diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b45dde5de1e4cafdbc02a15c4b775b763d5447bd..9f8c131968c050fb18001b5dc7c5468d0ed26dae 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -22,7 +22,7 @@
variables:
DEPLOY_REF: dev
- CI_REGISTRY_IMAGE: $CI_REGISTRY/caosdb/caosdb-pylib/testenv:latest
+ CI_REGISTRY_IMAGE: $CI_REGISTRY/caosdb/src/caosdb-pylib/testenv:latest
# When using dind, it's wise to use the overlayfs driver for
# improved performance.
@@ -65,7 +65,7 @@ trigger_build:
stage: deploy
script:
- /usr/bin/curl -X POST
- -F token=$DEPLOY_TRIGGER_TOKEN
+ -F token=$CI_JOB_TOKEN
-F "variables[F_BRANCH]=$CI_COMMIT_REF_NAME"
-F "variables[PYLIB]=$CI_COMMIT_REF_NAME"
-F "variables[TriggerdBy]=PYLIB"
@@ -92,15 +92,13 @@ build-testenv:
- docker push $CI_REGISTRY_IMAGE
# Build the sphinx documentation and make it ready for deployment by Gitlab Pages
-# documentation:
-# stage: deploy
-
# Special job for serving a static website. See https://docs.gitlab.com/ee/ci/yaml/README.html#pages
-pages:
+pages_prepare: &pages_prepare
+ tags: [ cached-dind ]
stage: deploy
only:
- # TODO this should be for master only, once releases are more regularly
- - dev
+ refs:
+ - /^release-.*$/i
script:
- echo "Deploying"
- make doc
@@ -108,3 +106,8 @@ pages:
artifacts:
paths:
- public
+pages:
+ <<: *pages_prepare
+ only:
+ refs:
+ - main
diff --git a/CHANGELOG.md b/CHANGELOG.md
index fd2bbfd27503488cbb7b2e7aef30ff959f3f323d..38b470db9d36675ffcef0b7e1434a08c3be7f407 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,11 +9,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added ###
-* Versioning support (experimental). The version db.Version class can
- represents particular entity versions and also the complete history of an
- entity.
-* Automated documentation builds: `make doc`
-
### Changed ###
### Deprecated ###
@@ -22,10 +17,91 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed ###
-* deepcopy of `_Messages` objects
+* #53 Documentation of inheritance
+
+### Security ###
+
+## [0.5.2] - 2021-06-03 ##
+
+### Added ###
+
+* Entity State support (experimental, no StateModel support yet). See the
+ `caosdb.State` class for more information.
+* `etag` property for the `caosdb.Query` class. The etag allows to debug the
+ caching and to decide whether the server has changed between queries.
+* function `_read_config_files` to read `pycaosdb.ini` files from different paths.
+
+### Changed ###
+
+* Updated error-handling tutorial in documentation to reflect the new
+ error classes
+
+### Deprecated ###
+
+### Removed ###
+
+### Fixed ###
+* #45 - test_config_ini_via_envvar
### Security ###
+## [0.5.1] - 2021-02-12 ##
+
+### Fixed ###
+
+* #43 - Error with `execute_query` when server doesn't support query caching.
+
+## [0.5.0] - 2021-02-11 ##
+
+### Added ###
+
+* New exceptions `HTTPForbiddenException` and
+ `HTTPResourceNotFoundException` for HTTP 403 and 404 errors,
+ respectively.
+* `BadQueryError`, `EmptyUniqueQueryError`, and `QueryNotUniqueError`
+ for bad (unique) queries.
+* Added `cache` paramter to `execute_query` and `Query.execute` which indicates
+ whether server may use the cache for the query execution.
+* Added `cached` property to the `Query` class which indicates whether the
+ server used the cache for the execution of the last query.
+* Documentation moved from wiki to this repository and enhanced.
+
+### Changed ###
+
+* Renaming of `URITooLongException` to `HTTPURITooLongError`.
+* Raising of entity exceptions and transaction errors. Whenever any
+ transaction fails, a `TransactionError` is raised. If one ore more
+ entities caused that failure, corresponding entity errors are
+ attached as direct and indirect children of the
+ `TransactionError`. They can be accessed via the `get_errors`
+ (direct children) and `get_all_errors` (direct and indirect
+ children) methods; the causing entities are accessed by
+ `get_entities` and `get_all_entities`. The `has_error` method can be
+ used to check whether a `TransactionError` was caused by a specific
+ `EntityError`.
+* Unique queries will now result in `EmptyUniqueQueryError` or
+ `QueryNotUniqueError` if no or more than one possible candidate is
+ found, respectively.
+
+### Removed ###
+
+* Dynamic exception type `EntityMultiError`.
+* `get_something` functions from all error object in `exceptions.py`
+* `AmbiguityException`
+
+## [0.4.1] - 2021-02-10 ##
+
+### Added ###
+
+* Versioning support (experimental). The version db.Version class can
+ represents particular entity versions and also the complete history of an
+ entity.
+* Automated documentation builds: `make doc`
+
+### Fixed ###
+
+* deepcopy of `_Messages` objects
+
## [0.4.0] - 2020-07-17##
### Added ###
@@ -79,7 +155,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
* import bugs in apiutils
-## [0.2.4] -- 2020-04-23
+## [0.2.4] - 2020-04-23
### Added
diff --git a/DEPENDENCIES.md b/DEPENDENCIES.md
new file mode 100644
index 0000000000000000000000000000000000000000..04e783a7fa31b1d5c3a600a1009c8f040db1620d
--- /dev/null
+++ b/DEPENDENCIES.md
@@ -0,0 +1,6 @@
+* caosdb-server == 0.3
+* Python >= 3.5
+* pip >= 20.0.2
+
+
+Any other dependencies are being installed via pip
diff --git a/README.md b/README.md
index ef26a604905d5140ae9a775065002af35ffe2121..04b34cbc07c98e73740b13200ed83fe067af99d2 100644
--- a/README.md
+++ b/README.md
@@ -1,25 +1,53 @@
-# Welcome
+
+# README
+
+## Welcome
This is the **CaosDB Python Client Library** repository and a part of the
CaosDB project.
-# Setup
+## Setup
Please read the [README_SETUP.md](README_SETUP.md) for instructions on how to
setup this code.
-# Further Reading
+## Further Reading
+
+Please refer to the [official documentation](https://docs.indiscale.com/caosdb-pylib/) for more information.
+
+## Contributing
+
+Thank you very much to all contributers—[past, present](https://gitlab.com/caosdb/caosdb/-/blob/dev/HUMANS.md), and prospective ones.
-Please refer to the [official gitlab repository of the CaosDB
-project](https://gitlab.com/caosdb/caosdb) for more information.
+### Code of Conduct
-# License
+By participating, you are expected to uphold our [Code of Conduct](https://gitlab.com/caosdb/caosdb/-/blob/dev/CODE_OF_CONDUCT.md).
-Copyright (C) 2018 Research Group Biomedical Physics, Max Planck Institute for
-Dynamics and Self-Organization Göttingen.
-Copyright (C) 2020 Indiscale GmbH <info@indiscale.com>
+### How to Contribute
+
+* You found a bug, have a question, or want to request a feature? Please
+[create an issue](https://gitlab.com/caosdb/caosdb-pylib/-/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.
+ * **Code style:** This project adhers to the PEP8 recommendations, you can test your code style
+ using the `autopep8` tool (`autopep8 -i -r ./`). Please write your doc strings following the
+ [NumpyDoc](https://numpydoc.readthedocs.io/en/latest/format.html) conventions.
+* If you have a suggestion for the [documentation](https://docs.indiscale.com/caosdb-pylib/),
+the preferred way is also a merge request as describe above (the documentation resides in `src/doc`).
+However, you can also create an issue for it.
+* You can also contact us at **info (AT) caosdb.de** and join the
+ CaosDB community on
+ [#caosdb: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) 2020-2021 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 481182d02d4c25acc5c5ed9607a282b22e861448..9da548395073643c16539cef180c4d6412dd8d46 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -30,6 +30,23 @@ packages you will ever need out of the box. If you prefer, you may also install
After installation, open an Anaconda prompt from the Windows menu and continue in the [Generic
installation](#generic-installation) section.
+#### iOS ####
+
+If there is no Python 3 installed yet, there are two main ways to obtain it: Either get the binary
+package from [python.org](https://www.python.org/downloads/) or, for advanced users, install via [Homebrew](https://brew.sh/). After installation
+from python.org, it is recommended to also update the TLS certificates for Python (this requires
+administrator rights for your user):
+
+```sh
+# Replace this with your Python version number:
+cd /Applications/Python\ 3.9/
+
+# This needs administrator rights:
+sudo ./Install\ Certificates.command
+```
+
+After these steps, you may continue with the [Generic installation](#generic-installation).
+
#### Generic installation ####
To install PyCaosDB locally, use `pip3` (also called `pip` on some systems):
@@ -58,7 +75,7 @@ current working directory will be read additionally, if it exists.
Here, we will look at the most common configuration options. For a full and
comprehensive description please check out
-[pycaosdb.ini file](https://gitlab.com/caosdb/caosdb-pylib/-/blob/master/examples/pycaosdb.ini)
+[pycaosdb.ini file](https://gitlab.com/caosdb/caosdb-pylib/-/blob/main/examples/pycaosdb.ini)
You can download this file and use it as a starting point.
@@ -67,7 +84,7 @@ Typically, you need to change at least the `url` and `username` fields as requir
you do not know what to put there, but for the demo instances https://demo.indiscale.com, `username=admin`
and `password=caosdb` should work).
-### Authentication ##
+### Authentication ###
The default configuration (that your are asked for your password when ever a connection is created
can be changed by setting `password_method`:
@@ -92,7 +109,7 @@ The following illustrates the recommended options:
#password_method=keyring
```
-### SSL Certificate ##
+### SSL Certificate ###
In some cases (especially if you are testing CaosDB) you might need to supply
an SSL certificate to allow SSL encryption.
@@ -101,9 +118,9 @@ an SSL certificate to allow SSL encryption.
cacert=/path/to/caosdb.ca.pem
```
-### Further Settings ##
+### Further Settings ###
As mentioned above, a complete list of options can be found in the
-[pycaosdb.ini file](https://gitlab.com/caosdb/caosdb-pylib/-/blob/master/examples/pycaosdb.ini) in
+[pycaosdb.ini file](https://gitlab.com/caosdb/caosdb-pylib/-/blob/main/examples/pycaosdb.ini) in
the examples folder of the source code.
## Try it out ##
@@ -121,21 +138,20 @@ Out[2]: Connection to CaosDB with 501 Records.
Note: This setup will ask you for your password whenever a new connection is created. If you do not
like this, check out the "Authentication" section in the [configuration documentation](configuration.md).
-Now would be a good time to continue with the [tutorials](tutorials.html).
+Now would be a good time to continue with the [tutorials](tutorials/index).
## Run Unit Tests
tox
-## Code Formatting
-
-autopep8 -i -r ./
-
-## Documentation #
+## Documentation ##
Build documentation in `build/` with `make doc`.
-### Requirements ##
+### Requirements ###
- `sphinx`
- `sphinx-autoapi`
- `recommonmark`
+
+### Troubleshooting ###
+If the client is to be executed directly from the `/src` folder, an initial `.\setup.py install --user` must be called.
diff --git a/RELEASE_GUIDELINES.md b/RELEASE_GUIDELINES.md
index 02be5c1ad19f6a3a405fb08d62e23dab350ad445..e015b598117abdcd575cf17e2f095fec459a4c4c 100644
--- a/RELEASE_GUIDELINES.md
+++ b/RELEASE_GUIDELINES.md
@@ -16,21 +16,27 @@ guidelines of the CaosDB Project
1. Create a release branch from the dev branch. This prevents further changes
to the code base and a never ending release process. Naming: `release-<VERSION>`
-2. Check all general prerequisites.
+2. Update CHANGELOG.md
-3. Prepare [setup.py](./setup.py): Update the `MAJOR`, `MINOR`, `MICRO`, `PRE`
+3. Check all general prerequisites.
+
+4. Prepare [setup.py](./setup.py): Check the `MAJOR`, `MINOR`, `MICRO`, `PRE`
variables and set `ISRELEASED` to `True`. Use the possibility to issue
pre-release versions for testing.
-4. Merge the release branch into the master branch.
+5. Merge the release branch into the main branch.
-5. Tag the latest commit of the master branch with `v<VERSION>`.
+6. Tag the latest commit of the main branch with `v<VERSION>`.
-6. Delete the release branch.
+7. Delete the release branch.
-7. Remove possibly existing `./dist` directory with old release.
+8. Remove possibly existing `./dist` directory with old release.
-8. Publish the release by executing `./release.sh` with uploads the caosdb
+9. Publish the release by executing `./release.sh` with uploads the caosdb
module to the Python Package Index [pypi.org](https://pypi.org).
-9. Merge the master branch back into the dev branch.
+10. Merge the main branch back into the dev branch.
+
+11. After the merge of main to dev, start a new development version by
+ setting `ISRELEASED` to `False` and by increasing at least the `MIRCO`
+ version in [setup.py](./setup.py)
diff --git a/examples/set_permissions.py b/examples/set_permissions.py
index 8b2b59f10ac033110af846eef0ed90356a09553d..8162b11bfefb41b1bcdbc74b8e314f99a61d1a4e 100755
--- a/examples/set_permissions.py
+++ b/examples/set_permissions.py
@@ -25,15 +25,13 @@
As a result, only a specific user or group may access it.
-This script assumes that data similar to the demo server of IndiScale (at
-demo.indiscale.com) exists on the server specified in the pycaosdb.ini
-configuration.
+This script assumes that the user specified in the pycaosdb.ini
+configuration can create new entities.
"""
import caosdb as db
from caosdb import administration as admin
-import lxml
def assert_user_and_role():
@@ -50,27 +48,27 @@ out : tuple
"""
try:
human_user = admin._retrieve_user("jane")
- _activate_user("jane")
- except db.EntityDoesNotExistError:
+ admin._update_user(name="jane", status="ACTIVE")
+ except db.HTTPResourceNotFoundError:
human_user = admin._insert_user(
"jane", password="Human_Rememberable_Password_1234", status="ACTIVE")
try:
alien_user = admin._retrieve_user("xaxys")
- _activate_user("xaxys")
- except db.EntityDoesNotExistError:
+ admin._update_user(name="xaxys", status="ACTIVE")
+ except db.HTTPResourceNotFoundError:
alien_user = admin._insert_user("xaxys", password="4321_Syxax",
status="ACTIVE")
# At the moment, the return value is only "ok" for successful insertions.
try:
human_role = admin._retrieve_role("human")
- except db.EntityDoesNotExistError:
+ except db.HTTPResourceNotFoundError:
human_role = admin._insert_role("human", "An Earthling.")
try:
alien_role = admin._retrieve_role("alien")
- except db.EntityDoesNotExistError:
+ except db.HTTPResourceNotFoundError:
alien_role = admin._insert_role("alien", "An Extra-terrestrial.")
admin._set_roles("jane", ["human"])
@@ -80,24 +78,6 @@ out : tuple
("xaxys", list(admin._get_roles("xaxys"))))
-def _activate_user(user):
- """Set the user state to "ACTIVE" if necessary.
-
-Parameters
-----------
-user : str
- The user to activate.
-
-Returns
--------
-None
-
- """
- user_xml = lxml.etree.fromstring(admin._retrieve_user(user))
- if user_xml.xpath("User")[0].attrib["status"] != "ACTIVE":
- admin._update_user(user, status="ACTIVE")
-
-
def get_entities(count=1):
"""Retrieve one or more entities.
@@ -111,9 +91,11 @@ Returns
out : Container
A container of retrieved entities, the length is given by the parameter count.
"""
- cont = db.execute_query("FIND RECORD Guitar", flags={"P": "0L{n}".format(n=count)})
+ cont = db.execute_query("FIND RECORD 'Human Food'", flags={
+ "P": "0L{n}".format(n=count)})
if len(cont) != count:
- raise db.CaosDBException(msg="Incorrect number of entitities returned.")
+ raise db.CaosDBException(
+ msg="Incorrect number of entitities returned.")
return cont
@@ -138,7 +120,8 @@ general : bool, optional
# Set general permissions
if general:
- grant = admin.PermissionRule(action="grant", permission="RETRIEVE:OWNER")
+ grant = admin.PermissionRule(
+ action="grant", permission="RETRIEVE:OWNER")
deny = admin.PermissionRule(action="deny", permission="RETRIEVE:FILE")
admin._set_permissions(role=role_grant, permission_rules=[grant])
@@ -189,9 +172,12 @@ None
for ent in cont:
ent.retrieve()
print("Successfully retrieved all entities.")
- except db.AuthorizationException:
- print(ent)
- print("Could not retrieve this entity although it should have been possible!")
+ except db.TransactionError as te:
+ if te.has_error(db.AuthorizationError):
+ print(ent)
+ print("Could not retrieve this entity although it should have been possible!")
+ else:
+ raise te
# Switch to user without permissions
db.configure_connection(username=denied_user[0], password=denied_user[1],
@@ -206,23 +192,45 @@ None
denied_all = False
print(ent)
print("Could retrieve this entity although it should not have been possible!")
- except db.AuthorizationException:
- pass
+ except db.TransactionError as te:
+ # Only do something if an error wasn't caused by an
+ # AuthorizationError
+ if not te.has_error(db.AuthorizationError):
+ raise te
if denied_all:
print("Retrieval of all entities was successfully denied.")
+def create_test_entities():
+ """Create some test entities.
+ After calling this function, there will be a RecordType "Human Food" with the corresponding Records
+ "Bread", "Tomatoes", and "Twinkies" inserted in the database.
+ """
+ rt = db.RecordType(
+ name="Human Food", description="Food that can be eaten only by humans").insert()
+ food = ("Bread", "Tomatoes", "Twinkies")
+
+ cont = db.Container()
+ for i in range(len(food)):
+ rec = db.Record(food[i])
+ rec.add_parent(name="Human Food")
+ cont.append(rec)
+
+ cont.insert()
+
+
def main():
"""The main function of this script."""
- db.connection.connection.get_connection()._login()
-
+ """Create some test entities"""
+ create_test_entities()
+ """Create new users"""
human, alien = assert_user_and_role()
-
- # public, private, undefined entities
+ """Load the newly created entities."""
entities = get_entities(count=3)
-
+ """Set permission for the entities (only humans are allowed to eat human food)"""
set_permission(human[1][0], alien[1][0], entities)
+ """Test the permissions"""
test_permission((human[0], "Human_Rememberable_Password_1234"),
(alien[0], "4321_Syxax"), entities)
diff --git a/release.sh b/release.sh
index a5f3654291743e5ac22fd3b938719e294b3a1e90..1af097f014de6cd9eb3d3e8ba5da34aea0fe1671 100755
--- a/release.sh
+++ b/release.sh
@@ -1,4 +1,4 @@
#!/bin/bash
-rm -r dist/ build/ .eggs/
+rm -rf dist/ build/ .eggs/
python setup.py sdist bdist_wheel
python -m twine upload -s dist/*
diff --git a/setup.py b/setup.py
index 4ab2d7669cc4f6d3f4873c0265da6c8cf06932ba..e1d39458ea8d1b0b17ea12a82ebd7133b27b045a 100755
--- a/setup.py
+++ b/setup.py
@@ -46,8 +46,8 @@ from setuptools import find_packages, setup
########################################################################
MAJOR = 0
-MINOR = 4
-MICRO = 1
+MINOR = 5
+MICRO = 3
PRE = "" # e.g. rc0, alpha.1, 0.beta-23
ISRELEASED = False
diff --git a/src/caosdb/__init__.py b/src/caosdb/__init__.py
index b83442f1bdf0f2b111a66d63e4549f68b6bedb69..7e06885fe495c1e8c4ccc99b7d0c0f8ff8c34b5b 100644
--- a/src/caosdb/__init__.py
+++ b/src/caosdb/__init__.py
@@ -37,7 +37,8 @@ from os.path import expanduser, join
import caosdb.apiutils
from caosdb.common import administration
from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER,
- REFERENCE, TEXT, LIST)
+ LIST, REFERENCE, TEXT)
+from caosdb.common.state import State, Transition
# Import of the basic API classes:
from caosdb.common.models import (ACL, ALL, FIX, NONE, OBLIGATORY, RECOMMENDED,
SUGGESTED, Container, DropOffBox, Entity,
@@ -45,15 +46,13 @@ from caosdb.common.models import (ACL, ALL, FIX, NONE, OBLIGATORY, RECOMMENDED,
Query, QueryTemplate, Record, RecordType,
delete, execute_query, get_global_acl,
get_known_permissions, raise_errors)
-from caosdb.configuration import configure, get_config
+from caosdb.configuration import _read_config_files, configure, get_config
from caosdb.connection.connection import configure_connection, get_connection
from caosdb.exceptions import *
-from caosdb.version import version as __version__
+try:
+ from caosdb.version import version as __version__
+except ModuleNotFoundError:
+ version = "uninstalled"
+ __version__ = version
-# read configuration these files
-
-if "PYCAOSDBINI" in environ:
- configure(expanduser(environ["PYCAOSDBINI"]))
-else:
- configure(expanduser('~/.pycaosdb.ini'))
-configure(join(getcwd(), "pycaosdb.ini"))
+_read_config_files()
diff --git a/src/caosdb/apiutils.py b/src/caosdb/apiutils.py
index bd279fcfe5c394b9b5cff787169cff5b9f2d3031..73074efc3057e0548c5abfd56ef3cf1ac9e9bf47 100644
--- a/src/caosdb/apiutils.py
+++ b/src/caosdb/apiutils.py
@@ -34,10 +34,10 @@ from collections.abc import Iterable
from subprocess import call
from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER,
- REFERENCE, TEXT)
+ REFERENCE, TEXT, is_reference)
from caosdb.common.models import (Container, Entity, File, Property, Query,
Record, RecordType, get_config,
- execute_query, is_reference)
+ execute_query)
def new_record(record_type, name=None, description=None,
@@ -244,6 +244,8 @@ class CaosDBPythonEntity(object):
return (val, False)
elif pr[0:4] == "LIST":
return self._type_converted_list(val, pr)
+ elif isinstance(val, Entity):
+ return (convert_to_python_object(val), False)
else:
return (int(val), True)
diff --git a/src/caosdb/common/administration.py b/src/caosdb/common/administration.py
index 7997088a102e86cbf2daeb42a996a1b6ae57f446..e7ba94182d7a4d8b60c6400cd1d804f62f7bf03c 100644
--- a/src/caosdb/common/administration.py
+++ b/src/caosdb/common/administration.py
@@ -30,8 +30,12 @@ from lxml import etree
from caosdb.common.utils import xml2str
from caosdb.connection.connection import get_connection
-from caosdb.exceptions import (AuthorizationException, ClientErrorException,
- EntityDoesNotExistError)
+from caosdb.exceptions import (HTTPClientError,
+ HTTPForbiddenError,
+ HTTPResourceNotFoundError,
+ EntityDoesNotExistError,
+ ServerConfigurationException,
+ )
def set_server_property(key, value):
@@ -52,9 +56,11 @@ def set_server_property(key, value):
None
"""
con = get_connection()
-
- con._form_data_request(method="POST", path="_server_properties",
- params={key: value}).read()
+ try:
+ con._form_data_request(method="POST", path="_server_properties",
+ params={key: value}).read()
+ except EntityDoesNotExistError:
+ raise ServerConfigurationException("Debug mode in server is probably disabled.") from None
def get_server_properties():
@@ -68,7 +74,11 @@ def get_server_properties():
The server properties.
"""
con = get_connection()
- body = con._http_request(method="GET", path="_server_properties").response
+ try:
+ body = con._http_request(method="GET", path="_server_properties").response
+ except EntityDoesNotExistError:
+ raise ServerConfigurationException("Debug mode in server is probably disabled.") from None
+
xml = etree.parse(body)
props = dict()
@@ -106,10 +116,10 @@ def _retrieve_user(name, realm=None, **kwargs):
con = get_connection()
try:
return con._http_request(method="GET", path="User/" + (realm + "/" + name if realm is not None else name), **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to retrieve this user."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "User does not exist."
raise
@@ -118,10 +128,10 @@ def _delete_user(name, **kwargs):
con = get_connection()
try:
return con._http_request(method="DELETE", path="User/" + name, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to delete this user."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "User does not exist."
raise
@@ -144,13 +154,13 @@ def _update_user(name, realm=None, password=None, status=None,
params["entity"] = str(entity)
try:
return con.put_form_data(entity_uri_segment="User/" + (realm + "/" + name if realm is not None else name), params=params, **kwargs).read()
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "User does not exist."
raise
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to update this user."
raise
- except ClientErrorException as e:
+ except HTTPClientError as e:
if e.status == 409:
e.msg = "Entity does not exist."
raise
@@ -173,10 +183,10 @@ def _insert_user(name, password=None, status=None, email=None, entity=None, **kw
params["entity"] = entity
try:
return con.post_form_data(entity_uri_segment="User", params=params, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to insert a new user."
raise e
- except ClientErrorException as e:
+ except HTTPClientError as e:
if e.status == 409:
e.msg = "User name is already in use."
@@ -189,10 +199,10 @@ def _insert_role(name, description, **kwargs):
con = get_connection()
try:
return con.post_form_data(entity_uri_segment="Role", params={"role_name": name, "role_description": description}, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to insert a new role."
raise
- except ClientErrorException as e:
+ except HTTPClientError as e:
if e.status == 409:
e.msg = "Role name is already in use. Choose a different name."
raise
@@ -202,10 +212,10 @@ def _update_role(name, description, **kwargs):
con = get_connection()
try:
return con.put_form_data(entity_uri_segment="Role/" + name, params={"role_description": description}, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to update this role."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "Role does not exist."
raise
@@ -214,10 +224,10 @@ def _retrieve_role(name, **kwargs):
con = get_connection()
try:
return con._http_request(method="GET", path="Role/" + name, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to retrieve this role."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "Role does not exist."
raise
@@ -226,10 +236,10 @@ def _delete_role(name, **kwargs):
con = get_connection()
try:
return con._http_request(method="DELETE", path="Role/" + name, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to delete this role."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "Role does not exist."
raise
@@ -243,14 +253,15 @@ def _set_roles(username, roles, realm=None, **kwargs):
body = xml2str(xml)
con = get_connection()
try:
- body = con._http_request(method="PUT", path="UserRoles/" + (realm + "/" + username if realm is not None else username), body=body, **kwargs).read()
- except AuthorizationException as e:
+ body = con._http_request(method="PUT", path="UserRoles/" + (realm + "/" +
+ username if realm is not None else username), body=body, **kwargs).read()
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to set this user's roles."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "User does not exist."
raise
- except ClientErrorException as e:
+ except HTTPClientError as e:
if e.status == 409:
e.msg = "Role does not exist."
raise
@@ -266,11 +277,12 @@ def _set_roles(username, roles, realm=None, **kwargs):
def _get_roles(username, realm=None, **kwargs):
con = get_connection()
try:
- body = con._http_request(method="GET", path="UserRoles/" + (realm + "/" + username if realm is not None else username), **kwargs).read()
- except AuthorizationException as e:
+ body = con._http_request(method="GET", path="UserRoles/" + (
+ realm + "/" + username if realm is not None else username), **kwargs).read()
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to retrieve this user's roles."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "User does not exist."
raise
ret = set()
@@ -310,10 +322,10 @@ Returns
con = get_connection()
try:
return con._http_request(method="PUT", path="PermissionRules/" + role, body=body, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to set this role's permissions."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "Role does not exist."
raise
@@ -322,10 +334,10 @@ def _get_permissions(role, **kwargs):
con = get_connection()
try:
return PermissionRule._parse_body(con._http_request(method="GET", path="PermissionRules/" + role, **kwargs).read())
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to retrieve this role's permissions."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "Role does not exist."
raise
diff --git a/src/caosdb/common/datatype.py b/src/caosdb/common/datatype.py
index 246485c3957462fc98ac83f9d904413ad7518302..eb8c1e4e0088f1924940a104ec3916b9d5d40f99 100644
--- a/src/caosdb/common/datatype.py
+++ b/src/caosdb/common/datatype.py
@@ -25,7 +25,7 @@
import re
-from ..exceptions import AmbiguityException, EntityDoesNotExistError
+from ..exceptions import EmptyUniqueQueryError, QueryNotUniqueError
DOUBLE = "DOUBLE"
REFERENCE = "REFERENCE"
@@ -91,9 +91,9 @@ def get_id_of_datatype(datatype):
Raises
------
- AmbiguityException
+ QueryNotUniqueError
If there are more than one entities with the same name as the datatype.
- EntityDoesNotExistError
+ EmptyUniqueQueryError
If there is no entity with the name of the datatype.
"""
from caosdb import execute_query
@@ -107,11 +107,11 @@ def get_id_of_datatype(datatype):
res = [el for el in res if el.name.lower() == datatype.lower()]
if len(res) > 1:
- raise AmbiguityException(
+ raise QueryNotUniqueError(
"Name {} did not lead to unique result; Missing "
"implementation".format(datatype))
elif len(res) != 1:
- raise EntityDoesNotExistError(
+ raise EmptyUniqueQueryError(
"No RecordType named {}".format(datatype))
return res[0].id
diff --git a/src/caosdb/common/models.py b/src/caosdb/common/models.py
index a5adf6af68b72663c0fe8cd6ab58c39cdcea5d27..6ec49df2722170805fb6230753f36503870a8821 100644
--- a/src/caosdb/common/models.py
+++ b/src/caosdb/common/models.py
@@ -5,8 +5,9 @@
#
# 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 Florian Spreckelsen <f.spreckelsen@indiscale.com>
# Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
-# Copyright (C) 2020 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
@@ -29,7 +30,6 @@ from __future__ import print_function, unicode_literals
import re
import sys
-import traceback
from builtins import str
from functools import cmp_to_key
from hashlib import sha512
@@ -40,24 +40,28 @@ from sys import hexversion
from tempfile import NamedTemporaryFile
from warnings import warn
-from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER,
- LIST, REFERENCE, TEXT, is_reference)
+from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, INTEGER, TEXT)
from caosdb.common.versioning import Version
+from caosdb.common.state import State
from caosdb.common.utils import uuid, xml2str
from caosdb.configuration import get_config
from caosdb.connection.connection import get_connection
from caosdb.connection.encode import MultipartParam, multipart_encode
-from caosdb.exceptions import (AmbiguityException, AuthorizationException,
- CaosDBException, ConnectionException,
- ConsistencyError, EntityDoesNotExistError,
- EntityError, EntityHasNoDatatypeError,
- TransactionError, UniqueNamesError,
+from caosdb.exceptions import (AmbiguousEntityError,
+ AuthorizationError,
+ CaosDBException, CaosDBConnectionError,
+ ConsistencyError,
+ EmptyUniqueQueryError,
+ EntityDoesNotExistError, EntityError,
+ EntityHasNoDatatypeError,
+ MismatchingEntitiesError,
+ QueryNotUniqueError, TransactionError,
+ UniqueNamesError,
UnqualifiedParentsError,
- UnqualifiedPropertiesError, URITooLongException)
+ UnqualifiedPropertiesError,
+ HTTPURITooLongError)
from lxml import etree
-from .datatype import is_reference
-
_ENTITY_URI_SEGMENT = "Entity"
# importances/inheritance
@@ -109,6 +113,7 @@ class Entity(object):
self.name = name
self.description = description
self.id = id
+ self.state = None
@property
def version(self):
@@ -426,14 +431,39 @@ class Entity(object):
def add_parent(self, parent=None, **kwargs): # @ReservedAssignment
"""Add a parent to this entity.
- The first parameter is meant to identify the parent entity. So the method expects an instance of
- Entity, an integer or a string here. Even though, by means of the **kwargs parameter you may pass
- more parameters to this method. Accepted keywords are: id, name, inheritance. Any other keyword is
- ignored right now but this may change in the future.
+ Parameters
+ ----------
+ parent : Entity or int or str or None
+ The parent entity, either specified by the Entity object
+ itself, or its id or its name. Default is None.
+ **kwargs : dict, optional
+ Additional keyword arguments for specifying the parent by
+ name or id, and for specifying the mode of inheritance.
+
+ id : int
+ Integer id of the parent entity. Ignored if `parent`
+ is not None.
+ name : str
+ Name of the parent entity. Ignored if `parent is not
+ none`.
+ inheritance : str
+ One of ``obligatory``, ``recommended``, ``suggested``, or ``fix``. Specifies the
+ minimum importance which parent properties need to have to be inherited by this
+ entity. If no `inheritance` is given, no properties will be inherited by the child.
+ This parameter is case-insensitive.
+
+ Note that the behaviour is currently not yet specified when assigning parents to
+ Records, it only works for inheritance of RecordTypes (and Properties).
+
+ For more information, it is recommended to look into the
+ :ref:`data insertion tutorial<tutorial-inheritance-properties>`.
+
+ Raises
+ ------
+ UserWarning
+ If neither a `parent` parameter, nor the `id`, nor `name`
+ parameter is passed to this method.
- @param parent: An entity, an id or a name.
- @param **kwargs: Accepted keywords: id, name, inheritance.
- @raise UserWarning: If neither a 'parent' parameter, nor the 'id', nor 'name' parameter is passed to this method.
"""
name = (kwargs['name'] if 'name' in kwargs else None)
pid = (kwargs['id'] if 'id' in kwargs else None)
@@ -637,7 +667,6 @@ class Entity(object):
if not isinstance(selector, (tuple, list)):
selector = [selector]
- val = None
ref = self
# there are some special selectors which can be applied to the
@@ -757,15 +786,14 @@ class Entity(object):
return ret
- def get_errors_deep(self, roots=[]):
+ def get_errors_deep(self, roots=None):
"""Get all error messages of this entity and all sub-entities /
- parents.
-
- / properties.
+ parents / properties.
@return A list of tuples. Tuple index 0 contains the error message
and tuple index 1 contains the tree.
"""
+ roots = [] if roots is None else roots
result_list = list()
ret_self = self.get_errors()
result_list.extend([
@@ -806,8 +834,7 @@ class Entity(object):
xml = etree.Element("Entity")
assert isinstance(xml, etree._Element)
- ''' unwrap wrapped entity '''
-
+ # unwrap wrapped entity
if self._wrapped_entity is not None:
xml = self._wrapped_entity.to_xml(xml, add_properties)
@@ -854,6 +881,8 @@ class Entity(object):
xml.append(v_elem)
elif self.value == "":
xml.append(etree.Element("EmptyString"))
+ elif str(self.value) == "nan":
+ xml.text = "NaN"
else:
xml.text = str(self.value)
@@ -907,6 +936,9 @@ class Entity(object):
if self.acl is not None:
xml.append(self.acl.to_xml())
+ if self.state is not None:
+ xml.append(self.state.to_xml())
+
return xml
@staticmethod
@@ -951,6 +983,8 @@ class Entity(object):
entity.add_message(child)
elif isinstance(child, Version):
entity.version = child
+ elif isinstance(child, State):
+ entity.state = child
elif child is None or hasattr(child, "encode"):
vals.append(child)
elif isinstance(child, Entity):
@@ -963,7 +997,7 @@ class Entity(object):
# add VALUE
value = None
- if len(vals):
+ if vals:
# The value[s] have been inside a <Value> tag.
value = vals
elif elem.text is not None and elem.text.strip() != "":
@@ -988,11 +1022,20 @@ class Entity(object):
if self.id is None:
c = Container().retrieve(query=self.name, sync=False)
- if len(c == 1):
+ if len(c) == 1:
e = c[0]
+ elif len(c) == 0:
+ ee = EntityDoesNotExistError(
+ "The entity to be updated does not exist on the server.",
+ entity=self
+ )
+ raise TransactionError(ee)
else:
- raise AmbiguityException(
- "Could not determine the desired Entity which is to be updated by its name.")
+ ae = AmbiguousEntityError(
+ "Could not determine the desired Entity which is to be updated by its name.",
+ entity=self
+ )
+ raise TransactionError(ae)
else:
e = Container().retrieve(query=self.id, sync=False)[0]
e.acl = ACL(self.acl.to_xml())
@@ -1031,13 +1074,12 @@ class Entity(object):
if len(c) == 1:
c[0].messages.extend(c.messages)
-
return c[0]
- else:
- raise AmbiguityException("This retrieval was not unique!!!")
- else:
- return Container().append(self).retrieve(
- unique=unique, raise_exception_on_error=raise_exception_on_error, flags=flags)
+
+ raise QueryNotUniqueError("This retrieval was not unique!!!")
+
+ return Container().append(self).retrieve(
+ unique=unique, raise_exception_on_error=raise_exception_on_error, flags=flags)
def insert(self, raise_exception_on_error=True, unique=True,
sync=True, strict=False, flags=None):
@@ -1070,7 +1112,7 @@ class Entity(object):
flags=flags)[0]
def update(self, strict=False, raise_exception_on_error=True,
- unique=True, flags=None):
+ unique=True, flags=None, sync=True):
"""Update this entity.
There are two possible work-flows to perform this update:
@@ -1104,6 +1146,7 @@ class Entity(object):
return Container().append(self).update(
strict=strict,
+ sync=sync,
raise_exception_on_error=raise_exception_on_error,
unique=unique,
flags=flags)[0]
@@ -1239,9 +1282,10 @@ class QueryTemplate():
self.is_valid = lambda: False
self.is_deleted = lambda: False
self.version = None
+ self.state = None
- def retrieve(self, strict=True, raise_exception_on_error=True,
- unique=True, sync=True, flags=None):
+ def retrieve(self, raise_exception_on_error=True, unique=True, sync=True,
+ flags=None):
return Container().append(self).retrieve(
raise_exception_on_error=raise_exception_on_error,
@@ -1386,8 +1430,7 @@ class Parent(Entity):
if xml is None:
xml = etree.Element("Parent")
- return super(Parent, self).to_xml(
- xml=xml, add_properties=add_properties)
+ return super().to_xml(xml=xml, add_properties=add_properties)
class _EntityWrapper(object):
@@ -1417,6 +1460,23 @@ class Property(Entity):
property=property, value=value, **copy_kwargs)
def add_parent(self, parent=None, **kwargs):
+ """Add a parent Entity to this Property.
+
+ Parameters
+ ----------
+ parent : Entity or int or str or None, optional
+ The parent entity
+ **kwargs : dict, optional
+ Additional keyword arguments specifying the parent Entity
+ by id or name, and specifying the inheritance level. See
+ :py:meth:`Entity.add_parent` for more information. Note
+ that by default, `inheritance` is set to ``fix``.
+
+ See Also
+ --------
+ Entity.add_parent
+
+ """
copy_kwargs = kwargs.copy()
if 'inheritance' not in copy_kwargs:
@@ -1452,7 +1512,7 @@ class Message(object):
if xml is None:
xml = etree.Element(str(self.type))
- if self.code:
+ if self.code is not None:
xml.set("code", str(self.code))
if self.description:
@@ -1468,7 +1528,7 @@ class Message(object):
def __eq__(self, obj):
if isinstance(obj, Message):
- return self.type == obj.type and self.code == obj.codes
+ return self.type == obj.type and self.code == obj.code
return False
@@ -1491,17 +1551,35 @@ class RecordType(Entity):
# set default importance
copy_kwargs['inheritance'] = FIX
- return super(RecordType, self).add_property(
- property=property, value=value, **copy_kwargs)
+ return super().add_property(property=property, value=value,
+ **copy_kwargs)
def add_parent(self, parent=None, **kwargs):
+ """Add a parent to this RecordType
+
+ Parameters
+ ----------
+ parent : Entity or int or str or None, optional
+ The parent entity, either specified by the Entity object
+ itself, or its id or its name. Default is None.
+ **kwargs : dict, optional
+ Additional keyword arguments specifying the parent Entity by id or
+ name, and specifying the inheritance level. See
+ :py:meth:`Entity.add_parent` for more information. Note
+ that by default, `inheritance` is set to ``obligatory``.
+
+ See Also
+ --------
+ Entity.add_parent
+
+ """
copy_kwargs = kwargs.copy()
if 'inheritance' not in copy_kwargs:
# set default importance
copy_kwargs['inheritance'] = OBLIGATORY
- return super(RecordType, self).add_parent(parent=parent, **copy_kwargs)
+ return super().add_parent(parent=parent, **copy_kwargs)
def __init__(self, name=None, id=None, description=None, datatype=None): # @ReservedAssignment
Entity.__init__(self, name=name, id=id, description=description,
@@ -1529,7 +1607,7 @@ class Record(Entity):
# set default importance
copy_kwargs['inheritance'] = FIX
- return super(Record, self).add_property(
+ return super().add_property(
property=property, value=value, **copy_kwargs)
def __init__(self, name=None, id=None, description=None): # @ReservedAssignment
@@ -1693,7 +1771,7 @@ class File(Record):
# set default importance
copy_kwargs['inheritance'] = FIX
- return super(File, self).add_property(
+ return super().add_property(
property=property, value=value, **copy_kwargs)
@@ -2018,7 +2096,8 @@ class _Messages(dict):
<<< del msgs["HelloWorld",2]
<<< assert msgs.get("HelloWorld",2) == None
- <<< # this Message has no code and no description (make easy things easy...)
+ # this Message has no code and no description (make easy things easy...)
+ <<<
<<< msgs["HelloWorld"] = "Hello!"
<<< assert msgs["HelloWorld"] == "Hello!"
@@ -2215,6 +2294,7 @@ def _basic_sync(e_local, e_remote):
e_local.is_valid = e_remote.is_valid
e_local.is_deleted = e_remote.is_deleted
e_local.version = e_remote.version
+ e_local.state = e_remote.state
if hasattr(e_remote, "query"):
e_local.query = e_remote.query
@@ -2227,15 +2307,19 @@ def _basic_sync(e_local, e_remote):
def _deletion_sync(e_local, e_remote):
if e_local is None or e_remote is None:
- return None
+ return
+
try:
- e_remote.get_messages()[('info', 10)]
- _basic_sync(e_local, e_remote)
- e_local.is_valid = lambda: False
- e_local.is_deleted = lambda: True
- e_local.id = None
+ e_remote.get_messages()["info", 10] # try and get the deletion info
except KeyError:
+ # deletion info wasn't there
e_local.messages = e_remote.messages
+ return
+
+ _basic_sync(e_local, e_remote)
+ e_local.is_valid = lambda: False
+ e_local.is_deleted = lambda: True
+ e_local.id = None
class Container(list):
@@ -2276,11 +2360,11 @@ class Container(list):
"""
if entity in self:
- super(Container, self).remove(entity)
+ super().remove(entity)
else:
for ee in self:
if entity == ee.id:
- super(Container, self).remove(ee)
+ super().remove(ee)
return ee
raise ValueError(
@@ -2398,13 +2482,13 @@ class Container(list):
"""
if isinstance(entity, Entity):
- super(Container, self).append(entity)
+ super().append(entity)
elif isinstance(entity, int):
- super(Container, self).append(Entity(id=entity))
+ super().append(Entity(id=entity))
elif hasattr(entity, "encode"):
- super(Container, self).append(Entity(name=entity))
+ super().append(Entity(name=entity))
elif isinstance(entity, QueryTemplate):
- super(Container, self).append(entity)
+ super().append(entity)
else:
raise TypeError(
"Entity was neither an id nor a name nor an entity." +
@@ -2420,8 +2504,8 @@ class Container(list):
@return xml element
"""
tmpid = 0
- ''' users might already have specified some tmpids. -> look for smallest.'''
+ # users might already have specified some tmpids. -> look for smallest.
for e in self:
tmpid = min(tmpid, Container._get_smallest_tmpid(e))
tmpid -= 1
@@ -2640,8 +2724,7 @@ class Container(list):
# list of remote entities which already have a local equivalent
used_remote_entities = []
- ''' match by cuid '''
-
+ # match by cuid
for local_entity in self:
sync_dict[local_entity] = None
@@ -2667,10 +2750,9 @@ class Container(list):
local_entity.add_message(Message("Error", None, msg))
if raise_exception_on_error:
- raise AmbiguityException(msg)
-
- ''' match by id '''
+ raise MismatchingEntitiesError(msg)
+ # match by id
for local_entity in self:
if sync_dict[local_entity] is None and local_entity.id is not None:
sync_remote_entities = []
@@ -2692,10 +2774,9 @@ class Container(list):
local_entity.add_message(Message("Error", None, msg))
if raise_exception_on_error:
- raise AmbiguityException(msg)
-
- ''' match by path '''
+ raise MismatchingEntitiesError(msg)
+ # match by path
for local_entity in self:
if (sync_dict[local_entity] is None
and local_entity.path is not None):
@@ -2722,10 +2803,9 @@ class Container(list):
local_entity.add_message(Message("Error", None, msg))
if raise_exception_on_error:
- raise AmbiguityException(msg)
-
- ''' match by name '''
+ raise MismatchingEntitiesError(msg)
+ # match by name
for local_entity in self:
if (sync_dict[local_entity] is None
and local_entity.name is not None):
@@ -2752,7 +2832,7 @@ class Container(list):
local_entity.add_message(Message("Error", None, msg))
if raise_exception_on_error:
- raise AmbiguityException(msg)
+ raise MismatchingEntitiesError(msg)
# add remaining entities to this remote_container
sync_remote_entities = []
@@ -2771,7 +2851,7 @@ class Container(list):
remote_container.add_message(Message("Error", None, msg))
if raise_exception_on_error:
- raise AmbiguityException(msg)
+ raise MismatchingEntitiesError(msg)
return sync_dict
@@ -2786,11 +2866,24 @@ class Container(list):
this happens, none of them will be deleted. It occurs an error
instead.
"""
+ chunk_size = 100
+ item_count = len(self)
+ # Split Container in 'chunk_size'-sized containers (if necessary) to avoid error 414 Request-URI Too Long
+ if item_count > chunk_size:
+ for i in range(0, int(item_count/chunk_size)+1):
+ chunk = Container()
+ for j in range(i*chunk_size, min(item_count, (i+1)*chunk_size)):
+ chunk.append(self[j])
+ if len(chunk):
+ chunk.delete()
+ return self
if len(self) == 0:
if raise_exception_on_error:
- raise TransactionError(
- self, "There are no entities to be deleted. This container is empty.")
+ te = TransactionError(
+ msg="There are no entities to be deleted. This container is empty.",
+ container=self)
+ raise te
return self
self.clear_server_messages()
@@ -2814,21 +2907,23 @@ class Container(list):
description="This entity has no identifier. It cannot be deleted."))
if raise_exception_on_error:
- raise EntityError(
+ ee = EntityError(
"This entity has no identifier. It cannot be deleted.", entity)
- else:
- entity.is_valid = lambda: False
+ raise TransactionError(ee)
+ entity.is_valid = lambda: False
if len(id_str) == 0:
if raise_exception_on_error:
- raise TransactionError(
- self, "There are no entities to be deleted.")
+ te = TransactionError(
+ msg="There are no entities to be deleted.",
+ container=self)
+ raise te
return self
entity_url_segments = [_ENTITY_URI_SEGMENT, "&".join(id_str)]
_log_request("DELETE: " + str(entity_url_segments) +
- ("?" + flags if flags is not None else ''))
+ ("?" + str(flags) if flags is not None else ''))
http_response = c.delete(entity_url_segments, query_dict=flags)
cresp = Container._response_to_entities(http_response)
@@ -2882,10 +2977,11 @@ class Container(list):
description="This entity has no identifier. It cannot be retrieved."))
if raise_exception_on_error:
- raise EntityError(
- "This entity has no identifier. It cannot be retrieved.", entity)
- else:
- entity.is_valid = lambda: False
+ ee = EntityError(
+ "This entity has no identifier. It cannot be retrieved.",
+ entity)
+ raise TransactionError(ee)
+ entity.is_valid = lambda: False
else:
entities_str.append(str(query))
@@ -2926,12 +3022,12 @@ class Container(list):
"&".join(entities))], query_dict=flags)
return Container._response_to_entities(http_response)
- except URITooLongException as uri_e:
+ except HTTPURITooLongError as uri_e:
try:
# split up
uri1, uri2 = Container._split_uri_string(entities)
- except ValueError:
- raise uri_e
+ except ValueError as val_e:
+ raise uri_e from val_e
c1 = self._retrieve(entities=uri1, flags=flags)
c2 = self._retrieve(entities=uri2, flags=flags)
c1.extend(c2)
@@ -2974,9 +3070,10 @@ class Container(list):
"""Update these entites."""
if len(self) < 1:
- raise TransactionError(
- container=self,
- msg="There are no entities to be updated. This container is empty.")
+ te = TransactionError(
+ msg="There are no entities to be updated. This container is empty.",
+ container=self)
+ raise te
self.clear_server_messages()
insert_xml = etree.Element("Update")
@@ -2993,8 +3090,10 @@ class Container(list):
for entity in self:
if (entity.id is None or entity.id < 0):
- raise TransactionError(
- self, "You tried to update an entity without a valid id.")
+ ee = EntityError(
+ "You tried to update an entity without a valid id.",
+ entity)
+ raise TransactionError(ee)
self._linearize()
@@ -3164,9 +3263,10 @@ class Container(list):
insert_xml.append(entity_xml)
if len(self) > 0 and len(insert_xml) < 1:
- raise TransactionError(
- container=self,
- msg="There are no entities to be inserted. This container contains existent entities only.")
+ te = TransactionError(
+ msg="There are no entities to be inserted. This container contains existent entities only.",
+ container=self)
+ raise te
_log_request("POST: " + _ENTITY_URI_SEGMENT +
('' if flags is None else "?" + str(flags)), insert_xml)
@@ -3402,6 +3502,22 @@ class ACL():
self.deny(username=username, realm=realm, role=role,
permission=permission, priority=priority)
+ def combine(self, other):
+ """ Combine and return new instance."""
+ result = ACL()
+ result._grants.update(other._grants)
+ result._grants.update(self._grants)
+ result._denials.update(other._denials)
+ result._denials.update(self._denials)
+ result._priority_grants.update(other._priority_grants)
+ result._priority_grants.update(self._priority_grants)
+ result._priority_denials.update(other._priority_denials)
+ result._priority_denials.update(self._priority_denials)
+ return result
+
+ def __eq__(self, other):
+ return isinstance(other, ACL) and other._grants == self._grants and self._denials == other._denials and self._priority_grants == other._priority_grants and self._priority_denials == other._priority_denials
+
def is_empty(self):
return len(self._grants) + len(self._priority_grants) + \
len(self._priority_denials) + len(self._denials) == 0
@@ -3611,6 +3727,23 @@ class ACL():
class Query():
+ """Query
+
+ Attributes
+ ----------
+ q : str
+ The query string.
+ flags : dict of str
+ A dictionary of flags to be send with the query request.
+ messages : _Messages()
+ A container of messages included in the last query response.
+ cached : bool
+ indicates whether the server used the query cache for the execution of
+ this query.
+ results : int or Container
+ The number of results (when this was a count query) or the container
+ with the resulting entities.
+ """
def putFlag(self, key, value=None):
self.flags[key] = value
@@ -3626,28 +3759,63 @@ class Query():
def __init__(self, q):
self.flags = dict()
self.messages = _Messages()
+ self.cached = None
+ self.etag = None
if isinstance(q, etree._Element):
self.q = q.get("string")
self.results = int(q.get("results"))
+ if q.get("cached") is None:
+ self.cached = False
+ else:
+ self.cached = q.get("cached").lower() == "true"
+ self.etag = q.get("etag")
+
for m in q:
if m.tag.lower() == 'warning' or m.tag.lower() == 'error':
self.messages.append(_parse_single_xml_element(m))
else:
self.q = q
- def execute(self, unique=False, raise_exception_on_error=True,
- **kwargs):
+ def execute(self, unique=False, raise_exception_on_error=True, cache=True):
+ """Execute a query (via a server-requests) and return the results.
+
+ Parameters
+ ----------
+
+ unique : bool
+ Whether the query is expected to have only one entity as result.
+ Defaults to False.
+ raise_exception_on_error : bool
+ Whether an exception should be raises when there are errors in the
+ resulting entities. Defaults to True.
+ cache : bool
+ Whether to use the query cache (equivalent to adding a "cache"
+ flag) to the Query object. Defaults to True.
+
+ Returns
+ -------
+ results : Container or integer
+ Returns an integer when it was a `COUNT` query. Otherwise, returns a
+ Container with the resulting entities.
+ """
connection = get_connection()
- query_dict = dict(self.flags)
+
+ flags = self.flags
+ if cache is False:
+ flags["cache"] = "false"
+ query_dict = dict(flags)
query_dict["query"] = str(self.q)
+
_log_request("GET Entity?" + str(query_dict), None)
http_response = connection.retrieve(
entity_uri_segments=["Entity"],
- query_dict=query_dict, **kwargs)
+ query_dict=query_dict)
cresp = Container._response_to_entities(http_response)
self.results = cresp.query.results
+ self.cached = cresp.query.cached
+ self.etag = cresp.query.etag
if self.q.lower().startswith('count') and len(cresp) == 0:
# this was a count query
@@ -3659,10 +3827,12 @@ class Query():
if unique:
if len(cresp) > 1 and raise_exception_on_error:
- raise AmbiguityException("This query wasn't unique")
- elif len(cresp) == 0 and raise_exception_on_error:
- raise EntityDoesNotExistError("No such entity found.")
- elif len(cresp) == 1:
+ raise QueryNotUniqueError(
+ "Query '{}' wasn't unique.".format(self.q))
+ if len(cresp) == 0 and raise_exception_on_error:
+ raise EmptyUniqueQueryError(
+ "Query '{}' found no results.".format(self.q))
+ if len(cresp) == 1:
r = cresp[0]
r.messages.extend(cresp.messages)
@@ -3672,8 +3842,32 @@ class Query():
return cresp
-def execute_query(q, unique=False, raise_exception_on_error=True, flags=None,
- **kwargs):
+def execute_query(q, unique=False, raise_exception_on_error=True, cache=True, flags=None):
+ """Execute a query (via a server-requests) and return the results.
+
+ Parameters
+ ----------
+
+ q : str
+ The query string.
+ unique : bool
+ Whether the query is expected to have only one entity as result.
+ Defaults to False.
+ raise_exception_on_error : bool
+ Whether an exception should be raises when there are errors in the
+ resulting entities. Defaults to True.
+ cache : bool
+ Whether to use the query cache (equivalent to adding a "cache" flag).
+ Defaults to True.
+ flags : dict of str
+ Flags to be added to the request.
+
+ Returns
+ -------
+ results : Container or integer
+ Returns an integer when it was a `COUNT` query. Otherwise, returns a
+ Container with the resulting entities.
+ """
query = Query(q)
if flags is not None:
@@ -3681,7 +3875,7 @@ def execute_query(q, unique=False, raise_exception_on_error=True, flags=None,
return query.execute(unique=unique,
raise_exception_on_error=raise_exception_on_error,
- **kwargs)
+ cache=cache)
class DropOffBox(list):
@@ -3735,7 +3929,7 @@ class Info():
c = get_connection()
try:
http_response = c.retrieve(["Info"])
- except ConnectionException as conn_e:
+ except CaosDBConnectionError as conn_e:
print(conn_e)
return
@@ -3850,11 +4044,15 @@ def _parse_single_xml_element(elem):
return entity
elif elem.tag.lower() == "version":
return Version.from_xml(elem)
+ elif elem.tag.lower() == "state":
+ return State.from_xml(elem)
elif elem.tag.lower() == "emptystring":
return ""
elif elem.tag.lower() == "value":
if len(elem) == 1 and elem[0].tag.lower() == "emptystring":
return ""
+ elif len(elem) == 1 and elem[0].tag.lower() in classmap:
+ return _parse_single_xml_element(elem[0])
elif elem.text is None or elem.text.strip() == "":
return None
@@ -3880,124 +4078,119 @@ def _parse_single_xml_element(elem):
"code"), description=elem.get("description"), body=elem.text)
-def raise_errors(arg0):
- if isinstance(arg0, (Entity, QueryTemplate)):
- entity_error = EntityError(
- entity=arg0, error=Message('Error', 0, 'EntityMultiError'))
- found114 = False
- found116 = False
+def _evaluate_and_add_error(parent_error, ent):
+ """Evaluate the error message(s) attached to entity and add a
+ corresponding exception to parent_error.
- for e in arg0.get_errors():
- try:
- if e.code is not None:
- if int(e.code) == 101: # arg0 does not exist
- raise EntityDoesNotExistError(error=e, entity=arg0)
- elif int(e.code) == 110: # entity has no data type
- raise EntityHasNoDatatypeError(error=e, entity=arg0)
- elif int(e.code) == 403: # Transaction not permitted
- raise AuthorizationException(error=e, entity=arg0)
- elif int(e.code) == 114: # unqualified properties
- found114 = True
- unqualified_properties_error = UnqualifiedPropertiesError(
- error=e, entity=arg0)
-
- for p in arg0.get_properties():
- try:
- raise_errors(p)
- except EntityError as pe:
- unqualified_properties_error.add_error(pe)
- raise unqualified_properties_error
- elif int(e.code) == 116: # unqualified parents
- found116 = True
- unqualified_parents_error = UnqualifiedParentsError(
- error=e, entity=arg0)
-
- for p in arg0.get_parents():
- try:
- raise_errors(p)
- except EntityError as pe:
- unqualified_parents_error.add_error(pe)
- raise unqualified_parents_error
- elif int(e.code) == 152: # name was not unique
- raise UniqueNamesError(error=e, entity=arg0)
- raise EntityError(error=e, entity=arg0)
- except EntityError as ee:
- entity_error.add_error(ee)
+ Parameters:
+ -----------
+ parent_error : TrancactionError
+ Parent error to which the new exception will be attached. This
+ exception will be a direct child.
+ ent : Entity
+ Entity that caused the TransactionError. An exception is
+ created depending on its error message(s).
- if not found114:
- for p in arg0.get_properties():
- try:
- raise_errors(p)
- except EntityError as pe:
- entity_error.add_error(pe)
+ Returns:
+ --------
+ TransactionError :
+ Parent error with new exception(s) attached to it.
+ """
+ if isinstance(ent, (Entity, QueryTemplate)):
+ # Check all error messages
+ found114 = False
+ found116 = False
+ for err in ent.get_errors():
+ # Evaluate specific EntityErrors depending on the error
+ # code
+ if err.code is not None:
+ if int(err.code) == 101: # ent doesn't exist
+ new_exc = EntityDoesNotExistError(entity=ent,
+ error=err)
+ elif int(err.code) == 110: # ent has no data type
+ new_exc = EntityHasNoDatatypeError(entity=ent,
+ error=err)
+ elif int(err.code) == 403: # no permission
+ new_exc = AuthorizationError(entity=ent,
+ error=err)
+ elif int(err.code) == 152: # name wasn't unique
+ new_exc = UniqueNamesError(entity=ent, error=err)
+ elif int(err.code) == 114: # unqualified properties
+ found114 = True
+ new_exc = UnqualifiedPropertiesError(entity=ent,
+ error=err)
+ for prop in ent.get_properties():
+ new_exc = _evaluate_and_add_error(new_exc,
+ prop)
+ elif int(err.code) == 116: # unqualified parents
+ found116 = True
+ new_exc = UnqualifiedParentsError(entity=ent,
+ error=err)
+ for par in ent.get_parents():
+ new_exc = _evaluate_and_add_error(new_exc,
+ par)
+ else: # General EntityError for other codes
+ new_exc = EntityError(entity=ent, error=err)
+ else: # No error code causes a general EntityError, too
+ new_exc = EntityError(entity=ent, error=err)
+ parent_error.add_error(new_exc)
+ # Check for possible errors in parents and properties that
+ # weren't detected up to here
+ if not found114:
+ dummy_err = EntityError(entity=ent)
+ for prop in ent.get_properties():
+ dummy_err = _evaluate_and_add_error(dummy_err, prop)
+ if dummy_err.errors:
+ parent_error.add_error(dummy_err)
if not found116:
- for p in arg0.get_parents():
- try:
- raise_errors(p)
- except EntityError as pe:
- entity_error.add_error(pe)
-
- if len(entity_error.get_errors()) == 1:
- r = entity_error.get_errors().pop()
- raise r
- elif len(entity_error.get_errors()) > 1:
- r = entity_error._convert()
- raise r
- elif isinstance(arg0, Container):
- transaction_error = TransactionError(
- container=arg0, msg="This transaction terminated with Errors.")
- doRaise = False
- found12 = False
-
- if arg0.get_errors() is not None:
- for er in arg0.get_errors():
- if er.code is not None:
- if int(er.code) == 12: # atomicity violation
- found12 = True
- atomic_error = TransactionError(
- container=arg0, error=er, msg=er.description)
-
- for e in arg0:
- try:
- raise_errors(e)
- except EntityError as ee:
- atomic_error.add_error(ee)
-
- if len(atomic_error.get_errors()) > 0:
- transaction_error.add_error(
- atomic_error._convert())
- doRaise = True
- else:
- transaction_error.add_error(atomic_error)
- doRaise = True
- else:
- te = TransactionError(
- container=arg0, error=er, msg=er.description)
- transaction_error.add_error(te)
- doRaise = True
-
- if len(transaction_error.get_errors()) == 1:
- transaction_error = transaction_error.get_errors().pop()
-
- if not found12:
- for e in arg0:
- try:
- raise_errors(e)
- except EntityError as ee:
- transaction_error.add_error(ee)
- doRaise = True
-
- if len(transaction_error.get_errors()) == 1:
- t = transaction_error.get_errors().pop()
- raise t
- elif len(transaction_error.get_errors()) > 1:
- t = transaction_error._convert()
- raise t
- elif doRaise:
- raise transaction_error
+ dummy_err = EntityError(entity=ent)
+ for par in ent.get_parents():
+ dummy_err = _evaluate_and_add_error(dummy_err, par)
+ if dummy_err.errors:
+ parent_error.add_error(dummy_err)
+
+ elif isinstance(ent, Container):
+ parent_error.container = ent
+ if ent.get_errors() is not None:
+ parent_error.code = ent.get_errors()[0].code
+ # In the highly unusual case of more than one error
+ # message, attach all of them.
+ parent_error.msg = '\n'.join(
+ [x.description for x in ent.get_errors()])
+ # Go through all container elements and add them:
+ for elt in ent:
+ parent_error = _evaluate_and_add_error(parent_error, elt)
+
else:
- raise TypeError("Parameter arg0 is to be an Entity or a Container")
+ raise TypeError("Parameter ent is to be an Entity or a Container")
+
+ return parent_error
+
+
+def raise_errors(arg0):
+ """Raise a TransactionError depending on the error code(s) inside
+ Entity, QueryTemplate or Container arg0. More detailed errors may
+ be attached to the TransactionError depending on the contents of
+ arg0.
+
+ Parameters:
+ -----------
+ arg0 : Entity, QueryTemplate, or Container
+ CaosDB object whose messages are evaluated according to their
+ error codes
+
+ """
+ transaction_error = _evaluate_and_add_error(TransactionError(),
+ arg0)
+ # Raise if any error was found
+ if len(transaction_error.all_errors) > 0:
+ raise transaction_error
+ # Cover the special case of an empty container with error
+ # message(s) (e.g. query syntax error)
+ if (transaction_error.container is not None and
+ transaction_error.container.has_errors()):
+ raise transaction_error
def delete(ids, raise_exception_on_error=True):
diff --git a/src/caosdb/common/state.py b/src/caosdb/common/state.py
new file mode 100644
index 0000000000000000000000000000000000000000..cb74022bef57a77c8270b2033c904eecabaadf83
--- /dev/null
+++ b/src/caosdb/common/state.py
@@ -0,0 +1,198 @@
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020 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/>.
+#
+# ** end header
+
+import copy
+from lxml import etree
+
+
+def _translate_to_state_acis(acis):
+ result = set()
+ for aci in acis:
+ aci = copy.copy(aci)
+ if aci.role:
+ aci.role = "?STATE?" + aci.role + "?"
+ result.add(aci)
+ return result
+
+
+class Transition:
+ """Transition
+
+ Represents allowed transitions from one state to another.
+
+ Properties
+ ----------
+ name : str
+ The name of the transition
+ description: str
+ The description of the transition
+ from_state : str
+ A state name
+ to_state : str
+ A state name
+ """
+
+ def __init__(self, name, from_state, to_state, description=None):
+ self._name = name
+ self._from_state = from_state
+ self._to_state = to_state
+ self._description = description
+
+ @property
+ def name(self):
+ return self._name
+
+ @property
+ def description(self):
+ return self._description
+
+ @property
+ def from_state(self):
+ return self._from_state
+
+ @property
+ def to_state(self):
+ return self._to_state
+
+ def __repr__(self):
+ return f'Transition(name="{self.name}", from_state="{self.from_state}", to_state="{self.to_state}", description="{self.description}")'
+
+ def __eq__(self, other):
+ return (isinstance(other, Transition)
+ and other.name == self.name
+ and other.to_state == self.to_state
+ and other.from_state == self.from_state)
+
+ def __hash__(self):
+ return 23472 + hash(self.name) + hash(self.from_state) + hash(self.to_state)
+
+ @staticmethod
+ def from_xml(xml):
+ to_state = [to.get("name") for to in xml
+ if to.tag.lower() == "tostate"]
+ from_state = [from_.get("name") for from_ in xml
+ if from_.tag.lower() == "fromstate"]
+ result = Transition(name=xml.get("name"),
+ description=xml.get("description"),
+ from_state=from_state[0] if from_state else None,
+ to_state=to_state[0] if to_state else None)
+ return result
+
+
+class State:
+ """State
+
+ Represents the state of an entity and take care of the serialization and
+ deserialization of xml for the entity state.
+
+ An entity state is always a State of a StateModel.
+
+ Properties
+ ----------
+ name : str
+ Name of the State
+ model : str
+ Name of the StateModel
+ description : str
+ Description of the State (read-only)
+ id : str
+ Id of the undelying State record (read-only)
+ transitions : set of Transition
+ All transitions which are available from this state (read-only)
+ """
+
+ def __init__(self, model, name):
+ self.name = name
+ self.model = model
+ self._id = None
+ self._description = None
+ self._transitions = None
+
+ @property
+ def id(self):
+ return self._id
+
+ @property
+ def description(self):
+ return self._description
+
+ @property
+ def transitions(self):
+ return self._transitions
+
+ def __eq__(self, other):
+ return (isinstance(other, State)
+ and self.name == other.name
+ and self.model == other.model)
+
+ def __hash__(self):
+ return hash(self.name) + hash(self.model)
+
+ def __repr__(self):
+ return f"State('{self.model}', '{self.name}')"
+
+ def to_xml(self):
+ """Serialize this State to xml.
+
+ Returns
+ -------
+ xml : etree.Element
+ """
+ xml = etree.Element("State")
+ if self.name is not None:
+ xml.set("name", self.name)
+ if self.model is not None:
+ xml.set("model", self.model)
+ return xml
+
+ @staticmethod
+ def from_xml(xml):
+ """Create a new State instance from an xml Element.
+
+ Parameters
+ ----------
+ xml : etree.Element
+
+ Returns
+ -------
+ state : State
+ """
+ name = xml.get("name")
+ model = xml.get("model")
+ result = State(name=name, model=model)
+ result._id = xml.get("id")
+ result._description = xml.get("description")
+ transitions = [Transition.from_xml(t) for t in xml if t.tag.lower() ==
+ "transition"]
+ if transitions:
+ result._transitions = set(transitions)
+
+ return result
+
+ @staticmethod
+ def create_state_acl(acl):
+ from .models import ACL
+ state_acl = ACL()
+ state_acl._grants = _translate_to_state_acis(acl._grants)
+ state_acl._denials = _translate_to_state_acis(acl._denials)
+ state_acl._priority_grants = _translate_to_state_acis(acl._priority_grants)
+ state_acl._priority_denials = _translate_to_state_acis(acl._priority_denials)
+ return state_acl
diff --git a/src/caosdb/configuration.py b/src/caosdb/configuration.py
index 59f6c6a094d2df88384eb360dc4789ec99e8d787..842f1ee62a5b3178b7305e4c1e0c281a2dbd3b38 100644
--- a/src/caosdb/configuration.py
+++ b/src/caosdb/configuration.py
@@ -28,6 +28,9 @@ except ImportError:
# python3
from configparser import ConfigParser
+from os import environ, getcwd
+from os.path import expanduser, join, isfile
+
def _reset_config():
global _pycaosdbconf
@@ -50,3 +53,20 @@ def configure(inifile):
def get_config():
global _pycaosdbconf
return _pycaosdbconf
+
+
+def _read_config_files():
+ """Function to read config files from different paths. Checks for path in $PYCAOSDBINI or home directory (.pycaosdb.ini) and in the current working directory (pycaosdb.ini).
+
+ Returns:
+ [list]: list with successfully parsed ini-files. Order: env_var or home directory, cwd. Used for testing the function.
+ """
+ return_var = []
+ if "PYCAOSDBINI" in environ:
+ return_var.extend(configure(expanduser(environ["PYCAOSDBINI"])))
+ else:
+ return_var.extend(configure(expanduser('~/.pycaosdb.ini')))
+
+ if isfile(join(getcwd(), "pycaosdb.ini")):
+ return_var.extend(configure(join(getcwd(), "pycaosdb.ini")))
+ return return_var
diff --git a/src/caosdb/connection/authentication/auth_token.py b/src/caosdb/connection/authentication/auth_token.py
index fbce78fb86d78e06d97ef00dd162c1ed57f7560d..688123867f68153d3631bb8559baa235f6f02da5 100644
--- a/src/caosdb/connection/authentication/auth_token.py
+++ b/src/caosdb/connection/authentication/auth_token.py
@@ -30,7 +30,7 @@ An Authentictor which only uses only a pre-supplied authentication token.
from __future__ import absolute_import, unicode_literals, print_function
from .interface import AbstractAuthenticator, CaosDBServerConnection
from caosdb.connection.utils import auth_token_to_cookie
-from caosdb.exceptions import LoginFailedException
+from caosdb.exceptions import LoginFailedError
def get_authentication_provider():
@@ -68,11 +68,11 @@ class AuthTokenAuthenticator(AbstractAuthenticator):
self._login()
def _login(self):
- raise LoginFailedException("The authentication token is expired or you "
- "have been logged out otherwise. The "
- "auth_token authenticator cannot log in "
- "again. You must provide a new "
- "authentication token.")
+ raise LoginFailedError("The authentication token is expired or you "
+ "have been logged out otherwise. The "
+ "auth_token authenticator cannot log in "
+ "again. You must provide a new "
+ "authentication token.")
def logout(self):
self._logout()
diff --git a/src/caosdb/connection/authentication/interface.py b/src/caosdb/connection/authentication/interface.py
index d9a9b4306b1dbdedbc67dfda81a3ca3d7b4aeb41..a364aeb564ee929d995b2f8098bd21e30e9733ab 100644
--- a/src/caosdb/connection/authentication/interface.py
+++ b/src/caosdb/connection/authentication/interface.py
@@ -31,7 +31,7 @@ import logging
from caosdb.connection.utils import urlencode
from caosdb.connection.interface import CaosDBServerConnection
from caosdb.connection.utils import parse_auth_token, auth_token_to_cookie
-from caosdb.exceptions import LoginFailedException
+from caosdb.exceptions import LoginFailedError
# meta class compatible with Python 2 *and* 3:
ABC = ABCMeta('ABC', (object, ), {'__slots__': ()})
@@ -197,9 +197,9 @@ class CredentialsAuthenticator(AbstractAuthenticator):
# we need a username for this:
if username is None:
- raise LoginFailedException("No username was given.")
+ raise LoginFailedError("No username was given.")
if password is None:
- raise LoginFailedException("No password was given")
+ raise LoginFailedError("No password was given")
headers = {}
headers["Content-Type"] = "application/x-www-form-urlencoded"
@@ -210,7 +210,7 @@ class CredentialsAuthenticator(AbstractAuthenticator):
response.read() # clear socket
if response.status != 200:
- raise LoginFailedException("LOGIN WAS NOT SUCCESSFUL")
+ raise LoginFailedError("LOGIN WAS NOT SUCCESSFUL")
self.on_response(response)
return response
diff --git a/src/caosdb/connection/authentication/keyring.py b/src/caosdb/connection/authentication/keyring.py
index 1dc986174acbe23191305632afda91cda0c718d2..d8be7ddf030577545230c9111fdad542b6d6e7e2 100644
--- a/src/caosdb/connection/authentication/keyring.py
+++ b/src/caosdb/connection/authentication/keyring.py
@@ -30,7 +30,7 @@ retrieve the password.
import sys
import imp
from getpass import getpass
-from caosdb.exceptions import ConfigurationException
+from caosdb.exceptions import ConfigurationError
from .external_credentials_provider import ExternalCredentialsProvider
from .interface import CredentialsAuthenticator
@@ -67,10 +67,10 @@ def _get_external_keyring():
def _call_keyring(**config):
if "username" not in config:
- raise ConfigurationException("Your configuration did not provide a "
- "`username` which is needed by the "
- "`KeyringCaller` to retrieve the "
- "password in question.")
+ raise ConfigurationError("Your configuration did not provide a "
+ "`username` which is needed by the "
+ "`KeyringCaller` to retrieve the "
+ "password in question.")
url = config.get("url")
username = config.get("username")
app = "caosdb — {}".format(url)
diff --git a/src/caosdb/connection/authentication/pass.py b/src/caosdb/connection/authentication/pass.py
index 9399fc4f4a76407ad94618785adcfbb945d4c788..853cdf0ed92039e7b5fc9beda8bb76cc0f3cc030 100644
--- a/src/caosdb/connection/authentication/pass.py
+++ b/src/caosdb/connection/authentication/pass.py
@@ -28,7 +28,7 @@ password.
"""
from subprocess import check_output, CalledProcessError
-from caosdb.exceptions import ConfigurationException
+from caosdb.exceptions import ConfigurationError
from .interface import CredentialsAuthenticator
from .external_credentials_provider import ExternalCredentialsProvider
@@ -50,10 +50,10 @@ def get_authentication_provider():
def _call_pass(**config):
if "password_identifier" not in config:
- raise ConfigurationException("Your configuration did not provide a "
- "`password_identifier` which is needed "
- "by the `PassCaller` to retrieve the "
- "password in question.")
+ raise ConfigurationError("Your configuration did not provide a "
+ "`password_identifier` which is needed "
+ "by the `PassCaller` to retrieve the "
+ "password in question.")
try:
return check_output(
diff --git a/src/caosdb/connection/authentication/unauthenticated.py b/src/caosdb/connection/authentication/unauthenticated.py
index 53a2756eb59259a0be012e41f2ea213735568838..65febae8fd8f02f3ee0d339fafb36af512fc7be7 100644
--- a/src/caosdb/connection/authentication/unauthenticated.py
+++ b/src/caosdb/connection/authentication/unauthenticated.py
@@ -30,7 +30,7 @@ cookies.
"""
from __future__ import absolute_import, unicode_literals, print_function
from .interface import AbstractAuthenticator, CaosDBServerConnection
-from caosdb.exceptions import LoginFailedException
+from caosdb.exceptions import LoginFailedError
def get_authentication_provider():
@@ -70,11 +70,11 @@ class Unauthenticated(AbstractAuthenticator):
self._login()
def _login(self):
- raise LoginFailedException("This caosdb client is configured to stay "
- "unauthenticated. Change your "
- "`password_method` and provide an "
- "`auth_token` or credentials if you want "
- "to authenticate this client.")
+ raise LoginFailedError("This caosdb client is configured to stay "
+ "unauthenticated. Change your "
+ "`password_method` and provide an "
+ "`auth_token` or credentials if you want "
+ "to authenticate this client.")
def logout(self):
self._logout()
diff --git a/src/caosdb/connection/connection.py b/src/caosdb/connection/connection.py
index 703897d62a40a820a6ff578869a862f6c7c4c019..9e273a56778737033fda9f342f967f56946b501b 100644
--- a/src/caosdb/connection/connection.py
+++ b/src/caosdb/connection/connection.py
@@ -33,12 +33,19 @@ from errno import EPIPE as BrokenPipe
from socket import error as SocketError
from caosdb.configuration import get_config
-from caosdb.exceptions import (AuthorizationException, CaosDBException,
- ClientErrorException, ConfigurationException,
- ConnectionException, EntityDoesNotExistError,
- LoginFailedException, ServerErrorException,
- URITooLongException)
-from caosdb.version import version
+from caosdb.exceptions import (CaosDBException, HTTPClientError,
+ ConfigurationError,
+ CaosDBConnectionError,
+ HTTPForbiddenError,
+ LoginFailedError,
+ HTTPResourceNotFoundError,
+ HTTPServerError,
+ HTTPURITooLongError)
+try:
+ from caosdb.version import version
+except ModuleNotFoundError:
+ version = "uninstalled"
+
from pkg_resources import resource_filename
from .interface import CaosDBHTTPResponse, CaosDBServerConnection
@@ -61,6 +68,10 @@ class _WrappedHTTPResponse(CaosDBHTTPResponse):
def __init__(self, response):
self.response = response
+ @property
+ def reason(self):
+ return self.response.reason
+
@property
def status(self):
return self.response.status
@@ -88,7 +99,8 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
"""
def __init__(self):
- self._useragent = ("caosdb-pylib/{version} - {implementation}".format(version=version, implementation=type(self).__name__))
+ self._useragent = ("caosdb-pylib/{version} - {implementation}".format(
+ version=version, implementation=type(self).__name__))
self._http_con = None
self._base_path = None
@@ -132,7 +144,7 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
self._http_con.request(method=method, url=self._base_path + path,
headers=headers, body=body)
except SocketError as socket_err:
- raise ConnectionException(
+ raise CaosDBConnectionError(
"Connection failed. Network or server down? " + str(socket_err)
)
@@ -156,7 +168,7 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
Raises
------
- ConnectionException
+ CaosDBConnectionError
If no url has been specified, or if the CA certificate cannot be
loaded.
"""
@@ -193,9 +205,9 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
try:
context.load_verify_locations(config["cacert"])
except Exception as exc:
- raise ConnectionException("Could not load the cacert in"
- "`{}`: {}".format(config["cacert"],
- exc))
+ raise CaosDBConnectionError("Could not load the cacert in"
+ "`{}`: {}".format(config["cacert"],
+ exc))
context.load_default_certs()
@@ -204,7 +216,7 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
host = parsed_url.netloc
self._base_path = parsed_url.path
else:
- raise ConnectionException(
+ raise CaosDBConnectionError(
"No connection url specified. Please "
"do so via caosdb.configure_connection(...) or in a config "
"file.")
@@ -276,7 +288,7 @@ def _get_authenticator(**config):
Raises
------
- ConnectionException
+ ConfigurationError
If the password_method string cannot be resolved to a CaosAuthenticator
class.
"""
@@ -292,10 +304,10 @@ def _get_authenticator(**config):
return auth_provider
except ImportError:
- raise ConfigurationException("Password method \"{}\" not implemented. "
- "Try `plain`, `pass`, `keyring`, or "
- "`auth_token`."
- .format(config["password_method"]))
+ raise ConfigurationError("Password method \"{}\" not implemented. "
+ "Try `plain`, `pass`, `keyring`, or "
+ "`auth_token`."
+ .format(config["password_method"]))
def configure_connection(**kwargs):
@@ -398,29 +410,24 @@ def _handle_response_status(http_response):
# emtpy response buffer
body = http_response.read()
+ if status == 404:
+ raise HTTPResourceNotFoundError("This resource has not been found.")
+ elif status > 499:
+ raise HTTPServerError(body=body)
+
+ reason = http_response.reason
+ standard_message = ("Request failed. The response returned with status "
+ "{} - {}.".format(status, reason))
if status == 401:
- raise LoginFailedException(
- "Request failed. The response returned with status "
- "{}.".format(status))
+ raise LoginFailedError(standard_message)
elif status == 403:
- raise AuthorizationException(
- "Request failed. The response returned with status "
- "{}.".format(status))
- elif status == 404:
- raise EntityDoesNotExistError("This entity does not exist.")
+ raise HTTPForbiddenError(standard_message)
elif status in (413, 414):
- raise URITooLongException(
- "Request failed. The response returned with status "
- "{}.".format(status))
+ raise HTTPURITooLongError(standard_message)
elif 399 < status < 500:
- raise ClientErrorException(msg=("Request failed. The response returned "
- "with status {}.").format(status), status=status, body=body)
- elif status > 499:
- raise ServerErrorException(body=body)
+ raise HTTPClientError(msg=standard_message, status=status, body=body)
else:
- raise CaosDBException(
- "Request failed. The response returned with status "
- "{}.".format(status))
+ raise CaosDBException(standard_message)
class _Connection(object): # pylint: disable=useless-object-inheritance
@@ -454,7 +461,7 @@ class _Connection(object): # pylint: disable=useless-object-inheritance
self.is_configured = True
if "implementation" not in config:
- raise ConfigurationException(
+ raise ConfigurationError(
"Missing CaosDBServerConnection implementation. You did not "
"specify an `implementation` for the connection.")
try:
@@ -465,20 +472,20 @@ class _Connection(object): # pylint: disable=useless-object-inheritance
raise TypeError("The `implementation` callable did not return "
"an instance of CaosDBServerConnection.")
except TypeError as type_err:
- raise ConfigurationException(
+ raise ConfigurationError(
"Bad CaosDBServerConnection implementation. The "
"implementation must be a callable object which returns an "
"instance of `CaosDBServerConnection` (e.g. a constructor "
- "or a factory).", type_err)
+ "or a factory).\n{}".format(type_err.args[0]))
self._delegate_connection.configure(**config)
if "auth_token" in config:
# deprecated, needed for older scripts
config["password_method"] = "auth_token"
if "password_method" not in config:
- raise ConfigurationException("Missing password_method. You did "
- "not specify a `password_method` for"
- "the connection.")
+ raise ConfigurationError("Missing password_method. You did "
+ "not specify a `password_method` for"
+ "the connection.")
self._authenticator = _get_authenticator(
connection=self._delegate_connection, **config)
@@ -554,8 +561,8 @@ class _Connection(object): # pylint: disable=useless-object-inheritance
uri_segments.extend(path.split("/"))
return self.retrieve(entity_uri_segments=uri_segments)
- except EntityDoesNotExistError:
- raise EntityDoesNotExistError("This file does not exist.")
+ except HTTPResourceNotFoundError:
+ raise HTTPResourceNotFoundError("This file does not exist.")
def _login(self):
self._authenticator.login()
@@ -576,7 +583,7 @@ class _Connection(object): # pylint: disable=useless-object-inheritance
headers=headers, body=body,
reconnect=False,
**kwargs)
- except LoginFailedException:
+ except LoginFailedError:
if kwargs.get("reconnect", True) is True:
self._login()
@@ -608,3 +615,11 @@ class _Connection(object): # pylint: disable=useless-object-inheritance
_handle_response_status(http_response)
return http_response
+
+ def get_username(self):
+ """
+ Return the username of the current connection.
+
+ Shortcut for: get_connection()._authenticator._credentials_provider.username
+ """
+ return self._authenticator._credentials_provider.username
diff --git a/src/caosdb/exceptions.py b/src/caosdb/exceptions.py
index 5763bef4ac805a7dd1dfde8da2f6f3b7e5fd4bd8..fdd2e11f1dfb8857f86942df2534d732bad9a793 100644
--- a/src/caosdb/exceptions.py
+++ b/src/caosdb/exceptions.py
@@ -5,6 +5,8 @@
#
# 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 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
@@ -21,6 +23,10 @@
#
# ** end header
#
+"""The exceptions module defines exceptions for HTTP Errors (4xx and 5xx and
+HTTP response codes) and for transaction errors (i.e. missing permissions,
+dependencies, non-passing consistency checks etc.).
+"""
from lxml import etree
@@ -28,13 +34,13 @@ from lxml import etree
class CaosDBException(Exception):
"""Base class of all CaosDB exceptions."""
- def __init__(self, msg=None, *args):
- Exception.__init__(self, msg, *args)
+ def __init__(self, msg):
+ Exception.__init__(self, msg)
self.msg = msg
-class ConfigurationException(CaosDBException):
- """ConfigurationException.
+class ConfigurationError(CaosDBException):
+ """ConfigurationError.
Indicates a misconfiguration.
@@ -43,7 +49,6 @@ class ConfigurationException(CaosDBException):
msg : str
A descriptin of the misconfiguration. The constructor adds
a few lines with explainingg where to find the configuration.
- *args
Attributes
----------
@@ -51,23 +56,32 @@ class ConfigurationException(CaosDBException):
A description of the misconfiguration.
"""
- def __init__(self, msg, *args):
- super(ConfigurationException, self).__init__(msg +
- ConfigurationException._INFO,
- *args)
+ def __init__(self, msg):
+ super().__init__(msg + ConfigurationError._INFO)
_INFO = ("\n\nPlease check your ~/.pycaosdb.ini and your $PWD/"
- ".pycaosdb.ini. Do at least one of them exist and are they correct?")
+ ".pycaosdb.ini. Does at least one of them exist and are they correct?")
-class ClientErrorException(CaosDBException):
+class ServerConfigurationException(CaosDBException):
+ """The server is configured in a different way than expected.
+
+ This can be for example unexpected flags or settings or missing extensions.
+ """
+
+
+class HTTPClientError(CaosDBException):
+ """HTTPClientError represents 4xx HTTP client errors."""
+
def __init__(self, msg, status, body):
self.status = status
self.body = body
CaosDBException.__init__(self, msg)
-class ServerErrorException(CaosDBException):
+class HTTPServerError(CaosDBException):
+ """HTTPServerError represents 5xx HTTP server errors."""
+
def __init__(self, body):
xml = etree.fromstring(body)
error = xml.xpath('/Response/Error')[0]
@@ -78,107 +92,126 @@ class ServerErrorException(CaosDBException):
CaosDBException.__init__(self, msg)
-class ConnectionException(CaosDBException):
+class CaosDBConnectionError(CaosDBException):
"""Connection is not configured or the network is down."""
def __init__(self, msg=None):
CaosDBException.__init__(self, msg)
-class URITooLongException(CaosDBException):
+class HTTPURITooLongError(HTTPClientError):
"""The URI of the last request was too long."""
def __init__(self, msg=None):
- CaosDBException.__init__(self, msg)
+ HTTPClientError.__init__(self, msg=msg, status=414, body=None)
+
+class LoginFailedError(CaosDBException):
+ """Login failed.
-class AmbiguityException(CaosDBException):
- """A retrieval of an entity that was supposed to be uniquely identifiable
- returned two or more entities."""
+ Probably, your username/password pair is wrong.
+ """
def __init__(self, msg=None):
- CaosDBException.__init__(self, msg)
+ CaosDBException.__init__(self, msg=msg)
-class LoginFailedException(CaosDBException):
- """Login failed.
+class HTTPForbiddenError(HTTPClientError):
+ """You're lacking the required permissions. Corresponds to HTTP status
+ 403.
- Probably, your username/password pair is wrong.
"""
def __init__(self, msg=None):
- CaosDBException.__init__(self, msg=msg)
+ HTTPClientError.__init__(self, msg=msg, status=403, body=None)
-class TransactionError(CaosDBException):
+class HTTPResourceNotFoundError(HTTPClientError):
+ """The requested resource doesn't exist; corresponds to HTTP status
+ 404.
- def _calc_bases(self):
- types = dict()
- # collect each class once
+ """
- for err in self.errors:
- types[id(type(err))] = type(err)
- # delete redundant super classes
+ def __init__(self, msg=None):
+ HTTPClientError.__init__(self, msg=msg, status=404, body=None)
- if len(types.values()) > 1:
- # remove TransactionError
- try:
- del types[id(TransactionError)]
- except KeyError:
- pass
- if len(types.values()) > 1:
- # remove EntityError
- try:
- del types[id(EntityError)]
- except KeyError:
- pass
+class MismatchingEntitiesError(CaosDBException):
+ """Mismatching entities were found during container sync."""
- ret = ()
- for t in types.values():
- ret += (t,)
+# ######################### Bad query errors ###########################
- if ret == ():
- ret = (type(self),)
- return ret
+class BadQueryError(CaosDBException):
+ """Base class for query errors that are not transaction errors."""
- def __init__(self, container=None, error=None, msg=None):
- self.container = container
- self.errors = []
- self.msg = msg if msg is not None else str(error)
- self.error = error
- def print_errs(self):
- print(self)
+class QueryNotUniqueError(BadQueryError):
+ """A unique query or retrieve found more than one entity."""
- for err in self.errors:
- err.print_errs()
- def _convert(self):
- t = self._calc_bases()
- try:
- newtype = type('TransactionError', t, {})
- except BaseException:
- self.print_errs()
- raise
- newinstance = newtype(container=self.container, error=self.msg)
- newinstance.errors = self.errors
- newinstance.get_entities = self.get_entities
+class EmptyUniqueQueryError(BadQueryError):
+ """A unique query or retrieve dound no result."""
- return newinstance
- def get_container(self):
- '''
- @return: The container that raised this TransactionError during the last
- transaction.
- '''
+# ######################### Transaction errors #########################
- return self.container
+
+class TransactionError(CaosDBException):
+ """An error of this type is raised whenever any transaction fails with
+ one or more entities between client and CaosDB server. More
+ detailed errors are collected as direct and indirect children in
+ the 'errors' list (direct children) and the 'all_errors' set (set
+ of all direct and indirect children).
+
+ """
+
+ def __init__(self, error=None,
+ msg="An error occured during the transaction.",
+ container=None):
+ CaosDBException.__init__(self, msg=msg)
+ self.errors = []
+ self.all_errors = set()
+ self.entities = []
+ self.all_entities = set()
+ self.container = container
+ # special case of faulty container
+ if container is not None and container.get_errors() is not None:
+ self.code = container.get_errors()[0].code
+ else:
+ self.code = None
+ if error is not None:
+ self.add_error(error)
+
+ def has_error(self, error_t, direct_children_only=False):
+ """Check whether this transaction error contains an error of type
+ error_t. If direct_children_only is True, only direct children
+ are checked.
+
+ Parameters
+ ----------
+ error_t : EntityError
+ error type to be checked
+ direct_children_only: bool, optional
+ If True, only direct children, i.e., all errors in
+ self.errors are checked. Else all direct and indirect
+ children, i.e., all errors in self.all_errors are
+ used. Default is false.
+
+ Returns
+ -------
+ has_error : bool
+ True if at least one of the children is of type error_t,
+ False otherwise.
+
+ """
+
+ test_set = self.errors if direct_children_only else self.all_errors
+ return any([isinstance(err, error_t) for err in test_set])
def add_error(self, error):
- """Add an error to this TransactionError.
+ """Add an error as a direct child to this TransactionError.
@param error: An EntityError or a list of EntityErrors.
@@ -189,35 +222,31 @@ class TransactionError(CaosDBException):
"""
if hasattr(error, "__iter__"):
- for e in error:
- self.add_error(e)
+ for err in error:
+ self.add_error(err)
return self
- elif isinstance(error, TransactionError):
+ elif isinstance(error, EntityError):
self.errors.append(error)
+ self.entities.append(error.entity)
+
+ self.all_errors.add(error)
+ self.all_errors.update(error.all_errors)
+ self.all_entities.add(error.entity)
+ self.all_entities.update(error.all_entities)
return self
else:
raise TypeError(
- "Argument is to be an TransactionError or a list of TransactionErrors.")
-
- def get_errors(self):
- '''
- @return: A list of all EntityError objects.
- '''
-
- if hasattr(self, 'errors'):
- return self.errors
-
- return None
+ "Argument is to be an EntityError or a list of EntityErrors.")
def _repr_reasons(self, indent):
- if self.get_errors() is not None and len(self.get_errors()) > 0:
+ if self.errors is not None and len(self.errors) > 0:
ret = "\n" + indent + " +--| REASONS |--"
- for c in self.get_errors():
+ for err in self.errors:
ret += '\n' + indent + ' | -> ' + \
- c.__str__(indent=indent + ' |')
+ err.__str__(indent=indent + ' |')
ret += "\n" + indent + " +----------------"
return ret
@@ -225,8 +254,11 @@ class TransactionError(CaosDBException):
return ''
def _repr_head(self, indent):
- return str(type(self).__name__) + ((': ' + self.msg)
- if hasattr(self, 'msg') and self.msg is not None else '')
+ return indent + str(type(self).__name__) + (
+ (': ' + self.msg)
+ if hasattr(self, 'msg') and self.msg is not None
+ else ''
+ )
def __str__(self, indent=''):
ret = self._repr_head(indent=indent)
@@ -237,58 +269,21 @@ class TransactionError(CaosDBException):
def __repr__(self):
return self.__str__()
- def get_entities(self):
- '''
- @return: A list of all Entity objects with errors.
- '''
- ret = []
-
- if hasattr(self, 'get_entity') and self.get_entity() is not None:
- ret.append(self.get_entity())
-
- for error in self.errors:
- if hasattr(error, 'get_entity'):
- if error.get_entity() not in ret:
- ret.append(error.get_entity())
-# if hasattr(error, 'get_entities'):
-# for e in error.get_entities():
-# if e not in ret:
-# ret.append(e)
- return ret
-
- def get_error(self):
- return self.error
-
class EntityError(TransactionError):
+ """This is the most basic entity error. It is constructed using an
+ entity that caused the error and the error message attached by the
+ server.
- @staticmethod
- def _sort_t(t):
- if len(t) > 1:
- ret = ()
- '''remove EntityError'''
-
- for i in range(len(t)):
- if t[i] != EntityError:
- ret += (t[i],)
- t = ret
-
- return t
-
- def _convert(self):
- t = self._calc_bases()
- # TODO is it really a good idea to create dynamically types here?
- newtype = type('EntityMultiError', t+(Exception,), {})
- newinstance = newtype(error=self.error, entity=self.entity)
- setattr(newinstance, 'msg', self.msg)
- setattr(newinstance, 'errors', self.errors)
- setattr(newinstance, 'container', self.container)
-
- return newinstance
+ """
- def __init__(self, error=None, container=None, entity=None):
- TransactionError.__init__(self, container=container)
+ def __init__(self, error=None, entity=None):
+ TransactionError.__init__(self)
self.error = error
+ if hasattr(error, "code"):
+ self.code = error.code
+ else:
+ self.code = None
self.entity = entity
if error is not None and hasattr(error, "encode"):
@@ -300,34 +295,17 @@ class EntityError(TransactionError):
else:
self.msg = str(error)
- def get_entity(self):
- '''
- @return: The entity that caused this error.
- '''
-
- if hasattr(self, 'entity'):
- return self.entity
-
- return None
-
@property
def description(self):
+ """The description of the error."""
return self.error.description if self.error is not None else None
- def get_code(self):
- return self.error.code if self.error is not None else None
-
- def get_error(self):
- '''
- @return: Error Message object of this Error.
- '''
-
- return self.error
-
def _repr_head(self, indent):
if hasattr(self, 'entity') and self.entity is not None:
- return str(type(self.entity).__name__).upper() + " (" + str(self.entity.id) + (("," + "'" + str(self.entity.name) + "'")
- if self.entity.name is not None else '') + ") CAUSED " + TransactionError._repr_head(self, indent)
+ return (str(type(self.entity).__name__).upper() + " (id: " +
+ str(self.entity.id) + ((", name: " + "'" + str(self.entity.name) + "'") if
+ self.entity.name is not None else '') + ") CAUSED " +
+ TransactionError._repr_head(self, indent))
else:
return TransactionError._repr_head(self, indent)
@@ -337,15 +315,19 @@ class UniqueNamesError(EntityError):
class UnqualifiedParentsError(EntityError):
- """This entity has unqualified parents (call 'get_errors()' for a list of
- errors of the parent entities or 'get_entities()' for a list of parent
- entities with errors)."""
+ """This entity has unqualified parents (see 'errors' attribute for a
+ list of errors of the parent entities or 'entities' attribute for
+ a list of parent entities with errors).
+
+ """
class UnqualifiedPropertiesError(EntityError):
- """This entity has unqualified properties (call 'get_errors()' for a list
- of errors of the properties or 'get_entities()' for a list of properties
- with errors)."""
+ """This entity has unqualified properties (see 'errors' attribute for
+ a list of errors of the properties or 'entities' attribute for a
+ list of properties with errors).
+
+ """
class EntityDoesNotExistError(EntityError):
@@ -357,11 +339,17 @@ class EntityHasNoDatatypeError(EntityError):
class ConsistencyError(EntityError):
- pass
+ """The transaction violates database consistency."""
-class AuthorizationException(EntityError):
+class AuthorizationError(EntityError):
"""You are not allowed to do what ever you tried to do.
- Maybe you need more privileges or a user account at all.
+ Maybe you need more privileges or a user account.
+ """
+
+
+class AmbiguousEntityError(EntityError):
+ """A retrieval of the entity was not possible because there is more
+ than one possible candidate.
"""
diff --git a/src/caosdb/utils/caosdb_admin.py b/src/caosdb/utils/caosdb_admin.py
index 250c2878d5d615b0815bdd7b0bb287d1567fe085..392d8bea2ce3d9a868c32854800ca6cb78f021ba 100755
--- a/src/caosdb/utils/caosdb_admin.py
+++ b/src/caosdb/utils/caosdb_admin.py
@@ -33,7 +33,7 @@ from argparse import ArgumentParser, RawDescriptionHelpFormatter
import caosdb as db
from caosdb import administration as admin
-from caosdb.exceptions import ClientErrorException
+from caosdb.exceptions import HTTPClientError
__all__ = []
__version__ = 0.3
@@ -73,7 +73,7 @@ def do_retrieve(args):
c.append(db.Entity(id=eid))
except ValueError:
c.append(db.Entity(name=i))
- c.retrieve()
+ c.retrieve(flags=eval(args.flags))
print(c)
@@ -123,7 +123,7 @@ def do_create_user(args):
try:
admin._insert_user(name=args.user_name,
email=args.user_email, password=password)
- except ClientErrorException as e:
+ except HTTPClientError as e:
print(e.msg)
@@ -141,20 +141,20 @@ def do_set_user_password(args):
def do_add_user_roles(args):
- roles = admin._get_roles(user=args.user_name, realm=None)
+ roles = admin._get_roles(username=args.user_name, realm=None)
for r in args.user_roles:
roles.add(r)
- admin._set_roles(user=args.user_name, roles=roles)
+ admin._set_roles(username=args.user_name, roles=roles)
def do_remove_user_roles(args):
- roles = admin._get_roles(user=args.user_name, realm=None)
+ roles = admin._get_roles(username=args.user_name, realm=None)
for r in args.user_roles:
if r in roles:
roles.remove(r)
- admin._set_roles(user=args.user_name, roles=roles)
+ admin._set_roles(username=args.user_name, roles=roles)
def do_set_user_entity(args):
@@ -178,7 +178,7 @@ def do_delete_user(args):
def do_retrieve_user_roles(args):
- print(admin._get_roles(user=args.user_name))
+ print(admin._get_roles(username=args.user_name))
def do_retrieve_role_permissions(args):
diff --git a/src/doc/Makefile b/src/doc/Makefile
index 5458c5300efc82e55686bc1cd6934182c5c8e39a..64219c5957ee963e84f9305685f2ec4e8ed3d761 100644
--- a/src/doc/Makefile
+++ b/src/doc/Makefile
@@ -32,6 +32,7 @@ PY_BASEDIR = ../caosdb
SOURCEDIR = .
BUILDDIR = ../../build/doc
+
.PHONY: doc-help Makefile
# Put it first so that "make" without argument is like "make help".
@@ -44,4 +45,4 @@ doc-help:
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
apidoc:
- @$(SPHINXAPIDOC) -o _apidoc $(PY_BASEDIR)
+ @$(SPHINXAPIDOC) -o _apidoc --separate $(PY_BASEDIR)
diff --git a/src/doc/administration.rst b/src/doc/administration.rst
new file mode 100644
index 0000000000000000000000000000000000000000..061acc8364d2ef62f743a20d7b9e6562baac0fc5
--- /dev/null
+++ b/src/doc/administration.rst
@@ -0,0 +1,14 @@
+Administration
+==============
+
+The Python script ``caosdb_admin.py`` should be used for administrative tasks.
+Call ``caosdb_admin.py --help`` to see how to use it.
+
+The most common task is to create a new user (in the CaosDB realm) and set a
+password for the user (note that a user typically needs to be activated)::
+
+ caosdb_admin.py create_user anna
+ caosdb_admin.py set_user_password anna
+ caosdb_admin.py add_user_roles anna administration
+ caosdb_admin.py activate_user anna
+
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 9e2924ae726e13aacd2f955ae1904b39ad73cbc3..b05fa1c71c1dcd0b59916594818449d2ebc574bd 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -8,16 +8,18 @@
# -- Path setup --------------------------------------------------------------
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
+# If extensions (or modules to document with autodoc) are in another directory, add these
+# directories to sys.path here. This is particularly necessary if this package is installed at a
+# different version, for example via `pip install`.
#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('../caosdb'))
-
+# If the directory is relative to the documentation root, use os.path.abspath to make it absolute,
+# like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
-import sphinx_rtd_theme
+import sphinx_rtd_theme # noqa: E402
# -- Project information -----------------------------------------------------
@@ -27,9 +29,10 @@ copyright = '2020, IndiScale GmbH'
author = 'Daniel Hornung'
# The short X.Y version
-version = '0.4.0'
+version = '0.5.2'
# The full version, including alpha/beta/rc tags
-release = '0.4.0-rc'
+# release = '0.5.2-rc2'
+release = '0.5.2'
# -- General configuration ---------------------------------------------------
@@ -43,6 +46,7 @@ release = '0.4.0-rc'
# ones.
extensions = [
'sphinx.ext.autodoc',
+ 'sphinx.ext.autosectionlabel',
'sphinx.ext.intersphinx',
'sphinx.ext.napoleon', # For Google style docstrings
"recommonmark", # For markdown files.
@@ -54,7 +58,6 @@ templates_path = ['_templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
-#
source_suffix = ['.rst', '.md']
# The master toctree document.
@@ -81,6 +84,7 @@ pygments_style = None
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
+
html_theme = "sphinx_rtd_theme"
# Theme options are theme-specific and customize the look and feel of a theme
@@ -182,10 +186,24 @@ epub_exclude_files = ['search.html']
# -- Extension configuration -------------------------------------------------
-# -- Options for intersphinx extension ---------------------------------------
+# True to prefix each section label with the name of the document it is in, followed by a colon. For
+# example, index:Introduction for a section called Introduction that appears in document
+# index.rst. Useful for avoiding ambiguity when the same section heading appears in different
+# documents.
+#
+# Note: This stops "normal" links from working, so it should be kept at False.
+# autosectionlabel_prefix_document = True
+
+# -- Options for intersphinx -------------------------------------------------
+
+# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_mapping
+intersphinx_mapping = {
+ "python": ("https://docs.python.org/", None),
+ "caosdb-mysqlbackend": ("https://docs.indiscale.com/caosdb-mysqlbackend/",
+ None),
+ "caosdb-server": ("https://docs.indiscale.com/caosdb-server/", None),
+}
-# Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
# TODO Which options do we want?
autodoc_default_options = {
diff --git a/src/doc/configuration.md b/src/doc/configuration.md
index b2de2781d5adff4d59cb3648cd912e142327f676..6e53542f661dcae94622fef24a67cecf7491df9c 100644
--- a/src/doc/configuration.md
+++ b/src/doc/configuration.md
@@ -50,5 +50,5 @@ debugging (which I hope will not be necessary for this tutorial) or if you want
the internals of the protocol.
A complete list of options can be found in the
-[pycaosdb.ini file](https://gitlab.com/caosdb/caosdb-pylib/-/blob/master/examples/pycaosdb.ini) in
+[pycaosdb.ini file](https://gitlab.com/caosdb/caosdb-pylib/-/blob/main/examples/pycaosdb.ini) in
the examples folder of the source code.
diff --git a/src/doc/index.rst b/src/doc/index.rst
index e8cc93aa398de36c30833bc97ca79ce20564daa6..bd29c6c56acf5c173e94ae6471a6aeba56ea4b93 100644
--- a/src/doc/index.rst
+++ b/src/doc/index.rst
@@ -10,13 +10,14 @@ Welcome to PyCaosDB's documentation!
Getting started <README_SETUP>
tutorials/index
Concepts <concepts>
- Configuration <configuration>
- API documentation<_apidoc/modules>
+ Configuration <configuration>
+ Administration <administration>
+ API documentation<_apidoc/caosdb>
This is the documentation for the Python client library for CaosDB, ``PyCaosDB``.
-This documentation helps you to :doc:`get started<getting_started>`, explains the most important
-:doc:`concepts<concepts>` and offers a range of :doc:`tutorials<tutorials>`.
+This documentation helps you to :doc:`get started<README_SETUP>`, explains the most important
+:doc:`concepts<concepts>` and offers a range of :doc:`tutorials<tutorials/index>`.
Indices and tables
diff --git a/src/doc/tutorials/Data-Insertion.rst b/src/doc/tutorials/Data-Insertion.rst
new file mode 100644
index 0000000000000000000000000000000000000000..22fb9461d6916003b2dad496ff3487df335c8dcc
--- /dev/null
+++ b/src/doc/tutorials/Data-Insertion.rst
@@ -0,0 +1,173 @@
+Data Insertion
+==============
+
+Data Models
+~~~~~~~~~~~
+
+Data is stored and structured in CaosDB using a concept of RecordTypes, Properties, Records etc. If
+you do not know what these are, please look at the chapter :doc:`Data
+Model<caosdb-server:Data-Model>` in the CaosDB server documentation.
+
+In order to insert some actual data, we need to create a data model
+using RecordTypes and Properties (You may skip this if you use a CaosDB
+instance that already has the required types). So, let’s create a simple
+Property called “a†of datatype double. This is very easy in pylib:
+
+.. code:: python
+
+ a = db.Property(name="a", datatype=db.DOUBLE)
+
+There are a few basic datatypes: db.INTEGER, db.TEXT. See `data
+type <Specification/Datatype>`__ for a full list.
+
+We can create our own small data model for e.g. a simulation by adding
+two more Properties and a RecordType:
+
+.. code:: python
+
+ b = db.Property(name="b", datatype=db.DOUBLE)
+ epsilon = db.Property(name="epsilon", datatype=db.DOUBLE)
+ recordtype = db.RecordType(name="BarkleySimulation")
+ recordtype.add_property(a)
+ recordtype.add_property(b)
+ recordtype.add_property(epsilon)
+ container = db.Container()
+ container.extend([a, b, epsilon, recordtype])
+ container.insert()
+
+.. _tutorial-inheritance-properties:
+
+Inheritance of Properties
+-------------------------
+
+Suppose you want to create a new RecordType “2D_BarkleySimulationâ€
+that denotes spatially extended Barkley simulations. This is a subtype
+of the “BarkleySimulation†RecordType above and should have all its
+parameters, i.e., properties. It may be assigned more, e.g., spatial
+resolution, but we'll omit this for the sake of brevity for now.
+
+.. code:: python
+
+ rt = db.RecordType(name="2D_BarkleySimulation",
+ description="Spatially extended Barkley simulation")
+ # inherit all properties from the BarkleySimulation RecordType
+ rt.add_parent(name="BarkleySimulation", inheritance="all")
+ rt.insert()
+
+ print(rt.get_property(name="epsilon").importance) ### rt has a "epsilon" property with the same importance as "BarkleySimulation"
+
+The parameter ``inheritance=(obligatory|recommended|fix|all|none)`` of
+:py:meth:`Entity.add_parent()<caosdb.common.models.Entity.add_parent>` tells the server to assign
+all properties of the parent RecordType with the chosen importance (and properties with a higher
+importance) to the child RecordType
+automatically upon insertion. See the chapter on `importance
+<https://docs.indiscale.com/caosdb-server/specification/RecordType.html#importance>`_ in the
+documentation of the CaosDB server for more information on the importance and inheritance of
+properties.
+
+.. note::
+
+ The inherited properties will only be visible after the insertion since they are set by the
+ CaosDB server, not by the Python client.
+
+
+Insert Actual Data
+~~~~~~~~~~~~~~~~~~
+
+Suppose the RecordType “Experiment†and the Property “date†exist in the
+database. You can then create single data Records by using the
+corresponding python class:
+
+.. code:: python
+
+ rec = db.Record()
+ rec.add_parent(name="Experiment")
+ rec.add_property(name="date", value="2020-01-07")
+ rec.insert()
+
+Here, the record has a parent: The RecordType “Experimentâ€. And a
+Property: date.
+
+Note, that if you want to use a property that is not a primitive
+datatype like db.INTEGER and so on, you need to use the ID of the Entity
+that you are referencing.
+
+.. code:: python
+
+ rec = db.Record()
+ rec.add_parent(name="Experiment")
+ rec.add_property(name="report", value=235507)
+ rec.add_property(name="Analysis", value=230007)
+ rec.insert()
+
+Of course, the IDs 235507 and 230007 need to exist in CaosDB. The first
+example shows how to use a db.REFERENCE Property (report) and the second
+shows that you can use any RecordType as Property to reference a Record
+that has such a parent.
+
+Most Records do not have name however it can absolutely make sense. In
+that case use the name argument when creating it. Another useful feature
+is the fact that properties can have units:
+
+.. code:: python
+
+ rec = db.Record("DeviceNo-AB110")
+ rec.add_parent(name="SlicingMachine")
+ rec.add_property(name="weight", value="1749", unit="kg")
+ rec.insert()
+
+If you are in some kind of analysis you can do this in batch mode with a
+container. E.g. if you have a python list ``analysis_results``:
+
+.. code:: python
+
+ cont = db.Container()
+ for date, result in analysis_results:
+ rec = db.Record()
+ rec.add_parent(name="Experiment")
+ rec.add_property(name="date", value=date)
+ rec.add_property(name="result", value=result)
+ cont.append(rec)
+
+ cont.insert()
+
+Useful is also, that you can insert directly tabular data.
+
+.. code:: python
+
+ from caosadvancedtools.table_converter import from_tsv
+
+ recs = from_tsv("test.csv", "Experiment")
+ print(recs)
+ recs.insert()
+
+With this example file
+`test.csv <uploads/4f2c8756a26a3984c0af09d206d583e5/test.csv>`__.
+
+
+File Update
+-----------
+
+Updating an existing file by uploading a new version.
+
+1. Retrieve the file record of interest, e.g. by ID:
+
+.. code:: python
+
+ import caosdb as db
+
+ file_upd = db.File(id=174).retrieve()
+
+2. Set the new local file path. The remote file path is stored in the
+ file object as ``file_upd.path`` while the local path can be found in
+ ``file_upd.file``.
+
+.. code:: python
+
+ file_upd.file = "./supplements.pdf"
+
+3. Update the file:
+
+.. code:: python
+
+ file_upd.update()
diff --git a/src/doc/tutorials/data-model-interface.md b/src/doc/tutorials/data-model-interface.md
new file mode 100644
index 0000000000000000000000000000000000000000..f6967c57a0a3de6e7c6fd3d2b64d3f59620526de
--- /dev/null
+++ b/src/doc/tutorials/data-model-interface.md
@@ -0,0 +1,36 @@
+# Data Models
+
+
+
+You also want to change the datamodel? Also call
+```bash
+pip3 install --user --no-deps .
+```
+in
+```bash
+CaosDB/data_models
+```
+
+Change to the appropriate directory
+```bash
+cd CaosDB/data_models
+```
+There are "data models" defined in
+```bash
+caosdb_models
+```
+having an ending like "_model.py"
+A set of data models is also considered to be a model
+You can create an UML representation of a model or a set of models by calling
+```bash
+./model_interface.py -u model_name [model_name2]
+```
+If you have troubles look at
+```bash
+./model_interface.py -h
+```
+You can change existing models (but be careful! I hope you know what you are doing) or add new ones by changing the appropriate files or adding a new XXXX_model.py
+Once you are done, you can sync your changes with the server
+```bash
+./model_interface.py -s model_name [model_name2]
+```
diff --git a/src/doc/tutorials/errors.rst b/src/doc/tutorials/errors.rst
new file mode 100644
index 0000000000000000000000000000000000000000..37c53c9b527a0435f9f24ae6c6e71687e73eb963
--- /dev/null
+++ b/src/doc/tutorials/errors.rst
@@ -0,0 +1,176 @@
+
+Error Handling
+==============
+
+In case of erroneous transactions, connection problems and a lot of
+other cases, PyCaosDB may raise specific errors in order to pinpoint
+the problem as precisely as possible. Some of these errors a
+representations of errors in the CaosDB server, others stem from
+problems that occurred on the client side.
+
+The errors and exceptions are ordered hierarchically form the most
+general exceptions to specific transaction or connection problems. The
+most important error types and the hierarchy will be explained in the
+following. For more information on specific error types, see also the
+:doc:`source code<../_apidoc/caosdb.exceptions>`.
+
+.. note::
+
+ Starting from PyCaosDB 0.5, the error handling has changed
+ significantly. New error classes have been introduced and the
+ behavior of ``TransactionError`` and ``EntityError`` has been
+ re-worked. In the following, only the "new" errors are
+ discussed. Please refer to the documentation of PyCaosDB 0.4.1 and
+ earlier for the old error handling.
+
+CaosDBException
+----------------
+
+``CaosDBException`` is the most generic exception and all other error classes inherit
+from this one. Because of its generality, it doesn't tell you much
+except that some component of PyCaosDB raised an exception. If you
+want to catch all possible CaosDB errors, this is the class to use.
+
+TransactionError
+----------------
+
+Every transaction (calling ``insert``, ``update``, ``retrieve``, or
+``delete`` on a container or an entity) may finish with errors. They
+indicate, for instance, that an entity does not exist or that you need
+to specify a data type for your property and much more. If and only if
+one or more errors occur during a transaction a ``TransactionError``
+will be raised by the transaction method. The ``TransactionError``
+class is a container for all errors which occur during a
+transaction. It usually contains one or more :ref:`entity
+errors<EntityError>` which you can inspect in order to learn why the
+transaction failed. For this inspection, there are some helpful
+attributes and methods provided by the ``TransactionError``:
+
+* ``entities``: a list of all entities that directly caused at least one error
+ in this transaction.
+
+* ``errors``: a list of all ``EntityError`` objects that directly caused the
+ transaction to fail.
+
+* ``all_entities``, ``all_errors``: sets of all entities and errors
+ that, directly or indirectly, caused either this ``TransactionError`` or any of the
+ ``EntityError`` objects it contains.
+
+* ``has_error(error_t)``: Check whether an error of type ``error_t``
+ occurred during the transaction.
+
+Additionally, ``print(transaction_error)`` prints a tree-like
+representation of all errors regarding the transaction in question.
+
+EntityError
+-----------
+
+An ``EntityError`` specifies the entity and the error proper that
+caused a transaction to fail. It is never raised on its own but is
+contained in a ``TransactionError`` (which may or may not contain
+other ``EntityError`` objects) which is then raised. ``EntityError``
+has several :ref:`subclasses<Special Errors>` that further specify the
+error that occurred.
+
+The ``EntityError`` class is in fact a subclass of
+``TransactionError``. Thus, it has the same methods and attributes as
+the ``TransactionError`` explained
+:ref:`above<TransactionError>`. This is important in case of an
+``EntityError`` that was caused by other faulty entities (e.g., broken
+parents or properties). In that case these problematic entities and
+errors can again be inspected by visiting the ``entities`` and
+``errors`` lists as above.
+
+Special Errors
+~~~~~~~~~~~~~~
+
+Subclasses of ``EntityError`` for special purposes:
+
+* ``EntityDoesNotExistError``
+
+* ``EntityHasNoDataTypeError``
+
+* ``UniqueNamesError``
+
+* ``UnqualifiedParentsError``
+
+* ``UnqualifiedPropertiesError``
+
+* ``ConsistencyError``
+
+* ``AuthorizationError``
+
+* ``AmbiguousEntityError``
+
+BadQueryError
+-------------
+
+A ``BadQueryError`` is raised when a query could not be processed by
+the server. In contrast to a ``TransactionError`` it is not
+necessarily caused by problematic entities or
+containers. ``BadQueryError`` has the two important subclasses
+``EmptyUniqueQueryError`` and ``QueryNotUniqueError`` for queries with
+``unique=True`` which found no or ambiguous entities, respectively.
+
+HTTP Errors
+-----------
+
+An ``HTTPClientError`` or an ``HTTPServerError`` is raised in case of
+http(s) connection problems caused by the Python client or the CaosDB
+server, respectively. There are the following subclasses of
+``HTTPClientError`` that are used to specify the connection problem:
+
+* ``HTTPURITooLongError``: The URI of the request was too long to be
+ processed by the server.
+
+* ``HTTPForbiddenError``: You're not allowed to access this resource.
+
+* ``HTTPResourceNotFoundError``: The requested resource doesn't exist.
+
+Other Errors
+------------
+
+There are further subclasses of ``CaosDBException`` that are raised in
+case of faulty configurations or other problems. They should be rather
+self-explanatory from their names; see the :doc:`source code<../_apidoc/caosdb.exceptions>`
+for further information.
+
+* ``ConfigurationError``
+
+* ``LoginFailedError``
+
+* ``MismatchingEntitiesError``
+
+* ``ServerConfigurationException``
+
+Examples
+--------
+
+.. code-block:: python3
+
+ import caosdb as db
+
+ def link_and_insert(entity, linked, link=True):
+ """Link the ENTITY to LINKED and insert it."""
+ if link:
+ entity.add_property(db.Property(name="link", value=linked))
+ try:
+ entity.insert()
+ except db.TransactionError as tre:
+ # Unique names problem may be worked around by using another name
+ if tre.has_error(db.UniqueNamesError):
+ for ent_error in tre.errors:
+ if (isinstance(ent_error, db.UniqueNamesError)
+ and entity in ent_error.entities):
+ entity.name = entity.name + "_new" # Try again with new name.
+ link_and_insert(entity, linked, link=False)
+ break
+ # Unqualified properties will be handled by the caller
+ elif tre.has_error(db.UnqualifiedPropertiesError):
+ for ent_error in tre.errors:
+ if (isinstance(ent_error, db.UnqualifiedPropertiesError_
+ and entity in ent_error.entities):
+ raise RuntimeError("One of the properties was unqualified: " + str(ent_error))
+ # Other problems are not covered by this tutorial
+ else:
+ raise NotImplementedError("Unhandled TransactionError: " + str(tre))
diff --git a/src/doc/tutorials/first_steps.rst b/src/doc/tutorials/first_steps.rst
index 3da05b05c4d4025f6d81490550fd1482ae147fb4..34b96bbeca416107fb34feb4707b9ef46fc49fe7 100644
--- a/src/doc/tutorials/first_steps.rst
+++ b/src/doc/tutorials/first_steps.rst
@@ -2,14 +2,15 @@ First Steps
===========
You should have a working connection to a CaosDB instance now. If not, please check out the
-:doc:`Getting Started secton</getting_started>`.
+:doc:`Getting Started secton</README_SETUP>`.
If you are not yet familiar with Records, RecordTypes and Properties used in CaosDB,
-please check out the respective part in the `Web Interface Tutorial`_.
-You should also know the basics of the CaosDB Query Language (a tutorial is here_).
+please check out the respective part in the `Web Interface tutorial`_.
+You should also know the basics of the CaosDB Query Language (a tutorial is
+`here <https://docs.indiscale.com/caosdb-webui/tutorials/query.html>`_).
-We recommend that you connect to the demo instance in order to try out the following
-examples. You can do this with
+We recommend that you connect to the `demo instance`_ (hosted by `Indiscale`_) in order to try out
+the following examples. You can do this with
>>> import caosdb as db
>>> _ = db.configure_connection(
@@ -19,7 +20,7 @@ examples. You can do this with
... password="caosdb")
or by using corresponding settings in the configuration file
-(see :doc:`Getting Started secton</getting_started>`.).
+(see :doc:`Getting Started secton</README_SETUP>`.).
However, you can also translate the examples to the data model that you have at hand.
Let's start with a simple query.
@@ -113,6 +114,8 @@ You can download files (if the LinkAhead server has access to them)
The file will be saved under target_path.
If the files are large data files, it is often a better idea to only retrieve the path of the file and access them via a local mount.
+
+
Summary
-------
@@ -122,9 +125,6 @@ the result Records and their properties.
The next tutorial shows how to make some meaningful use of this.
-
-.. _here: https://gitlabio.something
.. _`demo instance`: https://demo.indiscale.com
.. _`IndiScale`: https://indiscale.com
-.. _`Web Interface Tutorial`: https://caosdb.gitlab.io/caosdb-webui/tutorials/model.html
-.. _here: https://caosdb.gitlab.io/caosdb-webui/tutorials/cql.html
+.. _`Web Interface tutorial`: https://docs.indiscale.com/caosdb-webui/tutorials/first_steps.html
diff --git a/src/doc/tutorials/index.rst b/src/doc/tutorials/index.rst
index 311f7080045e8925dd26eb03c2da3b12b1dba6e4..3889edb8f47e973cc7ae25c9134d75cfeab95f65 100644
--- a/src/doc/tutorials/index.rst
+++ b/src/doc/tutorials/index.rst
@@ -12,4 +12,7 @@ advanced usage of the Python client.
first_steps
basic_analysis
+ Data-Insertion
+ errors
+ data-model-interface
diff --git a/unittests/docker/Dockerfile b/unittests/docker/Dockerfile
index e41fb91b3e9ae54cff277519c03f481c21264e9e..7fa3f75bd198724628dee48ab328829fa071a639 100644
--- a/unittests/docker/Dockerfile
+++ b/unittests/docker/Dockerfile
@@ -5,6 +5,6 @@ RUN apt-get update && \
curl pycodestyle \
python3-sphinx
ARG COMMIT="dev"
-RUN git clone -b dev https://gitlab.com/caosdb/caosdb-pylib.git && \
+RUN git clone -b dev https://gitlab.indiscale.com/caosdb/src/caosdb-pylib.git && \
cd caosdb-pylib && git checkout $COMMIT && pip3 install .
RUN pip3 install recommonmark sphinx-rtd-theme
diff --git a/unittests/test_authentication_auth_token.py b/unittests/test_authentication_auth_token.py
index 1eaf091863e23205c9ffca5373e51b654a5a42e4..15e54121fc0d7b5c2be645cdb88bc20804a10980 100644
--- a/unittests/test_authentication_auth_token.py
+++ b/unittests/test_authentication_auth_token.py
@@ -32,7 +32,7 @@ from unittest.mock import Mock
from caosdb.connection.authentication import auth_token as at
from caosdb.connection.mockup import MockUpServerConnection, MockUpResponse
from caosdb.connection.utils import parse_auth_token
-from caosdb.exceptions import LoginFailedException
+from caosdb.exceptions import LoginFailedError
from caosdb import configure_connection
@@ -73,7 +73,7 @@ def test_login_raises():
c = configure_connection(url="https://example.com",
password_method="auth_token",
auth_token="[auth_token]")
- with raises(LoginFailedException):
+ with raises(LoginFailedError):
c._login()
diff --git a/unittests/test_authentication_unauthenticated.py b/unittests/test_authentication_unauthenticated.py
index 9ea864a9999c5e3a74fa22fd3f6942c4e5806256..52146b08ed4e1026660eebacedf348aeb2ff2721 100644
--- a/unittests/test_authentication_unauthenticated.py
+++ b/unittests/test_authentication_unauthenticated.py
@@ -32,7 +32,7 @@ from unittest.mock import Mock
from caosdb.connection.authentication import unauthenticated
from caosdb.connection.mockup import MockUpServerConnection, MockUpResponse
from caosdb.connection.utils import parse_auth_token
-from caosdb.exceptions import LoginFailedException
+from caosdb.exceptions import LoginFailedError
from caosdb import configure_connection
from .test_authentication_auth_token import response_with_auth_token
@@ -67,5 +67,5 @@ def test_configure_connection():
def test_login_raises():
c = configure_connection(url="https://example.com",
password_method="unauthenticated")
- with raises(LoginFailedException):
+ with raises(LoginFailedError):
c._login()
diff --git a/unittests/test_configuration.py b/unittests/test_configuration.py
index 76445b6f262120d6a29c73527a9bf042f85f8a05..b135e7cd65b11be7cb6c4ef2237a41a6639ccbb7 100644
--- a/unittests/test_configuration.py
+++ b/unittests/test_configuration.py
@@ -22,19 +22,45 @@
# ** end header
#
+import pytest
import caosdb as db
+from os import environ, getcwd, remove
+from os.path import expanduser, isfile, join
from pytest import raises
-def test_config_ini_via_envvar():
- from os import environ
- from os.path import expanduser
+@pytest.fixture
+def temp_ini_files():
+ created_temp_ini_cwd = False
+ created_temp_ini_home = False
+ if not isfile(join(getcwd(), "pycaosdb.ini")):
+ open("pycaosdb.ini", 'a').close() # create temporary ini file
+ created_temp_ini_cwd = True
+ if not isfile(expanduser("~/.pycaosdb.ini")):
+ open(expanduser("~/.pycaosdb.ini"), 'a').close() # create temporary ini file in home directory
+ created_temp_ini_home = True
+ yield 0
+ if created_temp_ini_cwd:
+ remove("pycaosdb.ini")
+ if created_temp_ini_home:
+ remove(expanduser("~/.pycaosdb.ini"))
+ environ["PYCAOSDBINI"] = "~/.pycaosdb.ini"
+
+
+def test_config_ini_via_envvar(temp_ini_files):
with raises(KeyError):
environ["PYCAOSDBINI"]
environ["PYCAOSDBINI"] = "bla bla"
assert environ["PYCAOSDBINI"] == "bla bla"
- assert db.configuration.configure(environ["PYCAOSDBINI"]) == []
+ # test wrong configuration file in envvar
+ assert not expanduser(environ["PYCAOSDBINI"]) in db.configuration._read_config_files()
+ # test good configuration file in envvar
environ["PYCAOSDBINI"] = "~/.pycaosdb.ini"
- assert db.configuration.configure(expanduser(environ["PYCAOSDBINI"])) == [expanduser("~/.pycaosdb.ini")]
+ assert expanduser("~/.pycaosdb.ini") in db.configuration._read_config_files()
+ # test without envvar
+ environ.pop("PYCAOSDBINI")
+ assert expanduser("~/.pycaosdb.ini") in db.configuration._read_config_files()
+ # test configuration file in cwd
+ assert join(getcwd(), "pycaosdb.ini") in db.configuration._read_config_files()
diff --git a/unittests/test_connection.py b/unittests/test_connection.py
index 1dfd1fce730d4d4ba627eb4c27830b0c5156fb29..16370f00b7d5e3389582befaac1762b1d2992fcf 100644
--- a/unittests/test_connection.py
+++ b/unittests/test_connection.py
@@ -37,7 +37,7 @@ from caosdb.connection.connection import (CaosDBServerConnection,
from caosdb.connection.mockup import (MockUpResponse, MockUpServerConnection,
_request_log_message)
from caosdb.connection.utils import make_uri_path, quote, urlencode
-from caosdb.exceptions import ConfigurationException, LoginFailedException
+from caosdb.exceptions import ConfigurationError, LoginFailedError
from nose.tools import assert_equal as eq
from nose.tools import assert_false as falz
from nose.tools import assert_is_not_none as there
@@ -234,7 +234,7 @@ def test_test_request_with_two_responses():
def test_missing_implementation():
connection = configure_connection()
- with raises(ConfigurationException) as exc_info:
+ with raises(ConfigurationError) as exc_info:
connection.configure()
assert exc_info.value.args[0].startswith(
"Missing CaosDBServerConnection implementation.")
@@ -242,27 +242,26 @@ def test_missing_implementation():
def test_bad_implementation_not_callable():
connection = configure_connection()
- with raises(ConfigurationException) as exc_info:
+ with raises(ConfigurationError) as exc_info:
connection.configure(implementation=None)
assert exc_info.value.args[0].startswith(
"Bad CaosDBServerConnection implementation.")
- assert exc_info.value.args[1].args[0] == "'NoneType' object is not callable"
+ assert "'NoneType' object is not callable" in exc_info.value.args[0]
def test_bad_implementation_wrong_class():
connection = configure_connection()
- with raises(ConfigurationException) as exc_info:
+ with raises(ConfigurationError) as exc_info:
connection.configure(implementation=dict)
assert exc_info.value.args[0].startswith(
"Bad CaosDBServerConnection implementation.")
- assert exc_info.value.args[1].args[0] == (
- "The `implementation` callable did not return an instance of "
- "CaosDBServerConnection.")
+ assert ("The `implementation` callable did not return an instance of "
+ "CaosDBServerConnection.") in exc_info.value.args[0]
def test_missing_auth_method():
connection = configure_connection()
- with raises(ConfigurationException) as exc_info:
+ with raises(ConfigurationError) as exc_info:
connection.configure(implementation=MockUpServerConnection)
assert exc_info.value.args[0].startswith("Missing password_method.")
@@ -272,11 +271,12 @@ def test_missing_password():
connection.configure(implementation=setup_two_resources,
password_method="plain")
connection._authenticator.auth_token = "[test-auth-token]"
- assert connection.retrieve(["some"]).headers["Cookie"] == "SessionToken=%5Btest-auth-token%5D;"
+ assert connection.retrieve(
+ ["some"]).headers["Cookie"] == "SessionToken=%5Btest-auth-token%5D;"
connection.configure(implementation=setup_two_resources,
password_method="plain")
- with raises(LoginFailedException):
+ with raises(LoginFailedError):
connection.delete(["401"])
@@ -284,11 +284,13 @@ def test_auth_token_connection():
connection = configure_connection(auth_token="blablabla",
password_method="auth_token",
implementation=setup_two_resources)
- connection.retrieve(["some"]).headers["Cookie"] == "SessionToken=blablabla;"
+ connection.retrieve(
+ ["some"]).headers["Cookie"] == "SessionToken=blablabla;"
connection._logout()
- with raises(LoginFailedException) as cm:
- connection.retrieve(["some"]).headers["Cookie"] == "SessionToken=blablabla;"
+ with raises(LoginFailedError) as cm:
+ connection.retrieve(
+ ["some"]).headers["Cookie"] == "SessionToken=blablabla;"
assert cm.value.args[0] == ("The authentication token is expired or you "
"have been logged out otherwise. The "
"auth_token authenticator cannot log in "
diff --git a/unittests/test_connection_utils.py b/unittests/test_connection_utils.py
index c21b453e3a7588f30d86be8d2ed39bb4d7a1d31e..3890ae05cfe38b78a5ba0829753420246bdb560d 100644
--- a/unittests/test_connection_utils.py
+++ b/unittests/test_connection_utils.py
@@ -28,7 +28,7 @@ from pytest import raises
from nose.tools import (assert_equal as eq, assert_raises as raiz, assert_true
as tru, assert_is_not_none as there, assert_false as
falz)
-from caosdb.exceptions import ConfigurationException, LoginFailedException
+from caosdb.exceptions import ConfigurationError, LoginFailedError
from caosdb.connection.utils import parse_auth_token, auth_token_to_cookie
from caosdb.connection.connection import (
configure_connection, CaosDBServerConnection,
@@ -45,8 +45,10 @@ def setup_module():
def test_parse_auth_token():
- assert parse_auth_token("SessionToken=%5Bblablabla%5D; expires=bla; ...") == "[blablabla]"
+ assert parse_auth_token(
+ "SessionToken=%5Bblablabla%5D; expires=bla; ...") == "[blablabla]"
def test_auth_token_to_cookie():
- assert auth_token_to_cookie("[blablabla]") == "SessionToken=%5Bblablabla%5D;"
+ assert auth_token_to_cookie(
+ "[blablabla]") == "SessionToken=%5Bblablabla%5D;"
diff --git a/unittests/test_error_handling.py b/unittests/test_error_handling.py
new file mode 100644
index 0000000000000000000000000000000000000000..7f974e7db826d093e335b250953658b08db062cd
--- /dev/null
+++ b/unittests/test_error_handling.py
@@ -0,0 +1,317 @@
+# -*- encoding: utf-8 -*-
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2020 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2020 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/>.
+#
+# ** end header
+#
+"""Test the new (as of June 2020) error handling. All errors should
+be TransactionErrors at first which may have one or more level of
+children.
+
+"""
+import caosdb as db
+from caosdb.common.models import raise_errors
+from caosdb.exceptions import (AuthorizationError,
+ EntityDoesNotExistError, EntityError,
+ EntityHasNoDatatypeError,
+ TransactionError, UniqueNamesError,
+ UnqualifiedParentsError,
+ UnqualifiedPropertiesError)
+
+from pytest import raises
+
+
+# #################### Single Error Tests ####################
+
+
+def _add_error_message_to_entity(entity, code, description="Error message"):
+ """Attach error message with code and description to entity"""
+ message = db.Message(type="Error", code=code,
+ description=description)
+ entity.add_message(message)
+
+ return entity
+
+
+def test_has_no_datatype_error():
+ """Code 110; property without datatype"""
+ code = 110
+ prop = _add_error_message_to_entity(db.Property(name="TestProp"),
+ code)
+ with raises(TransactionError) as e:
+ raise_errors(prop)
+ # There should be exactly one child
+ assert len(e.value.errors) == 1
+ err = e.value.errors[0]
+ # check type and entity of only child
+ assert isinstance(err, EntityHasNoDatatypeError)
+ assert err.entity.name == prop.name
+
+
+def test_entity_does_not_exist_error():
+ """Code 101; entity does not exist"""
+ code = 101
+ ent = _add_error_message_to_entity(db.Entity(name="TestEnt"),
+ code)
+ with raises(TransactionError) as e:
+ raise_errors(ent)
+ # There should be exactly one child
+ assert len(e.value.errors) == 1
+ err = e.value.errors[0]
+ # check type and entity of only child
+ assert isinstance(err, EntityDoesNotExistError)
+ assert err.entity.name == ent.name
+
+
+def test_entity_error():
+ """Code 0; most basic."""
+ code = 0
+ ent = _add_error_message_to_entity(db.Entity(name="TestEnt"),
+ code)
+ with raises(TransactionError) as e:
+ raise_errors(ent)
+ assert len(e.value.errors) == 1
+ err = e.value.errors[0]
+ assert isinstance(err, EntityError)
+ assert err.entity.name == ent.name
+
+
+def test_unique_names_error():
+ """Code 152; name is not unique"""
+ code = 152
+ ent = _add_error_message_to_entity(db.Entity(name="TestEnt"),
+ code)
+ with raises(TransactionError) as e:
+ raise_errors(ent)
+ assert len(e.value.errors) == 1
+ err = e.value.errors[0]
+ assert isinstance(err, UniqueNamesError)
+ assert err.entity.name == ent.name
+
+
+def test_authorization_exception():
+ """Code 403; transaction not allowed"""
+ code = 403
+ ent = _add_error_message_to_entity(db.Entity(name="TestEnt"),
+ code)
+ with raises(TransactionError) as e:
+ raise_errors(ent)
+ assert len(e.value.errors) == 1
+ err = e.value.errors[0]
+ assert isinstance(err, AuthorizationError)
+ assert err.entity.name == ent.name
+
+
+def test_empty_container_with_error():
+ """Has to raise an error, even though container is empty."""
+ code = 0
+ cont = _add_error_message_to_entity(db.Container(), code)
+ with raises(TransactionError) as e:
+ raise_errors(cont)
+ # No entity errors
+ assert len(e.value.errors) == 0
+ assert e.value.container == cont
+ assert int(e.value.code) == code
+
+
+def test_faulty_container_with_healthy_entities():
+ """Raises a TransactionError without any EntityErrors since only the
+ container, but none of its entities has an error.
+
+ """
+ code = 0
+ cont = _add_error_message_to_entity(db.Container(), code)
+ cont.append(db.Entity("TestHealthyEnt1"))
+ cont.append(db.Entity("TestHealthyEnt2"))
+ with raises(TransactionError) as e:
+ raise_errors(cont)
+ # No entity errors
+ assert len(e.value.errors) == 0
+ assert len(e.value.entities) == 0
+ assert e.value.container == cont
+ assert int(e.value.code) == code
+
+
+# #################### Children with children ####################
+
+
+def test_unqualified_parents_error():
+ """Code 116; parent does not exist"""
+ code = 116
+ entity_does_not_exist_code = 101
+ parent = _add_error_message_to_entity(
+ db.RecordType(name="TestParent"),
+ entity_does_not_exist_code)
+ rec = _add_error_message_to_entity(db.Record(name="TestRecord"),
+ code)
+ rec.add_parent(parent)
+ with raises(TransactionError) as e:
+ raise_errors(rec)
+ te = e.value
+ # One direct child, two errors in total
+ assert len(te.errors) == 1
+ assert len(te.all_errors) == 2
+ # UnqualifiedParentsError in Record ...
+ assert isinstance(te.errors[0], UnqualifiedParentsError)
+ assert te.errors[0].entity.name == rec.name
+ # ... caused by non-existing parent
+ assert isinstance(te.errors[0].errors[0], EntityDoesNotExistError)
+ assert te.errors[0].errors[0].entity.name == parent.name
+
+
+def test_unqualified_properties_error():
+ """Code 114; properties do not exist or have wrong data types or
+ values.
+
+ """
+ code = 114
+ entity_code = 0
+ no_entity_code = 101
+ prop1 = _add_error_message_to_entity(db.Property(
+ name="TestProp1"), entity_code)
+ prop2 = _add_error_message_to_entity(db.Property(
+ name="TestProp2"), no_entity_code)
+ rec = _add_error_message_to_entity(db.Record(name="TestRecord"),
+ code)
+ rec.add_property(prop1).add_property(prop2)
+ with raises(TransactionError) as e:
+ raise_errors(rec)
+ te = e.value
+ assert len(te.errors) == 1
+ upe = te.errors[0]
+ assert upe.entity.name == rec.name
+ assert len(upe.errors) == 2
+ for error_t in [UnqualifiedPropertiesError, EntityError,
+ EntityDoesNotExistError]:
+ assert any([isinstance(x, error_t) for x in te.all_errors])
+ assert upe.code == code
+
+
+# #################### Multiple errors ####################
+
+def test_parent_and_properties_errors():
+ """Record with UnqualifiedParentsError and UnqualifiedPropertiesError,
+ and corresponding parent and properties with their errors as
+ above. Test whether all levels are in order.
+
+ """
+ prop_code = 114
+ parent_code = 116
+ entity_code = 0
+ no_entity_code = 101
+ parent = _add_error_message_to_entity(
+ db.RecordType(name="TestParent"), no_entity_code)
+ prop1 = _add_error_message_to_entity(db.Property(
+ name="TestProp1"), entity_code)
+ prop2 = _add_error_message_to_entity(db.Property(
+ name="TestProp2"), no_entity_code)
+ rec = _add_error_message_to_entity(db.Record(name="TestRecord"),
+ prop_code)
+ rec = _add_error_message_to_entity(rec, parent_code)
+ rec.add_parent(parent)
+ rec.add_property(prop1).add_property(prop2)
+ with raises(TransactionError) as e:
+ raise_errors(rec)
+ # Now there should be two direct children; both have to be
+ # displayed correctly.
+ te = e.value
+ # exactly two children:
+ assert len(te.errors) == 2
+ # both have to have the right codes and entities
+ found_parent = False
+ found_prop = False
+ for err in te.errors:
+ if err.code == parent_code:
+ found_parent = True
+ assert err.errors[0].entity.name == parent.name
+ assert prop1.name not in [x.name for x in
+ err.all_entities]
+ assert prop2.name not in [x.name for x in
+ err.all_entities]
+ elif err.code == prop_code:
+ found_prop = True
+ assert parent.name not in [x.name for x in
+ err.all_entities]
+ for sub_err in err.errors:
+ if sub_err.code == entity_code:
+ assert sub_err.entity.name == prop1.name
+ elif sub_err.code == no_entity_code:
+ assert sub_err.entity.name == prop2.name
+ assert found_parent
+ assert found_prop
+
+
+def test_container_with_faulty_elements():
+ """Code 12; container with valid and invalid entities. All faulty
+ entities have to be reflected correctly in the errors list of the
+ TransactionError raised by the container.
+
+ """
+ container_code = 12
+ prop_code = 114
+ parent_code = 116
+ name_code = 152
+ auth_code = 403
+ entity_code = 0
+ no_entity_code = 101
+ # Broken parents and properties
+ parent = _add_error_message_to_entity(
+ db.RecordType(name="TestParent"), no_entity_code)
+ prop1 = _add_error_message_to_entity(db.Property(
+ name="TestProp1"), entity_code)
+ prop2 = _add_error_message_to_entity(db.Property(
+ name="TestProp2"), no_entity_code)
+ cont = _add_error_message_to_entity(db.Container(),
+ container_code)
+ # healthy record and property
+ good_rec = db.Record(name="TestRecord1")
+ good_prop = db.Property(name="TestProp3")
+ cont.extend([good_rec, good_prop])
+ # broken records with single and multiole errors
+ rec_name = _add_error_message_to_entity(db.Record(name="TestRecord2"),
+ code=name_code)
+ rec_auth = _add_error_message_to_entity(db.Record(name="TestRecord3"),
+ code=auth_code)
+ rec_par_prop = _add_error_message_to_entity(
+ db.Record(name="TestRecord"), prop_code)
+ rec_par_prop = _add_error_message_to_entity(rec_par_prop, parent_code)
+ rec_par_prop.add_parent(parent)
+ rec_par_prop.add_property(prop1).add_property(prop2)
+ cont.extend([rec_name, rec_auth, rec_par_prop])
+ with raises(TransactionError) as e:
+ raise_errors(cont)
+ te = e.value
+ assert te.container == cont
+ assert te.code == container_code
+ # no healthy entity caused an error
+ for good in [good_rec, good_prop]:
+ assert good not in te.all_entities
+ # all records that caused problems
+ assert {rec_name, rec_auth, rec_par_prop}.issubset(te.all_entities)
+ # the container error contains the errors caused by the records
+ for err in te.errors:
+ if err.entity.name == rec_name.name:
+ assert isinstance(err, UniqueNamesError)
+ elif err.entity.name == rec_auth.name:
+ assert isinstance(err, AuthorizationError)
+ elif err.entity.name == rec_par_prop.name:
+ # record raises both of them
+ assert (isinstance(err, UnqualifiedParentsError) or
+ isinstance(err, UnqualifiedPropertiesError))
diff --git a/unittests/test_property.py b/unittests/test_property.py
index 8b2deeb4b06cfbf3d42881201307a1e2122124e3..752ee01f0eafef14dbffd1e62c99d1c816c45d05 100644
--- a/unittests/test_property.py
+++ b/unittests/test_property.py
@@ -84,3 +84,8 @@ def test_get_property_with_entity():
p = Property(id=1234)
r.add_property(id=1234, value="bla")
assert r.get_property(p).value == "bla"
+
+
+def test_selected_reference_list():
+ assert len(testrecord.get_property("Conductor").value) == 1
+ assert isinstance(testrecord.get_property("Conductor").value[0], Entity)
diff --git a/unittests/test_query.py b/unittests/test_query.py
new file mode 100644
index 0000000000000000000000000000000000000000..12622ea486dda717ca1fbc1255510575c5e0c8e6
--- /dev/null
+++ b/unittests/test_query.py
@@ -0,0 +1,48 @@
+# -*- encoding: utf-8 -*-
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2021 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2021 Timm Fitschen <f.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/>.
+#
+# ** end header
+#
+from lxml import etree
+import caosdb as db
+
+
+def test_query_parsing():
+ s = '<Query string="FIND bla" results="0" cached="true" etag="asdf"/>'
+ q = db.Query(etree.fromstring(s))
+ assert q.q == "FIND bla"
+ assert q.results == 0
+ assert q.cached is True
+ assert q.etag == "asdf"
+
+ s = '<Query string="COUNT bla" results="1" cached="false" etag="asdf"/>'
+ q = db.Query(etree.fromstring(s))
+ assert q.q == "COUNT bla"
+ assert q.results == 1
+ assert q.cached is False
+ assert q.etag == "asdf"
+
+ s = '<Query string="COUNT blub" results="4"/>'
+ q = db.Query(etree.fromstring(s))
+ assert q.q == "COUNT blub"
+ assert q.results == 4
+ assert q.cached is False
+ assert q.etag is None
diff --git a/unittests/test_record.xml b/unittests/test_record.xml
index e961bdc6b88eb8e62b92696b52d7ad6a2dbf8089..018c747c11027a2c3996c65d1deab1d18514e17b 100644
--- a/unittests/test_record.xml
+++ b/unittests/test_record.xml
@@ -328,4 +328,10 @@
<Value>45531</Value>
<Value>45532</Value>
</Property>
+ <Property datatype="LIST<Person>" description="DESCRIBE ME!" id="1634561234" importance="FIX" name="Conductor">
+ <Value>
+ <Record id="23456543">
+ </Record>
+ </Value>
+ </Property>
</Record>
diff --git a/unittests/test_state.py b/unittests/test_state.py
new file mode 100644
index 0000000000000000000000000000000000000000..202c7a02af3db28434406626e5164def46febed7
--- /dev/null
+++ b/unittests/test_state.py
@@ -0,0 +1,77 @@
+import pytest
+import caosdb as db
+from caosdb import State, Transition
+from caosdb.common.models import parse_xml, ACL
+from lxml import etree
+
+
+def test_state_xml():
+ state = State(model="model1", name="state1")
+ xml = etree.tostring(state.to_xml())
+
+ assert xml == b'<State name="state1" model="model1"/>'
+ state = State.from_xml(etree.fromstring(xml))
+ assert state.name == "state1"
+ assert state.model == "model1"
+
+ assert xml == etree.tostring(state.to_xml())
+
+
+def test_entity_xml():
+ r = db.Record()
+ assert r.state is None
+ r.state = State(model="model1", name="state1")
+
+ xml = etree.tostring(r.to_xml())
+ assert xml == b'<Record><State name="state1" model="model1"/></Record>'
+
+ r = parse_xml(xml)
+ assert r.state == State(model="model1", name="state1")
+
+
+def test_description():
+ xml = b'<State name="state1" model="model1"/>'
+ state = State.from_xml(etree.fromstring(xml))
+ assert state.description is None
+
+ with pytest.raises(AttributeError):
+ state.description = "test"
+
+ xml = b'<State name="state1" model="model1" description="test2"/>'
+ state = State.from_xml(etree.fromstring(xml))
+ assert state.description == "test2"
+
+
+def test_id():
+ xml = b'<State name="state1" model="model1"/>'
+ state = State.from_xml(etree.fromstring(xml))
+ assert state.id is None
+
+ with pytest.raises(AttributeError):
+ state.id = "2345"
+
+ xml = b'<State name="state1" model="model1" id="1234"/>'
+ state = State.from_xml(etree.fromstring(xml))
+ assert state.id == "1234"
+
+
+def test_create_state_acl():
+ acl = ACL()
+ acl.grant(role="role1", permission="DO:IT")
+ acl.grant(role="?OWNER?", permission="DO:THAT")
+ state_acl = State.create_state_acl(acl)
+ assert state_acl.get_permissions_for_role("?STATE?role1?") == {"DO:IT"}
+ assert state_acl.get_permissions_for_role("?STATE??OWNER??") == {"DO:THAT"}
+
+
+def test_transitions():
+ xml = b'<State name="state1" model="model1"/>'
+ state = State.from_xml(etree.fromstring(xml))
+ assert state.transitions is None
+
+ with pytest.raises(AttributeError):
+ state.transitions = []
+
+ xml = b'<State name="state1" model="model1" id="1234"><Transition name="t1"><FromState name="state1"/><ToState name="state2"/></Transition></State>'
+ state = State.from_xml(etree.fromstring(xml))
+ assert state.transitions == set([Transition(name="t1", from_state="state1", to_state="state2")])
diff --git a/unittests/test_utils.py b/unittests/test_utils.py
index f308445ed1a06331a54ebf67411dc154836557ca..42d18ba06eb7516bb318de54cb537f548cfe9081 100644
--- a/unittests/test_utils.py
+++ b/unittests/test_utils.py
@@ -24,7 +24,6 @@
"""Tests for caosdb.common.utils."""
from __future__ import unicode_literals
from lxml.etree import Element
-from nose.tools import assert_equals as eq
from caosdb.common.utils import xml2str
@@ -32,4 +31,4 @@ def test_xml2str():
name = 'Björn'
element = Element(name)
serialized = xml2str(element)
- eq(serialized, "<Björn/>\n")
+ assert serialized == "<Björn/>\n"