diff --git a/.copier-answers.yml b/.copier-answers.yml index c93dad0..2b84857 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,5 +1,5 @@ # Changes here will be overwritten by Copier -_commit: v8.5.0 +_commit: v8.5.0-3-g60fcc85 _src_path: gh:eccenca/cmem-plugin-template author_mail: cmempy-developer@eccenca.com author_name: eccenca GmbH diff --git a/CHANGELOG.md b/CHANGELOG.md index bcaf9d4..24717db 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,9 +5,15 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](https://semver.org/) -## [Unreleased] +## [2.3.0] 2026-08-17 -TODO: add at least one Added, Changed, Deprecated, Removed, Fixed or Security section +### Changed + +- Use cmem-client instead of cmempy for all Corporate Memory access + +### Removed + +- Remove cmem-cmempy dependency and `setup_cmempy_user_access` calls ## [2.2.7] 2026-07-22 diff --git a/cmem_plugin_reason/plugin_reason.py b/cmem_plugin_reason/plugin_reason.py index 24c461a..17b0e7d 100644 --- a/cmem_plugin_reason/plugin_reason.py +++ b/cmem_plugin_reason/plugin_reason.py @@ -7,8 +7,7 @@ from tempfile import TemporaryDirectory from uuid import uuid4 -from cmem.cmempy.dp.proxy.graph import get, get_graph_import_tree, get_graphs_list -from cmem.cmempy.dp.proxy.update import post +from cmem_plugin_base.dataintegration.client import get_client from cmem_plugin_base.dataintegration.context import ExecutionContext, ExecutionReport from cmem_plugin_base.dataintegration.description import Icon, Plugin, PluginParameter from cmem_plugin_base.dataintegration.entity import Entities @@ -17,7 +16,6 @@ from cmem_plugin_base.dataintegration.plugins import WorkflowPlugin from cmem_plugin_base.dataintegration.ports import FixedNumberOfInputs from cmem_plugin_base.dataintegration.types import BoolParameterType, StringParameterType -from cmem_plugin_base.dataintegration.utils import setup_cmempy_user_access from cmem_plugin_reason.doc import REASON_DOC from cmem_plugin_reason.utils import ( @@ -30,6 +28,7 @@ VALIDATE_PROFILES_PARAMETER, cancel_workflow, create_xml_catalog_file, + fetch_graph, get_file_with_datetime, get_output_graph_label, is_valid_uri, @@ -401,17 +400,19 @@ def underscore(word: str) -> str: def get_graphs(self, graphs: dict, missing: list) -> None: """Get graphs from CMEM""" for iri, filename in graphs.items(): - with (Path(self.temp) / filename).open("w", encoding="utf-8") as file: - if iri not in missing: - self.log.info(f"Fetching graph {iri}.") - setup_cmempy_user_access(self.context.user) - file.write(get(iri).text) - if iri == self.data_graph_iri: - file.write( - f"\n<{iri}> " - " " - f"<{self.ontology_graph_iri}> ." - ) + path = Path(self.temp) / filename + if iri in missing: + path.touch() + continue + self.log.info(f"Fetching graph {iri}.") + fetch_graph(self.client, iri, path) + if iri == self.data_graph_iri: + with path.open("a", encoding="utf-8") as file: + file.write( + f"\n<{iri}> " + " " + f"<{self.ontology_graph_iri}> ." + ) def get_graphs_tree(self) -> tuple[dict, list]: # noqa: C901 """Get graph import tree. Last item in graph_iris is output_graph_iri which is excluded""" @@ -420,15 +421,15 @@ def get_graphs_tree(self) -> tuple[dict, list]: # noqa: C901 for graph_iri in [self.data_graph_iri, self.ontology_graph_iri]: if graph_iri not in graphs: graphs[graph_iri] = f"{uuid4().hex}.nt" - tree = get_graph_import_tree(graph_iri) - for value in tree["tree"].values(): + tree = self.client.graph_imports.get_import_tree(graph_iri) + for value in tree.tree.values(): for iri in value: if iri not in graphs: if iri == self.ontology_graph_iri: self.data_imports_ontology = True elif iri == self.output_graph_iri: raise ImportError("Input graph imports output graph.") - if iri not in self.graphs_dict: + if iri not in self.client.graphs: missing.append(iri) graphs[iri] = f"{uuid4().hex}.nt" if missing: @@ -483,7 +484,7 @@ def add_result_import(self) -> None: }} }} """ - post(query=query) + self.client.store.sparql.update(query) def remove_ontology_import(self) -> None: """Remove ontology graph import from output graph""" @@ -495,11 +496,10 @@ def remove_ontology_import(self) -> None: }} }} """ - post(query=query) + self.client.store.sparql.update(query) def _execute(self) -> None: """`Execute plugin""" - setup_cmempy_user_access(self.context.user) graphs, missing = self.get_graphs_tree() self.get_graphs(graphs, missing) if cancel_workflow(self): @@ -508,8 +508,7 @@ def _execute(self) -> None: self.reason(graphs) if cancel_workflow(self): return - setup_cmempy_user_access(self.context.user) - send_result(self.output_graph_iri, get_file_with_datetime(self)) + send_result(self.client, self.output_graph_iri, get_file_with_datetime(self)) if self.validate_profile: if self.input_profiles: valid_profiles = self.valid_profiles.split(",") @@ -518,7 +517,6 @@ def _execute(self) -> None: post_profiles(self, valid_profiles) post_provenance(self) - setup_cmempy_user_access(self.context.user) if self.imports == "import_result": self.add_result_import() if self.imports != "import_ontology" and not self.data_imports_ontology: @@ -534,17 +532,16 @@ def _execute(self) -> None: def execute(self, inputs: Sequence[Entities], context: ExecutionContext) -> None: # noqa: ARG002 """Execute plugin with temporary directory""" - setup_cmempy_user_access(context.user) - self.graphs_dict = {_["iri"]: _ for _ in get_graphs_list()} - not_exist = [] - if self.data_graph_iri not in self.graphs_dict: - not_exist.append(self.data_graph_iri) - if self.ontology_graph_iri not in self.graphs_dict: - not_exist.append(self.ontology_graph_iri) + self.context = context + self.client = get_client(context) + not_exist = [ + iri + for iri in (self.data_graph_iri, self.ontology_graph_iri) + if iri not in self.client.graphs + ] if not_exist: raise ValueError(f"Graphs do not exist: {', '.join(not_exist)}") - self.context = context context.report.update( ExecutionReport( operation="reason", diff --git a/cmem_plugin_reason/plugin_validate.py b/cmem_plugin_reason/plugin_validate.py index c407f17..a3b3a34 100644 --- a/cmem_plugin_reason/plugin_validate.py +++ b/cmem_plugin_reason/plugin_validate.py @@ -6,8 +6,8 @@ from tempfile import TemporaryDirectory from uuid import uuid4 -from cmem.cmempy.dp.proxy.graph import get, get_graph_import_tree, get_graphs_list -from cmem.cmempy.workspace.projects.resources.resource import create_resource +from cmem_client.repositories.protocols.import_item import ImportConflictPolicy +from cmem_plugin_base.dataintegration.client import get_client from cmem_plugin_base.dataintegration.context import ExecutionContext, ExecutionReport from cmem_plugin_base.dataintegration.description import Icon, Plugin, PluginParameter from cmem_plugin_base.dataintegration.entity import Entities, Entity, EntityPath, EntitySchema @@ -16,7 +16,6 @@ from cmem_plugin_base.dataintegration.plugins import WorkflowPlugin from cmem_plugin_base.dataintegration.ports import FixedNumberOfInputs, FixedSchemaPort from cmem_plugin_base.dataintegration.types import BoolParameterType, StringParameterType -from cmem_plugin_base.dataintegration.utils import setup_cmempy_user_access from pathvalidate import is_valid_filepath from cmem_plugin_reason.doc import VALIDATE_DOC @@ -30,6 +29,7 @@ VALIDATE_REASONER_PARAMETER, cancel_workflow, create_xml_catalog_file, + fetch_graph, get_file_with_datetime, get_output_graph_label, is_valid_uri, @@ -183,12 +183,12 @@ def generate_output_schema(self) -> EntitySchema: def get_graphs(self, graphs: dict, missing: list) -> None: """Get graphs from CMEM""" for iri, filename in graphs.items(): + path = Path(self.temp) / filename + if iri in missing: + path.touch() + continue self.log.info(f"Fetching graph {iri}.") - with (Path(self.temp) / filename).open("w", encoding="utf-8") as file: - if iri not in missing: - self.log.info(f"Fetching graph {iri}.") - setup_cmempy_user_access(self.context.user) - file.write(get(iri).text) + fetch_graph(self.client, iri, path) def get_graphs_tree(self) -> tuple[dict, list]: """Get graph import tree. Last item in graph_iris is output_graph_iri which is excluded""" @@ -196,13 +196,13 @@ def get_graphs_tree(self) -> tuple[dict, list]: graphs = {} if self.ontology_graph_iri not in graphs: graphs[self.ontology_graph_iri] = f"{uuid4().hex}.nt" - tree = get_graph_import_tree(self.ontology_graph_iri) - for value in tree["tree"].values(): + tree = self.client.graph_imports.get_import_tree(self.ontology_graph_iri) + for value in tree.tree.values(): for iri in value: if iri not in graphs: if iri == self.output_graph_iri: raise ImportError("Input graph imports output graph.") - if iri not in self.graphs_dict: + if iri not in self.client.graphs: missing.append(iri) graphs[iri] = f"{uuid4().hex}.nt" if missing: @@ -241,11 +241,10 @@ def explain(self, graphs: dict) -> None: def make_resource(self, context: ExecutionContext) -> None: """Make MD resource in project""" - create_resource( - project_name=context.task.project_id(), - resource_name=self.md_filename, - file_resource=(Path(self.temp) / self.md_filename).open("r", encoding="utf-8"), - replace=True, + self.client.files.import_item( + path=Path(self.temp) / self.md_filename, + key=f"{context.task.project_id()}:{self.md_filename}", + on_conflict=ImportConflictPolicy.REPLACE, ) def add_profiles(self, valid_profiles: list) -> list: @@ -274,7 +273,6 @@ def make_entities(self, text: str, valid_profiles: list) -> Entities: def _execute(self) -> Entities | None: """Run the workflow operator.""" - setup_cmempy_user_access(self.context.user) graphs, missing = self.get_graphs_tree() self.get_graphs(graphs, missing) if cancel_workflow(self): @@ -284,9 +282,7 @@ def _execute(self) -> Entities | None: if cancel_workflow(self): return None if self.output_graph_iri: - setup_cmempy_user_access(self.context.user) - send_result(self.output_graph_iri, get_file_with_datetime(self)) - setup_cmempy_user_access(self.context.user) + send_result(self.client, self.output_graph_iri, get_file_with_datetime(self)) post_provenance(self) if cancel_workflow(self): return None @@ -296,7 +292,6 @@ def _execute(self) -> Entities | None: if cancel_workflow(self): return None if self.write_md: - setup_cmempy_user_access(self.context.user) self.make_resource(self.context) text = (Path(self.temp) / self.md_filename).read_text() @@ -326,12 +321,11 @@ def _execute(self) -> Entities | None: def execute(self, inputs: Sequence[Entities], context: ExecutionContext) -> Entities | None: # noqa: ARG002 """Execute plugin with temporary directory""" - setup_cmempy_user_access(context.user) - self.graphs_dict = {_["iri"]: _ for _ in get_graphs_list()} - if self.ontology_graph_iri not in self.graphs_dict: + self.context = context + self.client = get_client(context) + if self.ontology_graph_iri not in self.client.graphs: raise ValueError(f"Ontology graph does not exist: {self.ontology_graph_iri}") - self.context = context context.report.update( ExecutionReport( operation="validate", diff --git a/cmem_plugin_reason/robot.jar b/cmem_plugin_reason/robot.jar index cd122d6..f661be5 100644 Binary files a/cmem_plugin_reason/robot.jar and b/cmem_plugin_reason/robot.jar differ diff --git a/cmem_plugin_reason/utils.py b/cmem_plugin_reason/utils.py index 3959bff..1d8faf9 100644 --- a/cmem_plugin_reason/utils.py +++ b/cmem_plugin_reason/utils.py @@ -1,11 +1,9 @@ """Common constants and functions""" -import json import re import shlex from collections import OrderedDict from datetime import UTC, datetime -from io import BytesIO from pathlib import Path from secrets import token_hex from subprocess import CompletedProcess, run @@ -13,9 +11,9 @@ from xml.etree.ElementTree import Element, SubElement, tostring import validators.url -from cmem.cmempy.dp.proxy.graph import get_graphs_list, post_streamed -from cmem.cmempy.dp.proxy.sparql import post as post_select -from cmem.cmempy.dp.proxy.update import post as post_update +from cmem_client.client import Client +from cmem_client.repositories.graphs import GraphExportConfig, GraphsRepository +from cmem_client.repositories.protocols.import_item import ImportConflictPolicy from cmem_plugin_base.dataintegration.context import ExecutionReport from cmem_plugin_base.dataintegration.description import PluginParameter from cmem_plugin_base.dataintegration.parameter.choice import ChoiceParameterType @@ -28,6 +26,8 @@ ROBOT = Path(__path__[0]) / "robot.jar" +NT_EXPORT_CONFIG = GraphExportConfig(serialization=GraphsRepository.formats["n-triples"]) + REASONERS = OrderedDict( { "elk": "ELK", @@ -111,16 +111,14 @@ def create_xml_catalog_file(dir_: str, graphs: dict) -> None: file.write(reparsed) -def send_result(iri: str | None, file: BytesIO) -> None: +def fetch_graph(client: Client, iri: str, path: Path) -> None: + """Fetch a graph from CMEM as N-Triples into path""" + client.graphs.export_item(key=iri, path=path, replace=True, configuration=NT_EXPORT_CONFIG) + + +def send_result(client: Client, iri: str | None, file: Path) -> None: """Send result""" - res = post_streamed( - iri, - file, - replace=True, - content_type="text/turtle", - ) - if res.status_code != 204: # noqa: PLR2004 - raise OSError(f"Error posting result graph (status code {res.status_code}).") + client.graphs.import_item(path=file, key=iri, on_conflict=ImportConflictPolicy.REPLACE) def post_provenance(plugin: WorkflowPlugin) -> None: @@ -143,7 +141,7 @@ def post_provenance(plugin: WorkflowPlugin) -> None: }} }} """ - post_update(query=insert_query) + plugin.client.store.sparql.update(insert_query) def get_provenance(plugin: WorkflowPlugin) -> dict | None: @@ -163,14 +161,14 @@ def get_provenance(plugin: WorkflowPlugin) -> dict | None: }} """ - result = json.loads(post_select(query=type_query)) + type_rows = list(plugin.client.store.sparql.query(type_query)) - try: - plugin_type = result["results"]["bindings"][0]["type"]["value"] - except IndexError: + if not type_rows: plugin.log.warning("Could not add provenance data to output graph.") return None + plugin_type = str(type_rows[0]["type"]) + param_split = ( plugin_type.replace( "https://vocab.eccenca.com/di/functions/Plugin_", @@ -190,22 +188,20 @@ def get_provenance(plugin: WorkflowPlugin) -> dict | None: new_plugin_iri = f"{'_'.join(plugin_iri.split('_')[:-1])}_{token_hex(8)}" label = f"{plugin.label} plugin" - result = json.loads(post_select(query=parameter_query)) + parameters = {} + + for row in plugin.client.store.sparql.query(parameter_query): + param_iri = str(row["parameter"]) + param_name = param_iri.split(param_split)[1] + parameters[param_name] = param_iri - prov = { + return { "plugin_iri": new_plugin_iri, "plugin_label": label, "plugin_type": plugin_type, - "parameters": {}, + "parameters": parameters, } - for binding in result["results"]["bindings"]: - param_iri = binding["parameter"]["value"] - param_name = param_iri.split(param_split)[1] - prov["parameters"][param_name] = param_iri - - return prov - def robot(cmd: str, max_ram_percentage: int) -> CompletedProcess: """Run robot.jar""" @@ -240,34 +236,27 @@ def post_profiles(plugin: WorkflowPlugin, valid_profiles: list) -> None: }} }} """ - post_update(query=query) + plugin.client.store.sparql.update(query) def get_output_graph_label(plugin: WorkflowPlugin, iri: str, add_string: str) -> str: """Create a label for the output graph""" - graphs = ( - plugin.graphs_dict - if hasattr(plugin, "graphs_dict") - else {_["iri"]: _ for _ in get_graphs_list()} - ) - try: - data_graph_label = graphs[iri]["label"]["title"] - data_graph_label += " - " - except KeyError: - data_graph_label = "" + graph = plugin.client.graphs.get(iri) + data_graph_label = f"{graph.label.title} - " if graph and graph.label else "" return f"{data_graph_label}{add_string}" -def get_file_with_datetime(plugin: WorkflowPlugin) -> BytesIO: - """Return result file with dcterms:created datetime""" +def get_file_with_datetime(plugin: WorkflowPlugin) -> Path: + """Return path of the result file with dcterms:created datetime""" utctime = str(datetime.fromtimestamp(int(time()), tz=UTC))[:-6].replace(" ", "T") + "Z" - file_content = ( + file = Path(plugin.temp) / "result_datetime.ttl" + file.write_text( (Path(plugin.temp) / "result.ttl").read_text() + f"\n<{plugin.output_graph_iri}> " - f'"{utctime}"^^xsd:dateTime .' - ).encode("utf-8") - - return BytesIO(file_content) + f'"{utctime}"^^xsd:dateTime .', + encoding="utf-8", + ) + return file def cancel_workflow(plugin: WorkflowPlugin) -> bool: diff --git a/poetry.lock b/poetry.lock index 74b8cec..e06db4a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,15 +1,15 @@ -# This file is automatically @generated by Poetry 2.4.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.3.3 and should not be changed by hand. [[package]] name = "annotated-types" -version = "0.7.0" +version = "0.8.0" description = "Reusable constraint types to use with typing.Annotated" optional = false -python-versions = ">=3.8" -groups = ["main", "dev"] +python-versions = ">=3.10" +groups = ["main"] files = [ - {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, - {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, + {file = "annotated_types-0.8.0-py3-none-any.whl", hash = "sha256:f072f4d804ea359e4eaf198b1af7a8b0943881a87f31bb764f8bf219bb9419e0"}, + {file = "annotated_types-0.8.0.tar.gz", hash = "sha256:13b2beaad985e05e2d6407ee4c4f35590b11f8d693a258a561055cac8f64cab7"}, ] [[package]] @@ -18,7 +18,7 @@ version = "4.14.2" description = "High-level concurrency and networking framework on top of asyncio or Trio" optional = false python-versions = ">=3.10" -groups = ["dev"] 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100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,10 +23,10 @@ python = "^3.13" validators = "^0.35.0" pathvalidate = "^3.3.1" defusedxml = "^0.7.1" -cmem-cmempy = "^25.5.0" +cmem-client = "^1.0.0" [tool.poetry.dependencies.cmem-plugin-base] -version = "^4.16.1" +version = "^4.19.0" allow-prereleases = false [tool.poetry.group.dev.dependencies.cmem-cmemc] diff --git a/tests/test_output_graph_label.py b/tests/test_output_graph_label.py index 27effaf..5e0d3d4 100644 --- a/tests/test_output_graph_label.py +++ b/tests/test_output_graph_label.py @@ -3,6 +3,7 @@ from cmem_plugin_reason.plugin_reason import ReasonPlugin from cmem_plugin_reason.plugin_validate import ValidatePlugin from cmem_plugin_reason.utils import get_output_graph_label +from tests.utils import get_test_client def test_reason_output_graph_label() -> None: @@ -18,6 +19,7 @@ def test_reason_output_graph_label() -> None: validate_profile=False, imports="none", ) + plugin.client = get_test_client() assert ( get_output_graph_label(plugin, plugin.data_graph_iri, "Reasoning Results") == "CMEM Shapes Catalog - Reasoning Results" @@ -37,6 +39,7 @@ def test_reason_output_graph_label_fail() -> None: validate_profile=False, imports="none", ) + plugin.client = get_test_client() assert ( get_output_graph_label(plugin, plugin.data_graph_iri, "Reasoning Results") == "Reasoning Results" @@ -50,6 +53,7 @@ def test_validate_output_graph_label() -> None: output_graph_iri="https://vocab.eccenca.com/shacl/output/", reasoner="hermit", ) + plugin.client = get_test_client() assert ( get_output_graph_label(plugin, plugin.ontology_graph_iri, "Validation Result") == "CMEM Shapes Catalog - Validation Result" @@ -63,6 +67,7 @@ def test_validate_output_graph_label_fail() -> None: output_graph_iri="https://vocab.eccenca.com/shacl/output/", reasoner="hermit", ) + plugin.client = get_test_client() assert ( get_output_graph_label(plugin, plugin.ontology_graph_iri, "Validation Result") == "Validation Result" diff --git a/tests/test_reason.py b/tests/test_reason.py index 6b6c884..056d8b0 100644 --- a/tests/test_reason.py +++ b/tests/test_reason.py @@ -1,19 +1,23 @@ """Plugin tests.""" -import json from collections.abc import Generator from typing import Any import pytest -from cmem.cmempy.dp.proxy.graph import delete -from cmem.cmempy.dp.proxy.sparql import get from cmem_plugin_base.testing import TestExecutionContext from rdflib import Graph from rdflib.compare import isomorphic from cmem_plugin_reason.plugin_reason import ReasonPlugin from cmem_plugin_reason.utils import REASONERS -from tests.utils import FIXTURE_DIR, UID, get_bytes_io, get_remote_graph, import_graph, replace_uuid +from tests.utils import ( + FIXTURE_DIR, + UID, + get_remote_graph, + get_test_client, + import_graph, + replace_uuid, +) REASON_DATA_GRAPH_IRI = f"https://ns.eccenca.com/reasoning/{UID}/data/" REASON_DATA_GRAPH_IRI_2 = f"https://ns.eccenca.com/reasoning/{UID}/data2/" @@ -39,32 +43,31 @@ def reasoner_parameter() -> str | None: @pytest.fixture def setup() -> Generator[None, Any]: """Set up Reason test""" - delete(REASON_RESULT_GRAPH_IRI) - - import_graph(REASON_DATA_GRAPH_IRI, get_bytes_io(f"{FIXTURE_DIR}/test_reason_data.ttl")) - import_graph(REASON_DATA_GRAPH_IRI_2, get_bytes_io(f"{FIXTURE_DIR}/test_reason_data_2.ttl")) - import_graph( - REASON_ONTOLOGY_GRAPH_IRI_1, get_bytes_io(f"{FIXTURE_DIR}/test_reason_ontology_1.ttl") - ) - import_graph( - REASON_ONTOLOGY_GRAPH_IRI_2, get_bytes_io(f"{FIXTURE_DIR}/test_reason_ontology_2.ttl") - ) - import_graph( - REASON_ONTOLOGY_GRAPH_IRI_3, get_bytes_io(f"{FIXTURE_DIR}/test_reason_ontology_3.ttl") - ) + client = get_test_client() + client.graphs.delete_item(REASON_RESULT_GRAPH_IRI, skip_if_missing=True) + + import_graph(client, REASON_DATA_GRAPH_IRI, f"{FIXTURE_DIR}/test_reason_data.ttl") + import_graph(client, REASON_DATA_GRAPH_IRI_2, f"{FIXTURE_DIR}/test_reason_data_2.ttl") + import_graph(client, REASON_ONTOLOGY_GRAPH_IRI_1, f"{FIXTURE_DIR}/test_reason_ontology_1.ttl") + import_graph(client, REASON_ONTOLOGY_GRAPH_IRI_2, f"{FIXTURE_DIR}/test_reason_ontology_2.ttl") + import_graph(client, REASON_ONTOLOGY_GRAPH_IRI_3, f"{FIXTURE_DIR}/test_reason_ontology_3.ttl") import_graph( - ONTOLOGY_GRAPH_IMPORT_FAIL_IRI, get_bytes_io(f"{FIXTURE_DIR}/test_reason_ontology_4.ttl") + client, ONTOLOGY_GRAPH_IMPORT_FAIL_IRI, f"{FIXTURE_DIR}/test_reason_ontology_4.ttl" ) yield - delete(REASON_DATA_GRAPH_IRI) - delete(REASON_DATA_GRAPH_IRI_2) - delete(REASON_ONTOLOGY_GRAPH_IRI_1) - delete(REASON_ONTOLOGY_GRAPH_IRI_2) - delete(REASON_ONTOLOGY_GRAPH_IRI_3) - delete(ONTOLOGY_GRAPH_IMPORT_FAIL_IRI) - delete(REASON_RESULT_GRAPH_IRI) + client = get_test_client() + for iri in ( + REASON_DATA_GRAPH_IRI, + REASON_DATA_GRAPH_IRI_2, + REASON_ONTOLOGY_GRAPH_IRI_1, + REASON_ONTOLOGY_GRAPH_IRI_2, + REASON_ONTOLOGY_GRAPH_IRI_3, + ONTOLOGY_GRAPH_IMPORT_FAIL_IRI, + REASON_RESULT_GRAPH_IRI, + ): + client.graphs.delete_item(iri, skip_if_missing=True) @pytest.mark.parametrize("reasoner_parameter", REASONERS) @@ -82,7 +85,7 @@ def test_reason(setup: None, reasoner_parameter: str) -> None: # noqa: ARG001 imports="import_ontology", ).execute(inputs=(), context=TestExecutionContext()) - result = get_remote_graph(REASON_RESULT_GRAPH_IRI) + result = get_remote_graph(get_test_client(), REASON_RESULT_GRAPH_IRI) test = Graph().parse( data=replace_uuid(f"{FIXTURE_DIR}/test_{reasoner_parameter}.ttl"), format="turtle" ) @@ -163,7 +166,7 @@ def test_reason_ontology_import(setup: None) -> None: # noqa: ARG001 ignore_missing_imports=True, ).execute(inputs=(), context=TestExecutionContext()) - assert not json.loads(get(query=ASK_QUERY)).get("boolean", True) + assert not get_test_client().store.sparql.query(ASK_QUERY).askAnswer def test_reason_ontology_import_2(setup: None) -> None: # noqa: ARG001 @@ -181,4 +184,4 @@ def test_reason_ontology_import_2(setup: None) -> None: # noqa: ARG001 ignore_missing_imports=True, ).execute(inputs=(), context=TestExecutionContext()) - assert json.loads(get(query=ASK_QUERY)).get("boolean", False) + assert get_test_client().store.sparql.query(ASK_QUERY).askAnswer diff --git a/tests/test_validate.py b/tests/test_validate.py index fe40bb4..4b02668 100644 --- a/tests/test_validate.py +++ b/tests/test_validate.py @@ -1,13 +1,10 @@ """Plugin tests.""" from collections.abc import Generator -from contextlib import suppress from typing import Any import pytest -from cmem.cmempy.dp.proxy.graph import delete -from cmem.cmempy.workspace.projects.project import delete_project, make_new_project -from cmem.cmempy.workspace.projects.resources.resource import get_resource +from cmem_client.models.project import Project from cmem_plugin_base.dataintegration.entity import Entities from cmem_plugin_base.testing import TestExecutionContext from rdflib import Graph @@ -15,7 +12,14 @@ from cmem_plugin_reason.plugin_validate import ValidatePlugin from cmem_plugin_reason.utils import REASONERS -from tests.utils import FIXTURE_DIR, UID, get_bytes_io, get_remote_graph, import_graph, replace_uuid +from tests.utils import ( + FIXTURE_DIR, + UID, + get_remote_graph, + get_test_client, + import_graph, + replace_uuid, +) VALIDATE_ONTOLOGY_GRAPH_IRI_1 = f"https://ns.eccenca.com/validateontology/{UID}/vocab/" VALIDATE_ONTOLOGY_GRAPH_IRI_2 = f"https://ns.eccenca.com/validateontology/{UID}/vocab2/" @@ -44,32 +48,36 @@ def reasoner_parameter() -> str | None: @pytest.fixture def setup() -> Generator[None, Any]: """Set up Validate test""" - with suppress(Exception): - delete_project(PROJECT_ID) - delete(VALIDATE_RESULT_GRAPH_IRI) + client = get_test_client() + client.projects.delete_item(PROJECT_ID, skip_if_missing=True) + client.graphs.delete_item(VALIDATE_RESULT_GRAPH_IRI, skip_if_missing=True) - make_new_project(PROJECT_ID) + client.projects.create_item(Project(name=PROJECT_ID)) import_graph( - VALIDATE_ONTOLOGY_GRAPH_IRI_1, get_bytes_io(f"{FIXTURE_DIR}/test_validate_ontology_1.ttl") + client, VALIDATE_ONTOLOGY_GRAPH_IRI_1, f"{FIXTURE_DIR}/test_validate_ontology_1.ttl" ) import_graph( - VALIDATE_ONTOLOGY_GRAPH_IRI_2, get_bytes_io(f"{FIXTURE_DIR}/test_validate_ontology_2.ttl") + client, VALIDATE_ONTOLOGY_GRAPH_IRI_2, f"{FIXTURE_DIR}/test_validate_ontology_2.ttl" ) import_graph( - VALIDATE_ONTOLOGY_GRAPH_IRI_3, get_bytes_io(f"{FIXTURE_DIR}/test_validate_ontology_3.ttl") + client, VALIDATE_ONTOLOGY_GRAPH_IRI_3, f"{FIXTURE_DIR}/test_validate_ontology_3.ttl" ) import_graph( - ONTOLOGY_GRAPH_IMPORT_FAIL_IRI, get_bytes_io(f"{FIXTURE_DIR}/test_reason_ontology_4.ttl") + client, ONTOLOGY_GRAPH_IMPORT_FAIL_IRI, f"{FIXTURE_DIR}/test_reason_ontology_4.ttl" ) yield - delete(VALIDATE_ONTOLOGY_GRAPH_IRI_1) - delete(VALIDATE_ONTOLOGY_GRAPH_IRI_2) - delete(VALIDATE_ONTOLOGY_GRAPH_IRI_3) - delete(ONTOLOGY_GRAPH_IMPORT_FAIL_IRI) - delete(VALIDATE_RESULT_GRAPH_IRI) - delete_project(PROJECT_ID) + client = get_test_client() + for iri in ( + VALIDATE_ONTOLOGY_GRAPH_IRI_1, + VALIDATE_ONTOLOGY_GRAPH_IRI_2, + VALIDATE_ONTOLOGY_GRAPH_IRI_3, + ONTOLOGY_GRAPH_IMPORT_FAIL_IRI, + VALIDATE_RESULT_GRAPH_IRI, + ): + client.graphs.delete_item(iri, skip_if_missing=True) + client.projects.delete_item(PROJECT_ID, skip_if_missing=True) @pytest.mark.parametrize("reasoner_parameter", REASONERS) @@ -85,9 +93,10 @@ def test_validate(setup: None, reasoner_parameter: str) -> None: # noqa: ARG001 mode="inconsistency", ).execute(inputs=(), context=TestExecutionContext(PROJECT_ID)) + client = get_test_client() md_test = replace_uuid(f"{FIXTURE_DIR}/test_validate_{reasoner_parameter}.md") value_dict = get_value_dict(result) - output_graph = get_remote_graph(VALIDATE_RESULT_GRAPH_IRI) + output_graph = get_remote_graph(client, VALIDATE_RESULT_GRAPH_IRI) test = Graph().parse( data=replace_uuid(f"{FIXTURE_DIR}/test_validate_output_{reasoner_parameter}.ttl"), format="turtle", @@ -102,7 +111,7 @@ def test_validate(setup: None, reasoner_parameter: str) -> None: # noqa: ARG001 val_errors += 'EntityPath "reasoner" output error. ' if value_dict["valid_profiles"] != "Full,DL,EL,QL,RL": val_errors += 'EntityPath "valid_profiles" output error. ' - if md_test != get_resource(PROJECT_ID, MD_FILENAME).decode(): + if md_test != client.files.read(f"{PROJECT_ID}:{MD_FILENAME}").decode(): val_errors += "Markdown file error. " if not isomorphic(output_graph, test): val_errors += "Output graph error. " diff --git a/tests/utils.py b/tests/utils.py index 6710397..348e662 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -1,39 +1,52 @@ """Common functions""" -from io import BytesIO from pathlib import Path +from tempfile import TemporaryDirectory -from cmem.cmempy.dp.proxy.graph import get, post_streamed +from cmem_client.client import Client +from cmem_client.repositories.graphs import GraphExportConfig, GraphsRepository +from cmem_client.repositories.protocols.import_item import ImportConflictPolicy +from cmem_plugin_base.dataintegration.client import get_client +from cmem_plugin_base.testing import TestPluginContext from rdflib import DCTERMS, OWL, RDF, Graph, URIRef UID = "e02aaed014c94e0c91bf960fed127750" FIXTURE_DIR = Path(__file__).parent / "fixture_dir" +TTL_EXPORT_CONFIG = GraphExportConfig(serialization=GraphsRepository.formats["turtle"]) -def get_remote_graph(iri: str) -> Graph: + +def get_test_client() -> Client: + """Get a cmem-client for the test user + + A new client with a new context is returned on every call: TestUserContext requests + its access token once on creation and never refreshes it, and the client's + repositories cache the remote state on first access, while the plugins under test + change that state with their own client. + """ + return get_client(TestPluginContext()) + + +def get_remote_graph(client: Client, iri: str) -> Graph: """Get remote graph IRI""" - graph = Graph().parse( - data=get(iri, owl_imports_resolution=False).text, - format="turtle", - ) + with TemporaryDirectory() as temp: + path = Path(temp) / "graph.ttl" + client.graphs.export_item(key=iri, path=path, configuration=TTL_EXPORT_CONFIG) + graph = Graph().parse(source=path, format="turtle") graph.remove((URIRef(iri), DCTERMS.created, None)) graph.remove((None, RDF.type, OWL.AnnotationProperty)) return graph -def import_graph(iri: str, file: BytesIO) -> None: +def import_graph(client: Client, iri: str, filepath: str) -> None: """Import graph to CMEM""" - res = post_streamed(iri, file, replace=True) - if res.status_code != 204: # noqa: PLR2004 - raise ValueError(f"Response {res.status_code}: {res.url}") + with TemporaryDirectory() as temp: + path = Path(temp) / Path(filepath).name + path.write_text(replace_uuid(filepath), encoding="utf-8") + client.graphs.import_item(path=path, key=iri, on_conflict=ImportConflictPolicy.REPLACE) def replace_uuid(filepath: str) -> str: """Replace {uuid} in input files""" return Path(filepath).read_text().replace("{uuid}", UID) - - -def get_bytes_io(filepath: str) -> BytesIO: - """Get BytesIO object from filepath""" - return BytesIO(replace_uuid(filepath).encode(encoding="utf-8"))