pyicat-plus 2.2.0__tar.gz → 2.3.0__tar.gz

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyicat-plus
-Version: 2.2.0
+Version: 2.3.0
 Summary: Python client to ICAT+
 Author-email: ESRF <dau-pydev@esrf.fr>
 License: GNU Lesser General Public License
@@ -186,14 +186,10 @@ Requires-Dist: numpy
 Requires-Dist: querypool
 Requires-Dist: requests
 Requires-Dist: stompest
-Requires-Dist: tqdm
 Requires-Dist: pillow
 Requires-Dist: xsdata==24.9; python_version == "3.8"
 Requires-Dist: xsdata; python_version >= "3.9"
-Provides-Extra: bliss
-Requires-Dist: blissdata[beacon]; extra == "bliss"
 Provides-Extra: test
-Requires-Dist: pyicat-plus[bliss]; extra == "test"
 Requires-Dist: pytest>=7; extra == "test"
 Requires-Dist: pytest-timeout>=2.1; extra == "test"
 Requires-Dist: numpy>=1.15; extra == "test"
@@ -203,10 +199,7 @@ Requires-Dist: stomp.py>=7; extra == "test"
 Requires-Dist: h5py>=3.5; extra == "test"
 Provides-Extra: dev
 Requires-Dist: pyicat-plus[test]; extra == "dev"
-Requires-Dist: black>=25; extra == "dev"
-Requires-Dist: flake8>=4; extra == "dev"
-Requires-Dist: pep8-naming; extra == "dev"
-Requires-Dist: isort; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
 Requires-Dist: xsdata[cli]; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: doc
@@ -217,7 +210,10 @@ Requires-Dist: pydata-sphinx-theme; extra == "doc"
 Requires-Dist: sphinx-copybutton; extra == "doc"
 Dynamic: license-file
 
-# PyIcat-Plus
+<h1>
+  <img src="doc/_static/images/pyicatplus-logo.svg" alt="PyIcat-Plus logo" height="52">
+  PyIcat-Plus
+</h1>
 
 A python client for ICAT+.
 

pyicat_plus-2.3.0/README.md

@@ -0,0 +1,10 @@
+<h1>
+  <img src="doc/_static/images/pyicatplus-logo.svg" alt="PyIcat-Plus logo" height="52">
+  PyIcat-Plus
+</h1>
+
+A python client for ICAT+.
+
+## Documentation
+
+https://pyicat-plus.readthedocs.io/

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyicat-plus"
-version = "2.2.0"
+version = "2.3.0"
 authors = [{name = "ESRF", email = "dau-pydev@esrf.fr"}]
 description = "Python client to ICAT+"
 readme = {file = "README.md", content-type = "text/markdown"}
@@ -26,7 +26,6 @@ dependencies = [
     "querypool",
     "requests",
     "stompest",
-    "tqdm",
     "pillow",
     "xsdata==24.9; python_version == '3.8'",  # latest version that supports Python 3.8
     "xsdata; python_version >= '3.9'",
@@ -40,11 +39,7 @@ Issues = "https://gitlab.esrf.fr/icat/pyicat-plus/issues"
 Changelog = "https://gitlab.esrf.fr/icat/pyicat-plus/-/blob/main/CHANGELOG.md"
 
 [project.optional-dependencies]
-bliss = [
-    "blissdata[beacon]",
-]
 test = [
-    "pyicat-plus[bliss]",
     "pytest >=7",
     "pytest-timeout >=2.1",
     "numpy >=1.15",
@@ -55,10 +50,7 @@ test = [
 ]
 dev = [
     "pyicat-plus[test]",
-    "black >=25",
-    "flake8 >=4",
-    "pep8-naming",
-    "isort",
+    "ruff",
     "xsdata[cli]",
     "pre-commit",
 ]
@@ -83,13 +75,36 @@ where = ["src"]
 [tool.coverage.run]
 omit = ['*/tests/*']
 
-[tool.isort]
-profile = "black"
-force_single_line = true
+[tool.ruff]
+line-length = 88
+
+[tool.ruff.lint]
+select = [
+    "E", # pycodestyle errors
+    "F", # pyflakes
+    "I", # isort
+    "N", # pep8-naming
+    "S", # flake8-bandit
+]
+ignore = ["E501"]
+
+[tool.ruff.lint.per-file-ignores]
+"**/tests/**" = [
+    "S101", # allow asserts
+]
+"src/pyicat_plus_pytest_plugin/**" = [
+    "S101", # allow asserts
+]
+
+[tool.ruff.lint.isort]
+force-single-line = true
+known-first-party = ["pyicat_plus", "pyicat_plus_pytest_plugin"]
+
+[project.entry-points."pytest11"]
+"pyicat_plus" = "pyicat_plus_pytest_plugin.pytest_plugin"
 
 [project.scripts]
 icat-store-raw = "pyicat_plus.apps.store_raw:main"
-icat-sync-raw = "pyicat_plus.apps.sync_raw:main"
 icat-store-processed = "pyicat_plus.apps.store_processed:main"
 icat-store-from-file = "pyicat_plus.apps.store_from_file:main"
 icat-nexus-definitions = "pyicat_plus.apps.icat_as_nexus:main"

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/_icat_messaging/deserializers/xml.py

@@ -16,7 +16,7 @@ def deserialize_message(data: bytes) -> Tuple[str, Dict[str, Any]]:
     """
     :raises xml.etree.ElementTree.ParseError:
     """
-    root = ElementTree.fromstring(data)
+    root = ElementTree.fromstring(data)  # noqa: S314 -- trusted internal ICAT messaging broker
     root_tag = root.tag.split("}", 1)[-1]
 
     if root_tag == "dataset":

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/apps/store_processed.py

@@ -9,7 +9,7 @@ def main(argv=None):
     if argv is None:
         argv = sys.argv
 
-    parser = argparse.ArgumentParser(description="Register raw data with ICAT")
+    parser = argparse.ArgumentParser(description="Register processed data with ICAT")
 
     store_raw.add_store_parameters(parser)
     add_process_parameters(parser)
@@ -27,6 +27,7 @@ def main(argv=None):
         path=args.path,
         metadata=args.metadata,
         raw=args.raw,
+        store_filename=args.store_filename,
     )
 
     client.disconnect()
@@ -37,7 +38,7 @@ def add_process_parameters(parser):
         "--raw",
         action="append",
         required=True,
-        help="Raw dataset directories",
+        help="Input dataset directories, raw or processed",
     )
 
 

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/apps/store_raw.py

@@ -25,6 +25,7 @@ def main(argv=None):
         dataset=args.dataset,
         path=args.path,
         metadata=args.metadata,
+        store_filename=args.store_filename,
     )
     client.disconnect()
 
@@ -64,6 +65,11 @@ def add_store_parameters(parser):
         default=[],
     )
 
+    parser.add_argument(
+        "--store-filename",
+        help="Store in an XML file instead of sending to ActiveMQ",
+    )
+
 
 def apply_store_parameters(args):
     if args.metadatafile:

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/client/defaults.py

@@ -1,6 +1,6 @@
 from typing import List
 
-ELOGBOOK_TOKEN: str = "elogbook-00000000-0000-0000-0000-000000000000"
+ELOGBOOK_TOKEN: str = "elogbook-00000000-0000-0000-0000-000000000000"  # noqa: S105 -- placeholder default, not a secret
 
 METADATA_QUEUE: str = "icatIngest"
 METADATA_BROKERS: List[str] = ["bcu-mq-01.esrf.fr:61613", "bcu-mq-02.esrf.fr:61613"]

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/client/icatplus_restricted.py

@@ -8,6 +8,8 @@ import requests
 
 from ..utils.url import normalize_url
 from .deprecation_utils import deprecated_argument
+from .deprecation_utils import deprecated_method
+from .types import InvestigationType
 from .types import InvestigationUser
 from .types import SampleMetadata
 
@@ -41,6 +43,7 @@ class IcatPlusRestrictedClient:
 
     def _init_urls(self, url: str):
         self._investigation_url = urljoin(url, "catalogue/{session_id}/investigation")
+        self._investigation_types_url = urljoin(url, "catalogue/investigationtypes")
         self._sample_url = urljoin(url, "catalogue/{session_id}/samples")
         self._dataset_url = urljoin(url, "catalogue/datasets")
         self._parcel_url = urljoin(url, "tracking/{session_id}/parcel")
@@ -65,7 +68,7 @@ class IcatPlusRestrictedClient:
         }
         if username is not None:
             credentials["username"] = username
-        response = requests.post(self._authentication_url, json=credentials)
+        response = requests.post(self._authentication_url, json=credentials)  # noqa: S113 -- trusted internal ICAT+ service
         response.raise_for_status()
         authentication_response = response.json()
         self._session_id = authentication_response["sessionId"]
@@ -115,7 +118,12 @@ class IcatPlusRestrictedClient:
         params = {k: v for k, v in params.items() if v is not None}
 
         url = self._investigation_url.format(session_id=self.session_id)
-        response = requests.get(url, params=params)
+        response = requests.get(url, params=params)  # noqa: S113 -- trusted internal ICAT+ service
+        response.raise_for_status()
+        return response.json()
+
+    def get_investigation_types(self) -> List[InvestigationType]:
+        response = requests.get(self._investigation_types_url)  # noqa: S113 -- trusted internal ICAT+ service
         response.raise_for_status()
         return response.json()
 
@@ -127,7 +135,7 @@ class IcatPlusRestrictedClient:
         params = {"investigationId": investigation_id}
 
         url = self._parcel_url.format(session_id=self.session_id)
-        response = requests.get(url, params=params)
+        response = requests.get(url, params=params)  # noqa: S113 -- trusted internal ICAT+ service
         response.raise_for_status()
         return response.json()
 
@@ -161,7 +169,7 @@ class IcatPlusRestrictedClient:
             "Authorization": f"Bearer {self.session_id}",
         }
         url = self._dataset_url
-        response = requests.get(url, params=params, headers=headers)
+        response = requests.get(url, params=params, headers=headers)  # noqa: S113 -- trusted internal ICAT+ service
         response.raise_for_status()
         return response.json()
 
@@ -173,7 +181,7 @@ class IcatPlusRestrictedClient:
         :raises RuntimeError: No session ID is available.
         """
         url = self._session_info_url.format(session_id=self.session_id)
-        response = requests.get(url)
+        response = requests.get(url)  # noqa: S113 -- trusted internal ICAT+ service
         response.raise_for_status()
         return response.json()
 
@@ -209,7 +217,7 @@ class IcatPlusRestrictedClient:
         params = {k: v for k, v in params.items() if v is not None}
 
         url = self._sample_url.format(session_id=self.session_id)
-        response = requests.get(url, params=params)
+        response = requests.get(url, params=params)  # noqa: S113 -- trusted internal ICAT+ service
         response.raise_for_status()
         return response.json()
 
@@ -227,15 +235,35 @@ class IcatPlusRestrictedClient:
             params["parameters"] = filter
 
         url = self._sample_metadata_url.format(session_id=self.session_id)
-        response = requests.get(url, params=params)
+        response = requests.get(url, params=params)  # noqa: S113 -- trusted internal ICAT+ service
         response.raise_for_status()
         return response.json()
 
+    @deprecated_method
     def get_sample_files_information_by(self, sample_id: str) -> dict:
-        params = {"sampleId": sample_id}
+        """DEPRECATED: This method is deprecated and may be removed in future versions.
+        Use `get_sample_information_list_by` instead.
+
+        Returns a single sample's file information, or an empty dict when not found.
+        """
+        results = self.get_sample_information_list_by(sample_id=sample_id)
+        return results[0] if results else {}
+
+    def get_sample_information_list_by(
+        self,
+        sample_id: Optional[str] = None,
+        investigation_id: Optional[str] = None,
+    ) -> List[dict]:
+        if sample_id is None and investigation_id is None:
+            raise ValueError(
+                "Either 'sample_id' or 'investigation_id' must be provided."
+            )
+
+        params = {"sampleId": sample_id, "investigationId": investigation_id}
+        params = {k: v for k, v in params.items() if v is not None}
 
         url = self._sample_files_url.format(session_id=self.session_id)
-        response = requests.get(url, params=params)
+        response = requests.get(url, params=params)  # noqa: S113 -- trusted internal ICAT+ service
         response.raise_for_status()
         return response.json()
 
@@ -250,7 +278,7 @@ class IcatPlusRestrictedClient:
 
         url = self._download_file_url.format(session_id=self.session_id)
         if use_chunks:
-            with requests.get(url, params=params, stream=True) as response:
+            with requests.get(url, params=params, stream=True) as response:  # noqa: S113 -- trusted internal ICAT+ service
                 response.raise_for_status()
                 return b"".join(
                     chunk
@@ -258,7 +286,7 @@ class IcatPlusRestrictedClient:
                     if chunk
                 )
         else:
-            response = requests.get(url, params=params)
+            response = requests.get(url, params=params)  # noqa: S113 -- trusted internal ICAT+ service
             response.raise_for_status()
             return response.content
 
@@ -269,7 +297,7 @@ class IcatPlusRestrictedClient:
         url = self._investigation_users_url.format(
             session_id=self.session_id, investigation_id=investigation_id
         )
-        response = requests.get(url)
+        response = requests.get(url)  # noqa: S113 -- trusted internal ICAT+ service
         response.raise_for_status()
         return response.json()
 

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/client/interface.py

@@ -14,6 +14,7 @@ from .types import ArchiveStatusType as StatusType  # noqa F401 deprecated
 from .types import Dataset
 from .types import DatasetId
 from .types import DatasetMetadata  # noqa F401
+from .types import InvestigationType
 from .types import InvestigationUser
 from .types import SampleMetadata
 
@@ -143,7 +144,7 @@ class IcatClientInterface:
         store_filename: Optional[str] = None,
     ):
         """
-        Request icat to store raw dataset.
+        Request icat to store a raw dataset, i.e. a dataset without other datasets as input.
 
         :param beamline str: beamline name like id01, id15a, bm18...
         :param proposal str: proposal name like in1169, blc14795, ihma429...
@@ -166,14 +167,14 @@ class IcatClientInterface:
         store_filename: Optional[str] = None,
     ):
         """
-        Request icat to store a processed dataset.
+        Request icat to store a processed dataset, i.e. a dataset with other datasets as input.
 
         :param beamline str: beamline name like id01, id15a, bm18...
         :param proposal str: proposal name like in1169, blc14795, ihma429...
         :param str dataset: dataset name like sample_XYZ.
         :param str path: path to the processed dataset to store. Can be a file or a folder.
         :param dict metadata: metadata to associate with the dataset. Must contain keys defined by the appropriate application definition, available at https://icat-esrf-definitions.readthedocs.io.
-        :param tuple raw: Path(s) to the raw dataset(s). Should point to the 'bliss dataset' folder(s).
+        :param tuple raw: Path(s) to the input dataset(s), raw or processed. Should point to the dataset folder(s).
                           If processing relies on multiple datasets, all corresponding folders must be provided.
         :param str store_filename: xml file with metadata to be stored.
         """
@@ -413,6 +414,15 @@ class IcatClientInterface:
         """
         raise NotImplementedError
 
+    def get_investigation_types(self) -> List[InvestigationType]:
+        """
+        Returns a list of investigation types. Does not require authentication.
+        API Reference: https://icatplus.esrf.fr/api-docs/#/Catalogue/get_catalogue_investigationtypes
+
+        :returns: list of investigation types.
+        """
+        raise NotImplementedError
+
     def get_parcels_by(self, investigation_id: str) -> List[dict]:
         """
         Returns the list of parcels associated to an investigation.
@@ -448,12 +458,31 @@ class IcatClientInterface:
         """
         raise NotImplementedError
 
+    @deprecated_method
     def get_sample_files_information_by(self, sample_id: str) -> dict:
-        """
+        """DEPRECATED: This method is deprecated and may be removed in future versions.
+        Use `get_sample_information_list_by` instead.
+
         Returns the sample file information for a given sample.
 
         :param sample_id: Sample identifier.
-        :returns: Sample file information as dict.
+        :returns: Sample file information as dict, or an empty dict when no match is found.
+        """
+        raise NotImplementedError
+
+    def get_sample_information_list_by(
+        self,
+        sample_id: Optional[str] = None,
+        investigation_id: Optional[str] = None,
+    ) -> List[dict]:
+        """
+        Returns the list of sample file information for a given sample and/or
+        investigation.
+
+        :param sample_id: Sample identifier.
+        :param investigation_id: Investigation identifier.
+        :returns: List of sample file information.
+        :raises ValueError: Neither `sample_id` nor `investigation_id` is provided.
         """
         raise NotImplementedError
 

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/client/main.py

@@ -23,6 +23,7 @@ from .types import ArchiveStatusType
 from .types import ArchiveStatusType as StatusType  # noqa F401 deprecated
 from .types import Dataset
 from .types import DatasetId
+from .types import InvestigationType
 from .types import InvestigationUser
 from .types import SampleMetadata
 from .update_metadata import IcatUpdateMetadataClient
@@ -666,7 +667,8 @@ class IcatClient(IcatClientInterface):
         :param dataset: The dataset name.
         :param path: The path to the dataset on disk.
         :param metadata: A dictionary of metadata to be attached to the dataset.
-        :param raw: shorthand for ``metadata = {'input_datasets': ...}``.
+        :param raw: Path(s) to the input dataset(s), raw or processed. Shorthand for
+                    ``metadata = {'input_datasets': ...}``.
         :param store_filename: Save metadata in this file instead of sending it to ICAT.
         :param strict: Strict metadata validation.
 
@@ -687,7 +689,7 @@ class IcatClient(IcatClientInterface):
             else:
                 metadata["input_datasets"] = [raw]
         if not metadata.get("input_datasets"):
-            raise ValueError("Provide 'raw' dataset directories")
+            raise ValueError("Provide 'raw' input dataset directories")
         self.store_dataset(
             beamline=beamline,
             proposal=proposal,
@@ -890,6 +892,9 @@ class IcatClient(IcatClientInterface):
             parameters=parameters,
         )
 
+    def get_investigation_types(self) -> List[InvestigationType]:
+        return self._icatplus_restricted_client.get_investigation_types()
+
     def get_samples_by(
         self,
         investigation_id: Optional[str] = None,
@@ -929,6 +934,15 @@ class IcatClient(IcatClientInterface):
             sample_id
         )
 
+    def get_sample_information_list_by(
+        self,
+        sample_id: Optional[str] = None,
+        investigation_id: Optional[str] = None,
+    ) -> List[dict]:
+        return self._icatplus_restricted_client.get_sample_information_list_by(
+            sample_id, investigation_id
+        )
+
     def download_file_by(
         self,
         sample_id: str,

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/client/messaging.py

@@ -26,7 +26,7 @@ class IcatMessagingClient:
     MONITOR_SCHEME = "http"
     DEFAULT_MONITOR_PORT = 8778
     MONITOR_USER = "user"
-    MONITOR_PWD = "user"
+    MONITOR_PWD = "user"  # noqa: S105 -- default placeholder credential, not a secret
 
     def __init__(
         self,
@@ -112,7 +112,7 @@ class IcatMessagingClient:
     @property
     def _consumer_count(self):
         url = self.__consumer_count_url.format(host=self._host)
-        response = requests.get(url, headers=self.__jolokia_headers)
+        response = requests.get(url, headers=self.__jolokia_headers)  # noqa: S113 -- trusted internal ActiveMQ broker
         if not response.ok:
             raise RuntimeError(
                 response, "Failed to retrieve the ActiveMQ consumer count"

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/client/null.py

@@ -91,6 +91,9 @@ class IcatNullClient(IcatClientInterface):
     def get_sample_files_information_by(self, *args, **kwargs) -> None:
         pass
 
+    def get_sample_information_list_by(self, *args, **kwargs) -> None:
+        pass
+
     def download_file_by(self, *args, **kwargs) -> None:
         pass
 

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/client/types.py

@@ -73,3 +73,13 @@ class InvestigationUser(TypedDict):
     orcid: Optional[str]
     affiliation: Optional[str]
     role: str
+
+
+class InvestigationType(TypedDict):
+    """
+    Investigation type information
+    """
+
+    id: str
+    name: str
+    description: Optional[str]

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/metadata/definitions.py

@@ -314,7 +314,6 @@ def load_group(in_node: ElementTree.Element, **node_attributes) -> IcatFieldGrou
         nodes[icat_item.name] = icat_item
 
     for group_name, element in groups:
-
         technique_names = _GROUP_NAME_TO_TECHNIQUES.get(group_name, None)
         if technique_names:
             metadata_generator = technique.get_technique_metadata(*technique_names)
@@ -367,7 +366,7 @@ def icat_fields_source(url: Optional[str] = None) -> Union[str, StringIO]:
     if url.startswith("file://") or url.startswith("xml://"):
         return re.sub(r"^[a-z]+://", "", url)
     try:
-        response = requests.get(url)
+        response = requests.get(url)  # noqa: S113 -- trusted ESRF-hosted definitions URL
         response.raise_for_status()
     except Exception:
         working_url = "https://gitlab.esrf.fr/icat/hdf5-master-config/-/raw/master/src/icat_esrf_definitions/hdf5_cfg.xml"
@@ -385,7 +384,7 @@ def load_icat_fields(url: Optional[str] = None) -> IcatFieldGroup:
                 "file://", "xml://" or anything the `requests` library can handle.
     :returns: a mapping object representing the tree relationship of ICAT fields
     """
-    tree = ElementTree.parse(icat_fields_source(url=url))
+    tree = ElementTree.parse(icat_fields_source(url=url))  # noqa: S314 -- trusted ESRF-hosted definitions file
     in_node = tree.getroot()
     return load_group(
         in_node, name="", parent=IcatNodeId(), NX_class="NXentry", techniques=set()

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/tests/conftest.py

@@ -5,7 +5,6 @@ from esrf_ontologies import technique
 
 from ..errors import IcatMetadataFutureWarning
 from ..metadata.definitions import load_icat_fields
-from .fixtures.icat import *  # noqa F401
 
 pytest.register_assert_rewrite("pyicat_plus.tests.utils.compare")
 

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/tests/test_icat_investigations.py

@@ -377,7 +377,7 @@ class _Investigations:
         investigation = {
             "id": len(self._investigations),
             "startDate": startdate.astimezone().isoformat(),
-            "unique": random.uniform(0, 1),
+            "unique": random.uniform(0, 1),  # noqa: S311 -- test data, not crypto
         }
         if end_offset is not None:
             enddate = self._date + end_offset

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/tests/test_icat_restricted.py

@@ -27,7 +27,11 @@ def test_login(icatplus_restricted_client):
 def test_login_with_username_plugin(icatplus_restricted_client):
     client, messages = icatplus_restricted_client
 
-    result = client.login(password="correct", username="john", plugin="db")
+    result = client.login(
+        password="correct",  # noqa: S106 -- test server sentinel value
+        username="john",
+        plugin="db",
+    )
 
     assert result["sessionId"] == client.session_id
     assert messages.empty()
@@ -230,13 +234,41 @@ def test_get_sample_files_information_by(icatplus_restricted_client):
 
     sample_id = generate.icat_id()
 
+    with pytest.warns(DeprecationWarning, match="get_sample_files_information_by"):
+        with pytest.raises(RuntimeError, match="Login is required."):
+            _ = client.get_sample_files_information_by(sample_id)
+
+    assert client.login("correct")
+
+    with pytest.warns(DeprecationWarning, match="get_sample_files_information_by"):
+        sample_files = client.get_sample_files_information_by(sample_id)
+
+    assert sample_files == {}
+    assert messages.empty()
+
+
+def test_get_sample_information_list_by(icatplus_restricted_client):
+    client, messages = icatplus_restricted_client
+
+    sample_id = generate.icat_id()
+    investigation_id = generate.icat_id()
+
     with pytest.raises(RuntimeError, match="Login is required."):
-        _ = client.get_sample_files_information_by(sample_id)
+        _ = client.get_sample_information_list_by(sample_id=sample_id)
 
     assert client.login("correct")
 
-    sample_files = client.get_sample_files_information_by(sample_id)
+    with pytest.raises(
+        ValueError, match="Either 'sample_id' or 'investigation_id' must be provided."
+    ):
+        client.get_sample_information_list_by()
+
+    sample_files = client.get_sample_information_list_by(sample_id=sample_id)
+    assert sample_files == []
 
+    sample_files = client.get_sample_information_list_by(
+        investigation_id=investigation_id
+    )
     assert sample_files == []
     assert messages.empty()
 
@@ -292,6 +324,16 @@ def test_get_investigation_users(icatplus_restricted_client):
     assert messages.empty()
 
 
+def test_get_investigation_types(icatplus_restricted_client):
+    client, messages = icatplus_restricted_client
+
+    investigation_types = client.get_investigation_types()
+
+    assert isinstance(investigation_types, list)
+    assert investigation_types
+    assert messages.empty()
+
+
 def _release_date_from_start_date(start_date_str: str) -> datetime.date:
     start = datetime.datetime.fromisoformat(start_date_str[:19])
     return start.date().replace(year=start.year + 3)

{pyicat_plus-2.2.0 → pyicat_plus-2.3.0}/src/pyicat_plus/tests/utils/compare.py

@@ -83,7 +83,7 @@ def _set_expected_value(expected: dict, value: str, *keys) -> None:
 
             if not isinstance(param_list, list):
                 raise TypeError(
-                    f"Expected list at '{'.'.join(keys[:i+1])}', got {type(param_list).__name__}"
+                    f"Expected list at '{'.'.join(keys[: i + 1])}', got {type(param_list).__name__}"
                 )
 
             # Do not overwrite existing parameter
@@ -127,7 +127,7 @@ def _set_expected_to_actual_value(actual: dict, expected: dict, *keys: str) -> N
 
             if not isinstance(value, list):
                 raise TypeError(
-                    f"Expected list at '{'.'.join(keys[:i+1])}', "
+                    f"Expected list at '{'.'.join(keys[: i + 1])}', "
                     f"got {type(value).__name__}"
                 )
 

pyicat_plus-2.3.0/src/pyicat_plus/tests/utils/generate.py

@@ -0,0 +1,5 @@
+import random
+
+
+def icat_id() -> int:
+    return random.randint(1000000000, 9999999999)  # noqa: S311 -- test data, not crypto