java.io.FileNotFoundException;
@@ -28,22 +28,22 @@ import java.io.IOException;
import java.io.PrintStream;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.transaction.FileStorageConsistencyCheck;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.transaction.Transaction;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.Undoable;
import org.jdom2.Document;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.transaction.FileStorageConsistencyCheck;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.transaction.Transaction;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.Undoable;
@JobAnnotation(
flag = "fileStorageConsistency",
@@ -55,7 +55,7 @@ import org.jdom2.output.XMLOutputter;
+ " - a test case which can be run if the server is in debug mode (prefixed\n"
+ " -c)\n"
+ " - a filesystem location whose children are checked recursively,\n"
- + " relative to the caosroot dilesystem location.\n")
+ + " relative to the linkaheadroot file system location.\n")
public class CheckFileStorageConsistency extends FlagJob {
public static final Pattern parseArgs =
@@ -81,7 +81,7 @@ public class CheckFileStorageConsistency extends FlagJob {
} catch (final NumberFormatException e) {
}
}
- if (matcher.group(2) != null && CaosDBServer.isDebugMode()) {
+ if (matcher.group(2) != null && LinkAheadServer.isDebugMode()) {
// group two is TestCase (-c$testcase)
try {
test(TestCase.valueOf(matcher.group(2)));
@@ -208,7 +208,7 @@ public class CheckFileStorageConsistency extends FlagJob {
+ "test_file_storage_consistecy"
+ Integer.toString(hashCode()));
- final Undoable undo2 = org.caosdb.server.utils.FileUtils.rename(f2, tmp2);
+ final Undoable undo2 = org.linkahead.server.utils.FileUtils.rename(f2, tmp2);
final File overridden = new File(oldPath2);
overridden.createNewFile();
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckNamePresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckNamePresent.java
index 3166057c95671273efe27357ce11b2ffe10e2c78..600841947ae18537a85e54ec7d7c8dbd32a6c3cc 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckNamePresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckNamePresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether an entity has a name.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java
index fb6919649242a906b36526e3725fc25e710c9d60..3cd840c59f4ac6d821b8c7425de824f22be3dd6d 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java
@@ -1,14 +1,14 @@
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.HashSet;
import java.util.Objects;
import java.util.Set;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(
flag = "noAdditionalProperties",
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckNoOverridesPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckNoOverridesPresent.java
index d6cae3ee40222d3b3d6eb89e1b2d0c8bce1da0e5..d7967f38a218444d3b3275d8ced5987a4a44f0e9 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckNoOverridesPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckNoOverridesPresent.java
@@ -1,10 +1,10 @@
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(
flag = "noOverrides",
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
index e6ba9da430e6218e5c40fba968c309ed94152bf6..46ea9ee71e01179d2fe817402d30d217b6cb7331 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,17 +19,17 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether an entity implements all obligatory properties of all parents.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckParPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckParPresent.java
index 058710c6bbbf5c2bbd3f95f7ae70a243d3bfcd20..7bd122079320259bd40c3ade5c09a2e1070072aa 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckParPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckParPresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether an entity has at least one parent.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
index 8895ae9adb4d12da2f7789a8798ca0fb9d183c05..64affc9bcbbb3f0304777309f9a8aeba084216ea 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,24 +20,24 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import com.google.common.base.Objects;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.entity.Affiliation;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.entity.Affiliation;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether all parents of an entity are valid/qualified.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckPropPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckPropPresent.java
index cc23d980152c44cfdbf88500e9041044a0418034..e7a810890ad122f1c539376be9c4566e9780a05b 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckPropPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckPropPresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether at least one property is present.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java
index 23a92340f5befbfbe7ded2fe95d3244b5ff78594..835fb1b7ed32b45a4ac4936b316be2cb1d2ac65e 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,23 +20,23 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import static org.caosdb.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST;
+import static org.linkahead.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST;
import com.google.common.base.Objects;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether all properties of an entity are valid or qualified.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckQueryTemplate.java b/src/main/java/org/caosdb/server/jobs/core/CheckQueryTemplate.java
index 42dccf552d69bbba6bee2ab909eaf31b5159041f..9d7579ccb4962e06117dd030d9583b94e1383ded 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckQueryTemplate.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckQueryTemplate.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.ParsingException;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.ParsingException;
+import org.linkahead.server.utils.ServerMessages;
public class CheckQueryTemplate extends EntityJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckReferenceDependencyExistent.java b/src/main/java/org/caosdb/server/jobs/core/CheckReferenceDependencyExistent.java
index 2edbc5a270db93312c73b8c960c615a161e8907b..ff72e207e89ef98656b3d698e2b9b21e5b567623 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckReferenceDependencyExistent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckReferenceDependencyExistent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
import java.util.Objects;
-import org.caosdb.server.database.backend.transaction.GetDependentEntities;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.backend.transaction.GetDependentEntities;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether an entity is referenced by other entities. In the event that someone wants to
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java b/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
index 0b8ba45b1cae19812641ed733be7aacc2fb78575..f2f556df5f2a1da17cec0ee36d58b56f6f7a231a 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,25 +20,25 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.FileDatatype;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.FileDatatype;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check if the referenced entity is in the scope of the data type. E.g. if the data type is
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckRefidPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckRefidPresent.java
index 17d9bc7c9fbbfd37d64446a8b21ff65afca9391d..346290ee9576b555d022188e86f6c45240d07643 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckRefidPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckRefidPresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.EntityJob;
+import org.linkahead.server.jobs.EntityJob;
public class CheckRefidPresent extends EntityJob {
@Override
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
index 12b545b8e6fd608e20851d37f34e809acfcd1544..fdba66431ebc1bf4040a99b520d77a058d882e71 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,23 +22,23 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether a reference property is pointing to a valid entity.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckStateTransition.java b/src/main/java/org/caosdb/server/jobs/core/CheckStateTransition.java
index a43face9ae14f3fac57890ccb8617e5637c95c16..381dd72d2f4e458b5329f911e0758a1d2c3e20a0 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckStateTransition.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckStateTransition.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,19 +18,19 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.Map;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check if the attempted state transition is allowed.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java
index 28b914e61d33847e7beb46881c0dac4d9b17f9f0..e13007b987fe69e74885468ef2f89a255f01d39a 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether the target path of a file entity is valid. That is, the target path is in the file
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java
index 85eb3259dcc17cfdfd2a03aeb3d3360fb04f3908..19195c475dbb61fe7774a4ed965552ff13a5f3c3 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.MagicTypes;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.MagicTypes;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether this entity has a unit property.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckValueParsable.java b/src/main/java/org/caosdb/server/jobs/core/CheckValueParsable.java
index 1dd457143f8cc23c0136f2c51cb40edf8552ba15..b1af70a433e6bf850433864345587f3bd3c23fe1 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckValueParsable.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckValueParsable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
/**
* Check whether the value of an entity is parsable according to the entity's data type. This job
diff --git a/src/main/java/org/caosdb/server/jobs/core/DebugCalls.java b/src/main/java/org/caosdb/server/jobs/core/DebugCalls.java
index 8e0ae7435693ba1010f023da6c585911825f5a5e..e38226084adeb4b44400320609326cadd1ae2787 100644
--- a/src/main/java/org/caosdb/server/jobs/core/DebugCalls.java
+++ b/src/main/java/org/caosdb/server/jobs/core/DebugCalls.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
@JobAnnotation(
flag = "debug",
@@ -40,7 +40,7 @@ public class DebugCalls extends FlagJob {
@Override
protected void job(final String value) {
- if (CaosDBServer.isDebugMode()) {
+ if (LinkAheadServer.isDebugMode()) {
if (value != null) {
if (value.equalsIgnoreCase(ex_null_p)) {
throw new NullPointerException();
diff --git a/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java b/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java
index a4c50f8893935d7bbd6091b970b32a8811a08d93..4dc817c7cefa06c4da24deea3b87992d9406b263 100644
--- a/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java
+++ b/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,7 +18,7 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.ArrayList;
import java.util.HashMap;
@@ -33,31 +33,31 @@ import java.util.Map.Entry;
import java.util.Objects;
import java.util.Set;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.TextDatatype;
-import org.caosdb.server.entity.ClientMessage;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.permissions.EntityACI;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.utils.EntityStatus;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.datatype.TextDatatype;
+import org.linkahead.server.entity.ClientMessage;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.permissions.EntityACI;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.utils.EntityStatus;
/**
* The EntityStateJob is the abstract base class for four EntityJobs:
@@ -338,7 +338,7 @@ public abstract class EntityStateJob extends EntityJob {
final int end = aci.getResponsibleAgent().toString().length() - 1;
final String role = aci.getResponsibleAgent().toString().substring(7, end);
rules.add(
- new EntityACI(org.caosdb.server.permissions.Role.create(role), aci.getBitSet()));
+ new EntityACI(org.linkahead.server.permissions.Role.create(role), aci.getBitSet()));
}
}
return new EntityACL(rules);
diff --git a/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java b/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java
index 2d7a45d099fa5bec35586b58257eb2c71d61cbe0..ce0ca985f9b0b9a76f2e933eb163f1b765bcc443 100644
--- a/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java
+++ b/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.ParsingException;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.ParsingException;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(flag = "query", stage = TransactionStage.INIT, transaction = Retrieve.class)
public class ExecuteQuery extends FlagJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/History.java b/src/main/java/org/caosdb/server/jobs/core/History.java
index c1215db5c9e99b0dbdf43a3dc5ce8bf54bfbeb19..16872e4918e8b68f2a2b412b3fb8c9854c9fcf27 100644
--- a/src/main/java/org/caosdb/server/jobs/core/History.java
+++ b/src/main/java/org/caosdb/server/jobs/core/History.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.backend.transaction.RetrieveVersionHistory;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.backend.transaction.RetrieveVersionHistory;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Retrieves the complete version history of each entity and appends it to the entity.
diff --git a/src/main/java/org/caosdb/server/jobs/core/InheritInitialState.java b/src/main/java/org/caosdb/server/jobs/core/InheritInitialState.java
index b905bfa0fcbf98f107506d1fb1e7d2142b3b8657..353bae3fda917d4ea379d685f68a5e89f6d25b94 100644
--- a/src/main/java/org/caosdb/server/jobs/core/InheritInitialState.java
+++ b/src/main/java/org/caosdb/server/jobs/core/InheritInitialState.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,15 +17,15 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.utils.EntityStatus;
@JobAnnotation(stage = TransactionStage.CHECK)
public class InheritInitialState extends EntityStateJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/Inheritance.java b/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
index a1bd800c7ca40b28d7b9ff27dd8f828ed112891f..35e94ad2048a31e660f3ded114e46405fcff851d 100644
--- a/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
+++ b/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,23 +22,23 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.ScheduledJob;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.ScheduledJob;
+import org.linkahead.server.utils.EntityStatus;
/**
* Add all those properties from the parent to the child which have the same importance (or higher).
diff --git a/src/main/java/org/caosdb/server/jobs/core/InitEntityStateJobs.java b/src/main/java/org/caosdb/server/jobs/core/InitEntityStateJobs.java
index 5cd6d67aa7eca6a231eecf627606f272ac0f0775..f687b1b185e38a066206c4e82aa40a51ac425abb 100644
--- a/src/main/java/org/caosdb/server/jobs/core/InitEntityStateJobs.java
+++ b/src/main/java/org/caosdb/server/jobs/core/InitEntityStateJobs.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,29 +17,29 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.entity.ClientMessage;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.WritableEntity;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.entity.ClientMessage;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.WritableEntity;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
/**
* Initialize the other entity jobs by converting the client message with type "State" or
@@ -59,7 +59,7 @@ public class InitEntityStateJobs extends EntityStateJob implements Observer {
@Override
protected void run() {
- if ("ENABLED".equals(CaosDBServer.getServerProperty(SERVER_PROPERTY_EXT_ENTITY_STATE))) {
+ if ("ENABLED".equals(LinkAheadServer.getServerProperty(SERVER_PROPERTY_EXT_ENTITY_STATE))) {
State newState = handleNewState();
State oldState = handleOldState(newState);
if (newState != null || oldState != null) {
diff --git a/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java b/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java
index 6390ad7cf6da2483a1589432b2c82ba7dfd1dfae..13dd3466037ea3623d5338ca65e5812997bb4bb6 100644
--- a/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java
+++ b/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.io.File;
import java.io.IOException;
@@ -30,30 +30,30 @@ import java.util.LinkedList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.RollBackHandler;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.transaction.WriteTransactionInterface;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.Undoable;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.RollBackHandler;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.transaction.WriteTransactionInterface;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.Undoable;
+import org.linkahead.server.utils.Utils;
@JobAnnotation(
flag = "InsertFilesInDir",
@@ -80,7 +80,7 @@ public class InsertFilesInDir extends FlagJob {
private static LinkedList<File> getAllowedFolders() {
final String[] dirs =
- CaosDBServer.getServerProperty(ServerProperties.KEY_INSERT_FILES_IN_DIR_ALLOWED_DIRS)
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_INSERT_FILES_IN_DIR_ALLOWED_DIRS)
.split("\\s*,?\\s*");
final LinkedList<File> ret = new LinkedList<File>();
for (final String dir : dirs) {
@@ -174,7 +174,7 @@ public class InsertFilesInDir extends FlagJob {
try {
final Undoable delete = FileUtils.delete(InsertFilesInDir.this.tmp, true);
delete.cleanUp();
- } catch (final IOException | CaosDBException | InterruptedException e) {
+ } catch (final IOException | LinkAheadException | InterruptedException e) {
e.printStackTrace();
}
}
@@ -184,7 +184,7 @@ public class InsertFilesInDir extends FlagJob {
try {
final Undoable delete = FileUtils.delete(InsertFilesInDir.this.tmp, true);
delete.cleanUp();
- } catch (final IOException | CaosDBException | InterruptedException e) {
+ } catch (final IOException | LinkAheadException | InterruptedException e) {
e.printStackTrace();
}
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/JobFailureSeverity.java b/src/main/java/org/caosdb/server/jobs/core/JobFailureSeverity.java
index e95bef34b7b9bea8e1b2b2126da196c1c7c53c12..843c0fae11e09074aa303db5395aba07f9c9db70 100644
--- a/src/main/java/org/caosdb/server/jobs/core/JobFailureSeverity.java
+++ b/src/main/java/org/caosdb/server/jobs/core/JobFailureSeverity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
/**
* Describes the severity of a failure of a job (esp. consitency checks).
diff --git a/src/main/java/org/caosdb/server/jobs/core/LoadContainerFlagJobs.java b/src/main/java/org/caosdb/server/jobs/core/LoadContainerFlagJobs.java
index a07862c0a8ced52a8caa1af2e845497eb64badd7..417281d7993b15466e7896f7a2b440fea88aabe4 100644
--- a/src/main/java/org/caosdb/server/jobs/core/LoadContainerFlagJobs.java
+++ b/src/main/java/org/caosdb/server/jobs/core/LoadContainerFlagJobs.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.Map.Entry;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
@JobAnnotation(stage = TransactionStage.INIT)
public class LoadContainerFlagJobs extends ContainerJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/MakeStateMessage.java b/src/main/java/org/caosdb/server/jobs/core/MakeStateMessage.java
index d497a2ab5d955f0d6db0205b360a1a56ef90a4b7..a50937174ed7bcc18d564dab91371121fcc33ae7 100644
--- a/src/main/java/org/caosdb/server/jobs/core/MakeStateMessage.java
+++ b/src/main/java/org/caosdb/server/jobs/core/MakeStateMessage.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,18 +17,18 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
import java.util.Map;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.Retrieve;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.Retrieve;
/**
* Remove the state property from the entity and, iff necessary, convert it into a State instance
@@ -50,7 +50,7 @@ public class MakeStateMessage extends EntityStateJob {
@Override
protected void run() {
- if ("ENABLED".equals(CaosDBServer.getServerProperty(SERVER_PROPERTY_EXT_ENTITY_STATE))) {
+ if ("ENABLED".equals(LinkAheadServer.getServerProperty(SERVER_PROPERTY_EXT_ENTITY_STATE))) {
try {
// fetch all state properties and remove them from the entity (indicated by "true")
List<Property> stateProperties = getStateProperties(true);
diff --git a/src/main/java/org/caosdb/server/jobs/core/MakeStateProperty.java b/src/main/java/org/caosdb/server/jobs/core/MakeStateProperty.java
index c2aebc681b38a9902bede69883cce4025bc8afe6..0b0a8f54d08450aa76f6071933ccf5f2ae7af9e6 100644
--- a/src/main/java/org/caosdb/server/jobs/core/MakeStateProperty.java
+++ b/src/main/java/org/caosdb/server/jobs/core/MakeStateProperty.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -21,12 +21,12 @@
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.WriteTransaction;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.WriteTransaction;
/**
* This job constructs an ordinary Property from the State right before the entity is being written
diff --git a/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java b/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java
index 249fc0b17ebe908a9a7ab9d13bfdb00d869ec630..0866e661cb2846cce510d0c505790fd0cc2574df 100644
--- a/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java
+++ b/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.jobs.FilesJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.jobs.FilesJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.ServerMessages;
/**
* Match the checksum and the size of a file record to the uploaded file's checksum and size.
diff --git a/src/main/java/org/caosdb/server/jobs/core/NoCache.java b/src/main/java/org/caosdb/server/jobs/core/NoCache.java
index e408330ee2639d1c5d7dc5f145848e292daa9b3b..e22f3df614c29a2b31b5dd7dce26d94f83ad6366 100644
--- a/src/main/java/org/caosdb/server/jobs/core/NoCache.java
+++ b/src/main/java/org/caosdb/server/jobs/core/NoCache.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
@JobAnnotation(
flag = "cache",
diff --git a/src/main/java/org/caosdb/server/jobs/core/Paging.java b/src/main/java/org/caosdb/server/jobs/core/Paging.java
index aa918ecfe2ac20b90b019b5ace91bde05ccac9ef..b390cf32f5700a4cbab637de834027f8ffe0697e 100644
--- a/src/main/java/org/caosdb/server/jobs/core/Paging.java
+++ b/src/main/java/org/caosdb/server/jobs/core/Paging.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
@JobAnnotation(flag = "P", stage = TransactionStage.INIT, transaction = Retrieve.class)
public class Paging extends FlagJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/ParseUnit.java b/src/main/java/org/caosdb/server/jobs/core/ParseUnit.java
index 8e0a7818ea3c7567456115dafe5b3b2593f7511b..57b78ef72f3b14ca6fd80ee7cde6e3a0e21ce097 100644
--- a/src/main/java/org/caosdb/server/jobs/core/ParseUnit.java
+++ b/src/main/java/org/caosdb/server/jobs/core/ParseUnit.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import de.timmfitschen.easyunits.parser.ParserException;
-import org.caosdb.server.datatype.SingleValue;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.MagicTypes;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.unit.CaosDBSystemOfUnits;
-import org.caosdb.unit.Unit;
-import org.caosdb.unit.UnknownUnit;
+import org.linkahead.server.datatype.SingleValue;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.MagicTypes;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.unit.LinkAheadSystemOfUnits;
+import org.linkahead.unit.Unit;
+import org.linkahead.unit.UnknownUnit;
public class ParseUnit extends EntityJob {
@@ -43,7 +43,7 @@ public class ParseUnit extends EntityJob {
try {
Unit unit;
- unit = CaosDBSystemOfUnits.getUnit(unitStr);
+ unit = LinkAheadSystemOfUnits.getUnit(unitStr);
if (unit instanceof UnknownUnit) {
getEntity().addWarning(ServerMessages.UNKNOWN_UNIT);
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/PickUp.java b/src/main/java/org/caosdb/server/jobs/core/PickUp.java
index b0e04529fa059be33b5af99c47286a3d2a469cdb..deba4b92dd6d1e811efda5ee309450c539e721fd 100644
--- a/src/main/java/org/caosdb/server/jobs/core/PickUp.java
+++ b/src/main/java/org/caosdb/server/jobs/core/PickUp.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.io.File;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
@JobAnnotation(stage = TransactionStage.INIT)
public class PickUp extends EntityJob implements Observer {
diff --git a/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java b/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java
index 7196f04edc99cf1269603e820975a96703639965..085562b5d3e18a1539da60a84a0684adaf1331d7 100644
--- a/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java
+++ b/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,25 +20,25 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import static org.caosdb.server.entity.MagicTypes.NAME;
+import static org.linkahead.server.entity.MagicTypes.NAME;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* To be called after CheckPropValid and Inheritance.
diff --git a/src/main/java/org/caosdb/server/jobs/core/RemoveDuplicates.java b/src/main/java/org/caosdb/server/jobs/core/RemoveDuplicates.java
index 3d3adcc1e1175d7aed95bba64d9d81d13b70f495..92e57e1921cdb4d0837aa5adf1d608c30a6b2313 100644
--- a/src/main/java/org/caosdb/server/jobs/core/RemoveDuplicates.java
+++ b/src/main/java/org/caosdb/server/jobs/core/RemoveDuplicates.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.HashSet;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.ContainerJob;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.ContainerJob;
public class RemoveDuplicates extends ContainerJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java b/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java
index 5ab722c7176e89485e2bd40dfd515a77bc09e38b..79ecf3412bc11eba4ce747c9d089ef9076f38eca 100644
--- a/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java
+++ b/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.database.backend.transaction.GetIDByName;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.backend.transaction.GetIDByName;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class ResolveNames extends ContainerJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/RetrieveACL.java b/src/main/java/org/caosdb/server/jobs/core/RetrieveACL.java
index 0f25071818ff7de041016942e51705a66c9b7cb5..69021f5ffa300cdca9a3fcf26f31b3d91725ca23 100644
--- a/src/main/java/org/caosdb/server/jobs/core/RetrieveACL.java
+++ b/src/main/java/org/caosdb/server/jobs/core/RetrieveACL.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(
stage = TransactionStage.POST_TRANSACTION,
diff --git a/src/main/java/org/caosdb/server/jobs/core/RetrieveAllJob.java b/src/main/java/org/caosdb/server/jobs/core/RetrieveAllJob.java
index a89385e29f458ad3ad15eea0d9e6b6bf7640bca6..8112dcda3e7a8cf290d7ba51e9266100ead23997 100644
--- a/src/main/java/org/caosdb/server/jobs/core/RetrieveAllJob.java
+++ b/src/main/java/org/caosdb/server/jobs/core/RetrieveAllJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.database.backend.transaction.RetrieveAll;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.backend.transaction.RetrieveAll;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
@JobAnnotation(flag = "all", stage = TransactionStage.INIT, transaction = Retrieve.class)
public class RetrieveAllJob extends FlagJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/RetrieveOwner.java b/src/main/java/org/caosdb/server/jobs/core/RetrieveOwner.java
index fa094b28ba9a6ed1387710a751be160fa6f53d47..1712e17f3eaf921fb5ac30065e56eee16f555fac 100644
--- a/src/main/java/org/caosdb/server/jobs/core/RetrieveOwner.java
+++ b/src/main/java/org/caosdb/server/jobs/core/RetrieveOwner.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.permissions.ResponsibleAgent;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.permissions.ResponsibleAgent;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(
stage = TransactionStage.POST_TRANSACTION,
diff --git a/src/main/java/org/caosdb/server/jobs/core/RetriveAllNames.java b/src/main/java/org/caosdb/server/jobs/core/RetriveAllNames.java
index b5787246cbafba0df31056d2da15adb330ef0c50..ef15f9cf0ec17896e659a2f751e292c63efc814a 100644
--- a/src/main/java/org/caosdb/server/jobs/core/RetriveAllNames.java
+++ b/src/main/java/org/caosdb/server/jobs/core/RetriveAllNames.java
@@ -1,12 +1,12 @@
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.database.backend.transaction.GetAllNames;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.backend.transaction.GetAllNames;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
/**
* A jobs which retrieves all known names for which the requesting user has the RETRIEVE_ENTITY
diff --git a/src/main/java/org/caosdb/server/jobs/core/SetImpToFix.java b/src/main/java/org/caosdb/server/jobs/core/SetImpToFix.java
index f0047d02f861ef26cbad12b4e6a5963d51415eec..e6624a78179f674fc1ef6b6b1e003c7ddd3c7339 100644
--- a/src/main/java/org/caosdb/server/jobs/core/SetImpToFix.java
+++ b/src/main/java/org/caosdb/server/jobs/core/SetImpToFix.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.jobs.EntityJob;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.jobs.EntityJob;
/**
* Set the statement status of all properties of an entity to the value "FIX".
diff --git a/src/main/java/org/caosdb/server/jobs/core/SetImpToRecByDefault.java b/src/main/java/org/caosdb/server/jobs/core/SetImpToRecByDefault.java
index dd6cfc0820d9cd15281897a200f82d2c7d9d02bb..93d551b57825a01207ba9427c443232dd7e1b87f 100644
--- a/src/main/java/org/caosdb/server/jobs/core/SetImpToRecByDefault.java
+++ b/src/main/java/org/caosdb/server/jobs/core/SetImpToRecByDefault.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.jobs.EntityJob;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.jobs.EntityJob;
/**
* Set the statement status of all properties of an entity which do not have a statement status to
diff --git a/src/main/java/org/caosdb/server/jobs/core/Strict.java b/src/main/java/org/caosdb/server/jobs/core/Strict.java
index bb69063c116e5c14aa9fad2b0bbf881d2481b394..ccf2b50ade581622683ab6c29715abc2ffb2b042 100644
--- a/src/main/java/org/caosdb/server/jobs/core/Strict.java
+++ b/src/main/java/org/caosdb/server/jobs/core/Strict.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(stage = TransactionStage.POST_CHECK)
public class Strict extends ContainerJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/TestMail.java b/src/main/java/org/caosdb/server/jobs/core/TestMail.java
index 793e6fe211f18c2d576501597c1189dac2444d46..8a5a34015795bbadc61a8e799313e69222c069d7 100644
--- a/src/main/java/org/caosdb/server/jobs/core/TestMail.java
+++ b/src/main/java/org/caosdb/server/jobs/core/TestMail.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
-import org.caosdb.server.utils.mail.Mail;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
+import org.linkahead.server.utils.mail.Mail;
@JobAnnotation(
flag = "testMail",
@@ -38,13 +38,13 @@ import org.caosdb.server.utils.mail.Mail;
public class TestMail extends FlagJob {
private static final String NAME =
- CaosDBServer.getServerProperty(ServerProperties.KEY_NO_REPLY_NAME);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_NO_REPLY_NAME);
private static final String EMAIL =
- CaosDBServer.getServerProperty(ServerProperties.KEY_NO_REPLY_EMAIL);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_NO_REPLY_EMAIL);
@Override
protected void job(final String recipient) {
- if (CaosDBServer.isDebugMode() && recipient != null) {
+ if (LinkAheadServer.isDebugMode() && recipient != null) {
if (Utils.isRFC822Compliant(recipient)) {
final Mail m = new Mail(NAME, EMAIL, null, recipient, "Test mail", "This is a test mail.");
m.send();
diff --git a/src/main/java/org/caosdb/server/jobs/core/UniqueName.java b/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
index 86e6c37e35ec91db647e14e30896abb6b884555b..166177344857915475727ec47cebbd9027d572d3 100644
--- a/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
+++ b/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(flag = "uniquename", stage = TransactionStage.PRE_CHECK)
public class UniqueName extends FlagJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/UpdateUnitConverters.java b/src/main/java/org/caosdb/server/jobs/core/UpdateUnitConverters.java
index 0b71d2102c98188d875d52d3bbc3e0f79a23043b..3b97dd40ef1c1e895ffdd22356b5c8f44d0fa4bf 100644
--- a/src/main/java/org/caosdb/server/jobs/core/UpdateUnitConverters.java
+++ b/src/main/java/org/caosdb/server/jobs/core/UpdateUnitConverters.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.database.backend.transaction.InsertLinCon;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.unit.Converter;
-import org.caosdb.unit.LinearConverter;
-import org.caosdb.unit.Unit;
+import org.linkahead.server.database.backend.transaction.InsertLinCon;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.unit.Converter;
+import org.linkahead.unit.LinearConverter;
+import org.linkahead.unit.Unit;
@JobAnnotation(stage = TransactionStage.PRE_TRANSACTION)
public class UpdateUnitConverters extends EntityJob {
diff --git a/src/main/java/org/caosdb/server/logging/RequestErrorLogMessage.java b/src/main/java/org/caosdb/server/logging/RequestErrorLogMessage.java
index 4f0e57a46155c51076d4a134c3559d0f773811a1..58e8e91bd35fa953c9c701b7fec0ce3f3b0ee8e9 100644
--- a/src/main/java/org/caosdb/server/logging/RequestErrorLogMessage.java
+++ b/src/main/java/org/caosdb/server/logging/RequestErrorLogMessage.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.logging;
+package org.linkahead.server.logging;
import java.io.IOException;
import java.io.Serializable;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
-import org.caosdb.server.resource.ReReadableRepresentation;
+import org.linkahead.server.resource.ReReadableRepresentation;
import org.restlet.Message;
import org.restlet.Request;
import org.restlet.Response;
diff --git a/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java b/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java
index 4416227f9672a9b3be3ffb34306e78de04a20a2f..0db1ad679c5641be52619aa4c11b4e08ce3425ce 100644
--- a/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java
+++ b/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.logging.log4j;
+package org.linkahead.server.logging.log4j;
import java.io.File;
import java.net.URI;
@@ -30,7 +30,7 @@ public class CustomConfigurationFactory extends PropertiesConfigurationFactory {
private List<String> getConfigFiles() {
List<String> configFiles = new ArrayList<>(10);
configFiles.add(core_default.getAbsolutePath());
- if (Boolean.getBoolean("caosdb.debug")) {
+ if (Boolean.getBoolean("linkahead.debug")) {
configFiles.add(core_debug.getAbsolutePath());
}
if (ext_file.exists()) {
diff --git a/src/main/java/org/caosdb/server/permissions/AbstractEntityACLFactory.java b/src/main/java/org/caosdb/server/permissions/AbstractEntityACLFactory.java
index d5d818fd42b6a9b65af07df8bab627be2aeb1551..4705bbc6004c21812a19560f65eaae01c5c4deef 100644
--- a/src/main/java/org/caosdb/server/permissions/AbstractEntityACLFactory.java
+++ b/src/main/java/org/caosdb/server/permissions/AbstractEntityACLFactory.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.ArrayList;
import java.util.Collection;
diff --git a/src/main/java/org/caosdb/server/permissions/CaosPermission.java b/src/main/java/org/caosdb/server/permissions/CaosPermission.java
index 615b4d1a9c26c1addb955506ab1debddb729db9c..31746874a56f5b3dca56c620f0ef49d65f85e454 100644
--- a/src/main/java/org/caosdb/server/permissions/CaosPermission.java
+++ b/src/main/java/org/caosdb/server/permissions/CaosPermission.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.Collection;
import java.util.HashSet;
@@ -28,9 +28,9 @@ import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-public class CaosPermission extends HashSet<PermissionRule> implements Permission {
+public class LinkAheadPermission extends HashSet<PermissionRule> implements Permission {
- public CaosPermission(final HashSet<PermissionRule> rules) {
+ public LinkAheadPermission(final HashSet<PermissionRule> rules) {
super(rules);
}
diff --git a/src/main/java/org/caosdb/server/permissions/EntityACI.java b/src/main/java/org/caosdb/server/permissions/EntityACI.java
index 34d713eb69179cf7e88103cca2dd901077ffc092..f668b9c19b00843d82fc0096dca804bf987bc879 100644
--- a/src/main/java/org/caosdb/server/permissions/EntityACI.java
+++ b/src/main/java/org/caosdb/server/permissions/EntityACI.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.HashMap;
import java.util.Set;
diff --git a/src/main/java/org/caosdb/server/permissions/EntityACL.java b/src/main/java/org/caosdb/server/permissions/EntityACL.java
index f959ba89bd08cd5996af18540a484292a5046f94..ff94b7564fa4b71a68ee48fdfc9cd659a8a772e6 100644
--- a/src/main/java/org/caosdb/server/permissions/EntityACL.java
+++ b/src/main/java/org/caosdb/server/permissions/EntityACL.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,10 +21,10 @@
*
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
-import static org.caosdb.server.permissions.Role.OTHER_ROLE;
-import static org.caosdb.server.permissions.Role.OWNER_ROLE;
+import static org.linkahead.server.permissions.Role.OTHER_ROLE;
+import static org.linkahead.server.permissions.Role.OWNER_ROLE;
import java.io.File;
import java.io.IOException;
@@ -37,17 +37,17 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.exceptions.TransactionException;
import org.eclipse.jetty.util.ajax.JSON;
import org.jdom2.DataConversionException;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.exceptions.TransactionException;
public class EntityACL {
@@ -68,7 +68,7 @@ public class EntityACL {
SAXBuilder saxBuilder = new SAXBuilder();
File file =
new File(
- CaosDBServer.getServerProperty(ServerProperties.KEY_GLOBAL_ENTITY_PERMISSIONS_FILE)
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_GLOBAL_ENTITY_PERMISSIONS_FILE)
.trim());
try {
@@ -94,7 +94,7 @@ public class EntityACL {
public static final EntityACL getOwnerACLFor(final Subject subject) {
// TODO handle the case where a valid non-guest user (e.g. me@PAM,
- // you@CaosDB) is (just temporarily) authenticated via a
+ // you@LinkAhead) is (just temporarily) authenticated via a
// OneTimeAuthenticationToken
if (AuthenticationUtils.isAnonymous(subject)
|| AuthenticationUtils.isFromOneTimeTokenRealm(subject)) {
diff --git a/src/main/java/org/caosdb/server/permissions/EntityACLFactory.java b/src/main/java/org/caosdb/server/permissions/EntityACLFactory.java
index 08e4ae45cf07baac91b98205c1098d823b878b21..bc53019377006250543fc7df0922f51b1fc17051 100644
--- a/src/main/java/org/caosdb/server/permissions/EntityACLFactory.java
+++ b/src/main/java/org/caosdb/server/permissions/EntityACLFactory.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.Collection;
diff --git a/src/main/java/org/caosdb/server/permissions/EntityPermission.java b/src/main/java/org/caosdb/server/permissions/EntityPermission.java
index 1cfe9901ad2fdf0067d7cd58712c2caa506ac73b..789d9a76514afbf2fdb3105570c847b6997c74b4 100644
--- a/src/main/java/org/caosdb/server/permissions/EntityPermission.java
+++ b/src/main/java/org/caosdb/server/permissions/EntityPermission.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.ArrayList;
import java.util.HashSet;
@@ -28,16 +28,16 @@ import java.util.List;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.entity.xml.ToElementable;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.entity.xml.ToElementable;
public class EntityPermission extends Permission {
private static final long serialVersionUID = -8935713878537140286L;
private static List<EntityPermission> instances = new ArrayList<>();
private final int bitNumber;
- private final org.caosdb.api.entity.v1.EntityPermission mapping;
+ private final org.linkahead.api.entity.v1.EntityPermission mapping;
public static final Permission EDIT_PRIORITY_ACL =
new Permission(
"ADMIN:ENTITY:EDIT:PRIORITY_ACL",
@@ -66,16 +66,16 @@ public class EntityPermission extends Permission {
final String shortName,
final String description,
final int bitNumber,
- org.caosdb.api.entity.v1.EntityPermission mapping) {
+ org.linkahead.api.entity.v1.EntityPermission mapping) {
super(shortName, description);
this.bitNumber = bitNumber;
this.mapping = mapping;
if (bitNumber > 61) {
- throw new CaosDBException(
+ throw new LinkAheadException(
"This bitNumber is too big. This implementation only handles bitNumbers up to 61.");
}
if (instances.contains(this)) {
- throw new CaosDBException("This EntityPermission is defined already.");
+ throw new LinkAheadException("This EntityPermission is defined already.");
} else {
instances.add(this);
}
@@ -113,7 +113,7 @@ public class EntityPermission extends Permission {
}
public static EntityPermission getEntityPermission(
- final org.caosdb.api.entity.v1.EntityPermission permission) {
+ final org.linkahead.api.entity.v1.EntityPermission permission) {
for (final EntityPermission p : instances) {
if (p.getMapping() == permission) {
return p;
@@ -136,7 +136,7 @@ public class EntityPermission extends Permission {
return ret;
}
- public org.caosdb.api.entity.v1.EntityPermission getMapping() {
+ public org.linkahead.api.entity.v1.EntityPermission getMapping() {
return mapping;
}
@@ -147,144 +147,144 @@ public class EntityPermission extends Permission {
"RETRIEVE:ENTITY",
"Permission to retrieve the full entity (name, description, data type, ...) with all parents and properties (unless prohibited by another rule on the property level).",
4,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ENTITY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ENTITY);
public static final EntityPermission RETRIEVE_ACL =
new EntityPermission(
"RETRIEVE:ACL",
"Permission to retrieve the full and final ACL of this entity.",
5,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ACL);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ACL);
public static final EntityPermission RETRIEVE_HISTORY =
new EntityPermission(
"RETRIEVE:HISTORY",
"Permission to retrieve the history of this entity.",
6,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_HISTORY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_HISTORY);
public static final EntityPermission RETRIEVE_OWNER =
new EntityPermission(
"RETRIEVE:OWNER",
"Permission to retrieve the owner(s) of this entity.",
9,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_OWNER);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_OWNER);
public static final EntityPermission RETRIEVE_FILE =
new EntityPermission(
"RETRIEVE:FILE",
"Permission to download the file belonging to this entity.",
10,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_FILE);
public static final EntityPermission DELETE =
new EntityPermission(
"DELETE",
"Permission to delete this entity.",
1,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_DELETE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_DELETE);
public static final EntityPermission EDIT_ACL =
new EntityPermission(
"EDIT:ACL",
"Permission to change the user-specified part of this entity's ACL. Roles with this Permission are called 'Owners'.",
0,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_EDIT_ACL);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_EDIT_ACL);
public static final EntityPermission UPDATE_DESCRIPTION =
new EntityPermission(
"UPDATE:DESCRIPTION",
"Permission to change the value of this entity.",
11,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DESCRIPTION);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DESCRIPTION);
public static final EntityPermission UPDATE_VALUE =
new EntityPermission(
"UPDATE:VALUE",
"Permission to change the value of this entity.",
12,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_VALUE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_VALUE);
public static final EntityPermission UPDATE_ROLE =
new EntityPermission(
"UPDATE:ROLE",
"Permission to change the role of this entity.",
13,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ROLE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ROLE);
public static final EntityPermission UPDATE_REMOVE_PARENT =
new EntityPermission(
"UPDATE:PARENT:REMOVE",
"Permission to remove parents from this entity.",
14,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PARENT);
public static final EntityPermission UPDATE_ADD_PARENT =
new EntityPermission(
"UPDATE:PARENT:ADD",
"Permission to add a parent to this entity.",
15,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PARENT);
public static final EntityPermission UPDATE_REMOVE_PROPERTY =
new EntityPermission(
"UPDATE:PROPERTY:REMOVE",
"Permission to remove properties from this entity.",
16,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PROPERTY);
public static final EntityPermission UPDATE_ADD_PROPERTY =
new EntityPermission(
"UPDATE:PROPERTY:ADD",
"Permission to add a property to this entity.",
17,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PROPERTY);
public static final EntityPermission UPDATE_NAME =
new EntityPermission(
"UPDATE:NAME",
"Permission to change the name of this entity.",
19,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_NAME);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_NAME);
public static final EntityPermission UPDATE_DATA_TYPE =
new EntityPermission(
"UPDATE:DATA_TYPE",
"Permission to change the data type of this entity.",
20,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DATA_TYPE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DATA_TYPE);
public static final EntityPermission UPDATE_REMOVE_FILE =
new EntityPermission(
"UPDATE:FILE:REMOVE",
"Permission to delete the file of this entity.",
21,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_FILE);
public static final EntityPermission UPDATE_ADD_FILE =
new EntityPermission(
"UPDATE:FILE:ADD",
"Permission to set a file for this entity.",
22,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_FILE);
public static final EntityPermission UPDATE_MOVE_FILE =
new EntityPermission(
"UPDATE:FILE:MOVE",
"Permission to move an existing file to a new location.",
23,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_MOVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_MOVE_FILE);
public static final EntityPermission USE_AS_REFERENCE =
new EntityPermission(
"USE:AS_REFERENCE",
"Permission to refer to this entity via a reference property.",
24,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_REFERENCE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_REFERENCE);
public static final EntityPermission USE_AS_PROPERTY =
new EntityPermission(
"USE:AS_PROPERTY",
"Permission to implement this entity as a property.",
25,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PROPERTY);
public static final EntityPermission USE_AS_PARENT =
new EntityPermission(
"USE:AS_PARENT",
"Permission to use this entity as a super type for other entities.",
26,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PARENT);
public static final EntityPermission USE_AS_DATA_TYPE =
new EntityPermission(
"USE:AS_DATA_TYPE",
"Permission to use this entity as a data type for reference properties.",
27,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_DATA_TYPE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_DATA_TYPE);
public static final EntityPermission UPDATE_QUERY_TEMPLATE_DEFINITION =
new EntityPermission(
"UPDATE:QUERY_TEMPLATE_DEFINITION",
"Permission to update the query template definition of this QueryTemplate",
28,
- org.caosdb.api.entity.v1.EntityPermission
+ org.linkahead.api.entity.v1.EntityPermission
.ENTITY_PERMISSION_UPDATE_QUERY_TEMPLATE_DEFINITION);
}
diff --git a/src/main/java/org/caosdb/server/permissions/Permission.java b/src/main/java/org/caosdb/server/permissions/Permission.java
index e8f33a3ae3f9eb0956bae6bc7c7eceefdc5663b7..3721be99fcc7e30fa8e18af3ff4112159954449f 100644
--- a/src/main/java/org/caosdb/server/permissions/Permission.java
+++ b/src/main/java/org/caosdb/server/permissions/Permission.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import org.apache.shiro.authz.permission.WildcardPermission;
diff --git a/src/main/java/org/caosdb/server/permissions/PermissionRule.java b/src/main/java/org/caosdb/server/permissions/PermissionRule.java
index 2e8b6984509761d649acb27b5482c8df7bff9933..815e3c39946a2b9fd8c6f704d88b8e2439427a07 100644
--- a/src/main/java/org/caosdb/server/permissions/PermissionRule.java
+++ b/src/main/java/org/caosdb/server/permissions/PermissionRule.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,15 +21,15 @@
*
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.HashMap;
import java.util.Map;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.authz.permission.WildcardPermission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.Principal;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.Principal;
public class PermissionRule {
diff --git a/src/main/java/org/caosdb/server/permissions/ResponsibleAgent.java b/src/main/java/org/caosdb/server/permissions/ResponsibleAgent.java
index 3f8fd3bbbe800b1ce43d240da53344512feb5e01..7b164ebfaa2a0c572adcd60c9acb4b2077dc5192 100644
--- a/src/main/java/org/caosdb/server/permissions/ResponsibleAgent.java
+++ b/src/main/java/org/caosdb/server/permissions/ResponsibleAgent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.HashMap;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/permissions/Role.java b/src/main/java/org/caosdb/server/permissions/Role.java
index f7f4e55e195d72ba3a42a8b909d2c87944bcbf81..ca278daf3a6d9844cdead55195c568bf1abe2af6 100644
--- a/src/main/java/org/caosdb/server/permissions/Role.java
+++ b/src/main/java/org/caosdb/server/permissions/Role.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.HashMap;
import org.jdom2.Attribute;
diff --git a/src/main/java/org/caosdb/server/query/Backreference.java b/src/main/java/org/caosdb/server/query/Backreference.java
index b801ffaf396a3ba9f98531ca06fc274b05c70b96..3f29ec03d793472daefd0aa7f0452e9a20363b77 100644
--- a/src/main/java/org/caosdb/server/query/Backreference.java
+++ b/src/main/java/org/caosdb/server/query/Backreference.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
@@ -34,11 +34,11 @@ import java.sql.Types;
import java.util.HashMap;
import java.util.Map.Entry;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.query.Query.Pattern;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.query.Query.Pattern;
+import org.linkahead.server.query.Query.QueryException;
public class Backreference implements EntityFilterInterface, QueryInterface {
diff --git a/src/main/java/org/caosdb/server/query/CQLLexer.g4 b/src/main/java/org/caosdb/server/query/CQLLexer.g4
index be6dcfa99d2f9c48cba8a0f7fccb7f97b277e01d..20dc44382da628ffe4a2f89546af9cf90ec198d7 100644
--- a/src/main/java/org/caosdb/server/query/CQLLexer.g4
+++ b/src/main/java/org/caosdb/server/query/CQLLexer.g4
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/src/main/java/org/caosdb/server/query/CQLParser.g4 b/src/main/java/org/caosdb/server/query/CQLParser.g4
index 8615bae31fae67eb0bd3315f664bfa708db61618..d042b5bfbc5b50cb5bfe0542d55632eb3f36d3b0 100644
--- a/src/main/java/org/caosdb/server/query/CQLParser.g4
+++ b/src/main/java/org/caosdb/server/query/CQLParser.g4
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/src/main/java/org/caosdb/server/query/CQLParsingErrorListener.java b/src/main/java/org/caosdb/server/query/CQLParsingErrorListener.java
index c2b453e5836a18628904302f2157f0a41a190068..66b764756fd057de681e9b8443be4abc09dff35e 100644
--- a/src/main/java/org/caosdb/server/query/CQLParsingErrorListener.java
+++ b/src/main/java/org/caosdb/server/query/CQLParsingErrorListener.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.util.ArrayList;
import java.util.BitSet;
diff --git a/src/main/java/org/caosdb/server/query/Conjunction.java b/src/main/java/org/caosdb/server/query/Conjunction.java
index 59dfd57b20ed8bce443e670e767dc42bb91ac6ac..f6e199cf675ff52355dc887e281f7e91474a4363 100644
--- a/src/main/java/org/caosdb/server/query/Conjunction.java
+++ b/src/main/java/org/caosdb/server/query/Conjunction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
@@ -30,9 +30,9 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.query.Query.QueryException;
public class Conjunction extends EntityFilterContainer
implements QueryInterface, EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/Disjunction.java b/src/main/java/org/caosdb/server/query/Disjunction.java
index 925ef85952e2d31783a6f7447074d0384e508a98..ff4dd8e6ddcdf2511b099c3cf4071f34e545814f 100644
--- a/src/main/java/org/caosdb/server/query/Disjunction.java
+++ b/src/main/java/org/caosdb/server/query/Disjunction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
@@ -30,9 +30,9 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.query.Query.QueryException;
public class Disjunction extends EntityFilterContainer
implements QueryInterface, EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/EntityFilterContainer.java b/src/main/java/org/caosdb/server/query/EntityFilterContainer.java
index 1b270e9b120f2c336381db16c88769862b68a725..7e1ecc9516f233e0645c7a15b802ea00090b2193 100644
--- a/src/main/java/org/caosdb/server/query/EntityFilterContainer.java
+++ b/src/main/java/org/caosdb/server/query/EntityFilterContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.util.LinkedList;
diff --git a/src/main/java/org/caosdb/server/query/EntityFilterInterface.java b/src/main/java/org/caosdb/server/query/EntityFilterInterface.java
index be8484c2f122ae301ea78a014c771e116b0fc012..92c704b3a4167db4b2402bdc7f3996f866a8e12c 100644
--- a/src/main/java/org/caosdb/server/query/EntityFilterInterface.java
+++ b/src/main/java/org/caosdb/server/query/EntityFilterInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.query.Query.QueryException;
public interface EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/IDFilter.java b/src/main/java/org/caosdb/server/query/IDFilter.java
index ce01f5f242f914c6f6f812f0875332f7ca004c07..663cb6ca4192ad6ae7a4a86130fe97135ce2bde7 100644
--- a/src/main/java/org/caosdb/server/query/IDFilter.java
+++ b/src/main/java/org/caosdb/server/query/IDFilter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static java.sql.Types.CHAR;
import static java.sql.Types.INTEGER;
@@ -29,8 +29,8 @@ import static java.sql.Types.VARCHAR;
import java.sql.CallableStatement;
import java.sql.Connection;
import java.sql.SQLException;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.query.Query.QueryException;
public class IDFilter implements EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/Negation.java b/src/main/java/org/caosdb/server/query/Negation.java
index 431124df7b995faf6aa493363a51095e7028b9b8..7aad2caee4914bb4a9f221c14b0a4f455fd28d7e 100644
--- a/src/main/java/org/caosdb/server/query/Negation.java
+++ b/src/main/java/org/caosdb/server/query/Negation.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
@@ -30,9 +30,9 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.query.Query.QueryException;
public class Negation implements EntityFilterInterface, QueryInterface {
diff --git a/src/main/java/org/caosdb/server/query/POV.java b/src/main/java/org/caosdb/server/query/POV.java
index ebc35a16b1495accf8cd4a114dd688c2b2529c1b..8374b2d83c6c07a3f4a63f26aeefbeb4decf932f 100644
--- a/src/main/java/org/caosdb/server/query/POV.java
+++ b/src/main/java/org/caosdb/server/query/POV.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static java.sql.Types.DOUBLE;
import static java.sql.Types.INTEGER;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import de.timmfitschen.easyunits.parser.ParserException;
import java.sql.CallableStatement;
@@ -39,14 +39,14 @@ import java.util.Map.Entry;
import java.util.Stack;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.datetime.DateTimeFactory2;
-import org.caosdb.datetime.DateTimeInterface;
-import org.caosdb.datetime.Interval;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.query.Query.QueryException;
-import org.caosdb.unit.CaosDBSystemOfUnits;
-import org.caosdb.unit.Unit;
import org.jdom2.Element;
+import org.linkahead.datetime.DateTimeFactory2;
+import org.linkahead.datetime.DateTimeInterface;
+import org.linkahead.datetime.Interval;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.query.Query.QueryException;
+import org.linkahead.unit.LinkAheadSystemOfUnits;
+import org.linkahead.unit.Unit;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -78,7 +78,7 @@ public class POV implements EntityFilterInterface {
private final Stack<String> prefix = new Stack<>();
private Unit getUnit(final String s) throws ParserException {
- return CaosDBSystemOfUnits.getUnit(s);
+ return LinkAheadSystemOfUnits.getUnit(s);
}
/**
diff --git a/src/main/java/org/caosdb/server/query/Query.java b/src/main/java/org/caosdb/server/query/Query.java
index abaca4365e54c21ee2ba8cf8bf7727fe746c7277..5ed794fce4c1524aa5e8d8866cf48d94170a2fd8 100644
--- a/src/main/java/org/caosdb/server/query/Query.java
+++ b/src/main/java/org/caosdb/server/query/Query.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,9 +19,9 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.io.Serializable;
import java.sql.CallableStatement;
@@ -46,35 +46,35 @@ import org.antlr.v4.runtime.CharStreams;
import org.antlr.v4.runtime.CommonTokenStream;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.apache.shiro.subject.Subject;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLHelper;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.database.backend.transaction.RetrieveSparseEntity;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.query.CQLParser.CqContext;
-import org.caosdb.server.query.CQLParsingErrorListener.ParsingError;
-import org.caosdb.server.transaction.TransactionInterface;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.ResultSetIterator;
import org.jdom2.Element;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLHelper;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.database.backend.transaction.RetrieveSparseEntity;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.query.CQLParser.CqContext;
+import org.linkahead.server.query.CQLParsingErrorListener.ParsingError;
+import org.linkahead.server.transaction.TransactionInterface;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.ResultSetIterator;
import org.slf4j.Logger;
public class Query implements QueryInterface, ToElementable, TransactionInterface {
@@ -259,7 +259,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
}
private final boolean filterEntitiesWithoutRetrievePermisions =
- !CaosDBServer.getServerProperty(
+ !LinkAheadServer.getServerProperty(
ServerProperties.KEY_QUERY_FILTER_ENTITIES_WITHOUT_RETRIEVE_PERMISSIONS)
.equalsIgnoreCase("FALSE");
@@ -602,13 +602,13 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
try {
this.role =
Role.valueOf(
- CaosDBServer.getServerProperty(ServerProperties.KEY_FIND_QUERY_DEFAULT_ROLE));
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_FIND_QUERY_DEFAULT_ROLE));
} catch (IllegalArgumentException e) {
addError(
"Unsupportet value of the server property "
+ ServerProperties.KEY_FIND_QUERY_DEFAULT_ROLE
+ ": "
- + CaosDBServer.getServerProperty(ServerProperties.KEY_FIND_QUERY_DEFAULT_ROLE));
+ + LinkAheadServer.getServerProperty(ServerProperties.KEY_FIND_QUERY_DEFAULT_ROLE));
throw new UnsupportedOperationException(e);
}
}
@@ -645,7 +645,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
private String generateSelectStatementForResultSet(
final String resultSetTableName, final boolean versioned) {
// TODO remove the entities.role part when
- // https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/issues/245 is resolved
+ // https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/issues/245 is resolved
if (resultSetTableName.equals("entities")) {
final String baseStatement =
"SELECT entities.id, entity_acl.acl FROM entities INNER JOIN entity_acl ON entity_acl.id=entities.acl WHERE entities.role!='DOMAIN'";
diff --git a/src/main/java/org/caosdb/server/query/QueryInterface.java b/src/main/java/org/caosdb/server/query/QueryInterface.java
index 0f2db9a97094ddc26062a9c9922907c183a26413..bef36cceb3d2dceb44609ab94d7d23e4241c02bd 100644
--- a/src/main/java/org/caosdb/server/query/QueryInterface.java
+++ b/src/main/java/org/caosdb/server/query/QueryInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.sql.Connection;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
+import org.linkahead.server.database.access.Access;
public interface QueryInterface {
diff --git a/src/main/java/org/caosdb/server/query/RoleFilter.java b/src/main/java/org/caosdb/server/query/RoleFilter.java
index 97d1b1eab3bcc9e21adab4fa5e2a5204411e58fb..eb73e48ff6648f327a77c309acef2f22fdc092bb 100644
--- a/src/main/java/org/caosdb/server/query/RoleFilter.java
+++ b/src/main/java/org/caosdb/server/query/RoleFilter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.query.Query.QueryException;
-import org.caosdb.server.query.Query.Role;
import org.jdom2.Element;
+import org.linkahead.server.query.Query.QueryException;
+import org.linkahead.server.query.Query.Role;
public class RoleFilter implements EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/StoredAt.java b/src/main/java/org/caosdb/server/query/StoredAt.java
index 90adc188b61e375a30721b605cb91b93fe76a88b..c0731f8889f045e23aaffbc20717a0aadc83cca8 100644
--- a/src/main/java/org/caosdb/server/query/StoredAt.java
+++ b/src/main/java/org/caosdb/server/query/StoredAt.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static java.sql.Types.VARCHAR;
@@ -30,8 +30,8 @@ import java.sql.CallableStatement;
import java.sql.SQLException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.query.Query.QueryException;
public class StoredAt implements EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/SubProperty.java b/src/main/java/org/caosdb/server/query/SubProperty.java
index d5ce923449b45cb45dab77e4c30b5d8b343e01e3..00ff7ab461b01398466b141169893b859a2f52d4 100644
--- a/src/main/java/org/caosdb/server/query/SubProperty.java
+++ b/src/main/java/org/caosdb/server/query/SubProperty.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,19 +20,19 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.query.Query.QueryException;
public class SubProperty implements QueryInterface, EntityFilterInterface {
private final EntityFilterInterface filter;
diff --git a/src/main/java/org/caosdb/server/query/TransactionFilter.java b/src/main/java/org/caosdb/server/query/TransactionFilter.java
index 2099639b0fc862edb2fc0bceecfa17bad6dad167..9c4443c64a9c94a78024839f165bc3993c012e70 100644
--- a/src/main/java/org/caosdb/server/query/TransactionFilter.java
+++ b/src/main/java/org/caosdb/server/query/TransactionFilter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.sql.CallableStatement;
import java.sql.Connection;
import java.sql.SQLException;
import java.sql.Types;
-import org.caosdb.datetime.Date;
-import org.caosdb.datetime.DateTimeFactory2;
-import org.caosdb.datetime.Interval;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.datetime.Date;
+import org.linkahead.datetime.DateTimeFactory2;
+import org.linkahead.datetime.Interval;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.query.Query.QueryException;
public class TransactionFilter implements EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/Utils.java b/src/main/java/org/caosdb/server/query/Utils.java
index 661cee12585d8f4b07ca3a9fea364943aa1d9c6b..b5180c6beb89cea3142a46a90f08266a5603735c 100644
--- a/src/main/java/org/caosdb/server/query/Utils.java
+++ b/src/main/java/org/caosdb/server/query/Utils.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.io.PrintStream;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/query/VersionFilter.java b/src/main/java/org/caosdb/server/query/VersionFilter.java
index aa391778ce20c089a9fa6dae88caf77e0f797703..b6f24038a0f49ecad68eaeacb6da4c10148eb519 100644
--- a/src/main/java/org/caosdb/server/query/VersionFilter.java
+++ b/src/main/java/org/caosdb/server/query/VersionFilter.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.query;
+package org.linkahead.server.query;
public class VersionFilter {
diff --git a/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java b/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java
index 44ebfa22d08c975031f5bf5bfca325d6b706af24..ba20d6542f2433faed819264b781690b2815e944 100644
--- a/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java
+++ b/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static java.net.URLDecoder.decode;
@@ -41,17 +41,17 @@ import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.WebinterfaceUtils;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.WebinterfaceUtils;
import org.restlet.data.Form;
import org.restlet.data.Header;
import org.restlet.data.Parameter;
@@ -69,7 +69,7 @@ import org.restlet.util.Series;
*
* @author Timm Fitschen
*/
-public abstract class AbstractCaosDBServerResource extends ServerResource {
+public abstract class AbstractLinkAheadServerResource extends ServerResource {
private final HashMap<String, String> flags = new HashMap<String, String>();
private Long timestamp = null;
@@ -243,7 +243,7 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
protected abstract Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception;
@Post
@@ -277,7 +277,7 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, Exception {
getResponse().setStatus(Status.CLIENT_ERROR_METHOD_NOT_ALLOWED);
return null;
@@ -293,7 +293,7 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
protected Representation httpPostInChildClass(final Representation entity)
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, xmlNotWellFormedException, JDOMException, Exception {
getResponse().setStatus(Status.CLIENT_ERROR_METHOD_NOT_ALLOWED);
return null;
@@ -314,7 +314,7 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
protected String getXSLScript() {
- return this.utils.getWebinterfaceURI("webcaosdb.xsl");
+ return this.utils.getWebinterfaceURI("weblinkahead.xsl");
}
/** Wrap an element for an "OK" response. */
diff --git a/src/main/java/org/caosdb/server/resource/AuthenticationResource.java b/src/main/java/org/caosdb/server/resource/AuthenticationResource.java
index ed60d7906b1cda003ed2a84f0e22200049d96c25..f38a9d66c509d58a49130bca1829a870f1c3c45f 100644
--- a/src/main/java/org/caosdb/server/resource/AuthenticationResource.java
+++ b/src/main/java/org/caosdb/server/resource/AuthenticationResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
@@ -31,28 +31,28 @@ import org.apache.shiro.authc.AccountException;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authc.CredentialsException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.RealmUsernamePasswordToken;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.RealmUsernamePasswordToken;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Form;
import org.restlet.data.Reference;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
-public class AuthenticationResource extends AbstractCaosDBServerResource {
+public class AuthenticationResource extends AbstractLinkAheadServerResource {
/** Returns single "Login" element. XSLT will create a form. */
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final Document doc = new Document();
final Element rootElem = generateRootElement();
@@ -66,7 +66,7 @@ public class AuthenticationResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, Exception {
final Subject user = SecurityUtils.getSubject();
if (user.isAuthenticated()) {
@@ -112,7 +112,7 @@ public class AuthenticationResource extends AbstractCaosDBServerResource {
} catch (final CredentialsException | AccountException e) {
getLogger().log(Level.INFO, "LOGIN_FAILED", e);
} catch (final AuthenticationException e) {
- if (CaosDBServer.isDebugMode()) {
+ if (LinkAheadServer.isDebugMode()) {
getLogger().log(Level.INFO, "LOGIN_FAILED", e);
} else {
getLogger().log(Level.INFO, "LOGIN_FAILED\t" + e.getMessage());
diff --git a/src/main/java/org/caosdb/server/resource/DefaultResource.java b/src/main/java/org/caosdb/server/resource/DefaultResource.java
index 488cd667c8832e4b90277e07144c65cbb7e4036d..5cdad9b88c322148c465ae31e27fae0ee093076c 100644
--- a/src/main/java/org/caosdb/server/resource/DefaultResource.java
+++ b/src/main/java/org/caosdb/server/resource/DefaultResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
import org.jdom2.Document;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
import org.restlet.representation.Representation;
-public class DefaultResource extends AbstractCaosDBServerResource {
+public class DefaultResource extends AbstractLinkAheadServerResource {
private Element responseBody = null;
@@ -43,7 +43,7 @@ public class DefaultResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final Document doc = new org.jdom2.Document();
final Element root = generateRootElement();
diff --git a/src/main/java/org/caosdb/server/resource/EntityOwnerResource.java b/src/main/java/org/caosdb/server/resource/EntityOwnerResource.java
index 41f92a5631d9cabb04ee5498373848b516885424..304c8f75dfaf413bbe456eee233bb0cf4da39324 100644
--- a/src/main/java/org/caosdb/server/resource/EntityOwnerResource.java
+++ b/src/main/java/org/caosdb/server/resource/EntityOwnerResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,12 +22,12 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.resource.transaction.RetrieveEntityResource;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.resource.transaction.RetrieveEntityResource;
/**
* Resource which returns the entity with the owner information attached to it.
diff --git a/src/main/java/org/caosdb/server/resource/EntityPermissionsResource.java b/src/main/java/org/caosdb/server/resource/EntityPermissionsResource.java
index 1f5ee5f7d8a28a235de02bbc33f826da32af0615..144eabe6ead2f480df8a770f8afb9e9156683aab 100644
--- a/src/main/java/org/caosdb/server/resource/EntityPermissionsResource.java
+++ b/src/main/java/org/caosdb/server/resource/EntityPermissionsResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,11 +22,11 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.resource.transaction.RetrieveEntityResource;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.resource.transaction.RetrieveEntityResource;
/**
* Resource which appends the entity permissions (esp. the global ones) to the normal entity
diff --git a/src/main/java/org/caosdb/server/resource/FileSystemResource.java b/src/main/java/org/caosdb/server/resource/FileSystemResource.java
index 9c0d615833148f706b190d7dfbc1aafdca61a75f..69653780eeff21ec433ec01595d3880d9957b95c 100644
--- a/src/main/java/org/caosdb/server/resource/FileSystemResource.java
+++ b/src/main/java/org/caosdb/server/resource/FileSystemResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,27 +20,27 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static java.net.URLDecoder.decode;
-import static org.caosdb.server.FileSystem.getFromFileSystem;
+import static org.linkahead.server.FileSystem.getFromFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.transaction.RetrieveSparseEntityByPath;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Attribute;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.transaction.RetrieveSparseEntityByPath;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Disposition;
import org.restlet.data.MediaType;
import org.restlet.data.Status;
@@ -53,7 +53,7 @@ import org.restlet.representation.Representation;
*
* @author Timm Fitschen
*/
-public class FileSystemResource extends AbstractCaosDBServerResource {
+public class FileSystemResource extends AbstractLinkAheadServerResource {
public static Message ORPHANED_FILE_WARNING =
new Message(
@@ -61,7 +61,7 @@ public class FileSystemResource extends AbstractCaosDBServerResource {
"Orphaned file. The file is not tracked. This is probably a harmless inconsistency but it might be a sign of other problems.");
/**
- * Download a File from the CaosDBFileSystem. Only one File per Request.
+ * Download a File from the LinkAheadFileSystem. Only one File per Request.
*
* @author Timm Fitschen
* @return InputRepresentation
diff --git a/src/main/java/org/caosdb/server/resource/InfoResource.java b/src/main/java/org/caosdb/server/resource/InfoResource.java
index 452ea7956d75ff8ea4d9a5f3cf8e24df1980caf3..1d4239053fdb771c19e2de1ad35579d3d3bfa234 100644
--- a/src/main/java/org/caosdb/server/resource/InfoResource.java
+++ b/src/main/java/org/caosdb/server/resource/InfoResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,21 +20,21 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.util.TimeZone;
-import org.caosdb.datetime.UTCTimeZoneShift;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.utils.FlagInfo;
-import org.caosdb.server.utils.Info;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.datetime.UTCTimeZoneShift;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.utils.FlagInfo;
+import org.linkahead.server.utils.Info;
import org.restlet.representation.Representation;
-/** This class represents the information retrieved by /Info requests (only GET) to CaosDB. */
-public class InfoResource extends AbstractCaosDBServerResource {
+/** This class represents the information retrieved by /Info requests (only GET) to LinkAhead. */
+public class InfoResource extends AbstractLinkAheadServerResource {
/**
* The response to the HTTP GET request is generated here.
diff --git a/src/main/java/org/caosdb/server/resource/JdomRepresentation.java b/src/main/java/org/caosdb/server/resource/JdomRepresentation.java
index 4be6743d9ff959c278f80322c92fe2ee9f42d7cd..b1a146d95eeb5963ff297716cb9becabd6e7a3b2 100644
--- a/src/main/java/org/caosdb/server/resource/JdomRepresentation.java
+++ b/src/main/java/org/caosdb/server/resource/JdomRepresentation.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.io.OutputStream;
import java.io.Writer;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.ProcessingInstruction;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.restlet.data.MediaType;
import org.restlet.data.Reference;
import org.restlet.representation.WriterRepresentation;
@@ -82,7 +82,7 @@ public class JdomRepresentation extends WriterRepresentation {
public static final String getWebUIRef(final Reference reference) {
return reference.getHostIdentifier()
- + CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT)
+ + LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT)
+ "/webinterface/";
}
diff --git a/src/main/java/org/caosdb/server/resource/LogoutResource.java b/src/main/java/org/caosdb/server/resource/LogoutResource.java
index 1659f751a4710fbf99fc473b586cc3b180c8a62c..524d7b29d3d1989ddb1c0d6ceffa0afb9b28be50 100644
--- a/src/main/java/org/caosdb/server/resource/LogoutResource.java
+++ b/src/main/java/org/caosdb/server/resource/LogoutResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
import org.restlet.representation.Representation;
public class LogoutResource extends AuthenticationResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
return super.httpDeleteInChildClass();
}
diff --git a/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java b/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java
index 8d2aa1720aaefcdbaccee18c6a1626a912319b6a..61b380ac02c917878a2cb6f954ad42cc9c8fb15a 100644
--- a/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java
+++ b/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,31 +20,31 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
import java.util.HashSet;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.transaction.RetrievePermissionRulesTransaction;
-import org.caosdb.server.transaction.UpdatePermissionRulesTransaction;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.transaction.RetrievePermissionRulesTransaction;
+import org.linkahead.server.transaction.UpdatePermissionRulesTransaction;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
import org.restlet.representation.StringRepresentation;
-public class PermissionRulesResource extends AbstractCaosDBServerResource {
+public class PermissionRulesResource extends AbstractLinkAheadServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final String role = getRequestedItems()[0];
diff --git a/src/main/java/org/caosdb/server/resource/ReReadableRepresentation.java b/src/main/java/org/caosdb/server/resource/ReReadableRepresentation.java
index 3620eef2167073f479c9df63c415e01857db3ea1..f0d16d8218c5e21708da82331dccc5cba60ba5c9 100644
--- a/src/main/java/org/caosdb/server/resource/ReReadableRepresentation.java
+++ b/src/main/java/org/caosdb/server/resource/ReReadableRepresentation.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import com.google.common.base.Charsets;
import java.io.IOException;
diff --git a/src/main/java/org/caosdb/server/resource/RolesResource.java b/src/main/java/org/caosdb/server/resource/RolesResource.java
index ad1544da3a326f1c16e0b01238985d10e93b0581..f189e10acf1838f683ee5c882ce7968bdf7e656d 100644
--- a/src/main/java/org/caosdb/server/resource/RolesResource.java
+++ b/src/main/java/org/caosdb/server/resource/RolesResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,33 +20,33 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.transaction.DeleteRoleTransaction;
-import org.caosdb.server.transaction.InsertRoleTransaction;
-import org.caosdb.server.transaction.RetrieveRoleTransaction;
-import org.caosdb.server.transaction.UpdateRoleTransaction;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.transaction.DeleteRoleTransaction;
+import org.linkahead.server.transaction.InsertRoleTransaction;
+import org.linkahead.server.transaction.RetrieveRoleTransaction;
+import org.linkahead.server.transaction.UpdateRoleTransaction;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Form;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
import org.restlet.representation.StringRepresentation;
-public class RolesResource extends AbstractCaosDBServerResource {
+public class RolesResource extends AbstractLinkAheadServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final Element root = generateRootElement();
final Document document = new Document();
@@ -74,7 +74,7 @@ public class RolesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, Exception {
if (getRequestedItems().length > 0) {
final String name = getRequestedItems()[0];
@@ -97,7 +97,7 @@ public class RolesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpPostInChildClass(final Representation entity)
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, xmlNotWellFormedException, JDOMException, Exception {
String name = null;
diff --git a/src/main/java/org/caosdb/server/resource/ScriptingResource.java b/src/main/java/org/caosdb/server/resource/ScriptingResource.java
index 6e7cf721cb11bf95df23396bc79d5691335708a6..42a8aeb1e6523bfc5b6e4d68f463c43128a10b20 100644
--- a/src/main/java/org/caosdb/server/resource/ScriptingResource.java
+++ b/src/main/java/org/caosdb/server/resource/ScriptingResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import com.ibm.icu.text.Collator;
import java.io.IOException;
@@ -38,19 +38,19 @@ import org.apache.commons.fileupload.FileItemStream;
import org.apache.commons.fileupload.FileUploadException;
import org.apache.commons.fileupload.disk.DiskFileItemFactory;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.OneTimeAuthenticationToken;
-import org.caosdb.server.accessControl.SessionToken;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.scripting.CallerSerializer;
-import org.caosdb.server.scripting.ScriptingPermissions;
-import org.caosdb.server.scripting.ServerSideScriptingCaller;
-import org.caosdb.server.utils.Serializer;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
import org.jdom2.Element;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.OneTimeAuthenticationToken;
+import org.linkahead.server.accessControl.SessionToken;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.scripting.CallerSerializer;
+import org.linkahead.server.scripting.ScriptingPermissions;
+import org.linkahead.server.scripting.ServerSideScriptingCaller;
+import org.linkahead.server.utils.Serializer;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
import org.restlet.data.CharacterSet;
import org.restlet.data.Form;
import org.restlet.data.MediaType;
@@ -60,7 +60,7 @@ import org.restlet.engine.header.ContentType;
import org.restlet.ext.fileupload.RestletFileUpload;
import org.restlet.representation.Representation;
-public class ScriptingResource extends AbstractCaosDBServerResource {
+public class ScriptingResource extends AbstractLinkAheadServerResource {
private ServerSideScriptingCaller caller;
private Collection<FileProperties> deleteFiles = new LinkedList<>();
diff --git a/src/main/java/org/caosdb/server/resource/ServerLogsResource.java b/src/main/java/org/caosdb/server/resource/ServerLogsResource.java
index f304f10062209d62855a0bff21e0c8cad54e1962..bbbd82676a336f595551001aa262b8cb91e2186c 100644
--- a/src/main/java/org/caosdb/server/resource/ServerLogsResource.java
+++ b/src/main/java/org/caosdb/server/resource/ServerLogsResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
@@ -29,19 +29,19 @@ import java.util.List;
import java.util.logging.Level;
import java.util.logging.LogRecord;
import java.util.logging.XMLFormatter;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.transaction.RetrieveLogRecordTransaction;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.transaction.RetrieveLogRecordTransaction;
import org.restlet.data.Form;
import org.restlet.data.MediaType;
import org.restlet.representation.Representation;
import org.restlet.representation.StringRepresentation;
-public class ServerLogsResource extends AbstractCaosDBServerResource {
+public class ServerLogsResource extends AbstractLinkAheadServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
Level level = null;
diff --git a/src/main/java/org/caosdb/server/resource/ServerPropertiesResource.java b/src/main/java/org/caosdb/server/resource/ServerPropertiesResource.java
index 5b4e83162ab2e2a701a8497eeb85225def94cff1..1d4916cfc40769cf9e9bc97d6f9e090e062d1d9e 100644
--- a/src/main/java/org/caosdb/server/resource/ServerPropertiesResource.java
+++ b/src/main/java/org/caosdb/server/resource/ServerPropertiesResource.java
@@ -1,14 +1,14 @@
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerPropertiesSerializer;
-import org.caosdb.server.accessControl.ACMPermissions;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerPropertiesSerializer;
+import org.linkahead.server.accessControl.ACMPermissions;
import org.restlet.data.Form;
import org.restlet.data.Parameter;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
-public class ServerPropertiesResource extends AbstractCaosDBServerResource {
+public class ServerPropertiesResource extends AbstractLinkAheadServerResource {
@Override
protected void doInit() {
@@ -22,24 +22,24 @@ public class ServerPropertiesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpGetInChildClass() {
- if (CaosDBServer.isDebugMode()) {
+ if (LinkAheadServer.isDebugMode()) {
getUser().checkPermission(ACMPermissions.PERMISSION_ACCESS_SERVER_PROPERTIES);
return super.ok(
- new ServerPropertiesSerializer().serialize(CaosDBServer.getServerProperties()));
+ new ServerPropertiesSerializer().serialize(LinkAheadServer.getServerProperties()));
}
return error(Status.CLIENT_ERROR_NOT_FOUND);
}
@Override
protected Representation httpPostInChildClass(Representation entity) {
- if (CaosDBServer.isDebugMode()) {
+ if (LinkAheadServer.isDebugMode()) {
getUser().checkPermission(ACMPermissions.PERMISSION_ACCESS_SERVER_PROPERTIES);
Form form = new Form(entity);
for (Parameter param : form) {
- CaosDBServer.setProperty(param.getName(), param.getValue());
+ LinkAheadServer.setProperty(param.getName(), param.getValue());
}
return super.ok(
- new ServerPropertiesSerializer().serialize(CaosDBServer.getServerProperties()));
+ new ServerPropertiesSerializer().serialize(LinkAheadServer.getServerProperties()));
}
return error(Status.CLIENT_ERROR_NOT_FOUND);
}
diff --git a/src/main/java/org/caosdb/server/resource/SharedFileResource.java b/src/main/java/org/caosdb/server/resource/SharedFileResource.java
index 971dff6901e771cce13dac87d1d0a1ac30dde83e..4bfed91a518c381d58a404789ac75a0667f181f1 100644
--- a/src/main/java/org/caosdb/server/resource/SharedFileResource.java
+++ b/src/main/java/org/caosdb/server/resource/SharedFileResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,17 +22,17 @@
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static java.net.URLDecoder.decode;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.JDOMException;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Disposition;
import org.restlet.data.MediaType;
import org.restlet.data.Status;
@@ -44,7 +44,7 @@ import org.restlet.representation.Representation;
*
* @author Daniel Hornung
*/
-public class SharedFileResource extends AbstractCaosDBServerResource {
+public class SharedFileResource extends AbstractLinkAheadServerResource {
/**
* Download a File from the tempfiles folder. Only one File per Request.
diff --git a/src/main/java/org/caosdb/server/resource/ThumbnailsResource.java b/src/main/java/org/caosdb/server/resource/ThumbnailsResource.java
index c74251a1c31b2b3ec13bb72618b9c53d222e0cdf..9396c13fa05744142daeb654bcfd607256eb9260 100644
--- a/src/main/java/org/caosdb/server/resource/ThumbnailsResource.java
+++ b/src/main/java/org/caosdb/server/resource/ThumbnailsResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,25 +20,25 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
-import static org.caosdb.server.FileSystem.getFromFileSystem;
+import static org.linkahead.server.FileSystem.getFromFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.JDOMException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Disposition;
import org.restlet.data.MediaType;
import org.restlet.data.Status;
import org.restlet.representation.FileRepresentation;
import org.restlet.representation.Representation;
-public class ThumbnailsResource extends AbstractCaosDBServerResource {
+public class ThumbnailsResource extends AbstractLinkAheadServerResource {
/**
- * Download a File from the CaosDBFileSystem. Only one File per Request.
+ * Download a File from the LinkAheadFileSystem. Only one File per Request.
*
* @author Timm Fitschen
* @return InputRepresentation
diff --git a/src/main/java/org/caosdb/server/resource/UserResource.java b/src/main/java/org/caosdb/server/resource/UserResource.java
index de07331e9637549285d71ca2fd910916cd13316a..b8b0f5e8b4a53ac747eb0c6c6a3414cb5db1b2ad 100644
--- a/src/main/java/org/caosdb/server/resource/UserResource.java
+++ b/src/main/java/org/caosdb/server/resource/UserResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,27 +20,27 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.accessControl.UserStatus;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.transaction.DeleteUserTransaction;
-import org.caosdb.server.transaction.InsertUserTransaction;
-import org.caosdb.server.transaction.RetrieveUserTransaction;
-import org.caosdb.server.transaction.UpdateUserTransaction;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.accessControl.UserStatus;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.transaction.DeleteUserTransaction;
+import org.linkahead.server.transaction.InsertUserTransaction;
+import org.linkahead.server.transaction.RetrieveUserTransaction;
+import org.linkahead.server.transaction.UpdateUserTransaction;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Form;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
@@ -50,11 +50,11 @@ import org.restlet.representation.Representation;
*
* @author Timm Fitschen
*/
-public class UserResource extends AbstractCaosDBServerResource {
+public class UserResource extends AbstractLinkAheadServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final Document doc = new Document();
@@ -148,7 +148,8 @@ public class UserResource extends AbstractCaosDBServerResource {
UserStatus.valueOf(
form.getFirstValue(
"status",
- CaosDBServer.getServerProperty(ServerProperties.KEY_NEW_USER_DEFAULT_ACTIVITY))
+ LinkAheadServer.getServerProperty(
+ ServerProperties.KEY_NEW_USER_DEFAULT_ACTIVITY))
.toUpperCase());
Integer userEntity = null;
if (form.getFirst("entity") != null) {
@@ -177,7 +178,7 @@ public class UserResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, Exception {
final Document doc = new Document();
diff --git a/src/main/java/org/caosdb/server/resource/UserRolesResource.java b/src/main/java/org/caosdb/server/resource/UserRolesResource.java
index 4eb7f6143038bb6e4b0c3fda4646e2730acfea04..8ba2044206d87c85687112977df0c5c2c1f7fa14 100644
--- a/src/main/java/org/caosdb/server/resource/UserRolesResource.java
+++ b/src/main/java/org/caosdb/server/resource/UserRolesResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,32 +20,32 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.List;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.transaction.RetrieveUserRolesTransaction;
-import org.caosdb.server.transaction.UpdateUserRolesTransaction;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.transaction.RetrieveUserRolesTransaction;
+import org.linkahead.server.transaction.UpdateUserRolesTransaction;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
-public class UserRolesResource extends AbstractCaosDBServerResource {
+public class UserRolesResource extends AbstractLinkAheadServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final String user = getRequestedItems()[0];
final String realm =
diff --git a/src/main/java/org/caosdb/server/resource/Webinterface.java b/src/main/java/org/caosdb/server/resource/Webinterface.java
index 95901260937a5364a68ed3e9e6849210bd67d6b3..bf7812178f36d58d564c5f20470b9f67115ff34c 100644
--- a/src/main/java/org/caosdb/server/resource/Webinterface.java
+++ b/src/main/java/org/caosdb/server/resource/Webinterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.utils.WebinterfaceUtils;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.utils.WebinterfaceUtils;
import org.restlet.data.CacheDirective;
import org.restlet.data.Header;
import org.restlet.data.MediaType;
@@ -98,7 +98,8 @@ public class Webinterface extends ServerResource {
cacheDirectives.add(
new CacheDirective(
HeaderConstants.CACHE_MAX_AGE,
- CaosDBServer.getServerProperty(ServerProperties.KEY_WEBUI_HTTP_HEADER_CACHE_MAX_AGE)));
+ LinkAheadServer.getServerProperty(
+ ServerProperties.KEY_WEBUI_HTTP_HEADER_CACHE_MAX_AGE)));
getResponse().setCacheDirectives(cacheDirectives);
return ret;
}
diff --git a/src/main/java/org/caosdb/server/resource/WebinterfaceBuildNumber.java b/src/main/java/org/caosdb/server/resource/WebinterfaceBuildNumber.java
index 22f1a46e4fd314b0dcaebde7abdcc1d41a9f50f0..428cbe1442823a3105619bb5bc2530ab4fbfd49c 100644
--- a/src/main/java/org/caosdb/server/resource/WebinterfaceBuildNumber.java
+++ b/src/main/java/org/caosdb/server/resource/WebinterfaceBuildNumber.java
@@ -1,5 +1,5 @@
/**
- * ** header v3.0 This file is a part of the CaosDB Project.
+ * ** header v3.0 This file is a part of the LinkAhead Project.
*
* <p>Copyright (c) 2019 IndiScale GmbH Copyright (c) 2019 Daniel Hornung <d.hornung@indiscale.com>
*
@@ -16,9 +16,9 @@
*
* <p>** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
-import org.caosdb.server.utils.WebinterfaceUtils;
+import org.linkahead.server.utils.WebinterfaceUtils;
import org.restlet.data.Status;
import org.restlet.resource.Get;
import org.restlet.resource.ResourceException;
diff --git a/src/main/java/org/caosdb/server/resource/transaction/EntityNamesResource.java b/src/main/java/org/caosdb/server/resource/transaction/EntityNamesResource.java
index 0c66485ea3d62286d633d9580c1362ba33435095..7fd729062bf847daaec7b0f29ffd54931f624fd7 100644
--- a/src/main/java/org/caosdb/server/resource/transaction/EntityNamesResource.java
+++ b/src/main/java/org/caosdb/server/resource/transaction/EntityNamesResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,9 +22,9 @@
*
* ** end header
*/
-package org.caosdb.server.resource.transaction;
+package org.linkahead.server.resource.transaction;
-import org.caosdb.server.entity.container.RetrieveContainer;
+import org.linkahead.server.entity.container.RetrieveContainer;
/**
* Resource which returns only the names of entities.
diff --git a/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java b/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java
index 4cd7b2fcbd4ae9e9dd3d047555194172c4224d38..d2a54274e2e3d535675dc9a9997822ff1162b5b6 100644
--- a/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java
+++ b/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.resource.transaction;
+package org.linkahead.server.resource.transaction;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
@@ -28,22 +28,22 @@ import org.apache.commons.fileupload.FileItemIterator;
import org.apache.commons.fileupload.FileItemStream;
import org.apache.commons.fileupload.FileUploadException;
import org.apache.commons.fileupload.disk.DiskFileItemFactory;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.WritableContainer;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.transaction.WriteTransactionInterface;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.WritableContainer;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.transaction.WriteTransactionInterface;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.MediaType;
import org.restlet.ext.fileupload.RestletFileUpload;
import org.restlet.representation.Representation;
@@ -130,7 +130,7 @@ public class EntityResource extends RetrieveEntityResource {
*/
private Element parseMultipartEntity(final WritableContainer container)
throws FileUploadException, IOException, Message, xmlNotWellFormedException,
- NoSuchAlgorithmException, CaosDBException {
+ NoSuchAlgorithmException, LinkAheadException {
final DiskFileItemFactory factory = new DiskFileItemFactory();
factory.setSizeThreshold(1000240);
final RestletFileUpload upload = new RestletFileUpload(factory);
diff --git a/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java b/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java
index 6527376d71ba31718394f887b7335615d80db5c6..0a24366a2b3d887dd0574fafc1ca0daa86ff8498 100644
--- a/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java
+++ b/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,19 +19,19 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.resource.transaction;
+package org.linkahead.server.resource.transaction;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.resource.AbstractCaosDBServerResource;
-import org.caosdb.server.transaction.Retrieve;
import org.jdom2.Document;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.resource.AbstractLinkAheadServerResource;
+import org.linkahead.server.transaction.Retrieve;
import org.restlet.representation.Representation;
/**
@@ -40,7 +40,7 @@ import org.restlet.representation.Representation;
*
* @author Timm Fitschen (t.fitschen@indiscale.com)
*/
-public abstract class RetrieveEntityResource extends AbstractCaosDBServerResource {
+public abstract class RetrieveEntityResource extends AbstractLinkAheadServerResource {
/**
* Parse the segment which specifies the entities which are to be retrieved
@@ -74,7 +74,7 @@ public abstract class RetrieveEntityResource extends AbstractCaosDBServerResourc
/** Handle the GET request. */
@Override
protected final Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final RetrieveContainer entityContainer =
diff --git a/src/main/java/org/caosdb/server/scripting/CallerSerializer.java b/src/main/java/org/caosdb/server/scripting/CallerSerializer.java
index b133ad5cf02afa0194beb175883b999e75810efe..710f78607e8dd31b94dfae98cfb9f9848fffe88b 100644
--- a/src/main/java/org/caosdb/server/scripting/CallerSerializer.java
+++ b/src/main/java/org/caosdb/server/scripting/CallerSerializer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,12 +21,12 @@
*
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
import java.io.IOException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.utils.Serializer;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.utils.Serializer;
/**
* Serializes the result of calling a server-side script into XML.
@@ -49,14 +49,14 @@ public class CallerSerializer implements Serializer<ServerSideScriptingCaller, E
try {
stdout.addContent(caller.getStdOut());
} catch (IOException e) {
- throw new CaosDBException(e);
+ throw new LinkAheadException(e);
}
Element stderr = new Element("stderr");
try {
stderr.addContent(caller.getStdErr());
} catch (IOException e) {
- throw new CaosDBException(e);
+ throw new LinkAheadException(e);
}
Element tmpdir = new Element("shareddir");
diff --git a/src/main/java/org/caosdb/server/scripting/ScriptingPermissions.java b/src/main/java/org/caosdb/server/scripting/ScriptingPermissions.java
index 0af49e9faf6ec8ad9a4107d72554a44744184661..9b09785d4958a427e539c674b8f5cb4ffb308aff 100644
--- a/src/main/java/org/caosdb/server/scripting/ScriptingPermissions.java
+++ b/src/main/java/org/caosdb/server/scripting/ScriptingPermissions.java
@@ -1,6 +1,6 @@
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
-import org.caosdb.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.ACMPermissions;
public class ScriptingPermissions extends ACMPermissions {
diff --git a/src/main/java/org/caosdb/server/scripting/ScriptingUtils.java b/src/main/java/org/caosdb/server/scripting/ScriptingUtils.java
index c9a0b522d949a4ba3c36ae4f867661263a0185d3..5cc3b459398baba6f33cc0a12c12312f83756a5c 100644
--- a/src/main/java/org/caosdb/server/scripting/ScriptingUtils.java
+++ b/src/main/java/org/caosdb/server/scripting/ScriptingUtils.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ConfigurationException;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ConfigurationException;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
public class ScriptingUtils {
@@ -40,11 +40,11 @@ public class ScriptingUtils {
public ScriptingUtils() {
ArrayList<File> new_bin_dirs = new ArrayList<>();
String bin_dirs_str =
- CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_BIN_DIRS);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_BIN_DIRS);
if (bin_dirs_str == null) {
// fall-back for old server property
bin_dirs_str =
- CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_BIN_DIR);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_BIN_DIR);
}
// split and process
@@ -75,7 +75,8 @@ public class ScriptingUtils {
this.working =
new File(
- CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_WORKING_DIR));
+ LinkAheadServer.getServerProperty(
+ ServerProperties.KEY_SERVER_SIDE_SCRIPTING_WORKING_DIR));
if (!working.exists()) {
working.mkdirs();
diff --git a/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java b/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java
index edb6b39a4e92466e5a3e5a489669d366bbe8ce37..a64378c350d774bcda02663bbf8aae5a1116ecb9 100644
--- a/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java
+++ b/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
import java.io.File;
import java.io.FileNotFoundException;
@@ -34,13 +34,13 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.io.FileUtils;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
/**
* Calls server-side scripting scripts.
@@ -163,7 +163,7 @@ public class ServerSideScriptingCaller {
}
void putFilesInWorkingDir(final Collection<FileProperties> files)
- throws FileNotFoundException, CaosDBException {
+ throws FileNotFoundException, LinkAheadException {
if (files == null) {
return;
}
@@ -174,13 +174,13 @@ public class ServerSideScriptingCaller {
}
for (final FileProperties f : files) {
if (f.getPath() == null || f.getPath().isEmpty()) {
- throw new CaosDBException("The path must not be null or empty!");
+ throw new LinkAheadException("The path must not be null or empty!");
}
File link = getUploadFilesDir().toPath().resolve(f.getPath()).toFile();
if (!link.getParentFile().exists()) {
link.getParentFile().mkdirs();
}
- org.caosdb.server.utils.FileUtils.createSymlink(link, f.getFile());
+ org.linkahead.server.utils.FileUtils.createSymlink(link, f.getFile());
}
}
@@ -196,7 +196,7 @@ public class ServerSideScriptingCaller {
}
/**
- * Create a writable "home like" directory, needed for some Python libs, e.g. caosdb-pylib.
+ * Create a writable "home like" directory, needed for some Python libs, e.g. linkahead-pylib.
*
* <p>The temporary working directory must exist when this method is called.
*/
@@ -212,7 +212,7 @@ public class ServerSideScriptingCaller {
}
File srcDir =
new File(
- CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_HOME_DIR));
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_HOME_DIR));
FileUtils.copyDirectory(srcDir, this.tmpHome);
}
diff --git a/src/main/java/org/caosdb/server/scripting/TimeoutException.java b/src/main/java/org/caosdb/server/scripting/TimeoutException.java
index 31b9b7e989989677653e5938cc6bd531878f5299..bbe0e7718b32432c2782b27d58beab3bb4a719aa 100644
--- a/src/main/java/org/caosdb/server/scripting/TimeoutException.java
+++ b/src/main/java/org/caosdb/server/scripting/TimeoutException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
public class TimeoutException extends Exception {
diff --git a/src/main/java/org/caosdb/server/scripting/TimeoutProcess.java b/src/main/java/org/caosdb/server/scripting/TimeoutProcess.java
index c867ca3b7f0190b1cd5d6b6be4f595be10d2891a..2e1ce29de7d5760dc722a950989ab6ab4f2bd793 100644
--- a/src/main/java/org/caosdb/server/scripting/TimeoutProcess.java
+++ b/src/main/java/org/caosdb/server/scripting/TimeoutProcess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
import java.io.InputStream;
diff --git a/src/main/java/org/caosdb/server/transaction/AccessControlTransaction.java b/src/main/java/org/caosdb/server/transaction/AccessControlTransaction.java
index 1cf9f8f70df2eaa384e4074cc3b80a4816a88142..3dd742641203d418934d4fd1e1f0258ab3d81e6f 100644
--- a/src/main/java/org/caosdb/server/transaction/AccessControlTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/AccessControlTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.misc.RollBackHandler;
-import org.caosdb.server.entity.Message;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.misc.RollBackHandler;
+import org.linkahead.server.entity.Message;
public abstract class AccessControlTransaction implements TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/ChecksumUpdater.java b/src/main/java/org/caosdb/server/transaction/ChecksumUpdater.java
index 1f52ca8d8d19abd16848e6506eaa5d3ada32cb6a..6b74221418d1ec1d2c87fd4f38f6e3d7ccafb799 100644
--- a/src/main/java/org/caosdb/server/transaction/ChecksumUpdater.java
+++ b/src/main/java/org/caosdb/server/transaction/ChecksumUpdater.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,23 +20,23 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.GetUpdateableChecksums;
-import org.caosdb.server.database.backend.transaction.RetrieveSparseEntity;
-import org.caosdb.server.database.backend.transaction.SetFileChecksum;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.container.WritableContainer;
-import org.caosdb.server.utils.FileUtils;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.GetUpdateableChecksums;
+import org.linkahead.server.database.backend.transaction.RetrieveSparseEntity;
+import org.linkahead.server.database.backend.transaction.SetFileChecksum;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.container.WritableContainer;
+import org.linkahead.server.utils.FileUtils;
/**
* Retrieves all file without a checksum, calculates one and stores it to the database (method
@@ -108,7 +108,7 @@ public class ChecksumUpdater extends WriteTransaction
private boolean wasChangedInTheMeantime(
final EntityInterface fileEntity, final Access access, final long lastModified)
- throws NoSuchAlgorithmException, IOException, CaosDBException, Message {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException, Message {
final EntityInterface checkEntity =
execute(new RetrieveSparseEntity(fileEntity), access).getEntity();
final FileProperties thatFP = checkEntity.getFileProperties();
@@ -126,7 +126,7 @@ public class ChecksumUpdater extends WriteTransaction
e.printStackTrace();
} catch (final IOException e) {
e.printStackTrace();
- } catch (final CaosDBException e) {
+ } catch (final LinkAheadException e) {
e.printStackTrace();
}
return null;
diff --git a/src/main/java/org/caosdb/server/transaction/DeleteRoleTransaction.java b/src/main/java/org/caosdb/server/transaction/DeleteRoleTransaction.java
index 2e7e5b2a5ad4354b517dc7020f44f5ece459cc35..532a4afa5b3c8f0f4409908dd4b3ae8d57dfa857 100644
--- a/src/main/java/org/caosdb/server/transaction/DeleteRoleTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/DeleteRoleTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,16 +21,16 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.backend.transaction.DeleteRole;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.SetPermissionRules;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.backend.transaction.DeleteRole;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.SetPermissionRules;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
public class DeleteRoleTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java b/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java
index 24aac16b9c529130520518822e6bf3a6a3e8b72d..200277a3ffc2ae359615340f3c3b7c9c69ce1893 100644
--- a/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,20 +21,20 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.backend.transaction.DeletePassword;
-import org.caosdb.server.database.backend.transaction.DeleteUser;
-import org.caosdb.server.database.backend.transaction.RetrievePasswordValidator;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.backend.transaction.DeletePassword;
+import org.linkahead.server.database.backend.transaction.DeleteUser;
+import org.linkahead.server.database.backend.transaction.RetrievePasswordValidator;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
public class DeleteUserTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java b/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java
index 59d12c73ccdcf620f0e7c2f2f3bbb51233f51d84..54f42f9d2b3b4dcec260a061325518b3a4942196 100644
--- a/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java
+++ b/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.ArrayList;
import java.util.HashMap;
@@ -28,22 +28,22 @@ import java.util.Iterator;
import java.util.List;
import java.util.Map.Entry;
import java.util.TimeZone;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.FileConsistencyCheck;
-import org.caosdb.server.database.backend.transaction.GetFileIterator;
-import org.caosdb.server.database.backend.transaction.GetFileRecordByPath;
-import org.caosdb.server.database.backend.transaction.RetrieveAllUncheckedFiles;
-import org.caosdb.server.database.backend.transaction.SetFileCheckedTimestamp;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.utils.SHA512;
import org.jdom2.Element;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.FileConsistencyCheck;
+import org.linkahead.server.database.backend.transaction.GetFileIterator;
+import org.linkahead.server.database.backend.transaction.GetFileRecordByPath;
+import org.linkahead.server.database.backend.transaction.RetrieveAllUncheckedFiles;
+import org.linkahead.server.database.backend.transaction.SetFileCheckedTimestamp;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.utils.SHA512;
public class FileStorageConsistencyCheck extends Thread
implements ToElementable, TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/InsertLogRecordTransaction.java b/src/main/java/org/caosdb/server/transaction/InsertLogRecordTransaction.java
index 950d9b8d25688e47833b60c01335f8dd525a0630..a7ecbb40a8f360d318784b39434c8aa9ad92449f 100644
--- a/src/main/java/org/caosdb/server/transaction/InsertLogRecordTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/InsertLogRecordTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.List;
import java.util.logging.LogRecord;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.InsertLogRecord;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.InsertLogRecord;
public class InsertLogRecordTransaction implements TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/InsertRoleTransaction.java b/src/main/java/org/caosdb/server/transaction/InsertRoleTransaction.java
index 44288af5888c2dacbf9e97c235a76e0d9992a969..173907d8b2909a7115a1a8ea3c9d0a01ebbb7af6 100644
--- a/src/main/java/org/caosdb/server/transaction/InsertRoleTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/InsertRoleTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.backend.transaction.InsertRole;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.SetPermissionRules;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.backend.transaction.InsertRole;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.SetPermissionRules;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
public class InsertRoleTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java b/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java
index f3f4c7f5fd583ff0ff16d4fd1ce583394258f35b..1ef9e9f7edf40f7a9e122ec938b092194fb6f8b8 100644
--- a/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,24 +21,24 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.accessControl.UserStatus;
-import org.caosdb.server.database.backend.transaction.SetPassword;
-import org.caosdb.server.database.backend.transaction.UpdateUser;
-import org.caosdb.server.database.backend.transaction.UpdateUserRoles;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.accessControl.UserStatus;
+import org.linkahead.server.database.backend.transaction.SetPassword;
+import org.linkahead.server.database.backend.transaction.UpdateUser;
+import org.linkahead.server.database.backend.transaction.UpdateUserRoles;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
public class InsertUserTransaction extends AccessControlTransaction {
@@ -92,10 +92,10 @@ public class InsertUserTransaction extends AccessControlTransaction {
* Check requirements for user names (length, character set). Default config is POSIX compliant.
*/
private void checkUserName(String name) throws Message {
- String regex = CaosDBServer.getServerProperty(ServerProperties.KEY_USER_NAME_VALID_REGEX);
+ String regex = LinkAheadServer.getServerProperty(ServerProperties.KEY_USER_NAME_VALID_REGEX);
if (!name.matches(regex)) {
throw ServerMessages.INVALID_USER_NAME(
- CaosDBServer.getServerProperty(ServerProperties.KEY_USER_NAME_INVALID_MESSAGE));
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_USER_NAME_INVALID_MESSAGE));
}
if (UserSources.isUserExisting(new Principal(this.user.realm, this.user.name))) {
diff --git a/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java b/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java
index ed3cd3cc5a154e82946e76f9934ee8608fe6980c..3abd2dd75f5743e81f691459425936ddd01cfa06 100644
--- a/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,17 +19,17 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Iterator;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.backend.transaction.ListRoles;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.backend.transaction.ListRoles;
+import org.linkahead.server.database.proto.ProtoUser;
public class ListRolesTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java b/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java
index 2ade4e8595f159d1fc6996c1e04913f4195ecd97..c14051a422a8f402bb130db5eddd821847791201 100644
--- a/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,15 +19,15 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.backend.transaction.ListUsers;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.backend.transaction.ListUsers;
+import org.linkahead.server.database.proto.ProtoUser;
public class ListUsersTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/LogUserVisitTransaction.java b/src/main/java/org/caosdb/server/transaction/LogUserVisitTransaction.java
index dff0d34fed5bab445bfd761817aecc474def6025..a08bc1f135e342ae877cd50e5230e6a2b60548d8 100644
--- a/src/main/java/org/caosdb/server/transaction/LogUserVisitTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/LogUserVisitTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,9 +17,9 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import org.caosdb.server.database.backend.transaction.LogUserVisit;
+import org.linkahead.server.database.backend.transaction.LogUserVisit;
public class LogUserVisitTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/Retrieve.java b/src/main/java/org/caosdb/server/transaction/Retrieve.java
index 643c1201b530af9821c9a5c1a7b62f7c5d04cf52..3f11f976d8367edf6ac433bcd3071d5e8b034716 100644
--- a/src/main/java/org/caosdb/server/transaction/Retrieve.java
+++ b/src/main/java/org/caosdb/server/transaction/Retrieve.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,21 +20,21 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.entity.xml.IdAndServerMessagesOnlyStrategy;
-import org.caosdb.server.jobs.ScheduledJob;
-import org.caosdb.server.jobs.core.JobFailureSeverity;
-import org.caosdb.server.jobs.core.RemoveDuplicates;
-import org.caosdb.server.jobs.core.ResolveNames;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.entity.xml.IdAndServerMessagesOnlyStrategy;
+import org.linkahead.server.jobs.ScheduledJob;
+import org.linkahead.server.jobs.core.JobFailureSeverity;
+import org.linkahead.server.jobs.core.RemoveDuplicates;
+import org.linkahead.server.jobs.core.ResolveNames;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class Retrieve extends Transaction<RetrieveContainer> {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveACL.java b/src/main/java/org/caosdb/server/transaction/RetrieveACL.java
index ac0a2896451a43ca10985bd38787ad4f847a05cc..d905a19390788065aaf26105eb2864c7d7b2ac0c 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveACL.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveACL.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,19 +19,19 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import com.google.protobuf.ProtocolStringList;
import java.util.UUID;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.backend.transaction.RetrieveEntityACLTransaction;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.permissions.EntityPermission;
+import org.linkahead.server.database.backend.transaction.RetrieveEntityACLTransaction;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.permissions.EntityPermission;
public class RetrieveACL extends Transaction<TransactionContainer> {
@@ -75,7 +75,7 @@ public class RetrieveACL extends Transaction<TransactionContainer> {
&& acl.isPermitted(getTransactor(), EntityPermission.RETRIEVE_ENTITY)) {
throw new AuthorizationException("You are not permitted to update this entity's ACL.");
} else {
- e.addError(org.caosdb.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST);
+ e.addError(org.linkahead.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST);
}
}
}
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveLogRecordTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrieveLogRecordTransaction.java
index 2f6cafd6e4e55ab868f69f1d3414a2196f0a4fea..d33d82a2458c2ea019337a8a4b25cf46d3410b39 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveLogRecordTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveLogRecordTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.LogRecord;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.RetrieveLogRecord;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.RetrieveLogRecord;
public class RetrieveLogRecordTransaction implements TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrievePasswordValidatorTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrievePasswordValidatorTransaction.java
index bb1e136bcb62c28800d0b7c2c0d88c9a2ee34634..9d01ecf111b2869a899e37b15ba3477948c55cf0 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrievePasswordValidatorTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrievePasswordValidatorTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.database.backend.transaction.RetrievePasswordValidator;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.database.backend.transaction.RetrievePasswordValidator;
+import org.linkahead.server.utils.ServerMessages;
public class RetrievePasswordValidatorTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrievePermissionRulesTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrievePermissionRulesTransaction.java
index 225d068895d6484448b149d6b925facaabbf75fb..f3fea603615f544fb5c9c399363ae864a74bd5be 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrievePermissionRulesTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrievePermissionRulesTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.HashSet;
-import org.caosdb.server.database.backend.transaction.RetrievePermissionRules;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.backend.transaction.RetrievePermissionRules;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.utils.ServerMessages;
public class RetrievePermissionRulesTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveRoleTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrieveRoleTransaction.java
index 8e92a347f869b2a6a3e6f2be58d9124e6a9442d7..a60b6bb322140c3e255000e0676b6ab5fd92cefa 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveRoleTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveRoleTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Iterator;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.utils.ServerMessages;
public class RetrieveRoleTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveSparseEntityByPath.java b/src/main/java/org/caosdb/server/transaction/RetrieveSparseEntityByPath.java
index eca97ce64c7f235fe5b7ec6d26e003301bb53bff..902f5f679c26fa244af338e03075adcc8c866ea5 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveSparseEntityByPath.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveSparseEntityByPath.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import org.caosdb.server.database.backend.transaction.GetFileRecordByPath;
-import org.caosdb.server.database.backend.transaction.RetrieveSparseEntity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.TransactionContainer;
+import org.linkahead.server.database.backend.transaction.GetFileRecordByPath;
+import org.linkahead.server.database.backend.transaction.RetrieveSparseEntity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.TransactionContainer;
public class RetrieveSparseEntityByPath extends Transaction<TransactionContainer> {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveUserRolesTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrieveUserRolesTransaction.java
index e26e29830a6e3c5f135b467f4622febda195da89..acc3bdd93bbea59078bb3ecfafc8f6b054e95a35 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveUserRolesTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveUserRolesTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Set;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.utils.ServerMessages;
public class RetrieveUserRolesTransaction implements TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java
index eb24fb24db4f1b6a50a279cfcd9e158003a70948..41562e0e579169f21a06668eb022fe7a0b51025c 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,18 +21,18 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.backend.transaction.RetrieveUser;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.backend.transaction.RetrieveUser;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.utils.ServerMessages;
public class RetrieveUserTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/Transaction.java b/src/main/java/org/caosdb/server/transaction/Transaction.java
index 5fc06f5ec82066d3515cbf524e64beb001ba0fcd..21ccb9dfb4cf049c69ed11348c8419fd3612248d 100644
--- a/src/main/java/org/caosdb/server/transaction/Transaction.java
+++ b/src/main/java/org/caosdb/server/transaction/Transaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,34 +19,34 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.HashMap;
import java.util.List;
import org.apache.shiro.subject.Subject;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.InsertTransactionHistory;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.Schedule;
-import org.caosdb.server.jobs.ScheduledJob;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.jobs.core.AccessControl;
-import org.caosdb.server.jobs.core.CheckDatatypePresent;
-import org.caosdb.server.jobs.core.CheckEntityACLRoles;
-import org.caosdb.server.jobs.core.JobFailureSeverity;
-import org.caosdb.server.jobs.core.PickUp;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.utils.AbstractObservable;
-import org.caosdb.server.utils.Info;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.InsertTransactionHistory;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.Schedule;
+import org.linkahead.server.jobs.ScheduledJob;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.jobs.core.AccessControl;
+import org.linkahead.server.jobs.core.CheckDatatypePresent;
+import org.linkahead.server.jobs.core.CheckEntityACLRoles;
+import org.linkahead.server.jobs.core.JobFailureSeverity;
+import org.linkahead.server.jobs.core.PickUp;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.utils.AbstractObservable;
+import org.linkahead.server.utils.Info;
+import org.linkahead.server.utils.Observer;
public abstract class Transaction<C extends TransactionContainer> extends AbstractObservable
implements TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/TransactionInterface.java b/src/main/java/org/caosdb/server/transaction/TransactionInterface.java
index 8e01c7d9b407927ebdb6a0528f7dcbc6d5bea40d..68b0073ba48d3cff8c15e117a8b17b8df5689ca3 100644
--- a/src/main/java/org/caosdb/server/transaction/TransactionInterface.java
+++ b/src/main/java/org/caosdb/server/transaction/TransactionInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.misc.RollBackHandler;
-import org.caosdb.server.database.misc.TransactionBenchmark;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.misc.RollBackHandler;
+import org.linkahead.server.database.misc.TransactionBenchmark;
public interface TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/UpdateACL.java b/src/main/java/org/caosdb/server/transaction/UpdateACL.java
index 84c73080550d8899f4f1a5156bebb2a44c39df6a..5a8471acde15612524493e32bbcdd35bad02f4fd 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdateACL.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdateACL.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,22 +19,22 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import static org.caosdb.server.query.Query.clearCache;
+import static org.linkahead.server.query.Query.clearCache;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.database.backend.transaction.UpdateEntityTransaction;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.core.CheckEntityACLRoles;
-import org.caosdb.server.jobs.core.JobFailureSeverity;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.database.backend.transaction.UpdateEntityTransaction;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.core.CheckEntityACLRoles;
+import org.linkahead.server.jobs.core.JobFailureSeverity;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
public class UpdateACL extends Transaction<TransactionContainer>
implements WriteTransactionInterface {
@@ -104,7 +104,7 @@ public class UpdateACL extends Transaction<TransactionContainer>
"You are not permitted to change permission rules of this entity.");
} else {
// we pretend this entity doesn't exist
- result.addError(org.caosdb.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST);
+ result.addError(org.linkahead.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST);
}
return result;
});
diff --git a/src/main/java/org/caosdb/server/transaction/UpdatePermissionRulesTransaction.java b/src/main/java/org/caosdb/server/transaction/UpdatePermissionRulesTransaction.java
index 4f8c9369fe915675e24c55e9fc7e0052ede360b3..929d8200273b1aeb15437c73c8b9d383a2a240c1 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdatePermissionRulesTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdatePermissionRulesTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.SetPermissionRules;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.SetPermissionRules;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.utils.ServerMessages;
public class UpdatePermissionRulesTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/UpdateRoleTransaction.java b/src/main/java/org/caosdb/server/transaction/UpdateRoleTransaction.java
index a62aff5bb6e90120e6cfd6651acde231cf3519b1..02b8ec267252b939d8bafdb0aef7776506f54f35 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdateRoleTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdateRoleTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,19 +21,19 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.backend.transaction.InsertRole;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.SetPermissionRules;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.backend.transaction.InsertRole;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.SetPermissionRules;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.utils.ServerMessages;
public class UpdateRoleTransaction extends AccessControlTransaction {
@@ -58,7 +58,9 @@ public class UpdateRoleTransaction extends AccessControlTransaction {
Set<PermissionRule> oldPermissions = Set.copyOf(oldRole.permission_rules);
Set<PermissionRule> newPermissions = Set.copyOf(role.permission_rules);
if (!oldPermissions.equals(newPermissions)) {
- if (org.caosdb.server.permissions.Role.ADMINISTRATION.toString().equals(this.role.name)) {
+ if (org.linkahead.server.permissions.Role.ADMINISTRATION
+ .toString()
+ .equals(this.role.name)) {
throw ServerMessages.SPECIAL_ROLE_PERMISSIONS_CANNOT_BE_CHANGED();
}
subject.checkPermission(ACMPermissions.PERMISSION_UPDATE_ROLE_PERMISSIONS(this.role.name));
diff --git a/src/main/java/org/caosdb/server/transaction/UpdateUserRolesTransaction.java b/src/main/java/org/caosdb/server/transaction/UpdateUserRolesTransaction.java
index a74d875fc8b4d14821de24522e8b9bc531416ee5..74fa1b544acfac79b03e336dcdd6f2339c50dc5a 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdateUserRolesTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdateUserRolesTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.HashSet;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.UpdateUserRoles;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.UpdateUserRoles;
+import org.linkahead.server.utils.ServerMessages;
public class UpdateUserRolesTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java b/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java
index 6808968f20574242cfdaa9b87793d7a4ad4b6914..0fa8216d9176456e89f43a31b6cab70a6b224805 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,32 +21,32 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.HashSet;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.accessControl.UserStatus;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.RetrieveUser;
-import org.caosdb.server.database.backend.transaction.SetPassword;
-import org.caosdb.server.database.backend.transaction.UpdateUser;
-import org.caosdb.server.database.backend.transaction.UpdateUserRoles;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.accessControl.UserStatus;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.RetrieveUser;
+import org.linkahead.server.database.backend.transaction.SetPassword;
+import org.linkahead.server.database.backend.transaction.UpdateUser;
+import org.linkahead.server.database.backend.transaction.UpdateUserRoles;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
/**
* This transaction also checks if the current user has sufficient permissions to make the update.
@@ -67,7 +67,7 @@ public class UpdateUserTransaction extends AccessControlTransaction {
final String password) {
this.user = new ProtoUser();
this.user.realm =
- realm == null
+ realm == null // If there was no definite realm to be found, use the internal realm's name.
? UserSources.guessRealm(username, UserSources.getInternalRealm().getName())
: realm;
this.user.name = username;
@@ -102,7 +102,7 @@ public class UpdateUserTransaction extends AccessControlTransaction {
+ this.user.realm
+ "' cannot be updated. Only the users from the realm '"
+ UserSources.getInternalRealm().getName()
- + "' can change their passwords from within caosdb.");
+ + "' can change their passwords from within LinkAhead.");
}
SecurityUtils.getSubject()
diff --git a/src/main/java/org/caosdb/server/transaction/WriteTransaction.java b/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
index 47b7a53c71ddebb7c1b062c2c8599cf44eabe039..22b8ac0c7818caa2eb88f7c4d68f551213c94af3 100644
--- a/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
@@ -30,34 +30,34 @@ import java.util.Objects;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.DeleteEntityTransaction;
-import org.caosdb.server.database.backend.transaction.InsertEntityTransaction;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.database.backend.transaction.UpdateEntityTransaction;
-import org.caosdb.server.database.misc.RollBackHandler;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.container.WritableContainer;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.Schedule;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.permissions.Permission;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.DeleteEntityTransaction;
+import org.linkahead.server.database.backend.transaction.InsertEntityTransaction;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.database.backend.transaction.UpdateEntityTransaction;
+import org.linkahead.server.database.misc.RollBackHandler;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.container.WritableContainer;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.Schedule;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.permissions.Permission;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* This class is responsible for inserting, updating and deleting entities which are held in the
@@ -362,13 +362,13 @@ public class WriteTransaction extends Transaction<WritableContainer>
*
* @param newEntity
* @param oldEntity
- * @throws CaosDBException
+ * @throws LinkAheadException
* @throws IOException
* @throws NoSuchAlgorithmException
*/
public HashSet<Permission> deriveUpdate(
final EntityInterface newEntity, final EntityInterface oldEntity)
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final HashSet<Permission> needPermissions = new HashSet<>();
boolean updatetable = false;
diff --git a/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java b/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java
index 4e2938e18d061cbd1a7575baa59322356731859a..44662633f20abe2faf3c8986663bf78d5f98cf6b 100644
--- a/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java
+++ b/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java
@@ -1,7 +1,7 @@
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
+import org.linkahead.server.database.access.Access;
public interface WriteTransactionInterface extends TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/utils/AbstractObservable.java b/src/main/java/org/caosdb/server/utils/AbstractObservable.java
index abc7f0a0ae1cdcbeff613c2778637de97a507c57..996fd0b4f9176d8448fcff50d009a159824f4185 100644
--- a/src/main/java/org/caosdb/server/utils/AbstractObservable.java
+++ b/src/main/java/org/caosdb/server/utils/AbstractObservable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.util.Iterator;
import org.eclipse.jetty.util.ConcurrentHashSet;
diff --git a/src/main/java/org/caosdb/server/utils/AsynchronousHasher.java b/src/main/java/org/caosdb/server/utils/AsynchronousHasher.java
index 47dad864835e8c370ddef31988205a113665b6c1..35524bf2533e3165ca3e4c06ebbe4df58df1c7a3 100644
--- a/src/main/java/org/caosdb/server/utils/AsynchronousHasher.java
+++ b/src/main/java/org/caosdb/server/utils/AsynchronousHasher.java
@@ -1,7 +1,7 @@
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@ package org.caosdb.server.utils;
*
* ** end header
*/
-// package org.caosdb.server.utils;
+// package org.linkahead.server.utils;
//
// import java.io.File;
//
diff --git a/src/main/java/org/caosdb/server/utils/ConfigurationException.java b/src/main/java/org/caosdb/server/utils/ConfigurationException.java
index df04ac169f3c8113443a69795840a50774bef0b1..509658fc5736ff04b076c2acfc99100a3c574af2 100644
--- a/src/main/java/org/caosdb/server/utils/ConfigurationException.java
+++ b/src/main/java/org/caosdb/server/utils/ConfigurationException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public class ConfigurationException extends RuntimeException {
diff --git a/src/main/java/org/caosdb/server/utils/CronJob.java b/src/main/java/org/caosdb/server/utils/CronJob.java
index 8110a51752d996fc2f4fd2af3e5b7350f3e4d01f..a0ac9703ac1dbb2847f77a3e7c1d22fdf77264a2 100644
--- a/src/main/java/org/caosdb/server/utils/CronJob.java
+++ b/src/main/java/org/caosdb/server/utils/CronJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.util.HashMap;
-import org.caosdb.server.CaosDBServer;
+import org.linkahead.server.LinkAheadServer;
public class CronJob {
@@ -44,7 +44,7 @@ public class CronJob {
}
}
if (onShutdown) {
- CaosDBServer.addPreShutdownHook(
+ LinkAheadServer.addPreShutdownHook(
new Runnable() {
@Override
public void run() {
diff --git a/src/main/java/org/caosdb/server/utils/EntityStatus.java b/src/main/java/org/caosdb/server/utils/EntityStatus.java
index d6658ef12535bca15a6af7b1d16a4d3d8c0b5e58..34f917b51bdc2488f06cfd23ed40c8ba6c92ae0a 100644
--- a/src/main/java/org/caosdb/server/utils/EntityStatus.java
+++ b/src/main/java/org/caosdb/server/utils/EntityStatus.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
/**
* The order of the EntityStatus values matters, in that everything later than "QUALIFIED" also
diff --git a/src/main/java/org/caosdb/server/utils/FileUtils.java b/src/main/java/org/caosdb/server/utils/FileUtils.java
index eb4270f8d33abf933dbe24001bfa9b02ce45639b..ee29ef7b9f0a6b29075ac407959f51793488dd3c 100644
--- a/src/main/java/org/caosdb/server/utils/FileUtils.java
+++ b/src/main/java/org/caosdb/server/utils/FileUtils.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import static java.nio.file.Files.isSameFile;
import static java.nio.file.Files.isSymbolicLink;
@@ -37,13 +37,13 @@ import java.nio.file.LinkOption;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.Arrays;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
import org.eclipse.jetty.io.RuntimeIOException;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
public class FileUtils {
@@ -188,12 +188,12 @@ public class FileUtils {
}
public static String chownScript =
- CaosDBServer.getServerProperty(ServerProperties.KEY_CHOWN_SCRIPT);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CHOWN_SCRIPT);
public static void runChownScript(final File file) {
if (chown_enabled) {
try {
- final String sudopw = CaosDBServer.getServerProperty(ServerProperties.KEY_SUDO_PASSWORD);
+ final String sudopw = LinkAheadServer.getServerProperty(ServerProperties.KEY_SUDO_PASSWORD);
final Process cmd =
Runtime.getRuntime()
.exec(
@@ -208,7 +208,7 @@ public class FileUtils {
+ file.getAbsolutePath()
});
if (cmd.waitFor() != 0) {
- throw new TransactionException("caosdb_chown_dropoffbox failed.");
+ throw new TransactionException("linkahead_chown_dropoffbox failed.");
}
} catch (final InterruptedException e) {
throw new TransactionException(e);
@@ -222,11 +222,12 @@ public class FileUtils {
* @deprecated Soon to be removed.
* @throws IOException
* @throws InterruptedException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Deprecated
- public static void testChownScript() throws IOException, InterruptedException, CaosDBException {
- final String sudopw = CaosDBServer.getServerProperty(ServerProperties.KEY_SUDO_PASSWORD);
+ public static void testChownScript()
+ throws IOException, InterruptedException, LinkAheadException {
+ final String sudopw = LinkAheadServer.getServerProperty(ServerProperties.KEY_SUDO_PASSWORD);
final Process cmd =
Runtime.getRuntime()
.exec(
@@ -311,7 +312,7 @@ public class FileUtils {
}
private static void moveReplace(File file, File target)
- throws IOException, CaosDBException, InterruptedException {
+ throws IOException, LinkAheadException, InterruptedException {
if (exists(target)) {
org.apache.commons.io.FileUtils.forceDelete(target);
}
@@ -329,10 +330,10 @@ public class FileUtils {
* @param newlink
* @throws IOException
* @throws InterruptedException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
private static void moveSymlink(File oldlink, File newlink)
- throws IOException, CaosDBException, InterruptedException {
+ throws IOException, LinkAheadException, InterruptedException {
File target = oldlink.toPath().toRealPath().toFile();
createSymlink(newlink, target);
callPosixUnlink(oldlink);
@@ -408,7 +409,7 @@ public class FileUtils {
}
public static Undoable delete(final File file)
- throws IOException, CaosDBException, InterruptedException {
+ throws IOException, LinkAheadException, InterruptedException {
return delete(file, false);
}
@@ -423,10 +424,10 @@ public class FileUtils {
* @return
* @throws IOException
* @throws InterruptedException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
public static Undoable delete(final File file, final boolean recursive)
- throws IOException, CaosDBException, InterruptedException {
+ throws IOException, LinkAheadException, InterruptedException {
if (file.exists() && file.isFile()) {
// delete file
final File backup = getTmpFile(file.getName());
@@ -527,7 +528,7 @@ public class FileUtils {
private static void callPosixUnlink(File file) throws IOException, InterruptedException {
final Process cmd = Runtime.getRuntime().exec(new String[] {"unlink", file.getAbsolutePath()});
if (cmd.waitFor() != 0) {
- throw new CaosDBException("could not unlink " + file.getAbsolutePath());
+ throw new LinkAheadException("could not unlink " + file.getAbsolutePath());
}
}
diff --git a/src/main/java/org/caosdb/server/utils/FlagInfo.java b/src/main/java/org/caosdb/server/utils/FlagInfo.java
index 60697cb90df0bcf0da0588c580c49664ec0b0f52..be6a86796460958ac91d759e9ba3bc5737d71d37 100644
--- a/src/main/java/org/caosdb/server/utils/FlagInfo.java
+++ b/src/main/java/org/caosdb/server/utils/FlagInfo.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.lang.annotation.Annotation;
import java.util.ArrayList;
import java.util.Set;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.transaction.TransactionInterface;
import org.jdom2.Element;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.transaction.TransactionInterface;
import org.reflections.Reflections;
public class FlagInfo {
@@ -38,7 +38,7 @@ public class FlagInfo {
public static ArrayList<JobAnnotation> scan() {
final ArrayList<JobAnnotation> as = new ArrayList<JobAnnotation>();
- final Reflections jobPackage = new Reflections("org.caosdb.server.jobs.core");
+ final Reflections jobPackage = new Reflections("org.linkahead.server.jobs.core");
final Set<Class<? extends FlagJob>> allClassesSet = jobPackage.getSubTypesOf(FlagJob.class);
for (final Class<? extends Job> c : allClassesSet) {
for (final Annotation a : c.getAnnotations()) {
diff --git a/src/main/java/org/caosdb/server/utils/HashAlgorithm.java b/src/main/java/org/caosdb/server/utils/HashAlgorithm.java
index 6bf517fc5b906b4199219bde5654dbdebf3c5ecb..1989c2b6c4ce78a838c30e3ef773a2a780ccd2e5 100644
--- a/src/main/java/org/caosdb/server/utils/HashAlgorithm.java
+++ b/src/main/java/org/caosdb/server/utils/HashAlgorithm.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.File;
diff --git a/src/main/java/org/caosdb/server/utils/HashException.java b/src/main/java/org/caosdb/server/utils/HashException.java
index 46c3ecc6fba5cceac03605f80f4154e8f6a97594..e0ebd41eaedce60aee94b2157f27790fb8ee42df 100644
--- a/src/main/java/org/caosdb/server/utils/HashException.java
+++ b/src/main/java/org/caosdb/server/utils/HashException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
-import org.caosdb.server.CaosDBException;
+import org.linkahead.server.LinkAheadException;
-public class HashException extends CaosDBException {
+public class HashException extends LinkAheadException {
/** */
private static final long serialVersionUID = 5478908505951882613L;
diff --git a/src/main/java/org/caosdb/server/utils/HashNotReadyException.java b/src/main/java/org/caosdb/server/utils/HashNotReadyException.java
index 7b52a92406d53f54ba11c257353c255bded46696..264d5084a8c54dd79e941ce68ec06f6f76aa1315 100644
--- a/src/main/java/org/caosdb/server/utils/HashNotReadyException.java
+++ b/src/main/java/org/caosdb/server/utils/HashNotReadyException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public class HashNotReadyException extends HashException {
diff --git a/src/main/java/org/caosdb/server/utils/HashTimeoutException.java b/src/main/java/org/caosdb/server/utils/HashTimeoutException.java
index 4733ae5314d235cab9c7ee3e98400bd90483f277..b7c3a1af579ff981a77341db8eaed3c9bea738ae 100644
--- a/src/main/java/org/caosdb/server/utils/HashTimeoutException.java
+++ b/src/main/java/org/caosdb/server/utils/HashTimeoutException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public class HashTimeoutException extends HashException {
diff --git a/src/main/java/org/caosdb/server/utils/Hasher.java b/src/main/java/org/caosdb/server/utils/Hasher.java
index 9eb009cd6e3445f3cc87639e8fc6d14793f386f2..1b36b9db06a1f8eb5a99b803f4b7923dc1a34f88 100644
--- a/src/main/java/org/caosdb/server/utils/Hasher.java
+++ b/src/main/java/org/caosdb/server/utils/Hasher.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.File;
import java.io.IOException;
diff --git a/src/main/java/org/caosdb/server/utils/Info.java b/src/main/java/org/caosdb/server/utils/Info.java
index 644239fc662c1b6a05dc1aac37af1bfe26e7972e..9d31cfffd2979c6519ecd33f773a472d77cd2409 100644
--- a/src/main/java/org/caosdb/server/utils/Info.java
+++ b/src/main/java/org/caosdb/server/utils/Info.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.File;
import java.io.IOException;
@@ -28,18 +28,18 @@ import java.sql.SQLException;
import java.util.LinkedList;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.GetInfo;
-import org.caosdb.server.database.backend.transaction.SyncStats;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoInfo;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.transaction.TransactionInterface;
import org.jdom2.Element;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.GetInfo;
+import org.linkahead.server.database.backend.transaction.SyncStats;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoInfo;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.transaction.TransactionInterface;
public class Info extends AbstractObservable implements Observer, TransactionInterface {
@@ -184,7 +184,7 @@ public class Info extends AbstractObservable implements Observer, TransactionInt
}
/**
- * Generates an XML element showing the information for the /Info resource in CaosDB.
+ * Generates an XML element showing the information for the /Info resource in LinkAhead.
*
* @return An XML element containing:
* <ul>
@@ -212,7 +212,7 @@ public class Info extends AbstractObservable implements Observer, TransactionInt
counts.setAttribute("files", Integer.toString(filesCount));
counts.setAttribute("fssize", fssize);
counts.setAttribute("tmpfiles", Integer.toString(tmpFilesCount));
- if (CaosDBServer.isDebugMode()) {
+ if (LinkAheadServer.isDebugMode()) {
counts.setAttribute("debug", "true");
}
final Element e = new Element("dropOffBox");
diff --git a/src/main/java/org/caosdb/server/utils/Initialization.java b/src/main/java/org/caosdb/server/utils/Initialization.java
index 4f28f206bd5f272887fb78b661c6dc46d5cff6bc..2c79499bc2a948d65979b27a2ad21e50c2ff97b9 100644
--- a/src/main/java/org/caosdb/server/utils/Initialization.java
+++ b/src/main/java/org/caosdb/server/utils/Initialization.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,12 +22,12 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.transaction.TransactionInterface;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.transaction.TransactionInterface;
public final class Initialization implements TransactionInterface, AutoCloseable {
diff --git a/src/main/java/org/caosdb/server/utils/NullPrintStream.java b/src/main/java/org/caosdb/server/utils/NullPrintStream.java
index 9256bdee5af75af1a141c2f1dbdbee54cf1b64e2..c26f386a77a1b28c0c722a0cd178e6cf9af9ac4e 100644
--- a/src/main/java/org/caosdb/server/utils/NullPrintStream.java
+++ b/src/main/java/org/caosdb/server/utils/NullPrintStream.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.PrintStream;
import org.apache.commons.io.output.NullOutputStream;
diff --git a/src/main/java/org/caosdb/server/utils/Observable.java b/src/main/java/org/caosdb/server/utils/Observable.java
index a43822eb9725232f068c6cdb26764994033366a3..4dbeed65a02779e75e0de84f71935f2daaeed59a 100644
--- a/src/main/java/org/caosdb/server/utils/Observable.java
+++ b/src/main/java/org/caosdb/server/utils/Observable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public interface Observable {
public boolean acceptObserver(Observer o);
diff --git a/src/main/java/org/caosdb/server/utils/ObservableWrapper.java b/src/main/java/org/caosdb/server/utils/ObservableWrapper.java
index 9a1833db95220919102b7ec434971ce9057d86dd..dc2bf92dbdc6e717f9df93a07ab2d4c7d2bb9d3b 100644
--- a/src/main/java/org/caosdb/server/utils/ObservableWrapper.java
+++ b/src/main/java/org/caosdb/server/utils/ObservableWrapper.java
@@ -1,7 +1,7 @@
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@ package org.caosdb.server.utils;
*
* ** end header
*/
-// package org.caosdb.server.utils;
+// package org.linkahead.server.utils;
//
//
// public class ObservableWrapper<T> extends AbstractObservable {
diff --git a/src/main/java/org/caosdb/server/utils/Observer.java b/src/main/java/org/caosdb/server/utils/Observer.java
index b4c8f5444b957a1d18efc7f864c67b3daff8ca33..a058db676a988489abeac2e51c71934bc3561d05 100644
--- a/src/main/java/org/caosdb/server/utils/Observer.java
+++ b/src/main/java/org/caosdb/server/utils/Observer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public interface Observer {
diff --git a/src/main/java/org/caosdb/server/utils/Releasable.java b/src/main/java/org/caosdb/server/utils/Releasable.java
index f81a029ae319af057c4bc06e3d0501b6eedbe38c..42d49b65f109edd75fc2b37877c91ab2f7bf1820 100644
--- a/src/main/java/org/caosdb/server/utils/Releasable.java
+++ b/src/main/java/org/caosdb/server/utils/Releasable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public interface Releasable {
diff --git a/src/main/java/org/caosdb/server/utils/ResultSetIterator.java b/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
index 71429f1a704299555ab1d86be0695e3104be828d..42da71d9f7b183dc87b1273699c990c5d64375be 100644
--- a/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
+++ b/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
@@ -1,13 +1,13 @@
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Iterator;
import java.util.NoSuchElementException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.query.Query.IdVersionAclTriplet;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.query.Query.IdVersionAclTriplet;
/**
* A class for iterating over {@link ResultSet}
diff --git a/src/main/java/org/caosdb/server/utils/SHA512.java b/src/main/java/org/caosdb/server/utils/SHA512.java
index a461d95ed9e38baf350b0ee53e059b10ee13a177..acbab54b524fc493b4b5e0504571d77bae5eb678 100644
--- a/src/main/java/org/caosdb/server/utils/SHA512.java
+++ b/src/main/java/org/caosdb/server/utils/SHA512.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.File;
import java.io.IOException;
diff --git a/src/main/java/org/caosdb/server/utils/Serializer.java b/src/main/java/org/caosdb/server/utils/Serializer.java
index c58ca23ebfd439e5681289e451da5651d459abc7..1ad9f5828715524870c125e9e34c29e60d0ab34c 100644
--- a/src/main/java/org/caosdb/server/utils/Serializer.java
+++ b/src/main/java/org/caosdb/server/utils/Serializer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public interface Serializer<T, S> {
diff --git a/src/main/java/org/caosdb/server/utils/ServerMessages.java b/src/main/java/org/caosdb/server/utils/ServerMessages.java
index 9e18ca9065ec407d2dfc795d173e8d97f11682be..7ed0be5e6642e0816b7310dcfae800a1698f0502 100644
--- a/src/main/java/org/caosdb/server/utils/ServerMessages.java
+++ b/src/main/java/org/caosdb/server/utils/ServerMessages.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics, Max-Planck-Institute
* for Dynamics and Self-Organization Göttingen
@@ -21,13 +21,13 @@
*
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
public class ServerMessages {
@@ -469,7 +469,7 @@ public class ServerMessages {
public static Message UNKNOWN_ERROR(final String requestID) {
return UNKNOWN_ERROR(
- requestID, CaosDBServer.getServerProperty(ServerProperties.KEY_BUGTRACKER_URI));
+ requestID, LinkAheadServer.getServerProperty(ServerProperties.KEY_BUGTRACKER_URI));
}
public static Message UNKNOWN_ERROR(final String sRID, final String reportTo) {
diff --git a/src/main/java/org/caosdb/server/utils/ServerStat.java b/src/main/java/org/caosdb/server/utils/ServerStat.java
index 8b5526335208f07b084e8d61e5d4244b3c235da2..28f6da2a7c37f2d6cf3c6e434c071a8e4496a0eb 100644
--- a/src/main/java/org/caosdb/server/utils/ServerStat.java
+++ b/src/main/java/org/caosdb/server/utils/ServerStat.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.Serializable;
diff --git a/src/main/java/org/caosdb/server/utils/TransactionLogMessage.java b/src/main/java/org/caosdb/server/utils/TransactionLogMessage.java
index 368e09085fce6cc77ac703cd7e2f51f9f4f32d22..b38bf21cf39dd8bf24f6748598283208ac110223 100644
--- a/src/main/java/org/caosdb/server/utils/TransactionLogMessage.java
+++ b/src/main/java/org/caosdb/server/utils/TransactionLogMessage.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.util.TimeZone;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.entity.EntityInterface;
import org.jdom2.Element;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.entity.EntityInterface;
public class TransactionLogMessage {
diff --git a/src/main/java/org/caosdb/server/utils/UncloseableOutputStream.java b/src/main/java/org/caosdb/server/utils/UncloseableOutputStream.java
index 3f70f2826cbed4547282d2e809ccdaa0068e3ebe..cd39a7a1d0d0b867f720fc32529c6fa077420997 100644
--- a/src/main/java/org/caosdb/server/utils/UncloseableOutputStream.java
+++ b/src/main/java/org/caosdb/server/utils/UncloseableOutputStream.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.IOException;
import java.io.OutputStream;
diff --git a/src/main/java/org/caosdb/server/utils/UndoHandler.java b/src/main/java/org/caosdb/server/utils/UndoHandler.java
index 2102784711a1ebd5e879d1562eda26715a19f6b2..681923054b82144145025ae43a8a489860ef00ba 100644
--- a/src/main/java/org/caosdb/server/utils/UndoHandler.java
+++ b/src/main/java/org/caosdb/server/utils/UndoHandler.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.util.ArrayDeque;
import java.util.Deque;
diff --git a/src/main/java/org/caosdb/server/utils/Undoable.java b/src/main/java/org/caosdb/server/utils/Undoable.java
index 2bbbcb17abf77556cbc6160cfe60335364c61de3..671df33a93e7b0e5c124fcabc6a41a1b36e9df18 100644
--- a/src/main/java/org/caosdb/server/utils/Undoable.java
+++ b/src/main/java/org/caosdb/server/utils/Undoable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public interface Undoable {
diff --git a/src/main/java/org/caosdb/server/utils/Utils.java b/src/main/java/org/caosdb/server/utils/Utils.java
index 07a7e9618aa5b9e45f0086e837acfe1bf427173f..119f733a48b1c3f881a8cebf62ec2439eef96cb7 100644
--- a/src/main/java/org/caosdb/server/utils/Utils.java
+++ b/src/main/java/org/caosdb/server/utils/Utils.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import static java.net.URLDecoder.decode;
import static java.net.URLEncoder.encode;
@@ -35,13 +35,13 @@ import java.text.DecimalFormat;
import java.util.Scanner;
import java.util.regex.Pattern;
import org.apache.commons.codec.binary.Base32;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.Message;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.Message;
/** Utility functions. */
public class Utils {
@@ -306,7 +306,7 @@ public class Utils {
* @param password The password to be checked.
*/
public static void checkPasswordStrength(final String password) throws Message {
- String regex = CaosDBServer.getServerProperty(ServerProperties.KEY_PASSWORD_STRENGTH_REGEX);
+ String regex = LinkAheadServer.getServerProperty(ServerProperties.KEY_PASSWORD_STRENGTH_REGEX);
if (password.equals("correcthorsebatterystaple")) {
throw ServerMessages.PASSWORD_TOO_WEAK("PWNED!");
@@ -314,7 +314,7 @@ public class Utils {
if (!password.matches(regex)) {
throw ServerMessages.PASSWORD_TOO_WEAK(
- CaosDBServer.getServerProperty(ServerProperties.KEY_PASSWORD_WEAK_MESSAGE));
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_PASSWORD_WEAK_MESSAGE));
}
}
}
diff --git a/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java b/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java
index 6c583fccce77471ae4a4272f35d94ec2c886afd3..1d4c8a1808c18578e2fcf8b2d06f2fec7759ba84 100644
--- a/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java
+++ b/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java
@@ -1,5 +1,5 @@
/**
- * ** header v3.0 This file is a part of the CaosDB Project.
+ * ** header v3.0 This file is a part of the LinkAhead Project.
*
* <p>Copyright (c) 2019 IndiScale GmbH Copyright (c) 2019 Daniel Hornung <d.hornung@indiscale.com>
*
@@ -16,7 +16,7 @@
*
* <p>** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.File;
import java.io.IOException;
@@ -29,10 +29,10 @@ import java.util.Map;
import java.util.stream.Stream;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.resource.AbstractCaosDBServerResource;
-import org.caosdb.server.resource.Webinterface;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.resource.AbstractLinkAheadServerResource;
+import org.linkahead.server.resource.Webinterface;
import org.restlet.Request;
import org.restlet.data.Reference;
@@ -41,15 +41,15 @@ import org.restlet.data.Reference;
* <li>Resolving relative paths of files of the web interface to {@link File} objects.
* <li>Generating URIs to public files of the web interface from relative string paths.
*
- * <p>Especially the {@link AbstractCaosDBServerResource} and the {@link Webinterface} use this
- * class for these tasks.
+ * <p>Especially the {@link AbstractLinkAheadServerResource} and the {@link Webinterface} use
+ * this class for these tasks.
*
* @author Timm Fitschen (t.fitschen@indiscale.com)
*/
public class WebinterfaceUtils {
private Logger logger = LogManager.getLogger(this.getClass());
- public static final String DEFAULT_WEBUI_PUBLIC = "caosdb-webui/public";
+ public static final String DEFAULT_WEBUI_PUBLIC = "linkahead-webui/public";
public static final String DEFAULT_BUILD_NUMBER_FILE = ".build_number";
public static final String DEFAULT_ROUTE = "webinterface";
private final String host;
@@ -162,7 +162,7 @@ public class WebinterfaceUtils {
WebinterfaceUtils(String host) {
this(
host,
- CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT),
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT),
DEFAULT_WEBUI_PUBLIC,
DEFAULT_ROUTE,
DEFAULT_BUILD_NUMBER_FILE);
diff --git a/src/main/java/org/caosdb/server/utils/mail/Mail.java b/src/main/java/org/caosdb/server/utils/mail/Mail.java
index 36588fc1b3611efad17b80c9122208aa2292870f..5004b706a437ecc0a11a1844320955c51a936760 100644
--- a/src/main/java/org/caosdb/server/utils/mail/Mail.java
+++ b/src/main/java/org/caosdb/server/utils/mail/Mail.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
import java.util.Date;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
public class Mail {
private static MailHandler handler = null;
static {
- String clazz = CaosDBServer.getServerProperty(ServerProperties.KEY_MAIL_HANDLER_CLASS);
+ String clazz = LinkAheadServer.getServerProperty(ServerProperties.KEY_MAIL_HANDLER_CLASS);
try {
@SuppressWarnings("unchecked")
Class<? extends MailHandler> mailHandlerClass =
diff --git a/src/main/java/org/caosdb/server/utils/mail/MailFormatter.java b/src/main/java/org/caosdb/server/utils/mail/MailFormatter.java
index 2e31724d32527a3f171285513b2014be123e0921..52b68e04e41b143c3aa8da3b3bc0a523119827f7 100644
--- a/src/main/java/org/caosdb/server/utils/mail/MailFormatter.java
+++ b/src/main/java/org/caosdb/server/utils/mail/MailFormatter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
public interface MailFormatter {
diff --git a/src/main/java/org/caosdb/server/utils/mail/MailHandler.java b/src/main/java/org/caosdb/server/utils/mail/MailHandler.java
index ebdf88dad42028c223784501216002cb5f5196a9..e97d1be4416bb92666ae70fd0b2796011fa08bfa 100644
--- a/src/main/java/org/caosdb/server/utils/mail/MailHandler.java
+++ b/src/main/java/org/caosdb/server/utils/mail/MailHandler.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
public interface MailHandler {
diff --git a/src/main/java/org/caosdb/server/utils/mail/Mailable.java b/src/main/java/org/caosdb/server/utils/mail/Mailable.java
index fc679aac61afee3cc8d5d47610a6c84ed0be36c0..4549997c38b12e767b4f2293fb2330344e93d109 100644
--- a/src/main/java/org/caosdb/server/utils/mail/Mailable.java
+++ b/src/main/java/org/caosdb/server/utils/mail/Mailable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
public interface Mailable {
diff --git a/src/main/java/org/caosdb/server/utils/mail/SendMailHandler.java b/src/main/java/org/caosdb/server/utils/mail/SendMailHandler.java
index 88a487c5b02ed9279520d5584fc13582e967a770..d22ef6f4113e3f2f5326118bee6cfc076ddd7cd9 100644
--- a/src/main/java/org/caosdb/server/utils/mail/SendMailHandler.java
+++ b/src/main/java/org/caosdb/server/utils/mail/SendMailHandler.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
import java.io.BufferedWriter;
import java.io.IOException;
diff --git a/src/main/java/org/caosdb/server/utils/mail/SimpleMailFormatter.java b/src/main/java/org/caosdb/server/utils/mail/SimpleMailFormatter.java
index c1d5ce6b9967c41f82ecf24539f435af87a0899c..85c4a47cc3c6ef9381db579b9dd58acbd8776d59 100644
--- a/src/main/java/org/caosdb/server/utils/mail/SimpleMailFormatter.java
+++ b/src/main/java/org/caosdb/server/utils/mail/SimpleMailFormatter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
import javax.mail.internet.MailDateFormat;
diff --git a/src/main/java/org/caosdb/server/utils/mail/ToFileHandler.java b/src/main/java/org/caosdb/server/utils/mail/ToFileHandler.java
index 24a6da787925a352b2675edf3000ad7f5d1f8dbb..e6af1de2df43c03ab6014a8211014b362f56096a 100644
--- a/src/main/java/org/caosdb/server/utils/mail/ToFileHandler.java
+++ b/src/main/java/org/caosdb/server/utils/mail/ToFileHandler.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintWriter;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
public class ToFileHandler implements MailHandler {
@@ -37,7 +37,7 @@ public class ToFileHandler implements MailHandler {
@Override
public void handleMail(final Mail mail) {
final String loc =
- CaosDBServer.getServerProperty(ServerProperties.KEY_MAIL_TO_FILE_HANDLER_LOC);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_MAIL_TO_FILE_HANDLER_LOC);
File f = new File(loc);
if ((f.exists() && f.isDirectory()) || !f.exists() && loc.endsWith("/")) {
f = new File(f.getAbsolutePath() + "/OUTBOX");
diff --git a/src/main/java/org/caosdb/unit/CaosDBSystemOfUnits.java b/src/main/java/org/caosdb/unit/CaosDBSystemOfUnits.java
index ed78c5cf41225ddc7adb36869a779d1c4ec57d67..f9b1ba87f14b794411ecb25642868cf2b317802d 100644
--- a/src/main/java/org/caosdb/unit/CaosDBSystemOfUnits.java
+++ b/src/main/java/org/caosdb/unit/CaosDBSystemOfUnits.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
import de.timmfitschen.easyunits.BaseUnit;
import de.timmfitschen.easyunits.DefaultSystemOfUnitsFactory;
@@ -31,7 +31,7 @@ import de.timmfitschen.easyunits.UnknownUnitException;
import de.timmfitschen.easyunits.conversion.Prefix;
import de.timmfitschen.easyunits.parser.ParserException;
-public class CaosDBSystemOfUnits {
+public class LinkAheadSystemOfUnits {
public static Unit getUnit(final String s) throws ParserException {
try {
@@ -43,7 +43,7 @@ public class CaosDBSystemOfUnits {
private static SystemOfUnits system = createSystemOfUnits();
- private CaosDBSystemOfUnits() {}
+ private LinkAheadSystemOfUnits() {}
private static SystemOfUnits createSystemOfUnits() {
final DefaultSystemOfUnitsFactory f = new DefaultSystemOfUnitsFactory();
diff --git a/src/main/java/org/caosdb/unit/Converter.java b/src/main/java/org/caosdb/unit/Converter.java
index dfe63477d9c3e9639a58845b8034028befb039bb..290b1023ff0d7017f87793f8916b014c44bc8a07 100644
--- a/src/main/java/org/caosdb/unit/Converter.java
+++ b/src/main/java/org/caosdb/unit/Converter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,6 +20,6 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
public interface Converter {}
diff --git a/src/main/java/org/caosdb/unit/LinearConverter.java b/src/main/java/org/caosdb/unit/LinearConverter.java
index 8eac2d7e07dbe9f1594b368968b06d00034ea95e..91936e667ba2d4678a532b26586a3d45cac3d4c7 100644
--- a/src/main/java/org/caosdb/unit/LinearConverter.java
+++ b/src/main/java/org/caosdb/unit/LinearConverter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
public interface LinearConverter extends Converter {
diff --git a/src/main/java/org/caosdb/unit/Unit.java b/src/main/java/org/caosdb/unit/Unit.java
index 9e676773013f30d5aa30b60a1357a130f3c5a941..40f7045eff1023e0c8aaa5ed5b9686a2e45440c1 100644
--- a/src/main/java/org/caosdb/unit/Unit.java
+++ b/src/main/java/org/caosdb/unit/Unit.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
public interface Unit {
diff --git a/src/main/java/org/caosdb/unit/UnknownUnit.java b/src/main/java/org/caosdb/unit/UnknownUnit.java
index 70ad3546ece269efbdc224b7d6d12f9448a21938..383c0e5f284736683d33d8c4881a5b00ada59fa2 100644
--- a/src/main/java/org/caosdb/unit/UnknownUnit.java
+++ b/src/main/java/org/caosdb/unit/UnknownUnit.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
public class UnknownUnit extends WrappedUnit implements Unit {
diff --git a/src/main/java/org/caosdb/unit/WrappedConverter.java b/src/main/java/org/caosdb/unit/WrappedConverter.java
index f23be0394daa4a680e642a3d5f018e8b21db4235..3f2b727c587cb980919c34d8fb43f1ec0cbbdd66 100644
--- a/src/main/java/org/caosdb/unit/WrappedConverter.java
+++ b/src/main/java/org/caosdb/unit/WrappedConverter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
public class WrappedConverter implements Converter {
diff --git a/src/main/java/org/caosdb/unit/WrappedLinearConverter.java b/src/main/java/org/caosdb/unit/WrappedLinearConverter.java
index b90b32ccee7395800f62ad91cdc960c4b93d0813..b72c65b7b865e72f32d47227660c153f28281643 100644
--- a/src/main/java/org/caosdb/unit/WrappedLinearConverter.java
+++ b/src/main/java/org/caosdb/unit/WrappedLinearConverter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
diff --git a/src/main/java/org/caosdb/unit/WrappedUnit.java b/src/main/java/org/caosdb/unit/WrappedUnit.java
index c29ee5b5853423d14cd602c393c779673f6b0ed4..0af35f46b3483304cbb2f88cbc2bf7daa5a52160 100644
--- a/src/main/java/org/caosdb/unit/WrappedUnit.java
+++ b/src/main/java/org/caosdb/unit/WrappedUnit.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
import de.timmfitschen.easyunits.conversion.LinearConverter;
diff --git a/src/test/java/org/caosdb/datetime/DateTimeTest.java b/src/test/java/org/caosdb/datetime/DateTimeTest.java
index 49e883fb0d2a2c3f62e0417a2a246841c4e6c9bb..7f7d68d1f6b4c1c0bab2a45630693fa751b58200 100644
--- a/src/test/java/org/caosdb/datetime/DateTimeTest.java
+++ b/src/test/java/org/caosdb/datetime/DateTimeTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -33,22 +33,22 @@ import java.sql.Timestamp;
import java.time.ZoneId;
import java.util.GregorianCalendar;
import java.util.TimeZone;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
public class DateTimeTest {
@BeforeAll
public static void setup() throws InterruptedException, IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.initTimeZone();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.initTimeZone();
}
@Test
public void testGetTimeZoneFromDate() throws InterruptedException, IOException {
- String tz = CaosDBServer.getTimeZoneFromDate();
+ String tz = LinkAheadServer.getTimeZoneFromDate();
ZoneId of = java.time.ZoneId.of(tz);
assertNotNull(of);
}
diff --git a/src/test/java/org/caosdb/datetime/UTCTimeZoneShiftTest.java b/src/test/java/org/caosdb/datetime/UTCTimeZoneShiftTest.java
index 9cfa98b144d5f3a4c66a008722d0f03f8d626840..bfb67d4ec7c5fe43b1a28c4130a8123b0114a68d 100644
--- a/src/test/java/org/caosdb/datetime/UTCTimeZoneShiftTest.java
+++ b/src/test/java/org/caosdb/datetime/UTCTimeZoneShiftTest.java
@@ -1,4 +1,4 @@
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import static org.junit.jupiter.api.Assertions.assertEquals;
diff --git a/src/test/java/org/caosdb/server/Misc.java b/src/test/java/org/caosdb/server/Misc.java
index 0b39327e6371fcc619f70d10c67bb4d7269589cd..62aff10999f627c3f3c512e3e241588bf439bcba 100644
--- a/src/test/java/org/caosdb/server/Misc.java
+++ b/src/test/java/org/caosdb/server/Misc.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -38,18 +38,18 @@ import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.jobs.core.CheckFileStorageConsistency;
-import org.caosdb.server.utils.CronJob;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.jvnet.libpam.PAMException;
import org.jvnet.libpam.UnixUser;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.jobs.core.CheckFileStorageConsistency;
+import org.linkahead.server.utils.CronJob;
public class Misc {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
@@ -289,7 +289,7 @@ public class Misc {
@Test
public void testShiro() {
- CaosDBServer.initShiro();
+ LinkAheadServer.initShiro();
final Subject subject = SecurityUtils.getSubject();
diff --git a/src/test/java/org/caosdb/server/accessControl/TestDefaultPamScriptCaller.java b/src/test/java/org/caosdb/server/accessControl/TestDefaultPamScriptCaller.java
index a893b46afa0e855c281103022a1553d3cb47675b..30418c171c58cb2c78653ba2015689c5ff57e1f5 100644
--- a/src/test/java/org/caosdb/server/accessControl/TestDefaultPamScriptCaller.java
+++ b/src/test/java/org/caosdb/server/accessControl/TestDefaultPamScriptCaller.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
diff --git a/src/test/java/org/caosdb/server/authentication/AuthTokenTest.java b/src/test/java/org/caosdb/server/authentication/AuthTokenTest.java
index d83651a3b202be77a2bab7abbab37c6281f1b0b2..4f4a175d504c024c9955ad7f73498e65b6c2f073 100644
--- a/src/test/java/org/caosdb/server/authentication/AuthTokenTest.java
+++ b/src/test/java/org/caosdb/server/authentication/AuthTokenTest.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.authentication;
+package org.linkahead.server.authentication;
import static org.junit.jupiter.api.Assertions.assertArrayEquals;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -45,35 +45,35 @@ import org.apache.commons.io.input.CharSequenceInputStream;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Config;
-import org.caosdb.server.accessControl.OneTimeAuthenticationToken;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.SelfValidatingAuthenticationToken;
-import org.caosdb.server.accessControl.SessionToken;
-import org.caosdb.server.accessControl.SessionTokenRealm;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.grpc.AuthInterceptor;
-import org.caosdb.server.resource.TestScriptingResource.RetrievePasswordValidator;
-import org.caosdb.server.resource.TestScriptingResource.RetrievePermissionRules;
-import org.caosdb.server.resource.TestScriptingResource.RetrieveRoleMockup;
-import org.caosdb.server.resource.TestScriptingResource.RetrieveUserMockUp;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Config;
+import org.linkahead.server.accessControl.OneTimeAuthenticationToken;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.SelfValidatingAuthenticationToken;
+import org.linkahead.server.accessControl.SessionToken;
+import org.linkahead.server.accessControl.SessionTokenRealm;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.grpc.AuthInterceptor;
+import org.linkahead.server.resource.TestScriptingResource.RetrievePasswordValidator;
+import org.linkahead.server.resource.TestScriptingResource.RetrievePermissionRules;
+import org.linkahead.server.resource.TestScriptingResource.RetrieveRoleMockup;
+import org.linkahead.server.resource.TestScriptingResource.RetrieveUserMockUp;
public class AuthTokenTest {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@BeforeAll
@@ -84,8 +84,8 @@ public class AuthTokenTest {
BackendTransaction.setImpl(
RetrievePasswordValidatorImpl.class, RetrievePasswordValidator.class);
- CaosDBServer.initServerProperties();
- CaosDBServer.initShiro();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.initShiro();
}
@BeforeEach
@@ -284,7 +284,7 @@ public class AuthTokenTest {
assertEquals(
Integer.parseInt(
- CaosDBServer.getServerProperty(ServerProperties.KEY_ONE_TIME_TOKEN_EXPIRES_MS)),
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_ONE_TIME_TOKEN_EXPIRES_MS)),
config.getExpiresAfter());
assertEquals(1, config.getMaxReplays());
assertNull(config.getPurpose(), "no purpose");
@@ -405,7 +405,7 @@ public class AuthTokenTest {
OneTimeAuthenticationToken.initConfig(new CharSequenceInputStream(testYaml, "utf-8"));
Subject anonymous = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
anonymous.login(AnonymousAuthenticationToken.getInstance());
OneTimeAuthenticationToken token =
diff --git a/src/test/java/org/caosdb/server/caching/TestCaching.java b/src/test/java/org/caosdb/server/caching/TestCaching.java
index 1aba2ff6f16cea7a1f62e84e50e2cc9797114e27..b75bd09e893c9ac8fd91c7fa675491384371b5a6 100644
--- a/src/test/java/org/caosdb/server/caching/TestCaching.java
+++ b/src/test/java/org/caosdb/server/caching/TestCaching.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.caching;
+package org.linkahead.server.caching;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertSame;
@@ -6,17 +6,17 @@ import static org.junit.jupiter.api.Assertions.assertSame;
import java.io.IOException;
import org.apache.commons.jcs.JCS;
import org.apache.commons.jcs.access.CacheAccess;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.accessControl.Pam;
-import org.caosdb.server.database.backend.transaction.RetrieveProperties;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.accessControl.Pam;
+import org.linkahead.server.database.backend.transaction.RetrieveProperties;
public class TestCaching {
@BeforeAll
public static void init() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
JCSCacheHelper.init();
}
diff --git a/src/test/java/org/caosdb/server/caching/TestNoCaching.java b/src/test/java/org/caosdb/server/caching/TestNoCaching.java
index 4fc73adf89f9355d1ff6addcd0f71fd9eda4e653..c696531ac5322d48a02fefb654c698f794cfa00c 100644
--- a/src/test/java/org/caosdb/server/caching/TestNoCaching.java
+++ b/src/test/java/org/caosdb/server/caching/TestNoCaching.java
@@ -1,22 +1,22 @@
-package org.caosdb.server.caching;
+package org.linkahead.server.caching;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import org.apache.commons.jcs.JCS;
import org.apache.commons.jcs.access.CacheAccess;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.database.backend.transaction.RetrieveProperties;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.database.backend.transaction.RetrieveProperties;
public class TestNoCaching {
@BeforeAll
public static void init() throws IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.setProperty(ServerProperties.KEY_CACHE_DISABLE, "TRUE");
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.setProperty(ServerProperties.KEY_CACHE_DISABLE, "TRUE");
JCSCacheHelper.init();
}
diff --git a/src/test/java/org/caosdb/server/database/DatabaseAccessManagerTest.java b/src/test/java/org/caosdb/server/database/DatabaseAccessManagerTest.java
index 9d682ce3b2e2d6fe233095baa7095ebef2602ba4..29156f79d866259a81efb829020ce45c7061d2fe 100644
--- a/src/test/java/org/caosdb/server/database/DatabaseAccessManagerTest.java
+++ b/src/test/java/org/caosdb/server/database/DatabaseAccessManagerTest.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
diff --git a/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
index 03bd185c8884822f89f8ff323a1c32125b66f88b..46324a4c87b6adf8137f98840bc77224ea7642a8 100644
--- a/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
+++ b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,30 +20,30 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage1Inserts;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage2Inserts;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage1Inserts;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage2Inserts;
import java.util.ArrayDeque;
import java.util.Deque;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.SingleValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Property;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.datatype.SingleValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.wrapper.Property;
public class InsertTest {
diff --git a/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java b/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java
index 72c84d1f7b262a854a257c8ae764d4e3da9b8e80..c538f7fb8acb1f42fc39d604d33f53e12e82f0b3 100644
--- a/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java
+++ b/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -28,15 +28,15 @@ import static org.junit.jupiter.api.Assertions.assertNull;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.PropertyToElementStrategyTest;
-import org.caosdb.server.query.Query.Selection;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.PropertyToElementStrategyTest;
+import org.linkahead.server.query.Query.Selection;
public class RetrieveFullEntityTest {
diff --git a/src/test/java/org/caosdb/server/database/backend/transactions/TestGetAllNames.java b/src/test/java/org/caosdb/server/database/backend/transactions/TestGetAllNames.java
index 90efd31063bd480e0c1a4f36cf1a12c1b0c058a3..a3242b96ee8179f479f80528b391986a7231f1f4 100644
--- a/src/test/java/org/caosdb/server/database/backend/transactions/TestGetAllNames.java
+++ b/src/test/java/org/caosdb/server/database/backend/transactions/TestGetAllNames.java
@@ -1,20 +1,20 @@
-package org.caosdb.server.database.backend.transactions;
+package org.linkahead.server.database.backend.transactions;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetAllNamesImpl;
-import org.caosdb.server.database.backend.transaction.GetAllNames;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityInterface;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetAllNamesImpl;
+import org.linkahead.server.database.backend.transaction.GetAllNames;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityInterface;
public class TestGetAllNames {
@@ -48,7 +48,7 @@ public class TestGetAllNames {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
BackendTransaction.init();
BackendTransaction.setImpl(GetAllNamesImpl.class, GetAllNamesBackend.class);
}
diff --git a/src/test/java/org/caosdb/server/datatype/testBoolean.java b/src/test/java/org/caosdb/server/datatype/testBoolean.java
index a8b3913089b797bcc3d1f4217c228120aec37b49..679f3a4e72bfa059ecaf7915f4dbaab85a337a85 100644
--- a/src/test/java/org/caosdb/server/datatype/testBoolean.java
+++ b/src/test/java/org/caosdb/server/datatype/testBoolean.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,23 +20,23 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
public class testBoolean {
@Test
- public void testCaosEnumCI() {
- CaosEnum ce = new CaosEnum("TRUE", "FALSE", "NEITHER");
+ public void testLinkAheadEnumCI() {
+ LinkAheadEnum ce = new LinkAheadEnum("TRUE", "FALSE", "NEITHER");
assertNotNull(ce.valueOf("TRUE"));
assertNotNull(ce.valueOf("true"));
assertNotNull(ce.valueOf("TRue"));
@@ -56,8 +56,8 @@ public class testBoolean {
}
@Test
- public void testCaosEnumCS() {
- CaosEnum ce = new CaosEnum(true, "TRUE", "FALSE", "NEITHER", "neither");
+ public void testLinkAheadEnumCS() {
+ LinkAheadEnum ce = new LinkAheadEnum(true, "TRUE", "FALSE", "NEITHER", "neither");
assertNotNull(ce.valueOf("TRUE"));
assertNotNull(ce.valueOf("FALSE"));
assertNotNull(ce.valueOf("NEITHER"));
diff --git a/src/test/java/org/caosdb/server/entity/EntityTest.java b/src/test/java/org/caosdb/server/entity/EntityTest.java
index 3a923315529bfc6e17f52bf932d942344b32b68b..ab5b8248a7c1dd913611eff0b9880ebbab6c612c 100644
--- a/src/test/java/org/caosdb/server/entity/EntityTest.java
+++ b/src/test/java/org/caosdb/server/entity/EntityTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
-import org.caosdb.server.datatype.IntegerDatatype;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.IntegerDatatype;
public class EntityTest {
diff --git a/src/test/java/org/caosdb/server/entity/SelectionTest.java b/src/test/java/org/caosdb/server/entity/SelectionTest.java
index 8772063805ea9f8d6b3916d8d029a33a9c580bb2..d6da1cbfb44eaf913717d631a68346d8e4cc1eb0 100644
--- a/src/test/java/org/caosdb/server/entity/SelectionTest.java
+++ b/src/test/java/org/caosdb/server/entity/SelectionTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,25 +22,25 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.IOException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.Selection;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.Selection;
public class SelectionTest {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
diff --git a/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java b/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java
index a8ccdbdc9f7a9522020332e01cba96a1667d70b6..60eed2c3c8637fb84b499ae1e691de40d2ee1c40 100644
--- a/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java
+++ b/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
@@ -20,22 +20,22 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import static org.junit.jupiter.api.Assertions.assertEquals;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.PropertyToElementStrategyTest;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
import org.jdom2.Element;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.PropertyToElementStrategyTest;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
public class PropertyContainerTest {
diff --git a/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java b/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
index a2c9676b9759fc55fb0d1e089808ab50d016288e..f11b905a39d041355ed1113c938bc03b4d1a864b 100644
--- a/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
+++ b/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
@@ -20,22 +20,22 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
import static org.junit.jupiter.api.Assertions.assertEquals;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.query.Query.Selection;
import org.jdom2.Element;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.query.Query.Selection;
public class PropertyToElementStrategyTest {
diff --git a/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java b/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
index d46c187324b76e179ef8d562cd5a150ab7968a45..97fa6671866a241467ae70984ee8b639db04fa75 100644
--- a/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
+++ b/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
@@ -1,34 +1,34 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.util.TimeZone;
-import org.caosdb.api.entity.v1.Value.Builder;
-import org.caosdb.datetime.DateTimeFactory2;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.IdAndServerMessagesOnlyStrategy;
-import org.caosdb.server.query.Query.Selection;
import org.junit.jupiter.api.Test;
-
-public class CaosDBToGrpcConvertersTest {
+import org.linkahead.api.entity.v1.Value.Builder;
+import org.linkahead.datetime.DateTimeFactory2;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.IdAndServerMessagesOnlyStrategy;
+import org.linkahead.server.query.Query.Selection;
+
+public class LinkAheadToGrpcConvertersTest {
@Test
public void testConvertScalarValue_Datetime() {
TimeZone timeZone = TimeZone.getTimeZone("UTC");
DateTimeFactory2 factory = new DateTimeFactory2(timeZone);
- CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(timeZone);
+ LinkAheadToGrpcConverters converters = new LinkAheadToGrpcConverters(timeZone);
Value value = null;
assertEquals(
converters.convertScalarValue(value).toString(),
@@ -60,7 +60,7 @@ public class CaosDBToGrpcConvertersTest {
@Test
public void testConvertEntity_FileDescriptor() {
RetrieveEntity entity = new RetrieveEntity();
- CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(null);
+ LinkAheadToGrpcConverters converters = new LinkAheadToGrpcConverters(null);
assertEquals(converters.convert(entity).toString(), "entity {\n}\n");
entity.setFileProperties(new FileProperties("checksum1234", "the/path", 1024L));
assertEquals(
@@ -94,7 +94,7 @@ public class CaosDBToGrpcConvertersTest {
p.setValue(new GenericValue("don print"));
entity.addProperty(p);
- CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(null);
+ LinkAheadToGrpcConverters converters = new LinkAheadToGrpcConverters(null);
// first test the normal SerializeFieldStrategy instead
entity.setSerializeFieldStrategy(null);
@@ -115,7 +115,7 @@ public class CaosDBToGrpcConvertersTest {
RetrieveEntity entity = new RetrieveEntity();
entity.addProperty(p);
- CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(null);
+ LinkAheadToGrpcConverters converters = new LinkAheadToGrpcConverters(null);
Builder value = converters.getSelectedValue(new Selection("p0"), entity);
assertEquals(
"scalar_value {\n" + " special_value: SPECIAL_VALUE_UNSPECIFIED\n" + "}\n",
@@ -155,7 +155,7 @@ public class CaosDBToGrpcConvertersTest {
RetrieveEntity entity = new RetrieveEntity();
entity.addProperty(p);
- CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(null);
+ LinkAheadToGrpcConverters converters = new LinkAheadToGrpcConverters(null);
Builder value =
converters.getSelectedValue(
new Selection("Person").setSubSelection(new Selection("full name")), entity);
diff --git a/src/test/java/org/caosdb/server/jobs/JobConfigTest.java b/src/test/java/org/caosdb/server/jobs/JobConfigTest.java
index e176c2111189fb52ca9946e10ae5ec705549b6c8..333f6cce68fd6253c8ff4dc2a3e8183b2bceb000 100644
--- a/src/test/java/org/caosdb/server/jobs/JobConfigTest.java
+++ b/src/test/java/org/caosdb/server/jobs/JobConfigTest.java
@@ -1,24 +1,24 @@
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.UpdateEntity;
import org.jdom2.Element;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.UpdateEntity;
public class JobConfigTest {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
diff --git a/src/test/java/org/caosdb/server/jobs/ScheduleTest.java b/src/test/java/org/caosdb/server/jobs/ScheduleTest.java
index 7033ac35bf10391c85745d74a7184f065d8f6e38..20ca6782a6226e05631614d7ce7f620f9489f141 100644
--- a/src/test/java/org/caosdb/server/jobs/ScheduleTest.java
+++ b/src/test/java/org/caosdb/server/jobs/ScheduleTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import static org.junit.jupiter.api.Assertions.fail;
import java.io.IOException;
-import org.caosdb.server.CaosDBServer;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
public class ScheduleTest {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
/** The problem of ticket #297 was that a CHECK job was executed during the ROLL_BACK stage. */
diff --git a/src/test/java/org/caosdb/server/jobs/core/TestInsertFilesInDir.java b/src/test/java/org/caosdb/server/jobs/core/TestInsertFilesInDir.java
index a7202be9e7f8a4cfea5c050f403f15025511d09c..144743b73a832ef9915789184e1bd06f0371ef06 100644
--- a/src/test/java/org/caosdb/server/jobs/core/TestInsertFilesInDir.java
+++ b/src/test/java/org/caosdb/server/jobs/core/TestInsertFilesInDir.java
@@ -1,18 +1,18 @@
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.CaosDBServer;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
public class TestInsertFilesInDir {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
diff --git a/src/test/java/org/caosdb/server/logging/TestLogging.java b/src/test/java/org/caosdb/server/logging/TestLogging.java
index 0f67ebeae074c21712567c45cdd60948350a77bf..704a4bde7bb1ad9484e938879b55a810ebeb9481 100644
--- a/src/test/java/org/caosdb/server/logging/TestLogging.java
+++ b/src/test/java/org/caosdb/server/logging/TestLogging.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.logging;
+package org.linkahead.server.logging;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -7,9 +7,9 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.File;
import java.io.IOException;
import org.apache.commons.io.FileUtils;
-import org.caosdb.server.CaosDBServer;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
import org.restlet.Request;
import org.restlet.Response;
import org.slf4j.Logger;
@@ -19,8 +19,8 @@ public class TestLogging {
private Logger logger = LoggerFactory.getLogger(getClass());
private Logger request_errors_logger =
- LoggerFactory.getLogger(CaosDBServer.REQUEST_ERRORS_LOGGER);
- private Logger request_time_logger = LoggerFactory.getLogger(CaosDBServer.REQUEST_TIME_LOGGER);
+ LoggerFactory.getLogger(LinkAheadServer.REQUEST_ERRORS_LOGGER);
+ private Logger request_time_logger = LoggerFactory.getLogger(LinkAheadServer.REQUEST_TIME_LOGGER);
@BeforeAll
public static void setup() throws IOException {
@@ -35,7 +35,7 @@ public class TestLogging {
logger.info("info");
logger.debug("debug");
logger.trace("trace");
- assertEquals(logger.getName(), "org.caosdb.server.logging.TestLogging");
+ assertEquals(logger.getName(), "org.linkahead.server.logging.TestLogging");
assertTrue(logger.isErrorEnabled());
assertTrue(logger.isWarnEnabled());
assertTrue(logger.isInfoEnabled());
@@ -54,7 +54,7 @@ public class TestLogging {
@Test
public void testRequestTimeLogger() {
- assertTrue(CaosDBServer.isDebugMode());
+ assertTrue(LinkAheadServer.isDebugMode());
assertFalse(request_time_logger.isErrorEnabled());
assertFalse(request_time_logger.isTraceEnabled());
}
diff --git a/src/test/java/org/caosdb/server/permissions/EntityACLTest.java b/src/test/java/org/caosdb/server/permissions/EntityACLTest.java
index 5feab38f5a465844b52946ef4bb9e3ce32c6dd5c..aa07da20adb8bc410c1f48eaf9fe6d176c32dfa2 100644
--- a/src/test/java/org/caosdb/server/permissions/EntityACLTest.java
+++ b/src/test/java/org/caosdb/server/permissions/EntityACLTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -34,31 +34,31 @@ import java.util.LinkedList;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Config;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.accessControl.OneTimeAuthenticationToken;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.resource.AbstractCaosDBServerResource;
-import org.caosdb.server.resource.AbstractCaosDBServerResource.XMLParser;
-import org.caosdb.server.utils.Utils;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Config;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.accessControl.OneTimeAuthenticationToken;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.resource.AbstractLinkAheadServerResource;
+import org.linkahead.server.resource.AbstractLinkAheadServerResource.XMLParser;
+import org.linkahead.server.utils.Utils;
public class EntityACLTest {
@@ -158,8 +158,8 @@ public class EntityACLTest {
@BeforeAll
public static void init() throws IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.initShiro();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.initShiro();
assertNotNull(EntityACL.GLOBAL_PERMISSIONS);
BackendTransaction.setImpl(
@@ -318,7 +318,7 @@ public class EntityACLTest {
return false;
}
- public static AbstractCaosDBServerResource.XMLParser parser = new XMLParser();
+ public static AbstractLinkAheadServerResource.XMLParser parser = new XMLParser();
public Element stringToJdom(final String s) throws JDOMException, IOException {
return parser.parse(Utils.String2InputStream(s)).getRootElement();
@@ -327,7 +327,7 @@ public class EntityACLTest {
@Test
public void testEntityACLForAnonymous() {
Subject anonymous = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
anonymous.login(AnonymousAuthenticationToken.getInstance());
assertTrue(AuthenticationUtils.isAnonymous(anonymous));
EntityACL acl = EntityACL.getOwnerACLFor(anonymous);
@@ -339,14 +339,16 @@ public class EntityACLTest {
public void testFactory() {
final AbstractEntityACLFactory<EntityACL> f = new EntityACLFactory();
- org.caosdb.server.permissions.Role role1 = org.caosdb.server.permissions.Role.create("role1");
+ org.linkahead.server.permissions.Role role1 =
+ org.linkahead.server.permissions.Role.create("role1");
Config config1 = new Config();
config1.setRoles(new String[] {role1.toString()});
OneTimeAuthenticationToken token1 = OneTimeAuthenticationToken.generate(config1);
Subject user1 = SecurityUtils.getSecurityManager().createSubject(null);
user1.login(token1);
- org.caosdb.server.permissions.Role role2 = org.caosdb.server.permissions.Role.create("role2");
+ org.linkahead.server.permissions.Role role2 =
+ org.linkahead.server.permissions.Role.create("role2");
Config config2 = new Config();
config2.setRoles(new String[] {role2.toString()});
OneTimeAuthenticationToken token2 = OneTimeAuthenticationToken.generate(config2);
@@ -382,41 +384,48 @@ public class EntityACLTest {
@Test
public void testRemove() {
EntityACLFactory f = new EntityACLFactory();
- f.grant(org.caosdb.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
- f.deny(org.caosdb.server.permissions.Role.create("role2"), false, EntityPermission.EDIT_ACL);
+ f.grant(org.linkahead.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
+ f.deny(org.linkahead.server.permissions.Role.create("role2"), false, EntityPermission.EDIT_ACL);
f.grant(
- org.caosdb.server.permissions.Role.create("role3"), true, EntityPermission.RETRIEVE_ACL);
+ org.linkahead.server.permissions.Role.create("role3"), true, EntityPermission.RETRIEVE_ACL);
f.deny(
- org.caosdb.server.permissions.Role.create("role4"), true, EntityPermission.RETRIEVE_ENTITY);
+ org.linkahead.server.permissions.Role.create("role4"),
+ true,
+ EntityPermission.RETRIEVE_ENTITY);
EntityACL other = f.create();
- f.grant(org.caosdb.server.permissions.Role.create("role2"), false, EntityPermission.EDIT_ACL);
f.grant(
- org.caosdb.server.permissions.Role.create("role5"), false, EntityPermission.RETRIEVE_FILE);
+ org.linkahead.server.permissions.Role.create("role2"), false, EntityPermission.EDIT_ACL);
+ f.grant(
+ org.linkahead.server.permissions.Role.create("role5"),
+ false,
+ EntityPermission.RETRIEVE_FILE);
f.remove(other); // normalize and remove "other"
EntityACL tester = f.create();
assertEquals(1, tester.getRules().size()); // Permissions array has been written and read
for (EntityACI aci : tester.getRules()) {
- assertEquals(aci.getResponsibleAgent(), org.caosdb.server.permissions.Role.create("role5"));
+ assertEquals(
+ aci.getResponsibleAgent(), org.linkahead.server.permissions.Role.create("role5"));
}
}
@Test
public void testNormalize() {
EntityACLFactory f = new EntityACLFactory();
- f.grant(org.caosdb.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
- f.deny(org.caosdb.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
- f.grant(org.caosdb.server.permissions.Role.create("role1"), true, EntityPermission.DELETE);
- f.deny(org.caosdb.server.permissions.Role.create("role1"), true, EntityPermission.DELETE);
+ f.grant(org.linkahead.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
+ f.deny(org.linkahead.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
+ f.grant(org.linkahead.server.permissions.Role.create("role1"), true, EntityPermission.DELETE);
+ f.deny(org.linkahead.server.permissions.Role.create("role1"), true, EntityPermission.DELETE);
// priority denail overrides everything else
EntityACL denyDelete = f.create();
assertEquals(1, denyDelete.getRules().size());
for (EntityACI aci : denyDelete.getRules()) {
- assertEquals(org.caosdb.server.permissions.Role.create("role1"), aci.getResponsibleAgent());
+ assertEquals(
+ org.linkahead.server.permissions.Role.create("role1"), aci.getResponsibleAgent());
assertTrue(EntityACL.isDenial(aci.getBitSet()));
assertTrue(EntityACL.isPriorityBitSet(aci.getBitSet()));
}
@@ -426,9 +435,11 @@ public class EntityACLTest {
public void testOwnership() {
EntityACLFactory f = new EntityACLFactory();
f.grant(
- org.caosdb.server.permissions.Role.create("the_owner"), false, EntityPermission.EDIT_ACL);
+ org.linkahead.server.permissions.Role.create("the_owner"),
+ false,
+ EntityPermission.EDIT_ACL);
f.deny(
- org.caosdb.server.permissions.Role.create("someone_else"),
+ org.linkahead.server.permissions.Role.create("someone_else"),
false,
EntityPermission.EDIT_ACL);
EntityACL acl = f.create();
@@ -439,12 +450,12 @@ public class EntityACLTest {
@Test
public void testPermissionsFor() {
EntityACLFactory f = new EntityACLFactory();
- f.deny(org.caosdb.server.permissions.Role.ANONYMOUS_ROLE, false, EntityPermission.EDIT_ACL);
- f.grant(org.caosdb.server.permissions.Role.OWNER_ROLE, false, "*");
+ f.deny(org.linkahead.server.permissions.Role.ANONYMOUS_ROLE, false, EntityPermission.EDIT_ACL);
+ f.grant(org.linkahead.server.permissions.Role.OWNER_ROLE, false, "*");
EntityACL acl = f.create();
Subject anonymous = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
anonymous.login(AnonymousAuthenticationToken.getInstance());
assertTrue(AuthenticationUtils.isAnonymous(anonymous));
diff --git a/src/test/java/org/caosdb/server/permissions/EntityPermissionTest.java b/src/test/java/org/caosdb/server/permissions/EntityPermissionTest.java
index 8699a4311a27172904878d461f2b708b2a7d18ab..17bc0e2cd2986c8b41ebecf2f9370644a22dea12 100644
--- a/src/test/java/org/caosdb/server/permissions/EntityPermissionTest.java
+++ b/src/test/java/org/caosdb/server/permissions/EntityPermissionTest.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import static org.junit.jupiter.api.Assertions.*;
@@ -10,83 +10,83 @@ public class EntityPermissionTest {
public void testGRPCMapping() {
assertEquals(
EntityPermission.EDIT_ACL.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_EDIT_ACL);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_EDIT_ACL);
assertEquals(
EntityPermission.DELETE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_DELETE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_DELETE);
assertEquals(
EntityPermission.USE_AS_DATA_TYPE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_DATA_TYPE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_DATA_TYPE);
assertEquals(
EntityPermission.USE_AS_PARENT.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PARENT);
assertEquals(
EntityPermission.USE_AS_PROPERTY.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PROPERTY);
assertEquals(
EntityPermission.USE_AS_REFERENCE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_REFERENCE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_REFERENCE);
assertEquals(
EntityPermission.RETRIEVE_ENTITY.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ENTITY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ENTITY);
assertEquals(
EntityPermission.RETRIEVE_ACL.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ACL);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ACL);
assertEquals(
EntityPermission.RETRIEVE_OWNER.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_OWNER);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_OWNER);
assertEquals(
EntityPermission.RETRIEVE_HISTORY.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_HISTORY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_HISTORY);
assertEquals(
EntityPermission.RETRIEVE_FILE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_FILE);
assertEquals(
EntityPermission.UPDATE_VALUE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_VALUE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_VALUE);
assertEquals(
EntityPermission.UPDATE_DESCRIPTION.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DESCRIPTION);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DESCRIPTION);
assertEquals(
EntityPermission.UPDATE_DATA_TYPE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DATA_TYPE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DATA_TYPE);
assertEquals(
EntityPermission.UPDATE_NAME.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_NAME);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_NAME);
assertEquals(
EntityPermission.UPDATE_QUERY_TEMPLATE_DEFINITION.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission
+ org.linkahead.api.entity.v1.EntityPermission
.ENTITY_PERMISSION_UPDATE_QUERY_TEMPLATE_DEFINITION);
assertEquals(
EntityPermission.UPDATE_ROLE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ROLE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ROLE);
assertEquals(
EntityPermission.UPDATE_ADD_PARENT.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PARENT);
assertEquals(
EntityPermission.UPDATE_REMOVE_PARENT.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PARENT);
assertEquals(
EntityPermission.UPDATE_ADD_PROPERTY.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PROPERTY);
assertEquals(
EntityPermission.UPDATE_REMOVE_PROPERTY.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PROPERTY);
assertEquals(
EntityPermission.UPDATE_ADD_FILE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_FILE);
assertEquals(
EntityPermission.UPDATE_REMOVE_FILE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_FILE);
assertEquals(
EntityPermission.UPDATE_MOVE_FILE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_MOVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_MOVE_FILE);
}
}
diff --git a/src/test/java/org/caosdb/server/query/POVTest.java b/src/test/java/org/caosdb/server/query/POVTest.java
index 7212423bbaf2ac4d3c5e33543d3e6ffe4e70b5e4..2e9223dc3219a2b5ec3125bb73577590e77d20b8 100644
--- a/src/test/java/org/caosdb/server/query/POVTest.java
+++ b/src/test/java/org/caosdb/server/query/POVTest.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
diff --git a/src/test/java/org/caosdb/server/query/QueryTest.java b/src/test/java/org/caosdb/server/query/QueryTest.java
index 986122ca46307173c6c9f80b2085db3f1776904a..e6a514c817b76c090b4ac06765a6dfca97dfc1de 100644
--- a/src/test/java/org/caosdb/server/query/QueryTest.java
+++ b/src/test/java/org/caosdb/server/query/QueryTest.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,7 +17,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
@@ -28,20 +28,20 @@ import static org.junit.jupiter.api.Assertions.fail;
import java.io.IOException;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.database.access.InitAccess;
-import org.caosdb.server.transaction.WriteTransaction;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.database.access.InitAccess;
+import org.linkahead.server.transaction.WriteTransaction;
public class QueryTest {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.initShiro();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.initShiro();
}
String getCacheKey(String query) {
@@ -52,7 +52,7 @@ public class QueryTest {
String getCacheKeyWithUser(String query) {
Subject anonymous = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
anonymous.login(AnonymousAuthenticationToken.getInstance());
Query q = new Query(query, anonymous);
q.parse();
diff --git a/src/test/java/org/caosdb/server/query/TestCQL.java b/src/test/java/org/caosdb/server/query/TestCQL.java
index 8d7a7e8fb219f286d6cdaffc4b28240a7b2897d5..f8c3fadc7563c102254738425bd20f9f0454da26 100644
--- a/src/test/java/org/caosdb/server/query/TestCQL.java
+++ b/src/test/java/org/caosdb/server/query/TestCQL.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -37,24 +37,24 @@ import org.antlr.v4.runtime.CharStreams;
import org.antlr.v4.runtime.CommonTokenStream;
import org.antlr.v4.runtime.Token;
import org.antlr.v4.runtime.tree.ParseTree;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.query.CQLParser.CqContext;
-import org.caosdb.server.query.Query.Pattern;
-import org.caosdb.server.query.Query.QueryException;
-import org.caosdb.server.utils.Initialization;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.query.CQLParser.CqContext;
+import org.linkahead.server.query.Query.Pattern;
+import org.linkahead.server.query.Query.QueryException;
+import org.linkahead.server.utils.Initialization;
public class TestCQL {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
static Access access = Initialization.setUp().getAccess();
@@ -268,7 +268,7 @@ public class TestCQL {
String queryMR56 = "FIND ENTITY WITH ((p0 = v0 OR p1=v1) AND p2=v2)";
String versionedQuery1 = "FIND ANY VERSION OF ENTITY e1";
- // https://gitlab.com/caosdb/caosdb-server/-/issues/131
+ // https://gitlab.com/linkahead/linkahead-server/-/issues/131
String issue131a = "FIND ename WITH pname1.x AND pname2";
String issue131b = "FIND ename WITH (pname1.x < 10) AND (pname1.x)";
String issue131c = "FIND ename WITH pname2 AND pname1.x ";
@@ -277,7 +277,7 @@ public class TestCQL {
String issue131f = "FIND ename WITH (pname1.pname2 > 30) AND pname1.pname2 < 40";
String issue144 = "FIND ename WITH pname = ";
- // https://gitlab.com/caosdb/caosdb-server/-/issues/130
+ // https://gitlab.com/linkahead/linkahead-server/-/issues/130
String issue130a =
"SELECT 'name with spaces.and dot', 'name with spaces'.name, name with spaces.name, name with\\,comma and\\.dot and \\'single_quote.sub FROM ENTITY";
String issue130b = "SELECT 'Wrapper' FROM RECORD TestRT";
@@ -7074,7 +7074,7 @@ public class TestCQL {
/**
* Test that brackets around 'has pname' do not cause filter to become subproperty filter.
*
- * <p>https://gitlab.com/caosdb/caosdb-server/-/issues/203
+ * <p>https://gitlab.com/linkahead/linkahead-server/-/issues/203
*/
@Test
public void testIssue203() {
diff --git a/src/test/java/org/caosdb/server/resource/FileSystemResourceTest.java b/src/test/java/org/caosdb/server/resource/FileSystemResourceTest.java
index 63c10c1f3e3f7e44e34ece9248bf87b4cbfa139f..936bd542449b8c8ce6cf774d8903c3e51bf3464a 100644
--- a/src/test/java/org/caosdb/server/resource/FileSystemResourceTest.java
+++ b/src/test/java/org/caosdb/server/resource/FileSystemResourceTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static org.junit.jupiter.api.Assertions.assertThrows;
diff --git a/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java b/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java
index ca4fbb0954f469055c2da3d0bf00b03cdc9dd563..a8fc04cc2de0d2c6e263f24b8f06e1c9999b8716 100644
--- a/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java
+++ b/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -14,29 +14,29 @@ import java.util.HashSet;
import org.apache.shiro.mgt.DefaultSecurityManager;
import org.apache.shiro.subject.Subject;
import org.apache.shiro.subject.support.DelegatingSubject;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AnonymousRealm;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.utils.WebinterfaceUtils;
import org.jdom2.Element;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AnonymousRealm;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.utils.WebinterfaceUtils;
import org.restlet.data.Reference;
import org.restlet.representation.Representation;
-public class TestAbstractCaosDBServerResource {
+public class TestAbstractLinkAheadServerResource {
/** a no-op mock-up which resolved all rules to an empty set of permissions. */
public static class RetrievePermissionRulesMockup implements RetrievePermissionRulesImpl {
@@ -78,7 +78,7 @@ public class TestAbstractCaosDBServerResource {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
BackendTransaction.setImpl(
RetrievePermissionRulesImpl.class, RetrievePermissionRulesMockup.class);
@@ -88,14 +88,14 @@ public class TestAbstractCaosDBServerResource {
@Test
public void testReponseRootElement(@TempDir Path tmpDir) throws IOException {
final Subject user = new DelegatingSubject(new DefaultSecurityManager(new AnonymousRealm()));
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
user.login(AnonymousAuthenticationToken.getInstance());
- AbstractCaosDBServerResource s =
- new AbstractCaosDBServerResource() {
+ AbstractLinkAheadServerResource s =
+ new AbstractLinkAheadServerResource() {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
// TODO Auto-generated method stub
return null;
@@ -158,7 +158,7 @@ public class TestAbstractCaosDBServerResource {
+ "defaultRealm = PAM\n"
+ "\n"
+ "[PAM]\n"
- + "class = org.caosdb.server.accessControl.Pam\n"
+ + "class = org.linkahead.server.accessControl.Pam\n"
+ "default_status = ACTIVE\n"
+ "include.user = admin\n"
+ ";include.group = [uncomment and put your groups here]\n"
@@ -169,6 +169,6 @@ public class TestAbstractCaosDBServerResource {
+ "user.admin.roles = administration";
Files.write(Paths.get(usersourcesFileName), usersourcesContent.getBytes());
- CaosDBServer.setProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE, usersourcesFileName);
+ LinkAheadServer.setProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE, usersourcesFileName);
}
}
diff --git a/src/test/java/org/caosdb/server/resource/TestScriptingResource.java b/src/test/java/org/caosdb/server/resource/TestScriptingResource.java
index 31d4a384c4a2a7e12b48c99073119cb7a38e3acc..88b66c5f2439241bdcc94a54c6d6c979b5d13e7a 100644
--- a/src/test/java/org/caosdb/server/resource/TestScriptingResource.java
+++ b/src/test/java/org/caosdb/server/resource/TestScriptingResource.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -31,29 +31,29 @@ import java.util.HashSet;
import java.util.List;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.scripting.ScriptingPermissions;
-import org.caosdb.server.scripting.ServerSideScriptingCaller;
import org.jdom2.Element;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.scripting.ScriptingPermissions;
+import org.linkahead.server.scripting.ServerSideScriptingCaller;
import org.restlet.Request;
import org.restlet.Response;
import org.restlet.data.Form;
@@ -153,8 +153,8 @@ public class TestScriptingResource {
@BeforeAll
public static void setupShiro() throws IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.initShiro();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.initShiro();
BackendTransaction.setImpl(RetrieveRoleImpl.class, RetrieveRoleMockup.class);
BackendTransaction.setImpl(RetrievePermissionRulesImpl.class, RetrievePermissionRules.class);
@@ -171,7 +171,7 @@ public class TestScriptingResource {
public int callScript(
java.util.List<String> invokation,
Integer timeout_ms,
- java.util.List<org.caosdb.server.entity.FileProperties> files,
+ java.util.List<org.linkahead.server.entity.FileProperties> files,
Object authToken)
throws Message {
if (invokation.get(0).equals("anonymous_ok")) {
@@ -206,7 +206,7 @@ public class TestScriptingResource {
@Test
public void testAnonymousWithOutPermission() {
Subject user = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
user.login(AnonymousAuthenticationToken.getInstance());
Form form = new Form("call=anonymous_no_permission");
Representation entity = form.getWebRepresentation();
@@ -224,7 +224,7 @@ public class TestScriptingResource {
@Test
public void testAnonymousWithPermission() {
Subject user = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
user.login(AnonymousAuthenticationToken.getInstance());
Form form = new Form("call=anonymous_ok");
Representation entity = form.getWebRepresentation();
@@ -257,7 +257,7 @@ public class TestScriptingResource {
@Test
public void testHandleForm() throws Message, IOException {
Subject user = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
user.login(AnonymousAuthenticationToken.getInstance());
Form form = new Form("call=anonymous_ok");
assertEquals(0, resource.handleForm(form));
diff --git a/src/test/java/org/caosdb/server/resource/TestSharedFileResource.java b/src/test/java/org/caosdb/server/resource/TestSharedFileResource.java
index 6b9fab19af6a899629e0338f7274f09f4baec7b4..988ba24da1fb99517cd5a57cb9d1ffc6b4981c67 100644
--- a/src/test/java/org/caosdb/server/resource/TestSharedFileResource.java
+++ b/src/test/java/org/caosdb/server/resource/TestSharedFileResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2019 IndiScale GmbH
*
@@ -20,7 +20,7 @@
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -38,14 +38,14 @@ import net.jcip.annotations.NotThreadSafe;
import org.apache.shiro.mgt.DefaultSecurityManager;
import org.apache.shiro.subject.Subject;
import org.apache.shiro.subject.support.DelegatingSubject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AnonymousRealm;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AnonymousRealm;
import org.restlet.Request;
import org.restlet.Response;
import org.restlet.data.Disposition;
@@ -75,7 +75,7 @@ public class TestSharedFileResource {
@BeforeAll
public static void setup() throws Exception {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
String tmpStr = FileSystem.getTmp();
illegalTopLevelFile = new File(tmpStr, illegalTopLevelString);
@@ -109,7 +109,7 @@ public class TestSharedFileResource {
provideUserSourcesFile(tmpDir);
final Subject user = new DelegatingSubject(new DefaultSecurityManager(new AnonymousRealm()));
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
user.login(AnonymousAuthenticationToken.getInstance());
SharedFileResource resource =
new SharedFileResource() {
@@ -176,7 +176,7 @@ public class TestSharedFileResource {
+ "defaultRealm = PAM\n"
+ "\n"
+ "[PAM]\n"
- + "class = org.caosdb.server.accessControl.Pam\n"
+ + "class = org.linkahead.server.accessControl.Pam\n"
+ "default_status = ACTIVE\n"
+ "include.user = admin\n"
+ ";include.group = [uncomment and put your groups here]\n"
@@ -187,6 +187,6 @@ public class TestSharedFileResource {
+ "user.admin.roles = administration";
Files.write(Paths.get(usersourcesFileName), usersourcesContent.getBytes());
- CaosDBServer.setProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE, usersourcesFileName);
+ LinkAheadServer.setProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE, usersourcesFileName);
}
}
diff --git a/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java b/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java
index 0d37928231f139b40b9c3c17d6753fac7368b233..227733557cc5d14dd423a3fca55fb3ed9c410faa 100644
--- a/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java
+++ b/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -39,19 +39,19 @@ import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.TimeUnit;
import org.apache.commons.io.FileUtils;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.Timeout;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
public class TestServerSideScriptingCaller {
@@ -63,8 +63,8 @@ public class TestServerSideScriptingCaller {
@BeforeAll
public static void setupTestFolder() throws IOException {
testFolder = Files.createTempDirectory(".TestDir_ServerSideScripting").toFile();
- CaosDBServer.initServerProperties();
- CaosDBServer.getServerProperties()
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.getServerProperties()
.setProperty(
ServerProperties.KEY_SERVER_SIDE_SCRIPTING_BIN_DIRS, testFolder.getAbsolutePath());
@@ -163,10 +163,10 @@ public class TestServerSideScriptingCaller {
* Throw {@link FileNotFoundException} because PWD does not exist.
*
* @throws IOException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Test()
- public void testPutFilesInWorkingDirFailure1() throws IOException, CaosDBException {
+ public void testPutFilesInWorkingDirFailure1() throws IOException, LinkAheadException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -177,13 +177,13 @@ public class TestServerSideScriptingCaller {
}
/**
- * Throw {@link CaosDBException} because tmpIdentifier is null or empty.
+ * Throw {@link LinkAheadException} because tmpIdentifier is null or empty.
*
* @throws FileNotFoundException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Test
- public void testPutFilesInWorkingDirFailure2() throws FileNotFoundException, CaosDBException {
+ public void testPutFilesInWorkingDirFailure2() throws FileNotFoundException, LinkAheadException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -200,10 +200,10 @@ public class TestServerSideScriptingCaller {
* Throw {@link NullPointerException} because file is null.
*
* @throws FileNotFoundException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Test
- public void testPutFilesInWorkingDirFailure3() throws FileNotFoundException, CaosDBException {
+ public void testPutFilesInWorkingDirFailure3() throws FileNotFoundException, LinkAheadException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -223,10 +223,10 @@ public class TestServerSideScriptingCaller {
* Throw {@link TransactionException} because file does not exist.
*
* @throws FileNotFoundException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Test
- public void testPutFilesInWorkingDirFailure4() throws FileNotFoundException, CaosDBException {
+ public void testPutFilesInWorkingDirFailure4() throws FileNotFoundException, LinkAheadException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -247,10 +247,10 @@ public class TestServerSideScriptingCaller {
* putFilesInWorkingDir returns silently because files is null.
*
* @throws IOException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Test()
- public void testPutFilesInWorkingDirReturnSilently() throws IOException, CaosDBException {
+ public void testPutFilesInWorkingDirReturnSilently() throws IOException, LinkAheadException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -259,7 +259,7 @@ public class TestServerSideScriptingCaller {
}
@Test
- public void testPutFilesInWorkingDirOk() throws CaosDBException, IOException {
+ public void testPutFilesInWorkingDirOk() throws LinkAheadException, IOException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -405,7 +405,7 @@ public class TestServerSideScriptingCaller {
@Override
public void putFilesInWorkingDir(final Collection<FileProperties> files)
- throws FileNotFoundException, CaosDBException {}
+ throws FileNotFoundException, LinkAheadException {}
@Override
public int callScript(
@@ -431,8 +431,8 @@ public class TestServerSideScriptingCaller {
@Override
public void putFilesInWorkingDir(final Collection<FileProperties> files)
- throws FileNotFoundException, CaosDBException {
- throw new CaosDBException("");
+ throws FileNotFoundException, LinkAheadException {
+ throw new LinkAheadException("");
}
@Override
@@ -460,7 +460,7 @@ public class TestServerSideScriptingCaller {
@Override
public void putFilesInWorkingDir(final Collection<FileProperties> files)
- throws FileNotFoundException, CaosDBException {}
+ throws FileNotFoundException, LinkAheadException {}
@Override
public void createTmpHomeDir() throws Exception {}
@@ -490,7 +490,7 @@ public class TestServerSideScriptingCaller {
@Override
public void putFilesInWorkingDir(final Collection<FileProperties> files)
- throws FileNotFoundException, CaosDBException {}
+ throws FileNotFoundException, LinkAheadException {}
@Override
public int callScript(
@@ -614,9 +614,9 @@ public class TestServerSideScriptingCaller {
cmd, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
caller.createWorkingDir();
// Create source folder in working directory
- String scriptingHomeDir = CaosDBServer.getServerProperty("SERVER_SIDE_SCRIPTING_HOME_DIR");
+ String scriptingHomeDir = LinkAheadServer.getServerProperty("SERVER_SIDE_SCRIPTING_HOME_DIR");
File tempHomeDirSrc = new File(caller.getTmpWorkingDir(), "home_source");
- CaosDBServer.setProperty("SERVER_SIDE_SCRIPTING_HOME_DIR", tempHomeDirSrc.toString());
+ LinkAheadServer.setProperty("SERVER_SIDE_SCRIPTING_HOME_DIR", tempHomeDirSrc.toString());
tempHomeDirSrc.mkdir();
String testFileName = "testfile.txt";
String testContent = "sloikdfgu89w4t78930tvgyum9q238456t27ht2";
@@ -631,6 +631,6 @@ public class TestServerSideScriptingCaller {
String expectedFileContent = FileUtils.readFileToString(expectedFile, "UTF-8");
assertEquals(expectedFileContent, testContent);
caller.cleanup();
- CaosDBServer.setProperty("SERVER_SIDE_SCRIPTING_HOME_DIR", scriptingHomeDir);
+ LinkAheadServer.setProperty("SERVER_SIDE_SCRIPTING_HOME_DIR", scriptingHomeDir);
}
}
diff --git a/src/test/java/org/caosdb/server/transaction/RetrieveTest.java b/src/test/java/org/caosdb/server/transaction/RetrieveTest.java
index a3ac40e1bf1e0fe6489a74f45d6c253b903b4478..c8ae9417aad7d39f02bca4e7020c5476bbbcfdfe 100644
--- a/src/test/java/org/caosdb/server/transaction/RetrieveTest.java
+++ b/src/test/java/org/caosdb/server/transaction/RetrieveTest.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -7,34 +7,34 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.IOException;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.entity.xml.IdAndServerMessagesOnlyStrategy;
-import org.caosdb.server.permissions.EntityACLFactory;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.entity.xml.IdAndServerMessagesOnlyStrategy;
+import org.linkahead.server.permissions.EntityACLFactory;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class RetrieveTest {
// @review Florian Spreckelsen 2022-03-22
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "TRUE");
- CaosDBServer.initShiro();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "TRUE");
+ LinkAheadServer.initShiro();
BackendTransaction.setImpl(RetrieveRoleImpl.class, RetrieveRoleMockup.class);
}
diff --git a/src/test/java/org/caosdb/server/transaction/UpdateTest.java b/src/test/java/org/caosdb/server/transaction/UpdateTest.java
index a0891a3eb34e1759100c78916d0fb250de149ef8..ace94c5a5323c6993bc3893d4d1396594e0804b3 100644
--- a/src/test/java/org/caosdb/server/transaction/UpdateTest.java
+++ b/src/test/java/org/caosdb/server/transaction/UpdateTest.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,44 +19,44 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import static org.caosdb.server.utils.EntityStatus.QUALIFIED;
-import static org.caosdb.server.utils.EntityStatus.VALID;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.linkahead.server.utils.EntityStatus.QUALIFIED;
+import static org.linkahead.server.utils.EntityStatus.VALID;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.util.HashSet;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.permissions.Permission;
-import org.caosdb.server.utils.EntityStatus;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.permissions.Permission;
+import org.linkahead.server.utils.EntityStatus;
public class UpdateTest {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
public void testDeriveUpdate_SameName()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final Entity newEntity = new RetrieveEntity("Name");
final Entity oldEntity = new RetrieveEntity("Name");
new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
@@ -65,7 +65,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_DifferentName()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final Entity newEntity = new RetrieveEntity("NewName");
final Entity oldEntity = new RetrieveEntity("OldName");
new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
@@ -74,7 +74,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_SameProperty()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final Entity newEntity = new RetrieveEntity(new EntityID(1234));
final Property newProperty = new Property(new RetrieveEntity(new EntityID(1)));
newEntity.addProperty(newProperty);
@@ -88,7 +88,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_AnotherProperty()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final Entity newEntity = new RetrieveEntity(new EntityID(1234));
final Property newProperty = new Property(new RetrieveEntity(new EntityID(1)));
final Property newProperty2 = new Property(new RetrieveEntity(new EntityID(2)));
@@ -106,7 +106,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_SameUnit()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final EntityInterface magicUnit = new RetrieveEntity(new EntityID(1234));
magicUnit.setName("Unit");
magicUnit.setId(new EntityID(24));
@@ -148,7 +148,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_DifferentUnit()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final EntityInterface magicUnit = new RetrieveEntity(new EntityID(1234));
magicUnit.setName("Unit");
magicUnit.setId(new EntityID(24));
@@ -189,7 +189,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_Collections()
- throws NoSuchAlgorithmException, CaosDBException, IOException {
+ throws NoSuchAlgorithmException, LinkAheadException, IOException {
final Entity newEntity = new UpdateEntity();
final Property newProperty = new Property(new UpdateEntity(new EntityID(1)));
@@ -264,7 +264,7 @@ public class UpdateTest {
/** For issue #217: Server gets list property datatype wrong if description is updated. */
@Test
public void testDeriveUpdate_UpdateList()
- throws NoSuchAlgorithmException, CaosDBException, IOException {
+ throws NoSuchAlgorithmException, LinkAheadException, IOException {
// @review Florian Spreckelsen 2022-03-15
final Property oldProperty = new Property(new UpdateEntity(new EntityID(1)));
final Property newProperty = new Property(new UpdateEntity(new EntityID(1)));
diff --git a/src/test/java/org/caosdb/server/utils/FileUtilsTest.java b/src/test/java/org/caosdb/server/utils/FileUtilsTest.java
index e05a3c7f6f082f2432137737c5937e67ff75d4ef..8079a2c469f7b8051ca7925ef00f1dc12c936658 100644
--- a/src/test/java/org/caosdb/server/utils/FileUtilsTest.java
+++ b/src/test/java/org/caosdb/server/utils/FileUtilsTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -38,34 +38,34 @@ import java.security.NoSuchAlgorithmException;
import java.util.Iterator;
import java.util.regex.Pattern;
import net.jcip.annotations.NotThreadSafe;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckHash;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckSize;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileExists;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileWasModifiedAfter;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator.FileNameIterator;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemHelper;
-import org.caosdb.server.database.backend.interfaces.FileCheckHash;
-import org.caosdb.server.database.backend.interfaces.FileCheckSize;
-import org.caosdb.server.database.backend.interfaces.FileExists;
-import org.caosdb.server.database.backend.interfaces.FileWasModifiedAfter;
-import org.caosdb.server.database.backend.interfaces.GetFileIteratorImpl;
-import org.caosdb.server.database.backend.transaction.FileConsistencyCheck;
-import org.caosdb.server.database.backend.transaction.GetFileIterator;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
import org.eclipse.jetty.io.RuntimeIOException;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckHash;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckSize;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileExists;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileWasModifiedAfter;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator.FileNameIterator;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemHelper;
+import org.linkahead.server.database.backend.interfaces.FileCheckHash;
+import org.linkahead.server.database.backend.interfaces.FileCheckSize;
+import org.linkahead.server.database.backend.interfaces.FileExists;
+import org.linkahead.server.database.backend.interfaces.FileWasModifiedAfter;
+import org.linkahead.server.database.backend.interfaces.GetFileIteratorImpl;
+import org.linkahead.server.database.backend.transaction.FileConsistencyCheck;
+import org.linkahead.server.database.backend.transaction.GetFileIterator;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
@NotThreadSafe
public class FileUtilsTest {
@@ -76,7 +76,7 @@ public class FileUtilsTest {
public static File someFile;
public static File someDir_someFile;
public static File linkToSomeFile;
- public static File tmpFolderCaosDB;
+ public static File tmpFolderLinkAhead;
private static File newFolder(String name) throws IOException {
Path ret = Files.createTempDirectory(tempDirectory, name);
@@ -84,8 +84,8 @@ public class FileUtilsTest {
}
@BeforeAll
- public static void setup() throws Message, IOException, CaosDBException, InterruptedException {
- CaosDBServer.initServerProperties();
+ public static void setup() throws Message, IOException, LinkAheadException, InterruptedException {
+ LinkAheadServer.initServerProperties();
BackendTransaction.setImpl(FileExists.class, UnixFileSystemFileExists.class);
BackendTransaction.setImpl(GetFileIteratorImpl.class, UnixFileSystemGetFileIterator.class);
BackendTransaction.setImpl(
@@ -95,7 +95,7 @@ public class FileUtilsTest {
tempDirectory = Files.createTempDirectory(null);
testRoot = newFolder("fileutils_testfolder");
- File basePath = newFolder("caosdbRoot");
+ File basePath = newFolder("linkaheadRoot");
File dropOffBox = newFolder("dropOffBox");
someDir = testRoot.toPath().resolve("some_dir").toFile();
linkToSomeDir = testRoot.toPath().resolve("link_to_some_dir").toFile();
@@ -103,10 +103,10 @@ public class FileUtilsTest {
someDir_someFile = someDir.toPath().resolve("someFile").toFile();
linkToSomeFile = testRoot.toPath().resolve("link_to_some_file").toFile();
- tmpFolderCaosDB = newFolder("tmpFolderCaosDB");
- CaosDBServer.setProperty(ServerProperties.KEY_FILE_SYSTEM_ROOT, basePath.toString());
- CaosDBServer.setProperty(ServerProperties.KEY_DROP_OFF_BOX, dropOffBox.toString());
- CaosDBServer.setProperty(ServerProperties.KEY_TMP_FILES, tmpFolderCaosDB.toString());
+ tmpFolderLinkAhead = newFolder("tmpFolderLinkAhead");
+ LinkAheadServer.setProperty(ServerProperties.KEY_FILE_SYSTEM_ROOT, basePath.toString());
+ LinkAheadServer.setProperty(ServerProperties.KEY_DROP_OFF_BOX, dropOffBox.toString());
+ LinkAheadServer.setProperty(ServerProperties.KEY_TMP_FILES, tmpFolderLinkAhead.toString());
FileSystem.init();
basePath = new File(FileSystem.getBasepath());
@@ -130,7 +130,7 @@ public class FileUtilsTest {
}
@AfterAll
- public static void teardown() throws IOException, CaosDBException, InterruptedException {
+ public static void teardown() throws IOException, LinkAheadException, InterruptedException {
FileUtils.delete(testRoot, true);
deleteTmp();
assertFalse(testRoot.exists());
@@ -141,10 +141,10 @@ public class FileUtilsTest {
/**
* @throws InterruptedException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@BeforeEach
- public void testTmpEmpty() throws IOException, CaosDBException, InterruptedException {
+ public void testTmpEmpty() throws IOException, LinkAheadException, InterruptedException {
if (new File(FileSystem.getTmp()).exists()) {
if (0 != new File(FileSystem.getTmp()).list().length) {
System.err.println("TMP not empty, aborting test!");
@@ -159,7 +159,7 @@ public class FileUtilsTest {
}
}
- public static void deleteTmp() throws IOException, CaosDBException, InterruptedException {
+ public static void deleteTmp() throws IOException, LinkAheadException, InterruptedException {
File tmpDir = new File(FileSystem.getTmp());
if (tmpDir.exists())
for (File f : tmpDir.listFiles()) {
@@ -169,7 +169,7 @@ public class FileUtilsTest {
}
@AfterEach
- public void callDeleteTmp() throws IOException, CaosDBException, InterruptedException {
+ public void callDeleteTmp() throws IOException, LinkAheadException, InterruptedException {
deleteTmp();
}
@@ -196,7 +196,8 @@ public class FileUtilsTest {
}
@Test
- public void testGetMimeTypeSymlink() throws IOException, InterruptedException, CaosDBException {
+ public void testGetMimeTypeSymlink()
+ throws IOException, InterruptedException, LinkAheadException {
final File symlink = testRoot.toPath().resolve("simlink").toFile();
try {
@@ -241,7 +242,7 @@ public class FileUtilsTest {
}
@Test
- public void testSymlinkRoot() throws IOException, InterruptedException, CaosDBException {
+ public void testSymlinkRoot() throws IOException, InterruptedException, LinkAheadException {
final File symlink_root = linkToSomeDir;
assertTrue(symlink_root.exists());
assertTrue(symlink_root.isDirectory());
@@ -283,7 +284,7 @@ public class FileUtilsTest {
}
@Test
- public void TestChownScript() throws IOException, InterruptedException, CaosDBException {
+ public void TestChownScript() throws IOException, InterruptedException, LinkAheadException {
FileUtils.testChownScript();
final File f = new File(FileSystem.getDropOffBox() + "chown_test_file");
@@ -465,7 +466,7 @@ public class FileUtilsTest {
}
@Test
- public void testSymlinkBehavior() throws IOException, InterruptedException, CaosDBException {
+ public void testSymlinkBehavior() throws IOException, InterruptedException, LinkAheadException {
// root dir for this test
final String rootPath = "./testSymlinkBehavior/";
@@ -721,11 +722,11 @@ public class FileUtilsTest {
String existingDirStr = "existingDir";
String existingFileStr = "existingFile";
String newDirStr = "newDir/";
- File existingDir = new File(tmpFolderCaosDB, existingDirStr);
+ File existingDir = new File(tmpFolderLinkAhead, existingDirStr);
existingDir.mkdir();
- File existingFile = new File(tmpFolderCaosDB, existingFileStr);
+ File existingFile = new File(tmpFolderLinkAhead, existingFileStr);
existingFile.createNewFile();
- File newDir = new File(tmpFolderCaosDB, newDirStr);
+ File newDir = new File(tmpFolderLinkAhead, newDirStr);
// Existing directory
assertEquals(existingDir.toString(), FileSystem.assertDir(existingDirStr));
diff --git a/src/test/java/org/caosdb/server/utils/UtilsTest.java b/src/test/java/org/caosdb/server/utils/UtilsTest.java
index 562d592756b8cf075dd421913dabb193d734af12..6f5c71ef382417dec5e16737739a0ebdde5f270d 100644
--- a/src/test/java/org/caosdb/server/utils/UtilsTest.java
+++ b/src/test/java/org/caosdb/server/utils/UtilsTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2019 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
diff --git a/src/test/java/org/caosdb/server/utils/WebinterfaceUtilsTest.java b/src/test/java/org/caosdb/server/utils/WebinterfaceUtilsTest.java
index c607afd02c7651f0631283be77a3745d44121a3b..f812287e8245468c481d0ae5fec0acef4f46d083 100644
--- a/src/test/java/org/caosdb/server/utils/WebinterfaceUtilsTest.java
+++ b/src/test/java/org/caosdb/server/utils/WebinterfaceUtilsTest.java
@@ -1,21 +1,21 @@
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import java.io.IOException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.restlet.data.Reference;
public class WebinterfaceUtilsTest {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
@@ -23,7 +23,7 @@ public class WebinterfaceUtilsTest {
WebinterfaceUtils utils = new WebinterfaceUtils(new Reference("https://host:2345/some_path"));
String buildNumber = utils.getBuildNumber();
String ref = utils.getWebinterfaceURI("sub");
- String contextRoot = CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT);
+ String contextRoot = LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT);
contextRoot =
contextRoot != null && contextRoot.length() > 0
? "/" + contextRoot.replaceFirst("^/", "").replaceFirst("/$", "")
diff --git a/src/test/java/org/caosdb/server/utils/mail/TestMail.java b/src/test/java/org/caosdb/server/utils/mail/TestMail.java
index 05cf5bf5698831ffbb68fc3a76836c4587d15f14..415ee72d4aa32ac480a2f51bd7826e16bcddfa04 100644
--- a/src/test/java/org/caosdb/server/utils/mail/TestMail.java
+++ b/src/test/java/org/caosdb/server/utils/mail/TestMail.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import org.apache.commons.io.FileUtils;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
public class TestMail {
@@ -40,9 +40,9 @@ public class TestMail {
public static void setupUp() throws IOException {
testDir = Files.createTempDirectory(".TestDir_Mail").toFile();
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
// output mails to the test dir
- CaosDBServer.setProperty(
+ LinkAheadServer.setProperty(
ServerProperties.KEY_MAIL_TO_FILE_HANDLER_LOC, testDir.getAbsolutePath());
}