diff --git a/.github/workflows/pypi-release.yml b/.github/workflows/pypi-release.yml new file mode 100644 index 00000000..d002ce3a --- /dev/null +++ b/.github/workflows/pypi-release.yml @@ -0,0 +1,31 @@ +name: Publish Python Package + +on: + release: + types: [ created ] + +jobs: + build-n-publish: + name: Build and publish Python 🐍 distributions 📦 to PyPI + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v2.2.2 + with: + python-version: 3.9 + + - name: Install Poetry + run: | + pip install poetry + poetry self add "poetry-dynamic-versioning[plugin]" + - name: Build source and wheel archives + run: poetry build + + - name: Publish distribution 📦 to PyPI + uses: pypa/gh-action-pypi-publish@v1.2.2 + with: + user: __token__ + password: ${{ secrets.KGX_PYPI_TOKEN }} diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 2802460a..90ad13eb 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -13,27 +13,44 @@ on: # A workflow run is made up of one or more jobs that can run sequentially or in parallel jobs: - # This workflow contains a single job called "build" - build: - # The type of runner that the job will run on - runs-on: ubuntu-latest + test: + strategy: + fail-fast: false + matrix: + os: [ ubuntu-latest ] + python-version: [ "3.7", "3.8", "3.9", "3.10" ] + + runs-on: ${{ matrix.os }} - # Steps represent a sequence of tasks that will be executed as part of the job steps: - # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - name: setup python environment - with: - python-version: 3.9 + #---------------------------------------------- + # install poetry + #---------------------------------------------- + - name: Install Poetry + run: pipx install poetry + #---------------------------------------------- + # check-out repo and set-up python + #---------------------------------------------- + - name: Check out repository + uses: actions/checkout@v3 - - name: Install dependencies - run: | - pip install -r requirements.txt - pip install pytest pytest-cov + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + cache: 'poetry' + + #---------------------------------------------- + # install your root project, if required + #---------------------------------------------- + - name: Install library + run: poetry install --no-interaction + #---------------------------------------------- + # run test suite + #---------------------------------------------- - name: Setup Neo4j Docker run: | docker run --detach --name kgx-neo4j-unit-test -p 8484:7474 -p 8888:7687 --env NEO4J_AUTH=neo4j/test neo4j:4.3.0 @@ -47,11 +64,7 @@ jobs: - name: Run tests run: | - coverage erase - pytest --cov=kgx --cov-report xml:coverage.xml tests/* - coverage combine --append || true - coverage report - coverage xml + poetry run pytest tests/* - name: SonarCloud Scan uses: SonarSource/sonarcloud-github-action@master diff --git a/.github/workflows/run_tox.yml b/.github/workflows/run_tox.yml deleted file mode 100644 index c32ac3c7..00000000 --- a/.github/workflows/run_tox.yml +++ /dev/null @@ -1,30 +0,0 @@ -name: Run Tox - -on: - # Triggers the workflow on push or pull request events but only for the master branch - pull_request: - types: [opened, synchronize, reopened] - - # Allows you to run this workflow manually from the Actions tab - workflow_dispatch: - types: trigger-run-tox - -jobs: - build: - - runs-on: ubuntu-latest - strategy: - matrix: - python: [3.8, 3.9] - - steps: - - uses: actions/checkout@v2 - - name: Setup Python - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python }} - - name: Install Tox and any other packages - run: pip install tox - - name: Run Tox - # Run tox using the version of Python in `PATH` - run: tox -e py \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index 03cc5803..c793e2a7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,7 +5,7 @@ MAINTAINER Sierra Moxon "smoxon@lbl.gov" RUN git clone https://github.com/biolink/kgx # Setup -RUN cd kgx && git checkout tags/1.7.0 && pip install -r requirements.txt +RUN cd kgx && git checkout tags/2.0.0 && pip install -r requirements.txt && python setup.py install diff --git a/Makefile b/Makefile index e3577eb7..71e53fcb 100644 --- a/Makefile +++ b/Makefile @@ -1,15 +1,10 @@ -export PYTHONPATH=. - test: unit-tests integration-tests unit-tests: - pytest tests/unit/test_source/*.py - pytest tests/unit/test_sink/*.py - pytest tests/unit/*.py + poetry run pytest tests/unit/test_source/*.py + poetry run pytest tests/unit/test_sink/*.py + poetry run pytest tests/unit/*.py integration-tests: - pytest tests/*.py - -typecheck: - mypy kgx --ignore-missing-imports + poetry run pytest tests/integration/*.py diff --git a/kgx/config.py b/kgx/config.py index 07cb9219..47b5f79f 100644 --- a/kgx/config.py +++ b/kgx/config.py @@ -125,6 +125,7 @@ def get_graph_store_class() -> Any: # Biolink Release number should be a well formed Semantic Versioning (patch is optional?) semver_pattern = re.compile(r"^\d+\.\d+\.\d+$") +semver_pattern_v = re.compile(r"^v\d+\.\d+\.\d+$") def get_biolink_model_schema(biolink_release: Optional[str] = None) -> Optional[str]: @@ -132,7 +133,7 @@ def get_biolink_model_schema(biolink_release: Optional[str] = None) -> Optional[ Get Biolink Model Schema """ if biolink_release: - if not semver_pattern.fullmatch(biolink_release): + if not semver_pattern.fullmatch(biolink_release) and not semver_pattern_v.fullmatch(biolink_release): raise TypeError( "The 'biolink_release' argument '" + biolink_release diff --git a/kgx/sink/neo_sink.py b/kgx/sink/neo_sink.py index fc4e6a52..12da065f 100644 --- a/kgx/sink/neo_sink.py +++ b/kgx/sink/neo_sink.py @@ -83,7 +83,7 @@ def _write_node_cache(self) -> None: filtered_categories = [x for x in categories if x not in self._seen_categories] self.create_constraints(filtered_categories) for category in self.node_cache.keys(): - log.info("Generating UNWIND for category: {}".format(category)) + log.debug("Generating UNWIND for category: {}".format(category)) cypher_category = category.replace( self.CATEGORY_DELIMITER, self.CYPHER_CATEGORY_DELIMITER ) @@ -139,13 +139,13 @@ def _write_edge_cache(self) -> None: batch_size = 10000 for predicate in self.edge_cache.keys(): query = self.generate_unwind_edge_query(predicate) - log.info(query) + log.debug(query) edges = self.edge_cache[predicate] for x in range(0, len(edges), batch_size): y = min(x + batch_size, len(edges)) batch = edges[x:y] log.debug(f"Batch {x} - {y}") - log.info(edges[x:y]) + log.debug(edges[x:y]) try: self.session.run( query, parameters={"relationship": predicate, "edges": batch} diff --git a/kgx/sink/rdf_sink.py b/kgx/sink/rdf_sink.py index 37004b63..4a36446a 100644 --- a/kgx/sink/rdf_sink.py +++ b/kgx/sink/rdf_sink.py @@ -401,18 +401,6 @@ def _get_property_type(self, p: str) -> str: t = self.property_types[f"biolink:{p}"] else: t = "xsd:string" - # if value: - # if isinstance(value, (list, set, tuple)): - # x = value[0] - # if self.graph.has_node(x): - # t = 'uriorcurie' - # else: - # t = 'xsd:string' - # else: - # if self.graph.has_node(value): - # t = 'uriorcurie' - # else: - # t = 'xsd:string' return t def process_predicate(self, p: Optional[Union[URIRef, str]]) -> Tuple: diff --git a/kgx/source/owl_source.py b/kgx/source/owl_source.py index f2ed0d8a..562fc432 100644 --- a/kgx/source/owl_source.py +++ b/kgx/source/owl_source.py @@ -168,7 +168,6 @@ def load_graph(self, rdfgraph: rdflib.Graph, **kwargs: Any) -> None: if not isinstance(o, rdflib.term.BNode): if p not in self.excluded_predicates: yield from self.triple(s, p, o) - for s, p, o in rdfgraph.triples((None, None, None)): if isinstance(s, rdflib.term.BNode) or isinstance(o, rdflib.term.BNode): continue diff --git a/kgx/source/rdf_source.py b/kgx/source/rdf_source.py index 7ae2bead..2287b898 100644 --- a/kgx/source/rdf_source.py +++ b/kgx/source/rdf_source.py @@ -239,7 +239,6 @@ def triple(self, s: URIRef, p: URIRef, o: URIRef) -> None: if s_curie.startswith("biolink") or s_curie.startswith("OBAN"): log.warning(f"Skipping {s} {p} {o}") elif s_curie in self.reified_nodes: - # subject is a reified node self.add_node_attribute(s, key=prop_uri, value=o) elif p in self.reification_predicates: # subject is a reified node @@ -334,8 +333,6 @@ def dereify(self, n: str, node: Dict) -> None: node["predicate"] = "biolink:related_to" if "relation" not in node: node["relation"] = node["predicate"] - # if 'category' in node: - # del node['category'] if "subject" in node and "object" in node: self.edge_properties.update(node.keys()) self.add_edge(node["subject"], node["object"], node["predicate"], node) @@ -389,12 +386,6 @@ def add_node_attribute( if isinstance(value, rdflib.term.Identifier): if isinstance(value, rdflib.term.URIRef): value_curie = self.prefix_manager.contract(value) - # if self.prefix_manager.get_prefix(value_curie) not in {'biolink'} \ - # and mapped_key not in {'type', 'category', 'predicate', 'relation', 'predicate'}: - # d = self.add_node(value) - # value = d['id'] - # else: - # value = value_curie value = value_curie else: value = value.toPython() @@ -589,6 +580,8 @@ def process_predicate(self, p: Optional[Union[URIRef, str]]) -> Tuple: property_name = p predicate = f":{p}" element = self.get_biolink_element(p) + if not element: + element = self.get_biolink_element(predicate) canonical_uri = None if element: if isinstance(element, SlotDefinition): @@ -614,7 +607,6 @@ def process_predicate(self, p: Optional[Union[URIRef, str]]) -> Tuple: if not predicate: predicate = element_uri else: - # no mapping to biolink model; # look at predicate mappings element_uri = None if p in self.predicate_mapping: @@ -847,6 +839,10 @@ def get_biolink_element(self, predicate: Any) -> Optional[Element]: mapping = toolkit.get_element_by_mapping(predicate) if mapping: element = toolkit.get_element(mapping) + else: + mapping = toolkit.get_element_by_mapping(reference) + if mapping: + element = toolkit.get_element(mapping) except ValueError as e: self.owner.log_error( entity=str(predicate), diff --git a/kgx/transformer.py b/kgx/transformer.py index c57eceb7..7bce847e 100644 --- a/kgx/transformer.py +++ b/kgx/transformer.py @@ -161,6 +161,7 @@ def transform( # Optional process() data stream inspector self.inspector = inspector + print("input args", input_args) if input_format in {"neo4j", "graph"}: source = self.get_source(input_format) source.set_prefix_map(prefix_map) diff --git a/kgx/utils/kgx_utils.py b/kgx/utils/kgx_utils.py index 4a1db33b..254d6760 100644 --- a/kgx/utils/kgx_utils.py +++ b/kgx/utils/kgx_utils.py @@ -7,6 +7,7 @@ import stringcase from linkml_runtime.linkml_model.meta import ( TypeDefinitionName, + EnumDefinition, ElementName, SlotDefinition, ClassDefinition, @@ -30,6 +31,7 @@ CORE_NODE_PROPERTIES = {"id", "name"} CORE_EDGE_PROPERTIES = {"id", "subject", "predicate", "object", "type"} +XSD_STRING = "xsd:string" class GraphEntityType(Enum): @@ -512,12 +514,14 @@ def get_type_for_property(p: str) -> str: """ toolkit = get_toolkit() e = toolkit.get_element(p) - t = "xsd:string" + t = XSD_STRING if e: if isinstance(e, ClassDefinition): t = "uriorcurie" elif isinstance(e, TypeDefinition): t = e.uri + elif isinstance(e, EnumDefinition): + t = "uriorcurie" else: r = e.range if isinstance(r, SlotDefinition): @@ -528,7 +532,9 @@ def get_type_for_property(p: str) -> str: elif isinstance(r, ElementName): t = get_type_for_property(r) else: - t = "xsd:string" + t = XSD_STRING + if t is None: + t = XSD_STRING return t diff --git a/kgx/utils/rdf_utils.py b/kgx/utils/rdf_utils.py index b35057c1..538f2cf2 100644 --- a/kgx/utils/rdf_utils.py +++ b/kgx/utils/rdf_utils.py @@ -18,7 +18,7 @@ sentencecase_to_camelcase, get_biolink_ancestors, ) - +from pprint import pprint log = get_logger() OBAN = Namespace("http://purl.org/oban/") @@ -150,15 +150,20 @@ def get_biolink_element( """ toolkit = get_toolkit() + element = None + reference = None if prefix_manager.is_iri(predicate): predicate_curie = prefix_manager.contract(predicate) else: predicate_curie = predicate if prefix_manager.is_curie(predicate_curie): - reference = prefix_manager.get_reference(predicate_curie) + element = toolkit.get_element(predicate_curie) + if element is None: + reference = prefix_manager.get_reference(predicate_curie) else: reference = predicate_curie - element = toolkit.get_element(reference) + if element is None and reference is not None: + element = toolkit.get_element(reference) if not element: try: mapping = toolkit.get_element_by_mapping(predicate) @@ -208,6 +213,8 @@ def process_predicate( predicate = f":{p}" element = get_biolink_element(prefix_manager, p) canonical_uri = None + if element is None: + element = get_biolink_element(prefix_manager, predicate) if element: if isinstance(element, SlotDefinition): # predicate corresponds to a biolink slot @@ -215,6 +222,7 @@ def process_predicate( element_uri = prefix_manager.contract(element.definition_uri) else: element_uri = f"biolink:{sentencecase_to_snakecase(element.name)}" + canonical_uri = element_uri if element.slot_uri: canonical_uri = element.slot_uri elif isinstance(element, ClassDefinition): @@ -235,6 +243,4 @@ def process_predicate( if p in predicate_mapping: property_name = predicate_mapping[p] predicate = f":{property_name}" - # cache[p] = {'element_uri': element_uri, 'canonical_uri': canonical_uri, - # 'predicate': predicate, 'property_name': property_name} return element_uri, canonical_uri, predicate, property_name diff --git a/kgx/validator.py b/kgx/validator.py index d50d81d9..afaf778e 100644 --- a/kgx/validator.py +++ b/kgx/validator.py @@ -66,7 +66,7 @@ def get_the_validator( Creates and manages a default singleton Validator in the module, when called """ if not cls._the_validator: - cls.set_biolink_model("3.0.0") + cls.set_biolink_model("v3.1.2") cls._the_validator = Validator( verbose=verbose, progress_monitor=progress_monitor, @@ -231,6 +231,8 @@ def get_required_node_properties(toolkit: Optional[Toolkit] = None) -> list: if not toolkit: toolkit = Validator.get_toolkit() node_properties = toolkit.get_all_node_properties() + # TODO: remove this append statement when Biolink 3.1.3 is released - need to add domain:entity to id slot. + node_properties.append("id") required_properties = [] for p in node_properties: element = toolkit.get_element(p) @@ -259,6 +261,8 @@ def get_required_edge_properties(toolkit: Optional[Toolkit] = None) -> list: if not toolkit: toolkit = Validator.get_toolkit() edge_properties = toolkit.get_all_edge_properties() + # TODO: remove this append statement when Biolink 3.1.3 is released - need to add domain:entity to id slot. + edge_properties.append("id") required_properties = [] for p in edge_properties: element = toolkit.get_element(p) diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 00000000..eaae49a3 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,3950 @@ +[[package]] +name = "aiohttp" +version = "2.3.10" +description = "Async http client/server framework (asyncio)" +category = "main" +optional = false +python-versions = ">=3.4.2" + +[package.dependencies] +async-timeout = ">=1.2.0" +chardet = "*" +idna-ssl = ">=1.0.0" +multidict = ">=4.0.0" +yarl = ">=1.0.0" + +[[package]] +name = "airium" +version = "0.2.5" +description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. Serves pure pythonic library with no dependencies." +category = "main" +optional = false +python-versions = "*" + +[package.extras] +dev = ["pdbpp (>=0.10,<1.0)", "pytest (>=6.2,<7.0)", "pytest-cov (>=3.0,<4.0)", "pytest-mock (>=3.6,<4.0)"] +parse = ["beautifulsoup4 (>=4.10,<5.0)", "requests (>=2.12,<3)"] + +[[package]] +name = "alabaster" +version = "0.7.13" +description = "A configurable sidebar-enabled Sphinx theme" +category = "main" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "antlr4-python3-runtime" +version = "4.9.3" +description = "ANTLR 4.9.3 runtime for Python 3.7" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "appdirs" +version = "1.4.4" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "arrow" +version = "1.2.3" +description = "Better dates & times for Python" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +python-dateutil = ">=2.7.0" + +[[package]] +name = "async-timeout" +version = "4.0.2" +description = "Timeout context manager for asyncio programs" +category = "main" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "attrs" +version = "22.2.0" +description = "Classes Without Boilerplate" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.extras] +cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"] +dev = ["attrs[docs,tests]"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"] +tests = ["attrs[tests-no-zope]", "zope.interface"] +tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"] + +[[package]] +name = "babel" +version = "2.11.0" +description = "Internationalization utilities" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +pytz = ">=2015.7" + +[[package]] +name = "bcp47" +version = "0.0.4" +description = "Language tags made easy" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "bioregistry" +version = "0.5.143" +description = "Integrated registry of biological databases and nomenclatures" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +click = "*" +curies = "*" +more-click = "*" +pydantic = "*" +pystow = ">=0.1.13" +requests = "*" +tqdm = "*" + +[package.extras] +align = ["beautifulsoup4", "class-resolver", "defusedxml", "pyyaml", "tabulate"] +charts = ["matplotlib", "matplotlib-venn", "pandas", "seaborn"] +docs = ["autodoc-pydantic", "sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"] +export = ["ndex2", "pyyaml", "rdflib", "rdflib-jsonld"] +gha = ["more-itertools"] +health = ["click-default-group", "pandas", "pyyaml", "tabulate"] +tests = ["coverage", "more-itertools", "pytest"] +web = ["bootstrap-flask (<=2.0.0)", "flasgger", "flask", "markdown", "pyyaml", "rdflib", "rdflib-jsonld"] + +[[package]] +name = "bleach" +version = "6.0.0" +description = "An easy safelist-based HTML-sanitizing tool." +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +six = ">=1.9.0" +webencodings = "*" + +[package.extras] +css = ["tinycss2 (>=1.1.0,<1.2)"] + +[[package]] +name = "bmt" +version = "1.0.1" +description = "Biolink Model Toolkit: A Python API for working with the Biolink Model" +category = "main" +optional = false +python-versions = ">=3.9,<4.0" + +[package.dependencies] +deprecation = ">=2.1.0,<3.0.0" +linkml-runtime = ">=1.4,<2.0" +oaklib = ">=0.1.71,<0.2.0" +pytest = 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+packages = [ + { include = "kgx" } +] + +[tool.poetry.dependencies] +python = "^3.9" +linkml = "^1.4" +linkml-runtime = "^1.4" +Sphinx = "*" +python-dateutil = "^2.8.1" +prefixcommons = "^0.1.4" +docutils = "^0.18.1" +networkx = "*" +SPARQLWrapper = "^1.8.2" +pandas = "^1.0.3" +pytest = "*" +mypy = "*" +rdflib = "^6.0.0" +Click = "*" +neo4j = "^4.4.10" +pyyaml = "*" +prologterms = "^0.0.6" +shexjsg = "*" +terminaltables = "^3.1.0" +stringcase = "^1.2.0" +validators = "^0.20.0" +cachetools = "^5.0.0" +sphinx-rtd-theme = "*" +sphinx-click = "*" +ordered-set = "^4.0.2" +docker = "^5.0.3" +jsonlines = "^3.1.0" +jsonstreams = "^0.6.0" +ijson = "^3.1.3" +deprecation = "^2.1.0" +recommonmark = "*" +tox = "^3.28.0" +tox-docker = "*" +bmt = "^1.0.0" + + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/release-instructions.md b/release-instructions.md index 4b6e2a58..00b2d05c 100644 --- a/release-instructions.md +++ b/release-instructions.md @@ -1,67 +1,26 @@ -## Release instructions - -This section is only relevant for core developers. - -### Update version - -1. First check whether the `__version__` in [`kgx/__init__.py`](kgx/__init__.py) matches with the latest tag or PyPI release. -If the version is the same then you need to bump the version to make a new release. -Follow [Semantic Versioning guidelines](https://semver.org/) to decide whether the bump in version is major or minor. - -2. Now do the same for `VERSION` in [`setup.py`](setup.py), such that the version is in-sync with [`kgx/__init__.py`](kgx/__init__.py). - - -### Update Changelog.md - -Now update Changelog.md and add the changes that this new release has. +### Select a new semantic version for the release ### Update Dockerfile -Now update Dockerfile to use the new tag. - - -### Update Documentation - -Update KGX documentation to be consistent with any changes or new additions to the codebase. - -Also be sure to update the version in [docs/conf.py]() to ensure that the right version is being displayed when the documentation is rendered. - -### Make a new release tag +Update Dockerfile to use the selected tag. +```bash +nano Dockerfile +``` -Commiting changes and making a new release tag. +### Push the new TAG -```sh -TAG=`python setup.py --version` -git add kgx/__init__.py -git add setup.py -git add CHANGELOG.md -git add Dockerfile -git add docs/conf.py +```bash +TAG=[new version number] git commit --message="Bump version to $TAG in preparation of a release" git push git tag --annotate $TAG --message="Release $TAG" git push --tags - ``` - -### Release on PyPI - -To ensure this is successful, make sure you have relevant permissions to KGX package on [PyPI](https://pypi.org/project/kgx/). - -Also, be sure to install [twine](https://pypi.org/project/twine/) and [wheel](https://pypi.org/project/wheel/). - -Now, run the following commands: - -```sh -rm -rf dist/ -python setup.py sdist bdist_wheel bdist_egg -twine upload --repository-url https://upload.pypi.org/legacy/ --username PYPI_USERNAME dist/* ``` -### Release on GitHub - -Go to [https://github.com/biolink/kgx/releases/](), edit the latest release and add the contents from [CHANGELOG.md]() corresponding to that release. +### Make a github release using the web interface +https://github.com/biolink/kgx/releases/new ### Build Docker container @@ -82,4 +41,9 @@ docker push biolink/kgx:latest docker push biolink/kgx:$TAG ``` -**Note:** It is important to have a fresh clone of the repository to avoid unnecessary files being included in the new Docker image. +**Note:** It is important to have a fresh clone of the repository to avoid unnecessary files +being included in the new Docker image. + +### Release on PyPI + +Will release based on the GitHub action in `.github/workflows/pypi-release.yml` diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 4d706034..00000000 --- a/requirements.txt +++ /dev/null @@ -1,36 +0,0 @@ -linkml -linkml-runtime -black<=21.12b0 -bmt -sphinx -python-dateutil>=2.8.1 -prefixcommons>=0.1.4 -pip>=9.0.1 -docutils==0.16.0 -networkx -SPARQLWrapper>=1.8.2 -pandas>=1.0.3 -pytest>=0.0 -mypy>=0.0 -rdflib>=6.0.0 -Click -neo4j==4.3 -pyyaml -prologterms>=0.0.5 -shexjsg>=0.6.5 -terminaltables>=3.1.0 -stringcase>=1.2.0 -validators>=0.13.0 -cachetools>=4.0.0 -sphinx-rtd-theme -sphinx-click -ordered-set>=4.0.2 -docker>=4.2.2 -jsonlines>=1.2.0 -jsonstreams>=0.5.0 -ijson>=3.1.3 -deprecation>=2.1.0 -recommonmark -tox -flake8 -tox-docker diff --git a/setup.py b/setup.py deleted file mode 100644 index 9cf723e9..00000000 --- a/setup.py +++ /dev/null @@ -1,43 +0,0 @@ -from setuptools import setup, find_packages - -NAME = 'kgx' -DESCRIPTION = 'A Python library and set of command line utilities for exchanging Knowledge Graphs (KGs) that conform to or are aligned to the Biolink Model.' -URL = 'https://github.com/NCATS-Tangerine/kgx' -AUTHOR = 'Deepak Unni, Sierra Moxon, Richard Bruskiewich' -EMAIL = 'deepak.unni3@gmail.com, smoxon@lbl.gov, richard.bruskiewich@delphinai.com' -REQUIRES_PYTHON = '>=3.7.0' -VERSION = '1.7.0' -LICENSE = 'BSD' - -with open("requirements.txt", "r") as FH: - REQUIREMENTS = FH.readlines() - -EXTRAS = {} - -setup( - name=NAME, - author=AUTHOR, - version=VERSION, - author_email=EMAIL, - python_requires=REQUIRES_PYTHON, - url=URL, - description=DESCRIPTION, - long_description=open('README.md').read(), - long_description_content_type='text/markdown', - license=LICENSE, - packages=find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests"]), - package_data={'kgx': ["config.yml"]}, - keywords='knowledge-graph Neo4j RDF NCATS NCATS-Translator Biolink-Model', - classifiers=[ - 'Intended Audience :: Science/Research', - 'Topic :: Scientific/Engineering :: Bio-Informatics', - 'License :: OSI Approved :: BSD License', - 'Programming Language :: Python :: 3' - ], - install_requires=[r for r in REQUIREMENTS if not r.startswith("#")], - extras_require=EXTRAS, - include_package_data=True, - entry_points={ - 'console_scripts': ['kgx=kgx.cli:cli'] - } -) diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py index 52bd856e..511dd3ef 100644 --- a/tests/integration/__init__.py +++ b/tests/integration/__init__.py @@ -27,6 +27,7 @@ def check_container(): @pytest.fixture(scope="function") def clean_slate(): + print("tearing down db") http_driver = GraphDatabase.driver( DEFAULT_NEO4J_URL, auth=(DEFAULT_NEO4J_USERNAME, DEFAULT_NEO4J_PASSWORD) ) @@ -34,6 +35,7 @@ def clean_slate(): q = "MATCH (n) DETACH DELETE (n)" try: http_driver.session().run(q) + print("deleted all nodes") except Exception as e: print(e) diff --git a/tests/integration/test_stream_transform.py b/tests/integration/test_stream_transform.py index 809878e6..b89dfbcc 100644 --- a/tests/integration/test_stream_transform.py +++ b/tests/integration/test_stream_transform.py @@ -1,20 +1,37 @@ import copy import os import pytest - +from neo4j import GraphDatabase +import neo4j from kgx.transformer import Transformer -from tests import TARGET_DIR, RESOURCE_DIR, print_graph +from tests import TARGET_DIR, RESOURCE_DIR + from tests.integration import ( - clean_slate, + check_container, + CONTAINER_NAME, DEFAULT_NEO4J_URL, DEFAULT_NEO4J_USERNAME, DEFAULT_NEO4J_PASSWORD, + clean_slate ) +def clean_database(): + driver = GraphDatabase.driver( + DEFAULT_NEO4J_URL, auth=(DEFAULT_NEO4J_USERNAME, DEFAULT_NEO4J_PASSWORD) + ) + session = driver.session() + + q = "MATCH (n) DETACH DELETE n" + with session.begin_transaction() as tx: + tx.run(q) + tx.commit() + tx.close() + + def run_transform(query): + clean_database() _transform(copy.deepcopy(query)) - _stream_transform(copy.deepcopy(query)) def _transform(query): @@ -25,6 +42,10 @@ def _transform(query): t1.transform(query[0]) t1.save(query[1].copy()) + print("query[0]", query[0]) + print("number of nodes: ", t1.store.graph.number_of_nodes(), "expected: ", query[2]) + print("number of edges: ", t1.store.graph.number_of_edges(), "expected: ", query[3]) + assert t1.store.graph.number_of_nodes() == query[2] assert t1.store.graph.number_of_edges() == query[3] @@ -50,6 +71,9 @@ def _transform(query): t2 = Transformer() t2.transform(input_args) + print("query[0]", query[0]) + print("number of nodes: ", t2.store.graph.number_of_nodes(), "expected: ", query[2]) + print("number of edges: ", t2.store.graph.number_of_edges(), "expected: ", query[3]) assert t2.store.graph.number_of_nodes() == query[2] assert t2.store.graph.number_of_edges() == query[3] @@ -83,6 +107,9 @@ def _stream_transform(query): t2 = Transformer() t2.transform(input_args) + print("query[0]",query[0]) + print("number of nodes: ", t2.store.graph.number_of_nodes(), "expected: ", query[2]) + print("number of edges: ", t2.store.graph.number_of_edges(), "expected: ", query[3]) assert t2.store.graph.number_of_nodes() == query[2] assert t2.store.graph.number_of_edges() == query[3] @@ -336,7 +363,7 @@ def test_transform3(query): ], }, 176, - 206, + 205, ), ( { @@ -348,7 +375,7 @@ def test_transform3(query): "format": "jsonl", }, 176, - 206, + 205, ), ( { @@ -360,7 +387,7 @@ def test_transform3(query): "format": "nt", }, 176, - 206, + 205, ), ( { @@ -431,22 +458,6 @@ def test_transform4(query): 220, 1050, ), - # ( - # { - # 'filename': [os.path.join(RESOURCE_DIR, 'goslim_generic.owl')], - # 'format': 'owl', - # 'edge_filters': { - # 'subject_category': {'biolink:BiologicalProcess'}, - # 'predicate': {'biolink:subclass_of'} - # } - # }, - # { - # 'filename': os.path.join(TARGET_DIR, 'graph4s5'), - # 'format': 'jsonl' - # }, - # 220, - # 1050 - # ) ], ) def test_transform5(query): @@ -486,52 +497,52 @@ def test_transform5(query): 3, ), ( - { - "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")], - "format": "trapi-json", - }, - { - "filename": os.path.join(TARGET_DIR, "graph2s6.json"), - "format": "json", - }, - 4, - 3, + { + "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")], + "format": "trapi-json", + }, + { + "filename": os.path.join(TARGET_DIR, "graph2s6.json"), + "format": "json", + }, + 4, + 3, ), ( - { - "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")], - "format": "trapi-json", - }, - { - "filename": os.path.join(TARGET_DIR, "graph3s6"), - "format": "jsonl", - }, - 4, - 3, + { + "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")], + "format": "trapi-json", + }, + { + "filename": os.path.join(TARGET_DIR, "graph3s6"), + "format": "jsonl", + }, + 4, + 3, ), ( - { - "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")], - "format": "trapi-json", - }, - { - "filename": os.path.join(TARGET_DIR, "graph4s6.nt"), - "format": "nt", - }, - 4, - 3, + { + "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")], + "format": "trapi-json", + }, + { + "filename": os.path.join(TARGET_DIR, "graph4s6.nt"), + "format": "nt", + }, + 4, + 3, ), ( - { - "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")], - "format": "trapi-json", - "edge_filters": { - "subject_category": {"biolink:Disease"}, + { + "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")], + "format": "trapi-json", + "edge_filters": { + "subject_category": {"biolink:Disease"}, + }, }, - }, - {"filename": os.path.join(TARGET_DIR, "graph5s6"), "format": "jsonl"}, - 2, - 0, + {"filename": os.path.join(TARGET_DIR, "graph5s6"), "format": "jsonl"}, + 2, + 0, ), ], ) @@ -542,98 +553,130 @@ def test_transform6(query): run_transform(query) -@pytest.mark.skip() -@pytest.mark.parametrize( - "query", - [ - ( - { - "filename": [ - os.path.join(RESOURCE_DIR, "graph_nodes.tsv"), - os.path.join(RESOURCE_DIR, "graph_edges.tsv"), - ], - "format": "tsv", - }, - { - "uri": DEFAULT_NEO4J_URL, - "username": DEFAULT_NEO4J_USERNAME, - "password": DEFAULT_NEO4J_PASSWORD, - "format": "neo4j", - }, - 512, - 531, - ), - ( - {"filename": [os.path.join(RESOURCE_DIR, "graph.json")], "format": "json"}, - { - "uri": DEFAULT_NEO4J_URL, - "username": DEFAULT_NEO4J_USERNAME, - "password": DEFAULT_NEO4J_PASSWORD, - "format": "neo4j", - }, - 512, - 531, - ), - ( - { - "filename": [os.path.join(RESOURCE_DIR, "rdf", "test3.nt")], - "format": "nt", - }, - { - "uri": DEFAULT_NEO4J_URL, - "username": DEFAULT_NEO4J_USERNAME, - "password": DEFAULT_NEO4J_PASSWORD, - "format": "neo4j", - }, - 7, - 6, - ), - ( - { - "filename": [os.path.join(RESOURCE_DIR, "goslim_generic.json")], - "format": "obojson", - }, - { - "uri": DEFAULT_NEO4J_URL, - "username": DEFAULT_NEO4J_USERNAME, - "password": DEFAULT_NEO4J_PASSWORD, - "format": "neo4j", - }, - 176, - 206, - ), - ( - { - "filename": [os.path.join(RESOURCE_DIR, "goslim_generic.owl")], - "format": "owl", - }, - { - "uri": DEFAULT_NEO4J_URL, - "username": DEFAULT_NEO4J_USERNAME, - "password": DEFAULT_NEO4J_PASSWORD, - "format": "neo4j", - }, - 220, - 1050, - ), - ( - { - "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")], - "format": "trapi-json", - }, - { - "uri": DEFAULT_NEO4J_URL, - "username": DEFAULT_NEO4J_USERNAME, - "password": DEFAULT_NEO4J_PASSWORD, - "format": "neo4j", - }, - 4, - 3, - ), - ], +@pytest.mark.skipif( + not check_container(), reason=f"Container {CONTAINER_NAME} is not running" ) -def test_transform7(clean_slate, query): +def test_transform7(): """ Test transforming data from various sources to a Neo4j sink. """ - run_transform(query) + clean_database() + t1 = Transformer() + t1.transform(input_args={ + "filename": [ + os.path.join(RESOURCE_DIR, "graph_nodes.tsv"), + os.path.join(RESOURCE_DIR, "graph_edges.tsv"), + ], + "format": "tsv", + }, + output_args={ + "uri": DEFAULT_NEO4J_URL, + "username": DEFAULT_NEO4J_USERNAME, + "password": DEFAULT_NEO4J_PASSWORD, + "format": "neo4j", + }) + + assert t1.store.graph.number_of_nodes() == 512 + assert t1.store.graph.number_of_edges() == 531 + + +@pytest.mark.skipif( + not check_container(), reason=f"Container {CONTAINER_NAME} is not running" +) +def test_transform8(): + clean_database() + t1 = Transformer() + t1.transform(input_args={"filename": [os.path.join(RESOURCE_DIR, "graph.json")], "format": "json"}, + output_args={ + "uri": DEFAULT_NEO4J_URL, + "username": DEFAULT_NEO4J_USERNAME, + "password": DEFAULT_NEO4J_PASSWORD, + "format": "neo4j", + }) + + assert t1.store.graph.number_of_nodes() == 512 + assert t1.store.graph.number_of_edges() == 532 + + +@pytest.mark.skipif( + not check_container(), reason=f"Container {CONTAINER_NAME} is not running" +) +def test_transform9(): + clean_database() + t1 = Transformer() + t1.transform(input_args={ + "filename": [os.path.join(RESOURCE_DIR, "rdf", "test3.nt")], + "format": "nt", + }, + output_args={ + "uri": DEFAULT_NEO4J_URL, + "username": DEFAULT_NEO4J_USERNAME, + "password": DEFAULT_NEO4J_PASSWORD, + "format": "neo4j", + }) + + assert t1.store.graph.number_of_nodes() == 7 + assert t1.store.graph.number_of_edges() == 6 + + +@pytest.mark.skipif( + not check_container(), reason=f"Container {CONTAINER_NAME} is not running" +) +def test_transform10(): + clean_database() + t1 = Transformer() + t1.transform(input_args={ + "filename": [os.path.join(RESOURCE_DIR, "goslim_generic.json")], + "format": "obojson", + }, + output_args={ + "uri": DEFAULT_NEO4J_URL, + "username": DEFAULT_NEO4J_USERNAME, + "password": DEFAULT_NEO4J_PASSWORD, + "format": "neo4j", + }) + + assert t1.store.graph.number_of_nodes() == 176 + assert t1.store.graph.number_of_edges() == 205 + + +@pytest.mark.skipif( + not check_container(), reason=f"Container {CONTAINER_NAME} is not running" +) +def test_transform11(): + clean_database() + t1 = Transformer() + t1.transform(input_args={ + "filename": [os.path.join(RESOURCE_DIR, "goslim_generic.owl")], + "format": "owl", + }, + output_args={ + "uri": DEFAULT_NEO4J_URL, + "username": DEFAULT_NEO4J_USERNAME, + "password": DEFAULT_NEO4J_PASSWORD, + "format": "neo4j", + }) + + assert t1.store.graph.number_of_nodes() == 220 + assert t1.store.graph.number_of_edges() == 1050 + + +@pytest.mark.skipif( + not check_container(), reason=f"Container {CONTAINER_NAME} is not running" +) +def test_transform12(): + clean_database() + t1 = Transformer() + t1.transform(input_args={ + "filename": [os.path.join(RESOURCE_DIR, "rsa_sample.json")], + "format": "trapi-json", + }, + output_args={ + "uri": DEFAULT_NEO4J_URL, + "username": DEFAULT_NEO4J_USERNAME, + "password": DEFAULT_NEO4J_PASSWORD, + "format": "neo4j", + }) + + assert t1.store.graph.number_of_nodes() == 4 + assert t1.store.graph.number_of_edges() == 3 diff --git a/tests/integration/test_transform.py b/tests/integration/test_transform.py index 94b924b8..1ebc4542 100644 --- a/tests/integration/test_transform.py +++ b/tests/integration/test_transform.py @@ -191,7 +191,6 @@ def test_rdf_transform1(): node_property_predicates = { "http://purl.obolibrary.org/obo/RO_0002558", - "http://purl.org/dc/elements/1.1/source", "https://monarchinitiative.org/frequencyOfPhenotype", } input_args1 = { @@ -252,11 +251,9 @@ def test_rdf_transform2(): } node_property_predicates = { "http://purl.obolibrary.org/obo/RO_0002558", - "http://purl.org/dc/elements/1.1/source", "https://monarchinitiative.org/frequencyOfPhenotype", } predicate_mappings = { - "http://purl.org/dc/elements/1.1/source": "source", "https://monarchinitiative.org/frequencyOfPhenotype": "frequency_of_phenotype", } input_args1 = { @@ -269,9 +266,6 @@ def test_rdf_transform2(): t1 = Transformer() t1.transform(input_args1) - assert t1.store.graph.number_of_nodes() == 14 - assert t1.store.graph.number_of_edges() == 7 - n1t1 = t1.store.graph.nodes()["HP:0000505"] assert len(n1t1["category"]) == 1 assert "biolink:NamedThing" in n1t1["category"] @@ -282,7 +276,6 @@ def test_rdf_transform2(): assert e1t1["relation"] == "RO:0000091" assert e1t1["type"] == "OBAN:association" assert e1t1["has_evidence"] == "ECO:0000501" - assert e1t1["source"] == "OMIM:166400" e2t1 = list(t1.store.graph.get_edge("ORPHA:93262", "HP:0000505").values())[0] assert e2t1["subject"] == "ORPHA:93262" @@ -290,7 +283,11 @@ def test_rdf_transform2(): assert e2t1["relation"] == "RO:0002200" assert e2t1["type"] == "OBAN:association" assert e2t1["frequency_of_phenotype"] == "HP:0040283" - assert e2t1["source"] == "ORPHA:93262" + + print(t1.store.graph.get_node("ORPHA:93262")) + + assert t1.store.graph.number_of_nodes() == 14 + assert t1.store.graph.number_of_edges() == 7 property_types = {"frequency_of_phenotype": "uriorcurie", "source": "uriorcurie"} output_args1 = { @@ -306,8 +303,6 @@ def test_rdf_transform2(): } t2 = Transformer() t2.transform(input_args2) - assert t2.store.graph.number_of_nodes() == 14 - assert t2.store.graph.number_of_edges() == 7 n1t2 = t2.store.graph.nodes()["HP:0000505"] assert len(n1t2["category"]) == 1 @@ -319,7 +314,6 @@ def test_rdf_transform2(): assert e1t2["relation"] == "RO:0000091" assert e1t2["type"] == "biolink:Association" assert e1t2["has_evidence"] == "ECO:0000501" - assert e1t2["source"] == "OMIM:166400" e2t2 = list(t2.store.graph.get_edge("ORPHA:93262", "HP:0000505").values())[0] assert e2t2["subject"] == "ORPHA:93262" @@ -327,7 +321,9 @@ def test_rdf_transform2(): assert e2t2["relation"] == "RO:0002200" assert e2t2["type"] == "biolink:Association" assert e2t2["frequency_of_phenotype"] == "HP:0040283" - assert e2t2["source"] == "ORPHA:93262" + + assert t2.store.graph.number_of_nodes() == 19 + assert t2.store.graph.number_of_edges() == 12 input_args3 = { "filename": [os.path.join(TARGET_DIR, "oban-export.nt")], @@ -335,8 +331,6 @@ def test_rdf_transform2(): } t3 = Transformer() t3.transform(input_args3) - assert t3.store.graph.number_of_nodes() == 14 - assert t3.store.graph.number_of_edges() == 7 n1t3 = t1.store.graph.nodes()["HP:0000505"] assert len(n1t3["category"]) == 1 @@ -348,7 +342,6 @@ def test_rdf_transform2(): assert e1t3["relation"] == "RO:0000091" assert e1t3["type"] == "biolink:Association" assert e1t3["has_evidence"] == "ECO:0000501" - assert e1t3["source"] == "OMIM:166400" e2t3 = list(t3.store.graph.get_edge("ORPHA:93262", "HP:0000505").values())[0] assert e2t3["subject"] == "ORPHA:93262" @@ -356,7 +349,9 @@ def test_rdf_transform2(): assert e2t3["relation"] == "RO:0002200" assert e2t3["type"] == "biolink:Association" assert e2t3["frequency_of_phenotype"] == "HP:0040283" - assert e2t3["source"] == "ORPHA:93262" + + assert t3.store.graph.number_of_nodes() == 19 + assert t3.store.graph.number_of_edges() == 12 def test_rdf_transform3(): diff --git a/tests/integration/test_validator.py b/tests/integration/test_validator.py index 5d13baae..4fb03f8e 100644 --- a/tests/integration/test_validator.py +++ b/tests/integration/test_validator.py @@ -5,6 +5,9 @@ from kgx.graph.nx_graph import NxGraph from kgx.transformer import Transformer from tests import RESOURCE_DIR +from bmt import Toolkit + +toolkit = Toolkit() def test_validator_bad(): @@ -90,7 +93,7 @@ def test_validator_explicit_biolink_version(): "CHEMBL.COMPOUND:1222250", id="CHEMBL.COMPOUND:1222250", name="Dextrose", - category=["Carbohydrate"], + category=["NamedThing"] ) G.add_node( "UBERON:0000001", id="UBERON:0000001", name="fake", category=["NamedThing"] @@ -105,7 +108,7 @@ def test_validator_explicit_biolink_version(): object="UBERON:0000001", category=["biolink:Association"], ) - Validator.set_biolink_model(version="1.8.2") + Validator.set_biolink_model(toolkit.get_model_version()) validator = Validator(verbose=True) validator.validate(G) print(validator.get_errors()) @@ -126,7 +129,7 @@ def test_validator(): "aggregator_knowledge_source": True, } - Validator.set_biolink_model("1.8.2") + Validator.set_biolink_model(toolkit.get_model_version()) # Validator assumes the currently set Biolink Release validator = Validator() diff --git a/tests/unit/test_clique_merge.py b/tests/unit/test_clique_merge.py index 1c915eb7..a64bb1d3 100644 --- a/tests/unit/test_clique_merge.py +++ b/tests/unit/test_clique_merge.py @@ -7,6 +7,7 @@ ) from kgx.utils.kgx_utils import get_biolink_ancestors, generate_edge_key, get_toolkit from tests import print_graph +from bmt import Toolkit def test_check_categories(): @@ -69,9 +70,6 @@ def test_check_all_categories2(): """ Test check_all_categories method. """ - # explicitly pin the release of Biolink to a - # specific one with known category ancestry - get_toolkit(biolink_release="3.0.0") categories = get_biolink_ancestors("biolink:Gene") vbc, ibc, ic = check_all_categories(categories) diff --git a/tests/unit/test_config.py b/tests/unit/test_config.py index f07064b0..92276357 100644 --- a/tests/unit/test_config.py +++ b/tests/unit/test_config.py @@ -5,12 +5,23 @@ def test_valid_biolink_version(): try: - schema = get_biolink_model_schema("2.2.5") + schema = get_biolink_model_schema("v3.2.1") except TypeError as te: assert False, "test failure!" assert ( schema - == "https://raw.githubusercontent.com/biolink/biolink-model/2.2.5/biolink-model.yaml" + == "https://raw.githubusercontent.com/biolink/biolink-model/v3.2.1/biolink-model.yaml" + ) + + +def test_valid_biolink_version_no_v(): + try: + schema = get_biolink_model_schema("2.0.1") + except TypeError as te: + assert False, "test failure!" + assert ( + schema + == "https://raw.githubusercontent.com/biolink/biolink-model/2.0.1/biolink-model.yaml" ) diff --git a/tests/unit/test_rdf_utils.py b/tests/unit/test_rdf_utils.py index 794f2f87..448086e3 100644 --- a/tests/unit/test_rdf_utils.py +++ b/tests/unit/test_rdf_utils.py @@ -1,6 +1,7 @@ import os import pytest from rdflib import URIRef, Graph +from pprint import pprint from kgx.prefix_manager import PrefixManager from kgx.utils.rdf_utils import infer_category, process_predicate @@ -89,7 +90,15 @@ def test_process_predicate(query): Test behavior of process_predicate method. """ pm = PrefixManager() + pprint(query[0]) x = process_predicate(pm, query[0]) + # x = "element_uri", "canonical_uri", "predicate", "property_name" + # print("x: ", x) + # print("query[0]", query[0]) + # print("x[0]: ", x[0], "query[1]: ", query[1]) + # print("x[1]: ", x[1], "query[2]: ", query[2]) + # print("x[2]: ", x[2], "query[3]: ", query[3]) + # print("x[3]: ", x[3], "query[4]: ", query[4]) assert x[0] == query[1] assert x[1] == query[2] assert x[2] == query[3] diff --git a/tests/unit/test_source/test_obograph_source.py b/tests/unit/test_source/test_obograph_source.py index 2c4097e2..7a7d4481 100644 --- a/tests/unit/test_source/test_obograph_source.py +++ b/tests/unit/test_source/test_obograph_source.py @@ -27,7 +27,7 @@ def test_read_obograph1(): nodes[rec[0]] = rec[1] assert len(nodes) == 176 - assert len(edges) == 206 + assert len(edges) == 205 n1 = nodes["GO:0003677"] assert n1["id"] == "GO:0003677" @@ -77,7 +77,7 @@ def test_read_jsonl2(): nodes[rec[0]] = rec[1] assert len(nodes) == 176 - assert len(edges) == 206 + assert len(edges) == 205 n1 = nodes["GO:0003677"] assert n1["id"] == "GO:0003677" diff --git a/tests/unit/test_source/test_owl_source.py b/tests/unit/test_source/test_owl_source.py index 7fa3d693..d3a93b25 100644 --- a/tests/unit/test_source/test_owl_source.py +++ b/tests/unit/test_source/test_owl_source.py @@ -3,6 +3,7 @@ from kgx.source import OwlSource from kgx.transformer import Transformer from tests import RESOURCE_DIR +from pprint import pprint def test_read_owl1(): @@ -27,21 +28,21 @@ def test_read_owl1(): n1 = nodes["GO:0008150"] assert n1["name"] == "biological_process" - assert "synonym" in n1 and "biological process" in n1["synonym"] + assert "has_exact_synonym" in n1 and "biological process" in n1["has_exact_synonym"] assert "description" in n1 assert "comment" in n1 assert "has_alternative_id" in n1 and "GO:0044699" in n1["has_alternative_id"] n2 = nodes["GO:0003674"] n2["name"] = "molecular_function" - assert "synonym" in n2 and "molecular function" in n2["synonym"] + assert "has_exact_synonym" in n2 and "molecular function" in n2["has_exact_synonym"] assert "description" in n2 assert "comment" in n2 assert "has_alternative_id" in n2 and "GO:0005554" in n2["has_alternative_id"] n3 = nodes["GO:0005575"] n3["name"] = "cellular_component" - assert "synonym" in n3 and "cellular component" in n3["synonym"] + assert "has_exact_synonym" in n3 and "cellular component" in n3["has_exact_synonym"] assert "description" in n3 assert "comment" in n3 assert "has_alternative_id" in n3 and "GO:0008372" in n3["has_alternative_id"] @@ -77,7 +78,7 @@ def test_read_owl2(): n1 = nodes["GO:0008150"] assert n1["name"] == "biological_process" - assert "synonym" in n1 and "biological process" in n1["synonym"] + assert "has_exact_synonym" in n1 and "biological process" in n1["has_exact_synonym"] assert "description" in n1 assert "comment" in n1 assert "has_alternative_id" in n1 and "GO:0044699" in n1["has_alternative_id"] @@ -85,7 +86,7 @@ def test_read_owl2(): n2 = nodes["GO:0003674"] n2["name"] = "molecular_function" - assert "synonym" in n2 and "molecular function" in n2["synonym"] + assert "has_exact_synonym" in n2 and "molecular function" in n2["has_exact_synonym"] assert "description" in n2 assert "comment" in n2 assert "has_alternative_id" in n2 and "GO:0005554" in n2["has_alternative_id"] @@ -93,7 +94,7 @@ def test_read_owl2(): n3 = nodes["GO:0005575"] n3["name"] = "cellular_component" - assert "synonym" in n3 and "cellular component" in n3["synonym"] + assert "has_exact_synonym" in n3 and "cellular component" in n3["has_exact_synonym"] assert "description" in n3 assert "comment" in n3 assert "has_alternative_id" in n3 and "GO:0008372" in n3["has_alternative_id"] @@ -141,7 +142,7 @@ def test_read_owl3(): n1 = nodes["GO:0008150"] assert n1["name"] == "biological_process" assert "subsets" in n1 and "GOP:goslim_generic" in n1["subsets"] - assert "synonym" in n1 and "biological process" in n1["synonym"] + assert "has_exact_synonym" in n1 and "biological process" in n1["has_exact_synonym"] assert "description" in n1 assert "comment" in n1 assert "xref" in n1 and "GO:0044699" in n1["xref"] @@ -149,7 +150,7 @@ def test_read_owl3(): n2 = nodes["GO:0003674"] n2["name"] = "molecular_function" assert "subsets" in n2 and "GOP:goslim_generic" in n2["subsets"] - assert "synonym" in n2 and "molecular function" in n2["synonym"] + assert "has_exact_synonym" in n2 and "molecular function" in n2["has_exact_synonym"] assert "description" in n2 assert "comment" in n2 assert "xref" in n2 and "GO:0005554" in n2["xref"] @@ -157,7 +158,7 @@ def test_read_owl3(): n3 = nodes["GO:0005575"] n3["name"] = "cellular_component" assert "subsets" in n3 and "GOP:goslim_generic" in n3["subsets"] - assert "synonym" in n3 and "cellular component" in n3["synonym"] + assert "has_exact_synonym" in n3 and "cellular component" in n3["has_exact_synonym"] assert "description" in n3 assert "comment" in n3 assert "xref" in n3 and "GO:0008372" in n3["xref"] diff --git a/tests/unit/test_source/test_rdf_source.py b/tests/unit/test_source/test_rdf_source.py index 31fb3706..4238592b 100644 --- a/tests/unit/test_source/test_rdf_source.py +++ b/tests/unit/test_source/test_rdf_source.py @@ -1,5 +1,5 @@ import os -import pprint +from pprint import pprint import pytest diff --git a/tox.ini b/tox.ini index e4ee6224..605fd4ba 100644 --- a/tox.ini +++ b/tox.ini @@ -1,48 +1,11 @@ -# TODO explain tox and testenv reserved words [tox] -envlist = python3.8 - python3.9 - black-diff - flake8 - docker-tests +envlist = py39, py310 +isolated_build = true +skipsdist = true -[testenv] -extras = - jupyter -deps = -rrequirements.txt -commands = pytest -allowlist_externals = - /usr/bin/make - /bin/cat - /bin/cp - /bin/mkdir - /usr/bin/git - -[testenv:black-diff] -line_length = 120 -commands = - black --check --diff kgx tests - -[testenv:black] -line_length = 120 -commands = - black kgx tests - -[testenv:flake8] -commands = - flake8 kgx tests -[flake8] -ignore = E501 -max_line_length = 70 -max-complexity = 10 -per-file-ignores = __init__.py:F401 - - -[testenv:example] -deps = - -rrequirements.txt -setenv = - PYTHONPATH=. -commands = - python examples/edgelabel.py +[testenv] +whitelist_externals = poetry +commands= + poetry install -v + poetry run pytest