feat: Add API ontology querying module

.github/workflows/generate_all_ontology.yml

@@ -3,7 +3,7 @@ name: Updates to Ontology Files
 on:
   push:
     paths:
-      - "**/tools/ontology-builder/src/ontology-references/ontology_info.yml"
+      - "**/api/python/src/cellxgene_ontology_guide/fixtures/ontology_info.yml"
     branches-ignore:
       - main
 
@@ -36,7 +36,7 @@ jobs:
       - name: ontology-processing
         run: |
           python3 ./tools/ontology-builder/src/all_ontology_generator.py
-          git add ./tools/ontology-builder/src/ontology-references/all_ontology.json.gz
+          git add ./api/python/src/cellxgene_ontology_guide/fixtures/all_ontology.json.gz
       - name: Commit
         run: |
           git commit -m "AUTO: update ontologies"

api/python/pyproject.toml

@@ -12,9 +12,7 @@ authors = [
 license = { text = "MIT" }
 readme = "README.md"
 requires-python = "~= 3.11"
-dependencies = [
-    "owlready2"
-]
+dependencies = []
 
 [project.optional-dependencies]
 test = ["pytest"]

api/python/src/cellxgene_ontology_guide/env.py

@@ -0,0 +1,5 @@
+import os
+
+PACKAGE_ROOT = os.path.dirname(os.path.realpath(__file__))
+ALL_ONTOLOGY_JSON = os.path.join(PACKAGE_ROOT, "fixtures/all_ontology.json.gz")
+ONTOLOGY_INFO_YML = os.path.join(PACKAGE_ROOT, "fixtures/ontology_info.yml")

api/python/src/cellxgene_ontology_guide/query.py

@@ -0,0 +1,16 @@
+from typing import List
+
+import env
+import gzip
+import json
+
+with gzip.open(env.ALL_ONTOLOGY_JSON, "rt") as f:
+    ONTOLOGY_DICT = json.load(f)
+
+
+def get_ancestors(term_id: str) -> List[str]:
+    # TODO: Support List input, Dict return?
+    # TODO: Regex input validation?
+    # TODO: docstring
+    ontology_name = term_id.split(":")[0]
+    return ONTOLOGY_DICT[ontology_name][term_id]["ancestors"]

api/python/tests/test_query.py

@@ -0,0 +1,6 @@
+from cellxgene_ontology_guide import query
+
+
+def test_get_ancestors():
+    ancestors = query.get_ancestors("UBERON:0000966")
+    assert len(ancestors) == 39

tools/ontology-builder/src/env.py

@@ -1,7 +1,9 @@
 import os
 
 PACKAGE_ROOT = os.path.dirname(os.path.realpath(__file__))
+ROOT_DIR = os.path.dirname(os.path.dirname(os.path.dirname(PACKAGE_ROOT)))
+FIXTURES_ROOT = os.path.join(ROOT_DIR, "api/python/src/cellxgene_ontology_guide/fixtures")
 ONTOLOGY_REF_DIR = os.path.join(PACKAGE_ROOT, "ontology-references")
 RAW_ONTOLOGY_DIR = os.path.join(ONTOLOGY_REF_DIR, "raw-files")
-ONTO_INFO_YAML = os.path.join(ONTOLOGY_REF_DIR, "ontology_info.yml")
-PARSED_ONTOLOGIES_FILE = os.path.join(ONTOLOGY_REF_DIR, "all_ontology.json.gz")
+ONTO_INFO_YAML = os.path.join(FIXTURES_ROOT, "ontology_info.yml")
+PARSED_ONTOLOGIES_FILE = os.path.join(FIXTURES_ROOT, "all_ontology.json.gz")