diff --git a/kgx/error_detection.py b/kgx/error_detection.py index 3f586277..3e3a547f 100644 --- a/kgx/error_detection.py +++ b/kgx/error_detection.py @@ -119,14 +119,9 @@ def log_error( if error not in self.errors[level]: self.errors[level][error] = dict() - - # don't record duplicate instances of error type and - # messages for entity identifiers... - if message not in self.errors[level][error]: - self.errors[level][error][message] = [entity] - else: - if entity not in self.errors[level][error][message]: - self.errors[level][error][message].append(entity) + + self.errors[level][error][message] = [entity] + self.errors[level][error][message].append(entity) def get_errors(self, level: str = None) -> Dict: """ diff --git a/kgx/sink/rdf_sink.py b/kgx/sink/rdf_sink.py index 4a36446a..70627913 100644 --- a/kgx/sink/rdf_sink.py +++ b/kgx/sink/rdf_sink.py @@ -237,8 +237,12 @@ def write_edge(self, record: Dict) -> None: value_uri = self._prepare_object(prop, prop_type, value) self._write_triple(URIRef(n), prop_uri, value_uri) else: + if "type" in record: + for type in record["type"]: + if type in associations: + at_least_one_type_in_associations = True if ( - ("type" in record and record["type"] in associations) + ("type" in record and at_least_one_type_in_associations) or ( "association_type" in record and record["association_type"] in associations diff --git a/kgx/utils/kgx_utils.py b/kgx/utils/kgx_utils.py index 83afae85..74561b65 100644 --- a/kgx/utils/kgx_utils.py +++ b/kgx/utils/kgx_utils.py @@ -21,7 +21,6 @@ import numpy as np from prefixcommons.curie_util import contract_uri from prefixcommons.curie_util import expand_uri - from kgx.config import get_logger, get_jsonld_context, get_biolink_model_schema from kgx.graph.base_graph import BaseGraph @@ -34,6 +33,8 @@ CORE_EDGE_PROPERTIES = {"id", "subject", "predicate", "object", "type"} XSD_STRING = "xsd:string" +tk = Toolkit() + class GraphEntityType(Enum): GRAPH = "graph" @@ -53,6 +54,7 @@ class GraphEntityType(Enum): "provided_by": list, } + column_types = { "publications": list, "qualifiers": list, @@ -833,6 +835,7 @@ def _sanitize_import_property(key: str, value: Any, list_delimiter: str) -> Any: Sanitized value """ + if key in column_types: if column_types[key] == list: if isinstance(value, (list, set, tuple)): @@ -843,7 +846,7 @@ def _sanitize_import_property(key: str, value: Any, list_delimiter: str) -> Any: new_value = list(value) elif isinstance(value, str): value = value.replace("\n", " ").replace("\t", " ") - new_value = [x for x in value.split(list_delimiter) if x] if list_delimiter else value + new_value = [x for x in value.split(list_delimiter) if x] if list_delimiter else [value] else: new_value = [str(value).replace("\n", " ").replace("\t", " ")] # remove duplication in the list @@ -871,9 +874,12 @@ def _sanitize_import_property(key: str, value: Any, list_delimiter: str) -> Any: ] new_value = list(value) elif isinstance(value, str): + multivalued_slots = [sentencecase_to_snakecase(x) for x in tk.get_all_multivalued_slots()] if list_delimiter and list_delimiter in value: value = value.replace("\n", " ").replace("\t", " ") new_value = [x for x in value.split(list_delimiter) if x] + elif key in multivalued_slots: + new_value = [value] else: new_value = value.replace("\n", " ").replace("\t", " ") elif isinstance(value, bool): diff --git a/poetry.lock b/poetry.lock index c60f5289..dcb9bda1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -142,24 +142,9 @@ 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 = "1.0.4" +version = "1.0.7" description = "Biolink Model Toolkit: A Python API for working with the Biolink Model" category = "main" optional = false @@ -168,18 +153,9 @@ python-versions = ">=3.9,<4.0" [package.dependencies] deprecation = ">=2.1.0,<3.0.0" linkml-runtime = ">=1.4.9,<2.0.0" -oaklib = ">=0.2.1,<0.3.0" -pytest = ">=7.2.2,<8.0.0" +oaklib = ">=0.3.1,<0.4.0" recommonmark = ">=0.7.1,<0.8.0" -sphinx-autodoc-typehints = ">=1.19.5,<2.0.0" -sphinx-click = ">=4.3.0,<5.0.0" -sphinx-rtd-theme = ">=1.1.1,<2.0.0" -sphinxcontrib-napoleon = ">=0.7,<0.8" stringcase = ">=1.2.0,<2.0.0" -twine = ">=4.0.1,<5.0.0" - -[package.extras] -docs = ["Sphinx (>=5.3.0,<6.0.0)"] [[package]] name = "cachetools" @@ -197,17 +173,6 @@ category = "main" optional = false python-versions = ">=3.6" -[[package]] -name = "cffi" -version = "1.15.1" -description = "Foreign Function Interface for Python calling C code." -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -pycparser = "*" - [[package]] name = "cfgraph" version = "0.2.1" @@ -283,27 +248,6 @@ python-versions = "*" [package.extras] test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"] -[[package]] -name = "cryptography" -version = "39.0.2" -description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." -category = "main" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -cffi = ">=1.12" - -[package.extras] -docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=1.1.1)"] -docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"] -pep8test = ["black", "check-manifest", "mypy", "ruff", "types-pytz", "types-requests"] -sdist = ["setuptools-rust (>=0.11.4)"] -ssh = ["bcrypt (>=3.1.5)"] -test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-shard (>=0.1.2)", "pytest-subtests", "pytest-xdist", "pytz"] -test-randomorder = ["pytest-randomly"] -tox = ["tox"] - [[package]] name = "curies" version = "0.4.5" @@ -421,7 +365,7 @@ python-versions = ">=3.7" [[package]] name = "filelock" -version = "3.10.0" +version = "3.10.7" description = "A platform independent file lock." category = "main" optional = false @@ -429,7 +373,7 @@ python-versions = ">=3.7" [package.extras] docs = ["furo (>=2022.12.7)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"] -testing = ["covdefaults (>=2.3)", "coverage (>=7.2.1)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"] +testing = ["covdefaults (>=2.3)", "coverage (>=7.2.2)", "diff-cover (>=7.5)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"] [[package]] name = "fqdn" @@ -607,33 +551,6 @@ python-versions = ">=3.7" [package.dependencies] arrow = ">=0.15.0" -[[package]] -name = "jaraco-classes" -version = "3.2.3" -description = "Utility functions for Python class constructs" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -more-itertools = "*" - -[package.extras] -docs = ["jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] -testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] - -[[package]] -name = "jeepney" -version = "0.8.0" -description = "Low-level, pure Python DBus protocol wrapper." -category = "main" -optional = false -python-versions = ">=3.7" - -[package.extras] -test = ["async-timeout", "pytest", "pytest-asyncio (>=0.17)", "pytest-trio", "testpath", "trio"] -trio = ["async_generator", "trio"] - [[package]] name = "jinja2" version = "3.1.2" @@ -761,26 +678,6 @@ six = "*" recomended = ["simplejson"] test = ["tox"] -[[package]] -name = "keyring" -version = "23.13.1" -description = "Store and access your passwords safely." -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -importlib-metadata = {version = ">=4.11.4", markers = "python_version < \"3.12\""} -"jaraco.classes" = "*" -jeepney = {version = ">=0.4.2", markers = "sys_platform == \"linux\""} -pywin32-ctypes = {version = ">=0.2.0", markers = "sys_platform == \"win32\""} -SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""} - -[package.extras] -completion = ["shtab"] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] -testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] - [[package]] name = "kgcl-rdflib" version = "0.3.0" @@ -822,7 +719,7 @@ regex = ["regex"] [[package]] name = "linkml" -version = "1.4.10" +version = "1.5.0" description = "Linked Open Data Modeling Language" category = "main" optional = false @@ -838,7 +735,7 @@ jinja2 = ">=3.1.0" jsonasobj2 = ">=1.0.3,<2.0.0" jsonschema = {version = ">=4.0.0", extras = ["format"]} linkml-dataops = "*" -linkml-runtime = ">=1,<2" +linkml-runtime = ">=1.5.0" myst-parser = "*" openpyxl = "*" parse = "*" @@ -895,7 +792,7 @@ docs = ["myst-parser[docs] (>=0.18.1,<0.19.0)", "sphinx-autodoc-typehints[docs] [[package]] name = "linkml-runtime" -version = "1.4.9" +version = "1.5.0" description = "Runtime environment for LinkML, the Linked open data modeling language" category = "main" optional = false @@ -982,14 +879,6 @@ click = "*" [package.extras] tests = ["coverage", "pytest"] -[[package]] -name = "more-itertools" -version = "9.1.0" -description = "More routines for operating on iterables, beyond itertools" -category = "main" -optional = false -python-versions = ">=3.7" - [[package]] name = "multidict" version = "6.0.4" @@ -1119,7 +1008,7 @@ viz = ["pygraphviz"] [[package]] name = "oaklib" -version = "0.2.5" +version = "0.3.1" description = "Ontology Access Kit: Python library for common ontology operations over a variety of backends" category = "main" optional = false @@ -1262,20 +1151,9 @@ category = "main" optional = false python-versions = "*" -[[package]] -name = "pkginfo" -version = "1.9.6" -description = "Query metadata from sdists / bdists / installed packages." -category = "main" -optional = false -python-versions = ">=3.6" - -[package.extras] -testing = ["pytest", "pytest-cov"] - [[package]] name = "platformdirs" -version = "3.1.1" +version = "3.2.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "main" optional = false @@ -1283,7 +1161,7 @@ python-versions = ">=3.7" [package.extras] docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"] -test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] [[package]] name = "pluggy" @@ -1305,17 +1183,6 @@ category = "main" optional = false python-versions = "*" -[[package]] -name = "pockets" -version = "0.9.1" -description = "A collection of helpful Python tools!" -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -six = ">=1.5.2" - [[package]] name = "prefixcommons" version = "0.1.12" @@ -1372,17 +1239,9 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -[[package]] -name = "pycparser" -version = "2.21" -description = "C parser in Python" -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" - [[package]] name = "pydantic" -version = "1.10.6" +version = "1.10.7" description = "Data validation and settings management using python type hints" category = "main" optional = false @@ -1548,7 +1407,7 @@ sortedcontainers = "*" [[package]] name = "pytz" -version = "2022.7.1" +version = "2023.2" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -1556,20 +1415,12 @@ python-versions = "*" [[package]] name = "pywin32" -version = "305" +version = "306" description = "Python for Window Extensions" category = "main" optional = false python-versions = "*" -[[package]] -name = "pywin32-ctypes" -version = "0.2.0" -description = "" -category = "main" -optional = false -python-versions = "*" - [[package]] name = "pyyaml" version = "6.0" @@ -1588,7 +1439,7 @@ python-versions = "*" [[package]] name = "rdflib" -version = "6.3.1" +version = "6.3.2" description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information." category = "main" optional = false @@ -1627,22 +1478,6 @@ python-versions = ">=3.7" rdflib = ">=5.0.0" rdflib-jsonld = "0.6.1" -[[package]] -name = "readme-renderer" -version = "37.3" -description = "readme_renderer is a library for rendering \"readme\" descriptions for Warehouse" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -bleach = ">=2.1.0" -docutils = ">=0.13.1" -Pygments = ">=2.5.1" - -[package.extras] -md = ["cmarkgfm (>=0.8.0)"] - [[package]] name = "recommonmark" version = "0.7.1" @@ -1696,17 +1531,6 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.dependencies] six = "*" -[[package]] -name = "rfc3986" -version = "2.0.0" -description = "Validating URI References per RFC 3986" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.extras] -idna2008 = ["idna"] - [[package]] name = "rfc3987" version = "1.3.8" @@ -1715,21 +1539,6 @@ category = "main" optional = false python-versions = "*" -[[package]] -name = "rich" -version = "13.3.2" -description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal" -category = "main" -optional = false -python-versions = ">=3.7.0" - -[package.dependencies] -markdown-it-py = ">=2.2.0,<3.0.0" -pygments = ">=2.13.0,<3.0.0" - -[package.extras] -jupyter = ["ipywidgets (>=7.5.1,<9)"] - [[package]] name = "ruamel-yaml" version = "0.17.21" @@ -1769,18 +1578,6 @@ dev = ["flake8", "mypy", "pycodestyle", "typing_extensions"] doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-panels (>=0.5.2)", "sphinx-tabs"] test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] -[[package]] -name = "secretstorage" -version = "3.3.3" -description = "Python bindings to FreeDesktop.org Secret Service API" -category = "main" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -cryptography = ">=2.0" -jeepney = ">=0.6" - [[package]] name = "semsql" version = "0.3.2" @@ -1901,22 +1698,6 @@ docs = ["sphinxcontrib-websupport"] lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-simplify", "isort", "mypy (>=0.990)", "ruff", "sphinx-lint", "types-requests"] test = ["cython", "html5lib", "pytest (>=4.6)"] -[[package]] -name = "sphinx-autodoc-typehints" -version = "1.22" -description = "Type hints (PEP 484) support for the Sphinx autodoc extension" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -sphinx = ">=5.3" - -[package.extras] -docs = ["furo (>=2022.12.7)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.21)"] -testing = ["covdefaults (>=2.2.2)", "coverage (>=7.0.5)", "diff-cover (>=7.3)", "nptyping (>=2.4.1)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "sphobjinv (>=2.3.1)", "typing-extensions (>=4.4)"] -type-comment = ["typed-ast (>=1.5.4)"] - [[package]] name = "sphinx-click" version = "4.4.0" @@ -2004,18 +1785,6 @@ python-versions = ">=3.5" [package.extras] test = ["flake8", "mypy", "pytest"] -[[package]] -name = "sphinxcontrib-napoleon" -version = "0.7" -description = "Sphinx \"napoleon\" extension." -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -pockets = ">=0.3" -six = ">=1.5.2" - [[package]] name = "sphinxcontrib-qthelp" version = "1.0.3" @@ -2201,25 +1970,6 @@ notebook = ["ipywidgets (>=6)"] slack = ["slack-sdk"] telegram = ["requests"] -[[package]] -name = "twine" -version = "4.0.2" -description = "Collection of utilities for publishing packages on PyPI" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -importlib-metadata = ">=3.6" -keyring = ">=15.1" -pkginfo = ">=1.8.1" -readme-renderer = ">=35.0" -requests = ">=2.20" -requests-toolbelt = ">=0.8.0,<0.9.0 || >0.9.0" -rfc3986 = ">=1.4.0" -rich = ">=12.0.0" -urllib3 = ">=1.26.0" - [[package]] name = "typing-extensions" version = "4.5.0" @@ -2296,19 +2046,15 @@ watchmedo = ["PyYAML (>=3.10)"] [[package]] name = "webcolors" -version = "1.12" -description = "A library for working with color names and color values formats defined by HTML and CSS." +version = "1.13" +description = "A library for working with the color formats defined by HTML and CSS." category = "main" optional = false python-versions = ">=3.7" -[[package]] -name = "webencodings" -version = "0.5.1" -description = "Character encoding aliases for legacy web content" -category = "main" -optional = false -python-versions = "*" +[package.extras] +docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"] +tests = ["pytest", "pytest-cov"] [[package]] name = "websocket-client" @@ -2358,7 +2104,7 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more [metadata] lock-version = "1.1" python-versions = "^3.9" -content-hash = "aa524874e6007b3f5fad3a24d3d8f403d22f73eb5525edcd51585481bc89c994" +content-hash = "2a175ebca6272901e61063448d3897c1b5119d7e6fa6c42c64c450095ea84432" [metadata.files] aiohttp = [ @@ -2493,13 +2239,9 @@ bioregistry = [ {file = 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"sha256:3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40"}, diff --git a/pyproject.toml b/pyproject.toml index 4c84b761..87bf8cd5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,7 +50,7 @@ ijson = "^3.1.3" deprecation = "^2.1.0" recommonmark = "*" tox = "^3.0" -bmt = "^1.0" +bmt = "^1.0.5" inflection = "^0.5.1" [tool.poetry-dynamic-versioning] diff --git a/tests/integration/test_transform.py b/tests/integration/test_transform.py index 1ebc4542..6aa5f424 100644 --- a/tests/integration/test_transform.py +++ b/tests/integration/test_transform.py @@ -212,14 +212,14 @@ def test_rdf_transform1(): assert e1["subject"] == "OMIM:166400" assert e1["object"] == "HP:0000006" assert e1["relation"] == "RO:0000091" - assert e1["type"] == "OBAN:association" - assert e1["has_evidence"] == "ECO:0000501" + assert e1["type"] == ["OBAN:association"] + assert e1["has_evidence"] == ["ECO:0000501"] e2 = list(t1.store.graph.get_edge("ORPHA:93262", "HP:0000505").values())[0] assert e2["subject"] == "ORPHA:93262" assert e2["object"] == "HP:0000505" assert e2["relation"] == "RO:0002200" - assert e2["type"] == "OBAN:association" + assert e2["type"] == ["OBAN:association"] assert e2["frequencyOfPhenotype"] == "HP:0040283" output_args = { @@ -274,14 +274,14 @@ def test_rdf_transform2(): assert e1t1["subject"] == "OMIM:166400" assert e1t1["object"] == "HP:0000006" assert e1t1["relation"] == "RO:0000091" - assert e1t1["type"] == "OBAN:association" - assert e1t1["has_evidence"] == "ECO:0000501" + assert e1t1["type"] == ['OBAN:association'] + assert e1t1["has_evidence"] == ["ECO:0000501"] e2t1 = list(t1.store.graph.get_edge("ORPHA:93262", "HP:0000505").values())[0] assert e2t1["subject"] == "ORPHA:93262" assert e2t1["object"] == "HP:0000505" assert e2t1["relation"] == "RO:0002200" - assert e2t1["type"] == "OBAN:association" + assert e2t1["type"] == ['OBAN:association'] assert e2t1["frequency_of_phenotype"] == "HP:0040283" print(t1.store.graph.get_node("ORPHA:93262")) @@ -312,14 +312,14 @@ def test_rdf_transform2(): assert e1t2["subject"] == "OMIM:166400" assert e1t2["object"] == "HP:0000006" assert e1t2["relation"] == "RO:0000091" - assert e1t2["type"] == "biolink:Association" - assert e1t2["has_evidence"] == "ECO:0000501" + assert e1t2["type"] == ['biolink:Association'] + assert e1t2["has_evidence"] == ["ECO:0000501"] e2t2 = list(t2.store.graph.get_edge("ORPHA:93262", "HP:0000505").values())[0] assert e2t2["subject"] == "ORPHA:93262" assert e2t2["object"] == "HP:0000505" assert e2t2["relation"] == "RO:0002200" - assert e2t2["type"] == "biolink:Association" + assert e2t2["type"] == ['biolink:Association'] assert e2t2["frequency_of_phenotype"] == "HP:0040283" assert t2.store.graph.number_of_nodes() == 19 @@ -340,14 +340,14 @@ def test_rdf_transform2(): assert e1t3["subject"] == "OMIM:166400" assert e1t3["object"] == "HP:0000006" assert e1t3["relation"] == "RO:0000091" - assert e1t3["type"] == "biolink:Association" - assert e1t3["has_evidence"] == "ECO:0000501" + assert e1t3["type"] == ['biolink:Association'] + assert e1t3["has_evidence"] == ["ECO:0000501"] e2t3 = list(t3.store.graph.get_edge("ORPHA:93262", "HP:0000505").values())[0] assert e2t3["subject"] == "ORPHA:93262" assert e2t3["object"] == "HP:0000505" assert e2t3["relation"] == "RO:0002200" - assert e2t3["type"] == "biolink:Association" + assert e2t3["type"] == ['biolink:Association'] assert e2t3["frequency_of_phenotype"] == "HP:0040283" assert t3.store.graph.number_of_nodes() == 19 @@ -386,7 +386,7 @@ def test_rdf_transform3(): n1t2 = t2.store.graph.nodes()["ENSEMBL:ENSG0000000000001"] n1t3 = t2.store.graph.nodes()["ENSEMBL:ENSG0000000000001"] - assert n1t1["type"] == n1t2["type"] == n1t3["type"] == "SO:0000704" + assert n1t1["type"] == n1t2["type"] == n1t3["type"] == ["SO:0000704"] assert len(n1t1["category"]) == len(n1t2["category"]) == len(n1t3["category"]) == 4 assert ( "biolink:Gene" in n1t1["category"] @@ -454,7 +454,7 @@ def test_rdf_transform4(): n1t1 = t1.store.graph.nodes()["ENSEMBL:ENSG0000000000001"] n1t2 = t2.store.graph.nodes()["ENSEMBL:ENSG0000000000001"] - assert n1t1["type"] == n1t2["type"] == "SO:0000704" + assert n1t1["type"] == n1t2["type"] == ["SO:0000704"] assert len(n1t1["category"]) == len(n1t2["category"]) == 4 assert "biolink:Gene" in n1t1["category"] and "biolink:Gene" in n1t2["category"] assert ( @@ -486,7 +486,7 @@ def test_rdf_transform4(): assert e1t1["object"] == e1t2["object"] == "ENSEMBL:ENSP0000000000002" assert e1t1["predicate"] == e1t2["predicate"] == "biolink:interacts_with" assert e1t1["relation"] == e1t2["relation"] == "biolink:interacts_with" - assert e1t1["type"] == e1t2["type"] == "biolink:Association" + assert e1t1["type"] == e1t2["type"] == ["biolink:Association"] assert e1t1["id"] == e1t2["id"] == "urn:uuid:fcf76807-f909-4ccb-b40a-3b79b49aa518" assert e1t1["fusion"] == e1t2["fusion"] == "0" assert e1t1["homology"] == e1t2["homology"] == "0.0" @@ -536,7 +536,7 @@ def test_rdf_transform5(): n1t1 = t1.store.graph.nodes()["ENSEMBL:ENSG0000000000001"] n1t2 = t2.store.graph.nodes()["ENSEMBL:ENSG0000000000001"] - assert n1t1["type"] == n1t2["type"] == "SO:0000704" + assert n1t1["type"] == n1t2["type"] == ["SO:0000704"] assert len(n1t1["category"]) == len(n1t2["category"]) == 4 assert "biolink:Gene" in n1t1["category"] and "biolink:Gene" in n1t2["category"] assert ( @@ -568,7 +568,7 @@ def test_rdf_transform5(): assert e1t1["object"] == e1t2["object"] == "ENSEMBL:ENSP0000000000002" assert e1t1["predicate"] == e1t2["predicate"] == "biolink:interacts_with" assert e1t1["relation"] == e1t2["relation"] == "biolink:interacts_with" - assert e1t1["type"] == e1t2["type"] == "biolink:Association" + assert e1t1["type"] == e1t2["type"] == ["biolink:Association"] assert e1t1["id"] == e1t2["id"] == "urn:uuid:fcf76807-f909-4ccb-b40a-3b79b49aa518" assert "test3.nt" in e1t1["knowledge_source"] assert e1t2["fusion"] == 0.0 diff --git a/tests/resources/graph_validate_nodes.tsv b/tests/resources/graph_validate_nodes.tsv new file mode 100644 index 00000000..eb8dd7cf --- /dev/null +++ b/tests/resources/graph_validate_nodes.tsv @@ -0,0 +1,6 @@ +id name category taxon +HGNC:10848 SHH biolink:Gene NCBITaxon:9606 +HGNC:20738 SYVN1 biolink:Gene NCBITaxon:9606 +HGNC:20635 PSME4 biolink:Gene NCBITaxon:9606 +HGNC:20634 PSME5 +GO:0005576 cellular_component biolink:CellularComponent NCBITaxon:9606 \ No newline at end of file diff --git a/tests/resources/monarch-tiny_edges.tsv b/tests/resources/monarch-tiny_edges.tsv new file mode 100644 index 00000000..02b47144 --- /dev/null +++ b/tests/resources/monarch-tiny_edges.tsv @@ -0,0 +1,501 @@ +id original_subject predicate original_object category aggregator_knowledge_source primary_knowledge_source publications provided_by has_evidence stage_qualifier relation knowledge_source frequency_qualifier negated onset_qualifier sex_qualifier qualifiers subject object +uuid:7739dc2c-45f8-11ed-b722-f133c15addd7 biolink:has_phenotype 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+uuid:7739de19-45f8-11ed-b722-f133c15addd7 biolink:has_phenotype biolink:GeneToPhenotypicFeatureAssociation infores:monarchinitiative infores:pombase PMID:11676915 pombase_gene_to_phenotype_edges PomBase:SPCC1739.11c FYPO:0002912 +uuid:7739de1a-45f8-11ed-b722-f133c15addd7 biolink:has_phenotype biolink:GeneToPhenotypicFeatureAssociation infores:monarchinitiative infores:pombase PMID:20473289 pombase_gene_to_phenotype_edges FYECO:0000137|FYECO:0000005 PomBase:SPCC1739.11c FYPO:0002061 +uuid:7739de1b-45f8-11ed-b722-f133c15addd7 biolink:has_phenotype biolink:GeneToPhenotypicFeatureAssociation infores:monarchinitiative infores:pombase PMID:23697806 pombase_gene_to_phenotype_edges FYECO:0000137|FYECO:0000005 PomBase:SPCC1739.11c FYPO:0002061 +uuid:7739de1c-45f8-11ed-b722-f133c15addd7 biolink:has_phenotype biolink:GeneToPhenotypicFeatureAssociation infores:monarchinitiative infores:pombase PMID:11676915 pombase_gene_to_phenotype_edges PomBase:SPCC1739.11c FYPO:0002061 +uuid:7739de1d-45f8-11ed-b722-f133c15addd7 biolink:has_phenotype biolink:GeneToPhenotypicFeatureAssociation infores:monarchinitiative infores:pombase PMID:11676915 pombase_gene_to_phenotype_edges PomBase:SPCC1739.11c FYPO:0001368 +uuid:7739de1e-45f8-11ed-b722-f133c15addd7 biolink:has_phenotype biolink:GeneToPhenotypicFeatureAssociation infores:monarchinitiative infores:pombase PMID:11676915 pombase_gene_to_phenotype_edges PomBase:SPCC1739.11c FYPO:0002967 +uuid:7739de1f-45f8-11ed-b722-f133c15addd7 biolink:has_phenotype biolink:GeneToPhenotypicFeatureAssociation infores:monarchinitiative infores:pombase PMID:11676915 pombase_gene_to_phenotype_edges PomBase:SPCC1739.11c FYPO:0002967 diff --git a/tests/unit/test_cli_utils.py b/tests/unit/test_cli_utils.py index d2ed7059..1b4b4f92 100644 --- a/tests/unit/test_cli_utils.py +++ b/tests/unit/test_cli_utils.py @@ -414,7 +414,7 @@ def test_validate_exception_triggered_error_exit_code(): """ Test graph validate error exit code. """ - test_input = os.path.join(RESOURCE_DIR, "graph_nodes.tsv") + test_input = os.path.join(RESOURCE_DIR, "graph_tiny_nodes.tsv") runner = CliRunner() result = runner.invoke( cli, diff --git a/tests/unit/test_source/test_rdf_source.py b/tests/unit/test_source/test_rdf_source.py index 4238592b..5aed80b4 100644 --- a/tests/unit/test_source/test_rdf_source.py +++ b/tests/unit/test_source/test_rdf_source.py @@ -22,7 +22,7 @@ def test_read_nt1(): assert len(edges) == 1 n1 = nodes["ENSEMBL:ENSG0000000000001"] - assert n1["type"] == "SO:0000704" + assert n1["type"] == ["SO:0000704"] assert len(n1["category"]) == 4 assert "biolink:Gene" in n1["category"] assert "biolink:GenomicEntity" in n1["category"] @@ -32,7 +32,7 @@ def test_read_nt1(): assert "Test Dataset" in n1["provided_by"] n2 = nodes["ENSEMBL:ENSG0000000000002"] - assert n2["type"] == "SO:0000704" + assert n2["type"] == ["SO:0000704"] assert len(n2["category"]) == 4 assert "biolink:Gene" in n2["category"] assert "biolink:GenomicEntity" in n2["category"] @@ -66,7 +66,7 @@ def test_read_nt2(): assert len(edges) == 1 n1 = nodes["ENSEMBL:ENSG0000000000001"] - assert n1["type"] == "SO:0000704" + assert n1["type"] == ["SO:0000704"] assert len(n1["category"]) == 4 assert "biolink:Gene" in n1["category"] assert "biolink:GenomicEntity" in n1["category"] @@ -76,7 +76,7 @@ def test_read_nt2(): assert "Test Dataset" in n1["provided_by"] n2 = nodes["ENSEMBL:ENSG0000000000002"] - assert n2["type"] == "SO:0000704" + assert n2["type"] == ["SO:0000704"] assert len(n2["category"]) == 4 assert "biolink:Gene" in n2["category"] assert "biolink:GenomicEntity" in n2["category"] @@ -115,7 +115,7 @@ def test_read_nt3(): assert len(edges) == 3 n1 = nodes["ENSEMBL:ENSG0000000000001"] - assert n1["type"] == "SO:0000704" + assert n1["type"] == ["SO:0000704"] assert len(n1["category"]) == 4 assert "biolink:Gene" in n1["category"] assert "biolink:GenomicEntity" in n1["category"] @@ -125,7 +125,7 @@ def test_read_nt3(): assert "Test Dataset" in n1["provided_by"] n2 = nodes["ENSEMBL:ENSG0000000000002"] - assert n2["type"] == "SO:0000704" + assert n2["type"] == ["SO:0000704"] assert len(n2["category"]) == 4 assert "biolink:Gene" in n2["category"] assert "biolink:GenomicEntity" in n2["category"] @@ -139,7 +139,7 @@ def test_read_nt3(): assert e1["object"] == "ENSEMBL:ENSP0000000000002" assert e1["predicate"] == "biolink:interacts_with" assert e1["relation"] == "biolink:interacts_with" - assert e1["type"] == "biolink:Association" + assert e1["type"] == ["biolink:Association"] assert e1["id"] == "urn:uuid:fcf76807-f909-4ccb-b40a-3b79b49aa518" assert e1["fusion"] == "0" assert e1["homology"] == "0.0" @@ -169,7 +169,7 @@ def test_read_nt4(): assert len(edges.keys()) == 6 n1 = nodes["ENSEMBL:ENSG0000000000001"] - assert n1["type"] == "SO:0000704" + assert n1["type"] == ["SO:0000704"] assert len(n1["category"]) == 4 assert "biolink:Gene" in n1["category"] assert "biolink:GenomicEntity" in n1["category"] @@ -179,7 +179,7 @@ def test_read_nt4(): assert "Test Dataset" in n1["provided_by"] n2 = nodes["ENSEMBL:ENSG0000000000002"] - assert n2["type"] == "SO:0000704" + assert n2["type"] == ["SO:0000704"] assert len(n2["category"]) == 4 assert "biolink:Gene" in n2["category"] assert "biolink:GenomicEntity" in n2["category"] @@ -193,7 +193,7 @@ def test_read_nt4(): assert e1["object"] == "ENSEMBL:ENSP0000000000002" assert e1["predicate"] == "biolink:interacts_with" assert e1["relation"] == "biolink:interacts_with" - assert e1["type"] == "biolink:Association" + assert e1["type"] == ["biolink:Association"] assert e1["id"] == "urn:uuid:fcf76807-f909-4ccb-b40a-3b79b49aa518" assert e1["fusion"] == "0" assert e1["homology"] == "0.0" @@ -247,14 +247,14 @@ def test_read_nt5(): assert e1["subject"] == "OMIM:166400" assert e1["object"] == "HP:0000006" assert e1["relation"] == "RO:0000091" - assert e1["type"] == "OBAN:association" - assert e1["has_evidence"] == "ECO:0000501" + assert e1["type"] == ["OBAN:association"] + assert e1["has_evidence"] == ["ECO:0000501"] e2 = edges["ORPHA:93262", "HP:0000505"][0] assert e2["subject"] == "ORPHA:93262" assert e2["object"] == "HP:0000505" assert e2["relation"] == "RO:0002200" - assert e2["type"] == "OBAN:association" + assert e2["type"] == ["OBAN:association"] assert e2["frequencyOfPhenotype"] == "HP:0040283" @@ -294,14 +294,14 @@ def test_read_nt6(): assert e1["subject"] == "OMIM:166400" assert e1["object"] == "HP:0000006" assert e1["relation"] == "RO:0000091" - assert e1["type"] == "OBAN:association" - assert e1["has_evidence"] == "ECO:0000501" + assert e1["type"] == ["OBAN:association"] + assert e1["has_evidence"] == ["ECO:0000501"] e2 = edges["ORPHA:93262", "HP:0000505"][0] assert e2["subject"] == "ORPHA:93262" assert e2["object"] == "HP:0000505" assert e2["relation"] == "RO:0002200" - assert e2["type"] == "OBAN:association" + assert e2["type"] == ["OBAN:association"] assert e2["frequency_of_phenotype"] == "HP:0040283"