Merge pull request #65 from TheJacksonLaboratory/G3-247-update-genese…

…t-get-endpoint-to-include-ontology-term-filter

Adding the ontology term filter to genesets

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.5.0"
+version = "0.6.0a0"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <[email protected]>",
@@ -20,7 +20,7 @@ python = "^3.9"
 geneweaver-core = "^0.9.1"
 fastapi = {extras = ["all"], version = "^0.99.1"}
 uvicorn = {extras = ["standard"], version = "^0.24.0"}
-geneweaver-db = "^0.3.8"
+geneweaver-db = "0.4.0a1"
 psycopg-pool = "^3.1.7"
 requests = "^2.31.0"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}

src/geneweaver/api/controller/genesets.py

@@ -63,6 +63,7 @@ def get_visible_genesets(
         ),
     ] = None,
     gene_id_type: Optional[GeneIdentifier] = None,
+    ontology_term: Optional[str] = None,
     search_text: Annotated[
         Optional[str], Query(description=api_message.SEARCH_TEXT)
     ] = None,
@@ -102,6 +103,7 @@ def get_visible_genesets(
         gene_id_type=gene_id_type,
         search_text=search_text,
         with_publication_info=with_publication_info,
+        ontology_term=ontology_term,
         only_my_genesets=only_my_genesets,
         limit=limit,
         offset=offset,

src/geneweaver/api/services/geneset.py

@@ -27,14 +27,17 @@ def get_visible_genesets(
     pubmed_id: Optional[int] = None,
     gene_id_type: Optional[GeneIdentifier] = None,
     search_text: Optional[str] = None,
+    ontology_term: Optional[str] = None,
     limit: Optional[int] = None,
     offset: Optional[int] = None,
     with_publication_info: bool = True,
 ) -> dict:
     """Get genesets from the database.
 
     :param cursor: A database cursor.
+    :param user: The user requesting the genesets.
     :param gs_id: Show only results with this geneset ID.
+    :param only_my_genesets: Show only results owned by the user.
     :param curation_tier: Show only results of this curation tier.
     :param species: Show only results associated with this species.
     :param name: Show only results with this name.
@@ -44,6 +47,7 @@ def get_visible_genesets(
     :param gene_id_type: Show only results with this gene ID type.
     :param search_text: Return genesets that match this search text (using PostgreSQL
                         full-text search).
+    :param ontology_term: Show only results associated with this ontology term.
     :param limit: Limit the number of results.
     :param offset: Offset the results.
     :param with_publication_info: Include publication info in the return.
@@ -70,6 +74,7 @@ def get_visible_genesets(
             gene_id_type=gene_id_type,
             search_text=search_text,
             with_publication_info=with_publication_info,
+            ontology_term=ontology_term,
             limit=limit,
             offset=offset,
         )