diff --git a/latest/_modules/hpotk/store/_api.html b/latest/_modules/hpotk/store/_api.html index 3ad8fa3..2b79a79 100644 --- a/latest/_modules/hpotk/store/_api.html +++ b/latest/_modules/hpotk/store/_api.html @@ -172,8 +172,8 @@

Source code for hpotk.store._api

 [docs]
     @abc.abstractmethod
     def fetch_tags(
-            self,
-            ontology_type: OntologyType,
+        self,
+        ontology_type: OntologyType,
     ) -> typing.Iterable[str]:
         """
         Fetch sequence of tags for an ontology.
@@ -194,10 +194,10 @@ 
Source code for hpotk.store._api
     """
 
     def __init__(
-            self,
-            store_dir: str,
-            ontology_release_service: OntologyReleaseService,
-            remote_ontology_service: RemoteOntologyService,
+        self,
+        store_dir: str,
+        ontology_release_service: OntologyReleaseService,
+        remote_ontology_service: RemoteOntologyService,
     ):
         self._logger = logging.getLogger(__name__)
         self._store_dir = store_dir
diff --git a/latest/_modules/hpotk/store/_config.html b/latest/_modules/hpotk/store/_config.html
index 16db102..0e6baf0 100644
--- a/latest/_modules/hpotk/store/_config.html
+++ b/latest/_modules/hpotk/store/_config.html
@@ -88,9 +88,9 @@ 
Source code for hpotk.store._config
 

 [docs]
 def configure_ontology_store(
-        store_dir: typing.Optional[str] = None,
-        ontology_release_service: OntologyReleaseService = GitHubOntologyReleaseService(),
-        remote_ontology_service: RemoteOntologyService = GitHubRemoteOntologyService(),
+    store_dir: typing.Optional[str] = None,
+    ontology_release_service: OntologyReleaseService = GitHubOntologyReleaseService(),
+    remote_ontology_service: RemoteOntologyService = GitHubRemoteOntologyService(),
 ) -> OntologyStore:
     """
     Configure and create the default ontology store.
@@ -107,7 +107,7 @@ 
Source code for hpotk.store._config
         store_dir = get_default_ontology_store_dir()
     else:
         if not os.path.isdir(store_dir):
-            raise ValueError(f'`store_dir` must point to an existing directory')
+            raise ValueError('`store_dir` must point to an existing directory')
     return OntologyStore(
         store_dir=store_dir,
         ontology_release_service=ontology_release_service,
diff --git a/latest/_modules/hpotk/store/_github.html b/latest/_modules/hpotk/store/_github.html
index e443739..3d95f4d 100644
--- a/latest/_modules/hpotk/store/_github.html
+++ b/latest/_modules/hpotk/store/_github.html
@@ -78,6 +78,7 @@ 
Source code for hpotk.store._github
 import io
 import json
 import logging
+import re
 import ssl
 import typing
 from urllib.request import urlopen
@@ -87,22 +88,31 @@ 
Source code for hpotk.store._github
 from ._api import OntologyType, OntologyReleaseService, RemoteOntologyService
 
 
+production_tag_pt = r'^v(?P<year>\d{4})-(?P<month>\d{2})-(?P<day>\d{2})$'
+"""
+A tag pattern to ensure we only include the "production" tags (e.g. not `v2024-12-12X`).
+"""
+
+
 ONTOLOGY_CREDENTIALS = {
         OntologyType.HPO: {
             'owner': 'obophenotype',
             'repo': 'human-phenotype-ontology',
+            'tag_pt': production_tag_pt,
         },
         OntologyType.MAxO: {
             'owner': 'monarch-initiative',
             'repo': 'MAxO',
+            'tag_pt': production_tag_pt,
         },
         OntologyType.MONDO: {
             'owner': 'monarch-initiative',
             'repo': 'mondo',
+            'tag_pt': production_tag_pt,
         },
     }
 """
-The default ontology credentials that only include HPO at the time.
+The default ontology credentials that only include HPO, MAxO, and MONDO at this time.
 """
 
 
@@ -114,9 +124,9 @@ 
Source code for hpotk.store._github
     """
 
     def __init__(
-            self,
-            timeout: int = 10,
-            ontology_credentials: typing.Mapping[OntologyType, typing.Mapping[str, str]] = ONTOLOGY_CREDENTIALS,
+        self,
+        timeout: int = 10,
+        ontology_credentials: typing.Mapping[OntologyType, typing.Mapping[str, str]] = ONTOLOGY_CREDENTIALS,
     ):
         self._logger = logging.getLogger(__name__)
         self._timeout = timeout
@@ -137,21 +147,23 @@ 
Source code for hpotk.store._github
         return self._get_tag_names(
             owner=credentials['owner'],
             repo=credentials['repo'],
+            tag_pt=credentials['tag_pt'],
         )

 
 
     def _get_tag_names(
-            self,
-            owner: str,
-            repo: str,
+        self,
+        owner: str,
+        repo: str,
+        tag_pt: str,
     ) -> typing.Iterable[str]:
         tag_url = self._tag_api_url.format(owner=owner, repo=repo)
         self._logger.debug('Pulling tag from %s', tag_url)
 
         with urlopen(
-                tag_url,
-                timeout=self._timeout,
-                context=self._ctx,
+            tag_url,
+            timeout=self._timeout,
+            context=self._ctx,
         ) as fh:
             tags = json.load(fh)
 
@@ -160,7 +172,11 @@ 
Source code for hpotk.store._github
         else:
             self._logger.debug('Fetched %d tags', len(tags))
 
-        return (tag['name'] for tag in tags)

+        pattern = re.compile(tag_pt)
+        return filter(
+            lambda tag: pattern.match(tag),
+            (tag['name'] for tag in tags),
+        )

 
 
 
diff --git a/latest/apidocs/hpotk.store.html b/latest/apidocs/hpotk.store.html
index bc236a9..e8e399c 100644
--- a/latest/apidocs/hpotk.store.html
+++ b/latest/apidocs/hpotk.store.html
@@ -366,7 +366,7 @@
 
 

 

-class hpotk.store.GitHubRemoteOntologyService(timeout: int = 10, ontology_credentials: Mapping[OntologyType, Mapping[str, str]] = {OntologyType.HPO: {'owner': 'obophenotype', 'repo': 'human-phenotype-ontology'}, OntologyType.MAxO: {'owner': 'monarch-initiative', 'repo': 'MAxO'}, OntologyType.MONDO: {'owner': 'monarch-initiative', 'repo': 'mondo'}})[source]

+class hpotk.store.GitHubRemoteOntologyService(timeout: int = 10, ontology_credentials: Mapping[OntologyType, Mapping[str, str]] = {OntologyType.HPO: {'owner': 'obophenotype', 'repo': 'human-phenotype-ontology', 'tag_pt': '^v(?P<year>\\d{4})-(?P<month>\\d{2})-(?P<day>\\d{2})$'}, OntologyType.MAxO: {'owner': 'monarch-initiative', 'repo': 'MAxO', 'tag_pt': '^v(?P<year>\\d{4})-(?P<month>\\d{2})-(?P<day>\\d{2})$'}, OntologyType.MONDO: {'owner': 'monarch-initiative', 'repo': 'mondo', 'tag_pt': '^v(?P<year>\\d{4})-(?P<month>\\d{2})-(?P<day>\\d{2})$'}})[source]
 
Bases: RemoteOntologyService

 
GitHubRemoteOntologyService knows how to fetch ontology data from GitHub.

 
The Obographs JSON files are fetched and only HPO is supported as of now.

@@ -391,7 +391,7 @@
 
 

 

-class hpotk.store.GitHubOntologyReleaseService(timeout: int = 10, ontology_credentials: Mapping[OntologyType, Mapping[str, str]] = {OntologyType.HPO: {'owner': 'obophenotype', 'repo': 'human-phenotype-ontology'}, OntologyType.MAxO: {'owner': 'monarch-initiative', 'repo': 'MAxO'}, OntologyType.MONDO: {'owner': 'monarch-initiative', 'repo': 'mondo'}})[source]

+class hpotk.store.GitHubOntologyReleaseService(timeout: int = 10, ontology_credentials: Mapping[OntologyType, Mapping[str, str]] = {OntologyType.HPO: {'owner': 'obophenotype', 'repo': 'human-phenotype-ontology', 'tag_pt': '^v(?P<year>\\d{4})-(?P<month>\\d{2})-(?P<day>\\d{2})$'}, OntologyType.MAxO: {'owner': 'monarch-initiative', 'repo': 'MAxO', 'tag_pt': '^v(?P<year>\\d{4})-(?P<month>\\d{2})-(?P<day>\\d{2})$'}, OntologyType.MONDO: {'owner': 'monarch-initiative', 'repo': 'mondo', 'tag_pt': '^v(?P<year>\\d{4})-(?P<month>\\d{2})-(?P<day>\\d{2})$'}})[source]
 
Bases: OntologyReleaseService

 
GitHubOntologyReleaseService can fetch the ontology tags from GitHub.

 

diff --git a/latest/searchindex.js b/latest/searchindex.js
index f9ca571..0b613ed 100644
--- a/latest/searchindex.js
+++ b/latest/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"API reference": [[24, null]], "Augmenting term with ancestors/descendants": [[31, "augmenting-term-with-ancestors-descendants"]], "Contents:": [[25, null], [27, null]], "Disease model": [[28, "disease-model"]], "Do not use obsolete term ids": [[33, "do-not-use-obsolete-term-ids"]], "Feedback": [[25, "feedback"]], "HPO annotations": [[28, null]], "Hierarchical sorting": [[30, "hierarchical-sorting"]], "Hierarchy traversals": [[31, "hierarchy-traversals"]], "Hierarchy-based tests": [[31, "hierarchy-based-tests"]], "Indices and tables": [[25, "indices-and-tables"]], "Iterators vs. collections": [[31, "iterators-vs-collections"]], "Load HPO annotations": [[28, "id1"]], "Load ontology": [[29, null]], "Loading other ontologies": [[29, "loading-other-ontologies"]], "Low level loader": [[29, "low-level-loader"]], "Minimal ontology": [[32, "minimal-ontology"]], "Next steps": [[29, "next-steps"]], "Ontology": [[32, "ontology"]], "Ontology loaders": [[29, "ontology-loaders"]], "Ontology store": [[29, "ontology-store"]], "Phenotypic features should be descendants of Phenotypic abnormality": [[33, "phenotypic-features-should-be-descendants-of-phenotypic-abnormality"]], "Phenotypic features should not violate the annotation propagation rule": [[33, "phenotypic-features-should-not-violate-the-annotation-propagation-rule"]], "Run benches": [[26, "run-benches"]], "Run tests": [[26, "run-tests"]], "Setup": [[26, null]], "Sorting term IDs": [[30, null]], "Stable code": [[26, "stable-code"]], "Submodules": [[7, "submodules"]], "Subpackages": [[0, "subpackages"], [1, "subpackages"], [3, "subpackages"], [4, "subpackages"], [6, "subpackages"], [14, "subpackages"], [17, "subpackages"], [18, "subpackages"], [21, "subpackages"]], "Support for other ontologies": [[29, "support-for-other-ontologies"]], "The bleeding edge code": [[26, "the-bleeding-edge-code"]], "Use ontology": [[32, null]], "Use ontology hierarchy": [[31, null]], "User guide": [[27, null]], "Validate phenotypic features": [[33, null]], "Validation pipeline": [[33, "validation-pipeline"]], "Welcome to HPO Toolkit\u2019s documentation!": [[25, null]], "hpotk package": [[0, null]], "hpotk.algorithm package": [[1, null]], "hpotk.algorithm.similarity package": [[2, null]], "hpotk.annotations package": [[3, null]], "hpotk.annotations.load package": [[4, null]], "hpotk.annotations.load.hpoa package": [[5, null]], "hpotk.constants package": [[6, null]], "hpotk.constants.hpo package": [[7, null]], "hpotk.constants.hpo.base module": [[8, null]], "hpotk.constants.hpo.frequency module": [[9, null]], "hpotk.constants.hpo.inheritance module": [[10, null]], "hpotk.constants.hpo.onset module": [[11, null]], "hpotk.constants.hpo.organ_system module": [[12, null]], "hpotk.constants.hpo.severity module": [[13, null]], "hpotk.graph package": [[14, null]], "hpotk.graph.csr package": [[15, null]], "hpotk.model package": [[16, null]], "hpotk.ontology package": [[17, null]], "hpotk.ontology.load package": [[18, null]], "hpotk.ontology.load.obographs package": [[19, null]], "hpotk.store package": [[20, null]], "hpotk.util package": [[21, null]], "hpotk.util.sort package": [[22, null]], "hpotk.validate package": [[23, null]]}, "docnames": ["apidocs/hpotk", "apidocs/hpotk.algorithm", "apidocs/hpotk.algorithm.similarity", "apidocs/hpotk.annotations", "apidocs/hpotk.annotations.load", "apidocs/hpotk.annotations.load.hpoa", "apidocs/hpotk.constants", "apidocs/hpotk.constants.hpo", "apidocs/hpotk.constants.hpo.base", "apidocs/hpotk.constants.hpo.frequency", "apidocs/hpotk.constants.hpo.inheritance", "apidocs/hpotk.constants.hpo.onset", "apidocs/hpotk.constants.hpo.organ_system", "apidocs/hpotk.constants.hpo.severity", "apidocs/hpotk.graph", "apidocs/hpotk.graph.csr", "apidocs/hpotk.model", "apidocs/hpotk.ontology", "apidocs/hpotk.ontology.load", "apidocs/hpotk.ontology.load.obographs", "apidocs/hpotk.store", "apidocs/hpotk.util", "apidocs/hpotk.util.sort", 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(hpotk.model.frequencyawarefeature static method)": [[16, "hpotk.model.FrequencyAwareFeature.check_numerator_and_denominator", false]], "clear() (hpotk.ontologystore method)": [[0, "hpotk.OntologyStore.clear", false]], "clear() (hpotk.store.ontologystore method)": [[20, "hpotk.store.OntologyStore.clear", false]], "clinical_modifier (in module hpotk.constants.hpo.base)": [[8, "hpotk.constants.hpo.base.CLINICAL_MODIFIER", false]], "cohort_size (hpotk.annotations.load.hpoa.simplehpoadiseaseloader property)": [[5, "hpotk.annotations.load.hpoa.SimpleHpoaDiseaseLoader.cohort_size", false]], "comment (hpotk.model.term property)": [[16, "hpotk.model.Term.comment", false]], "comment (hpotk.term property)": [[0, "hpotk.Term.comment", false]], "configure_ontology_store() (in module hpotk)": [[0, "hpotk.configure_ontology_store", false]], "configure_ontology_store() (in module hpotk.store)": [[20, "hpotk.store.configure_ontology_store", false]], "create_graph() (hpotk.graph.csrindexedgraphfactory 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"ye": 33, "year": 20, "yet": [0, 20], "you": [0, 14, 16, 26, 31], "your": [25, 26]}, "titles": ["hpotk package", "hpotk.algorithm package", "hpotk.algorithm.similarity package", "hpotk.annotations package", "hpotk.annotations.load package", "hpotk.annotations.load.hpoa package", "hpotk.constants package", "hpotk.constants.hpo package", "hpotk.constants.hpo.base module", "hpotk.constants.hpo.frequency module", "hpotk.constants.hpo.inheritance module", "hpotk.constants.hpo.onset module", "hpotk.constants.hpo.organ_system module", "hpotk.constants.hpo.severity module", "hpotk.graph package", "hpotk.graph.csr package", "hpotk.model package", "hpotk.ontology package", "hpotk.ontology.load package", "hpotk.ontology.load.obographs package", "hpotk.store package", "hpotk.util package", "hpotk.util.sort package", "hpotk.validate package", "API reference", "Welcome to HPO Toolkit\u2019s documentation!", "Setup", "User guide", "HPO annotations", "Load ontology", "Sorting term IDs", "Use ontology 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