diff --git a/.docker/Dockerfile b/.docker/Dockerfile
index 5c49eb7e9c88346b8423a611dc14aca2e85cf346..f9a4145fdf1a70e7be1ede3649261757a12d2c65 100644
--- a/.docker/Dockerfile
+++ b/.docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM debian:buster
+FROM debian:bookworm
RUN apt-get update \
&& \
apt-get install -y \
@@ -11,4 +11,8 @@ RUN apt-get update \
python3-sqlparse \
python3-sphinx \
doxygen
-RUN pip3 install breathe sphinx-rtd-theme recommonmark
+RUN pip3 install --break-system-packages \
+ breathe \
+ sphinx-rtd-theme \
+ pytest \
+ recommonmark
diff --git a/.docker/docker-compose.yml b/.docker/docker-compose.yml
new file mode 100644
index 0000000000000000000000000000000000000000..8c6555eb457a992f69625c55bfced34d9b1c51fd
--- /dev/null
+++ b/.docker/docker-compose.yml
@@ -0,0 +1,23 @@
+version: '3.6'
+services:
+ sqldb:
+ image: mariadb:11.4
+ volumes:
+ - type: volume
+ source: "caosdb-sqldata"
+ target: /var/lib/mysql
+ environment:
+ MYSQL_ROOT_PASSWORD: caosdb1234
+ networks:
+ # available on port 3306, host name 'sqldb'
+ - caosnet
+ ports:
+ - 3306:3306
+
+
+# A well-defined network for caosdb
+volumes:
+ caosdb-sqldata:
+networks:
+ caosnet:
+ driver: bridge
diff --git a/.gitignore b/.gitignore
index 26060c8b9c3986ed5a0803bcf1e1e2a88acee1a3..6f952db9ec3600b624a0151d97db6d299cbd53ca 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,4 +13,5 @@ libs/*
# Generated files
_doxygen/
_generated/
-/build/
\ No newline at end of file
+/build/
+*~
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1e54f4c213acfb9f2b67e01b2ad38b64171c31c0..3137b6ad8ddc686c563e78e6e2c5ee3f0a6ca3fe 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,7 +3,9 @@
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Copyright (C) 2024 Indiscale GmbH <info@indiscale.com>
# Copyright (C) 2019 Henrik tom Wörden
+# Copyright (C) 2024 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
@@ -59,43 +61,35 @@ unittests-mariadb:
tags: [ docker ]
stage: test
services:
- - mariadb:10.4
-
+ - mariadb:10.11
script:
- make pipeline-test SQL_HOST=mariadb
-# Run the unit tests with MySQL 8
-unittests-mysql-8:
- tags: [ docker ]
- stage: test
- # Should not stop the pipeline from continuing.
- allow_failure: true
- services:
- - name: mysql:8.0
- command: ["--default-authentication-plugin=mysql_native_password"]
-
- script:
- - sed "s/NO_AUTO_CREATE_USER,//" -i tests/example.dump.sql
- - rm tests/test_autotap.sql
- - make pipeline-test SQL_HOST=mysql
-
-# Run the unit tests with MySQL 5
-unittests-mysql-5:
+# Run the dump update tests
+test-dump-update:
tags: [ docker ]
stage: test
- # Should not stop the pipeline from continuing.
- allow_failure: true
- services:
- - name: mysql:5.7
- command: ["--default-authentication-plugin=mysql_native_password"]
-
script:
- # remove some lines from autotap because the checks of column default
- # values don't work with mysql-5
- - sed -i "/col_default_is.*NULL/d" tests/test_autotap.sql
- - sed -i "/col_default_is.*INACTIVE/d" tests/test_autotap.sql
- - sed -i "/col_default_is.*SHA/d" tests/test_autotap.sql
- - make pipeline-test SQL_HOST=mysql
+ - make test-dump-update
+
+# # Run the unit tests with MySQL 5
+# unittests-mysql-5:
+# tags: [ docker ]
+# stage: test
+# # Should not stop the pipeline from continuing.
+# allow_failure: true
+# services:
+# - name: mysql:5.7.36
+# command: ["--default-authentication-plugin=mysql_native_password"]
+#
+# script:
+# # remove some lines from autotap because the checks of column default
+# # values don't work with mysql-5
+# - sed -i "/col_default_is.*NULL/d" tests/test_autotap.sql
+# - sed -i "/col_default_is.*INACTIVE/d" tests/test_autotap.sql
+# - sed -i "/col_default_is.*SHA/d" tests/test_autotap.sql
+# - sed -i "s/utf8mb3/utf8/" tests/test_autotap.sql
+# - make pipeline-test SQL_HOST=mysql
######## Deploy ########
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 22588269882a81dd299b2e56120576d2382d9426..3bd316eb5605e52ad4c4ee60e84a6d40db5512c9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,31 +5,166 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-## [Unreleased] ##
+## [Unreleased]
+
+### Added
+
+- New version requirement: MariaDB 11.2 or later.
+
+### Changed
+
+* Changed names from CaosDB to LinkAhead.
+
+### Deprecated
+
+### Removed
+
+- MySQL support. See the deprecation in the 7.0.0 release.
+
+### Fixed
+
+- [SQL dump migration can now be applied
+ twice](https://gitlab.indiscale.com/caosdb/src/caosdb-mysqlbackend/-/issues/60):
+ Fixed an error in the regex.
+- [linkahead-server#264](https://gitlab.com/linkahead/linkahead-server/-/issues/264)
+ Queries ignore accents and umlauts: Changed to more appropriate
+ collation and character sets. This requires MariaDB 11.2 or later,
+ see above.
+
+### Security
+
+## [8.0.0] - 2024-10-24 ##
+
+### Added ###
+
+- Script to update outdated database dumps.
+
+### Changed ###
+
+- `OFFSET` is a reserved keyword in MariaDB 10.6, so the former
+ `OFFSET` parameter name in the `get_head_relative` function was
+ changed to HeadOffset. See
+ [`update_dumps/README.md`](update_dumps/README.md) for information
+ on how to update old SQL dumps to be compatible with this renaming
+ and MariaDB >= 10.6.
+
+## [7.0.2] - 2023-12-12 ##
+(Timm Fitschen)
+
+### Fixed ###
+
+* make install: Could not connect to MariaDB in local docker
+ container
+ [linkahead-mariadbbackend](https://gitlab.com/linkahead/linkahead-mariadbbackend/-/issues/33)
+* Wrong ids in data_type table due to a bug in the `linkahead-server < v0.11.0`
+ which has been fixed but left broken data. This resulted in server errors
+ [linkahead-mariadbbackend#34](https://gitlab.com/linkahead/linkahead-mariadbbackend/-/issues/34)
+
+## [7.0.1] - 2023-11-01
+(Timm Fitschen)
### Added ###
+* Sanity checks during `make install` and `make upgrade`.
+
+## [7.0.0] - 2023-10-25 ##
+(Timm Fitschen)
+
### Changed ###
-* Changed names from CaosDB to LinkAhead.
+* Change signature of procedure `insertEntityDataType`: expect the data type ID
+ instead of the name.
+* Change result set of procedure `retrieveEntity`: Rename column `Datatype` to
+ `DatatypeName` and add column `DatatypeID`.
+* Change result set of procedure `retrieveOverrides`: Rename column
+ `type_override` to `type_name_override` and add `type_id_override`.
+* Change signature of procedure `updateEntity`: expect the data type ID instead
+ to the name.
+* Internal ids, when returned by `retrieveEntityProperties`,
+ `registerReplacementIds`, or `retrieveOverrides`, are prefixed by a special
+ character which serves as a ephemeral marker. Currently this is `$` but this
+ may change in the future if there is a more suitable candidate.
### Deprecated ###
-### Removed ###
+* MySQL Support. Last version which is known to work well with LinkAhead is MySQL 5.7.36
### Fixed ###
-### Security ###
+* Unknown Server Error when inserting an Entity.
+ [linkahead-mariadbbackend#48](https://gitlab.indiscale.com/caosdb/src/caosdb-mysqlbackend/-/issues/48).
+* Fix broken `initEntity` procedure (and change the first parameters type from
+ INT UNSIGNED to VARCHAR(255) which is non-breaking).
-## [5.0.0] - 2021-10-28 ##
+## [6.0.1 2023-10-18] ##
+
+### Fixed ###
+* Old passwords table is removed from dumps where it still exists.
+
+## [6.0.0 2023-10-17] ##
+
+This is a major update. Switching from integer ids for internal and external use to string ids for the external use while keeping the old integer ids for internal use.
### Added ###
-* #33 CI pipeline for MySQL (was only MariaDB before).
+* Table `entity_ids`
+* Procedure `getIdByName`
+* Procedure `insertEntityDataType` and `insertEntityCollection`
+* Procedure `setFileProperties`.
### Changed ###
-### Deprecated ###
+* Rename PROCEDURE `registerSubdomain` to `registerReplacementIds`.
+* Change column `entities.role` datatype: replace 'DOMAIN' enum value with `_REPLACEMENT`.
+* Change column `transactions_log.entity_id` to VARCHAR(255)
+* Change column `user_info.entity` to VARCHAR(255)
+* Change signature of procedure `applyIDFilter` - `EntityID VARCHAR(255)`
+* Change signature of procedure `initBackreference` - `EntityID VARCHAR(255)` and `PropertyID VARCHAR(255)`
+* Change signature of procedure `initPOVPropertiesTable` - `PropertyID VARCHAR(255)`
+* Change signature of procedure `initPOVRefidsTable` - `PropertyID VARCHAR(255)`
+* Change signature of procedure `initSubEntity` - `EntityID VARCHAR(255)`
+* Change signature of procedure `deleteEntity` - `EntityID VARCHAR(255)`
+* Change signature of procedure `deleteEntityProperties` - `EntityID VARCHAR(255)`
+* Change signature of procedure `get_primary_parent_version` - `EntityID VARCHAR(255)`
+* Change signature of procedure `get_version_timestamp` - `EntityID VARCHAR(255)`
+* Change signature of procedure `get_head_version` - `EntityID VARCHAR(255)`
+* Change signature of procedure `get_head_relative` - `EntityID VARCHAR(255)`
+* Change signature of procedure `get_version_history` - `EntityID VARCHAR(255)`
+* Change signature of procedure `retrieveQueryTemplateDef` - `EntityID VARCHAR(255)`
+* Change signature of procedure `getDependentEntities` - `EntityID VARCHAR(255)`
+* Change signature of procedure `insertEntity` - Add parameter `EntityID VARCHAR(255)`
+* Change signature of procedure `insertEntityProperty` - `EntityID VARCHAR(255)` and `PropertyID VARCHAR(255)`, `DomainID VARCHAR(255)`, `DatatypeOverride VARCHAR(255)`
+* Change signature of procedure `insertIsa` - `ChildID VARCHAR(255)`, `ParentID VARCHAR(255)`.
+* Change signature of procedure `isSubtype` - `ChildID VARCHAR(255)`, `ParentID VARCHAR(255)`.
+* Change signature of procedure `retrieveEntity` - `EntityID VARCHAR(255)`
+* Change signature of procedure `retrieveOverrides` - `EntityID VARCHAR(255)`, `DomainID VARCHAR(255)`
+* Change signature of procedure `retrieveEntityParents` - `EntityID VARCHAR(255)`
+* Change signature of procedure `retrieveEntityProperties` - `EntityID VARCHAR(255)`, `DomainID VARCHAR(255)`
+* Change signature of procedure `updateEntity` - `EntityID VARCHAR(255)`
+
+### Removed ###
+
+* Deactivate procedure `delete_all_entity_versions`. This might be used in the
+ future, that is why we keep the code in a comment.
+* Drop procedure `retrieveSubEntity`
+* Drop procedure `retrieveDatatype`
+* Drop procedure `retrieveGroup`
+* Drop procedure `getInfo`
+* Drop procedure `getRole`
+* Drop procedure `setPassword`
+* Drop procedure `initAutoIncrement`
+* Delete special entity 50 (SQLite Datatype)
+* Delete special entity 99 (Work-around for the auto-increment)
+
+### Fixed ###
+
+* Change signature of procedure `getFileIdByPath` - `FilePath TEXT` - this length is needed for the path column of `file_entities`.
+
+## [5.0.0] - 2021-10-28 ##
+
+### Added ###
+
+* #33 CI pipeline for MySQL (was only MariaDB before).
### Removed ###
@@ -43,8 +178,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
* #32 Removed unused `groups` table from installation routines which prevented
the installation with MySQL 8.
-### Security ###
-
## [4.1.0] - 2021-06-11 ##
### Added ###
@@ -65,31 +198,29 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
* `get_version_history` returns two additional columns, `child_username` and
`child_realm`.
* Added a `versioned` flag to the following procedures:
- * `applyBackReference`
- * `applyIDFilter`
- * `applyPOV`
- * `applyRefPOV`
- * `makeStmt`
- * `calcComplementUnion`
- * `calcDifference`
- * `calcIntersection`
- * `finishSubProperty`
- * `getChildren`
- * `initEmptyTargetSet`
- * `initDisjunctionFilter`
- * `initEntity`
- * `initQuery`
- * `createTmpTable`
+ * `applyBackReference`
+ * `applyIDFilter`
+ * `applyPOV`
+ * `applyRefPOV`
+ * `makeStmt`
+ * `calcComplementUnion`
+ * `calcDifference`
+ * `calcIntersection`
+ * `finishSubProperty`
+ * `getChildren`
+ * `initEmptyTargetSet`
+ * `initDisjunctionFilter`
+ * `initEntity`
+ * `initQuery`
+ * `createTmpTable`
* Added a `direct` column to `archive_isa` table
-### Deprecated ###
-
### Removed ###
* unused procedures:
- * `initNegationFilter`
- * `initConjunctionFilter`
- * `finishNegationFilter`
+ * `initNegationFilter`
+ * `initConjunctionFilter`
+ * `finishNegationFilter`
### Fixed ###
@@ -109,8 +240,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
version resultet in an error. See corresponding test in `linkahead-pyinttest`
`tests/test_versioning.py::test_datatype_without_name`
-### Security ###
-
## [3.0.0] - 2020-09-01 ##
### Added ###
@@ -128,20 +257,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
with a lot of additions to the API. E.g.
* New `entity_version`.
* All `*_data` tables have a new twin, the `archive_*_data` table, where all
- old versions of entities are stored. The `*_data` tables only contain the
- data of the latest version.
+ old versions of entities are stored. The `*_data` tables only contain the
+ data of the latest version.
* Additional `archive_isa` for the history entities' parents.
* Additional `_iversion` column for the `reference_data` table for storing
- references to particular versions of an entity.
+ references to particular versions of an entity.
* New `setFileProperties` and `retrieveQueryTemplateDef` procedures which reduce server code and let the
- backend decide which tables to use. Also, this is necessary for the
- versioning, because these procedures behave differently depending on the
- ENTITY_VERSIONING feature being enabled or disabled.
+ backend decide which tables to use. Also, this is necessary for the
+ versioning, because these procedures behave differently depending on the
+ ENTITY_VERSIONING feature being enabled or disabled.
* Several functions and procedures for the interaction with the
- `entity_version` table and the `transactions` table. E.g.
- `insert_single_child_version`, `delete_all_entity_versions`,
- `get_iversion`, `get_primary_parent_version`, `get_version_timestamp`,
- `get_head_version`, `get_head_relative`, `get_version_history`.
+ `entity_version` table and the `transactions` table. E.g.
+ `insert_single_child_version`, `delete_all_entity_versions`,
+ `get_iversion`, `get_primary_parent_version`, `get_version_timestamp`,
+ `get_head_version`, `get_head_relative`, `get_version_history`.
The versions are tracked internally by the `_iversion` field which is an
integer and which should not be used outside of the backend.
* New makefile targets for testing with MariaDB instance from Docker image: call
@@ -164,5 +293,3 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
* Bug in `updateEntity.sql` (when updating the primary name without a prior call
to `deleteEntityProperties`). Same thing for `deleteEntity`.
* #21 Bug which prevented deletion of deeply inheriting entities, if versioning was enabled.
-
-### Security ###
diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000000000000000000000000000000000000..3d997f969ded2b5b3b8f9975835e51be7e86b30a
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,28 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+ - family-names: Fitschen
+ given-names: Timm
+ orcid: https://orcid.org/0000-0002-4022-432X
+ - family-names: Schlemmer
+ given-names: Alexander
+ orcid: https://orcid.org/0000-0003-4124-9649
+ - family-names: Hornung
+ given-names: Daniel
+ orcid: https://orcid.org/0000-0002-7846-6375
+ - family-names: tom Wörden
+ given-names: Henrik
+ orcid: https://orcid.org/0000-0002-5549-578X
+ - family-names: Spreckelsen
+ given-names: Florian
+ orcid: https://orcid.org/0000-0002-6856-2910
+ - family-names: Parlitz
+ given-names: Ulrich
+ orcid: https://orcid.org/0000-0003-3058-1435
+ - family-names: Luther
+ given-names: Stefan
+ orcid: https://orcid.org/0000-0001-7214-8125
+title: "LinkAhead - MariaDB Backend"
+version: 8.0.0
+doi: 10.3390/data4020083
+date-released: 2024-10-10
diff --git a/Makefile b/Makefile
index e776ee0babe292158c9e886730b4a41448375ac2..c2cbce0edc270234c9af76167eeaa0b6fe777abc 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,7 @@
+# This file is a part of the Linkahead Project.
#
-# ** header v3.0
-# This file is a part of the LinkAhead Project.
-#
+# Copyright (C) 2025 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2025 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
#
@@ -18,8 +18,7 @@
# 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/>.
#
-# ** end header
-#
+
SHELL=/bin/bash
INSTALL_SQL_FILE=db_5_0.sql
@@ -34,6 +33,7 @@ test-connection:
.PHONY: upgrade
upgrade:
@cd patches; ./applyPatches.sh --env=../.config
+ @./utils/make_db sanity_check
.PHONY: install
install: _install _grant upgrade
@@ -55,23 +55,26 @@ drop-%:
test:
./utils/make_db test --fresh
-# Run tests with a database which is started in a Docker container
+.PHONY: test-dump-update
+test-dump-update:
+ pytest dump_updates
+
+# Run tests with a database which is started in a MariaDB Docker container
.PHONY: test-docker
test-docker:
@docker kill linkahead-mysqlserver-test || true
- @docker container rm linkahead-mysqlserver-test || true
+ @docker container rm -v linkahead-mysqlserver-test || true
@docker run --name linkahead-mysqlserver-test -p "3306:3306" \
- -e MYSQL_ROOT_PASSWORD="pass-for-test" -d mariadb
+ -e MYSQL_ROOT_PASSWORD="pass-for-test" -d mariadb:11.4
@sleep 10
MAINPATH=$(realpath tests/docker_env) utils/make_db test --fresh
- @docker kill linkahead-mysqlserver-test
- @docker container rm linkahead-mysqlserver-test
+ make test-docker-stop
# if automatic stopping failed
.PHONY: test-docker-stop
test-docker-stop:
docker kill linkahead-mysqlserver-test
- docker container rm linkahead-mysqlserver-test
+ docker container rm -v linkahead-mysqlserver-test
# Compile the standalone documentation
.PHONY: doc
@@ -85,7 +88,9 @@ pipeline-test:
echo 'DATABASE_USER_HOST_LIST="%,"' >> .config
echo "MYSQL_USER_PASSWORD=$(MYSQL_ROOT_PASSWORD)" >> .config
echo "MYSQL_HOST=$(SQL_HOST)" >> .config
+ echo "MYSQL_OPTS=--protocol=TCP" >> .config
sleep 10
make install
./utils/make_db restore_db tests/example.dump.sql
+ make upgrade
./tests/test_utils.sh
diff --git a/README.md b/README.md
index 9e9d7c929cf872f8f8662e8912a3bec310cf293c..3c714592bc1ce7f71a7492c7c6ab53cbea48d5fc 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
## Welcome
-This is the **LinkAhead MySQL Backend** repository and a part of the
+This is the **LinkAhead MariaDB Backend** repository and a part of the
LinkAhead project.
## Setup
@@ -18,30 +18,32 @@ Please refer to the [official documentation](https://docs.linkahead.org/linkahea
## Contributing
-Thank you very much to all contributers—[past, present](https://gitlab.com/linkahead/linkahead/-/blob/dev/HUMANS.md), and prospective ones.
+Thank you very much to all contributers—[past,
+present](https://gitlab.com/linkahead/linkahead/-/blob/main/HUMANS.md), and prospective
+ones.
### Code of Conduct
-By participating, you are expected to uphold our [Code of Conduct](https://gitlab.com/linkahead/linkahead/-/blob/dev/CODE_OF_CONDUCT.md).
+By participating, you are expected to uphold our [Code of
+Conduct](https://gitlab.com/linkahead/linkahead/-/blob/main/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/linkahead/linkahead-mysqlbackend/-/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/linkahead-mysqlbackend/),
-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) linkahead.org**.
+* You found a bug, have a question, or want to request a feature? Please
+[create an issue](https://gitlab.com/linkahead/linkahead-mariadbbackend/-/issues).
+* You want to contribute code?
+ * **Forking:** 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.
+* You can also join the LinkAhead community on
+ [#linkahead:matrix.org](https://matrix.to/#/!unwwlTfOznjEnMMXxf:matrix.org).
## License
* Copyright (C) 2018 Research Group Biomedical Physics, Max Planck Institute
for Dynamics and Self-Organization Göttingen.
-* Copyright (C) 2020-2023 Indiscale GmbH <info@indiscale.com>
+* Copyright (C) 2020-2025 Indiscale GmbH <info@indiscale.com>
All files in this repository are licensed under a [GNU Affero General Public
License](LICENCE.md) (version 3 or later).
diff --git a/README_SETUP.md b/README_SETUP.md
index 88fbe41de13229faac502a89a4b767c15ae013e3..689852903dc4e0530fc464fe9e1cb95e2f3e5455 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -1,9 +1,9 @@
-# Setup of the LinkAhead SQL back end
+# Setup of the LinkAhead MariaDB backend
## Dependencies
-* `MariaDB Client 10.1`, `MySQL Client 5.5`, or later versions. In the case of
- MySQL, version 5.6 is recommended.
-- make
+
+* `MariaDB Client 11.2` or later.
+* make
## Create the configuration
* Create an empty `.config` file. For the default values and the meaning of
@@ -12,7 +12,7 @@
parameter that you want to change, add a corresponding line in your `.config`
file. You probably want to change the passwords. As the passwords are stored
unencrypted in the `.config` file, make sure nobody else can read it.
- * If there is no `mysql-config-editor` (`MySQL 5.5`. and `MariaDB`) then the
+ * If there is no `mysql-config-editor` program, then the
`MYSQL_USER_PASSWORD` must be provided, that is the password of the
`MYSQL_USER`.
* If you are using MariaDB and the `root` database user uses pam
@@ -22,7 +22,7 @@
## Setup the SQL database for LinkAhead
-* Run `make install`. If a there is a database with the name you have choosen
+* Run `make install`. If a there is a database with the name you have chosen
during the configuration, you need to reconfigure or delete the database
first.
* *Required database privileges:*
@@ -88,19 +88,46 @@ with the then current version of the stored entities.
* Alternatively, to run the tests in a containerized MariaDB instance, run `make test-docker`,
followed by `make test-docker-stop`.
+
+### Running in a Docker Container
+
+You can use `.docker/docker-compose.yml` to start a docker container
+(`docker-compose -f .docker/docker-compose.yml up -d`) that runs mariadb. You
+need appropriate settings in `.config`:
+* `MYSQL_OPTS="--protocol=TCP"` and
+* `DATABASE_USER_HOST_LIST=%,`
+After the first start, you need to install the database: `make install`.
+Then, you can connect to it with `mariadb --protocol=TCP -u caosdb -prandom1234
+caosdb`.
+
+### Developing tests ###
+
+To use the mytap framework:
+
+```console
+$ cd libs; unzip mytap-1.0.zip; cd mytap-1.0
+# Use the necessary mariadb options for connecting to the server in the following commands
+$ mariadb ... < mytap.sql # Set up the "tap" database and functions.
+$ mariadb ... < scripts/autotap.sql # Insert the "autotap" function.
+# Create autotap file (for comparison with current state)
+$ mariadb ... --raw -B --skip-column-names -e "call tap.autotap('_caosdb_schema_unit_tests')" > test_autotap.current.sql
+# Run the autotap tests (may fail unfortunately with current MariaDB):
+$ mariadb ... < test_autotap.current.sql
+```
+
### Troubleshooting
-#### MySQL has failing tests
+#### Failure to restore a database dump created with an older MariaDB version ####
-Our test suite is developed with MariaDB. That is why some tests, those which
-check constraints based on auto-generated names, fail because MySQL generates
-other names.
+Have a look into the `dump_updates/README.md`. In cases of version
+incompatibilities, the necessary steps to migrate the dump are
+probably described there and scripts for the migrations are provided
+in the same directory.
-Also some test fail with the message "Expected: NULL / Was: NULL" which is
-obviously what was expected.
+#### MySQL has failing tests
-Please look carefully through the tests. If something more serious than that
-comes up, please report a bug.
+*Note: Since we switched from MySQL to MariaDB, the two DBMS projects have diverged quite far. As a
+result, we no longer support MySQL.
## Documentation #
diff --git a/RELEASE_GUIDELINES.md b/RELEASE_GUIDELINES.md
index 9b06342c9d4a91f1add4bd61559ecd1d8e94546a..41c47136c1ab7160578950a384ce9c6ab2182b5b 100644
--- a/RELEASE_GUIDELINES.md
+++ b/RELEASE_GUIDELINES.md
@@ -1,12 +1,13 @@
-# Release Guidelines for the LinkAhead MySQL Backend
+# Release Guidelines for the LinkAhead MariaDB backend
This document specifies release guidelines in addition to the general release
-guidelines of the LinkAhead Project
-([RELEASE_GUIDELINES.md](https://gitlab.com/linkahead/linkahead/blob/dev/RELEASE_GUIDELINES.md))
+guidelines of the CaosDB Project
+([RELEASE_GUIDELINES.md](https://gitlab.com/caosdb/caosdb-meta/-/blob/dev/RELEASE_GUIDELINES.md))
## General Prerequisites
-* All tests are passing.
+* All tests are passing. (Note that pipelines may fail if the major
+ version increased. Rely on manual tests in that case.)
* (FEATURES.md is up-to-date and a public API is being declared in that document.)
* CHANGELOG.md is up-to-date.
* (DEPENDENCIES.md is up-to-date.)
@@ -19,10 +20,23 @@ guidelines of the LinkAhead Project
2. Check all general prerequisites.
-4. Merge the release branch into the main branch.
+3. Assure that the latest patch actually updates the CaosDBVersion() procedure
+ and that the version matches the version you are about to release.
-5. Tag the latest commit of the main branch with `v<VERSION>`.
+4. Update version in `doc/conf.py` and in `CITATION.cff`.
-6. Delete the release branch.
+5. Merge the release branch into the main branch.
-7. Merge the main branch back into the dev branch.
+6. Wait for the main branch pipeline to pass.
+
+7. Tag the latest commit of the main branch with `v<VERSION>`.
+
+8. Delete the release branch.
+
+9. Merge the main branch back into the dev branch and add the `[UNRELEASED]`
+ section to the CHANGELOG.
+
+10. Create a release at the [gitlab repo](https://gitlab.com/linkahead/linkahead-mariadbbackend/-/releases)
+
+11. If necessary, i.e., if the patch or major versions were increased
+ with the release, do a LinkAhead server release.
diff --git a/config.defaults b/config.defaults
index 79ebcba154f01dd86ad3b4399bca2eb84656632b..aba6e0c25d6d275c653f6e6b063d8d25bd281678 100644
--- a/config.defaults
+++ b/config.defaults
@@ -1,7 +1,7 @@
-#
-# ** header v2.0
# This file is a part of the LinkAhead Project.
#
+# Copyright (C) 2024 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2024 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
#
@@ -15,11 +15,9 @@
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
-# You should have received a copy of the GNU General Public License
+# 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/>.
#
-# ** end header
-#
# # Commands
# The MySQL client program.
@@ -40,6 +38,12 @@ MYSQL_PORT=3306
# which will then be used by the LinkAhead Server.
MYSQL_USER=root
MYSQL_USER_PASSWORD=caosdb1234
+# Additional options for the connection
+# e.g. if you want to connect a dockerized MariaDB at localhost you need to put
+# "--protocol=TCP" here because when host=localhost the connection defaults to
+# SOCKET.
+# MYSQL_OPTS='--protocol=TCP'
+MYSQL_OPTS=
# # DATABASE
# The name of the SQL database.
diff --git a/doc/Maintenance.rst b/doc/Maintenance.rst
index fbdef943a3b579c2457b746d09cfcd6d530c128a..ec8d8f3f6a677527a5a581096dc9bbd9c7068d97 100644
--- a/doc/Maintenance.rst
+++ b/doc/Maintenance.rst
@@ -1,12 +1,9 @@
-
Maintenance
===========
-
Creating a Backup
-----------------
-
You can use the Python script ``utils/backup.py`` to create a backup (SQL dump)
of the SQL-Backend::
diff --git a/doc/conf.py b/doc/conf.py
index 20f21f40728038c43e98725f6929bd1905d66dc6..1c33c3faa66aae1a78f2c9cd333b442ed227f7f3 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -22,13 +22,13 @@ import sphinx_rtd_theme
# -- Project information -----------------------------------------------------
project = 'linkahead-mysqlbackend'
-copyright = '2023, IndiScale GmbH'
+copyright = '2021 - 2024, IndiScale GmbH'
author = 'Daniel Hornung'
# The short X.Y version
-version = '6.0'
+version = '8.0.1'
# The full version, including alpha/beta/rc tags
-release = '6.0.0-SNAPSHOT'
+release = '8.0.1-SNAPSHOT'
# -- General configuration ---------------------------------------------------
diff --git a/doc/index.rst b/doc/index.rst
index 652b8556ca4cbbf29a6d29063e0d6d12d9b8b83e..fc6fd46750fa5cd4459f440e7ca7ac5afc041cb3 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -10,7 +10,9 @@ Welcome to documentation of LinkAhead's MySQL Backend!
Getting started <README_SETUP>
Concepts <concepts>
Maintenance
- API documentation<functions>
+ API documentation <functions>
+ Related Projects <related_projects/index>
+ Back to Overview <https://docs.indiscale.com/>
This documentation helps you to :doc:`get started<README_SETUP>`, explains the most important
:doc:`concepts<concepts>` .
diff --git a/doc/related_projects/index.rst b/doc/related_projects/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..78abfd939a097245042a8487eee8ae0d6b4d9e44
--- /dev/null
+++ b/doc/related_projects/index.rst
@@ -0,0 +1,25 @@
+Related Projects
+++++++++++++++++
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+ :hidden:
+
+.. container:: projects
+
+ For in-depth documentation for users, administrators and developers, you may want to visit the subproject-specific documentation pages for:
+
+ :`Server <https://docs.indiscale.com/caosdb-server>`_: The Java part of the LinkAhead server.
+
+ :`WebUI <https://docs.indiscale.com/caosdb-webui>`_: The default web frontend for the LinkAhead server.
+
+ :`PyLinkAhead <https://docs.indiscale.com/caosdb-pylib>`_: The LinkAhead Python library.
+
+ :`Advanced user tools <https://docs.indiscale.com/caosdb-advanced-user-tools>`_: The advanced Python tools for LinkAhead.
+
+ :`LinkAhead Crawler <https://docs.indiscale.com/caosdb-crawler/>`_: The crawler is the main tool for automatic data integration in LinkAhead.
+
+ :`LinkAhead <https://docs.indiscale.com/caosdb-deploy>`_: Your all inclusive LinkAhead software package.
+
+ :`Back to Overview <https://docs.indiscale.com/>`_: LinkAhead Documentation.
diff --git a/dump_updates/2024-10-02.dump_fix_mariadb_10_6.sh b/dump_updates/2024-10-02.dump_fix_mariadb_10_6.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8b9e4843c349a9281526953d6e0c40712a2b1c1a
--- /dev/null
+++ b/dump_updates/2024-10-02.dump_fix_mariadb_10_6.sh
@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+
+# This file is a part of the LinkAhead Project.
+#
+# Copyright (C) 2024 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2024 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
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# 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/>.
+
+# About this script
+# =================
+#
+# Fix the use of "offset" as a procedure parameter name. "OFFSET" became a reserved keyword in
+# MariaDB 10.6.
+#
+# This script takes an SQL dump from stdin and prints the fixed SQL to stdout.
+#
+# Usage
+# -----
+#
+# 2024-10-02.dump_fix_mariadb_10_6.sh < yourdump.sql > yourdump.fixed.sql
+
+set -euo pipefail
+IFS=$'\n\t'
+
+script='
+/^[[:blank:]]+Offset INT UNSIGNED/s/Offset INT UNSIGNED\) RETURNS varbinary\(255\)/HeadOffset INT UNSIGNED\) RETURNS varbinary(255)/
+s/LIMIT 1 OFFSET Offset/LIMIT 1 OFFSET HeadOffset/
+'
+
+sed -E -e "$script"
+
+unset script
diff --git a/dump_updates/README.md b/dump_updates/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..704ea80321a9a873185d0c6959e2000ad26fa10d
--- /dev/null
+++ b/dump_updates/README.md
@@ -0,0 +1,21 @@
+# SQL dump updates #
+
+## Dump ##
+
+This directory contains scripts to update database dumps to newer versions of the MariaDB server.
+
+## Background ##
+
+In some cases, restoring the database content from existing SQL dumps may not be possible in a
+straightforward manner. For those cases, this directory contains scripts to help with known issues.
+
+Examples for problems include:
+
+- New reserved keywords in MariaDB, that were previously used as identifiers in code.
+
+# Known issues and their fix #
+
+- SQL syntax error near `Offset INT UNSIGNED`: If a dump was made before MariaDB 10.6 (LinkAhead <
+ 0.15) and with the SQL backend before 7.0.3, there was a pramater named `Offset`. With MariaDB
+ 10.6 however, `OFFSET` became a reserved keyword. This can be fixed by running
+ `2024-10-02.dump_fix_mariadb_10_6.sh < yourdump.sql > yourdump.fixed.sql`
diff --git a/dump_updates/test/test_all.py b/dump_updates/test/test_all.py
new file mode 100644
index 0000000000000000000000000000000000000000..acdeeeceb341c396c91b764e60bd8b30a7bcd19d
--- /dev/null
+++ b/dump_updates/test/test_all.py
@@ -0,0 +1,85 @@
+#!/usr/bin/env python3
+
+# This file is a part of the LinkAhead Project.
+#
+# Copyright (C) 2024 IndiScale GmbH <www.indiscale.com>
+# Copyright (C) 2024 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
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# 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/>.
+
+"""Testing the dump update scripts
+
+As a general rule, dump updaters should be idempotent, so tests should run the update again after
+the first checks are successlful.
+
+TODO: Reduce the boilerplate for the tests.
+"""
+
+import filecmp
+from pathlib import Path
+from subprocess import run
+from tempfile import NamedTemporaryFile
+
+
+def get_basedir() -> str:
+ """Return the assumped base dir for the dump updates.
+ """
+ path = Path(__file__).parents[1]
+ return str(path)
+
+
+def get_test_data(basename: str) -> list[tuple[str, str]]:
+ """Return a list of [input, expectedoutput] tuples.
+
+ The output may be an empty string if no corresponding file can be found.
+ """
+ basedir = get_basedir()
+ datadir = Path(basedir) / "test" / "test_data"
+ results = []
+ for input_path in datadir.glob(f"{basename}.example*[0-9].sql"):
+ expected_path = datadir / f"{input_path.name[:-4]}.expected.sql"
+ if expected_path.exists():
+ expected = str(expected_path)
+ else:
+ expected = ""
+ results.append((str(input_path), expected))
+ return results
+
+
+def test_2024_10_02(tmpdir):
+ """``Offset`` became a reserved keyword in MariaDB 10.6.
+ """
+ script = "2024-10-02.dump_fix_mariadb_10_6.sh"
+ script_fullname = str(Path(get_basedir()) / script)
+ test_data = get_test_data(script[:-3])
+ for infile, expectedfile in test_data:
+ with (NamedTemporaryFile(dir=tmpdir, suffix=".sql", delete=True) as output,
+ open(infile, mode="rb") as infile_stream
+ ):
+ run([script_fullname],
+ stdin=infile_stream,
+ stdout=output,
+ check=True
+ )
+ assert filecmp.cmp(output.name, expectedfile), "Output does not match expected output."
+ with (NamedTemporaryFile(dir=tmpdir, suffix=".sql", delete=True) as output2,
+ open(output.name, mode="rb") as infile_stream
+ ):
+ run([script_fullname],
+ stdin=infile_stream,
+ stdout=output2,
+ check=True
+ )
+ assert filecmp.cmp(output2.name, expectedfile), (
+ "Run 2: Output does not match expected output.")
diff --git a/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.expected.sql b/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.expected.sql
new file mode 100644
index 0000000000000000000000000000000000000000..1a58223ba65827231ce658f1a655a68706bf8088
--- /dev/null
+++ b/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.expected.sql
@@ -0,0 +1,36 @@
+/* Just a short snippt with the problem */
+
+
+/*!50003 SET @saved_col_connection = @@collation_connection */ ;
+/*!50003 SET character_set_client = utf8 */ ;
+/*!50003 SET character_set_results = utf8 */ ;
+/*!50003 SET collation_connection = utf8_general_ci */ ;
+DELIMITER ;;
+CREATE DEFINER=`root`@`%` FUNCTION `get_head_relative`(EntityID VARCHAR(255),
+ HeadOffset INT UNSIGNED) RETURNS varbinary(255)
+ READS SQL DATA
+BEGIN
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
+
+
+
+
+ RETURN (
+ SELECT e.version
+ FROM entity_version AS e
+ WHERE e.entity_id = InternalEntityID
+ ORDER BY e._iversion DESC
+ LIMIT 1 OFFSET HeadOffset
+ );
+END ;;
+DELIMITER ;
+/*!50003 SET sql_mode = @saved_sql_mode */ ;
+/*!50003 SET character_set_client = @saved_cs_client */ ;
+/*!50003 SET character_set_results = @saved_cs_results */ ;
+/*!50003 SET collation_connection = @saved_col_connection */ ;
+/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
+/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
+/*!50003 D */
diff --git a/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.sql b/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.sql
new file mode 100644
index 0000000000000000000000000000000000000000..a5476af3268360476f2c1ef741cb25007e29ce5d
--- /dev/null
+++ b/dump_updates/test/test_data/2024-10-02.dump_fix_mariadb_10_6.example1.sql
@@ -0,0 +1,36 @@
+/* Just a short snippt with the problem */
+
+
+/*!50003 SET @saved_col_connection = @@collation_connection */ ;
+/*!50003 SET character_set_client = utf8 */ ;
+/*!50003 SET character_set_results = utf8 */ ;
+/*!50003 SET collation_connection = utf8_general_ci */ ;
+DELIMITER ;;
+CREATE DEFINER=`root`@`%` FUNCTION `get_head_relative`(EntityID VARCHAR(255),
+ Offset INT UNSIGNED) RETURNS varbinary(255)
+ READS SQL DATA
+BEGIN
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
+
+
+
+
+ RETURN (
+ SELECT e.version
+ FROM entity_version AS e
+ WHERE e.entity_id = InternalEntityID
+ ORDER BY e._iversion DESC
+ LIMIT 1 OFFSET Offset
+ );
+END ;;
+DELIMITER ;
+/*!50003 SET sql_mode = @saved_sql_mode */ ;
+/*!50003 SET character_set_client = @saved_cs_client */ ;
+/*!50003 SET character_set_results = @saved_cs_results */ ;
+/*!50003 SET collation_connection = @saved_col_connection */ ;
+/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
+/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
+/*!50003 D */
diff --git a/libs/mytap-1.0.zip b/libs/mytap-1.0.zip
index 9e04965cd40320bde2e598c585119ffa7f6b1eab..75341f8c8f8725fca94e2a34bc3dd58e8fa8e641 100644
Binary files a/libs/mytap-1.0.zip and b/libs/mytap-1.0.zip differ
diff --git a/patches/applyPatches.sh b/patches/applyPatches.sh
index ffaa06a782c3dfeababff092158bc5990f11220e..306e6d976aae09410c8c24db791448842a740162 100755
--- a/patches/applyPatches.sh
+++ b/patches/applyPatches.sh
@@ -47,4 +47,5 @@ do
done
cd ../
+
$UTILSPATH/update_sql_procedures.sh
diff --git a/patches/patch20170316-2.0.27/patch.sh b/patches/patch20170316-2.0.27/patch.sh
index 504b5dcca20004806cf49ec16b574f3128af8d5b..fb46b77407e819d7f0984752bfa4047858960ece 100755
--- a/patches/patch20170316-2.0.27/patch.sh
+++ b/patches/patch20170316-2.0.27/patch.sh
@@ -35,7 +35,12 @@ fi
check_version $OLD_VERSION
-mysql_execute 'DELETE FROM `entities` WHERE id=6; ALTER TABLE `entities` MODIFY COLUMN `role` ENUM("RECORDTYPE","RECORD","FILE","DOMAIN","PROPERTY","DATATYPE","ROLE","QUERYTEMPLATE") NOT NULL; INSERT INTO entities (id, name, description, role, acl) VALUES (8,"QUERYTEMPLATE","The QueryTemplate role.","ROLE",0); UPDATE `entities` SET role="ROLE" WHERE id<100 and name=role; CREATE TABLE `query_template_def` (id INT UNSIGNED PRIMARY KEY, definition MEDIUMTEXT NOT NULL, CONSTRAINT `query_template_def_ibfk_1` FOREIGN KEY (`id`) REFERENCES `entities` (`id`));'
+mysql_execute '
+DELETE FROM `entities` WHERE id=6;
+ALTER TABLE `entities` MODIFY COLUMN `role` ENUM("RECORDTYPE","RECORD","FILE","DOMAIN","PROPERTY","DATATYPE","ROLE","QUERYTEMPLATE") NOT NULL;
+INSERT INTO entities (id, name, description, role, acl) VALUES (8,"QUERYTEMPLATE","The QueryTemplate role.","ROLE",0);
+UPDATE `entities` SET role="ROLE" WHERE id<100 and name=role;
+CREATE TABLE `query_template_def` (id INT UNSIGNED PRIMARY KEY, definition MEDIUMTEXT NOT NULL, CONSTRAINT `query_template_def_ibfk_1` FOREIGN KEY (`id`) REFERENCES `entities` (`id`));'
update_version $NEW_VERSION
diff --git a/patches/patch20221122-6.0-SNAPSHOT/create_entity_ids_table.sql b/patches/patch20221122-6.0-SNAPSHOT/create_entity_ids_table.sql
new file mode 100644
index 0000000000000000000000000000000000000000..41297c918f0213017ebba22e1871ece2f515f782
--- /dev/null
+++ b/patches/patch20221122-6.0-SNAPSHOT/create_entity_ids_table.sql
@@ -0,0 +1,63 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2022-2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2022-2023 Timm Fitschen <t.fitschen@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
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * 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/>.
+ */
+
+-- a little bit of house keeping
+DROP PROCEDURE IF EXISTS retrieveSubEntity;
+DROP PROCEDURE IF EXISTS retrieveDatatype;
+DROP PROCEDURE IF EXISTS retrieveGroup;
+DROP PROCEDURE IF EXISTS getInfo;
+DROP PROCEDURE IF EXISTS getRole;
+DROP PROCEDURE IF EXISTS setPassword;
+DROP PROCEDURE IF EXISTS initAutoIncrement;
+DELETE FROM name_data WHERE entity_id=50;
+DELETE FROM entities WHERE id=50;
+DELETE FROM entities WHERE id=99;
+
+-- this simply is the more appropriate name
+ALTER TABLE entities MODIFY COLUMN
+ `role` enum('RECORDTYPE','RECORD','FILE','DOMAIN','PROPERTY','DATATYPE','ROLE','QUERYTEMPLATE', '_REPLACEMENT') COLLATE utf8_unicode_ci NOT NULL;
+ALTER TABLE archive_entities MODIFY COLUMN
+ `role` enum('RECORDTYPE','RECORD','FILE','DOMAIN','PROPERTY','DATATYPE','ROLE','QUERYTEMPLATE', '_REPLACEMENT') COLLATE utf8_unicode_ci NOT NULL;
+UPDATE entities SET role = "_REPLACEMENT" WHERE role="DOMAIN";
+UPDATE archive_entities SET role = "_REPLACEMENT" WHERE role="DOMAIN";
+ALTER TABLE entities MODIFY COLUMN
+ `role` enum('RECORDTYPE','RECORD','FILE','_REPLACEMENT','PROPERTY','DATATYPE','ROLE','QUERYTEMPLATE') COLLATE utf8_unicode_ci NOT NULL;
+ALTER TABLE archive_entities MODIFY COLUMN
+ `role` enum('RECORDTYPE','RECORD','FILE','_REPLACEMENT','PROPERTY','DATATYPE','ROLE','QUERYTEMPLATE') COLLATE utf8_unicode_ci NOT NULL;
+
+
+
+-- new entity_ids table
+DROP TABLE IF EXISTS `entity_ids`;
+CREATE TABLE `entity_ids` (
+ `id` VARCHAR(255) NOT NULL,
+ `internal_id` int(10) unsigned NOT NULL COMMENT 'Internal ID of an entity. This id is used internally in the *_data tables and elsewhere. This ID is never exposed via the CaosDB API.',
+ PRIMARY KEY `entity_ids_pk` (`id`),
+ CONSTRAINT `entity_ids_internal_id` FOREIGN KEY (`internal_id`) REFERENCES `entities` (`id`)
+) ENGINE=InnoDB COLLATE utf8mb4_bin;
+
+-- fill all existing entities into the new entity_ids table.
+INSERT INTO entity_ids (id, internal_id) SELECT id, id FROM entities WHERE id>0 AND role!="_REPLACEMENT";
+
+ALTER TABLE transaction_log MODIFY COLUMN `entity_id` VARCHAR(255) COLLATE utf8mb4_bin NOT NULL;
+
+ALTER TABLE user_info DROP FOREIGN KEY `subjects_ibfk_1`;
+ALTER TABle user_info MODIFY COLUMN `entity` VARCHAR(255) COLLATE utf8mb4_bin DEFAULT NULL;
+ALTER TABLE user_info ADD CONSTRAINT `subjects_ibfk_2` FOREIGN KEY (`entity`) REFERENCES `entity_ids` (`id`);
diff --git a/patches/patch20221122-6.0-SNAPSHOT/patch.sh b/patches/patch20221122-6.0-SNAPSHOT/patch.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9833f5ad953799afc33133014ec4db2ac6320beb
--- /dev/null
+++ b/patches/patch20221122-6.0-SNAPSHOT/patch.sh
@@ -0,0 +1,45 @@
+#!/bin/bash
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 Timm Fitschen <t.fitschen@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
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# 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/>.
+#
+
+# Update mysql schema to version v5.0.0
+# Drop the 'rules' table.
+
+NEW_VERSION="v6.0.0-SNAPSHOT-EXTIDS"
+OLD_VERSION="v5.0.0"
+
+DROP_TABLE_PASSWORDS='DROP TABLE IF EXISTS passwords;'
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+mysql_execute "$DROP_TABLE_PASSWORDS"
+mysql_execute_file $PATCH_DIR/create_entity_ids_table.sql
+
+update_version $NEW_VERSION
+
+
+success
+
diff --git a/patches/patch20231018-6.1.0/patch.sh b/patches/patch20231018-6.1.0/patch.sh
new file mode 100755
index 0000000000000000000000000000000000000000..e91f487216ce254fb3b1a78a911f38fcc263d8c7
--- /dev/null
+++ b/patches/patch20231018-6.1.0/patch.sh
@@ -0,0 +1,42 @@
+#!/bin/bash
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v6.1.0
+# No migration of the schema, updating procedures only
+
+NEW_VERSION="v6.1.0"
+OLD_VERSION="v6.0.0-SNAPSHOT-EXTIDS"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+# Drop insertUser procedure
+mysql_execute "DROP PROCEDURE IF EXISTS insertUser;"
+
+update_version $NEW_VERSION
+
+success
+
diff --git a/patches/patch20231025-7.0.0/patch.sh b/patches/patch20231025-7.0.0/patch.sh
new file mode 100755
index 0000000000000000000000000000000000000000..06a7dc85c75897b7c47e6094f634b5421f92c794
--- /dev/null
+++ b/patches/patch20231025-7.0.0/patch.sh
@@ -0,0 +1,39 @@
+#!/bin/bash
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v7.0.0
+# No migration of the schema, updating procedures only
+
+NEW_VERSION="v7.0.0"
+OLD_VERSION="v6.1.0"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+update_version $NEW_VERSION
+
+success
+
diff --git a/patches/patch20231101-7.0.1/patch.sh b/patches/patch20231101-7.0.1/patch.sh
new file mode 100755
index 0000000000000000000000000000000000000000..869a014317b3a51246562052560adcecb841eebe
--- /dev/null
+++ b/patches/patch20231101-7.0.1/patch.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v7.0.1
+# Removing remnant tables. This patch version also adds new sanity checks
+# during installation/upgrade
+
+NEW_VERSION="v7.0.1"
+OLD_VERSION="v7.0.0"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+mysql_execute "DROP TABLE IF EXISTS groups";
+mysql_execute "DROP TABLE IF EXISTS passwords";
+mysql_execute "DROP TABLE IF EXISTS logging";
+mysql_execute "DROP TABLE IF EXISTS isa";
+
+update_version $NEW_VERSION
+
+success
diff --git a/patches/patch20231211-7.0.2/patch.sh b/patches/patch20231211-7.0.2/patch.sh
new file mode 100755
index 0000000000000000000000000000000000000000..422fc00b9083808446d74776b446c072bdfd73bc
--- /dev/null
+++ b/patches/patch20231211-7.0.2/patch.sh
@@ -0,0 +1,41 @@
+#!/bin/bash
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v7.0.2
+# Patch the broken data_type table (fix id for file references as per
+# https://gitlab.com/linkahead/linkahead-server/-/issues/246)
+
+NEW_VERSION="v7.0.2"
+OLD_VERSION="v7.0.1"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+mysql_execute "UPDATE data_type SET datatype=17 WHERE datatype=3"
+
+update_version $NEW_VERSION
+
+success
diff --git a/patches/patch20241024-8.0.0/patch.sh b/patches/patch20241024-8.0.0/patch.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2573c95864518363088af121a705d87f786b07ca
--- /dev/null
+++ b/patches/patch20241024-8.0.0/patch.sh
@@ -0,0 +1,41 @@
+#!/bin/bash
+#
+# This file is a part of the LinkAhead Project.
+#
+# Copyright (C) 2024 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2024 Timm Fitschen <t.fitschen@indiscale.com>
+# Copyright (C) 2024 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v8.0.0
+#
+# The patch is empty because the change has to be applied manually
+# from ../../dump_updates/2024-10-02.dump_fix_mariadb_10_6.sh if necessary.
+
+NEW_VERSION="v8.0.0"
+OLD_VERSION="v7.0.2"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+update_version $NEW_VERSION
+
+success
diff --git a/patches/patch20250130-8.1.0/patch.sh b/patches/patch20250130-8.1.0/patch.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5a092150f217c44d100a15735523ef74ea613a8b
--- /dev/null
+++ b/patches/patch20250130-8.1.0/patch.sh
@@ -0,0 +1,99 @@
+#!/bin/bash
+#
+# This file is a part of the Linkahead Project.
+#
+# Copyright (C) 2025 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Daniel Hornung <d.hornung@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+# Update mysql schema to version v8.1.0
+#
+# Set the collation so that accents on characters become relevant.
+
+OLD_VERSION="v8.0.0"
+NEW_VERSION="v8.1.0"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+check_version $OLD_VERSION
+
+# Update charsets and collations.
+
+# Change database default.
+mysql_execute "ALTER DATABASE \`$DATABASE_NAME\` COLLATE = 'uca1400_as_ci';"
+
+# Some columns should be changed manually to prevent text length changes.
+mysql_execute "ALTER TABLE desc_overrides MODIFY description TEXT CHARACTER SET utf8mb4;"
+mysql_execute "ALTER TABLE entities MODIFY description TEXT CHARACTER SET utf8mb4;"
+mysql_execute "ALTER TABLE permissions MODIFY permissions MEDIUMTEXT CHARACTER SET utf8mb4 NOT NULL;"
+mysql_execute "ALTER TABLE query_template_def MODIFY definition MEDIUMTEXT CHARACTER SET utf8mb4 NOT NULL;"
+mysql_execute "ALTER TABLE roles MODIFY description MEDIUMTEXT CHARACTER SET utf8mb4;"
+mysql_execute "ALTER TABLE text_data MODIFY value TEXT CHARACTER SET utf8mb4 NOT NULL;"
+
+# Remove some constraints first.
+mysql_execute 'ALTER TABLE user_info DROP FOREIGN KEY `subjects_ibfk_2`;'
+
+# Get all tables, drop first line, take first column
+tables=$(mysql_execute "SHOW TABLE status where Collation='utf8mb3_unicode_ci';" -B | tail +2 | awk '{print $1}')
+for table in $tables; do
+ mysql_execute "ALTER TABLE $table CONVERT TO CHARACTER SET utf8mb4 COLLATE uca1400_as_ci;"
+done
+
+# Add constraints again.
+mysql_execute 'ALTER TABLE user_info MODIFY COLUMN `entity` VARCHAR(255) COLLATE utf8mb4_bin DEFAULT NULL;'
+mysql_execute 'ALTER TABLE user_info ADD CONSTRAINT `subjects_ibfk_2` FOREIGN KEY (`entity`) REFERENCES `entity_ids` (`id`);'
+
+# Set custom collations for columns
+mysql_execute "ALTER TABLE transaction_log MODIFY entity_id VARCHAR(255) CHARACTER SET utf8mb4 COLLATE utf8mb4_bin NOT NULL;"
+
+
+### Finished ###
+
+update_version $NEW_VERSION
+
+success
+
+
+##### Useful commands #####
+
+# cd git/caosdb-mysqlbackend/
+# UTILSPATH=utils
+# . utils/patch_header.sh
+
+
+# show table status where Collation='utf8mb3_unicode_ci';
+
+# name_data
+# text_data
+
+# show table status like 'name_data';
+# select * from name_data where value like 'Yield%';
+# update name_data SET value='Yield-stréss' where entity_id=354;
+# update name_data SET value='Yield-strés😋s' where entity_id=354;
+# select * from name_data where value='Yield-stress';
+
+# # Unicode 14.0.0
+# ALTER TABLE name_data CONVERT TO CHARACTER SET utf8mb4 COLLATE uca1400_as_ci;
+
+# FULL_COLLATION_NAME: utf8mb4_uca1400_as_ci;
+# COLLATION_NAME: uca1400_as_ci;
+
+# mariadb -h sqldb -u caosdb -prandom1234 --default-character-set=utf8mb4 caosdb
+
diff --git a/procedures/deleteEntity.sql b/procedures/deleteEntity.sql
index 7a195399b6c71ae68b26e2f74c53ab871ae05b0e..986a7908cb5ceb06c986c46cb7deac1b880e8f69 100644
--- a/procedures/deleteEntity.sql
+++ b/procedures/deleteEntity.sql
@@ -1,10 +1,10 @@
/*
- * ** header v3.0
* This 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) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020-2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@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
@@ -18,8 +18,6 @@
*
* 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/>.
- *
- * ** end header
*/
/* Delete a (sparse) Entity from the database.
@@ -31,37 +29,43 @@ have been deleted before. This can be done for example with the
Parameters
==========
-EntityID : UNSIGNED
-The ID of the Entity.
+EntityID : VARCHAR(255)
+ The ID of the Entity.
*/
DROP PROCEDURE IF EXISTS db_5_0.deleteEntity;
delimiter //
-CREATE PROCEDURE db_5_0.deleteEntity(in EntityID INT UNSIGNED)
+CREATE PROCEDURE db_5_0.deleteEntity(in EntityID VARCHAR(255))
BEGIN
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID from entity_ids WHERE id = EntityID;
-- detele file properties
- DELETE FROM files where file_id=EntityID;
+ DELETE FROM files where file_id=InternalEntityID;
-- delete datatype stuff
DELETE FROM data_type
WHERE ( domain_id = 0
AND entity_id = 0
- AND property_id = EntityID )
- OR datatype = EntityID;
+ AND property_id = InternalEntityID )
+ OR datatype = InternalEntityID;
DELETE FROM collection_type
WHERE domain_id = 0
AND entity_id = 0
- AND property_id = EntityID;
+ AND property_id = InternalEntityID;
-- delete primary name (in case this is called without a prior call to deleteEntityProperties)
DELETE FROM name_data
WHERE domain_id = 0
- AND entity_id = EntityID
+ AND entity_id = InternalEntityID
AND property_id = 20;
- DELETE FROM entities where id=EntityID;
+ DELETE FROM entity_ids
+ WHERE internal_id = InternalEntityID;
+
+ DELETE FROM entities where id=InternalEntityID;
-- clean up unused acl
DELETE FROM entity_acl
diff --git a/procedures/deleteEntityProperties.sql b/procedures/deleteEntityProperties.sql
index 916ddcba2751b9251ff2ddc387201e0ad9eebc3b..9216d9436c3b139ea68199940a5259512aa16133 100644
--- a/procedures/deleteEntityProperties.sql
+++ b/procedures/deleteEntityProperties.sql
@@ -1,11 +1,10 @@
/*
- * ** header v3.0
* This 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) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@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
@@ -19,23 +18,34 @@
*
* 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/>.
- *
- * ** end header
*/
DROP PROCEDURE IF EXISTS db_5_0.deleteEntityProperties;
delimiter //
-CREATE PROCEDURE db_5_0.deleteEntityProperties(in EntityID INT UNSIGNED)
+/*
+ * Delete all properties of an entity (i.e. remove them from the *_data tables
+ * and the isa_cache table).
+ *
+ * Parameters
+ * ==========
+ *
+ * EntityID : VARCHAR(255)
+ * The entity's id.
+ */
+CREATE PROCEDURE db_5_0.deleteEntityProperties(in EntityID VARCHAR(255))
BEGIN
DECLARE IVersion INT UNSIGNED DEFAULT NULL;
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID from entity_ids WHERE id = EntityID;
- CALL deleteIsa(EntityID);
+ CALL deleteIsa(InternalEntityID);
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
SELECT max(e._iversion) INTO IVersion -- What's the latest version?
FROM entity_version AS e
- WHERE e.entity_id = EntityID;
+ WHERE e.entity_id = InternalEntityID;
-- Copy the rows from *_data to archive_*_data ---------------------
INSERT INTO archive_reference_data (domain_id, entity_id,
@@ -43,142 +53,142 @@ BEGIN
SELECT domain_id, entity_id, property_id, value, value_iversion,
status, pidx, IVersion AS _iversion
FROM reference_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_null_data (domain_id, entity_id,
property_id, status, pidx, _iversion)
SELECT domain_id, entity_id, property_id, status,
pidx, IVersion AS _iversion
FROM null_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_text_data (domain_id, entity_id,
property_id, value, status, pidx, _iversion)
SELECT domain_id, entity_id, property_id, value, status,
pidx, IVersion AS _iversion
FROM text_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_name_data (domain_id, entity_id,
property_id, value, status, pidx, _iversion)
SELECT domain_id, entity_id, property_id, value, status,
pidx, IVersion AS _iversion
FROM name_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_enum_data (domain_id, entity_id,
property_id, value, status, pidx, _iversion)
SELECT domain_id, entity_id, property_id, value, status,
pidx, IVersion AS _iversion
FROM enum_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_integer_data (domain_id, entity_id,
property_id, value, status, pidx, _iversion, unit_sig)
SELECT domain_id, entity_id, property_id, value, status,
pidx, IVersion AS _iversion, unit_sig
FROM integer_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_double_data (domain_id, entity_id,
property_id, value, status, pidx, _iversion, unit_sig)
SELECT domain_id, entity_id, property_id, value, status,
pidx, IVersion AS _iversion, unit_sig
FROM double_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_datetime_data (domain_id, entity_id,
property_id, value, value_ns, status, pidx, _iversion)
SELECT domain_id, entity_id, property_id, value, value_ns,
status, pidx, IVersion AS _iversion
FROM datetime_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_date_data (domain_id, entity_id,
property_id, value, status, pidx, _iversion)
SELECT domain_id, entity_id, property_id, value, status,
pidx, IVersion AS _iversion
FROM date_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_name_overrides (domain_id, entity_id,
property_id, name, _iversion)
SELECT domain_id, entity_id, property_id, name,
IVersion AS _iversion
FROM name_overrides
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_desc_overrides (domain_id, entity_id,
property_id, description, _iversion)
SELECT domain_id, entity_id, property_id, description,
IVersion AS _iversion
FROM desc_overrides
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_data_type (domain_id, entity_id,
property_id, datatype, _iversion)
SELECT domain_id, entity_id, property_id, datatype,
IVersion AS _iversion
FROM data_type
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_collection_type (domain_id, entity_id,
property_id, collection, _iversion)
SELECT domain_id, entity_id, property_id, collection,
IVersion AS _iversion
FROM collection_type
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
+ WHERE (domain_id = 0 AND entity_id = InternalEntityID)
+ OR domain_id = InternalEntityID;
INSERT INTO archive_query_template_def (id, definition, _iversion)
SELECT id, definition, IVersion AS _iversion
FROM query_template_def
- WHERE id = EntityID;
+ WHERE id = InternalEntityID;
END IF;
DELETE FROM reference_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM null_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM text_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM name_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM enum_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM integer_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM double_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM datetime_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM date_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ where (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM name_overrides
- WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ WHERE (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM desc_overrides
- WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ WHERE (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM data_type
- WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ WHERE (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
DELETE FROM collection_type
- WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
+ WHERE (domain_id=0 AND entity_id=InternalEntityID) OR domain_id=InternalEntityID;
- DELETE FROM query_template_def WHERE id=EntityID;
+ DELETE FROM query_template_def WHERE id=InternalEntityID;
END;
//
diff --git a/procedures/deleteIsaCache.sql b/procedures/deleteIsaCache.sql
index cc9acd08059b2656ee934ba4a47f1c48dcdf5601..517912b73527ab7725d433c0cd91d7702b447e1c 100644
--- a/procedures/deleteIsaCache.sql
+++ b/procedures/deleteIsaCache.sql
@@ -1,11 +1,10 @@
/*
- * ** header v3.0
* This 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) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@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
@@ -19,8 +18,6 @@
*
* 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/>.
- *
- * ** end header
*/
SET GLOBAL log_bin_trust_function_creators = 1;
@@ -38,30 +35,30 @@ parameter entity is a child or inside the rpath.
Parameters
==========
-EntityID : UNSIGNED
-Child entity for which all parental relations should be deleted.
+InternalEntityID : UNSIGNED
+ Child entity for which all parental relations should be deleted.
*/
-CREATE PROCEDURE db_5_0.deleteIsa(IN EntityID INT UNSIGNED)
+CREATE PROCEDURE db_5_0.deleteIsa(IN InternalEntityID INT UNSIGNED)
BEGIN
DECLARE IVersion INT UNSIGNED DEFAULT NULL;
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
SELECT max(_iversion) INTO IVersion
FROM entity_version
- WHERE entity_id = EntityID;
+ WHERE entity_id = InternalEntityID;
-- move to archive_isa before deleting
INSERT IGNORE INTO archive_isa (child, child_iversion, parent, direct)
- SELECT e.child, IVersion AS child_iversion, e.parent, rpath = EntityID
+ SELECT e.child, IVersion AS child_iversion, e.parent, rpath = InternalEntityID
FROM isa_cache AS e
- WHERE e.child = EntityID;
+ WHERE e.child = InternalEntityID;
END IF;
DELETE FROM isa_cache
- WHERE child = EntityID
- OR rpath = EntityID
- OR rpath LIKE concat('%>', EntityID)
- OR rpath LIKE concat('%>', EntityID, '>%');
+ WHERE child = InternalEntityID
+ OR rpath = InternalEntityID
+ OR rpath LIKE concat('%>', InternalEntityID)
+ OR rpath LIKE concat('%>', InternalEntityID, '>%');
END;
//
diff --git a/procedures/entityVersioning.sql b/procedures/entityVersioning.sql
index 241474cb8dbf20f9caa9050aed9cbb600a8cef6d..a71c0c729f9fae5e710b8cfd8e37618e7615ff20 100644
--- a/procedures/entityVersioning.sql
+++ b/procedures/entityVersioning.sql
@@ -1,9 +1,9 @@
/*
* 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>
- *
+ * Copyright (C) 2020-2024 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2024 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
* published by the Free Software Foundation, either version 3 of the
@@ -27,23 +27,23 @@ DROP PROCEDURE IF EXISTS db_5_0.insert_single_child_version //
*
* Parameters
* ----------
- * EntityID
- * The ID of the versioned entity.
- * Hash
+ * InternalEntityID : INT UNSIGNED
+ * The internal ID of the versioned entity.
+ * Hash : VARBINARY(255)
* A hash of the entity. This is currently not implemented properly and only
* there for future use.
- * Version
+ * Version : VARBINARY(255)
* The new version ID of the entity, must be produced by the caller. Must be unique for each
* EntityID.
- * Parent
+ * Parent : VARBINARY(255)
* The version ID of the primary parent (i.e. predecessor). May be NULL; but if given, it must
* exist.
- * Transaction
+ * Transaction : VARBINARY(255)
* The transaction ID which created this entity version (by inserting
* or updating an entity).
*/
CREATE PROCEDURE db_5_0.insert_single_child_version(
- in EntityID INT UNSIGNED,
+ in InternalEntityID INT UNSIGNED,
in Hash VARBINARY(255),
in Version VARBINARY(255),
in Parent VARBINARY(255),
@@ -57,12 +57,12 @@ BEGIN
IF Parent IS NOT NULL THEN
SELECT e._iversion INTO newipparent
FROM entity_version AS e
- WHERE e.entity_id = EntityID
+ WHERE e.entity_id = InternalEntityID
AND e.version = Parent;
IF newipparent IS NULL THEN
-- throw error;
SELECT concat("This parent does not exists: ", Parent)
- FROM nonexisting;
+ FROM parent_version_does_not_exist;
END IF;
END IF;
@@ -70,7 +70,7 @@ BEGIN
-- generate _iversion
SELECT max(e._iversion)+1 INTO newiversion
FROM entity_version AS e
- WHERE e.entity_id=EntityID;
+ WHERE e.entity_id=InternalEntityID;
IF newiversion IS NULL THEN
SET newiversion = 1;
END IF;
@@ -78,7 +78,7 @@ BEGIN
INSERT INTO entity_version
(entity_id, hash, version, _iversion, _ipparent, srid)
VALUES
- (EntityID, Hash, Version, newiversion, newipparent, Transaction);
+ (InternalEntityID, Hash, Version, newiversion, newipparent, Transaction);
@@ -87,22 +87,28 @@ END;
DROP PROCEDURE IF EXISTS db_5_0.delete_all_entity_versions //
+/* THIS PROCEDURE HAS NEVER BEEN USED (outside of the tests). Reactivate when
+ * versioning's FORGET is being implemented. */
/**
* Remove all records in the entity_version table for the given entity.
*
* Parameters
* ----------
- * EntityID
+ * EntityID : VARCHAR(255)
* The id of the versioned entity.
*/
-CREATE PROCEDURE db_5_0.delete_all_entity_versions(
- in EntityID INT UNSIGNED)
+/* CREATE PROCEDURE db_5_0.delete_all_entity_versions(
+ in EntityID VARCHAR(255))
BEGIN
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
- DELETE FROM entity_version WHERE entity_id = EntityID;
+ DELETE FROM entity_version WHERE entity_id = InternalEntityID;
END;
//
+*/
DROP FUNCTION IF EXISTS db_5_0.get_iversion //
@@ -111,9 +117,9 @@ DROP FUNCTION IF EXISTS db_5_0.get_iversion //
*
* Parameters
* ----------
- * EntityID
- * The entity's id.
- * Version
+ * InternalEntityID : INT UNSIGNED
+ * The entity's internal id.
+ * Version : VARBINARY(255)
* The (official, externally used) version id.
*
* Returns
@@ -121,7 +127,7 @@ DROP FUNCTION IF EXISTS db_5_0.get_iversion //
* The internal version id.
*/
CREATE FUNCTION db_5_0.get_iversion(
- EntityID INT UNSIGNED,
+ InternalEntityID INT UNSIGNED,
Version VARBINARY(255))
RETURNS INT UNSIGNED
READS SQL DATA
@@ -129,7 +135,7 @@ BEGIN
RETURN (
SELECT e._iversion
FROM entity_version AS e
- WHERE e.entity_id = EntityID
+ WHERE e.entity_id = InternalEntityID
AND e.version = Version
);
END;
@@ -143,9 +149,9 @@ DROP FUNCTION IF EXISTS db_5_0.get_primary_parent_version //
*
* Parameters
* ----------
- * EntityID
+ * EntityID : VARCHAR(255)
* The entity id.
- * Version
+ * Version : VARBINARY(255)
* The version id.
*
* Returns
@@ -153,17 +159,21 @@ DROP FUNCTION IF EXISTS db_5_0.get_primary_parent_version //
* The id of the given version's primary parent version.
*/
CREATE FUNCTION db_5_0.get_primary_parent_version(
- EntityID INT UNSIGNED,
+ EntityID VARCHAR(255),
Version VARBINARY(255))
RETURNS VARBINARY(255)
READS SQL DATA
BEGIN
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
RETURN (
SELECT p.version
FROM entity_version AS e INNER JOIN entity_version AS p
ON (e._ipparent = p._iversion
AND e.entity_id = p.entity_id)
- WHERE e.entity_id = EntityID
+ WHERE e.entity_id = InternalEntityID
AND e.version = Version
);
END;
@@ -177,9 +187,9 @@ DROP FUNCTION IF EXISTS db_5_0.get_version_timestamp //
*
* Parameters
* ----------
- * EntityID
+ * EntityID : VARCHAR(255)
* The entity id.
- * Version
+ * Version : VARBINARY(255)
* The version id.
*
* Returns
@@ -188,16 +198,20 @@ DROP FUNCTION IF EXISTS db_5_0.get_version_timestamp //
* Note that the dot `.` here is not necessarily a decimal separator.
*/
CREATE FUNCTION db_5_0.get_version_timestamp(
- EntityID INT UNSIGNED,
+ EntityID VARCHAR(255),
Version VARBINARY(255))
RETURNS VARCHAR(255)
READS SQL DATA
BEGIN
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
RETURN (
SELECT concat(t.seconds, '.', t.nanos)
FROM entity_version AS e INNER JOIN transactions AS t
ON ( e.srid = t.srid )
- WHERE e.entity_id = EntityID
+ WHERE e.entity_id = InternalEntityID
AND e.version = Version
);
END;
@@ -210,7 +224,7 @@ DROP FUNCTION IF EXISTS db_5_0.get_head_version //
*
* Parameters
* ----------
- * EntityID
+ * EntityID : VARCHAR(255)
* The entity id.
*
* Returns
@@ -218,7 +232,7 @@ DROP FUNCTION IF EXISTS db_5_0.get_head_version //
* The version id of the HEAD.
*/
CREATE FUNCTION db_5_0.get_head_version(
- EntityID INT UNSIGNED)
+ EntityID VARCHAR(255))
RETURNS VARBINARY(255)
READS SQL DATA
BEGIN
@@ -233,15 +247,15 @@ DROP FUNCTION IF EXISTS db_5_0._get_head_iversion //
*
* Parameters
* ----------
- * EntityID
- * The entity id.
+ * InternalEntityID : INT UNSIGNED
+ * The entity's internal id.
*
* Returns
* -------
* The _iversion of the HEAD.
*/
CREATE FUNCTION db_5_0._get_head_iversion(
- EntityID INT UNSIGNED)
+ InternalEntityID INT UNSIGNED)
RETURNS INT UNSIGNED
READS SQL DATA
BEGIN
@@ -252,7 +266,7 @@ BEGIN
RETURN (
SELECT e._iversion
FROM entity_version AS e
- WHERE e.entity_id = EntityID
+ WHERE e.entity_id = InternalEntityID
ORDER BY e._iversion DESC
LIMIT 1
);
@@ -267,9 +281,9 @@ DROP FUNCTION IF EXISTS db_5_0.get_head_relative //
*
* Parameters
* ----------
- * EntityID
+ * EntityID : VARCHAR(255)
* The entity id.
- * Offset
+ * HeadOffset : INT UNSIGNED
* Distance in the sequence of primary parents of the entity. E.g. `0` is the
* HEAD itself. `1` is the primary parent of the HEAD. `2` is the primary
* parent of the primary parent of the HEAD, and so on.
@@ -279,11 +293,15 @@ DROP FUNCTION IF EXISTS db_5_0.get_head_relative //
* The version id of the HEAD.
*/
CREATE FUNCTION db_5_0.get_head_relative(
- EntityID INT UNSIGNED,
- Offset INT UNSIGNED)
+ EntityID VARCHAR(255),
+ HeadOffset INT UNSIGNED)
RETURNS VARBINARY(255)
READS SQL DATA
BEGIN
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
-- This implementation assumes that the distance from the head equals the
-- difference between the _iversion numbers. This will not be correct anymore
-- as soon as branches may split and merge. Then, a walk over the primary
@@ -291,9 +309,9 @@ BEGIN
RETURN (
SELECT e.version
FROM entity_version AS e
- WHERE e.entity_id = EntityID
+ WHERE e.entity_id = InternalEntityID
ORDER BY e._iversion DESC
- LIMIT 1 OFFSET Offset
+ LIMIT 1 OFFSET HeadOffset
);
END;
//
@@ -304,24 +322,24 @@ DROP FUNCTION IF EXISTS db_5_0._get_version //
*
* Parameters
* ----------
- * EntityID
- * The entity id.
+ * InternalEntityID : INT UNSIGNED
+ * The entity's internal id.
* IVersion
* Internal version id (integer).
*
* Returns
* -------
- * The version id.
+ * The (external) version id.
*/
CREATE FUNCTION db_5_0._get_version(
- EntityID INT UNSIGNED,
+ InternalEntityID INT UNSIGNED,
IVersion INT UNSIGNED)
RETURNS VARBINARY(255)
READS SQL DATA
BEGIN
RETURN (
SELECT version FROM entity_version
- WHERE entity_id = EntityID
+ WHERE entity_id = InternalEntityID
AND _iversion = IVersion
);
END;
@@ -335,7 +353,7 @@ DROP PROCEDURE IF EXISTS db_5_0.get_version_history //
*
* Parameters
* ----------
- * EntityID
+ * EntityID : VARCHAR(255)
* The entity id.
*
* Selects
@@ -344,8 +362,12 @@ DROP PROCEDURE IF EXISTS db_5_0.get_version_history //
* child_realm). `child` and `parent` are version IDs.
*/
CREATE PROCEDURE db_5_0.get_version_history(
- in EntityID INT UNSIGNED)
+ in EntityID VARCHAR(255))
BEGIN
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
-- retrieve root(s) (initial versions)
SELECT c.version AS child,
NULL as parent,
@@ -355,7 +377,7 @@ BEGIN
t.realm AS child_realm
FROM entity_version AS c INNER JOIN transactions as t
ON ( c.srid = t.srid )
- WHERE c.entity_id = EntityID
+ WHERE c.entity_id = InternalEntityID
AND c._ipparent is Null
-- TODO This first SELECT statement is necessary because the second one
@@ -375,7 +397,7 @@ BEGIN
ON (c._ipparent = p._iversion
AND c.entity_id = p.entity_id
AND t.srid = c.srid)
- WHERE p.entity_id = EntityID;
+ WHERE p.entity_id = InternalEntityID;
END;
//
@@ -412,56 +434,6 @@ BEGIN
END //
-
-DROP PROCEDURE IF EXISTS setFileProperties //
-/**
- * Insert/Update file properties.
- *
- * If ENTITY_VERSIONING is enabled the old file properties are moved to
- * `archive_files`.
- *
- * Parameters
- * ----------
- * EntityID
- * The file's id.
- * FilePath
- * Path of the file in the internal file system. If NULL, an existing file
- * entity is simply deleted.
- * FileSize
- * Size of the file in bytes.
- * FileHash
- * A Sha512 Hash of the file.
- */
-CREATE PROCEDURE setFileProperties (
- in EntityID INT UNSIGNED,
- in FilePath TEXT,
- in FileSize BIGINT UNSIGNED,
- in FileHash VARCHAR(255)
-)
-BEGIN
- DECLARE IVersion INT UNSIGNED DEFAULT NULL;
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
- SELECT max(e._iversion) INTO IVersion
- FROM entity_version AS e
- WHERE e.entity_id = EntityID;
-
- INSERT INTO archive_files (file_id, path, size, hash,
- _iversion)
- SELECT file_id, path, size, hash, IVersion AS _iversion
- FROM files
- WHERE file_id = EntityID;
- END IF;
-
- DELETE FROM files WHERE file_id = EntityID;
-
- IF FilePath IS NOT NULL THEN
- INSERT INTO files (file_id, path, size, hash)
- VALUES (EntityID, FilePath, FileSize, unhex(FileHash));
- END IF;
-
-END //
-
-
DROP PROCEDURE IF EXISTS retrieveQueryTemplateDef //
/**
@@ -469,9 +441,9 @@ DROP PROCEDURE IF EXISTS retrieveQueryTemplateDef //
*
* Parameters
* ----------
- * EntityID
+ * EntityID : VARCHAR(255)
* The QueryTemplate's id.
- * Version
+ * Version : VARBINARY(255)
* The QueryTemplate's version's id.
*
* Returns
@@ -480,12 +452,16 @@ DROP PROCEDURE IF EXISTS retrieveQueryTemplateDef //
* QueryTemplate.
*/
CREATE PROCEDURE retrieveQueryTemplateDef (
- in EntityID INT UNSIGNED,
+ in EntityID VARCHAR(255),
in Version VARBINARY(255))
retrieveQueryTemplateDefBody: BEGIN
DECLARE IVersion INT UNSIGNED DEFAULT NULL;
DECLARE IsHead BOOLEAN DEFAULT TRUE;
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
-- Are we at the head?
@@ -494,11 +470,7 @@ retrieveQueryTemplateDefBody: BEGIN
END IF;
IF IsHead IS FALSE THEN
- -- TODO Use get_iversion(EntityID, Version) instead? Or will that be much slower?
- SELECT e._iversion INTO IVersion
- FROM entity_version as e
- WHERE e.entity_id = EntityID
- AND e.version = Version;
+ SET IVersion = get_iversion(InternalEntityID, Version);
IF IVersion IS NULL THEN
-- RETURN EARLY - Version does not exist.
@@ -507,7 +479,7 @@ retrieveQueryTemplateDefBody: BEGIN
SELECT definition
FROM archive_query_template_def
- WHERE id = EntityID
+ WHERE id = InternalEntityID
AND _iversion = IVersion;
LEAVE retrieveQueryTemplateDefBody;
@@ -516,7 +488,7 @@ retrieveQueryTemplateDefBody: BEGIN
SELECT definition
FROM query_template_def
- WHERE id = EntityID;
+ WHERE id = InternalEntityID;
END //
diff --git a/procedures/getDependentEntities.sql b/procedures/getDependentEntities.sql
index b99d6a6c1e80831c392a11a3b4212538afad5887..1eae0729db3af3b8c06cf4ea27bebf77a17679a7 100644
--- a/procedures/getDependentEntities.sql
+++ b/procedures/getDependentEntities.sql
@@ -1,9 +1,10 @@
/*
- * ** header v3.0
* This 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 <www.indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@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
@@ -18,56 +19,76 @@
* 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/>.
*
- * ** end header
*/
-
DROP PROCEDURE IF EXISTS db_5_0.getDependentEntities;
delimiter //
-CREATE PROCEDURE db_5_0.getDependentEntities(in EntityID INT UNSIGNED)
+/*
+ * Return all entities which either reference the given entity, use the given
+ * reference as data type, or are direct children of the given entity.
+ *
+ * This function used to make sure that no entity can be deleted which
+ * is still needed by others.
+ *
+ * Parameters
+ * ----------
+ * EntityID : VARCHAR(255)
+ * The entity id.
+ *
+ * ResultSet
+ * ---------
+ * EntityID : VARCHAR(255)
+ *
+ */
+CREATE PROCEDURE db_5_0.getDependentEntities(in EntityID VARCHAR(255))
BEGIN
-DROP TEMPORARY TABLE IF EXISTS refering;
-CREATE TEMPORARY TABLE refering (
-id INT UNSIGNED UNIQUE
-);
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ DROP TEMPORARY TABLE IF EXISTS referring;
+ CREATE TEMPORARY TABLE referring (
+ id INT UNSIGNED UNIQUE
+ );
+
+ SELECT internal_id INTO InternalEntityID from entity_ids WHERE id = EntityID;
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM reference_data WHERE (value=EntityID OR property_id=EntityID) AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM reference_data WHERE (value=EntityID OR property_id=EntityID) AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
+ INSERT IGNORE INTO referring (id) SELECT entity_id FROM reference_data WHERE (value=InternalEntityID OR property_id=InternalEntityID) AND domain_id=0 AND entity_id!=InternalEntityID;
+ INSERT IGNORE INTO referring (id) SELECT domain_id FROM reference_data WHERE (value=InternalEntityID OR property_id=InternalEntityID) AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM text_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM text_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
+ INSERT IGNORE INTO referring (id) SELECT entity_id FROM text_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+ INSERT IGNORE INTO referring (id) SELECT domain_id FROM text_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM enum_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM enum_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
+ INSERT IGNORE INTO referring (id) SELECT entity_id FROM enum_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+ INSERT IGNORE INTO referring (id) SELECT domain_id FROM enum_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM name_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM name_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
+ INSERT IGNORE INTO referring (id) SELECT entity_id FROM name_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+ INSERT IGNORE INTO referring (id) SELECT domain_id FROM name_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM integer_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM integer_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
+ INSERT IGNORE INTO referring (id) SELECT entity_id FROM integer_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+ INSERT IGNORE INTO referring (id) SELECT domain_id FROM integer_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM double_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM double_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
+ INSERT IGNORE INTO referring (id) SELECT entity_id FROM double_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+ INSERT IGNORE INTO referring (id) SELECT domain_id FROM double_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM datetime_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM datetime_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
+ INSERT IGNORE INTO referring (id) SELECT entity_id FROM datetime_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+ INSERT IGNORE INTO referring (id) SELECT domain_id FROM datetime_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM date_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM date_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
+ INSERT IGNORE INTO referring (id) SELECT entity_id FROM date_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+ INSERT IGNORE INTO referring (id) SELECT domain_id FROM date_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM null_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM null_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
+ INSERT IGNORE INTO referring (id) SELECT entity_id FROM null_data WHERE property_id=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+ INSERT IGNORE INTO referring (id) SELECT domain_id FROM null_data WHERE property_id=InternalEntityID AND domain_id!=InternalEntityID AND entity_id!=InternalEntityID AND domain_id!=0;
-INSERT IGNORE INTO refering (id) SELECT entity_id from data_type WHERE datatype=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id from data_type WHERE datatype=EntityID;
+ INSERT IGNORE INTO referring (id) SELECT entity_id from data_type WHERE datatype=InternalEntityID AND domain_id=0 AND entity_id!=InternalEntityID;
+ INSERT IGNORE INTO referring (id) SELECT domain_id from data_type WHERE datatype=InternalEntityID;
+ INSERT IGNORE INTO referring (id) SELECT child FROM isa_cache WHERE parent = InternalEntityID AND rpath = child;
-Select id from refering WHERE id!=0 and id!=EntityID;
+ SELECT e.id FROM referring AS r LEFT JOIN entity_ids AS e ON r.id = e.internal_id WHERE r.id!=0 AND e.internal_id!=InternalEntityID;
-DROP TEMPORARY TABLE refering;
+ DROP TEMPORARY TABLE referring;
END;
//
diff --git a/procedures/getFileIdByPath.sql b/procedures/getFileIdByPath.sql
index 81326400f8ca54b8474f4b0ae20283a5f3a82ceb..d73a20698d67c7c94b5057cba305a4922ff64495 100644
--- a/procedures/getFileIdByPath.sql
+++ b/procedures/getFileIdByPath.sql
@@ -1,9 +1,10 @@
/*
- * ** header v3.0
* This 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 Timm Fitschen <t.fitschen@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
@@ -17,16 +18,27 @@
*
* 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/>.
- *
- * ** end header
*/
Drop Procedure if exists db_5_0.getFileIdByPath;
Delimiter //
-Create Procedure db_5_0.getFileIdByPath (in FilePath VARCHAR(255))
-BEGIN
-Select file_id as FileID from files where path=FilePath LIMIT 1;
+/*
+ * Return a file's id for a given path or nothing if the path is unknown.
+ *
+ * Parameters
+ * ----------
+ * FilePath : TEXT
+ * The file's path.
+ *
+ * Returns
+ * -------
+ * EntityID : VARCHAR(255)
+ */
+Create Procedure db_5_0.getFileIdByPath (in FilePath TEXT)
+BEGIN
+
+ SELECT e.id AS FileID FROM files AS f LEFT JOIN entity_ids ON e.internal_in = f.file_id WHERE f.path=FilePath LIMIT 1;
END;
//
diff --git a/procedures/getIdByName.sql b/procedures/getIdByName.sql
new file mode 100644
index 0000000000000000000000000000000000000000..781594eff9fba3b3582e2e2a4a828f3c7a98a10c
--- /dev/null
+++ b/procedures/getIdByName.sql
@@ -0,0 +1,63 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@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
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * 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/>.
+ */
+
+DROP PROCEDURE IF EXISTS db_5_0.getIdByName;
+DELIMITER //
+
+/*
+ * Return the Entity id(s) for a given name. Optionally, filter by role and set
+ * a limit.
+ *
+ * Parameters
+ * ----------
+ * Name : VARCHAR(255)
+ * The entity's name.
+ * Role : VARCHAR(255)
+ * E.g. RecordType, Record, Property,...
+ * Lmt : INT UNSIGNED
+ * Limit the number of returned entity ids.
+ *
+ * Returns
+ * -------
+ * EntityID : VARCHAR(255)
+ */
+CREATE PROCEDURE db_5_0.getIdByName(in Name VARCHAR(255), in Role VARCHAR(255), in Lmt INT UNSIGNED)
+BEGIN
+
+ SET @stmtStr = "SELECT e.id AS id FROM name_data AS n JOIN entity_ids AS e ON (n.domain_id=0 AND n.property_id=20 AND e.internal_id = n.entity_id) JOIN entities AS i ON (i.id = e.internal_id) WHERE n.value = ?";
+
+ IF Role IS NULL THEN
+ SET @stmtStr = CONCAT(@stmtStr, " AND i.role!='ROLE'");
+ ELSE
+ SET @stmtStr = CONCAT(@stmtStr, " AND i.role='", Role, "'");
+ END IF;
+
+ IF Lmt IS NOT NULL THEN
+ SET @stmtStr = CONCAT(@stmtStr, " LIMIT ", Lmt);
+ END IF;
+
+ SET @vName = Name;
+ PREPARE stmt FROM @stmtStr;
+ EXECUTE stmt USING @vName;
+ DEALLOCATE PREPARE stmt;
+
+END;
+//
+DELIMITER ;
diff --git a/procedures/getInfo.sql b/procedures/getInfo.sql
deleted file mode 100644
index 649127105aca34c56ae8fb7eac1433c3f0898714..0000000000000000000000000000000000000000
--- a/procedures/getInfo.sql
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the LinkAhead Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * 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/>.
- *
- * ** end header
- */
-#-- old procedure.
-Drop Procedure if exists db_5_0.getInfo;
diff --git a/procedures/getRole.sql b/procedures/getRole.sql
deleted file mode 100644
index ab1955d9416400d8d4ceeafc030bba29cd4ba2db..0000000000000000000000000000000000000000
--- a/procedures/getRole.sql
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the LinkAhead Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * 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/>.
- *
- * ** end header
- */
-
-
-
-
-
-
-
-DROP PROCEDURE IF EXISTS db_5_0.getRole;
-delimiter //
-CREATE PROCEDURE db_5_0.getRole(in RoleName VARCHAR(255))
-BEGIN
-
-Select e.id INTO @RoleID from entities e where e.name=RoleName AND e.role=RoleName LIMIT 1;
-
-call retrieveEntity(@RoleID);
-
-
-
-
-END;
-//
-delimiter ;
diff --git a/procedures/initAutoIncrement.sql b/procedures/initAutoIncrement.sql
deleted file mode 100644
index d1350175acd198cfd645c1a54ec478f5409d1832..0000000000000000000000000000000000000000
--- a/procedures/initAutoIncrement.sql
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the LinkAhead Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * 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/>.
- *
- * ** end header
- */
-
-DROP PROCEDURE IF EXISTS db_5_0.initAutoIncrement;
-delimiter //
-
-CREATE PROCEDURE db_5_0.initAutoIncrement()
-BEGIN
-
- SELECT @max := MAX(entity_id)+ 1 FROM transaction_log;
- IF @max IS NOT NULL THEN
- SET @stmtStr = CONCAT('ALTER TABLE entities AUTO_INCREMENT=',@max);
- PREPARE stmt FROM @stmtStr;
- EXECUTE stmt;
- DEALLOCATE PREPARE stmt;
- END IF;
-
-END;
-//
-delimiter ;
diff --git a/procedures/insertEntity.sql b/procedures/insertEntity.sql
index e05fdb4e008213b619ac47e4125fc3cc9844a47a..6b47b505f296d3dc662852bb609552643efc0dc1 100644
--- a/procedures/insertEntity.sql
+++ b/procedures/insertEntity.sql
@@ -1,11 +1,10 @@
/*
* ** header v3.0
- * This 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) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@indiscale>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -19,8 +18,6 @@
*
* 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/>.
- *
- * ** end header
*/
@@ -31,12 +28,14 @@ delimiter //
Parameters
==========
+EntityID : VARCHAR(255)
+ The entity id.
EntityName : VARCHAR(255)
EntityDesc : TEXT
EntityRole : VARCHAR(255)
-Currently one of 'RECORDTYPE', 'RECORD', 'FILE', 'DOMAIN', 'PROPERTY',
+Currently one of 'RECORDTYPE', 'RECORD', 'FILE', 'PROPERTY',
'DATATYPE', 'ROLE', 'QUERYTEMPLATE'
ACL : VARBINARY(65525)
@@ -44,17 +43,17 @@ ACL : VARBINARY(65525)
Select
======
-A tuple (EntityID, Version)
+(Version)
*/
-CREATE PROCEDURE db_5_0.insertEntity(in EntityName VARCHAR(255), in EntityDesc TEXT, in EntityRole VARCHAR(255), in ACL VARBINARY(65525))
+CREATE PROCEDURE db_5_0.insertEntity(in EntityID VARCHAR(255), in EntityName VARCHAR(255), in EntityDesc TEXT, in EntityRole VARCHAR(255), in ACL VARBINARY(65525))
BEGIN
- DECLARE NewEntityID INT UNSIGNED DEFAULT NULL;
DECLARE NewACLID INT UNSIGNED DEFAULT NULL;
DECLARE Hash VARBINARY(255) DEFAULT NULL;
DECLARE Version VARBINARY(255) DEFAULT NULL;
DECLARE Transaction VARBINARY(255) DEFAULT NULL;
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
- -- insert the acl. the new acl id is being written (c-style) into the
+ -- insert the acl. The new acl id is written (c-style) into the
-- variable NewACLID.
call entityACL(NewACLID, ACL);
@@ -63,13 +62,15 @@ BEGIN
VALUES (EntityDesc, EntityRole, NewACLID);
-- ... and return the generated id
- SET NewEntityID = LAST_INSERT_ID();
+ SET InternalEntityID = LAST_INSERT_ID();
+
+ INSERT INTO entity_ids (internal_id, id) VALUES (InternalEntityID, EntityID);
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
-- TODO this is transaction-scoped variable. Is this a good idea?
SET Transaction = @SRID;
SET Version = SHA1(UUID());
- CALL insert_single_child_version(NewEntityID, Hash, Version, Null, Transaction);
+ CALL insert_single_child_version(InternalEntityID, Hash, Version, Null, Transaction);
END IF;
-- insert the name of the entity into name_data table
@@ -77,10 +78,10 @@ BEGIN
IF EntityName IS NOT NULL THEN
INSERT INTO name_data
(domain_id, entity_id, property_id, value, status, pidx)
- VALUES (0, NewEntityID, 20, EntityName, "FIX", 0);
+ VALUES (0, InternalEntityID, 20, EntityName, "FIX", 0);
END IF;
- SELECT NewEntityID as EntityID, Version as Version;
+ SELECT Version as Version;
END;
//
diff --git a/procedures/insertEntityDataType.sql b/procedures/insertEntityDataType.sql
new file mode 100644
index 0000000000000000000000000000000000000000..bd75099ba5317d997ca7a6bc9b4ae00d5f0a04c7
--- /dev/null
+++ b/procedures/insertEntityDataType.sql
@@ -0,0 +1,71 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@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
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * 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/>.
+ */
+
+DROP PROCEDURE IF EXISTS db_5_0.insertEntityDataType;
+DELIMITER //
+
+/*
+ * Insert the (default) datatype of a property.
+ *
+ * Parameters
+ * ----------
+ * PropertyID : VARCHAR(255)
+ * The property id.
+ * DataTypeID : VARCHAR(255)
+ * The data type id (not the name!)
+ */
+CREATE PROCEDURE db_5_0.insertEntityDataType(in PropertyID VARCHAR(255), in DataTypeID VARCHAR(255))
+BEGIN
+ DECLARE InternalPropertyID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalPropertyID FROM entity_ids WHERE id=PropertyID;
+
+ INSERT INTO data_type (domain_id, entity_id, property_id, datatype) SELECT 0, 0, InternalPropertyID, ( SELECT internal_id FROM entity_ids WHERE id = DataTypeID);
+
+
+END;
+//
+DELIMITER ;
+
+
+DROP PROCEDURE IF EXISTS db_5_0.insertEntityCollection;
+DELIMITER //
+
+/*
+ * Insert the (default) collection type of a property.
+ *
+ * Parameters
+ * ----------
+ * PropertyID : VARCHAR(255)
+ * The property id.
+ * Collection : VARCHAR(255)
+ * The collection, e.g. "LIST"
+ */
+CREATE PROCEDURE db_5_0.insertEntityCollection(in PropertyID VARCHAR(255), in Collection VARCHAR(255))
+BEGIN
+ DECLARE InternalPropertyID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalPropertyID FROM entity_ids WHERE id=PropertyID;
+
+ INSERT INTO collection_type (domain_id, entity_id, property_id, collection) SELECT 0, 0, InternalPropertyID, Collection;
+
+END;
+//
+DELIMITER ;
diff --git a/procedures/insertEntityProperty.sql b/procedures/insertEntityProperty.sql
index b2e926a1659f76e50242e40e2d318062564dea17..872ee1d47dea7fca09b60586efbd4189a5a6149a 100644
--- a/procedures/insertEntityProperty.sql
+++ b/procedures/insertEntityProperty.sql
@@ -1,11 +1,10 @@
/*
- * ** header v3.0
* This 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) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@indiscale
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -19,112 +18,166 @@
*
* 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/>.
- *
- * ** end header
*/
DROP PROCEDURE IF EXISTS db_5_0.insertEntityProperty;
delimiter //
+
+
+/*
+ * Insert the property of an entity (level 1 and 2, only one *_data table entry at a time).
+ *
+ * Parameters
+ * ----------
+ * DomainID : VARCHAR(255)
+ * The domain id (0 or the entity's id for level-2-data)
+ * EntityID : VARCHAR(255)
+ * The entity id (or the property's id for level-2-data)
+ * PropertyID : VARCHAR(255)
+ * The property id (or the sub-property's id for level-2-data)
+ * Datatable : VARCHAR(255)
+ * Name of the *_data table, e.g. 'double_data'.
+ * PropertyValue : TEXT
+ * The property's value
+ * PropertyUnitSig : BIGINT
+ * The unit signature.
+ * PropertyStatus : VARCHAR(255)
+ * E.g. OBLIGATORY, FIX,...
+ * NameOverride : VARCHAR(255)
+ * The overridden name
+ * DescOverride : TEXT
+ * The overridden description
+ * DatatypeOverride : VARCHAR(255)
+ * The overridden datatype
+ * Collection : VARCHAR(255)
+ * The overridden collection (only if DatatypeOverride is present).
+ * PropertyIndex : INT UNSIGNED
+ * The property's index (for ordering of properties and values).
+ */
CREATE PROCEDURE db_5_0.insertEntityProperty(
- in DomainID INT UNSIGNED,
- in EntityID INT UNSIGNED,
- in PropertyID INT UNSIGNED,
+ in DomainID VARCHAR(255),
+ in EntityID VARCHAR(255),
+ in PropertyID VARCHAR(255),
in Datatable VARCHAR(255),
in PropertyValue TEXT,
in PropertyUnitSig BIGINT,
in PropertyStatus VARCHAR(255),
in NameOverride VARCHAR(255),
in DescOverride TEXT,
- in DatatypeOverride INT UNSIGNED,
+ in DatatypeOverride VARCHAR(255),
in Collection VARCHAR(255),
in PropertyIndex INT UNSIGNED)
BEGIN
DECLARE ReferenceValueIVersion INT UNSIGNED DEFAULT NULL;
DECLARE ReferenceValue INT UNSIGNED DEFAULT NULL;
DECLARE AT_PRESENT INTEGER DEFAULT NULL;
+ DECLARE InternalDataTypeID INT UNSIGNED DEFAULT NULL;
+ DECLARE InternalPropertyID INT UNSIGNED DEFAULT NULL;
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+ DECLARE InternalDomainID INT UNSIGNED DEFAULT 0;
+
+ SELECT internal_id INTO InternalDomainID FROM entity_ids WHERE id = DomainID;
+ -- When DomainID != 0 the EntityID could possibly be a 'replacement id'
+ -- which are internal ids by definition (and do not have external
+ -- equivalents).
+ IF LOCATE("$", EntityID) = 1 THEN
+ SET InternalEntityID=SUBSTRING(EntityID, 2);
+ ELSE
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+ END IF;
+ IF LOCATE("$", PropertyID) = 1 THEN
+ SET InternalPropertyID=SUBSTRING(PropertyID, 2);
+ ELSE
+ SELECT internal_id INTO InternalPropertyID FROM entity_ids WHERE id = PropertyID;
+ END IF;
CASE Datatable
WHEN 'double_data' THEN
INSERT INTO double_data
(domain_id, entity_id, property_id, value, unit_sig, status, pidx)
VALUES
- (DomainID, EntityID, PropertyID, PropertyValue, PropertyUnitSig, PropertyStatus, PropertyIndex);
+ (InternalDomainID, InternalEntityID, InternalPropertyID, PropertyValue, PropertyUnitSig, PropertyStatus, PropertyIndex);
WHEN 'integer_data' THEN
INSERT INTO integer_data
(domain_id, entity_id, property_id, value, unit_sig, status, pidx)
VALUES
- (DomainID, EntityID, PropertyID, PropertyValue, PropertyUnitSig, PropertyStatus, PropertyIndex);
+ (InternalDomainID, InternalEntityID, InternalPropertyID, PropertyValue, PropertyUnitSig, PropertyStatus, PropertyIndex);
WHEN 'datetime_data' THEN
INSERT INTO datetime_data
(domain_id, entity_id, property_id, value, value_ns, status, pidx)
VALUES
- (DomainID, EntityID, PropertyID, SUBSTRING_INDEX(PropertyValue, 'UTC', 1), IF(SUBSTRING_INDEX(PropertyValue, 'UTC', -1)='',NULL,SUBSTRING_INDEX(PropertyValue, 'UTC', -1)), PropertyStatus, PropertyIndex);
+ (InternalDomainID, InternalEntityID, InternalPropertyID, SUBSTRING_INDEX(PropertyValue, 'UTC', 1), IF(SUBSTRING_INDEX(PropertyValue, 'UTC', -1)='',NULL,SUBSTRING_INDEX(PropertyValue, 'UTC', -1)), PropertyStatus, PropertyIndex);
WHEN 'reference_data' THEN
-- special handling if versioning enabled and specific version of referenced entity is given.
SET AT_PRESENT=LOCATE("@", PropertyValue);
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") AND AT_PRESENT > 0 THEN
- SET ReferenceValue = SUBSTRING_INDEX(PropertyValue, '@', 1);
+ SELECT internal_id INTO ReferenceValue FROM entity_ids WHERE id = SUBSTRING_INDEX(PropertyValue, '@', 1);
SET ReferenceValueIVersion = get_iversion(ReferenceValue,
SUBSTRING_INDEX(PropertyValue, '@', -1));
- -- TODO raise error when @ present but iversion is null
IF ReferenceValueIVersion IS NULL THEN
+ -- Raise error when @ present but iversion is null
SELECT 0 from `ReferenceValueIVersion_WAS_NULL`;
END IF;
+ ELSEIF LOCATE("$", PropertyValue) = 1 THEN
+ SET ReferenceValue = SUBSTRING(PropertyValue, 2);
ELSE
- SET ReferenceValue = PropertyValue;
+ SELECT internal_id INTO ReferenceValue FROM entity_ids WHERE id = PropertyValue;
END IF;
+
INSERT INTO reference_data
(domain_id, entity_id, property_id, value, value_iversion, status,
pidx)
VALUES
- (DomainID, EntityID, PropertyID, ReferenceValue,
+ (InternalDomainID, InternalEntityID, InternalPropertyID, ReferenceValue,
ReferenceValueIVersion, PropertyStatus, PropertyIndex);
WHEN 'enum_data' THEN
INSERT INTO enum_data
(domain_id, entity_id, property_id, value, status, pidx)
VALUES
- (DomainID, EntityID, PropertyID, PropertyValue, PropertyStatus, PropertyIndex);
+ (InternalDomainID, InternalEntityID, InternalPropertyID, PropertyValue, PropertyStatus, PropertyIndex);
WHEN 'date_data' THEN
INSERT INTO date_data
(domain_id, entity_id, property_id, value, status, pidx)
VALUES
- (DomainID, EntityID, PropertyID, SUBSTRING_INDEX(PropertyValue, '.', 1), PropertyStatus, PropertyIndex);
+ (InternalDomainID, InternalEntityID, InternalPropertyID, SUBSTRING_INDEX(PropertyValue, '.', 1), PropertyStatus, PropertyIndex);
WHEN 'text_data' THEN
INSERT INTO text_data
(domain_id, entity_id, property_id, value, status, pidx)
VALUES
- (DomainID, EntityID, PropertyID, PropertyValue, PropertyStatus, PropertyIndex);
+ (InternalDomainID, InternalEntityID, InternalPropertyID, PropertyValue, PropertyStatus, PropertyIndex);
WHEN 'null_data' THEN
INSERT INTO null_data
(domain_id, entity_id, property_id, status, pidx)
VALUES
- (DomainID, EntityID, PropertyID, PropertyStatus, PropertyIndex);
+ (InternalDomainID, InternalEntityID, InternalPropertyID, PropertyStatus, PropertyIndex);
WHEN 'name_data' THEN
INSERT INTO name_data
(domain_id, entity_id, property_id, value, status, pidx)
VALUES
- (DomainID, EntityID, PropertyID, PropertyValue, PropertyStatus, PropertyIndex);
+ (InternalDomainID, InternalEntityID, InternalPropertyID, PropertyValue, PropertyStatus, PropertyIndex);
ELSE
+ -- raise error
SELECT * FROM table_does_not_exist;
END CASE;
IF DatatypeOverride IS NOT NULL THEN
- call overrideType(DomainID, EntityID, PropertyID, DatatypeOverride);
+ SELECT internal_id INTO InternalDataTypeID from entity_ids WHERE id = DatatypeOverride;
+ call overrideType(InternalDomainID, InternalEntityID, InternalPropertyID, InternalDataTypeID);
IF Collection IS NOT NULL THEN
- INSERT INTO collection_type (domain_id, entity_id, property_id, collection) VALUES (DomainID, EntityID, PropertyID, Collection);
+ INSERT INTO collection_type (domain_id, entity_id, property_id, collection) VALUES (InternalDomainID, InternalEntityID, InternalPropertyID, Collection);
END IF;
END IF;
IF NameOverride IS NOT NULL THEN
- call overrideName(DomainID, EntityID, PropertyID, NameOverride);
+ call overrideName(InternalDomainID, InternalEntityID, InternalPropertyID, NameOverride);
END IF;
IF DescOverride IS NOT NULL THEN
- call overrideDesc(DomainID, EntityID, PropertyID, DescOverride);
+ call overrideDesc(InternalDomainID, InternalEntityID, InternalPropertyID, DescOverride);
END IF;
END;
diff --git a/procedures/insertIsaCache.sql b/procedures/insertIsaCache.sql
index eaa83f104a273997f80f7276da548af3a812db50..d0273e39b88ce4c37ca2a9a2dcd32852403d199a 100644
--- a/procedures/insertIsaCache.sql
+++ b/procedures/insertIsaCache.sql
@@ -1,10 +1,10 @@
/*
- * ** header v3.0
* This 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) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@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
@@ -18,8 +18,6 @@
*
* 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/>.
- *
- * ** end header
*/
DROP PROCEDURE IF EXISTS db_5_0.insertIsa;
DELIMITER //
@@ -32,16 +30,22 @@ DELIMITER //
*
* Parameters
* ==========
- *
- * c : UNSIGNED
- * The child entity
- *
- * p : UNSIGNED
- * The parent entity
+ *
+ * ChildID : VARCHAR(255)
+ * The child entity.
+ *
+ * ParentID : VARCHAR(255)
+ * The parent entity.
*/
-CREATE PROCEDURE db_5_0.insertIsa(IN c INT UNSIGNED, IN p INT UNSIGNED)
+CREATE PROCEDURE db_5_0.insertIsa(IN ChildID VARCHAR(255), IN ParentID VARCHAR(255))
insert_is_a_proc: BEGIN
+ DECLARE c INT UNSIGNED DEFAULT NULL;
+ DECLARE p INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO c FROM entity_ids WHERE id = ChildID;
+ SELECT internal_id INTO p FROM entity_ids WHERE id = ParentID;
+
INSERT INTO isa_cache (child, parent, rpath) VALUES (c, p, c);
IF p = c THEN
@@ -69,17 +73,17 @@ insert_is_a_proc: BEGIN
INSERT IGNORE INTO isa_cache SELECT
l.child, -- Descendant as found in isa_cache
r.parent, -- Ancestor as found in isa_cache
- if(l.rpath=l.child and r.rpath=c, -- if distance=1 for left and right:
+ IF(l.rpath=l.child AND r.rpath=c, -- if distance=1 for left and right:
c, -- rpath = current child
- concat(if(l.rpath=l.child, -- if dist=1 for descendant:
+ concat(IF(l.rpath=l.child, -- if dist=1 for descendant:
c, -- rpath starts with c
concat(l.rpath, '>', c)), -- rpath starts with "desc.rpath > c"
- if(r.rpath=c, -- if dist=1 for ancestor
+ IF(r.rpath=c, -- if dist=1 for ancestor
'', -- rpath is finished
concat('>', r.rpath)))) -- rpath continuees with " > ancest.rpath"
AS rpath
FROM
- isa_cache as l INNER JOIN isa_cache as r
+ isa_cache AS l INNER JOIN isa_cache AS r
ON (l.parent = c AND c = r.child AND l.child != l.parent); -- Left: descendants of c, right: ancestors
END;
diff --git a/procedures/insertUser.sql b/procedures/insertUser.sql
deleted file mode 100644
index 392b6668c7e1fe8bb743afa37cb51f35e52b624c..0000000000000000000000000000000000000000
--- a/procedures/insertUser.sql
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the LinkAhead Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * 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/>.
- *
- * ** end header
- */
-
-Drop Procedure if exists db_5_0.insertUser;
-Delimiter //
-Create Procedure db_5_0.insertUser(in Name VARCHAR(255), in Password VARCHAR(255))
-
-BEGIN
-
-
-INSERT INTO entities (name, role, acl) VALUES (Name, 'USER', 0);
-
-SET @LAST_UserID = LAST_INSERT_ID();
-
-INSERT INTO passwords VALUES (@LAST_UserID, Password);
-
-Select @LAST_UserID as UserID;
-
-END;
-//
-
-
-delimiter ;
diff --git a/procedures/isSubtype.sql b/procedures/isSubtype.sql
index 489a63e47a1185d6e221fedbe5a3aec65f0470f3..98d9387077d89f3173fa939f6d7517bfbe95ebff 100644
--- a/procedures/isSubtype.sql
+++ b/procedures/isSubtype.sql
@@ -1,9 +1,10 @@
/*
- * ** header v3.0
* This 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 Timm Fitschen <t.fitschen@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
@@ -17,18 +18,37 @@
*
* 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/>.
- *
- * ** end header
*/
DROP PROCEDURE IF EXISTS db_5_0.isSubtype;
delimiter //
-CREATE PROCEDURE db_5_0.isSubtype(in c INT UNSIGNED, in p INT UNSIGNED)
+/*
+ * Return TRUE if the given Child is indeed a (direct or indirect) child of the
+ * given Parent.
+ *
+ * Parameters
+ * ----------
+ * ChildID : VARCHAR(255)
+ * The entity id of the child.
+ * ParentID : VARCHAR(255)
+ * The entity id of the parent.
+ *
+ * Returns
+ * -------
+ * ISA : BOOLEAN
+ */
+CREATE PROCEDURE db_5_0.isSubtype(in ChildID VARCHAR(255), in ParentID VARCHAR(255))
BEGIN
- DECLARE ret BOOLEAN DEFAULT FALSE;
- SELECT TRUE INTO ret FROM isa_cache AS i WHERE i.child=c AND i.parent=p LIMIT 1;
+ DECLARE c INT UNSIGNED DEFAULT NULL;
+ DECLARE p INT UNSIGNED DEFAULT NULL;
+ DECLARE ret BOOLEAN DEFAULT FALSE;
+
+ SELECT internal_id INTO c from entity_ids WHERE id = ChildID;
+ SELECT internal_id INTO p from entity_ids WHERE id = ParentID;
+
+ SELECT TRUE INTO ret FROM isa_cache AS i WHERE i.child=c AND i.parent=p LIMIT 1;
SELECT ret as ISA;
END;
//
diff --git a/procedures/overrideName.sql b/procedures/overrideName.sql
index 8ee39d25739220705d20688fe217a06fc0a18694..f8921330fcfa44c5f056dd2072fb8d781b7e2993 100644
--- a/procedures/overrideName.sql
+++ b/procedures/overrideName.sql
@@ -1,9 +1,10 @@
/*
- * ** header v3.0
* This 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 Timm Fitschen <t.fitschen@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
@@ -17,8 +18,6 @@
*
* 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/>.
- *
- * ** end header
*/
DROP PROCEDURE IF EXISTS db_5_0.overrideName;
@@ -26,21 +25,61 @@ DROP PROCEDURE IF EXISTS db_5_0.overrideDesc;
DROP PROCEDURE IF EXISTS db_5_0.overrideType;
DELIMITER //
-CREATE PROCEDURE db_5_0.overrideName(in DomainID INT UNSIGNED, in EntityID INT UNSIGNED, in PropertyID INT UNSIGNED, in Name VARCHAR(255))
+/*
+ * Insert a name override.
+ *
+ * Parameters
+ * ----------
+ * InternalDomainID : INT UNSIGNED
+ * The *internal* id of the domain.
+ * InternalEntityID : INT UNSIGNED
+ * The *internal* id of the entity.
+ * InternalPropertyID : INT UNSIGNED
+ * The *internal* id of the property.
+ * Name : VARCHAR(255)
+ */
+CREATE PROCEDURE db_5_0.overrideName(in InternalDomainID INT UNSIGNED, in InternalEntityID INT UNSIGNED, in InternalPropertyID INT UNSIGNED, in Name VARCHAR(255))
BEGIN
- INSERT INTO name_overrides (domain_id, entity_id, property_id, name) VALUES (DomainID, EntityID, PropertyID, Name);
+ INSERT INTO name_overrides (domain_id, entity_id, property_id, name) VALUES (InternalDomainID, InternalEntityID, InternalPropertyID, Name);
END;
//
-CREATE PROCEDURE db_5_0.overrideDesc(in DomainID INT UNSIGNED, in EntityID INT UNSIGNED, in PropertyID INT UNSIGNED, in Description TEXT)
+/*
+ * Insert a description override.
+ *
+ * Parameters
+ * ----------
+ * InternalDomainID : INT UNSIGNED
+ * The *internal* id of the domain.
+ * InternalEntityID : INT UNSIGNED
+ * The *internal* id of the entity.
+ * InternalPropertyID : INT UNSIGNED
+ * The *internal* id of the property.
+ * Description : TEXT
+ */
+CREATE PROCEDURE db_5_0.overrideDesc(in InternalDomainID INT UNSIGNED, in InternalEntityID INT UNSIGNED, in InternalPropertyID INT UNSIGNED, in Description TEXT)
BEGIN
- INSERT INTO desc_overrides (domain_id, entity_id, property_id, description) VALUES (DomainID, EntityID, PropertyID, Description);
+ INSERT INTO desc_overrides (domain_id, entity_id, property_id, description) VALUES (InternalDomainID, InternalEntityID, InternalPropertyID, Description);
END;
//
-CREATE PROCEDURE db_5_0.overrideType(in DomainID INT UNSIGNED, in EntityID INT UNSIGNED, in PropertyID INT UNSIGNED, in Datatype INT UNSIGNED)
+/*
+ * Insert a data type override.
+ *
+ * Parameters
+ * ----------
+ * InternalDomainID : INT UNSIGNED
+ * The *internal* id of the domain.
+ * InternalEntityID : INT UNSIGNED
+ * The *internal* id of the entity.
+ * InternalPropertyID : INT UNSIGNED
+ * The *internal* id of the property.
+ * InternalDatatypeID : INT UNSIGNED
+ * The *internal* id of the data type.
+ */
+CREATE PROCEDURE db_5_0.overrideType(in InternalDomainID INT UNSIGNED, in InternalEntityID INT UNSIGNED, in InternalPropertyID INT UNSIGNED, in InternalDataTypeID INT UNSIGNED)
BEGIN
- INSERT INTO data_type (domain_id, entity_id, property_id, datatype) VALUES (DomainID, EntityID, PropertyID, Datatype);
+ INSERT INTO data_type (domain_id, entity_id, property_id, datatype) VALUES (InternalDomainID, InternalEntityID, InternalPropertyID, InternalDataTypeID);
END;
//
diff --git a/procedures/query/applyIDFilter.sql b/procedures/query/applyIDFilter.sql
index 642e7806b47dae6848e77126f6a5c413ac9615db..062de92d9f1dc477a72dfda3285af9133b24ae98 100644
--- a/procedures/query/applyIDFilter.sql
+++ b/procedures/query/applyIDFilter.sql
@@ -1,9 +1,10 @@
/*
- * ** header v3.0
* This 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 Timm Fitschen <t.fitschen@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
@@ -17,8 +18,6 @@
*
* 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/>.
- *
- * ** end header
*/
DROP PROCEDURE IF EXISTS db_5_0.applyIDFilter;
@@ -32,71 +31,114 @@ DELIMITER //
*
* The `versioned` flag currently only has the effect that an `_iversion` column is also copied to
* the target.
+ *
+ * Parameters
+ * ----------
+ * sourceSet : VARCHAR(255)
+ * The name of the table from where we start.
+ * targetSet : VARCHAR(255)
+ * The name of the table where we collect all the "good" ids (or NULL or same as sourceSet).
+ * o : CHAR(2)
+ * The operator used for filtering, e.g. '=', '!=', '>', ...
+ * EntityID : VARCHAR(255)
+ * An entity id, existing or non-existing, which we use to compare the
+ * existing entities to using the operator.
+ * agg : CHAR(3)
+ * An aggregate function, e.g. 'max' or 'min'. This only makes sense for number-based ids.
+ * versioned : BOOLEAN
+ * The filter belongs to a version-aware query (e.g. FIND ANY VERSION OF
+ * ...) and hence the sourceSet and targetSet have an `_iversion` column.
*/
CREATE PROCEDURE db_5_0.applyIDFilter(in sourceSet VARCHAR(255), in targetSet VARCHAR(255),
- in o CHAR(2), in vInt BIGINT, in agg CHAR(3), in versioned BOOLEAN)
+ in o CHAR(2), in EntityID VARCHAR(255), in agg CHAR(3), in versioned BOOLEAN)
IDFILTER_LABEL: BEGIN
DECLARE data VARCHAR(20000) DEFAULT NULL;
DECLARE aggVal VARCHAR(255) DEFAULT NULL;
+DECLARE direction CHAR(4) DEFAULT NULL;
+DECLARE entity_id_type VARCHAR(255) DEFAULT "eids.id ";
#-- get aggVal if possible
IF agg IS NOT NULL THEN
IF versioned THEN
-- TODO versioned queries
SELECT 1 FROM id_agg_with_versioning_not_implemented;
+ ELSEIF agg = "max" THEN
+ SET direction = "DESC";
+ ELSEIF agg = "min" THEN
+ SET direction = "ASC ";
+ ELSE
+ SELECT 1 FROM unknown_agg_parameter;
END IF;
+
SET @stmtIDAggValStr = CONCAT(
- "SELECT ",
- agg,
- "(id) INTO @sAggVal FROM `",
+ "SELECT e.internal_id INTO @sAggVal FROM `",
sourceSet,
- "`");
+ "` AS s LEFT JOIN entity_ids AS e ON (s.id=e.internal_id) WHERE s.id>99 ORDER BY CAST(e.id AS UNSIGNED INT) ",
+ direction,
+ " LIMIT 1");
+
PREPARE stmtIDAggVal FROM @stmtIDAggValStr;
EXECUTE stmtIDAggVal;
DEALLOCATE PREPARE stmtIDAggVal;
SET aggVal = @sAggVal;
END IF;
+IF o = ">" OR o = ">=" OR o = "<" or o = "<=" THEN
+ SET entity_id_type = "CAST(eids.id AS UNSIGNED INT) ";
+END IF;
+
#-- generate stmt string
IF targetSet IS NULL OR targetSet = sourceSet THEN
SET data = CONCAT(
"DELETE FROM `",
sourceSet,
"` WHERE ",
- IF(o IS NULL OR vInt IS NULL,
+ IF(o IS NULL OR EntityID IS NULL,
"1=1",
- CONCAT("NOT id",
+ CONCAT("NOT EXISTS (SELECT 1 FROM entity_ids AS eids WHERE ",
+ entity_id_type,
o,
- vInt)),
+ ' "',
+ EntityID,
+ '" ',
+ " AND eids.internal_id = `",
+ sourceSet,
+ "`.id)"
+ )),
IF(aggVal IS NULL,
"",
- CONCAT(" AND id!=",
+ CONCAT(" AND `", sourceSet, "`.id!=",
aggVal)));
ELSEIF versioned AND sourceSet = "entities" THEN
-
-- ################# VERSIONING #####################
SET data = CONCAT(
"INSERT IGNORE INTO `",
targetSet,
- '` (id, _iversion) SELECT id, _get_head_iversion(id) FROM `entities` WHERE ',
- IF(o IS NULL OR vInt IS NULL,
+ '` (id, _iversion) SELECT e.id, _get_head_iversion(e.id) FROM `entities` AS e JOIN entity_ids AS eids ON (e.id = eids.internal_id) WHERE ',
+ IF(o IS NULL OR EntityID IS NULL,
"1=1",
- CONCAT("id",
+ CONCAT(entity_id_type,
o,
- vInt)),
+ ' "',
+ EntityID,
+ '"'
+ )),
IF(aggVal IS NULL,
"",
- CONCAT(" AND id=",
+ CONCAT(" AND e.id=",
aggVal)),
- ' UNION SELECT id, _iversion FROM `archive_entities` WHERE ',
- IF(o IS NULL OR vInt IS NULL,
+ ' UNION SELECT e.id, _iversion FROM `archive_entities` AS e JOIN entity_ids AS eids ON (e.id = eids.internal_id) WHERE ',
+ IF(o IS NULL OR EntityID IS NULL,
"1=1",
- CONCAT("id",
+ CONCAT(entity_id_type,
o,
- vInt)),
+ ' "',
+ EntityID,
+ '"'
+ )),
IF(aggVal IS NULL,
"",
- CONCAT(" AND id=",
+ CONCAT(" AND e.id=",
aggVal)));
-- ##################################################
@@ -108,12 +150,15 @@ ELSE
'` (id, _iversion) SELECT data.id, data._iversion FROM `',
'` (id) SELECT data.id FROM `'),
sourceSet,
- "` AS data WHERE ",
- IF(o IS NULL OR vInt IS NULL,
+ "` AS data JOIN entity_ids AS eids ON (eids.internal_id = data.id) WHERE ",
+ IF(o IS NULL OR EntityID IS NULL,
"1=1",
- CONCAT("data.id",
+ CONCAT(entity_id_type,
o,
- vInt)),
+ ' "',
+ EntityID,
+ '"'
+ )),
IF(aggVal IS NULL,
"",
CONCAT(" AND data.id=",
diff --git a/procedures/query/applyPOV.sql b/procedures/query/applyPOV.sql
index 9fb9101260e61b33439cb7d5ea6e2e3a9ff5ca2d..a038e4c7961c9c3a01f725c210dec4cfb9029eeb 100644
--- a/procedures/query/applyPOV.sql
+++ b/procedures/query/applyPOV.sql
@@ -1,5 +1,4 @@
/*
- * ** header v3.0
* This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
@@ -17,8 +16,6 @@
*
* 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/>.
- *
- * ** end header
*/
/* Documentation including (?) has to be checked by an expert. */
@@ -37,30 +34,31 @@ DELIMITER //
* ----------
*
* versioned : boolean
- * If True, sourceSet and targetSet have an _iversion column, otherwise that column will be
-* ignored (or only HEAD will be inserted into targetSet).
+ * If True, sourceSet and targetSet have an _iversion column, otherwise that column will be ignored
+ * (or only HEAD will be inserted into targetSet).
*/
-CREATE PROCEDURE db_5_0.applyPOV(in sourceSet VARCHAR(255), /* (?) Name of the table that the POV will be applied to. This can be a temporary table. */
- in targetSet VARCHAR(255), /* (?) Name of the result table of this POV. */
+CREATE PROCEDURE db_5_0.applyPOV(in sourceSet VARCHAR(255), /* Name of the table that the POV will be applied to. This can be a temporary table or the `entities` table */
+ in targetSet VARCHAR(255), /* Name of the result table of this POV. After the filter has been applied this table only contains matching
+ entity ids. This may be NULL or same as sourceSet. In that case the filter is applied in-place (delete non-matching). Otherwise the filter is applied by copying only the matching ids from the *source* set to the *target* set. */
in propertiesTable VARCHAR(255),
- in refIdsTable VARCHAR(255),
+ in refIdsTable VARCHAR(255), /* Name of a tmp table that contains all ids of children of the value interpreted as entity name or id */
in o CHAR(4), /* The operator for this operation. can be one of:
0 check for "equals NULL"
!0 check for "not NULL"
-> check whether a reference exists
- ( (?) check for datetime intervals
- !( (?) check for being outside of datetime intervals
- other operators (all SQL operators (?))
+ ( check for datetime interval (say "in")
+ !( check for being outside of datetime intervals (say "not in")
+ other operators (all valid SQL operators)
these other operators can be used either with or without an aggregation
to use an aggregation set agg to non-zero
all SQL aggregations can be used
*/
- in vText VARCHAR(255), /* (?) the text value to be checked against using operator o */
+ in vText VARCHAR(255), /* the text value to be checked against using operator o */
in vInt INT, /* the integer value to be checked against using operator o */
in vDouble DOUBLE, /* the double value to be checked against using operator o */
- in unit_sig BIGINT,
+ in unit_sig BIGINT, /* signatur of the unit given by the user. used when we need to convert units. */
in vDoubleStdUnit DOUBLE, /* The numeric value, converted according to the unit rules. */
- in stdUnit_sig BIGINT,
+ in stdUnit_sig BIGINT, /* signatur of the normalized/standardized unit, e.g when unit_sig is "km/h" this might be "m/s". */
in vDateTime VARCHAR(255),
in vDateTimeDotNotation VARCHAR(255),
in agg CHAR(3), /* an SQL aggregate function or NULL when no aggregation should be used */
@@ -84,6 +82,10 @@ POV_LABEL: BEGIN
DECLARE keepTabl VARCHAR(255) DEFAULT NULL;
DECLARE existence_op VARCHAR(255) DEFAULT "EXISTS";
+ #-- ######### HINT ##############
+ #-- first the appropriate statement is created which in the end prepared and executed
+ #-- #############################
+
IF o = '->' THEN
#-- special case: pure reference property
call applyRefPOV(sourceSet,targetSet, propertiesTable, refIdsTable, versioned);
@@ -232,6 +234,8 @@ POV_LABEL: BEGIN
IF o = "!=" AND refIdsTable IS NOT NULL THEN
SET existence_op = "NOT EXISTS";
END IF;
+ /* select all entities that reference the entity or a child of the
+ * value interpreted as ID*/
SET sRefData = IF(vText IS NULL,
' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `reference_data`',
IF(refIdsTable IS NULL,
@@ -246,6 +250,7 @@ POV_LABEL: BEGIN
END IF;
+ #-- create array of statement parts (and replace null with empty string) (?)
SET data = CONCAT('(',sTextData,
IF(sNameData IS NULL, '', sNameData),
IF(sEnumData IS NULL, '', sEnumData),
@@ -262,6 +267,7 @@ POV_LABEL: BEGIN
call createTmpTable(keepTabl, versioned);
IF versioned THEN
#-- generate statement from statement parts
+ #-- (versioned section)
SET @stmtPOVkeepTblStr = CONCAT(
'INSERT IGNORE INTO `', keepTabl, '` (id, _iversion) SELECT entity_id AS id, _iversion FROM ', data,
' as data', IF(propertiesTable IS NULL, '', CONCAT(
@@ -302,7 +308,14 @@ POV_LABEL: BEGIN
DEALLOCATE PREPARE stmtPOVkeepTbl;
ELSE
#-- generate statement from statement parts
- SET @stmtPOVkeepTblStr = CONCAT('INSERT IGNORE INTO `', keepTabl, '` (id) SELECT DISTINCT entity_id AS id FROM ', data, ' as data', IF(propertiesTable IS NULL, '', CONCAT(' WHERE EXISTS (Select 1 from `', propertiesTable, '` AS prop WHERE prop.id = data.property_id AND (prop.id2=data.entity_id OR prop.id2=0))')));
+ SET @stmtPOVkeepTblStr = CONCAT(
+ 'INSERT IGNORE INTO `', keepTabl,
+ '` (id) SELECT DISTINCT entity_id AS id FROM ', data, ' as data',
+ IF(propertiesTable IS NULL, '',
+ CONCAT(' WHERE EXISTS (Select 1 from `', propertiesTable,
+ '` AS prop WHERE prop.id = data.property_id AND
+ (prop.id2=data.entity_id OR prop.id2=0))')));
+ #-- (unversioned section)
SET @stmtPOVStr = CONCAT(
IF(targetSet IS NULL,
diff --git a/procedures/query/applyTransactionFilter.sql b/procedures/query/applyTransactionFilter.sql
index 63267a4505040c186721a367d141ac566cb30bc4..0d2490b43b17ecc4157156db0d2d2be84bd58d3b 100644
--- a/procedures/query/applyTransactionFilter.sql
+++ b/procedures/query/applyTransactionFilter.sql
@@ -1,9 +1,10 @@
/*
- * ** header v3.0
* This 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 Timm Fitschen <t.fitschen@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
@@ -17,37 +18,65 @@
*
* 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/>.
- *
- * ** end header
*/
DROP PROCEDURE IF EXISTS db_5_0.applyTransactionFilter;
DELIMITER //
+
+/*
+ * Apply a transaction filter to the sourceSet and collect the remaining
+ * entities in the targetSet.
+ *
+ * Parameters
+ * ----------
+ * sourceSet : VARCHAR(255)
+ * The name of the table from where we start.
+ * targetSet : VARCHAR(255)
+ * The name of the table where we collect all the "good" ids (or NULL or same as sourceSet).
+ * transaction : VARCHAR(255)
+ * The transaction's type (INSERT, UPDATE,...)
+ * operator_u : CHAR(2)
+ * The operator used for filtering by the user, e.g. '=', '!='.
+ * realm : VARCHAR(255)
+ * The user's realm (if filtering by the user).
+ * userName : VARCHAR(255)
+ * The user's name (if filtering by the user).
+ * ilb : BIGINT
+ * Inclusive Lower Bound of seconds for the transactions time.
+ * ilb_nanos : BIGINT
+ * Inclusive Lower Bound of nanoseconds for the transactions time.
+ * eub : BIGINT
+ * Exclusive Upper Bound of seconds for the transactions time.
+ * eub_nanos : BIGINT
+ * Exclusive Upper Bound of nanoseconds for the transactions time.
+ * operator_t : CHAR(2)
+ * The operator used for filtering by the transaction time, e.g. '=', '!=', '<', '>='.
+ */
CREATE PROCEDURE db_5_0.applyTransactionFilter(in sourceSet VARCHAR(255), targetSet VARCHAR(255), in transaction VARCHAR(255), in operator_u CHAR(2), in realm VARCHAR(255), in userName VARCHAR(255), in ilb BIGINT, in ilb_nanos INT UNSIGNED, in eub BIGINT, in eub_nanos INT UNSIGNED, in operator_t CHAR(2))
BEGIN
- DECLARE data TEXT default CONCAT('(SELECT entity_id FROM transaction_log AS t WHERE t.transaction=\'',
- transaction,
- '\'',
- IF(userName IS NOT NULL,
- CONCAT(' AND t.realm', operator_u, '? AND t.username', operator_u, '?'),
- ''
- ),
- IF(ilb IS NOT NULL,
- CONCAT(" AND", constructDateTimeWhereClauseForColumn("t.seconds", "t.nanos", ilb, ilb_nanos, eub, eub_nanos, operator_t)),
- ""
- ),
- ')'
- );
+ DECLARE data TEXT default CONCAT("(SELECT internal_id AS entity_id FROM transaction_log AS t JOIN entity_ids AS eids ON ( t.entity_id = eids.id ) WHERE t.transaction='",
+ transaction,
+ "'",
+ IF(userName IS NOT NULL,
+ CONCAT(' AND t.realm', operator_u, '? AND t.username', operator_u, '?'),
+ ''
+ ),
+ IF(ilb IS NOT NULL,
+ CONCAT(" AND", constructDateTimeWhereClauseForColumn("t.seconds", "t.nanos", ilb, ilb_nanos, eub, eub_nanos, operator_t)),
+ ""
+ ),
+ ')'
+ );
- SET @stmtTransactionStr = makeStmt(sourceSet, targetSet, data, NULL, FALSE);
- PREPARE stmtTransactionFilter from @stmtTransactionStr;
- IF userName IS NOT NULL THEN
- SET @userName = userName;
- SET @realm = realm;
- EXECUTE stmtTransactionFilter USING @realm, @userName;
- ELSE
- EXECUTE stmtTransactionFilter;
- END IF;
+ SET @stmtTransactionStr = makeStmt(sourceSet, targetSet, data, NULL, FALSE);
+ PREPARE stmtTransactionFilter from @stmtTransactionStr;
+ IF userName IS NOT NULL THEN
+ SET @userName = userName;
+ SET @realm = realm;
+ EXECUTE stmtTransactionFilter USING @realm, @userName;
+ ELSE
+ EXECUTE stmtTransactionFilter;
+ END IF;
END;
//
diff --git a/procedures/query/initBackReference.sql b/procedures/query/initBackReference.sql
index 777ddcc90f87b1a9cfe2d3ae70b64ce2c5ce25f7..6b3be3cdd2f97737ec8cb92a77040076027f1927 100644
--- a/procedures/query/initBackReference.sql
+++ b/procedures/query/initBackReference.sql
@@ -1,9 +1,10 @@
/*
- * ** header v3.0
* This 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 Timm Fitschen <t.fitschen@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
@@ -17,27 +18,52 @@
*
* 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/>.
- *
- * ** end header
*/
DROP PROCEDURE IF EXISTS db_5_0.initBackReference;
DELIMITER //
-CREATE PROCEDURE db_5_0.initBackReference(in pid INT UNSIGNED, in pname VARCHAR(255), in entity_id INT UNSIGNED, in ename VARCHAR(255))
+
+/*
+ * Create and initialize two new temporary tables.
+ *
+ * This is used to initialize the filterin for backreferences to a
+ * particular entity (specified by EntityID or EntityName) or using a
+ * particular property (specified by PropertyID or PropertyName).
+ *
+ * The propertiesTable contains all properties matching the PropertyID or
+ * PropertyName. The entitiesTable contains all entities matching EntityID or
+ * EntityName.
+
+ * Parameters
+ * ----------
+ * PropertyID : VARCHAR(255)
+ * The property's (external) id.
+ * PropertyName : VARCHAR(255)
+ * The property's name.
+ * EntityID : VARCHAR(255)
+ * The entity's (external) id.
+ * EntityName : VARCHAR(255)
+ * The entity's name.
+ *
+ * Select
+ * ------
+ * Tuple (propertiesTable, entitiesTable)
+ */
+CREATE PROCEDURE db_5_0.initBackReference(in PropertyID VARCHAR(255), in PropertyName VARCHAR(255), in EntityID VARCHAR(255), in EntityName VARCHAR(255))
BEGIN
DECLARE propertiesTable VARCHAR(255) DEFAULT NULL;
DECLARE entitiesTable VARCHAR(255) DEFAULT NULL;
- IF pname IS NOT NULL THEN
+ IF PropertyName IS NOT NULL THEN
-- TODO versioning for properties
call createTmpTable(propertiesTable, FALSE);
- call initSubEntity(pid, pname, propertiesTable);
+ call initSubEntity(PropertyID, PropertyName, propertiesTable);
END IF;
- IF ename IS NOT NULL THEN
+ IF EntityName IS NOT NULL THEN
-- TODO versioning for referencing entities
call createTmpTable(entitiesTable, FALSE);
- call initSubEntity(entity_id, ename, entitiesTable);
+ call initSubEntity(EntityID, EntityName, entitiesTable);
END IF;
SELECT propertiesTable, entitiesTable;
diff --git a/procedures/query/initEntity.sql b/procedures/query/initEntity.sql
index cb7822b8426d95dad2c159a23deaa1882c46cd78..cd1d35b1a4301b978ecc6bbd70653d222f949c96 100644
--- a/procedures/query/initEntity.sql
+++ b/procedures/query/initEntity.sql
@@ -30,7 +30,7 @@ DELIMITER //
* If `versioned` is `TRUE`, also add archived entities (for example if the name was changed in the
* past).
*/
-CREATE PROCEDURE db_5_0.initEntity(in eid INT UNSIGNED, in ename VARCHAR(255),
+CREATE PROCEDURE db_5_0.initEntity(in eid VARCHAR(255), in ename VARCHAR(255),
in enameLike VARCHAR(255), in enameRegexp VARCHAR(255),
in resultset VARCHAR(255), in versioned BOOLEAN)
initEntityLabel: BEGIN
@@ -78,11 +78,12 @@ initEntityLabel: BEGIN
'INSERT IGNORE INTO `',
resultset,
IF(versioned,
- '` (id, _iversion) SELECT id, _get_head_iversion(id) ',
- '` (id) SELECT id '),
- 'FROM entities WHERE id=',eid,';');
+ '` (id, _iversion) SELECT eids.internal_id, _get_head_iversion(eids.internal_id) ',
+ '` (id) SELECT eids.internal_id '),
+ 'FROM entity_ids AS eids WHERE eids.id=?;');
+ SET @query_param = eid;
PREPARE initEntityStmt FROM @initEntityStmtStr;
- EXECUTE initEntityStmt;
+ EXECUTE initEntityStmt USING @query_param;
DEALLOCATE PREPARE initEntityStmt;
END IF;
diff --git a/procedures/query/initPOV.sql b/procedures/query/initPOV.sql
index f5c1d1d95d63bde8d18de8f6065ded150213594c..4f132219c3c0dc9fdea76a76f943199551d6f079 100644
--- a/procedures/query/initPOV.sql
+++ b/procedures/query/initPOV.sql
@@ -1,9 +1,10 @@
/*
- * ** header v3.0
* This 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 Timm Fitschen <t.fitschen@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
@@ -17,15 +18,32 @@
*
* 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/>.
- *
- * ** end header
*/
DELIMITER //
DROP PROCEDURE IF EXISTS db_5_0.initPOVPropertiesTable//
-CREATE PROCEDURE db_5_0.initPOVPropertiesTable(in pid INT UNSIGNED, in pname VARCHAR(255), in sourceSet VARCHAR(255))
+/*
+ * Create and initialize a new temporary table.
+ *
+ * This is used to initialize the POV filtering. The resulting table
+ * contains all properties matching the Property component of the POV filter.
+ *
+ * Parameters
+ * ----------
+ * PropertyID : VARCHAR(255)
+ * The property's (external) id.
+ * PropertyName : VARCHAR(255)
+ * The property's name.
+ * sourceSet : VARCHAR(255)
+ * The name of the table which will be filtered by the POV filter.
+ *
+ * Select
+ * ------
+ * Tuple (propertiesTable, ... and a lot of debug output)
+ */
+CREATE PROCEDURE db_5_0.initPOVPropertiesTable(in PropertyID VARCHAR(255), in PropertyName VARCHAR(255), in sourceSet VARCHAR(255))
BEGIN
DECLARE propertiesTable VARCHAR(255) DEFAULT NULL; /*table for property ids*/
DECLARE replTbl VARCHAR(255) DEFAULT NULL;
@@ -38,24 +56,31 @@ BEGIN
DECLARE t6 BIGINT DEFAULT 0;
- IF pname is NOT NULL THEN
+ IF PropertyName is NOT NULL THEN
SELECT conv( concat( substring(uid,16,3), substring(uid,10,4), substring(uid,1,8)),16,10) div 10000 - (141427 * 24 * 60 * 60 * 1000) as current_mills INTO t1 from (select uuid() uid) as alias;
call createTmpTable2(propertiesTable);
- -- fill in all properties named "pname"
+ -- Fill in all properties (plus the domain id and entity id) named
+ -- "PropertyName", be it their default name or their overridden name.
+ -- We need *all* properties (mind, the properties of entities not
+ -- abstract properties) with the given name. If an abstract
+ -- property has the name "person" it might have the name "author" in
+ -- the "Article" record type. Now, if I want to collect all properties
+ -- of the Article named "author" I need to look into the name_overrides
+ -- table.
SET @initPOVPropertiesTableStmt1 = CONCAT('INSERT IGNORE INTO `', propertiesTable, '` (id, id2, domain) SELECT property_id, entity_id, domain_id from name_overrides WHERE name = ? UNION ALL SELECT entity_id, domain_id, 0 FROM name_data WHERE value = ?;');
PREPARE stmt FROM @initPOVPropertiesTableStmt1;
- SET @pname = pname;
- EXECUTE stmt USING @pname, @pname;
+ SET @PropertyName = PropertyName;
+ EXECUTE stmt USING @PropertyName, @PropertyName;
SET ecount = ROW_COUNT();
- -- fill in all properties with id="pid"
+ -- fill in all properties with id="PropertyID"
SELECT conv( concat( substring(uid,16,3), substring(uid,10,4), substring(uid,1,8)),16,10) div 10000 - (141427 * 24 * 60 * 60 * 1000) as current_mills INTO t2 from (select uuid() uid) as alias;
- IF pid IS NOT NULL THEN
+ IF PropertyID IS NOT NULL THEN
SET @initPOVPropertiesTableStmt2 = CONCAT('INSERT IGNORE INTO `', propertiesTable, '` (id, id2, domain) VALUES (?, 0, 0)');
PREPARE stmt FROM @initPOVPropertiesTableStmt2;
- SET @pid = pid;
- EXECUTE stmt USING @pid;
+ SET @PropertyID = PropertyID;
+ EXECUTE stmt USING @PropertyID;
SET ecount = ecount + ROW_COUNT();
END IF;
@@ -91,15 +116,33 @@ END //
DROP PROCEDURE IF EXISTS db_5_0.initPOVRefidsTable //
-CREATE PROCEDURE db_5_0.initPOVRefidsTable(in vInt INT UNSIGNED, in vText VARCHAR(255))
+/*
+ * Create and initialize a new temporary table.
+ *
+ * This used to initialize the POV filtering. The resulting table
+ * contains all entities matching the Value component of the POV filter (i.e.
+ * the referenced entities).
+ *
+ * Parameters
+ * ----------
+ * PropertyID : VARCHAR(255)
+ * The property's (external) id.
+ * PropertyName : VARCHAR(255)
+ * The property's name.
+ *
+ * Select
+ * ------
+ * Tuple (refIdsTable)
+ */
+CREATE PROCEDURE db_5_0.initPOVRefidsTable(in PropertyID VARCHAR(255), in PropertyName VARCHAR(255))
BEGIN
DECLARE refIdsTable VARCHAR(255) DEFAULT NULL; /*table for referenced entity ids*/
#-- for reference properties: the value is interpreted as a record type name.
- IF vText IS NOT NULL THEN
+ IF PropertyName IS NOT NULL THEN
-- TODO versioned queries
call createTmpTable(refIdsTable, FALSE);
- call initSubEntity(vInt, vText, refIdsTable);
+ call initSubEntity(PropertyID, PropertyName, refIdsTable);
#-- now, all ids are in the refIdsTable
END IF;
SELECT refIdsTable;
diff --git a/procedures/query/initSubEntity.sql b/procedures/query/initSubEntity.sql
index 27fa2b0669bb8d4d776fce8baf0583bf5b8039b8..a6c4955954908699710849f1cc12e4f45b101c30 100644
--- a/procedures/query/initSubEntity.sql
+++ b/procedures/query/initSubEntity.sql
@@ -1,9 +1,10 @@
/*
- * ** header v3.0
* This 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 Timm Fitschen <t.fitschen@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
@@ -17,20 +18,35 @@
*
* 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/>.
- *
- * ** end header
*/
DROP PROCEDURE IF EXISTS db_5_0.initSubEntity;
DELIMITER //
-
-CREATE PROCEDURE db_5_0.initSubEntity(in e_id INT UNSIGNED, in ename VARCHAR(255), in tableName VARCHAR(255))
+/*
+ * Initialize a new temporary table by loading an entity (by name or by id or
+ * both) and all of its children into the table (i.e. their internal ids).
+ *
+ * The table name has to be provided.
+ *
+ * This is used by initPOVRefidsTable and initBackReference for sub-property filtering.
+ *
+ * Parameters
+ * ----------
+ * EntityID : VARCHAR(255)
+ * The entity's (external) id.
+ * EntityName : VARCHAR(255)
+ * The entity's name.
+ * tableName : VARCHAR(255)
+ * The table which is to be initialized.
+ */
+CREATE PROCEDURE db_5_0.initSubEntity(in EntityID VARCHAR(255), in ename VARCHAR(255), in tableName VARCHAR(255))
BEGIN
DECLARE ecount INT DEFAULT 0;
DECLARE op VARCHAR(255) DEFAULT '=';
+
IF LOCATE("%", ename) > 0 THEN
SET op = "LIKE";
END IF;
@@ -47,10 +63,11 @@ BEGIN
SET ecount = ROW_COUNT();
DEALLOCATE PREPARE stmt;
- IF e_id IS NOT NULL THEN
- SET @stmtStr = CONCAT('INSERT IGNORE INTO `', tableName, '` (id) VALUES (', e_id, ')');
+ IF EntityID IS NOT NULL THEN
+ SET @stmtStr = CONCAT('INSERT IGNORE INTO `', tableName, '` (id) SELECT internal_id FROM entity_ids WHERE id = ?');
PREPARE stmt FROM @stmtStr;
- EXECUTE stmt;
+ SET @eid = EntityID;
+ EXECUTE stmt USING @eid;
SET ecount = ecount + ROW_COUNT();
DEALLOCATE PREPARE stmt;
END IF;
diff --git a/procedures/registerSubdomain.sql b/procedures/registerReplacementIds.sql
similarity index 70%
rename from procedures/registerSubdomain.sql
rename to procedures/registerReplacementIds.sql
index 03b0111dbcffea357ddadd8f1c4a1e842e7ad1a4..18d7082319866603a9abda158d357781112be37c 100644
--- a/procedures/registerSubdomain.sql
+++ b/procedures/registerReplacementIds.sql
@@ -1,9 +1,10 @@
/*
- * ** header v3.0
* This 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 <www.indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@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
@@ -17,33 +18,25 @@
*
* 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/>.
- *
- * ** end header
*/
-
-
-
-
-
-
-
-
DROP PROCEDURE IF EXISTS db_5_0.registerSubdomain;
+DROP PROCEDURE IF EXISTS db_5_0.registerReplacementIds;
delimiter //
-CREATE PROCEDURE db_5_0.registerSubdomain(in amount INT UNSIGNED)
+CREATE PROCEDURE db_5_0.registerReplacementIds(in amount INT UNSIGNED)
BEGIN
DECLARE ED INTEGER DEFAULT NULL;
- SELECT COUNT(id) INTO ED FROM entities WHERE Role='DOMAIN' AND id!=0;
+ SELECT COUNT(id) INTO ED FROM entities WHERE Role='_REPLACEMENT' AND id!=0;
WHILE ED < amount DO
INSERT INTO entities (description, role, acl) VALUES
- (NULL, 'DOMAIN', 0);
+ (NULL, '_REPLACEMENT', 0);
+
SET ED = ED + 1;
END WHILE;
- SELECT id as DomainID FROM entities WHERE Role='DOMAIN' and id!=0;
+ SELECT CONCAT("$", e.id) as ReplacementID FROM entities AS e WHERE e.Role='_REPLACEMENT' and e.id!=0;
END;
//
diff --git a/procedures/retrieveDatatype.sql b/procedures/retrieveDatatype.sql
deleted file mode 100644
index 1a32d7f92a23b88dce5b71efc6e10d4dc733f1a8..0000000000000000000000000000000000000000
--- a/procedures/retrieveDatatype.sql
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the LinkAhead Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * 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/>.
- *
- * ** end header
- */
-
-
-
-
-
-
-
-DROP PROCEDURE IF EXISTS db_5_0.retrieveDatatype;
-delimiter //
-CREATE PROCEDURE db_5_0.retrieveDatatype(in DatatypeName VARCHAR(255))
-BEGIN
-
-Select e.id INTO @DatatypeID from entities e where e.name=DatatypeName AND e.role='DATATYPE' LIMIT 1;
-
-call retrieveEntity(@DatatypeID);
-
-
-
-
-END;
-//
-delimiter ;
diff --git a/procedures/retrieveEntity.sql b/procedures/retrieveEntity.sql
index 8ecfea0c787f165970fe0cbf22e344dd0c7398c3..3e0aeb580cdb3ff26da6bee6167b9ba5ad63a94d 100644
--- a/procedures/retrieveEntity.sql
+++ b/procedures/retrieveEntity.sql
@@ -1,11 +1,10 @@
/*
- * ** header v3.0
* This 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) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@indiscale>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -19,8 +18,6 @@
*
* 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/>.
- *
- * ** end header
*/
@@ -36,30 +33,40 @@ drop procedure if exists db_5_0.retrieveEntity //
*
* Parameters
* ----------
- * EntityID
+ * EntityID : VARCHAR(255)
* The entity's id.
- * Version
+ * Version : VARBINARY(255)
* The version id. In this procedure only, the version may also be given as
* `HEAD` for the latest version or as `HEAD~n`, which retrieves the n-th
* ancestor of `HEAD`.
*
* ResultSet
* ---------
- * Tuple of (Datatype, Collection, EntityID, EntityName, EntityDesc,
- * EntityRole, FileSize, FilePath, FileHash, ACL, Version)
+ * Tuple of (DatatypeID, DatatypeName, Collection, EntityID, EntityName,
+ * EntityDesc, EntityRole, FileSize, FilePath, FileHash, ACL,
+ * Version)
*/
create procedure db_5_0.retrieveEntity(
- in EntityID INT UNSIGNED,
+ in EntityID VARCHAR(255),
in Version VARBINARY(255))
retrieveEntityBody: BEGIN
DECLARE FilePath VARCHAR(255) DEFAULT NULL;
DECLARE FileSize VARCHAR(255) DEFAULT NULL;
DECLARE FileHash VARCHAR(255) DEFAULT NULL;
- DECLARE DatatypeID INT UNSIGNED DEFAULT NULL;
+ DECLARE DatatypeID VARCHAR(255) DEFAULT NULL;
+ DECLARE InternalDatatypeID INT UNSIGNED DEFAULT NULL;
DECLARE CollectionName VARCHAR(255) DEFAULT NULL;
DECLARE IsHead BOOLEAN DEFAULT TRUE;
DECLARE IVersion INT UNSIGNED DEFAULT NULL;
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID from entity_ids WHERE id = EntityID;
+ IF InternalEntityID IS NULL THEN
+ -- RETURN EARLY - Entity does not exist.
+ SELECT 0 FROM entities WHERE 0 = 1;
+ LEAVE retrieveEntityBody;
+ END IF;
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
-- Find out head-ness and version
@@ -73,7 +80,7 @@ retrieveEntityBody: BEGIN
END IF;
IF IsHead IS FALSE THEN
- SET IVersion=get_iversion(EntityID, Version);
+ SET IVersion=get_iversion(InternalEntityID, Version);
IF IVersion IS NULL THEN
-- RETURN EARLY - Version does not exist.
@@ -84,16 +91,16 @@ retrieveEntityBody: BEGIN
SELECT path, size, HEX(hash)
INTO FilePath, FileSize, FileHash
FROM archive_files
- WHERE file_id = EntityID
+ WHERE file_id = InternalEntityID
AND _iversion = IVersion
LIMIT 1;
SELECT datatype
- INTO DatatypeID
+ INTO InternalDatatypeID
FROM archive_data_type
WHERE domain_id = 0
AND entity_id = 0
- AND property_id = EntityID
+ AND property_id = InternalEntityID
AND _iversion = IVersion
LIMIT 1;
@@ -102,7 +109,7 @@ retrieveEntityBody: BEGIN
FROM archive_collection_type
WHERE domain_id = 0
AND entity_id = 0
- AND property_id = EntityID
+ AND property_id = InternalEntityID
AND _iversion = IVersion
LIMIT 1;
@@ -111,18 +118,17 @@ retrieveEntityBody: BEGIN
( SELECT value FROM
( SELECT value FROM name_data
WHERE domain_id = 0
- AND entity_ID = DatatypeID
+ AND entity_id = InternalDatatypeID
AND property_id = 20
- UNION SELECT DatatypeID AS value
- ) AS tmp LIMIT 1 ) AS Datatype,
+ ) AS tmp LIMIT 1 ) AS DatatypeName,
+ ( SELECT id FROM entity_ids WHERE internal_id=InternalDatatypeID ) AS DatatypeID,
CollectionName AS Collection,
EntityID AS EntityID,
( SELECT value FROM archive_name_data
WHERE domain_id = 0
- AND entity_ID = EntityID
+ AND entity_ID = InternalEntityID
AND property_id = 20
AND _iversion = IVersion
- -- LIMIT 1 -- TODO Remove this line if all tests pass.
) AS EntityName,
e.description AS EntityDesc,
e.role AS EntityRole,
@@ -132,7 +138,7 @@ retrieveEntityBody: BEGIN
(SELECT acl FROM entity_acl AS a WHERE a.id = e.acl) AS ACL,
Version AS Version
FROM archive_entities AS e
- WHERE e.id = EntityID
+ WHERE e.id = InternalEntityID
AND e._iversion = IVersion
LIMIT 1;
@@ -145,33 +151,34 @@ retrieveEntityBody: BEGIN
SELECT path, size, hex(hash)
INTO FilePath, FileSize, FileHash
FROM files
- WHERE file_id = EntityID
+ WHERE file_id = InternalEntityID
LIMIT 1;
- SELECT datatype INTO DatatypeID
- FROM data_type
- WHERE domain_id=0
- AND entity_id=0
- AND property_id=EntityID
+ SELECT dt.datatype INTO InternalDatatypeID
+ FROM data_type as dt
+ WHERE dt.domain_id=0
+ AND dt.entity_id=0
+ AND dt.property_id=InternalEntityID
LIMIT 1;
SELECT collection INTO CollectionName
FROM collection_type
WHERE domain_id=0
AND entity_id=0
- AND property_id=EntityID
+ AND property_id=InternalEntityID
LIMIT 1;
SELECT
( SELECT value FROM name_data
WHERE domain_id = 0
- AND entity_ID = DatatypeID
- AND property_id = 20 LIMIT 1 ) AS Datatype,
+ AND entity_id = InternalDatatypeID
+ AND property_id = 20 LIMIT 1 ) AS DatatypeName,
+ ( SELECT id FROM entity_ids WHERE internal_id=InternalDatatypeID ) AS DatatypeID,
CollectionName AS Collection,
EntityID AS EntityID,
( SELECT value FROM name_data
WHERE domain_id = 0
- AND entity_ID = EntityID
+ AND entity_ID = InternalEntityID
AND property_id = 20 LIMIT 1) AS EntityName,
e.description AS EntityDesc,
e.role AS EntityRole,
@@ -180,7 +187,7 @@ retrieveEntityBody: BEGIN
FileHash AS FileHash,
(SELECT acl FROM entity_acl AS a WHERE a.id = e.acl) AS ACL,
Version AS Version
- FROM entities e WHERE id = EntityID LIMIT 1;
+ FROM entities e WHERE id = InternalEntityID LIMIT 1;
END;
//
diff --git a/procedures/retrieveEntityOverrides.sql b/procedures/retrieveEntityOverrides.sql
index ab3d1c11f34977fcea63f6d0b572c235366c19a7..d66e60a6bd8dbe509ff989522cc4e84b38b6f8cc 100644
--- a/procedures/retrieveEntityOverrides.sql
+++ b/procedures/retrieveEntityOverrides.sql
@@ -1,11 +1,10 @@
/*
- * ** header v3.0
* This 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) 2020 Indiscale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020,2023 Indiscale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@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
@@ -19,25 +18,61 @@
*
* 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/>.
- *
- * ** end header
*/
DROP PROCEDURE IF EXISTS db_5_0.retrieveOverrides;
delimiter //
+/*
+ * Retrieve the overridden (overriding the Abstract Property's) name, description, and datatype.
+ *
+ * Parameters
+ * ----------
+ *
+ * DomainID : VARCHAR(255)
+ * The domain id (0 or the entity'id for level-2-data)
+ * EntityID : VARCHAR(255)
+ * The entity id (or the property'id for level-2-data)
+ * Version : VARBINARY(255)
+ * The version of the entity. Optional
+ *
+ * ResultSet
+ * ---------
+ * collection_override, # e.g. LIST
+ * name_override, # the name
+ * desc_override, # the description
+ * type_name_override, # the datatype, e.g. DOUBLE
+ * type_id_override, # data type id.
+ * entity_id, # same as input EntityID
+ * InternalPropertyID, # internal property id, to be used when property_id
+ * # is NULL because a replacement is used.
+ * property_id, # the property id
+ */
CREATE PROCEDURE db_5_0.retrieveOverrides(
- in DomainID INT UNSIGNED,
- in EntityID INT UNSIGNED,
+ in DomainID VARCHAR(255),
+ in EntityID VARCHAR(255),
in Version VARBINARY(255))
retrieveOverridesBody: BEGIN
DECLARE IVersion INT UNSIGNED DEFAULT NULL;
DECLARE IsHead BOOLEAN DEFAULT TRUE;
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+ DECLARE InternalDomainID INT UNSIGNED DEFAULT 0;
+
+ -- When DomainID != 0 the EntityID could possibly be a 'replacement id'
+ -- which are internal ids by definition (and do not have external
+ -- equivalents).
+ IF LOCATE("$", EntityID) = 1 THEN
+ SET InternalEntityID=SUBSTRING(EntityID, 2);
+ ELSE
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+ END IF;
+ -- DomainID != 0 are always normal (i.e. external) Entity ids.
+ SELECT internal_id INTO InternalDomainID from entity_ids WHERE id = DomainID;
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
IF Version IS NOT NULL THEN
- IF DomainID = 0 THEN
+ IF InternalDomainID = 0 THEN
SELECT get_head_version(EntityID) = Version INTO IsHead;
ELSE
SELECT get_head_version(DomainID) = Version INTO IsHead;
@@ -47,8 +82,8 @@ retrieveOverridesBody: BEGIN
IF IsHead IS FALSE THEN
SELECT e._iversion INTO IVersion
FROM entity_version as e
- WHERE ((e.entity_id = EntityID AND DomainID = 0)
- OR (e.entity_id = DomainID))
+ WHERE ((e.entity_id = InternalEntityID AND InternalDomainID = 0)
+ OR (e.entity_id = InternalDomainID))
AND e.version = Version;
IF IVersion IS NULL THEN
@@ -61,12 +96,14 @@ retrieveOverridesBody: BEGIN
NULL AS collection_override,
name AS name_override,
NULL AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
+ NULL AS type_name_override,
+ NULL AS type_id_override,
+ EntityID AS entity_id,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS property_id
FROM archive_name_overrides
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion
UNION ALL
@@ -76,12 +113,14 @@ retrieveOverridesBody: BEGIN
NULL AS collection_override,
NULL AS name_override,
description AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
+ NULL AS type_name_override,
+ NULL AS type_id_override,
+ EntityID AS entity_id,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS property_id
FROM archive_desc_overrides
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion
UNION ALL
@@ -91,16 +130,18 @@ retrieveOverridesBody: BEGIN
NULL AS collection_override,
NULL AS name_override,
NULL AS desc_override,
- IFNULL((SELECT value FROM name_data
+ (SELECT value FROM name_data
WHERE domain_id = 0
AND entity_id = datatype
AND property_id = 20
- LIMIT 1), datatype) AS type_override,
- entity_id,
- property_id
+ LIMIT 1) AS type_name_override,
+ (SELECT id FROM entity_ids WHERE internal_id = datatype) AS type_id_override,
+ EntityID AS entity_id,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS property_id
FROM archive_data_type
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion
UNION ALL
@@ -110,12 +151,14 @@ retrieveOverridesBody: BEGIN
collection AS collection_override,
NULL AS name_override,
NULL AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
+ NULL AS type_name_override,
+ NULL AS type_id_override,
+ EntityID AS entity_id,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS property_id
FROM archive_collection_type
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion;
LEAVE retrieveOverridesBody;
@@ -126,12 +169,14 @@ retrieveOverridesBody: BEGIN
NULL AS collection_override,
name AS name_override,
NULL AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
+ NULL AS type_name_override,
+ NULL AS type_id_override,
+ EntityID AS entity_id,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS property_id
FROM name_overrides
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
UNION ALL
@@ -139,12 +184,14 @@ retrieveOverridesBody: BEGIN
NULL AS collection_override,
NULL AS name_override,
description AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
+ NULL AS type_name_override,
+ NULL AS type_id_override,
+ EntityID AS entity_id,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS property_id
FROM desc_overrides
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
UNION ALL
@@ -152,15 +199,17 @@ retrieveOverridesBody: BEGIN
NULL AS collection_override,
NULL AS name_override,
NULL AS desc_override,
- IFNULL((SELECT value FROM name_data
+ (SELECT value FROM name_data
WHERE domain_id = 0
AND entity_ID = datatype
- AND property_id = 20 LIMIT 1), datatype) AS type_override,
- entity_id,
- property_id
+ AND property_id = 20 LIMIT 1) AS type_name_override,
+ (SELECT id FROM entity_ids WHERE internal_id = datatype) AS type_id_override,
+ EntityID AS entity_id,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS property_id
FROM data_type
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
UNION ALL
@@ -168,12 +217,14 @@ retrieveOverridesBody: BEGIN
collection AS collection_override,
NULL AS name_override,
NULL AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
+ NULL AS type_name_override,
+ NULL AS type_id_override,
+ EntityID AS entity_id,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS property_id
FROM collection_type
- WHERE domain_id = DomainID
- AND entity_id = EntityID;
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID;
END;
diff --git a/procedures/retrieveEntityParents.sql b/procedures/retrieveEntityParents.sql
index c1378197b12b833b54f8fb22d41cb2d8ee2aa21e..5895a233a63bf51ac597b2e3c80a722e821a2f6c 100644
--- a/procedures/retrieveEntityParents.sql
+++ b/procedures/retrieveEntityParents.sql
@@ -1,11 +1,10 @@
/*
- * ** header v3.0
* This 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) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@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
@@ -19,8 +18,6 @@
*
* 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/>.
- *
- * ** end header
*/
@@ -28,37 +25,35 @@ DROP PROCEDURE IF EXISTS db_5_0.retrieveEntityParents;
DELIMITER //
/* Retrieve the parents of an Entity.
-
-Parameters
-==========
-
-EntityID : UNSIGNED
-Child entity for which all parental relations should be deleted.
-
-Returns
-=======
-ParentID : INT UNSIGNED
- Each parent's ID
-
-ParentName :
- The parent's name.
-
-ParentDescription :
- The parent's description.
-
-ParentRole :
- The parent's Role.
-
-ACL :
- Access control list something
+ *
+ * Parameters
+ * ----------
+ * EntityID : VARCHAR(255)
+ * Child entity for which all parental relations should be deleted.
+ *
+ * ResultSet
+ * ---------
+ * ParentID : VARCHAR(255)
+ * Each parent's ID
+ * ParentName : VARCHAR(255)
+ * The parent's name.
+ * ParentDescription : TEXT
+ * The parent's description.
+ * ParentRole : VARCHAR(255)
+ * The parent's Role.
+ * ACL : VARBINARY(65525)
+ * Access control list.
*/
CREATE PROCEDURE db_5_0.retrieveEntityParents(
- in EntityID INT UNSIGNED,
+ in EntityID VARCHAR(255),
in Version VARBINARY(255))
retrieveEntityParentsBody: BEGIN
DECLARE IVersion INT UNSIGNED DEFAULT NULL;
DECLARE IsHead BOOLEAN DEFAULT TRUE;
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID from entity_ids WHERE id = EntityID;
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
IF Version IS NOT NULL THEN
@@ -68,7 +63,7 @@ retrieveEntityParentsBody: BEGIN
IF IsHead IS FALSE THEN
SELECT e._iversion INTO IVersion
FROM entity_version as e
- WHERE e.entity_id = EntityID
+ WHERE e.entity_id = InternalEntityID
AND e.version = Version;
IF IVersion IS NULL THEN
@@ -77,10 +72,10 @@ retrieveEntityParentsBody: BEGIN
END IF;
SELECT
- i.parent AS ParentID,
+ ( SELECT id FROM entity_ids WHERE internal_id = i.parent) AS ParentID,
( SELECT value FROM name_data
WHERE domain_id = 0
- AND entity_id = ParentID
+ AND entity_id = i.parent
AND property_id = 20
) AS ParentName, -- This is not necessarily the name of the parent at the time of
-- IVersion but it is a good guess. Future implementations of the
@@ -92,7 +87,7 @@ retrieveEntityParentsBody: BEGIN
(SELECT acl FROM entity_acl AS a WHERE a.id = e.acl) AS ACL
FROM archive_isa AS i JOIN entities AS e
ON (i.parent = e.id)
- WHERE i.child = EntityID
+ WHERE i.child = InternalEntityID
AND i.child_iversion = IVersion
AND i.direct IS TRUE
;
@@ -102,18 +97,18 @@ retrieveEntityParentsBody: BEGIN
END IF;
SELECT
- i.parent AS ParentID,
+ ( SELECT id FROM entity_ids WHERE internal_id = i.parent) AS ParentID,
( SELECT value FROM name_data
WHERE domain_id = 0
- AND entity_id = ParentID
+ AND entity_id = i.parent
AND property_id = 20 ) AS ParentName,
e.description AS ParentDescription,
e.role AS ParentRole,
(SELECT acl FROM entity_acl AS a WHERE a.id = e.acl) AS ACL
FROM isa_cache AS i JOIN entities AS e
ON (i.parent = e.id)
- WHERE i.child = EntityID
- AND i.rpath = EntityID;
+ WHERE i.child = InternalEntityID
+ AND i.rpath = InternalEntityID;
END
//
diff --git a/procedures/retrieveEntityProperties.sql b/procedures/retrieveEntityProperties.sql
index 5eee63c6c8eb1353135bf269fe86bc10a7baa89c..7918f0eb3669b11ddcb1c1fd0e651fe3fd69b276 100644
--- a/procedures/retrieveEntityProperties.sql
+++ b/procedures/retrieveEntityProperties.sql
@@ -1,11 +1,10 @@
/*
- * ** header v3.0
* This 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) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020-2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@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
@@ -19,8 +18,6 @@
*
* 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/>.
- *
- * ** end header
*/
@@ -28,30 +25,70 @@ delimiter //
drop procedure if exists db_5_0.retrieveEntityProperties //
+/*
+ * Retrieve the properties of an entity (level 1 and 2).
+ *
+ * Parameters
+ * ----------
+ *
+ * DomainID : VARCHAR(255)
+ * The domain id (0 or the entity's id for level-2-data)
+ * EntityID : VARCHAR(255)
+ * The entity id (or the property's id for level-2-data)
+ * Version : VARBINARY(255)
+ * The version of the entity. Optional
+ *
+ * ResultSet
+ * ---------
+ * InternalPropertyID
+ * Internal property id, to be used when PropertyID
+ * is NULL because a replacement is used.
+ * PropertyID
+ * The property id
+ * PropertyValue
+ * The property value
+ * PropertyStatus
+ * E.g. OBLIGATORY, FIX, ...
+ * PropertyIndex
+ * The index of the property (for ordering).
+ * )
+ */
create procedure db_5_0.retrieveEntityProperties(
- in DomainID INT UNSIGNED,
- in EntityID INT UNSIGNED,
+ in DomainID VARCHAR(255),
+ in EntityID VARCHAR(255),
in Version VARBINARY(255))
retrieveEntityPropertiesBody: BEGIN
DECLARE IVersion INT UNSIGNED DEFAULT NULL;
DECLARE IsHead BOOLEAN DEFAULT TRUE;
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+ DECLARE InternalDomainID INT UNSIGNED DEFAULT 0;
+
+ -- When DomainID != 0 the EntityID could possibly be a 'replacement id'
+ -- which are internal ids by definition (and do not have external
+ -- equivalents).
+ IF LOCATE("$", EntityID) = 1 THEN
+ SET InternalEntityID=SUBSTRING(EntityID, 2);
+ ELSE
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+ END IF;
+ -- DomainID != 0 are always normal (i.e. external) Entity ids.
+ SELECT internal_id INTO InternalDomainID from entity_ids WHERE id = DomainID;
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
IF Version IS NOT NULL THEN
- IF DomainID = 0 THEN
+ IF InternalDomainID = 0 THEN
SELECT get_head_version(EntityID) = Version INTO IsHead;
ELSE
SELECT get_head_version(DomainID) = Version INTO IsHead;
END IF;
-
END IF;
IF IsHead IS FALSE THEN
SELECT e._iversion INTO IVersion
FROM entity_version as e
- WHERE ((e.entity_id = EntityID AND DomainID = 0)
- OR (e.entity_id = DomainID))
+ WHERE ((e.entity_id = InternalEntityID AND InternalDomainID = 0)
+ OR (e.entity_id = InternalDomainID))
AND e.version = Version;
IF IVersion IS NULL THEN
@@ -61,121 +98,135 @@ retrieveEntityPropertiesBody: BEGIN
#-- double properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
value AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM archive_double_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion
UNION ALL
#-- integer properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
value AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM archive_integer_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion
UNION ALL
#-- date properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
CONCAT(value, '.NULL.NULL') AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM archive_date_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion
UNION ALL
#-- datetime properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
CONCAT(value, 'UTC', IF(value_ns IS NULL, '', value_ns))
AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM archive_datetime_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion
UNION ALL
#-- text properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
value AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM archive_text_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion
UNION ALL
#-- enum properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
value AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM archive_enum_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion
UNION ALL
#-- reference properties
SELECT
- property_id AS PropertyID,
- IF(value_iversion IS NULL, value,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
+ IF(value_iversion IS NULL,
+ IF(status = "REPLACEMENT",
+ CONCAT("$", value),
+ ( SELECT id FROM entity_ids WHERE internal_id = value )),
-- make it "value@version" if necessary
- CONCAT(value, "@", _get_version(value, value_iversion)))
+ CONCAT(
+ ( SELECT id FROM entity_ids WHERE internal_id = value ),
+ "@", _get_version(value, value_iversion)))
AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM archive_reference_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion
UNION ALL
#-- null properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
NULL AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM archive_null_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND _iversion = IVersion
UNION ALL
#-- name properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
value AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM archive_name_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND property_id != 20
AND _iversion = IVersion;
@@ -185,115 +236,129 @@ retrieveEntityPropertiesBody: BEGIN
#-- double properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
value AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM double_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
UNION ALL
#-- integer properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
value AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM integer_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
UNION ALL
#-- date properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
CONCAT(value, '.NULL.NULL') AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM date_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
UNION ALL
#-- datetime properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
CONCAT(value, 'UTC', IF(value_ns IS NULL, '', value_ns))
AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM datetime_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
UNION ALL
#-- text properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
value AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM text_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
UNION ALL
#-- enum properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
value AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM enum_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
UNION ALL
#-- reference properties
SELECT
- property_id AS PropertyID,
- IF(value_iversion IS NULL, value,
- CONCAT(value, "@", _get_version(value, value_iversion)))
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
+ IF(value_iversion IS NULL,
+ IF(status = "REPLACEMENT",
+ CONCAT("$", value),
+ ( SELECT id FROM entity_ids WHERE internal_id = value )),
+ -- make it "value@version" if necessary
+ CONCAT(
+ ( SELECT id FROM entity_ids WHERE internal_id = value ),
+ "@", _get_version(value, value_iversion)))
AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM reference_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
UNION ALL
#-- null properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
NULL AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM null_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
UNION ALL
#-- name properties
SELECT
- property_id AS PropertyID,
+ CONCAT("$", property_id) AS InternalPropertyID,
+ ( SELECT id FROM entity_ids WHERE internal_id = property_id ) AS PropertyID,
value AS PropertyValue,
status AS PropertyStatus,
pidx AS PropertyIndex
FROM name_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
+ WHERE domain_id = InternalDomainID
+ AND entity_id = InternalEntityID
AND property_id != 20;
-
END;
//
diff --git a/procedures/retrieveGroup.sql b/procedures/retrieveGroup.sql
deleted file mode 100644
index 38504b093f40da27b01d82e51d2d4e1c308745c8..0000000000000000000000000000000000000000
--- a/procedures/retrieveGroup.sql
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the LinkAhead Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * 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/>.
- *
- * ** end header
- */
-
-Drop Procedure if exists db_5_0.retrieveGroup;
diff --git a/procedures/retrieveSubentity.sql b/procedures/retrieveSubentity.sql
deleted file mode 100644
index a7f2fb6b3bea081786cd65eec9ae253cbaa4b901..0000000000000000000000000000000000000000
--- a/procedures/retrieveSubentity.sql
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the LinkAhead Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * 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/>.
- *
- * ** end header
- */
-DELIMITER //
-DROP PROCEDURE IF EXISTS db_5_0.retrieveSubEntity //
-/**
-CREATE PROCEDURE db_5_0.retrieveSubEntity(in EntityID INT UNSIGNED, in DomainID INT UNSIGNED)
-BEGIN
- DECLARE FilePath VARCHAR(255) DEFAULT NULL;
- DECLARE FileSize VARCHAR(255) DEFAULT NULL;
- DECLARE FileHash VARCHAR(255) DEFAULT NULL;
-
- Select path, size, hex(hash) into FilePath, FileSize, FileHash from files where file_id = EntityID LIMIT 1;
- Select DomainID as DomainID,
- EntityID as EntityID,
- e.name as EntityName,
- e.description as EntityDesc,
- e.role as EntityRole,
- FileSize as FileSize,
- FilePath as FilePath,
- FileHash as FileHash
- from entities e where id = EntityID LIMIT 1;
-
-END;
-//
-
-**/
-DELIMITER ;
diff --git a/procedures/setFileProperties.sql b/procedures/setFileProperties.sql
new file mode 100644
index 0000000000000000000000000000000000000000..e1efa3f4c200f37a4d1c1769ca6db1d31d27f62a
--- /dev/null
+++ b/procedures/setFileProperties.sql
@@ -0,0 +1,73 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@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
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * 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/>.
+ */
+
+DROP PROCEDURE IF EXISTS setFileProperties;
+DELIMITER //
+/**
+ * Update file properties.
+ *
+ * If ENTITY_VERSIONING is enabled the old file properties are moved to
+ * `archive_files`.
+ *
+ * Parameters
+ * ----------
+ * EntityID : VARCHAR(255)
+ * The file's id.
+ * FilePath : TEXT
+ * Path of the file in the internal file system. If NULL, an existing file
+ * entity is simply deleted.
+ * FileSize : BIGINT UNSIGNED
+ * Size of the file in bytes.
+ * FileHash : VARCHAR(255)
+ * A Sha512 Hash of the file.
+ */
+CREATE PROCEDURE setFileProperties (
+ in EntityID VARCHAR(255),
+ in FilePath TEXT,
+ in FileSize BIGINT UNSIGNED,
+ in FileHash VARCHAR(255)
+)
+BEGIN
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+ DECLARE IVersion INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID FROM entity_ids WHERE id = EntityID;
+
+ IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
+ SELECT max(e._iversion) INTO IVersion
+ FROM entity_version AS e
+ WHERE e.entity_id = InternalEntityID;
+
+ INSERT INTO archive_files (file_id, path, size, hash,
+ _iversion)
+ SELECT file_id, path, size, hash, IVersion AS _iversion
+ FROM files
+ WHERE file_id = InternalEntityID;
+ END IF;
+
+ DELETE FROM files WHERE file_id = InternalEntityID;
+
+ IF FilePath IS NOT NULL THEN
+ INSERT INTO files (file_id, path, size, hash)
+ VALUES (InternalEntityID, FilePath, FileSize, unhex(FileHash));
+ END IF;
+
+END //
+DELIMITER ;
diff --git a/procedures/setPassword.sql b/procedures/setPassword.sql
deleted file mode 100644
index 0302dd69c6eae34fe38a0dfcc8ed56a8046ec809..0000000000000000000000000000000000000000
--- a/procedures/setPassword.sql
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the LinkAhead Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * 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/>.
- *
- * ** end header
- */
-
-
-DROP PROCEDURE IF EXISTS db_5_0.setPassword;
-delimiter //
-
-CREATE PROCEDURE db_5_0.setPassword(in EntityID INT UNSIGNED, in NewPassword VARCHAR(255))
-BEGIN
-
-
- DELETE FROM passwords where entity_id=EntityID;
- INSERT INTO passwords (entity_id, password) VALUES (EntityID, NewPassword);
-
-END;
-//
-delimiter ;
diff --git a/procedures/updateEntity.sql b/procedures/updateEntity.sql
index 96a140b2354a3ba17e8c7c6a5783729c4dbee21a..bdfe05b92cccb7c424e1a5b70759a15c7d9612dc 100644
--- a/procedures/updateEntity.sql
+++ b/procedures/updateEntity.sql
@@ -1,11 +1,10 @@
/*
- * ** header v3.0
* This 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) 2020 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@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
@@ -19,8 +18,6 @@
*
* 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/>.
- *
- * ** end header
*/
DROP PROCEDURE IF EXISTS db_5_0.updateEntity;
@@ -34,11 +31,11 @@ delimiter //
* Selects the new version identifier for the entity.
*/
CREATE PROCEDURE db_5_0.updateEntity(
- in EntityID INT UNSIGNED,
+ in EntityID VARCHAR(255),
in EntityName VARCHAR(255),
in EntityDescription TEXT,
in EntityRole VARCHAR(255),
- in Datatype VARCHAR(255),
+ in DatatypeID VARCHAR(255),
in Collection VARCHAR(255),
in ACL VARBINARY(65525))
BEGIN
@@ -48,20 +45,23 @@ BEGIN
DECLARE ParentVersion VARBINARY(255) DEFAULT NULL;
DECLARE Transaction VARBINARY(255) DEFAULT NULL;
DECLARE OldIVersion INT UNSIGNED DEFAULT NULL;
+ DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
+
+ SELECT internal_id INTO InternalEntityID from entity_ids WHERE id = EntityID;
call entityACL(ACLID, ACL);
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
SELECT max(_iversion) INTO OldIVersion
FROM entity_version
- WHERE entity_id = EntityID;
+ WHERE entity_id = InternalEntityID;
-- move old data to archives
INSERT INTO archive_entities (id, description, role,
acl, _iversion)
SELECT e.id, e.description, e.role, e.acl, OldIVersion
FROM entities AS e
- WHERE e.id = EntityID;
+ WHERE e.id = InternalEntityID;
INSERT INTO archive_data_type (domain_id, entity_id, property_id,
datatype, _iversion)
@@ -70,7 +70,7 @@ BEGIN
FROM data_type AS e
WHERE e.domain_id = 0
AND e.entity_id = 0
- AND e.property_id = EntityID;
+ AND e.property_id = InternalEntityID;
INSERT INTO archive_collection_type (domain_id, entity_id, property_id,
collection, _iversion)
@@ -79,16 +79,16 @@ BEGIN
FROM collection_type as e
WHERE e.domain_id = 0
AND e.entity_id = 0
- AND e.property_id = EntityID;
+ AND e.property_id = InternalEntityID;
SET Transaction = @SRID;
SELECT e.version INTO ParentVersion
FROM entity_version as e
- WHERE e.entity_id = EntityID
+ WHERE e.entity_id = InternalEntityID
AND e._iversion = OldIVersion;
CALL insert_single_child_version(
- EntityID, Hash, Version,
+ InternalEntityID, Hash, Version,
ParentVersion, Transaction);
END IF;
@@ -96,34 +96,33 @@ BEGIN
SET e.description = EntityDescription,
e.role=EntityRole,
e.acl = ACLID
- WHERE e.id = EntityID;
+ WHERE e.id = InternalEntityID;
-- clean up primary name, because updateEntity might be called without a
-- prior call to deleteEntityProperties.
DELETE FROM name_data
- WHERE domain_id = 0 AND entity_id = EntityID AND property_id = 20;
+ WHERE domain_id = 0 AND entity_id = InternalEntityID AND property_id = 20;
IF EntityName IS NOT NULL THEN
INSERT INTO name_data
(domain_id, entity_id, property_id, value, status, pidx)
- VALUES (0, EntityID, 20, EntityName, "FIX", 0);
+ VALUES (0, InternalEntityID, 20, EntityName, "FIX", 0);
END IF;
DELETE FROM data_type
- WHERE domain_id=0 AND entity_id=0 AND property_id=EntityID;
+ WHERE domain_id=0 AND entity_id=0 AND property_id=InternalEntityID;
DELETE FROM collection_type
- WHERE domain_id=0 AND entity_id=0 AND property_id=EntityID;
+ WHERE domain_id=0 AND entity_id=0 AND property_id=InternalEntityID;
- IF Datatype IS NOT NULL THEN
+ IF DatatypeID IS NOT NULL THEN
INSERT INTO data_type (domain_id, entity_id, property_id, datatype)
- SELECT 0, 0, EntityID,
- ( SELECT entity_id FROM name_data WHERE domain_id = 0
- AND property_id = 20 AND value = Datatype LIMIT 1 );
+ SELECT 0, 0, InternalEntityID,
+ ( SELECT internal_id FROM entity_ids WHERE id = DatatypeID );
IF Collection IS NOT NULL THEN
INSERT INTO collection_type (domain_id, entity_id, property_id,
collection)
- SELECT 0, 0, EntityID, Collection;
+ SELECT 0, 0, InternalEntityID, Collection;
END IF;
END IF;
diff --git a/tests/example.dump.sql b/tests/example.dump.sql
index 014e480e7a5423093b2a9f74b14cec4a7e54ad70..1fdb96dbf1e3fc35aba9b7d9ac7ad5e2fb45ad40 100644
--- a/tests/example.dump.sql
+++ b/tests/example.dump.sql
@@ -563,31 +563,6 @@ INSERT INTO `passwd` VALUES ('guest','3fe82ca86837d4f9ff765d2d4265ded96843314936
/*!40000 ALTER TABLE `passwd` ENABLE KEYS */;
UNLOCK TABLES;
---
--- Table structure for table `passwords`
---
-
-DROP TABLE IF EXISTS `passwords`;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `passwords` (
- `entity_id` int(10) unsigned NOT NULL COMMENT 'User ID.',
- `password` varchar(255) COLLATE utf8_unicode_ci NOT NULL COMMENT 'Password.',
- PRIMARY KEY (`entity_id`),
- CONSTRAINT `use_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Dumping data for table `passwords`
---
-
-LOCK TABLES `passwords` WRITE;
-/*!40000 ALTER TABLE `passwords` DISABLE KEYS */;
-INSERT INTO `passwords` VALUES (98,'37d7bd8a833261b4e4653644ee0a065f522b92b3738ca9ae2cb43a83844bf352c4a59c386a44965997a508c61988c9484c093775027425091d6d3d435c3c0e0c'),(99,'37d7bd8a833261b4e4653644ee0a065f522b92b3738ca9ae2cb43a83844bf352c4a59c386a44965997a508c61988c9484c093775027425091d6d3d435c3c0e0c');
-/*!40000 ALTER TABLE `passwords` ENABLE KEYS */;
-UNLOCK TABLES;
-
--
-- Table structure for table `permissions`
--
@@ -668,7 +643,7 @@ CREATE TABLE `reference_data` (
LOCK TABLES `reference_data` WRITE;
/*!40000 ALTER TABLE `reference_data` DISABLE KEYS */;
-INSERT INTO `reference_data` VALUES (0,243,233,119,'REPLACEMENT',6),(0,243,119,240,'FIX',0),(0,243,232,120,'REPLACEMENT',7),(0,243,120,241,'FIX',0),(0,243,234,121,'REPLACEMENT',8),(0,243,121,242,'FIX',0),(0,265,255,230,'FIX',3),(0,265,256,243,'FIX',4),(0,265,257,119,'REPLACEMENT',6),(0,265,119,262,'FIX',0),(0,265,260,120,'REPLACEMENT',7),(0,265,120,263,'FIX',0),(0,265,259,121,'REPLACEMENT',8),(0,265,121,264,'FIX',0),(0,270,257,119,'REPLACEMENT',1),(0,270,260,120,'REPLACEMENT',2),(0,271,257,119,'REPLACEMENT',1),(0,271,119,268,'FIX',0),(0,271,260,120,'REPLACEMENT',2),(0,271,120,269,'FIX',0),(0,271,267,266,'FIX',3),(0,273,222,271,'FIX',1),(0,277,222,230,'FIX',1),(0,279,222,243,'FIX',1),(0,278,222,265,'FIX',1),(0,276,222,99,'FIX',1),(0,230,221,119,'REPLACEMENT',3),(0,230,119,226,'FIX',0),(0,230,220,120,'REPLACEMENT',4),(0,230,120,227,'FIX',0),(0,230,218,121,'REPLACEMENT',5),(0,230,121,228,'FIX',0),(0,230,219,122,'REPLACEMENT',6),(0,230,122,229,'FIX',0);
+INSERT INTO `reference_data` VALUES (0,243,233,119,'REPLACEMENT',6),(0,243,119,240,'FIX',0),(0,243,232,120,'REPLACEMENT',7),(0,243,120,241,'FIX',0),(0,243,234,121,'REPLACEMENT',8),(0,243,121,242,'FIX',0),(0,265,255,230,'FIX',3),(0,265,256,243,'FIX',4),(0,265,257,119,'REPLACEMENT',6),(0,265,119,262,'FIX',0),(0,265,260,120,'REPLACEMENT',7),(0,265,120,263,'FIX',0),(0,265,259,121,'REPLACEMENT',8),(0,265,121,264,'FIX',0),(0,270,257,119,'REPLACEMENT',1),(0,270,260,120,'REPLACEMENT',2),(0,271,257,119,'REPLACEMENT',1),(0,271,119,268,'FIX',0),(0,271,260,120,'REPLACEMENT',2),(0,271,120,269,'FIX',0),(0,271,267,266,'FIX',3),(0,273,222,271,'FIX',1),(0,277,222,230,'FIX',1),(0,279,222,243,'FIX',1),(0,278,222,265,'FIX',1),(0,230,221,119,'REPLACEMENT',3),(0,230,119,226,'FIX',0),(0,230,220,120,'REPLACEMENT',4),(0,230,120,227,'FIX',0),(0,230,218,121,'REPLACEMENT',5),(0,230,121,228,'FIX',0),(0,230,219,122,'REPLACEMENT',6),(0,230,122,229,'FIX',0);
/*!40000 ALTER TABLE `reference_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2783,34 +2758,6 @@ BEGIN
INSERT IGNORE INTO units_lin_con (signature_from, signature_to, a, b_dividend, b_divisor, c) VALUES (signature_from, signature_to, a, b_dividend, b_divisor, c);
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `insertUser` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb4 */ ;
-/*!50003 SET character_set_results = utf8mb4 */ ;
-/*!50003 SET collation_connection = utf8mb4_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `insertUser`(in Name VARCHAR(255), in Password VARCHAR(255))
-BEGIN
-
-
-INSERT INTO entities (name, role, acl) VALUES (Name, 'USER', 0);
-
-SET @LAST_UserID = LAST_INSERT_ID();
-
-INSERT INTO passwords VALUES (@LAST_UserID, Password);
-
-Select @LAST_UserID as UserID;
-
END ;;
DELIMITER ;
/*!50003 SET sql_mode = @saved_sql_mode */ ;
@@ -3168,29 +3115,6 @@ BEGIN
SELECT collection as collection_override, NULL as name_override, NULL as desc_override, NULL as type_override, entity_id, property_id from collection_type where domain_id=DomainID and entity_id=EntityID;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `setPassword` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb4 */ ;
-/*!50003 SET character_set_results = utf8mb4 */ ;
-/*!50003 SET collation_connection = utf8mb4_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `setPassword`(in EntityID INT UNSIGNED, in NewPassword VARCHAR(255))
-BEGIN
-
-
- DELETE FROM passwords where entity_id=EntityID;
- INSERT INTO passwords (entity_id, password) VALUES (EntityID, NewPassword);
-
END ;;
DELIMITER ;
/*!50003 SET sql_mode = @saved_sql_mode */ ;
diff --git a/tests/test_autotap.sql b/tests/test_autotap.sql
index ebec7304fd753261775a40a8ccfd8e765136ec0e..6d62a0ced953fddc7afe1ccc06d45ef339e8f47e 100644
--- a/tests/test_autotap.sql
+++ b/tests/test_autotap.sql
@@ -38,7 +38,11 @@ SELECT tap.has_schema('_caosdb_schema_unit_tests','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','archive_isa','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','archive_isa','utf8_unicode_ci','');
+-- *******
+-- Collation testing of tables fails for uca1400 collations, see upstream issue:
+-- https://github.com/hepabolu/mytap/issues/58
+-- *******
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','archive_isa','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','archive_isa','InnoDB','');
-- COLUMNS
@@ -116,7 +120,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','archive_isa','archive_isa_i
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','collection_type','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','collection_type','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','collection_type','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','collection_type','InnoDB','');
-- COLUMNS
@@ -155,8 +159,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','collection_type','collection'
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','collection_type','collection','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','collection_type','collection','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','collection_type','collection',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','collection_type','collection','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','collection_type','collection','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','collection_type','collection','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','collection_type','collection','utf8mb4_uca1400_as_ci','');
-- INDEXES
SELECT tap.indexes_are('_caosdb_schema_unit_tests','collection_type','`domain_id`,`entity_id`,`property_id`','');
@@ -208,7 +212,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','collection_type','collectio
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','data_type','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','data_type','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','data_type','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','data_type','InnoDB','');
-- COLUMNS
@@ -300,7 +304,7 @@ SELECT tap.constraint_type_is('_caosdb_schema_unit_tests','data_type','datatype_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','date_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','date_data','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','date_data','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','date_data','InnoDB','');
-- COLUMNS
@@ -348,8 +352,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','date_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','date_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','date_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','date_data','status','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','date_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','date_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','date_data','status','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','date_data','status','utf8mb4_uca1400_as_ci','');
-- COLUMN date_data.pidx
@@ -398,7 +402,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','date_data','date_ov_forkey_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','datetime_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','datetime_data','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','datetime_data','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','datetime_data','InnoDB','');
-- COLUMNS
@@ -437,8 +441,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','datetime_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','datetime_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','datetime_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','datetime_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','datetime_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','datetime_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','datetime_data','status','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','datetime_data','status','utf8mb4_uca1400_as_ci','');
-- COLUMN datetime_data.pidx
@@ -505,7 +509,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','datetime_data','dat_propert
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','desc_overrides','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','desc_overrides','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','desc_overrides','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','desc_overrides','InnoDB','');
-- COLUMNS
@@ -544,8 +548,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','desc_overrides','description'
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','desc_overrides','description','text','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','desc_overrides','description','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','desc_overrides','description','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','desc_overrides','description','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','desc_overrides','description','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','desc_overrides','description','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','desc_overrides','description','utf8mb4_uca1400_as_ci','');
-- INDEXES
SELECT tap.indexes_are('_caosdb_schema_unit_tests','desc_overrides','`desc_ov_dom_ent_idx`','');
@@ -590,7 +594,7 @@ SELECT tap.constraint_type_is('_caosdb_schema_unit_tests','desc_overrides','desc
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','double_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','double_data','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','double_data','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','double_data','InnoDB','');
-- COLUMNS
@@ -638,8 +642,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','double_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','double_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','double_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','double_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','double_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','double_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','double_data','status','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','double_data','status','utf8mb4_uca1400_as_ci','');
-- COLUMN double_data.pidx
@@ -697,7 +701,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','double_data','dou_property_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','entities','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entities','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entities','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','entities','InnoDB','');
-- COLUMNS
@@ -718,17 +722,17 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','entities','description','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','entities','description','text','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','entities','description','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','entities','description','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','entities','description','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','entities','description','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','entities','description','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','entities','description','utf8mb4_uca1400_as_ci','');
-- COLUMN entities.role
SELECT tap.has_column('_caosdb_schema_unit_tests','entities','role','');
-SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','entities','role','enum(\'RECORDTYPE\',\'RECORD\',\'FILE\',\'DOMAIN\',\'PROPERTY\',\'DATATYPE\',\'ROLE\',\'QUERYTEMPLATE\')','');
+SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','entities','role','enum(\'RECORDTYPE\',\'RECORD\',\'FILE\',\'_REPLACEMENT\',\'PROPERTY\',\'DATATYPE\',\'ROLE\',\'QUERYTEMPLATE\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','entities','role','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','entities','role',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','entities','role','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','entities','role','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','entities','role','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','entities','role','utf8mb4_uca1400_as_ci','');
-- COLUMN entities.acl
@@ -760,7 +764,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','entities','`id`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','entity_acl','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entity_acl','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entity_acl','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','entity_acl','InnoDB','');
-- COLUMNS
@@ -807,7 +811,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','entity_acl','`id`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','enum_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','enum_data','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','enum_data','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','enum_data','InnoDB','');
-- COLUMNS
@@ -855,8 +859,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','enum_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','enum_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','enum_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','enum_data','status','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','enum_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','enum_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','enum_data','status','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','enum_data','status','utf8mb4_uca1400_as_ci','');
-- COLUMN enum_data.pidx
@@ -905,7 +909,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','enum_data','enum_ov_forkey_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','files','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','files','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','files','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','files','InnoDB','');
-- COLUMNS
@@ -926,8 +930,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','files','path','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','files','path','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','files','path','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','files','path',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','files','path','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','files','path','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','files','path','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','files','path','utf8mb4_uca1400_as_ci','');
-- COLUMN files.size
@@ -977,7 +981,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','files','`file_id`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','integer_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','integer_data','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','integer_data','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','integer_data','InnoDB','');
-- COLUMNS
@@ -1025,8 +1029,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','integer_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','integer_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','integer_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','integer_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','integer_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','integer_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','integer_data','status','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','integer_data','status','utf8mb4_uca1400_as_ci','');
-- COLUMN integer_data.pidx
@@ -1084,7 +1088,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','integer_data','int_property
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','isa_cache','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','isa_cache','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','isa_cache','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','isa_cache','InnoDB','');
-- COLUMNS
@@ -1114,8 +1118,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','isa_cache','rpath','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','isa_cache','rpath','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','isa_cache','rpath','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','isa_cache','rpath',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','isa_cache','rpath','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','isa_cache','rpath','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','isa_cache','rpath','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','isa_cache','rpath','utf8mb4_uca1400_as_ci','');
-- CONSTRAINTS
SELECT tap.constraints_are('_caosdb_schema_unit_tests','isa_cache','`PRIMARY`,`isa_cache_child_entity`,`isa_cache_parent_entity`','');
@@ -1145,7 +1149,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','isa_cache','`child`,`parent`,`
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','name_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','name_data','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','name_data','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','name_data','InnoDB','');
-- COLUMNS
@@ -1184,8 +1188,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','name_data','value','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','name_data','value','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','name_data','value','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','name_data','value',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_data','value','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_data','value','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_data','value','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_data','value','utf8mb4_uca1400_as_ci','');
-- COLUMN name_data.status
@@ -1193,8 +1197,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','name_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','name_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','name_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','name_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_data','status','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_data','status','utf8mb4_uca1400_as_ci','');
-- COLUMN name_data.pidx
@@ -1266,7 +1270,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','name_data','name_data_prope
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','name_overrides','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','name_overrides','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','name_overrides','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','name_overrides','InnoDB','');
-- COLUMNS
@@ -1305,8 +1309,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','name_overrides','name','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','name_overrides','name','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','name_overrides','name','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','name_overrides','name','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_overrides','name','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_overrides','name','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','name_overrides','name','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','name_overrides','name','utf8mb4_uca1400_as_ci','');
-- INDEXES
SELECT tap.indexes_are('_caosdb_schema_unit_tests','name_overrides','`name_ov_dom_ent_idx`','');
@@ -1351,7 +1355,7 @@ SELECT tap.constraint_type_is('_caosdb_schema_unit_tests','name_overrides','name
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','null_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','null_data','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','null_data','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','null_data','InnoDB','');
-- COLUMNS
@@ -1390,8 +1394,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','null_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','null_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','null_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','null_data','status','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','null_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','null_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','null_data','status','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','null_data','status','utf8mb4_uca1400_as_ci','');
-- COLUMN null_data.pidx
@@ -1440,7 +1444,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','null_data','null_forkey_pro
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','passwd','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','passwd','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','passwd','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','passwd','InnoDB','');
-- COLUMNS
@@ -1470,8 +1474,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','passwd','alg','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','passwd','alg','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','passwd','alg','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','passwd','alg','\'SHA-512\'','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','passwd','alg','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','passwd','alg','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','passwd','alg','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','passwd','alg','utf8mb4_uca1400_as_ci','');
-- COLUMN passwd.it
@@ -1505,7 +1509,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','passwd','`principal`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','permissions','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','permissions','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','permissions','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','permissions','InnoDB','');
-- COLUMNS
@@ -1526,8 +1530,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','permissions','permissions',''
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','permissions','permissions','mediumtext','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','permissions','permissions','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','permissions','permissions',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','permissions','permissions','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','permissions','permissions','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','permissions','permissions','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','permissions','permissions','utf8mb4_uca1400_as_ci','');
-- CONSTRAINTS
SELECT tap.constraints_are('_caosdb_schema_unit_tests','permissions','`PRIMARY`,`perm_name_roles`','');
@@ -1550,7 +1554,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','permissions','`role`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','query_template_def','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','query_template_def','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','query_template_def','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','query_template_def','InnoDB','');
-- COLUMNS
@@ -1571,8 +1575,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','query_template_def','definiti
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','query_template_def','definition','mediumtext','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','query_template_def','definition','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','query_template_def','definition',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','query_template_def','definition','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','query_template_def','definition','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','query_template_def','definition','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','query_template_def','definition','utf8mb4_uca1400_as_ci','');
-- CONSTRAINTS
SELECT tap.constraints_are('_caosdb_schema_unit_tests','query_template_def','`PRIMARY`,`query_template_def_ibfk_1`','');
@@ -1595,7 +1599,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','query_template_def','query_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','reference_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','reference_data','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','reference_data','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','reference_data','InnoDB','');
-- COLUMNS
@@ -1643,8 +1647,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','reference_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','reference_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','reference_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','reference_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','reference_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','reference_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','reference_data','status','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','reference_data','status','utf8mb4_uca1400_as_ci','');
-- COLUMN reference_data.pidx
@@ -1722,7 +1726,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','reference_data','reference_
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','roles','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','roles','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','roles','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','roles','InnoDB','');
-- COLUMNS
@@ -1743,8 +1747,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','roles','description','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','roles','description','mediumtext','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','roles','description','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','roles','description','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','roles','description','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','roles','description','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','roles','description','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','roles','description','utf8mb4_uca1400_as_ci','');
-- CONSTRAINTS
SELECT tap.constraints_are('_caosdb_schema_unit_tests','roles','`PRIMARY`','');
@@ -1760,7 +1764,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','roles','`name`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','stats','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','stats','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','stats','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','stats','InnoDB','');
-- COLUMNS
@@ -1772,8 +1776,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','stats','name','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','stats','name','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','stats','name','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','stats','name',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','stats','name','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','stats','name','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','stats','name','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','stats','name','utf8mb4_uca1400_as_ci','');
-- COLUMN stats.value
@@ -1798,7 +1802,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','stats','`name`','');
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','text_data','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','text_data','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','text_data','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','text_data','InnoDB','');
-- COLUMNS
@@ -1837,8 +1841,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','text_data','value','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','text_data','value','text','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','text_data','value','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','text_data','value',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','text_data','value','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','text_data','value','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','text_data','value','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','text_data','value','utf8mb4_uca1400_as_ci','');
-- COLUMN text_data.status
@@ -1846,8 +1850,8 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','text_data','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','text_data','status','enum(\'OBLIGATORY\',\'RECOMMENDED\',\'SUGGESTED\',\'FIX\',\'REPLACEMENT\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','text_data','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','text_data','status',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','text_data','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','text_data','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','text_data','status','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','text_data','status','utf8mb4_uca1400_as_ci','');
-- COLUMN text_data.pidx
@@ -1896,7 +1900,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','text_data','str_property_id
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','transaction_log','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','transaction_log','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','transaction_log','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','transaction_log','InnoDB','');
-- COLUMNS
@@ -1908,17 +1912,17 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','transaction_log','transaction
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','transaction_log','transaction','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','transaction_log','transaction','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','transaction_log','transaction',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','transaction_log','transaction','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','transaction_log','transaction','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','transaction_log','transaction','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','transaction_log','transaction','utf8mb4_uca1400_as_ci','');
-- COLUMN transaction_log.entity_id
SELECT tap.has_column('_caosdb_schema_unit_tests','transaction_log','entity_id','');
-SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','transaction_log','entity_id','int(10) unsigned','');
+SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','transaction_log','entity_id','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','transaction_log','entity_id','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','transaction_log','entity_id',NULL,'');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','transaction_log','entity_id',NULL,'');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','transaction_log','entity_id',NULL,'');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','transaction_log','entity_id','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','transaction_log','entity_id','utf8mb4_bin','');
-- COLUMN transaction_log.username
@@ -1970,7 +1974,7 @@ SELECT tap.is_indexed('_caosdb_schema_unit_tests','transaction_log','`entity_id`
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','units_lin_con','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','units_lin_con','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','units_lin_con','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','units_lin_con','InnoDB','');
-- COLUMNS
@@ -2044,7 +2048,7 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','units_lin_con','`signature_fro
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','user_info','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','user_info','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','user_info','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','user_info','InnoDB','');
-- COLUMNS
@@ -2083,17 +2087,17 @@ SELECT tap.has_column('_caosdb_schema_unit_tests','user_info','status','');
SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','user_info','status','enum(\'ACTIVE\',\'INACTIVE\')','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','user_info','status','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','user_info','status','\'INACTIVE\'','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','user_info','status','utf8','');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','user_info','status','utf8_unicode_ci','');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','user_info','status','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','user_info','status','utf8mb4_uca1400_as_ci','');
-- COLUMN user_info.entity
SELECT tap.has_column('_caosdb_schema_unit_tests','user_info','entity','');
-SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','user_info','entity','int(10) unsigned','');
+SELECT tap.col_column_type_is('_caosdb_schema_unit_tests','user_info','entity','varchar(255)','');
SELECT tap.col_extra_is('_caosdb_schema_unit_tests','user_info','entity','','');
SELECT tap.col_default_is('_caosdb_schema_unit_tests','user_info','entity','NULL','');
-SELECT tap.col_charset_is('_caosdb_schema_unit_tests','user_info','entity',NULL,'');
-SELECT tap.col_collation_is('_caosdb_schema_unit_tests','user_info','entity',NULL,'');
+SELECT tap.col_charset_is('_caosdb_schema_unit_tests','user_info','entity','utf8mb4','');
+SELECT tap.col_collation_is('_caosdb_schema_unit_tests','user_info','entity','utf8mb4_bin','');
-- INDEXES
SELECT tap.indexes_are('_caosdb_schema_unit_tests','user_info','`subject_entity`','');
@@ -2105,7 +2109,7 @@ SELECT tap.index_is_type('_caosdb_schema_unit_tests','user_info','subject_entity
SELECT tap.is_indexed('_caosdb_schema_unit_tests','user_info','`entity`','');
-- CONSTRAINTS
-SELECT tap.constraints_are('_caosdb_schema_unit_tests','user_info','`PRIMARY`,`subjects_ibfk_1`','');
+SELECT tap.constraints_are('_caosdb_schema_unit_tests','user_info','`PRIMARY`,`subjects_ibfk_2`','');
-- CONSTRAINT user_info.PRIMARY
@@ -2115,17 +2119,17 @@ SELECT tap.col_is_pk('_caosdb_schema_unit_tests','user_info','`realm`,`name`',''
-- CONSTRAINT user_info.subjects_ibfk_1
-SELECT tap.has_constraint('_caosdb_schema_unit_tests','user_info','subjects_ibfk_1','');
-SELECT tap.constraint_type_is('_caosdb_schema_unit_tests','user_info','subjects_ibfk_1','FOREIGN KEY','');
-SELECT tap.fk_on_delete('_caosdb_schema_unit_tests','user_info','subjects_ibfk_1','RESTRICT','');
-SELECT tap.fk_on_update('_caosdb_schema_unit_tests','user_info','subjects_ibfk_1','RESTRICT','');
+SELECT tap.has_constraint('_caosdb_schema_unit_tests','user_info','subjects_ibfk_2','');
+SELECT tap.constraint_type_is('_caosdb_schema_unit_tests','user_info','subjects_ibfk_2','FOREIGN KEY','');
+SELECT tap.fk_on_delete('_caosdb_schema_unit_tests','user_info','subjects_ibfk_2','RESTRICT','');
+SELECT tap.fk_on_update('_caosdb_schema_unit_tests','user_info','subjects_ibfk_2','RESTRICT','');
-- ***************************************************************
-- TABLE _caosdb_schema_unit_tests.user_roles
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','user_roles','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','user_roles','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','user_roles','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','user_roles','InnoDB','');
-- COLUMNS
@@ -2179,7 +2183,7 @@ SELECT tap.fk_on_update('_caosdb_schema_unit_tests','user_roles','user_roles_ibf
-- ***************************************************************
SELECT tap.has_table('_caosdb_schema_unit_tests','entity_version','');
-SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entity_version','utf8_unicode_ci','');
+-- SELECT tap.table_collation_is('_caosdb_schema_unit_tests','entity_version','utf8mb4_uca1400_as_ci','');
SELECT tap.table_engine_is('_caosdb_schema_unit_tests','entity_version','InnoDB','');
-- COLUMNS
@@ -2509,20 +2513,6 @@ SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','getFileIdByPa
SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','getFileIdByPath','DEFINER','');
SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','getFileIdByPath','CONTAINS SQL','');
--- PROCEDURES _caosdb_schema_unit_tests.getRole
-
-SELECT tap.has_procedure('_caosdb_schema_unit_tests','getRole','');
-SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','getRole','NO','');
-SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','getRole','DEFINER','');
-SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','getRole','CONTAINS SQL','');
-
--- PROCEDURES _caosdb_schema_unit_tests.initAutoIncrement
-
-SELECT tap.has_procedure('_caosdb_schema_unit_tests','initAutoIncrement','');
-SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','initAutoIncrement','NO','');
-SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','initAutoIncrement','DEFINER','');
-SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','initAutoIncrement','CONTAINS SQL','');
-
-- PROCEDURES _caosdb_schema_unit_tests.initBackReference
SELECT tap.has_procedure('_caosdb_schema_unit_tests','initBackReference','');
@@ -2586,13 +2576,6 @@ SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','insertLinCon'
SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','insertLinCon','DEFINER','');
SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','insertLinCon','CONTAINS SQL','');
--- PROCEDURES _caosdb_schema_unit_tests.insertUser
-
-SELECT tap.has_procedure('_caosdb_schema_unit_tests','insertUser','');
-SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','insertUser','NO','');
-SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','insertUser','DEFINER','');
-SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','insertUser','CONTAINS SQL','');
-
-- PROCEDURES _caosdb_schema_unit_tests.intersectTable
SELECT tap.has_procedure('_caosdb_schema_unit_tests','intersectTable','');
@@ -2649,12 +2632,12 @@ SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','raiseWarning'
SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','raiseWarning','DEFINER','');
SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','raiseWarning','CONTAINS SQL','');
--- PROCEDURES _caosdb_schema_unit_tests.registerSubdomain
+-- PROCEDURES _caosdb_schema_unit_tests.registerReplacementIds
-SELECT tap.has_procedure('_caosdb_schema_unit_tests','registerSubdomain','');
-SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','registerSubdomain','NO','');
-SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','registerSubdomain','DEFINER','');
-SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','registerSubdomain','CONTAINS SQL','');
+SELECT tap.has_procedure('_caosdb_schema_unit_tests','registerReplacementIds','');
+SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','registerReplacementIds','NO','');
+SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','registerReplacementIds','DEFINER','');
+SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','registerReplacementIds','CONTAINS SQL','');
-- PROCEDURES _caosdb_schema_unit_tests.initSubProperty
@@ -2677,13 +2660,6 @@ SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','registerTempT
SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','registerTempTableName','DEFINER','');
SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','registerTempTableName','CONTAINS SQL','');
--- PROCEDURES _caosdb_schema_unit_tests.retrieveDatatype
-
-SELECT tap.has_procedure('_caosdb_schema_unit_tests','retrieveDatatype','');
-SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','retrieveDatatype','NO','');
-SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','retrieveDatatype','DEFINER','');
-SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','retrieveDatatype','CONTAINS SQL','');
-
-- PROCEDURES _caosdb_schema_unit_tests.retrieveEntityParents
SELECT tap.has_procedure('_caosdb_schema_unit_tests','retrieveEntityParents','');
@@ -2691,13 +2667,6 @@ SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','retrieveEntit
SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','retrieveEntityParents','DEFINER','');
SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','retrieveEntityParents','CONTAINS SQL','');
--- PROCEDURES _caosdb_schema_unit_tests.setPassword
-
-SELECT tap.has_procedure('_caosdb_schema_unit_tests','setPassword','');
-SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','setPassword','NO','');
-SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','setPassword','DEFINER','');
-SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','setPassword','CONTAINS SQL','');
-
-- PROCEDURES _caosdb_schema_unit_tests.insertIsa
SELECT tap.has_procedure('_caosdb_schema_unit_tests','insertIsa','');
@@ -2754,12 +2723,5 @@ SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','insert_single
SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','insert_single_child_version','DEFINER','');
SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','insert_single_child_version','CONTAINS SQL','');
--- PROCEDURES _caosdb_schema_unit_tests.delete_all_entity_versions
-
-SELECT tap.has_procedure('_caosdb_schema_unit_tests', 'delete_all_entity_versions', '');
-SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','delete_all_entity_versions','NO','');
-SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','delete_all_entity_versions','DEFINER','');
-SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','delete_all_entity_versions','CONTAINS SQL','');
-
CALL tap.finish();
ROLLBACK;
diff --git a/tests/test_entity_versioning.sql b/tests/test_entity_versioning.sql
index f54e7d0526e47654fd1f06643b71b0b6d1aadc81..eb01deb2ec2a25b9117c3855c129d814f77f552b 100644
--- a/tests/test_entity_versioning.sql
+++ b/tests/test_entity_versioning.sql
@@ -1,9 +1,8 @@
/**
- * ** header v3.0
* 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>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@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
@@ -17,8 +16,6 @@
*
* 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/>.
- *
- * ** end header
*/
USE _caosdb_schema_unit_tests;
@@ -34,6 +31,13 @@ CALL tap.no_plan();
-- SETUP
+SET @EntityID1 = 10001;
+SET @EntityID2 = 10002;
+SET @EntityID3 = 10003;
+SET @EntityID4 = 10004;
+SET @EntityID5 = 10005;
+SET @EntityID6 = 10006;
+
-- Disable versioning because we want to test `insert_single_child_version`
-- separately from `insertEntity` but the former is called inside the latter
-- when versioning is enabled.
@@ -46,22 +50,22 @@ INSERT INTO transactions (srid,seconds,nanos,username,realm) VALUES
("SRIDblieb", 3456, 4576, "you", "home");
DELETE FROM entities WHERE id > 99;
CALL entityACL(@ACLID1, "{acl1}");
-CALL insertEntity("EntityName", "EntityDesc", "RECORDTYPE", "{acl1}");
-SELECT entity_id INTO @EntityID FROM name_data WHERE value="EntityName";
+CALL insertEntity(@EntityID1, "EntityName", "EntityDesc", "RECORDTYPE", "{acl1}");
+SELECT entity_id INTO @InternalEntityID1 FROM name_data WHERE value="EntityName";
-- TEST insert_single_child_version
SELECT count(*) INTO @x FROM entity_version;
SELECT tap.eq(@x, 0, "no versions there yet");
-CALL insert_single_child_version(@EntityID, "hashbla", "versionbla", NULL, "SRIDbla");
+CALL insert_single_child_version(@InternalEntityID1, "hashbla", "versionbla", NULL, "SRIDbla");
SELECT _ipparent INTO @x from entity_version WHERE version="versionbla";
SELECT tap.eq(@x, NULL, "no parent for the first version");
-- add a second version
SELECT count(*) INTO @x FROM entity_version;
SELECT tap.eq(@x, 1, "one version there already");
-CALL insert_single_child_version(@EntityID, "hashblub", "versionblub", "versionbla", "SRIDblub");
+CALL insert_single_child_version(@InternalEntityID1, "hashblub", "versionblub", "versionbla", "SRIDblub");
SELECT _ipparent INTO @x from entity_version WHERE version="versionblub";
SELECT tap.eq(@x, 1, "the original entity is the parent");
@@ -72,7 +76,7 @@ SELECT tap.eq(@x, 2, "two versions there already");
CALL tap._assert_throws(
concat("CALL insert_single_child_version(",
- @EntityID, ', "hashblieb", "versionblieb", "non-existing-parent", "SRIDBlieb")'),
+ @InternalEntityID1, ', "hashblieb", "versionblieb", "non-existing-parent", "SRIDBlieb")'),
"non existing parent throws");
SELECT count(*) INTO @x FROM entity_version;
@@ -80,21 +84,24 @@ SELECT tap.eq(@x, 2, "still two versions there");
-- TEST get_primary_parent_version
-SELECT tap.eq(get_primary_parent_version(@EntityID, "versionblub"), "versionbla", "returns correct parent for versionblub");
-SELECT tap.eq(get_primary_parent_version(@EntityID, "versionbla"), NULL, "versionbla has no parent");
+SELECT tap.eq(get_primary_parent_version(@EntityID1, "versionblub"), "versionbla", "returns correct parent for versionblub");
+SELECT tap.eq(get_primary_parent_version(@EntityID1, "versionbla"), NULL, "versionbla has no parent");
+-- Reactivate when versioning's FORGET is being implemented
-- TEST delete_all_entity_versions
SELECT count(*) INTO @x FROM entity_version;
SELECT tap.ok(@x > 0, "several versions in the table");
-CALL delete_all_entity_versions(@EntityID);
+-- CALL delete_all_entity_versions(@EntityID1);
+DELETE FROM entity_version WHERE entity_id = @InternalEntityID1;
SELECT count(*) INTO @x FROM entity_version;
SELECT tap.eq(@x, 0, "no versions there any more");
-- TEARDOWN clean up
DELETE FROM name_data WHERE entity_id > 99;
+DELETE FROM entity_ids WHERE internal_id > 99;
DELETE FROM entities WHERE id > 99;
-- #####################################################################
@@ -108,20 +115,20 @@ SELECT tap.eq(@x, 0, "before insertEntity, no versions there");
-- TEST insertEntity - should produce a version w/o parent
SET @SRID = "SRIDbla";
-CALL insertEntity("EntityName", "EntityDesc", "RECORDTYPE", "{acl1}");
-SELECT entity_id INTO @EntityID FROM name_data WHERE value="EntityName";
-CALL insertEntity("ParentName", "ParentDesc", "RECORDTYPE", "{acl1}");
+CALL insertEntity(@EntityID2, "EntityName", "EntityDesc", "RECORDTYPE", "{acl1}");
+SELECT entity_id INTO @InternalEntityID2 FROM name_data WHERE value="EntityName";
+CALL insertEntity(@EntityID3, "ParentName", "ParentDesc", "RECORDTYPE", "{acl1}");
SELECT entity_id INTO @ParentID FROM name_data WHERE value="ParentName";
-CALL insertIsa(@EntityID, @ParentID);
-CALL insertEntityProperty(0, @EntityID, 17, "null_data", NULL, NULL,
+CALL insertIsa(@EntityID2, @EntityID3);
+CALL insertEntityProperty(0, @EntityID2, 17, "null_data", NULL, NULL,
"RECOMMENDED", NULL, "DescOverride", NULL, NULL, 0);
-SELECT count(*) INTO @x FROM entity_version WHERE entity_id = @EntityID;
+SELECT count(*) INTO @x FROM entity_version WHERE entity_id = @InternalEntityID2;
SELECT tap.eq(@x, 1, "after insertEntity, a version is there.");
-SELECT _iversion INTO @x FROM entity_version WHERE entity_id = @EntityID and _ipparent is NULL;
+SELECT _iversion INTO @x FROM entity_version WHERE entity_id = @InternalEntityID2 and _ipparent is NULL;
SELECT tap.eq(@x, 1, "after insertEntity, the _iversion number is 1.");
-SELECT _ipparent INTO @x from entity_version WHERE entity_id = @EntityID;
+SELECT _ipparent INTO @x from entity_version WHERE entity_id = @InternalEntityID2;
SELECT tap.eq(@x, NULL, "no parent for the freshly inserted entity");
SELECT tap.eq(count(*), 0, "no entity in archive_entities before first update")
FROM archive_entities;
@@ -129,14 +136,14 @@ SELECT tap.eq(count(*), 0, "no entity in archive_entities before first update")
-- TEST updateEntity - should produce a version with a parent
SET @SRID = "SRIDblub";
-CALL deleteEntityProperties(@EntityID);
-CALL updateEntity(@EntityID, "NewEntityName", "NewEntityDesc", "RECORD", NULL, NULL, "{acl1}");
-SELECT count(*) INTO @x FROM entity_version WHERE entity_id = @EntityID;
+CALL deleteEntityProperties(@EntityID2);
+CALL updateEntity(@EntityID2, "NewEntityName", "NewEntityDesc", "RECORD", NULL, NULL, "{acl1}");
+SELECT count(*) INTO @x FROM entity_version WHERE entity_id = @InternalEntityID2;
SELECT tap.eq(@x, 2, "after updateEntity, a second version is there.");
-SELECT _iversion INTO @x FROM entity_version WHERE entity_id = @EntityID and _ipparent = 1;
+SELECT _iversion INTO @x FROM entity_version WHERE entity_id = @InternalEntityID2 and _ipparent = 1;
SELECT tap.eq(@x, 2, "after updateEntity, the _iversion number incremented.");
-SELECT _ipparent INTO @x FROM entity_version WHERE entity_id = @EntityID and _ipparent = 1;
+SELECT _ipparent INTO @x FROM entity_version WHERE entity_id = @InternalEntityID2 and _ipparent = 1;
SELECT tap.eq(@x, 1, "after updateEntity, the _pparent points to the first version");
SELECT tap.eq(count(*), 1, "after updateEntity, one entity in archive_entities")
@@ -144,60 +151,60 @@ SELECT tap.eq(count(*), 1, "after updateEntity, one entity in archive_entities")
-- TEST get_version_history
-CALL get_version_history(@EntityID);
+CALL get_version_history(@EntityID2);
-- TEST retrieveEntity
SELECT version INTO @x FROM entity_version
- WHERE entity_id = @EntityID
+ WHERE entity_id = @InternalEntityID2
AND _iversion = 2;
-CALL retrieveEntity(@EntityID, NULL);
-CALL retrieveEntity(@EntityID, "non-existing-version");
-CALL retrieveEntity(@EntityID, get_head_version(@EntityID));
-CALL retrieveEntity(@EntityID, @x);
+CALL retrieveEntity(@EntityID2, NULL);
+CALL retrieveEntity(@EntityID2, "non-existing-version");
+CALL retrieveEntity(@EntityID2, get_head_version(@EntityID2));
+CALL retrieveEntity(@EntityID2, @x);
-- TEST retrieveEntityParents
-CALL retrieveEntityParents(@EntityID, NULL);
-CALL retrieveEntityParents(@EntityID, "non-existing-version");
-CALL retrieveEntityParents(@EntityID, get_head_version(@EntityID));
-CALL retrieveEntityParents(@EntityID, @x);
+CALL retrieveEntityParents(@EntityID2, NULL);
+CALL retrieveEntityParents(@EntityID2, "non-existing-version");
+CALL retrieveEntityParents(@EntityID2, get_head_version(@EntityID2));
+CALL retrieveEntityParents(@EntityID2, @x);
-- TEST retrieveEntityProperties
-CALL retrieveEntityProperties(0, @EntityID, NULL);
-CALL retrieveEntityProperties(0, @EntityID, "non-existing-version");
-CALL retrieveEntityProperties(0, @EntityID, get_head_version(@EntityID));
-CALL retrieveEntityProperties(0, @EntityID, @x);
+CALL retrieveEntityProperties(0, @EntityID2, NULL);
+CALL retrieveEntityProperties(0, @EntityID2, "non-existing-version");
+CALL retrieveEntityProperties(0, @EntityID2, get_head_version(@EntityID2));
+CALL retrieveEntityProperties(0, @EntityID2, @x);
-- TEST retrieveOverrides
-CALL retrieveOverrides(0, @EntityID, NULL);
-CALL retrieveOverrides(0, @EntityID, "non-existing-version");
-CALL retrieveOverrides(0, @EntityID, get_head_version(@EntityID));
-CALL retrieveOverrides(0, @EntityID, @x);
+CALL retrieveOverrides(0, @EntityID2, NULL);
+CALL retrieveOverrides(0, @EntityID2, "non-existing-version");
+CALL retrieveOverrides(0, @EntityID2, get_head_version(@EntityID2));
+CALL retrieveOverrides(0, @EntityID2, @x);
-- and 2nd updateEntity
SET @SRID = "SRIDblieb";
-CALL updateEntity(@EntityID, "EntityName", "EntityDesc", "RECORDTYPE", NULL, NULL, "{acl1}");
-SELECT count(*) INTO @x FROM entity_version WHERE entity_id = @EntityID;
+CALL updateEntity(@EntityID2, "EntityName", "EntityDesc", "RECORDTYPE", NULL, NULL, "{acl1}");
+SELECT count(*) INTO @x FROM entity_version WHERE entity_id = @InternalEntityID2;
SELECT tap.eq(@x, 3, "after 2nd updateEntity, a 3rd version is there.");
-SELECT _iversion INTO @x FROM entity_version WHERE entity_id = @EntityID and _ipparent = 2;
+SELECT _iversion INTO @x FROM entity_version WHERE entity_id = @InternalEntityID2 and _ipparent = 2;
SELECT tap.eq(@x, 3, "after 2nd updateEntity, the _iversion number incremented again.");
-SELECT _ipparent INTO @x FROM entity_version WHERE entity_id = @EntityID and _iversion = 3;
+SELECT _ipparent INTO @x FROM entity_version WHERE entity_id = @InternalEntityID2 and _iversion = 3;
SELECT tap.eq(@x, 2, "after 2nd updateEntity, the _pparent points to the 2nd version");
-SELECT tap.eq("SRIDblieb", srid, "correct transaction was stored") FROM entity_version WHERE entity_id = @EntityID AND _ipparent = 2;
+SELECT tap.eq("SRIDblieb", srid, "correct transaction was stored") FROM entity_version WHERE entity_id = @InternalEntityID2 AND _ipparent = 2;
-- TEST deleteEntity - should remove all versions
-CALL deleteIsa(@EntityID);
-CALL deleteEntity(@EntityID);
-SELECT count(*) INTO @x FROM entity_version WHERE entity_id = @EntityID;
+CALL deleteIsa(@EntityID3);
+CALL deleteEntity(@EntityID2);
+SELECT count(*) INTO @x FROM entity_version WHERE entity_id = @InternalEntityID2;
SELECT tap.eq(@x, 0, "no versions there any more");
-CALL deleteEntity(@ParentID);
+CALL deleteEntity(@EntityID3);
CALL tap.finish();
ROLLBACK;
@@ -217,21 +224,21 @@ DELETE FROM transactions;
-- insert entity without versioning
DELETE FROM feature_config WHERE _key = "ENTITY_VERSIONING";
CALL entityACL(@ACLID1, "{acl1}");
-CALL insertEntity("EntityName", "EntityDesc", "RECORDTYPE", "{acl1}");
+CALL insertEntity(@EntityID4, "EntityName", "EntityDesc", "RECORDTYPE", "{acl1}");
SELECT count(*) INTO @NumOfEntities FROM entities;
-SELECT entity_id INTO @EntityID FROM name_data WHERE value="EntityName";
+SELECT entity_id INTO @InternalEntityID4 FROM name_data WHERE value="EntityName";
SET @TheUser = "TheUser"; -- used to identify the matching entry in transaction_log
-- fill transaction_log: one entity with two updates (and one insert) and another entity with insert and delete.
INSERT INTO transaction_log (transaction, entity_id, username, realm, seconds, nanos)
-- the first entry is the one which is be found by _fix_unversioned
VALUES
- ("Update", @EntityID, @TheUser, "CaosDB", 23458, 254),
+ ("Update", @InternalEntityID4, @TheUser, "CaosDB", 23458, 254),
-- the rest is dummy data
- ("Update", @EntityID, "OtherUser", "CaosDB", 2345, 633), -- not the latest transaction
- ("Insert", @EntityID, "OtherUser", "CaosDB", 245, 633), -- not the latest transaction
- ("Insert", @EntityID + 1, @TheUser, "CaosDB", 2325, 653), -- not the right entity, inserted before our target
- ("Delete", @EntityID + 1, @TheUser, "CaosDB", 232526, 653); -- not the right entity, deleted after our target
+ ("Update", @InternalEntityID4, "OtherUser", "CaosDB", 2345, 633), -- not the latest transaction
+ ("Insert", @InternalEntityID4, "OtherUser", "CaosDB", 245, 633), -- not the latest transaction
+ ("Insert", @InternalEntityID4 + 1, @TheUser, "CaosDB", 2325, 653), -- not the right entity, inserted before our target
+ ("Delete", @InternalEntityID4 + 1, @TheUser, "CaosDB", 232526, 653); -- not the right entity, deleted after our target
SELECT tap.eq(COUNT(*), 5, "five entries in transaction_log") FROM transaction_log;
@@ -251,11 +258,11 @@ SELECT tap.eq(COUNT(*), 2,
"after _fix_unversioned, one entry for our test entity in transactions, one for the standard entities.")
FROM transactions;
-SELECT tap.eq(entity_id, @EntityID, "versioned entity has correct id") FROM entity_version WHERE entity_id > 99;
+SELECT tap.eq(entity_id, @InternalEntityID4, "versioned entity has correct id") FROM entity_version WHERE entity_id > 99;
SELECT tap.ok(srid IS NOT NULL, "srid was generated and user/time matches entries from transaction_log")
FROM transactions AS t JOIN transaction_log AS l
ON (l.seconds = t.seconds AND l.nanos = t.nanos AND l.username = t.username AND l.realm = t.realm)
- WHERE l.entity_id = @EntityID AND l.username = @TheUser;
+ WHERE l.entity_id = @InternalEntityID4444 AND l.username = @TheUser;
CALL tap.finish();
ROLLBACK;
@@ -275,18 +282,18 @@ DELETE FROM transactions;
DELETE FROM feature_config WHERE _key = "ENTITY_VERSIONING";
CALL entityACL(@ACLID1, "{acl1}");
-CALL insertEntity("EntityName1", "EntityDesc1", "RECORDTYPE", "{acl1}");
-CALL insertEntity("EntityName2", "EntityDesc2", "RECORDTYPE", "{acl1}");
+CALL insertEntity(@EntityID5, "EntityName1", "EntityDesc1", "RECORDTYPE", "{acl1}");
+CALL insertEntity(@EntityID6, "EntityName2", "EntityDesc2", "RECORDTYPE", "{acl1}");
SELECT count(*) INTO @NumOfEntities FROM entities;
-SELECT entity_id INTO @EntityID1 FROM name_data WHERE value="EntityName1";
-SELECT entity_id INTO @EntityID2 FROM name_data WHERE value="EntityName2";
+SELECT entity_id INTO @InternalEntityID5 FROM name_data WHERE value="EntityName1";
+SELECT entity_id INTO @InternalEntityID6 FROM name_data WHERE value="EntityName2";
INSERT INTO transaction_log (transaction, entity_id, username, realm, seconds,
nanos)
-- the first entry is the one which will be found by _fix_unversioned
- VALUES ("INSERT", @EntityID1, "User", "CaosDB", 10000, 250),
- ("INSERT", @EntityID2, "User", "CaosDB", 10000, 250),
- ("UPDATE", @EntityID2, "User", "CaosDB", 20000, 250);
+ VALUES ("INSERT", @InternalEntityID5, "User", "CaosDB", 10000, 250),
+ ("INSERT", @InternalEntityID6, "User", "CaosDB", 10000, 250),
+ ("UPDATE", @InternalEntityID6, "User", "CaosDB", 20000, 250);
SELECT tap.eq(COUNT(*), 3, "three entries in transaction_log") FROM transaction_log;
@@ -309,10 +316,10 @@ SELECT tap.eq(COUNT(*), 3,
SELECT tap.eq(seconds, 10000, "version seconds of entity 1 is correct")
FROM entity_version AS v JOIN transactions AS t
- ON (v.srid = t.srid) WHERE v.entity_id = @EntityID1;
+ ON (v.srid = t.srid) WHERE v.entity_id = @InternalEntityID1;
SELECT tap.eq(seconds, 20000, "version seconds of entity 2 is correct")
FROM entity_version AS v JOIN transactions AS t
- ON (v.srid = t.srid) WHERE v.entity_id = @EntityID2;
+ ON (v.srid = t.srid) WHERE v.entity_id = @InternalEntityID2;
CALL tap.finish();
ROLLBACK;
diff --git a/tests/test_insert_update_delete.sql b/tests/test_insert_update_delete.sql
index a11b05e3d9a72d6038800adebf5b73c699c2a2b8..ff1e4ec3acc6fe0121ff168279fe7659e05a914c 100644
--- a/tests/test_insert_update_delete.sql
+++ b/tests/test_insert_update_delete.sql
@@ -1,9 +1,31 @@
+/**
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@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
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * 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/>.
+ */
USE _caosdb_schema_unit_tests;
BEGIN;
CALL tap.no_plan();
-- SETUP
+SET @EntityID1 = 10001;
+SET @EntityID2 = 10002;
+
-- Disable versioning and only test the non-versioning behavior
DELETE FROM feature_config WHERE _key = "ENTITY_VERSIONING";
@@ -16,31 +38,31 @@ SELECT entity_id into @TextDatatypeID FROM name_data WHERE value ="TEXT";
-- TEST insertEntity
SELECT tap.eq(COUNT(id), 0, "No entities")
FROM entities WHERE id>=100;
-CALL insertEntity("EntityName", "EntityDesc", "RECORDTYPE", "{acl1}");
+CALL insertEntity(@EntityID1, "EntityName", "EntityDesc", "RECORDTYPE", "{acl1}");
SELECT tap.eq(COUNT(entity_id), 1, "Entity has been inserted")
FROM name_data WHERE value="EntityName";
-SELECT entity_id INTO @EntityID FROM name_data WHERE value="EntityName";
-SELECT tap.ok(@EntityID >= 100, "EntityID greater 99");
+SELECT entity_id INTO @InternalEntityID FROM name_data WHERE value="EntityName";
+SELECT tap.ok(@InternalEntityID >= 100, "EntityID greater 99");
SELECT tap.eq(acl, @ACLID1, "correct acl id had been assigned")
- FROM entities WHERE id=@EntityID;
+ FROM entities WHERE id=@InternalEntityID;
-- TEST insertEntityProperty
-CALL insertEntity("AProperty", "APropDesc", "PROPERTY", "{acl1}");
-SELECT entity_id INTO @PropID FROM name_data WHERE value="AProperty";
-INSERT INTO data_type (domain_id, entity_id, property_id, datatype) VALUES (0, 0, @PropID, @TextDatatypeID);
+CALL insertEntity(@EntityID2, "AProperty", "APropDesc", "PROPERTY", "{acl1}");
+SELECT entity_id INTO @InternalPropertyID FROM name_data WHERE value="AProperty";
+INSERT INTO data_type (domain_id, entity_id, property_id, datatype) VALUES (0, 0, @InternalPropertyID, @TextDatatypeID);
SELECT COUNT(*) INTO @x FROM null_data;
SELECT tap.eq(@x, 0, "No data in null_data table");
-CALL insertEntityProperty(0, @EntityID, @PropID, "null_data", NULL, NULL, "RECOMMENDED", NULL, NULL, NULL, NULL, 0);
+CALL insertEntityProperty(0, @EntityID1, @EntityID2, "null_data", NULL, NULL, "RECOMMENDED", NULL, NULL, NULL, NULL, 0);
SELECT COUNT(*) INTO @x FROM null_data;
SELECT tap.eq(@x, 1, "One row in null_data table");
-- TEST updateEntity
-CALL updateEntity(@EntityID, "NewEntityName", "NewEntityDesc", "RECORD", NULL, NULL, "{acl2}");
+CALL updateEntity(@EntityID1, "NewEntityName", "NewEntityDesc", "RECORD", NULL, NULL, "{acl2}");
SELECT tap.eq(COUNT(entity_id), 0, "Old Entity name not present")
FROM name_data WHERE value="EntityName";
@@ -48,21 +70,21 @@ SELECT tap.eq(COUNT(entity_id), 1, "Entity name has been updated")
FROM name_data WHERE value="NewEntityName";
SELECT tap.eq(acl, @ACLID2, "acl has been updated")
- FROM entities WHERE id=@EntityID;
+ FROM entities WHERE id=@InternalEntityID;
-- CALL updateEntity again an update the Name
-CALL updateEntity(@EntityID, "NewerEntityName", "NewerEntityDesc", "RECORD", NULL, NULL, "{acl2}");
-CALL updateEntity(@EntityID, "NewEntityName", "NewEntityDesc", "RECORD", NULL, NULL, "{acl2}");
+CALL updateEntity(@EntityID2, "NewerEntityName", "NewerEntityDesc", "RECORD", NULL, NULL, "{acl2}");
+CALL updateEntity(@EntityID2, "NewEntityName", "NewEntityDesc", "RECORD", NULL, NULL, "{acl2}");
-- TEST deleteEntityProperties
-CALL deleteEntityProperties(@EntityID);
+CALL deleteEntityProperties(@EntityID1);
SELECT COUNT(*) INTO @x FROM null_data;
SELECT tap.eq(@x, 0, "data removed from null_data table");
-- TEST deleteEntity
-CALL deleteEntity(@EntityID);
-CALL deleteEntity(@PropID);
+CALL deleteEntity(@EntityID1);
+CALL deleteEntity(@EntityID2);
SELECT COUNT(id) INTO @x FROM entities WHERE id>100;
SELECT tap.eq(@x, 0, "entity deleted");
diff --git a/tests/test_issues.sql b/tests/test_issues.sql
index ea82fbdd3369c7c8cb1bdda6eee0242cd3231075..768d090245fc6a6a280377959e2c326a7f60ec59 100644
--- a/tests/test_issues.sql
+++ b/tests/test_issues.sql
@@ -1,9 +1,9 @@
/**
- * ** header v3.0
* This file is a part of the LinkAhead Project.
*
- * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@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
@@ -17,14 +17,16 @@
*
* 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/>.
- *
- * ** end header
*/
USE _caosdb_schema_unit_tests;
BEGIN;
CALL tap.no_plan();
+SET @EntityID1 = 10001;
+SET @EntityID2 = 10002;
+SET @EntityID3 = 10003;
+SET @EntityID4 = 10004;
-- ########################################################################
-- TEST Issues from https://gitlab.com/linkahead/linkahead-mysqlbackend/-/issues
@@ -42,23 +44,18 @@ INSERT INTO transactions (srid,seconds,nanos,username,realm) VALUES
CALL entityACL(@ACLID1, "{acl1}");
-- Insert entities and obtain IDs
-CALL insertEntity("A", "Desc A", "RECORDTYPE", "{acl1}");
-CALL insertEntity("B", "Desc B", "RECORDTYPE", "{acl1}");
-CALL insertEntity("C", "Desc C", "RECORDTYPE", "{acl1}");
-CALL insertEntity("rec", "Desc rec", "RECORD", "{acl1}");
-
-SELECT entity_id INTO @ID_A FROM name_data WHERE value="A";
-SELECT entity_id INTO @ID_B FROM name_data WHERE value="B";
-SELECT entity_id INTO @ID_C FROM name_data WHERE value="C";
-SELECT entity_id INTO @ID_rec FROM name_data WHERE value="rec";
+CALL insertEntity(@EntityID1, "A", "Desc A", "RECORDTYPE", "{acl1}");
+CALL insertEntity(@EntityID2, "B", "Desc B", "RECORDTYPE", "{acl1}");
+CALL insertEntity(@EntityID3, "C", "Desc C", "RECORDTYPE", "{acl1}");
+CALL insertEntity(@EntityID4, "rec", "Desc rec", "RECORD", "{acl1}");
-- Insert is-a relationships
-CALL insertIsA(@ID_A, @ID_B);
-CALL insertIsA(@ID_B, @ID_C);
-CALL insertIsA(@ID_rec, @ID_A);
+CALL insertIsA(@EntityID1, @EntityID2);
+CALL insertIsA(@EntityID2, @EntityID3);
+CALL insertIsA(@EntityID4, @EntityID1);
-- Try to delete last child
-- leads to failure in issue #21
-CALL deleteIsa(@ID_rec);
+CALL deleteIsa(@EntityID4);
ROLLBACK;
diff --git a/tests/test_reference_values.sql b/tests/test_reference_values.sql
index 1226229786d511824cd975053151ed78b7b91a61..1b77f7cb984742e40b50ad287789073042ad6daf 100644
--- a/tests/test_reference_values.sql
+++ b/tests/test_reference_values.sql
@@ -1,9 +1,8 @@
/**
- * ** header v3.0
* 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>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@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
@@ -17,8 +16,6 @@
*
* 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/>.
- *
- * ** end header
*/
USE _caosdb_schema_unit_tests;
@@ -37,9 +34,14 @@ INSERT INTO transactions (srid,seconds,nanos,username,realm) VALUES
("SRIDbla", 1234, 2345, "me", "home"),
("SRIDblub", 2345, 3465, "me", "home"),
("SRIDblieb", 3456, 4576, "you", "home");
-SET @EntityID=99;
+SET @EntityID="99";
SET @PropertyID=11;
SET @Value=50;
+SET @SRID="SRIDbla";
+call insertEntity(@EntityID, "TheName", "TheDesc", "RecordType", "{}");
+call insertEntity(@Value, "RefValue", "ValueDesc", "Record", "{}");
+SELECT internal_id INTO @InternalEntityID FROM entity_ids WHERE id = @EntityID;
+SELECT internal_id INTO @InternalValueID FROM entity_ids WHERE id = @Value;
-- switch off versioning
DELETE FROM feature_config WHERE _key = "ENTITY_VERSIONING";
@@ -49,16 +51,16 @@ CALL insertEntityProperty(0, @EntityID, @PropertyID, "reference_data", @Value,
NULL, "FIX", NULL, NULL, NULL, NULL, 0);
-- TODO switch expected/actual
-SELECT tap.eq(0, domain_id, "domain ok") FROM reference_data;
-SELECT tap.eq(99, entity_id, "entity ok") FROM reference_data;
-SELECT tap.eq(11, property_id, "property ok") FROM reference_data;
-SELECT tap.eq(50, value, "value ok") FROM reference_data;
+SELECT tap.eq("0", domain_id, "domain ok") FROM reference_data;
+SELECT tap.eq(@InternalEntityID, entity_id, "entity ok") FROM reference_data;
+SELECT tap.eq("11", property_id, "property ok") FROM reference_data;
+SELECT tap.eq(@InternalValueID, value, "value ok") FROM reference_data;
SELECT tap.eq("FIX", status, "status ok") FROM reference_data;
SELECT tap.eq("0", pidx, "pidx ok") FROM reference_data;
-SELECT tap.eq(NULL, value_iversion, "value_iversion ok") FROM reference_data;
+SELECT tap.eq(NULL, value_iversion, "value_iversion ok 1") FROM reference_data;
-- clean up
-DELETE FROM reference_data WHERE domain_id=0 AND entity_id=99;
+DELETE FROM reference_data WHERE domain_id=0 AND entity_id=@InternalValueID;
-- #####################################################################
-- TODO TEST insertEntityProperty with Versioning
@@ -69,39 +71,43 @@ INSERT INTO feature_config (_key, _value) VALUES ("ENTITY_VERSIONING", "ENABLED"
-- TEST insertEntityProperty with Versioning - REFERENCE HEAD
-SET @VALUE="50";
CALL insertEntityProperty(0, @EntityID, @PropertyID, "reference_data", @Value,
NULL, "FIX", NULL, NULL, NULL, NULL, 0);
-- TODO switch expected/actual
SELECT tap.eq(0, domain_id, "domain ok") FROM reference_data;
-SELECT tap.eq(99, entity_id, "entity ok") FROM reference_data;
+SELECT tap.eq(@InternalEntityID, entity_id, "entity ok") FROM reference_data;
SELECT tap.eq(11, property_id, "property ok") FROM reference_data;
-SELECT tap.eq(50, value, "value ok") FROM reference_data;
+SELECT tap.eq(@InternalValueID, value, "value ok") FROM reference_data;
SELECT tap.eq("FIX", status, "status ok") FROM reference_data;
SELECT tap.eq("0", pidx, "pidx ok") FROM reference_data;
-SELECT tap.eq(value_iversion, NULL, "value_iversion ok") FROM reference_data;
+SELECT tap.eq(value_iversion, NULL, "value_iversion ok 2") FROM reference_data;
-DELETE FROM reference_data WHERE domain_id=0 AND entity_id=99;
+DELETE FROM reference_data WHERE domain_id=0 AND entity_id=@InternalEntityID;
-- TEST insertEntityProperty with Versioning - Reference version
-CALL insert_single_child_version(50, "hashbla", "versionbla", NULL, "SRIDbla");
-CALL insert_single_child_version(50, "hashblub", "versionblub", "versionbla", "SRIDblub");
-
-SET @VALUE="50@versionbla";
+SELECT * FROM entity_ids;
+SELECT * FROM entity_version;
+SELECT e.version INTO @ParentVersion
+ FROM entity_version as e
+ WHERE e.entity_id = @InternalValueID
+ AND e._iversion = 1;
+CALL insert_single_child_version(@InternalValueID, "hashblub", "versionblub", @ParentVersion, "SRIDblub");
+
+SET @VALUE=CONCAT("50@", @ParentVersion);
CALL insertEntityProperty(0, @EntityID, @PropertyID, "reference_data", @Value,
NULL, "FIX", NULL, NULL, NULL, NULL, 0);
SELECT tap.eq(0, domain_id, "domain ok") FROM reference_data;
-SELECT tap.eq(99, entity_id, "entity ok") FROM reference_data;
+SELECT tap.eq(@InternalEntityID, entity_id, "entity ok") FROM reference_data;
SELECT tap.eq(11, property_id, "property ok") FROM reference_data;
-SELECT tap.eq(50, value, "value ok") FROM reference_data;
+SELECT tap.eq(@InternalValueID, value, "value ok") FROM reference_data;
SELECT tap.eq("FIX", status, "status ok") FROM reference_data;
SELECT tap.eq("0", pidx, "pidx ok") FROM reference_data;
-SELECT tap.eq(value_iversion, "1", "value_iversion ok") FROM reference_data;
+SELECT tap.eq(value_iversion, "1", "value_iversion ok 3") FROM reference_data;
-DELETE FROM reference_data WHERE domain_id=0 AND entity_id=99;
+DELETE FROM reference_data WHERE domain_id=0 AND entity_id=@InternalEntityID;
SET @VALUE="50@versionblub";
CALL insertEntityProperty(0, @EntityID, @PropertyID, "reference_data", @Value,
@@ -109,12 +115,12 @@ CALL insertEntityProperty(0, @EntityID, @PropertyID, "reference_data", @Value,
-- TODO switch expected/actual
SELECT tap.eq(0, domain_id, "domain ok") FROM reference_data;
-SELECT tap.eq(99, entity_id, "entity ok") FROM reference_data;
+SELECT tap.eq(@InternalEntityID, entity_id, "entity ok") FROM reference_data;
SELECT tap.eq(11, property_id, "property ok") FROM reference_data;
-SELECT tap.eq(50, value, "value ok") FROM reference_data;
+SELECT tap.eq(@InternalValueID, value, "value ok") FROM reference_data;
SELECT tap.eq("FIX", status, "status ok") FROM reference_data;
SELECT tap.eq("0", pidx, "pidx ok") FROM reference_data;
-SELECT tap.eq(value_iversion, "2", "value_iversion ok") FROM reference_data;
+SELECT tap.eq(value_iversion, "2", "value_iversion ok 4") FROM reference_data;
-- invalid values throw errors
diff --git a/utils/backup.sh b/utils/backup.sh
index 6f2872ef49b5f33698b723d0b3d8b2e05f14e588..7b0da2284578be303f852e664702ca033c754356 100755
--- a/utils/backup.sh
+++ b/utils/backup.sh
@@ -56,7 +56,7 @@ function backup() {
fi
echo "Dumping database $database to $backupfile ..."
- $MYSQLDUMP_CMD $(get_mysql_args_nodb) --opt --default-character-set=utf8 \
+ $MYSQLDUMP_CMD $(get_db_args_nodb) --opt --default-character-set=utf8 \
--routines "$database" > "$backupfile"
success
diff --git a/utils/helpers.sh b/utils/helpers.sh
index 1bb13f5bd4f4d8c57b152428acc07869fa4e0274..ff4b189bffeabf467e0725de9a4b62fe72cd6bf3 100644
--- a/utils/helpers.sh
+++ b/utils/helpers.sh
@@ -2,9 +2,9 @@
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright (C) 2019, 2020 Daniel Hornung (d.hornung@indiscale.com)
+# Copyright (C) 2019, 2020, 2024 Daniel Hornung (d.hornung@indiscale.com)
# Copyright (C) 2020 Henrik tom Wörden
-# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020, 2024 IndiScale GmbH <info@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
@@ -34,7 +34,7 @@
function mysql_execute {
#TODO is it meaningful that here always the database user is used???
set -e
- $MYSQL_CMD $(get_db_args) -e "$1"
+ $MYSQL_CMD $(get_db_args) -e "$@"
ret=${PIPESTATUS[0]}
if [ "$ret" -ne 0 ]; then
failure "MYSQL ERROR"
@@ -52,47 +52,31 @@ function mysql_execute_file {
fi
}
-
-function get_mysql_args {
- echo "$(get_mysql_args_nodb) --database=$DATABASE_NAME"
-}
-
+# Return the arguments from `get_db_args_nodb` and additionally the database name as
+# `--database=mydatabasename`.
function get_db_args {
echo "$(get_db_args_nodb) --database=$DATABASE_NAME"
}
+# Return arguments for user, password, host, port and additional options in MYSQL_OPTS.
+#
+# For example, the output may be:
+# --user=myuser --password=mypassword --host=example.com --port=1234 --other --option
function get_db_args_nodb {
- if [ "$DATABASE_USER" ]; then
- mysql_con_arguments="--user=$DATABASE_USER"
+ if [ -n "$MYSQL_USER" ]; then
+ mysql_con_arguments="--user=$MYSQL_USER"
fi
- if [ "$DATABASE_USER_PW" ]; then
- mysql_con_arguments="$mysql_con_arguments --password=$DATABASE_USER_PW"
+ if [ -n "$MYSQL_USER_PASSWORD" ]; then
+ mysql_con_arguments="$mysql_con_arguments --password=$MYSQL_USER_PASSWORD"
fi
- if [[ "$MYSQL_HOST" && ( "$MYSQL_HOST" != "localhost" ) ]]; then
+ if [ -n "$MYSQL_HOST" ] && [ "$MYSQL_HOST" != "localhost" ]; then
mysql_con_arguments="$mysql_con_arguments --host=$MYSQL_HOST"
- if [ "$MYSQL_PORT" ]; then
- mysql_con_arguments="$mysql_con_arguments --port=$MYSQL_PORT"
- fi
fi
- echo $mysql_con_arguments
-}
-
-function get_mysql_args_nodb {
- if [ "$LOGIN_PATH" ]; then
- mysql_con_arguments="--login-path=$LOGIN_PATH"
- else
- if [ "$MYSQL_USER" ]; then
- mysql_con_arguments="--user=$MYSQL_USER"
- fi
- if [ "$MYSQL_USER_PASSWORD" ]; then
- mysql_con_arguments="$mysql_con_arguments --password=$MYSQL_USER_PASSWORD"
- fi
- if [[ "$MYSQL_HOST" && ( "$MYSQL_HOST" != "localhost" ) ]]; then
- mysql_con_arguments="$mysql_con_arguments --host=$MYSQL_HOST"
- if [ "$MYSQL_PORT" ]; then
- mysql_con_arguments="$mysql_con_arguments --port=$MYSQL_PORT"
- fi
- fi
+ if [ -n "$MYSQL_PORT" ] && [ "$MYSQL_PORT" != "3306" ]; then
+ mysql_con_arguments="$mysql_con_arguments --port=$MYSQL_PORT"
+ fi
+ if [ -n "$MYSQL_OPTS" ] ; then
+ mysql_con_arguments="$mysql_con_arguments $MYSQL_OPTS"
fi
echo $mysql_con_arguments
}
diff --git a/utils/load_settings.sh b/utils/load_settings.sh
index 44d8f2d630270727a3a7cbd08f4b3ee037e6a7d7..8531113afa5f670400988f92692a59a031c91a11 100644
--- a/utils/load_settings.sh
+++ b/utils/load_settings.sh
@@ -2,9 +2,9 @@
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright (C) 2019, 2020 Daniel Hornung (d.hornung@indiscale.com)
+# Copyright (C) 2019, 2020, 2024 Daniel Hornung <d.hornung@indiscale.com>
# Copyright (C) 2020 Henrik tom Wörden
-# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020, 2024 IndiScale GmbH <info@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
@@ -62,9 +62,12 @@ export MYSQL_CMD
export MYSQLDUMP_CMD
export MYSQLADMIN_CMD
export MYSQL_CONFIG_EDITOR_CMD
+
export MYSQL_HOST
export MYSQL_PORT
export MYSQL_USER
+export MYSQL_OPTS
+
export DATABASE_NAME
export DATABASE_USER
export DATABASE_USER_PW
diff --git a/utils/make_db b/utils/make_db
index ea301acc6228344feb7f8b4f7e97a55cd1919048..c7f94fd2d57944758cb48f0aedb2ac2672ec16d3 100755
--- a/utils/make_db
+++ b/utils/make_db
@@ -1,10 +1,9 @@
#!/bin/bash
-# ** header v3.0
# This file is a part of the LinkAhead Project.
#
-# Copyright (C) 2021 Indiscale GmbH <info@indiscale.com>
-# Copyright (C) 2019, 2020, 2021 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2021, 2024 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2019, 2020, 2021, 2024 Daniel Hornung <d.hornung@indiscale.com>
# Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
# Copyright (C) 2020 IndiScale <info@indiscale.com>
@@ -22,7 +21,6 @@
# 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/>.
#
-# ** end header
# Although some sanity checks are performed, this script still allows lots of SQL injection
# possibilities.
@@ -87,7 +85,7 @@ function _install_unit_test_database () {
if _db_exists "$DATABASE_NAME"; then
echo "using $DATABASE_NAME"
else
- sed "s/db_5_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_mysql_args_nodb)
+ sed "s/db_5_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_db_args_nodb)
# create test user
grant
@@ -113,7 +111,7 @@ function _setup_mytap() {
pushd libs > /dev/null
unzip -u mytap*.zip > /dev/null
pushd mytap*/ > /dev/null
- $MYSQL_CMD $(get_mysql_args_nodb) < mytap.sql > /dev/null || exit 1
+ $MYSQL_CMD $(get_db_args_nodb) < mytap.sql > /dev/null || exit 1
popd > /dev/null
rm -r mytap*/
popd > /dev/null
@@ -129,13 +127,28 @@ name in your .config file "
exit 0
fi
- sed "s/db_5_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_mysql_args_nodb)
+ sed "s/db_5_0/$DATABASE_NAME/g" "$INSTALL_SQL_FILE" | $MYSQL_CMD $(get_db_args_nodb)
+}
+
+function sanity_check() {
+ trap "$(shopt -po errexit)" RETURN
+ set +e
+ echo -n "running sanity checks ..."
+ msg="$($MYSQL_CMD $(get_db_args) < "utils/sanity_check.sql" 2>/dev/null)"
+ code="$?"
+ if [ "$code" -eq "0" ] ; then
+ echo " [OK]"
+ else
+ echo " [FAILED]"
+ echo "$msg"
+ exit 1
+ fi
}
# Inserts the dump (arg 1) into the database
function restore_db() {
SQL_FILE="$1"
- $MYSQL_CMD $(get_mysql_args) < "$SQL_FILE"
+ $MYSQL_CMD $(get_db_args) < "$SQL_FILE"
cat <<EOF
If this is not the same SQL server where the SQL dump was originally created
from, make sure that a user with sufficient permissions exists. Note that you
@@ -144,7 +157,7 @@ EOF
}
function test-connection() {
- $MYSQL_CMD $(get_mysql_args_nodb) -e "select 0;"
+ $MYSQL_CMD $(get_db_args_nodb) -e "select 0;"
}
# Creates a user and grants it sufficient rights.
@@ -168,7 +181,7 @@ function grant() {
if [[ $1 = "--strict" ]] ; then
for host in ${DATABASE_USER_HOST_LIST//,/ } ; do
CMD="SELECT COUNT(*) FROM mysql.user WHERE user='${DATABASE_USER}' AND host='${host}';"
- [[ $($MYSQL_CMD $(get_mysql_args_nodb) -s -N -e "$CMD") = 0 ]] || {
+ [[ $($MYSQL_CMD $(get_db_args_nodb) -s -N -e "$CMD") = 0 ]] || {
echo "The user '${DATABASE_USER}@${host}' is already in the database."
echo "Please use another user or delete it, e.g. with"
echo "'mysql -u ${MYSQL_USER} -p -e \"DROP USER ${DATABASE_USER}@${host};\"'"
@@ -182,7 +195,7 @@ function grant() {
# FIXME Are all these permissions necessary? See
# https://gitlab.indiscale.com/caosdb/src/caosdb-mysqlbackend/-/issues/28 "Default
# installation target does not work for existing databases"
- $MYSQL_CMD $(get_mysql_args_nodb) <<EOF
+ $MYSQL_CMD $(get_db_args_nodb) <<EOF
CREATE USER IF NOT EXISTS
'$DATABASE_USER'@'$host' identified by '$DATABASE_USER_PW';
GRANT USAGE ON *.* TO '$DATABASE_USER'@'$host';
@@ -197,16 +210,16 @@ EOF
function drop() {
DROPDB="$1"
for host in ${DATABASE_USER_HOST_LIST//,/ } ; do
- $MYSQL_CMD $(get_mysql_args_nodb) -e "DROP USER '${DATABASE_USER}'@'${host}';" || true
+ $MYSQL_CMD $(get_db_args_nodb) -e "DROP USER '${DATABASE_USER}'@'${host}';" || true
done
- "$MYSQLADMIN_CMD" $(get_mysql_args_nodb) -f drop "$DROPDB"
+ "$MYSQLADMIN_CMD" $(get_db_args_nodb) -f drop "$DROPDB"
}
# Returns 0 or non-zero, depending on whether the database exists already.
# Optional parameter: [DATABASE_NAME], else $DATABASE_NAME is used.
function _db_exists() {
- $MYSQL_CMD $(get_mysql_args_nodb) -D "${1-${DATABASE_NAME}}" -e "show tables;" > /dev/null 2>&1 \
+ $MYSQL_CMD $(get_db_args_nodb) -D "${1-${DATABASE_NAME}}" -e "show tables;" > /dev/null 2>&1 \
&& return 0 || return 1
}
@@ -235,7 +248,7 @@ function grant-permission() {
fi
cmd="SELECT COUNT(1) from roles where name='${role}';"
- count=$($MYSQL_CMD $(get_mysql_args) -AN -e "$cmd")
+ count=$($MYSQL_CMD $(get_db_args) -AN -e "$cmd")
if [[ $count == "0" ]]; then
echo "Role not found!"
exit 1
@@ -244,7 +257,7 @@ function grant-permission() {
cmd="INSERT INTO permissions (role, permissions) VALUE ('${role}', '${permissions}')"
cmd+="ON DUPLICATE KEY UPDATE role='${role}', permissions='${permissions}'"
cmd+=";"
- $MYSQL_CMD $(get_mysql_args) -e "$cmd"
+ $MYSQL_CMD $(get_db_args) -e "$cmd"
}
@@ -256,5 +269,6 @@ case $1 in
"test-connection") test-connection ;;
"install_db") install_db ;;
"restore_db") restore_db $2 ;;
+ "sanity_check") sanity_check ;;
*) echo "Unknown action: $1"; exit 32
esac
diff --git a/utils/patch_header.sh b/utils/patch_header.sh
index 76896b067960f67a101bfa3954bbdecb4f41b31d..c7d25ae3f21ccbba30658182572177847d5610a7 100644
--- a/utils/patch_header.sh
+++ b/utils/patch_header.sh
@@ -1,12 +1,10 @@
-#
-# ** header v3.0
# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright (C) 2019, 2020 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2019, 2020, 2025 Daniel Hornung <d.hornung@indiscale.com>
# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
-# Copyright (C) 2020 IndiScale <info@indiscale.com>
+# Copyright (C) 2020, 2025 IndiScale <info@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -21,12 +19,20 @@
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
#
-# ** end header
-#
###############################################################################
# header for patch scripts #
###############################################################################
+#
+# This file defines the following functions (see below for more detailed descriptions):
+#
+# - check_version_or_exit: Check if the stored version is as expected.
+# - update_version: Set the stored version.
+# - dump_table: Store table content into a file.
+# - redo_table: Apply the table content stored by dump_table.
+#
+# This file also sets the `errexit` option (`set -e`).
+#
set -e
@@ -63,7 +69,7 @@ configuration make file. Notable examples are:
- DATABASE_USER_PW
EOF
- )
+ )
function _print_help() {
echo -e "$USAGE"
@@ -115,21 +121,51 @@ done
if [ -n "$PATCH" ]; then
echo -ne "applying patch $PATCH to $DATABASE_NAME ... "
fi
-# @param $1: db version string, e.g. v2.0.0
-# @return: 0 on success, 1 on failure
-function check_version {
+
+# usage: check_version_or_exit version
+#
+# Check if the version string is as expected. Otherwise, `exit 0`.
+#
+# Arguments
+# ---------
+#
+# version: str
+# The expected database version string, e.g. 'v2.0.0'
+#
+# Returns
+# -------
+#
+# 0 on success
+function check_version_or_exit {
local version=$($MYSQL_CMD $(get_db_args) -B -e "Select CaosDBVersion();")
- if [[ "$(echo $version | sed 's/^CaosDBVersion()\s//')" = "$1" ]]; then
+ local version="$(echo $version | sed 's/^CaosDBVersion()\s//')"
+ if [[ "$version" = "$1" ]]; then
return 0
fi
uptodate
}
-# @param $1: new version string
+# Deprecated name, call "check_version_or_exit" directly instead.
+function check_version {
+ check_version_or_exit "$1"
+}
+
+# usage: update_version version
+#
+# Set the version string.
+#
+# Arguments
+# ---------
+#
+# version: str
+# The new database version string, e.g. 'v2.0.0'
function update_version {
mysql_execute "DROP FUNCTION IF EXISTS CaosDBVersion; CREATE FUNCTION CaosDBVersion() RETURNS VARCHAR(255) DETERMINISTIC RETURN '$1';"
}
+# usage: dump_table table
+#
+# Dump the table given in the argument into file "caosdb.<table>.<OLD_VERSION>.dump.sql"
function dump_table {
if [[ -z $MYSQLDUMP_CMD ]]; then
echo "Cannot find mysqldump program!" >&2
@@ -139,6 +175,9 @@ function dump_table {
> ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
}
+# usage: redo_table table
+#
+# Apply the dump from `dump_table` to the database. Takes the same argument.
function redo_table {
$MYSQL_CMD $(get_db_args) < ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
}
diff --git a/utils/sanity_check.sql b/utils/sanity_check.sql
new file mode 100644
index 0000000000000000000000000000000000000000..5e3d580cc386feb44b5e97269ac384c050d6cf84
--- /dev/null
+++ b/utils/sanity_check.sql
@@ -0,0 +1,121 @@
+
+
+DROP PROCEDURE IF EXISTS sanity_check;
+delimiter //
+CREATE PROCEDURE sanity_check()
+sanityCheckBody: BEGIN
+ CREATE TEMPORARY TABLE expected_tables (table_name VARCHAR(255));
+ INSERT INTO expected_tables (table_name) VALUES
+("archive_collection_type"),
+("archive_data_type"),
+("archive_date_data"),
+("archive_datetime_data"),
+("archive_desc_overrides"),
+("archive_double_data"),
+("archive_entities"),
+("archive_enum_data"),
+("archive_files"),
+("archive_integer_data"),
+("archive_isa"),
+("archive_name_data"),
+("archive_name_overrides"),
+("archive_null_data"),
+("archive_query_template_def"),
+("archive_reference_data"),
+("archive_text_data"),
+("collection_type"),
+("data_type"),
+("date_data"),
+("datetime_data"),
+("desc_overrides"),
+("double_data"),
+("entities"),
+("entity_ids"),
+("entity_acl"),
+("entity_version"),
+("enum_data"),
+("feature_config"),
+("files"),
+("integer_data"),
+("isa_cache"),
+("name_data"),
+("name_overrides"),
+("null_data"),
+("passwd"),
+("permissions"),
+("query_template_def"),
+("reference_data"),
+("roles"),
+("stats"),
+("text_data"),
+("transaction_log"),
+("transactions"),
+("units_lin_con"),
+("user_info"),
+("user_roles")
+;
+
+SELECT COUNT(WRONG) INTO @count_wrong FROM (
+ SELECT l.table_name AS MATCHED,
+ r.table_name AS WRONG
+ FROM
+ expected_tables AS l
+ RIGHT OUTER JOIN
+ information_schema.tables AS r
+ ON (r.table_name COLLATE utf8_unicode_ci = l.table_name)
+ WHERE r.table_schema = database() AND r.table_type != 'TEMPORARY'
+ )
+ AS temp WHERE temp.MATCHED IS NULL;
+
+SELECT COUNT(MISSING) INTO @count_missing FROM (
+ SELECT l.table_name AS MISSING,
+ r.table_name AS MATCHED
+ FROM
+ expected_tables AS l
+ LEFT OUTER JOIN
+ information_schema.tables AS r
+ ON (r.table_name COLLATE utf8_unicode_ci = l.table_name)
+ WHERE r.table_schema = database() OR r.table_schema IS NULL
+ )
+ AS temp WHERE temp.MATCHED IS NULL;
+
+IF @count_missing = 0 AND @count_wrong = 0 THEN
+ LEAVE sanityCheckBody;
+END IF;
+
+SELECT "--------------";
+SELECT @count_missing AS "Number of missing tables";
+
+SELECT MISSING AS "Missing tables" FROM (
+ SELECT l.table_name AS MISSING, r.table_name AS MATCHED FROM
+ expected_tables AS l
+ LEFT OUTER JOIN
+ information_schema.tables AS r
+ ON (r.table_name COLLATE utf8_unicode_ci = l.table_name)
+ WHERE r.table_schema = database() OR r.table_schema IS NULL
+ )
+ AS temp WHERE temp.MATCHED IS NULL;
+
+SELECT "--------------";
+SELECT @count_wrong AS "Number of tables which should not exist";
+
+SELECT WRONG AS "Tables which should not exist" FROM (
+ SELECT expec.table_name AS MATCHED, info.table_name AS WRONG FROM
+ expected_tables AS expec
+ RIGHT OUTER JOIN
+ information_schema.tables AS info
+ ON (info.table_name COLLATE utf8_unicode_ci = expec.table_name)
+ WHERE info.table_schema = database() and info.table_type != 'TEMPORARY'
+ )
+ AS temp WHERE temp.MATCHED IS NULL;
+
+SELECT "--------------";
+SELECT "ERROR" from sanity_check_failed;
+
+END;
+//
+delimiter ;
+
+CALL sanity_check();
+
+DROP PROCEDURE sanity_check;
diff --git a/utils/update_sql_procedures.sh b/utils/update_sql_procedures.sh
index bbbbc15b299cf24bcfa4c72da6a4e49534655e67..2fe1febfc7d5bbe45a8bc68c630e13d1cef6707f 100755
--- a/utils/update_sql_procedures.sh
+++ b/utils/update_sql_procedures.sh
@@ -1,13 +1,12 @@
#!/bin/bash
#
-# ** header v3.0
# This 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) 2020 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2020, 2024 Daniel Hornung <d.hornung@indiscale.com>
# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@indiscale.com>
-# Copyright (C) 2020 IndiScale <info@indiscale.com>
+# Copyright (C) 2020, 2024 IndiScale <info@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
@@ -22,8 +21,6 @@
# 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/>.
#
-# ** end header
-#
# Updates all SQL procedures
@@ -37,7 +34,7 @@ fi
source $UTILSPATH/load_settings.sh
source $UTILSPATH/helpers.sh
-echo -n "updating procedures ... "
+echo "Updating procedures ... "
temp_proc_sql=$(mktemp --suffix=.sql)
sed -e "s/db_5_0/$DATABASE_NAME/g" procedures/*.sql procedures/query/*.sql \
> "$temp_proc_sql"