.gitlab-ci.yml

@@ -61,16 +61,6 @@ mypy:
     - make mypy
 
 # 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 .[test]
-    - python -m pytest unittests
 
 # This needs to be changed once Python 3.9 isn't the standard Python in Debian
 # anymore.
@@ -90,7 +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 ]
@@ -158,7 +152,7 @@ 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

@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 * New setup extra `test` which installs the dependencies for testing.
 * The Container class has a new member function `filter` which is based o `_filter_entity_list`.
+* The `Entity` properties `_cuid` and `_flags` are now available for read-only access
+  as `cuid` and `flags`, respectively.
 
 ### Changed ###
 
@@ -18,6 +20,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed ###
 
+* Support for Python 3.8
+
 ### Fixed ###
 
 * [#73](https://gitlab.com/linkahead/linkahead-pylib/-/issues/73)
@@ -33,6 +37,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * [#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
 
 ### Security ###
 

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

README_SETUP.md

@@ -4,7 +4,7 @@
 
 ### How to install ###
 
-First ensure that python with at least version 3.8 is installed. Should this not be
+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.
 
 #### Generic installation ####
@@ -39,7 +39,7 @@ entries `install_requires` and `extras_require`.
 
 #### 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.

setup.py

@@ -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",

src/linkahead/common/models.py

@@ -349,6 +349,15 @@ class Entity:
     def pickup(self, new_pickup):
         self.__pickup = new_pickup
 
+    @property   # getter for _cuid
+    def cuid(self):
+        # Set if None?
+        return self._cuid
+
+    @property   # getter for _flags
+    def flags(self):
+        return self._flags.copy()   # for dict[str, str] shallow copy is enough
+
     def grant(
         self,
         realm: Optional[str] = None,
@@ -1342,7 +1351,8 @@ class Entity:
                 else:
                     dt_str = xml2str(self.datatype.to_xml(visited_entities=visited_entities.copy()))
                     # Todo: Use for pretty-printing with calls from _repr_ only?
-                    # dt_str = dt_str.replace('<', 'ᐸ').replace('>', 'ᐳ').replace(' ', '⠀').replace('"', '\'').replace('\n', '')
+                    # dt_str = dt_str.replace('<', 'ᐸ').replace('>', 'ᐳ').replace(' ', '⠀').replace(
+                    # '"', '\'').replace('\n', '')
                     xml.set("datatype", dt_str)
             else:
                 xml.set("datatype", str(self.datatype))
@@ -3758,6 +3768,7 @@ class Container(list):
         """
         return _filter_entity_list(self, pid=pid, name=name, entity=entity,
                                    conjunction=conjunction)
+
     @staticmethod
     def _find_dependencies_in_container(container: Container):
         """Find elements in a container that are a dependency of another element of the same.

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
 
@@ -72,14 +81,40 @@ 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)
             else:
@@ -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/connection.py

@@ -39,7 +39,7 @@ from requests.adapters import HTTPAdapter
 from requests.exceptions import ConnectionError as HTTPConnectionError
 from urllib3.poolmanager import PoolManager
 
-from ..configuration import get_config
+from ..configuration import get_config, config_to_yaml
 from ..exceptions import (ConfigurationError, HTTPClientError,
                           HTTPForbiddenError, HTTPResourceNotFoundError,
                           HTTPServerError, HTTPURITooLongError,
@@ -422,8 +422,10 @@ def configure_connection(**kwargs):
         - "keyring"  Uses the `keyring` library.
         - "auth_token" Uses only a given auth_token.
 
-    timeout : int
+    timeout : int, tuple, or None
         A connection timeout in seconds. (Default: 210)
+        If a tuple is given, they are used as connect and read timeouts
+        respectively, timeout None disables the timeout.
 
     ssl_insecure : bool
         Whether SSL certificate warnings should be ignored. Only use this for
@@ -465,21 +467,29 @@ def configure_connection(**kwargs):
     global_conf = {}
     conf = get_config()
     # Convert config to dict, with preserving types
-    int_opts = ["timeout"]
+    int_opts = []
     bool_opts = ["ssl_insecure"]
+    other_opts = ["timeout"]
 
     if conf.has_section("Connection"):
         global_conf = dict(conf.items("Connection"))
-        # Integer options
 
+        # Integer options
         for opt in int_opts:
             if opt in global_conf:
                 global_conf[opt] = conf.getint("Connection", opt)
-        # Boolean options
 
+        # Boolean options
         for opt in bool_opts:
             if opt in global_conf:
                 global_conf[opt] = conf.getboolean("Connection", opt)
+
+        # Other options, defer parsing to configuration.config_to_yaml:
+        connection_config = config_to_yaml(conf)["Connection"]
+        for opt in other_opts:
+            if opt in global_conf:
+                global_conf[opt] = connection_config[opt]
+
     local_conf = _make_conf(_DEFAULT_CONF, global_conf, kwargs)
 
     connection = _Connection.get_instance()

src/linkahead/schema-pycaosdb-ini.yml

@@ -67,7 +67,13 @@ schema-pycaosdb-ini:
           description: This option is used internally and for testing. Do not override.
           examples: [_DefaultCaosDBServerConnection]
         timeout:
-          type: integer
+          oneOf:
+            - type: [integer, "null"]
+            - type: array
+              items:
+                type: [integer, "null"]
+              minItems: 2
+              maxItems: 2
       allOf:
         - if:
             properties:

unittests/test_configs/pylinkahead-timeout1.ini

+[Connection]
+url=https://localhost:10443/
+password_method = unauthenticated
+timeout = None

unittests/test_configs/pylinkahead-timeout2.ini

+[Connection]
+url=https://localhost:10443/
+password_method = unauthenticated
+timeout = (1,20)

unittests/test_configuration.py

@@ -24,6 +24,7 @@
 
 from os import environ, getcwd, remove
 from os.path import expanduser, isfile, join
+from pathlib import Path
 
 import linkahead as db
 import pytest
@@ -66,3 +67,18 @@ def test_config_ini_via_envvar(temp_ini_files):
     assert expanduser("~/.pylinkahead.ini") in db.configuration._read_config_files()
     # test configuration file in cwd
     assert join(getcwd(), "pylinkahead.ini") in db.configuration._read_config_files()
+
+
+def test_config_timeout_option():
+    expected_results = [None, (1, 20)]
+    # Iterate through timeout test configs
+    test_configs = Path(__file__).parent/'test_configs'
+    for test_config in test_configs.rglob('pylinkahead-timeout*.ini'):
+        # Test that test configs can be parsed
+        db.configure(str(test_config))
+        dct = db.configuration.config_to_yaml(db.get_config())
+        # Test that resulting dict has correct content for timeout
+        assert 'Connection' in dct
+        assert 'timeout' in dct['Connection']
+        assert dct['Connection']['timeout'] in expected_results
+        expected_results.remove(dct['Connection']['timeout'])

unittests/test_container.py

@@ -70,7 +70,8 @@ def test_get_property_values():
                                           )
     assert len(table) == 2
     house_row = table[0]
-    assert house_row == (house.name, 40.2, "ft", window.id, None, None, None, 20.5, 20.5, "m", owner.name)
+    assert house_row == (house.name, 40.2, "ft", window.id, None, None, None, 20.5, 20.5, "m",
+                         owner.name)
 
     owner_row = table[1]
     assert owner_row == (owner.name, None, None, None, None, None, None, None, None, None, None)
@@ -200,11 +201,12 @@ def test_container_slicing():
     with pytest.raises(TypeError):
         cont[[0, 2, 3]]
 
+
 def test_container_filter():
     # this is a very rudimentary test since filter is based on _filter_entity_list which is tested
     # separately
     cont = db.Container()
     cont.extend([db.Record(name=f"TestRec{ii+1}") for ii in range(5)])
     recs = cont.filter(name="TestRec2")
-    assert len(recs)==1
-    recs[0].name =="TestRec2"
+    assert len(recs) == 1
+    recs[0].name == "TestRec2"