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"sha256:837f2f0e0ca79481b92884962b914eba4e72b7a2daaf1f939c890ed0124b834b"}, - {file = "WTForms-3.0.1.tar.gz", hash = "sha256:6b351bbb12dd58af57ffef05bc78425d08d1914e0fd68ee14143b7ade023c5bc"}, -] +wtforms = [] yarl = [ {file = "yarl-1.7.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:f2a8508f7350512434e41065684076f640ecce176d262a7d54f0da41d99c5a95"}, {file = "yarl-1.7.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:da6df107b9ccfe52d3a48165e48d72db0eca3e3029b5b8cb4fe6ee3cb870ba8b"}, diff --git a/pyproject.toml b/pyproject.toml index df00c1d85..197a44b7d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,6 +26,7 @@ gilda = {version = "^0.10.1", optional = true} kgcl-rdflib = "^0.2.0" pystow = "^0.4.4" class-resolver = "^0.3.10" +ontoportal-client = "0.0.3" [tool.poetry.dev-dependencies] pytest = "^5.2" diff --git a/src/oaklib/implementations/bioportal/agroportal_implementation.py b/src/oaklib/implementations/bioportal/agroportal_implementation.py index 851e47050..196ae91d8 100644 --- a/src/oaklib/implementations/bioportal/agroportal_implementation.py +++ b/src/oaklib/implementations/bioportal/agroportal_implementation.py @@ -1,23 +1,17 @@ from dataclasses import dataclass -from oaklib.implementations import BioportalImplementation -from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface -from oaklib.interfaces.search_interface import SearchInterface -from oaklib.interfaces.text_annotator_interface import TextAnnotatorInterface +from ontoportal_client import AgroPortalClient + +from oaklib.implementations.ontoportal.ontoportal_implementation_base import ( + OntoPortalImplementationBase, +) @dataclass -class AgroportalImplementation( - BioportalImplementation, TextAnnotatorInterface, SearchInterface, MappingProviderInterface -): +class AgroportalImplementation(OntoPortalImplementationBase): """ Implementation over agroportal endpoint """ - @property - def _base_url(self) -> str: - return "http://data.agroportal.lirmm.fr/" - - def load_bioportal_api_key(self, path: str = None) -> None: - self.bioportal_api_key = "1de0a270-29c5-4dda-b043-7c3580628cd5" + ontoportal_client_class = AgroPortalClient diff --git a/src/oaklib/implementations/bioportal/bioportal_implementation.py b/src/oaklib/implementations/bioportal/bioportal_implementation.py index ea64ae0e1..eb262b9b8 100644 --- a/src/oaklib/implementations/bioportal/bioportal_implementation.py +++ b/src/oaklib/implementations/bioportal/bioportal_implementation.py @@ -1,285 +1,18 @@ -import logging -from dataclasses import dataclass, field -from typing import Any, Dict, Iterable, Iterator, List, Tuple, Union -from urllib.parse import quote +from dataclasses import dataclass -import requests -from sssom_schema import Mapping +from ontoportal_client import BioPortalClient -from oaklib.datamodels.search import SearchConfiguration -from oaklib.datamodels.text_annotator import TextAnnotation, TextAnnotationConfiguration -from oaklib.datamodels.vocabulary import SEMAPV -from oaklib.implementations.bioportal import SEARCH_CONFIG -from oaklib.interfaces.basic_ontology_interface import METADATA_MAP, PREFIX_MAP -from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface -from oaklib.interfaces.search_interface import SearchInterface -from oaklib.interfaces.text_annotator_interface import TextAnnotatorInterface -from oaklib.types import CURIE, URI -from oaklib.utilities.apikey_manager import get_apikey_value -from oaklib.utilities.rate_limiter import check_limit - -REST_URL = "http://data.bioontology.org" - -ANNOTATION = Dict[str, Any] - -# See: -# https://www.bioontology.org/wiki/BioPortal_Mappings -# https://github.com/agroportal/project-management/wiki/Mappings -SOURCE_TO_PREDICATE = { - "CUI": "skos:closeMatch", - "LOOM": "skos:closeMatch", - "REST": "skos:relatedMatch", # maybe?? - "SAME_URI": "skos:exactMatch", -} +from oaklib.implementations.ontoportal.ontoportal_implementation_base import ( + OntoPortalImplementationBase, +) @dataclass -class BioportalImplementation(TextAnnotatorInterface, SearchInterface, MappingProviderInterface): +class BioportalImplementation(OntoPortalImplementationBase): """ Implementation over bioportal endpoint See ``_ """ - bioportal_api_key: str = None - label_cache: Dict[CURIE, str] = field(default_factory=lambda: {}) - ontology_cache: Dict[URI, str] = field(default_factory=lambda: {}) - focus_ontology: str = None - - def __post_init__(self): - if self.focus_ontology is None: - if self.resource: - self.focus_ontology = self.resource.slug - - def prefix_map(self) -> PREFIX_MAP: - # TODO - return {} - - @property - def _base_url(self) -> str: - return REST_URL - - def load_bioportal_api_key(self, path: str = None) -> None: - self.bioportal_api_key = get_apikey_value("bioportal") - - def _headers(self) -> dict: - return {"Authorization": "apikey token=" + self.bioportal_api_key} - - def _bioportal_get(self, *args, raise_for_status=True, **kwargs): - if self.bioportal_api_key is None: - self.load_bioportal_api_key() - check_limit() - result = requests.get(*args, **kwargs, headers=self._headers()) - if raise_for_status: - result.raise_for_status() - # if result.status_code != 200: - # raise EnvironmentError - return result - - def ontologies(self) -> Iterable[CURIE]: - include = [] - include_str = ",".join(include) - params = {"include": include_str} - r = self._bioportal_get(self._base_url + "/ontologies", params=params) - results = r.json() - for result in results: - logging.debug(result) - yield result["acronym"] - - def ontology_versions(self, ontology: CURIE) -> Iterable[CURIE]: - r = self._bioportal_get(self._base_url + f"/ontologies/{ontology.upper()}/submissions") - r.raise_for_status() - for result in r.json(): - logging.debug(result) - yield result["version"] - - def ontology_metadata(self, ontology: CURIE) -> METADATA_MAP: - # TODO: normalize metadata - r = self._bioportal_get( - self._base_url + f"/ontologies/{ontology.upper()}/latest_submission" - ) - r.raise_for_status() - m = {} - submission_url = None - for k, v in r.json().items(): - if k == "@id": - k = "submission_uri" - submission_url = v - if k == "@type": - k = "type" - if isinstance(v, dict) or isinstance(v, list): - if k == "ontology": - if isinstance(v, dict): - m["id"] = v["acronym"] - m["title"] = v["name"] - else: - m[k] = v - if submission_url: - print(submission_url) - r = self._bioportal_get(f"{submission_url}/metrics") - r.raise_for_status() - for k, v in r.json().items(): - if isinstance(v, str) or isinstance(v, int) or isinstance(v, float): - if not k.startswith("@"): - m[k] = v - return m - - def labels(self, curies: Iterable[CURIE]) -> Iterable[Tuple[CURIE, str]]: - label_cache = self.label_cache - for curie in curies: - logging.debug(f"LOOKUP: {curie}") - if curie in label_cache: - yield curie, label_cache[curie] - else: - label = self.label(curie) - label_cache[curie] = label - yield curie, label - - def annotate_text( - self, text: str, configuration: TextAnnotationConfiguration = None - ) -> Iterator[TextAnnotation]: - if configuration is None: - configuration = TextAnnotationConfiguration() - logging.info(f"Annotating text: {text}") - # include =['prefLabel', 'synonym', 'definition', 'semanticType', 'cui'] - include = ["prefLabel", "semanticType", "cui"] - require_exact_match = True - include_str = ",".join(include) - params = {"include": include_str, "require_exact_match": require_exact_match, "text": text} - if self.resource and self.resource.slug: - params["ontologies"] = self.resource.slug.upper() - r = self._bioportal_get(self._base_url + "/annotator", params=params) - return self._annotator_json_to_results(r.json(), text, configuration) - - def _annotator_json_to_results( - self, json_list: List[Any], text: str, configuration: TextAnnotationConfiguration = None - ) -> Iterator[TextAnnotation]: - seen = {} - for obj in json_list: - ac_obj = obj["annotatedClass"] - for x in obj["annotations"]: - try: - ann = TextAnnotation( - subject_start=x["from"], - subject_end=x["to"], - subject_label=x["text"], - object_id=self.uri_to_curie(ac_obj["@id"]), - object_label=ac_obj["prefLabel"], - object_source=ac_obj["links"]["ontology"], - match_type=x["matchType"], - # info=str(obj) - ) - if len(text) == ann.subject_end and ann.subject_start == 1: - ann.matches_whole_text = True - if ( - configuration - and configuration.matches_whole_text - and not ann.matches_whole_text - ): - continue - uid = ann.subject_start, ann.subject_end, ann.object_id - if uid in seen: - logging.debug(f"Skipping duplicative annotation to {ann.object_source}") - continue - seen[uid] = True - yield ann - except KeyError: - # TODO: we should never catch exceptions in this way; - # this is temporary until we figure out why sometimes BP payloads - # lack some keys such as prefLabel - logging.error(f"Missing keys in annotation: {x} in {obj} when parsing {text}") - - # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - # Implements: SearchInterface - # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - def basic_search( - self, search_term: str, config: SearchConfiguration = SEARCH_CONFIG - ) -> Iterable[CURIE]: - params = {"q": search_term, "include": ["prefLabel"]} - if self.focus_ontology: - # Ontology acronyms in BioPortal are always uppercase - params["ontologies"] = self.focus_ontology.upper() - r = self._bioportal_get(self._base_url + "/search", params) - obj = r.json() - logging.debug(f"Search obj={obj}") - collection = obj["collection"] - while len(collection) > 0: - result = collection[0] - curie = self.uri_to_curie(result["@id"]) - label = result.get("prefLabel", None) - self.label_cache[curie] = label - logging.debug(f"M: {curie} => {label}") - yield curie - collection = collection[1:] - if len(collection) == 0: - next_page = obj["links"]["nextPage"] - if next_page: - check_limit() - r = requests.get(next_page, headers=self._headers()) - obj = r.json() - collection = obj["collection"] - - # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - # Implements: MappingProviderInterface - # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - def get_sssom_mappings_by_curie(self, id: Union[CURIE, URI]) -> Iterable[Mapping]: - ontology, class_uri = self._get_ontology_and_uri_from_id(id) - # This may return lots of duplicate mappings - # See: https://github.com/ncbo/ontologies_linked_data/issues/117 - quoted_class_uri = quote(class_uri, safe="") - req_url = f"{self._base_url}/ontologies/{ontology}/classes/{quoted_class_uri}/mappings" - logging.debug(req_url) - response = self._bioportal_get( - req_url, params={"display_context": "false"}, raise_for_status=False - ) - if response.status_code != requests.codes.ok: - logging.warning(f"Could not fetch mappings for {id}") - return [] - body = response.json() - for result in body: - yield self.result_to_mapping(result) - - def result_to_mapping(self, result: Dict[str, Any]) -> Mapping: - subject = result["classes"][0] - object = result["classes"][1] - self.add_uri_to_ontology_mapping(subject) - self.add_uri_to_ontology_mapping(object) - mapping = Mapping( - subject_id=subject["@id"], - predicate_id=SOURCE_TO_PREDICATE[result["source"]], - mapping_justification=SEMAPV.UnspecifiedMatching.value, - object_id=object["@id"], - mapping_provider=result["@type"], - mapping_tool=result["source"], - ) - return mapping - - def add_uri_to_ontology_mapping(self, ont_class: Dict[str, Any]) -> None: - ontology_url = ont_class["links"]["ontology"] - acronym = ontology_url.rsplit("/", 1)[-1] - self.ontology_cache[ont_class["@id"]] = acronym - - def ancestors(self, uri: URI) -> Iterable[URI]: - ontology, uri = self._get_ontology_and_uri_from_id(uri) - quoted_uri = quote(uri, safe="") - request_url = f"{self._base_url}/ontologies/{ontology}/classes/{quoted_uri}/ancestors" - logging.debug(request_url) - response = self._bioportal_get(request_url, params={"display_context": "false"}) - if response.status_code != requests.codes.ok: - logging.warning(f"Could not fetch ancestors for {uri}") - return [] - body = response.json() - for ancestor in body: - self.add_uri_to_ontology_mapping(ancestor) - yield ancestor["@id"] - - def _get_ontology_and_uri_from_id(self, id: Union[CURIE, URI]) -> Tuple[str, URI]: - if id in self.ontology_cache: - ontology = self.ontology_cache[id] - uri = id - else: - ontology = id.split(":", 1)[0] - uri = self.curie_to_uri(id) - return ontology, uri + ontoportal_client_class = BioPortalClient diff --git a/.tox/.package.lock b/src/oaklib/implementations/ontoportal/__init__.py old mode 100755 new mode 100644 similarity index 100% rename from .tox/.package.lock rename to src/oaklib/implementations/ontoportal/__init__.py diff --git a/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py b/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py new file mode 100644 index 000000000..554617a0b --- /dev/null +++ b/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py @@ -0,0 +1,266 @@ +import logging +from abc import ABC +from dataclasses import dataclass, field +from typing import Any, ClassVar, Dict, Iterable, Iterator, List, Tuple, Union +from urllib.parse import quote + +import requests +from ontoportal_client.api import PreconfiguredOntoPortalClient +from sssom_schema import Mapping + +from oaklib.datamodels.search import SearchConfiguration +from oaklib.datamodels.text_annotator import TextAnnotation, TextAnnotationConfiguration +from oaklib.datamodels.vocabulary import SEMAPV +from oaklib.interfaces import ( + MappingProviderInterface, + SearchInterface, + TextAnnotatorInterface, +) +from oaklib.interfaces.basic_ontology_interface import METADATA_MAP, PREFIX_MAP +from oaklib.types import CURIE, URI +from oaklib.utilities.apikey_manager import get_apikey_value +from oaklib.utilities.rate_limiter import check_limit + +SEARCH_CONFIG = SearchConfiguration() + +# See: +# https://www.bioontology.org/wiki/BioPortal_Mappings +# https://github.com/agroportal/project-management/wiki/Mappings +SOURCE_TO_PREDICATE = { + "CUI": "skos:closeMatch", + "LOOM": "skos:closeMatch", + "REST": "skos:relatedMatch", # maybe?? + "SAME_URI": "skos:exactMatch", +} + + +@dataclass +class OntoPortalImplementationBase( + TextAnnotatorInterface, SearchInterface, MappingProviderInterface, ABC +): + + ontoportal_client_class: ClassVar[type[PreconfiguredOntoPortalClient]] = None + + label_cache: Dict[CURIE, str] = field(default_factory=lambda: {}) + ontology_cache: Dict[URI, str] = field(default_factory=lambda: {}) + focus_ontology: str = None + + def __post_init__(self): + if self.focus_ontology is None: + if self.resource: + self.focus_ontology = self.resource.slug + if not self.ontoportal_client_class: + raise NotImplementedError("ontoportal_client_class not specified") + api_key = get_apikey_value(self.ontoportal_client_class.name) + self.client = self.ontoportal_client_class(api_key=api_key) + + def prefix_map(self) -> PREFIX_MAP: + # TODO + return {} + + def _get_response(self, *args, **kwargs): + check_limit() + return self.client.get_response(*args, **kwargs) + + def _get_json(self, *args, **kwargs): + response = self._get_response(*args, **kwargs) + return response.json() + + def ontologies(self) -> Iterable[CURIE]: + include = [] + include_str = ",".join(include) + params = {"include": include_str} + results = self._get_json("/ontologies", params=params) + for result in results: + logging.debug(result) + yield result["acronym"] + + def ontology_versions(self, ontology: CURIE) -> Iterable[CURIE]: + results = self._get_json(f"/ontologies/{ontology.upper()}/submissions") + for result in results: + logging.debug(result) + yield result["version"] + + def ontology_metadata(self, ontology: CURIE) -> METADATA_MAP: + # TODO: normalize metadata + results = self._get_json(f"/ontologies/{ontology.upper()}/latest_submission") + m = {} + submission_url = None + for k, v in results.items(): + if k == "@id": + k = "submission_uri" + submission_url = v + if k == "@type": + k = "type" + if isinstance(v, dict) or isinstance(v, list): + if k == "ontology": + if isinstance(v, dict): + m["id"] = v["acronym"] + m["title"] = v["name"] + else: + m[k] = v + if submission_url: + logging.info(submission_url) + results = self._get_json(f"{submission_url}/metrics") + for k, v in results.items(): + if isinstance(v, str) or isinstance(v, int) or isinstance(v, float): + if not k.startswith("@"): + m[k] = v + return m + + def labels(self, curies: Iterable[CURIE]) -> Iterable[Tuple[CURIE, str]]: + label_cache = self.label_cache + for curie in curies: + logging.debug(f"LOOKUP: {curie}") + if curie in label_cache: + yield curie, label_cache[curie] + else: + label = self.label(curie) + label_cache[curie] = label + yield curie, label + + def annotate_text( + self, text: str, configuration: TextAnnotationConfiguration = None + ) -> Iterator[TextAnnotation]: + if configuration is None: + configuration = TextAnnotationConfiguration() + logging.info(f"Annotating text: {text}") + # include =['prefLabel', 'synonym', 'definition', 'semanticType', 'cui'] + include = ["prefLabel", "semanticType", "cui"] + require_exact_match = True + include_str = ",".join(include) + params = {"include": include_str, "require_exact_match": require_exact_match, "text": text} + if self.resource and self.resource.slug: + params["ontologies"] = self.resource.slug.upper() + results = self._get_json("/annotator", params=params) + return self._annotator_json_to_results(results, text, configuration) + + def _annotator_json_to_results( + self, json_list: List[Any], text: str, configuration: TextAnnotationConfiguration = None + ) -> Iterator[TextAnnotation]: + seen = {} + for obj in json_list: + ac_obj = obj["annotatedClass"] + for x in obj["annotations"]: + try: + ann = TextAnnotation( + subject_start=x["from"], + subject_end=x["to"], + subject_label=x["text"], + object_id=self.uri_to_curie(ac_obj["@id"]), + object_label=ac_obj["prefLabel"], + object_source=ac_obj["links"]["ontology"], + match_type=x["matchType"], + # info=str(obj) + ) + if len(text) == ann.subject_end and ann.subject_start == 1: + ann.matches_whole_text = True + if ( + configuration + and configuration.matches_whole_text + and not ann.matches_whole_text + ): + continue + uid = ann.subject_start, ann.subject_end, ann.object_id + if uid in seen: + logging.debug(f"Skipping duplicative annotation to {ann.object_source}") + continue + seen[uid] = True + yield ann + except KeyError: + # TODO: we should never catch exceptions in this way; + # this is temporary until we figure out why sometimes BP payloads + # lack some keys such as prefLabel + logging.error(f"Missing keys in annotation: {x} in {obj} when parsing {text}") + + # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + # Implements: SearchInterface + # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + + def basic_search( + self, search_term: str, config: SearchConfiguration = SEARCH_CONFIG + ) -> Iterable[CURIE]: + params = {"q": search_term, "include": ["prefLabel"]} + if self.focus_ontology: + # Ontology acronyms in BioPortal are always uppercase + params["ontologies"] = self.focus_ontology.upper() + obj = self._get_json("/search", params) + logging.debug(f"Search obj={obj}") + collection = obj["collection"] + while len(collection) > 0: + result = collection[0] + curie = self.uri_to_curie(result["@id"]) + label = result.get("prefLabel", None) + self.label_cache[curie] = label + logging.debug(f"M: {curie} => {label}") + yield curie + collection = collection[1:] + if len(collection) == 0: + next_page = obj["links"]["nextPage"] + if next_page: + obj = self._get_json(next_page) + collection = obj["collection"] + + # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + # Implements: MappingProviderInterface + # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + + def get_sssom_mappings_by_curie(self, id: Union[CURIE, URI]) -> Iterable[Mapping]: + ontology, class_uri = self._get_ontology_and_uri_from_id(id) + # This may return lots of duplicate mappings + # See: https://github.com/ncbo/ontologies_linked_data/issues/117 + quoted_class_uri = quote(class_uri, safe="") + req_url = f"/ontologies/{ontology}/classes/{quoted_class_uri}/mappings" + logging.debug(req_url) + response = self._get_response( + req_url, params={"display_context": "false"}, raise_for_status=False + ) + if response.status_code != requests.codes.ok: + logging.warning(f"Could not fetch mappings for {id}") + return [] + body = response.json() + for result in body: + yield self.result_to_mapping(result) + + def result_to_mapping(self, result: Dict[str, Any]) -> Mapping: + subject = result["classes"][0] + object = result["classes"][1] + self.add_uri_to_ontology_mapping(subject) + self.add_uri_to_ontology_mapping(object) + mapping = Mapping( + subject_id=subject["@id"], + predicate_id=SOURCE_TO_PREDICATE[result["source"]], + mapping_justification=SEMAPV.UnspecifiedMatching.value, + object_id=object["@id"], + mapping_provider=result["@type"], + mapping_tool=result["source"], + ) + return mapping + + def add_uri_to_ontology_mapping(self, ont_class: Dict[str, Any]) -> None: + ontology_url = ont_class["links"]["ontology"] + acronym = ontology_url.rsplit("/", 1)[-1] + self.ontology_cache[ont_class["@id"]] = acronym + + def ancestors(self, uri: URI) -> Iterable[URI]: + ontology, uri = self._get_ontology_and_uri_from_id(uri) + quoted_uri = quote(uri, safe="") + request_url = f"/ontologies/{ontology}/classes/{quoted_uri}/ancestors" + logging.debug(request_url) + response = self._get_response(request_url, params={"display_context": "false"}) + if response.status_code != requests.codes.ok: + logging.warning(f"Could not fetch ancestors for {uri}") + return [] + body = response.json() + for ancestor in body: + self.add_uri_to_ontology_mapping(ancestor) + yield ancestor["@id"] + + def _get_ontology_and_uri_from_id(self, id: Union[CURIE, URI]) -> Tuple[str, URI]: + if id in self.ontology_cache: + ontology = self.ontology_cache[id] + uri = id + else: + ontology = id.split(":", 1)[0] + uri = self.curie_to_uri(id) + return ontology, uri diff --git a/tests/test_implementations/test_bioportal.py b/tests/test_implementations/test_bioportal.py index ecd1945fb..8a5225e10 100644 --- a/tests/test_implementations/test_bioportal.py +++ b/tests/test_implementations/test_bioportal.py @@ -7,6 +7,7 @@ from oaklib.implementations.bioportal.bioportal_implementation import ( BioportalImplementation, ) +from oaklib.utilities.apikey_manager import get_apikey_value from tests import DIGIT, HUMAN, NEURON, VACUOLE @@ -16,11 +17,12 @@ class TestBioportal(unittest.TestCase): """ def setUp(self) -> None: - impl = BioportalImplementation() + cls = BioportalImplementation try: - impl.load_bioportal_api_key() + get_apikey_value(cls.ontoportal_client_class.name) except ValueError: self.skipTest("Skipping bioportal tests, no API key set") + impl = cls() self.impl = impl def test_text_annotator(self): @@ -34,6 +36,11 @@ def test_search(self): results = list(itertools.islice(self.impl.basic_search("tentacle pocket"), 20)) assert "CEPH:0000259" in results + def test_search_pagination(self): + # bioportal defaults to pagesize=50 so this should require 3 pages of results + results = list(itertools.islice(self.impl.basic_search("brain"), 150)) + self.assertIn("CLAO:0001044", results) + def test_mappings(self): mappings = list(self.impl.get_sssom_mappings_by_curie(DIGIT)) for m in mappings: @@ -51,3 +58,24 @@ def test_ancestors(self): ancestors = list(self.impl.ancestors(VACUOLE)) assert "http://purl.obolibrary.org/obo/GO_0005575" in ancestors # cellular_component assert "http://purl.obolibrary.org/obo/GO_0005737" in ancestors # cytoplasm + + def test_ontologies(self): + ontologies = list(self.impl.ontologies()) + self.assertTrue(ontologies) + self.assertIn("OBI", ontologies) + self.assertIn("UBERON", ontologies) + + def test_ontology_versions(self): + versions = list(self.impl.ontology_versions("FMA")) + self.assertTrue(versions) + self.assertIn("5.0.0", versions) + self.assertIn("v3.2.1", versions) + + def test_ontology_metadata(self): + metadata = self.impl.ontology_metadata("OBI") + self.assertIn("title", metadata) + self.assertEqual(metadata["title"], "Ontology for Biomedical Investigations") + self.assertIn("homepage", metadata) + self.assertEqual(metadata["homepage"], "http://purl.obolibrary.org/obo/obi") + self.assertIn("classes", metadata) + self.assertIsInstance(metadata["classes"], int)