Merge pull request #82 from TheJacksonLaboratory/G3-301-api-add-ontol…

…ogy-term-to-gs

G3-301 endpoint to add ontology term to geneset

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.7.0a10"
+version = "0.7.0a11"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <alexander.berger@jax.org>",
@@ -20,7 +20,7 @@ python = "^3.9"
 geneweaver-core = "^0.10.0a3"
 fastapi = {extras = ["all"], version = "^0.111.0"}
 uvicorn = {extras = ["standard"], version = "^0.30.0"}
-geneweaver-db = "0.5.0a13"
+geneweaver-db = "0.5.0a15"
 psycopg-pool = "^3.1.7"
 requests = "^2.32.3"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}

src/geneweaver/api/controller/genesets.py

@@ -340,3 +340,33 @@ def get_geneset_ontology_terms(
             raise HTTPException(status_code=403, detail=api_message.ACCESS_FORBIDDEN)
 
     return terms_resp
+
+
+@router.put("/{geneset_id}/ontologies", status_code=204)
+def put_geneset_ontology_term(
+    geneset_id: Annotated[
+        int, Path(format="int64", minimum=0, maxiumum=9223372036854775807)
+    ],
+    ontology_ref_term_id: str,
+    user: UserInternal = Security(deps.full_user),
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+) -> None:
+    """Set geneset threshold for geneset owner."""
+    response = genset_service.add_geneset_ontology_term(
+        cursor=cursor,
+        geneset_id=geneset_id,
+        ref_term_id=ontology_ref_term_id,
+        user=user,
+    )
+
+    if "error" in response:
+        if response.get("message") == api_message.ACCESS_FORBIDDEN:
+            raise HTTPException(status_code=403, detail=api_message.ACCESS_FORBIDDEN)
+
+        if response.get("message") == api_message.RECORD_NOT_FOUND_ERROR:
+            raise HTTPException(
+                status_code=404, detail=api_message.RECORD_NOT_FOUND_ERROR
+            )
+
+        if response.get("message") == api_message.RECORD_EXISTS:
+            raise HTTPException(status_code=412, detail=api_message.RECORD_EXISTS)

src/geneweaver/api/services/geneset.py

@@ -5,15 +5,17 @@
 from fastapi.logger import logger
 from geneweaver.api.controller import message
 from geneweaver.api.core.exceptions import UnauthorizedException
-from geneweaver.api.schemas.auth import User
+from geneweaver.api.schemas.auth import AppRoles, User
 from geneweaver.core.enum import GeneIdentifier, GenesetTier, Species
 from geneweaver.core.schema.score import GenesetScoreType
 from geneweaver.db import gene as db_gene
 from geneweaver.db import geneset as db_geneset
 from geneweaver.db import geneset_value as db_geneset_value
 from geneweaver.db import ontology as db_ontology
 from geneweaver.db import threshold as db_threshold
-from psycopg import Cursor
+from psycopg import Cursor, errors
+
+ONTO_GSO_REF_TYPE = "GeneWeaver Primary Annotation"
 
 
 def determine_geneset_access(
@@ -434,3 +436,55 @@ def get_geneset_ontology_terms(
     except Exception as err:
         logger.error(err)
         raise err
+
+
+def add_geneset_ontology_term(
+    cursor: Cursor,
+    geneset_id: int,
+    ref_term_id: str,
+    user: User,
+    gso_ref_type: str = ONTO_GSO_REF_TYPE,
+) -> dict:
+    """Get geneset ontology terms by geneset id.
+
+    :param cursor: DB cursor
+    :param geneset_id: geneset identifier
+    :param ref_term_id ref term identifier
+    :param user: GW user
+    :param limit: Limit the number of results.
+    :param offset: Offset the results.
+    @return: persisted record  (geneset id, ontology term id).
+    """
+    try:
+        if user is None or user.id is None:
+            return {"error": True, "message": message.ACCESS_FORBIDDEN}
+
+        owner = db_geneset.user_is_owner(
+            cursor=cursor, user_id=user.id, geneset_id=geneset_id
+        )
+        curator = user.role is AppRoles.curator
+
+        if not owner and not curator:
+            return {"error": True, "message": message.ACCESS_FORBIDDEN}
+
+        onto_term = db_ontology.by_ontology_term(
+            cursor=cursor, onto_ref_term_id=ref_term_id
+        )
+
+        if onto_term is None:
+            return {"error": True, "message": message.RECORD_NOT_FOUND_ERROR}
+
+        results = db_ontology.add_ontology_term_to_geneset(
+            cursor=cursor,
+            geneset_id=geneset_id,
+            ontology_term_id=onto_term.get("onto_id"),
+            gso_ref_type=gso_ref_type,
+        )
+        return {"data": results}
+
+    except errors.UniqueViolation:
+        return {"error": True, "message": message.RECORD_EXISTS}
+
+    except Exception as err:
+        logger.error(err)
+        raise err

tests/controllers/test_genesets.py

@@ -310,3 +310,40 @@ def test_get_geneset_ontology_terms_errors(mock_get_genenset_onto_terms, client)
 
     response = client.get("/api/genesets/1234/ontologies")
     assert response.status_code == 403
+
+
+@patch("geneweaver.api.services.geneset.add_geneset_ontology_term")
+def test_add_geneset_ontology_term_response(mock_add_genenset_onto_terms, client):
+    """Test add geneset ontology_terms  response."""
+    mock_resp = test_ontology_data.get("geneset_ontology_terms")
+    mock_add_genenset_onto_terms.return_value = mock_resp
+
+    response = client.put("/api/genesets/1234/ontologies?ontology_ref_term_id=D001921")
+    assert response.status_code == 204
+
+
+@patch("geneweaver.api.services.geneset.add_geneset_ontology_term")
+def test_add_geneset_ontology_terms_errors(mock_add_genenset_onto_terms, client):
+    """Test add geneset ontology_terms errors."""
+    mock_resp = {
+        "error": True,
+        "message": message.ACCESS_FORBIDDEN,
+    }
+    mock_add_genenset_onto_terms.return_value = mock_resp
+
+    response = client.put("/api/genesets/1234/ontologies?ontology_ref_term_id=D001921")
+    assert response.status_code == 403
+
+    mock_add_genenset_onto_terms.return_value = {
+        "error": True,
+        "message": message.RECORD_NOT_FOUND_ERROR,
+    }
+    response = client.put("/api/genesets/1234/ontologies?ontology_ref_term_id=QEQWEWE")
+    assert response.status_code == 404
+
+    mock_add_genenset_onto_terms.return_value = {
+        "error": True,
+        "message": message.RECORD_EXISTS,
+    }
+    response = client.put("/api/genesets/1234/ontologies?ontology_ref_term_id=D001921")
+    assert response.status_code == 412

tests/data/publications.json

@@ -32,7 +32,7 @@
     "volume": "3",
     "pages": "565-76",
     "month": null,
-    "year": 1975
+    "year": "1975"
   },
   "add_pubmed_resp": {
     "pubmed_id": 1234,

tests/services/test_genset.py

@@ -472,3 +472,64 @@ def test_geneset_gene_value_w_gene_id_type_none_resp2(mock_db_geneset):
         None, user=mock_user, geneset_id=1234, gene_id_type=GeneIdentifier(2)
     )
     assert response == {"data": None}
+
+
+@patch("geneweaver.api.services.geneset.db_geneset")
+@patch("geneweaver.api.services.geneset.db_ontology")
+def test_add_genset_ontology_term(mock_db_ontology, mock_db_geneset):
+    """Test geneset gene value data response."""
+    mock_reponse = {"data": {"gs_id": 1234, "ont_id": 1}}
+    mock_db_ontology.by_ontology_term.return_value = {"onto_id": 123123}
+    mock_db_geneset.user_is_owner.return_value = True
+    mock_db_ontology.add_ontology_term_to_geneset.return_value = mock_reponse.get(
+        "data"
+    )
+
+    response = geneset.add_geneset_ontology_term(
+        cursor=None, user=mock_user, geneset_id=1234, ref_term_id="D001921"
+    )
+    assert response == mock_reponse
+
+
+@patch("geneweaver.api.services.geneset.db_geneset")
+@patch("geneweaver.api.services.geneset.db_ontology")
+def test_add_geneset_ontology_term_errors(mock_db_ontology, mock_db_geneset):
+    """Test geneset gene value data response."""
+    mock_reponse = {"data": {"gs_id": 1234, "ont_id": 1}}
+    mock_db_ontology.by_ontology_term.return_value = {"onto_id": 123123}
+    mock_db_geneset.user_is_owner.return_value = False
+    mock_db_ontology.add_ontology_term_to_geneset.return_value = mock_reponse.get(
+        "data"
+    )
+
+    # user is not the geneset owner
+    response = geneset.add_geneset_ontology_term(
+        cursor=None, user=mock_user, geneset_id=1234, ref_term_id="D001921"
+    )
+    assert response.get("error") is True
+    assert response.get("message") == message.ACCESS_FORBIDDEN
+
+    # user is not logged-in
+    response = geneset.add_geneset_ontology_term(
+        cursor=None, user=None, geneset_id=1234, ref_term_id="D001921"
+    )
+    assert response.get("error") is True
+    assert response.get("message") == message.ACCESS_FORBIDDEN
+
+    # Ontology term is not found
+    mock_db_ontology.by_ontology_term.return_value = None
+    mock_db_geneset.user_is_owner.return_value = True
+    response = geneset.add_geneset_ontology_term(
+        cursor=None, user=mock_user, geneset_id=1234, ref_term_id="D001921"
+    )
+    assert response.get("error") is True
+    assert response.get("message") == message.RECORD_NOT_FOUND_ERROR
+
+    # db error
+    mock_db_geneset.user_is_owner.return_value = True
+    mock_db_ontology.by_ontology_term.return_value = {"onto_id": 123123}
+    mock_db_ontology.add_ontology_term_to_geneset.side_effect = Exception("ERROR")
+    with pytest.raises(expected_exception=Exception):
+        geneset.add_geneset_ontology_term(
+            cursor=None, user=mock_user, geneset_id=1234, ref_term_id="D001921"
+        )