Merge pull request #84 from TheJacksonLaboratory/G3-303-api-delete-ge…

…neset-ontology-term G3 303 api delete geneset ontology term
TheJacksonLaboratory · Jul 31, 2024 · 8ae6c2b · 8ae6c2b
2 parents 7430ac3 + 4f8d045
commit 8ae6c2b
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Showing 6 changed files with 285 additions and 23 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.7.0"
+version = "0.8.0a1"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <alexander.berger@jax.org>",

diff --git a/src/geneweaver/api/controller/genesets.py b/src/geneweaver/api/controller/genesets.py
@@ -339,23 +339,34 @@ def get_geneset_ontology_terms(
         if terms_resp.get("message") == api_message.ACCESS_FORBIDDEN:
             raise HTTPException(status_code=403, detail=api_message.ACCESS_FORBIDDEN)
 
+        if terms_resp.get("message") == api_message.INACCESSIBLE_OR_FORBIDDEN:
+            raise HTTPException(
+                status_code=404, detail=api_message.INACCESSIBLE_OR_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)
+        int,
+        Path(
+            description=api_message.GENESET_ID,
+            format="int64",
+            minimum=0,
+            maxiumum=9223372036854775807,
+        ),
     ],
-    ontology_ref_term_id: str,
+    ontology_id: Annotated[str, Query(description=api_message.ONTOLOGY_ID)],
     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,
+        term_ref_id=ontology_id,
         user=user,
     )
 
@@ -370,3 +381,46 @@ def put_geneset_ontology_term(
 
         if response.get("message") == api_message.RECORD_EXISTS:
             raise HTTPException(status_code=412, detail=api_message.RECORD_EXISTS)
+
+        if response.get("message") == api_message.INACCESSIBLE_OR_FORBIDDEN:
+            raise HTTPException(
+                status_code=404, detail=api_message.INACCESSIBLE_OR_FORBIDDEN
+            )
+
+
+@router.delete("/{geneset_id}/ontologies/{ontology_id}", status_code=204)
+def delete_geneset_ontology_term(
+    geneset_id: Annotated[
+        int,
+        Path(
+            description=api_message.GENESET_ID,
+            format="int64",
+            minimum=0,
+            maxiumum=9223372036854775807,
+        ),
+    ],
+    ontology_id: Annotated[str, Path(description=api_message.ONTOLOGY_ID)],
+    user: UserInternal = Security(deps.full_user),
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+) -> None:
+    """Set geneset threshold for geneset owner."""
+    response = genset_service.delete_geneset_ontology_term(
+        cursor=cursor,
+        geneset_id=geneset_id,
+        term_ref_id=ontology_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.INACCESSIBLE_OR_FORBIDDEN:
+            raise HTTPException(
+                status_code=404, detail=api_message.INACCESSIBLE_OR_FORBIDDEN
+            )
diff --git a/src/geneweaver/api/controller/message.py b/src/geneweaver/api/controller/message.py
@@ -28,3 +28,4 @@
     "Gensets and/or publications search types ('genesets', 'publications') "
 )
 CHECK_DB_HEALTH = "Check DB health flag"
+ONTOLOGY_ID = "Ontology term reference ID"
diff --git a/src/geneweaver/api/services/geneset.py b/src/geneweaver/api/services/geneset.py
@@ -441,15 +441,15 @@ def get_geneset_ontology_terms(
 def add_geneset_ontology_term(
     cursor: Cursor,
     geneset_id: int,
-    ref_term_id: str,
+    term_ref_id: str,
     user: User,
     gso_ref_type: str = ONTO_GSO_REF_TYPE,
 ) -> dict:
-    """Get geneset ontology terms by geneset id.
+    """Add ontology term to a geneset.
 
     :param cursor: DB cursor
     :param geneset_id: geneset identifier
-    :param ref_term_id ref term identifier
+    :param term_ref_id ref term identifier
     :param user: GW user
     :param limit: Limit the number of results.
     :param offset: Offset the results.
@@ -459,6 +459,12 @@ def add_geneset_ontology_term(
         if user is None or user.id is None:
             return {"error": True, "message": message.ACCESS_FORBIDDEN}
 
+        is_gs_readable = db_geneset.is_readable(
+            cursor=cursor, user_id=user.id, geneset_id=geneset_id
+        )
+        if is_gs_readable is False:
+            return {"error": True, "message": message.INACCESSIBLE_OR_FORBIDDEN}
+
         owner = db_geneset.user_is_owner(
             cursor=cursor, user_id=user.id, geneset_id=geneset_id
         )
@@ -468,7 +474,7 @@ def add_geneset_ontology_term(
             return {"error": True, "message": message.ACCESS_FORBIDDEN}
 
         onto_term = db_ontology.by_ontology_term(
-            cursor=cursor, onto_ref_term_id=ref_term_id
+            cursor=cursor, onto_ref_term_id=term_ref_id
         )
 
         if onto_term is None:
@@ -488,3 +494,58 @@ def add_geneset_ontology_term(
     except Exception as err:
         logger.error(err)
         raise err
+
+
+def delete_geneset_ontology_term(
+    cursor: Cursor,
+    geneset_id: int,
+    term_ref_id: str,
+    user: User,
+    gso_ref_type: str = ONTO_GSO_REF_TYPE,
+) -> dict:
+    """Delete ontology term from a geneset.
+
+    :param cursor: DB cursor
+    :param geneset_id: geneset identifier
+    :param term_ref_id ref term identifier
+    :param user: GW user
+    :param limit: Limit the number of results.
+    :param offset: Offset the results.
+    @return: deleted record  (geneset id, ontology term id).
+    """
+    try:
+        if user is None or user.id is None:
+            return {"error": True, "message": message.ACCESS_FORBIDDEN}
+
+        is_gs_readable = db_geneset.is_readable(
+            cursor=cursor, user_id=user.id, geneset_id=geneset_id
+        )
+        if is_gs_readable is False:
+            return {"error": True, "message": message.INACCESSIBLE_OR_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=term_ref_id
+        )
+
+        if onto_term is None:
+            return {"error": True, "message": message.RECORD_NOT_FOUND_ERROR}
+
+        results = db_ontology.delete_ontology_term_from_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 Exception as err:
+        logger.error(err)
+        raise err
diff --git a/tests/controllers/test_genesets.py b/tests/controllers/test_genesets.py
@@ -311,14 +311,21 @@ 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
 
+    mock_get_genenset_onto_terms.return_value = {
+        "error": True,
+        "message": message.INACCESSIBLE_OR_FORBIDDEN,
+    }
+    response = client.get("/api/genesets/1234/ontologies")
+    assert response.status_code == 404
+
 
 @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")
+    response = client.put("/api/genesets/1234/ontologies?ontology_id=D001921")
     assert response.status_code == 204
 
 
@@ -331,19 +338,63 @@ def test_add_geneset_ontology_terms_errors(mock_add_genenset_onto_terms, client)
     }
     mock_add_genenset_onto_terms.return_value = mock_resp
 
-    response = client.put("/api/genesets/1234/ontologies?ontology_ref_term_id=D001921")
+    response = client.put("/api/genesets/1234/ontologies?ontology_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")
+    response = client.put("/api/genesets/1234/ontologies?ontology_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")
+    response = client.put("/api/genesets/1234/ontologies?ontology_id=D001921")
     assert response.status_code == 412
+
+    mock_add_genenset_onto_terms.return_value = {
+        "error": True,
+        "message": message.INACCESSIBLE_OR_FORBIDDEN,
+    }
+    response = client.put("/api/genesets/1234/ontologies?ontology_id=D001921")
+    assert response.status_code == 404
+
+
+@patch("geneweaver.api.services.geneset.delete_geneset_ontology_term")
+def test_delete_geneset_ontology_term_response(mock_delete_genenset_onto_terms, client):
+    """Test delete geneset ontology_terms  response."""
+    mock_resp = test_ontology_data.get("geneset_ontology_terms")
+    mock_delete_genenset_onto_terms.return_value = mock_resp
+
+    response = client.delete("/api/genesets/1234/ontologies/D001921")
+    assert response.status_code == 204
+
+
+@patch("geneweaver.api.services.geneset.delete_geneset_ontology_term")
+def test_delete_geneset_ontology_terms_errors(mock_delete_genenset_onto_terms, client):
+    """Test delete geneset ontology_terms errors."""
+    mock_resp = {
+        "error": True,
+        "message": message.ACCESS_FORBIDDEN,
+    }
+    mock_delete_genenset_onto_terms.return_value = mock_resp
+
+    response = client.delete("/api/genesets/1234/ontologies/D001921")
+    assert response.status_code == 403
+
+    mock_delete_genenset_onto_terms.return_value = {
+        "error": True,
+        "message": message.RECORD_NOT_FOUND_ERROR,
+    }
+    response = client.delete("/api/genesets/1234/ontologies/QEQWEWE")
+    assert response.status_code == 404
+
+    mock_delete_genenset_onto_terms.return_value = {
+        "error": True,
+        "message": message.INACCESSIBLE_OR_FORBIDDEN,
+    }
+    response = client.delete("/api/genesets/1234/ontologies/D001921")
+    assert response.status_code == 404