Merge branch 'dev' into f-remove-dropoffbox

.gitlab-ci.yml

@@ -57,22 +57,10 @@ mypy:
   tags: [ docker ]
   stage: linting
   script:
-    - pip install mypy types-PyYAML types-jsonschema types-requests types-setuptools types-lxml types-python-dateutil pytest
+    - pip install .[mypy,test]
     - make mypy
-  allow_failure: true
 
 # run unit tests
-unittest_py3.8:
-  tags: [ docker ]
-  stage: test
-  needs: [ ]
-  image: python:3.8
-  script: &python_test_script
-    # Python docker has problems with tox and pip so use plain pytest here
-    - touch ~/.pylinkahead.ini
-    - pip install pynose pytest pytest-cov jsonschema>=4.4.0 setuptools
-    - pip install .
-    - python -m pytest unittests
 
 # This needs to be changed once Python 3.9 isn't the standard Python in Debian
 # anymore.
@@ -92,7 +80,11 @@ unittest_py3.10:
   stage: test
   needs: [ ]
   image: python:3.10
-  script: *python_test_script
+  script: &python_test_script
+    # Python docker has problems with tox and pip so use plain pytest here
+    - touch ~/.pylinkahead.ini
+    - pip install .[test]
+    - python -m pytest unittests
 
 unittest_py3.11:
   tags: [ docker ]
@@ -109,19 +101,25 @@ unittest_py3.12:
   script: *python_test_script
 
 unittest_py3.13:
-  allow_failure: true
   tags: [ docker ]
   stage: test
   needs: [ ]
-  image: python:3.13-rc
-  script:
-    # TODO: Replace by '*python_test_script' as soon as 3.13 has been officially released.
-    # Python docker has problems with tox and pip so use plain pytest here
-    - apt update && apt install -y cargo
-    - touch ~/.pylinkahead.ini
-    - pip install pynose pytest pytest-cov jsonschema>=4.4.0 setuptools
-    - pip install .
-    - python -m pytest unittests
+  image: python:3.13
+  script: *python_test_script
+
+unittest_py3.14:
+  allow_failure: true   # remove on release
+  tags: [ docker ]
+  stage: test
+  needs: [ ]
+  image: python:3.14-rc
+  script:               # replace by '*python_test_script' on release
+    # Install cargo manually, source its env, and set it to accept 3.14 as interpreter
+    - curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+    - . "$HOME/.cargo/env"
+    - export PYO3_USE_ABI3_FORWARD_COMPATIBILITY=1
+    # Continue normally
+    - *python_test_script
 
 # Trigger building of server image and integration tests
 trigger_build:
@@ -167,7 +165,7 @@ build-testenv:
 pages_prepare: &pages_prepare
   tags: [ cached-dind ]
   stage: deploy
-  needs: [ code_style, pylint, unittest_py3.8, unittest_py3.9, unittest_py3.10 ]
+  needs: [ code_style, pylint, unittest_py3.9, unittest_py3.10 ]
   only:
     refs:
       - /^release-.*$/i

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased] ##
 
 ### Added ###
+- convenience functions `value_matches_versionid`, `get_id_from_versionid` and `get_versionid`
 
 ### Changed ###
 
@@ -23,6 +24,82 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Documentation ###
 
+* [#78](https://gitlab.com/linkahead/linkahead-pylib/-/issues/78) Fix
+  and extend test-registration docstrings.
+
+## [0.17.0] - 2025-01-14 ##
+
+### Added ###
+
+* New setup extra `test` which installs the dependencies for testing.
+* The Container class has a new member function `filter_by_identity`
+  which is based on `_filter_entity_list`.
+* The `Entity` properties `_cuid` and `_flags` are now available for read-only access
+  as `cuid` and `flags`, respectively.
+
+### Changed ###
+
+* Renamed the `filter` function of Container, ParentList and
+  PropertyList to `filter_by_identity`.
+
+### Deprecated ###
+
+* `ParentList.filter` and `PropertyList.filter` functions, use
+  `filter_by_identity` instead.
+
+### Removed ###
+
+* Support for Python 3.8
+
+### Fixed ###
+
+* [#73](https://gitlab.com/linkahead/linkahead-pylib/-/issues/73)
+  `Entity.to_xml` now detects potentially infinite recursion and prevents an error
+* [#89](https://gitlab.com/linkahead/linkahead-pylib/-/issues/89)
+  `to_xml` does not add `noscript` or `TransactionBenchmark` tags anymore
+* [#103](https://gitlab.com/linkahead/linkahead-pylib/-/issues/103)
+  `authentication/interface/on_response()` does not overwrite
+  `auth_token` if new value is `None`
+* [#119](https://gitlab.com/linkahead/linkahead-pylib/-/issues/119)
+  The diff returned by compare_entities now uses id instead of name as
+  key if either property does not have a name
+* [#87](https://gitlab.com/linkahead/linkahead-pylib/-/issues/87)
+  `XMLSyntaxError` messages when parsing (incomplete) responses in
+  case of certain connection timeouts.
+  The diff returned by compare_entities now uses id instead of name as key if either property does not have a name
+* [#127](https://gitlab.com/linkahead/linkahead-pylib/-/issues/127)
+  pylinkahead.ini now supports None and tuples as values for the `timeout` keyword
+
+## [0.16.0] - 2024-11-13 ##
+
+### Added ###
+
+* `ParentList` and `PropertyList` now have a `filter` function that allows to select a subset of
+  the contained elements by ID and/or name.
+* Official support for Python 3.13
+* Added arguments to `describe_diff` that allow customizing the labels for the 'old' and the 'new' diffs.
+* Optional `realm` argument for `linkahead_admin.py set_user_password`
+  which defaults to `None`, i.e., the server's default realm.
+
+### Changed ###
+
+* `compare_entities` is now case insensitive with respect to property and
+  recordtype names
+* `_ParentList` is now called `ParentList`
+* `_Properties` is now called `PropertyList`
+* `ParentList.remove` is now case insensitive when a name is used.
+
+### Deprecated ###
+
+* the use of the arguments `old_entity` and `new_entity` in `compare_entities`
+  is now deprecated. Please use `entity0` and `entity1` respectively instead.
+
+### Fixed ###
+
+* [gitlab.indiscale.com#200](https://gitlab.indiscale.com/caosdb/src/caosdb-pylib/-/issues/200)
+  ``linkahead_admin.py`` prints reasonable error messages when users
+  or roles don't exist.
+
 ## [0.15.1] - 2024-08-21 ##
 
 ### Deprecated ###

CITATION.cff

@@ -20,6 +20,6 @@ authors:
     given-names: Stefan
     orcid: https://orcid.org/0000-0001-7214-8125
 title: CaosDB - Pylib
-version: 0.15.1
+version: 0.17.0
 doi: 10.3390/data4020083
-date-released: 2024-08-21
+date-released: 2025-01-14

DEPENDENCIES.md

 * caosdb-server >= 0.12.0
-* Python >= 3.8
+* Python >= 3.9
 * pip >= 20.0.2
 
 Any other dependencies are defined in the setup.py and are being installed via pip

Makefile

@@ -40,7 +40,7 @@ style:
 .PHONY: style
 
 lint:
-	pylint --unsafe-load-any-extension=y -d all -e E,F src/linkahead/common
+	pylint --unsafe-load-any-extension=y -d all -e E,F src/linkahead
 .PHONY: lint
 
 mypy:

README.md

@@ -47,7 +47,7 @@ However, you can also create an issue for it.
 
 * Copyright (C) 2018 Research Group Biomedical Physics, Max Planck Institute
   for Dynamics and Self-Organization Göttingen.
-* Copyright (C) 2020-2022 Indiscale GmbH <info@indiscale.com>
+* Copyright (C) 2020-2025 Indiscale GmbH <info@indiscale.com>
 
 All files in this repository are licensed under a [GNU Affero General Public
 License](LICENCE.md) (version 3 or later).

README_SETUP.md

@@ -2,24 +2,44 @@
 
 ## Installation ##
 
-### Requirements ###
+### How to install ###
+
+First ensure that python with at least version 3.9 is installed. Should this not be
+the case, you can use the [Installing python](#installing-python-) guide for your OS.
 
-PyCaosDB needs at least Python 3.8.  Additionally, the following packages are required (they will
-typically be installed automatically):
+#### Generic installation ####
 
-- `lxml`
-- `PyYaml`
-- `PySocks`
+To install this LinkAhead python client locally, use `pip`/`pip3`:
 
-Optional packages:
-- `keyring`
+```sh
+pip install linkahead
+```
+
+#### Additional dependencies ####
+
+To test using tox, you also need to install tox:  
+`pip install tox`  
+
+To install dependencies used by optional functionality, the following pip extras 
+keywords are defined:
+- `test` for testing with pytest
+- `mypy` for mypy and types
 - `jsonschema` 
+- `keyring` 
 
-### How to install ###
+These extras can be installed using: 
+```sh
+pip install .[KEYWORD]
+```
+A current list of the dependencies installed with this program as well as those installed with 
+the keywords can be found in `setup.py`s `setup_package()` method, in the `metadata` dictionary
+entries `install_requires` and `extras_require`.
+
+### Installing python ###
 
 #### Linux ####
 
-Make sure that Python (at least version 3.8) and pip is installed, using your system tools and
+Make sure that Python (at least version 3.9) and pip is installed, using your system tools and
 documentation.
 
 Then open a terminal and continue in the [Generic installation](#generic-installation) section.
@@ -51,34 +71,7 @@ cd /Applications/Python\ 3.9/
 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):
-
-```sh
-pip3 install --user caosdb
-```
-
----
-
-Alternatively, obtain the sources from GitLab and install from there (`git` must be installed for
-this option):
-
-```sh
-git clone https://gitlab.com/caosdb/caosdb-pylib
-cd caosdb-pylib
-pip3 install --user .
-```
-
-For installation of optional packages, install with an additional option, e.g. for 
-validating with the caosdb json schema:
-
-```sh
-pip3 install --user .[jsonschema]
-```
+After these steps, you may continue with the [Generic installation](#generic-installation) section.
 
 ## Configuration ##
 
@@ -87,7 +80,7 @@ is described in detail in the [configuration section of the documentation](https
 
 ## Try it out ##
 
-Start Python and check whether the you can access the database. (You will be asked for the
+Start Python and check whether you can access the database. (You will be asked for the
 password):
 
 ```python
@@ -107,6 +100,7 @@ Now would be a good time to continue with the [tutorials](tutorials/index).
 - Run all tests: `tox` or `make unittest`
 - Run a specific test file: e.g. `tox -- unittests/test_schema.py`
 - Run a specific test function: e.g. `tox -- unittests/test_schema.py::test_config_files`
+- To run using pytest: `pytest .`
 
 ## Documentation ##
 We use sphinx to create the documentation. Docstrings in the code should comply
@@ -114,13 +108,6 @@ with the Googly style (see link below).
 
 Build documentation in `build/` with `make doc`.
 
-### Requirements ###
-
-- `sphinx`
-- `sphinx-autoapi`
-- `recommonmark`
-- `sphinx_rtd_theme`
-
 ### How to contribute ###
 
 - [Google Style Python Docstrings](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html)
@@ -128,7 +115,7 @@ Build documentation in `build/` with `make doc`.
 - [References to other documentation](https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#role-external)
 
 ### Troubleshooting ###
-If the client is to be executed directly from the `/src` folder, an initial `.\setup.py install --user` must be called.
+If the client is to be executed directly from the `/src` folder, an initial `.\setup.py install` must be called.
 
 ## Migration ##
 TODO

setup.py

@@ -48,8 +48,8 @@ from setuptools import find_packages, setup
 
 ISRELEASED = False
 MAJOR = 0
-MINOR = 15
-MICRO = 2
+MINOR = 17
+MICRO = 1
 # Do not tag as pre-release until this commit
 # https://github.com/pypa/packaging/pull/515
 # has made it into a release. Probably we should wait for pypa/packaging>=21.4
@@ -179,7 +179,7 @@ def setup_package():
             "Topic :: Scientific/Engineering :: Information Analysis",
         ],
         packages=find_packages('src'),
-        python_requires='>=3.8',
+        python_requires='>=3.9',
         package_dir={'': 'src'},
         install_requires=['lxml>=4.6.3',
                           "requests[socks]>=2.26",
@@ -187,11 +187,27 @@ def setup_package():
                           'PyYAML>=5.4.1',
                           'future',
                           ],
-        extras_require={'keyring': ['keyring>=13.0.0'],
-                        'jsonschema': ['jsonschema>=4.4.0']},
+        extras_require={
+            "jsonschema": ["jsonschema>=4.4.0"],
+            "keyring": ["keyring>=13.0.0"],
+            "mypy": [
+                "mypy",
+                "types-PyYAML",
+                "types-jsonschema",
+                "types-requests",
+                "types-setuptools",
+                "types-lxml",
+                "types-python-dateutil",
+            ],
+            "test": [
+                "pytest",
+                "pytest-cov",
+                "coverage>=4.4.2",
+                "jsonschema>=4.4.0",
+            ]
+
+        },
         setup_requires=["pytest-runner>=2.0,<3dev"],
-        tests_require=["pytest", "pytest-cov", "coverage>=4.4.2",
-                       "jsonschema>=4.4.0"],
         package_data={
             'linkahead': ['py.typed', 'cert/indiscale.ca.crt', 'schema-pycaosdb-ini.yml'],
         },

src/doc/conf.py

@@ -25,14 +25,14 @@ import sphinx_rtd_theme  # noqa: E402
 # -- Project information -----------------------------------------------------
 
 project = 'pylinkahead'
-copyright = '2023, IndiScale GmbH'
+copyright = '2024, IndiScale GmbH'
 author = 'Daniel Hornung'
 
 # The short X.Y version
-version = '0.15.2'
+version = '0.17.1'
 # The full version, including alpha/beta/rc tags
 # release = '0.5.2-rc2'
-release = '0.15.2-dev'
+release = '0.17.1-dev'
 
 
 # -- General configuration ---------------------------------------------------

src/doc/tutorials/complex_data_models.rst

@@ -75,3 +75,70 @@ Examples
    b = input("Press any key to cleanup.")
    # cleanup everything after the user presses any button.
    c.delete()
+
+
+Finding parents and properties
+------------------------------
+To find a specific parent or property of an Entity, its
+ParentList or PropertyList can be filtered using names, ids, or
+entities. A short example:
+
+.. code-block:: python3
+
+   import linkahead as db
+
+   # Setup a record with six properties
+   r = db.Record()
+   p1_1 = db.Property(id=101, name="Property 1")
+   p1_2 = db.Property(name="Property 1")
+   p2_1 = db.Property(id=102, name="Property 2")
+   p2_2 = db.Property(id=102)
+   p2_3 = db.Property(id=102, name="Other Property")
+   p3 = db.Property(id=104, name="Other Property")
+   r.add_property(p1_1).add_property(p1_2).add_property(p2_1)
+   r.add_property(p2_2).add_property(p2_3).add_property(p3)
+   properties = r.properties
+
+   # As r only has one property with id 101, this returns a list containing only p1_1
+   properties.filter_by_identity(pid=101)
+   # Result: [p1_1]
+
+   # Filtering with name="Property 1" returns both p1_1 and p1_2, as they share their name
+   properties.filter_by_identity(name="Property 1")
+   # Result: [p1_1, p1_2]
+
+   #  If both name and pid are given, matching is based only on pid for all entities that have an id
+   properties.filter_by_identity(pid="102", name="Other Property")
+   # Result: [p2_1, p2_2, p2_3]
+
+   # However, filter_by_identity with name="Property 1" and id=101 returns both p1_1 and p1_2, because
+   # p1_2 does not have an id and matches the name
+   properties.filter_by_identity(pid="101", name="Property 1")
+   # Result: [p1_1, p1_2]
+
+   # We can also filter using an entity, in which case the name and id of the entity are used:
+   properties.filter_by_identity(pid="102", name="Property 2") == properties.filter_by_identity(p2_1)
+   # Result: True
+
+   # If we only need properties that match both id and name, we can set the parameter
+   # conjunction to True:
+   properties.filter_by_identity(pid="102", name="Property 2", conjunction=True)
+   # Result: [p2_1]
+
+The filter function of ParentList works analogously.
+
+Finding entities in a Container
+-------------------------------
+In the same way as described above, Container can be filtered.
+A short example:
+
+.. code-block:: python3
+
+   import linkahead as db
+
+   # Setup a record with six properties
+   p1 = db.Property(id=101, name="Property 1")
+   p2 = db.Property(name="Property 2")
+   c = db.Container().extend([p1,p2])
+   c.filter_by_identity(name="Property 1")
+   # Result: [p1]

src/linkahead/__init__.py

@@ -42,7 +42,7 @@ from .common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER, LIST,
                               REFERENCE, TEXT)
 # Import of the basic  API classes:
 from .common.models import (ACL, ALL, FIX, NONE, OBLIGATORY, RECOMMENDED,
-                            SUGGESTED, Container, Entity, File,
+                            SUGGESTED, Container, Entity, File, Parent,
                             Info, Message, Permissions, Property, Query,
                             QueryTemplate, Record, RecordType, delete,
                             execute_query, get_global_acl,
@@ -55,7 +55,7 @@ from .utils.get_entity import (get_entity_by_id, get_entity_by_name,
                                get_entity_by_path)
 
 try:
-    from .version import version as __version__
+    from .version import version as __version__  # pylint: disable=import-error
 except ModuleNotFoundError:
     version = "uninstalled"
     __version__ = version

src/linkahead/cached.py

@@ -165,7 +165,8 @@ Returns
     -------
 
     out: named tuple
-  See the standard library :func:`functools.lru_cache` for details."""
+      See the standard library :func:`functools.lru_cache` for details.
+    """
     return _cached_access.cache_info()
 
 

src/linkahead/common/administration.py

@@ -91,7 +91,7 @@ def get_server_properties() -> dict[str, Optional[str]]:
     props: dict[str, Optional[str]] = dict()
 
     for elem in xml.getroot():
-        props[elem.tag] = elem.text
+        props[str(elem.tag)] = str(elem.text)
 
     return props
 
@@ -156,7 +156,10 @@ def generate_password(length: int):
 def _retrieve_user(name: str, realm: Optional[str] = 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()
+        return con._http_request(
+            method="GET",
+            path="User/" + (realm + "/" + name if realm is not None else name),
+            **kwargs).read()
     except HTTPForbiddenError as e:
         e.msg = "You are not permitted to retrieve this user."
         raise
@@ -198,7 +201,9 @@ def _update_user(name: str,
     if entity is not 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()
+        return con.put_form_data(entity_uri_segment="User/" + (realm + "/" +
+                                                               name if realm is not None else name),
+                                 params=params, **kwargs).read()
     except HTTPResourceNotFoundError as e:
         e.msg = "User does not exist."
         raise e
@@ -246,7 +251,9 @@ def _insert_user(name: str,
 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()
+        return con.post_form_data(entity_uri_segment="Role",
+                                  params={"role_name": name, "role_description": description},
+                                  **kwargs).read()
     except HTTPForbiddenError as e:
         e.msg = "You are not permitted to insert a new role."
         raise
@@ -259,7 +266,9 @@ def _insert_role(name, description, **kwargs):
 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()
+        return con.put_form_data(entity_uri_segment="Role/" + name,
+                                 params={"role_description": description},
+                                 **kwargs).read()
     except HTTPForbiddenError as e:
         e.msg = "You are not permitted to update this role."
         raise
@@ -301,8 +310,10 @@ 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()
+        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
@@ -369,7 +380,8 @@ Returns
     body = xml2str(xml)
     con = get_connection()
     try:
-        return con._http_request(method="PUT", path="PermissionRules/" + role, body=body, **kwargs).read()
+        return con._http_request(method="PUT", path="PermissionRules/" + role, body=body,
+                                 **kwargs).read()
     except HTTPForbiddenError as e:
         e.msg = "You are not permitted to set this role's permissions."
         raise
@@ -381,7 +393,9 @@ Returns
 def _get_permissions(role, **kwargs):
     con = get_connection()
     try:
-        return PermissionRule._parse_body(con._http_request(method="GET", path="PermissionRules/" + role, **kwargs).read())
+        return PermissionRule._parse_body(con._http_request(method="GET",
+                                                            path="PermissionRules/" + role,
+                                                            **kwargs).read())
     except HTTPForbiddenError as e:
         e.msg = "You are not permitted to retrieve this role's permissions."
         raise
@@ -429,7 +443,8 @@ priority : bool, optional
         if permission is None:
             raise ValueError(f"Permission is missing in PermissionRule xml: {elem}")
         priority = PermissionRule._parse_boolean(elem.get("priority"))
-        return PermissionRule(elem.tag, permission, priority if priority is not None else False)
+        return PermissionRule(str(elem.tag), permission,
+                              priority if priority is not None else False)
 
     @staticmethod
     def _parse_body(body: str):

src/linkahead/common/state.py

@@ -20,11 +20,11 @@
 # ** end header
 
 from __future__ import annotations  # Can be removed with 3.10.
-import copy
-from lxml import etree
 
+import copy
 from typing import TYPE_CHECKING
-import sys
+
+from lxml import etree
 
 if TYPE_CHECKING:
     from typing import Optional
@@ -87,7 +87,8 @@ class Transition:
         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}")'
+        return (f'Transition(name="{self.name}", from_state="{self.from_state}", '
+                f'to_state="{self.to_state}", description="{self.description}")')
 
     def __eq__(self, other):
         return (
@@ -103,9 +104,9 @@ class Transition:
     @staticmethod
     def from_xml(xml: etree._Element) -> "Transition":
         to_state = [to.get("name")
-                    for to in xml if to.tag.lower() == "tostate"]
+                    for to in xml if str(to.tag).lower() == "tostate"]
         from_state = [
-            from_.get("name") for from_ in xml if from_.tag.lower() == "fromstate"
+            from_.get("name") for from_ in xml if str(from_.tag).lower() == "fromstate"
         ]
         return Transition(
             name=xml.get("name"),
@@ -199,7 +200,7 @@ class State:
         result._id = xml.get("id")
         result._description = xml.get("description")
         transitions = [
-            Transition.from_xml(t) for t in xml if t.tag.lower() == "transition"
+            Transition.from_xml(t) for t in xml if str(t.tag).lower() == "transition"
         ]
         if transitions:
             result._transitions = set(transitions)

src/linkahead/common/versioning.py

@@ -101,11 +101,14 @@ class Version():
     # pylint: disable=redefined-builtin
     def __init__(self, id: Optional[str] = None, date: Optional[str] = None,
                  username: Optional[str] = None, realm: Optional[str] = None,
-                 predecessors: Optional[List[Version]] = None, successors: Optional[List[Version]] = None,
+                 predecessors: Optional[List[Version]] = None,
+                 successors: Optional[List[Version]] = None,
                  is_head: Union[bool, str, None] = False,
                  is_complete_history: Union[bool, str, None] = False):
-        """Typically the `predecessors` or `successors` should not "link back" to an existing Version
-object."""
+        """Typically the `predecessors` or `successors` should not "link back" to an existing
+        Version object.
+
+        """
         self.id = id
         self.date = date
         self.username = username
@@ -205,8 +208,8 @@ object."""
         version : Version
             a new version instance
         """
-        predecessors = [Version.from_xml(p) for p in xml if p.tag.lower() == "predecessor"]
-        successors = [Version.from_xml(s) for s in xml if s.tag.lower() == "successor"]
+        predecessors = [Version.from_xml(p) for p in xml if str(p.tag).lower() == "predecessor"]
+        successors = [Version.from_xml(s) for s in xml if str(s.tag).lower() == "successor"]
         return Version(id=xml.get("id"), date=xml.get("date"),
                        is_head=xml.get("head"),
                        is_complete_history=xml.get("completeHistory"),

src/linkahead/configuration.py

@@ -30,6 +30,15 @@ import yaml
 try:
     optional_jsonschema_validate: Optional[Callable] = None
     from jsonschema import validate as optional_jsonschema_validate
+
+    # Adapted from https://github.com/python-jsonschema/jsonschema/issues/148
+    # Defines Validator to allow parsing of all iterables as array in jsonschema
+    # CustomValidator can be removed if/once jsonschema allows tuples for arrays
+    from collections.abc import Iterable
+    from jsonschema import validators
+    default = validators.validator_for(True)   # Returns latest supported draft
+    t_c = (default.TYPE_CHECKER.redefine('array', lambda x, y: isinstance(y, Iterable)))
+    CustomValidator = validators.extend(default, type_checker=t_c)
 except ImportError:
     pass
 
@@ -72,13 +81,39 @@ def get_config() -> ConfigParser:
     return _pycaosdbconf
 
 
-def config_to_yaml(config: ConfigParser) -> dict[str, dict[str, Union[int, str, bool]]]:
-    valobj: dict[str, dict[str, Union[int, str, bool]]] = {}
+def config_to_yaml(config: ConfigParser) -> dict[str, dict[str, Union[int, str, bool, tuple, None]]]:
+    """
+    Generates and returns a dict with all config options and their values
+    defined in the config.
+    The values of the options 'debug', 'timeout', and 'ssl_insecure' are
+    parsed, all other values are saved as string.
+
+    Parameters
+    ----------
+    config : ConfigParser
+        The config to be converted to a dict
+
+    Returns
+    -------
+    valobj : dict
+        A dict with config options and their values as key value pairs
+    """
+    valobj: dict[str, dict[str, Union[int, str, bool, tuple, None]]] = {}
     for s in config.sections():
         valobj[s] = {}
         for key, value in config[s].items():
             # TODO: Can the type be inferred from the config object?
-            if key in ["timeout", "debug"]:
+            if key in ["debug"]:
+                valobj[s][key] = int(value)
+            elif key in ["timeout"]:
+                value = "".join(value.split())          # Remove whitespace
+                if str(value).lower() in ["none", "null"]:
+                    valobj[s][key] = None
+                elif value.startswith('(') and value.endswith(')'):
+                    content = [None if str(s).lower() in ["none", "null"] else int(s)
+                               for s in value[1:-1].split(',')]
+                    valobj[s][key] = tuple(content)
+                else:
                     valobj[s][key] = int(value)
             elif key in ["ssl_insecure"]:
                 valobj[s][key] = bool(value)
@@ -88,11 +123,12 @@ def config_to_yaml(config: ConfigParser) -> dict[str, dict[str, Union[int, str,
     return valobj
 
 
-def validate_yaml_schema(valobj: dict[str, dict[str, Union[int, str, bool]]]):
+def validate_yaml_schema(valobj: dict[str, dict[str, Union[int, str, bool, tuple, None]]]):
     if optional_jsonschema_validate:
         with open(os.path.join(os.path.dirname(__file__), "schema-pycaosdb-ini.yml")) as f:
             schema = yaml.load(f, Loader=yaml.SafeLoader)
-        optional_jsonschema_validate(instance=valobj, schema=schema["schema-pycaosdb-ini"])
+        optional_jsonschema_validate(instance=valobj, schema=schema["schema-pycaosdb-ini"],
+                                     cls=CustomValidator)
     else:
         warnings.warn("""
             Warning: The validation could not be performed because `jsonschema` is not installed.

src/linkahead/connection/authentication/interface.py

@@ -125,8 +125,9 @@ class AbstractAuthenticator(ABC):
         Returns
         -------
         """
-        self.auth_token = parse_auth_token(
-            response.getheader("Set-Cookie"))
+        new_token = parse_auth_token(response.getheader("Set-Cookie"))
+        if new_token is not None:
+            self.auth_token = new_token
 
     def on_request(self, method: str, path: str, headers: QueryDict, **kwargs):
         # pylint: disable=unused-argument
@@ -190,7 +191,7 @@ class CredentialsAuthenticator(AbstractAuthenticator):
     def _logout(self):
         self.logger.debug("[LOGOUT]")
         if self.auth_token is not None:
-            self._connection.request(method="DELETE", path="logout")
+            self._connection.request(method="GET", path="logout")
         self.auth_token = None
 
     def _login(self):