Merge pull request #77 from ielis:improve-release-tag-handling

Improve ontology release tag handling
ielis · Dec 12, 2024 · f1b8895 · f1b8895
2 parents 7d8bca6 + 10317b6
commit f1b8895
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Showing 4 changed files with 46 additions and 21 deletions.
diff --git a/src/hpotk/store/_api.py b/src/hpotk/store/_api.py
@@ -82,8 +82,8 @@ class OntologyReleaseService(metaclass=abc.ABCMeta):
 
     @abc.abstractmethod
     def fetch_tags(
-            self,
-            ontology_type: OntologyType,
+        self,
+        ontology_type: OntologyType,
     ) -> typing.Iterable[str]:
         """
         Fetch sequence of tags for an ontology.
@@ -100,10 +100,10 @@ class OntologyStore:
     """
 
     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/src/hpotk/store/_config.py b/src/hpotk/store/_config.py
@@ -9,9 +9,9 @@
 
 
 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.
@@ -28,7 +28,7 @@ def configure_ontology_store(
         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/src/hpotk/store/_github.py b/src/hpotk/store/_github.py
@@ -1,6 +1,7 @@
 import io
 import json
 import logging
+import re
 import ssl
 import typing
 from urllib.request import urlopen
@@ -10,22 +11,31 @@
 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.
 """
 
 
@@ -35,9 +45,9 @@ class GitHubOntologyReleaseService(OntologyReleaseService):
     """
 
     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
@@ -56,20 +66,22 @@ def fetch_tags(self, ontology_type: OntologyType) -> typing.Iterable[str]:
         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)
 
@@ -78,7 +90,11 @@ def _get_tag_names(
         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),
+        )
 
 
 class GitHubRemoteOntologyService(RemoteOntologyService):

diff --git a/tests/test_store.py b/tests/test_store.py
@@ -173,6 +173,15 @@ def initialize_store_dir(store_dir: Path):
         mondo_path.joinpath("x.txt").touch()
         mondo_path.joinpath("y.txt").touch()
 
+    @pytest.mark.skip("Just for manual debugging")
+    def test_resolve_store_path__latest(
+        self,
+        ontology_store: hpotk.OntologyStore,
+    ):
+        latest = ontology_store.resolve_store_path(hpotk.store.OntologyType.HPO)
+        print(latest)
+
+
 @pytest.mark.online
 class TestGitHubOntologyStoreOnline:
     """