Merge pull request #24 from TheJacksonLaboratory/GW-149-geneset-metadata

Gw 149 geneset metadata

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.2.0a1"
+version = "0.2.0a2"
 description = "description"
 authors = ["Jax Computational Sciences <[email protected]>"]
 packages = [

src/geneweaver/api/controller/genesets.py

@@ -99,3 +99,23 @@ def get_export_geneset_by_id_type(
         media_type="application/octet-stream",
         filename=geneset_filename,
     )
+
+
+@router.get("/{geneset_id}/metadata")
+def get_geneset_metadata(
+    geneset_id: Annotated[
+        int, Path(format="int64", minimum=0, maxiumum=9223372036854775807)
+    ],
+    user: UserInternal = Security(deps.full_user),
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+) -> dict:
+    """Get a geneset metadata by geneset id."""
+    response = genset_service.get_geneset_metadata(cursor, geneset_id, user)
+
+    if "error" in response:
+        if response.get("message") == api_message.ACCESS_FORBIDDEN:
+            raise HTTPException(status_code=403, detail=api_message.ACCESS_FORBIDDEN)
+        else:
+            raise HTTPException(status_code=500, detail=api_message.UNEXPECTED_ERROR)
+
+    return response

src/geneweaver/api/services/geneset.py

@@ -12,6 +12,26 @@
 from psycopg import Cursor
 
 
+def get_geneset_metadata(cursor: Cursor, geneset_id: int, user: User) -> dict:
+    """Get a geneset metadata by geneset id.
+
+    @param cursor: DB cursor
+    @param geneset_id: geneset identifier
+    @param user: GW user
+    @return: dictionary response (geneset).
+    """
+    try:
+        if not is_geneset_readable_by_user(cursor, geneset_id, user):
+            return {"error": True, "message": message.ACCESS_FORBIDDEN}
+
+        geneset = db_geneset.by_id(cursor, geneset_id)
+        return {"geneset": geneset}
+
+    except Exception as err:
+        logger.error(err)
+        raise err
+
+
 def get_geneset(cursor: Cursor, geneset_id: int, user: User) -> dict:
     """Get a geneset by ID.
 

tests/services/test_genset.py

@@ -96,3 +96,14 @@ def test_get_geneset_w_gene_id_type_reponse(
     assert (
         response.get("geneset_values") == geneset_w_gene_id_type_resp["geneset_values"]
     )
+
+
+@patch("geneweaver.api.services.geneset.db_geneset")
+@patch("geneweaver.api.services.geneset.is_geneset_readable_by_user")
+def test_get_geneset_metadata(mock_genset_readable_func, mock_db_geneset):
+    """Test get geneset metadata by geneset id."""
+    mock_genset_readable_func.return_value = True
+    mock_db_geneset.by_id.return_value = geneset_by_id_resp.get("geneset")
+    response = geneset.get_geneset_metadata(None, 1234, None)
+
+    assert response.get("geneset") == geneset_by_id_resp["geneset"]