G3-239 geneset threshold update endpoint

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.5.0a0"
+version = "0.5.0a1"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <[email protected]>",
@@ -17,11 +17,10 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.9"
-
 geneweaver-core = "^0.9.1"
 fastapi = {extras = ["all"], version = "^0.99.1"}
 uvicorn = {extras = ["standard"], version = "^0.24.0"}
-geneweaver-db = "^0.3.3"
+geneweaver-db = "^0.3.4"
 psycopg-pool = "^3.1.7"
 requests = "^2.31.0"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}

src/geneweaver/api/controller/genesets.py

@@ -13,8 +13,8 @@
 from geneweaver.api.schemas.auth import UserInternal
 from geneweaver.api.services import geneset as genset_service
 from geneweaver.api.services import publications as publication_service
-from geneweaver.core.schema.score import GenesetScoreType
 from geneweaver.core.enum import GeneIdentifier, GenesetTier, Species
+from geneweaver.core.schema.score import GenesetScoreType
 from typing_extensions import Annotated
 
 from . import message as api_message
@@ -277,13 +277,12 @@ def put_geneset_threshold(
     cursor: Optional[deps.Cursor] = Depends(deps.cursor),
 ) -> dict:
     """Set geneset threshold for geneset owner."""
-    response = genset_service.update_geneset_threshold(cursor, geneset_id, gene_score_type, user)
+    response = genset_service.update_geneset_threshold(
+        cursor, geneset_id, gene_score_type, 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

@@ -9,8 +9,8 @@
 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 threshold as db_threshold
 from geneweaver.db import geneset_value as db_geneset_value
+from geneweaver.db import threshold as db_threshold
 from psycopg import Cursor
 
 
@@ -250,18 +250,21 @@ def map_geneset_homology(
 def update_geneset_threshold(
     cursor: Cursor, geneset_id: int, geneset_score: GenesetScoreType, user: User
 ) -> dict:
-    """ set geneset threshold if user is the owner"""
-
+    """Set geneset threshold if user is the owner."""
     try:
         if user is None or user.id is None:
             return {"error": True, "message": message.ACCESS_FORBIDDEN}
 
-        # if not db_geneset.user_is_owner(cursor=cursor, user_id=user.id, geneset_id=geneset_id):
-        #     return {"error": True, "message": message.ACCESS_FORBIDDEN}
+        if not db_geneset.user_is_owner(
+            cursor=cursor, user_id=user.id, geneset_id=geneset_id
+        ):
+            return {"error": True, "message": message.ACCESS_FORBIDDEN}
 
-        db_threshold.set_geneset_threshold(cursor=cursor, geneset_id=geneset_id, geneset_score_type=geneset_score)
+        db_threshold.set_geneset_threshold(
+            cursor=cursor, geneset_id=geneset_id, geneset_score_type=geneset_score
+        )
+        return {}
 
     except Exception as err:
         logger.error(err)
         raise err
-

tests/controllers/test_genesets.py

@@ -1,5 +1,6 @@
 """Tests for geneset API."""
 
+import json
 from unittest.mock import patch
 
 from geneweaver.api.controller import message
@@ -11,6 +12,7 @@
 geneset_metadata_w_pub_info = test_geneset_data.get("geneset_metadata_w_pub_info")
 publication_by_id_resp = test_publication_data.get("publication_by_id")
 geneset_genes_values_resp = test_geneset_data.get("geneset_genes_values_resp_1")
+geneset_threshold_update_req = test_geneset_data.get("geneset_threshold_update_req")
 
 
 @patch("geneweaver.api.services.geneset.get_geneset")
@@ -228,3 +230,29 @@ def test_get_geneset_gene_values_errors(mock_get_geneset_gene_values, client):
     mock_get_geneset_gene_values.return_value = {"data": None}
     response = client.get("/api/genesets/1234/values")
     assert response.status_code == 404
+
+
+@patch("geneweaver.api.services.geneset.update_geneset_threshold")
+def test_set_geneset_endpoint_response(mock_update_geneset_threshold, client):
+    """Test set geneset threshold endpoint."""
+    mock_update_geneset_threshold.return_value = {}
+
+    response = client.put(
+        "/api/genesets/1234/threshold", data=json.dumps(geneset_threshold_update_req)
+    )
+    assert response.status_code == 200
+    assert response.json() == {}
+
+
+@patch("geneweaver.api.services.geneset.update_geneset_threshold")
+def test_set_geneset_endpoint_response_errors(mock_update_geneset_threshold, client):
+    """Test set geneset threshold endpoint errors."""
+    mock_update_geneset_threshold.return_value = {
+        "error": True,
+        "message": message.ACCESS_FORBIDDEN,
+    }
+
+    response = client.put(
+        "/api/genesets/1234/threshold", data=json.dumps(geneset_threshold_update_req)
+    )
+    assert response.status_code == 403

tests/data/__init__.py

@@ -47,6 +47,9 @@
     "geneset_genes_values_resp_1": json.loads(geneset_list_response_json).get(
         "geneset_genes_values_resp_1"
     ),
+    "geneset_threshold_update_req": json.loads(geneset_list_response_json).get(
+        "geneset_threshold_update_req"
+    ),
 }
 
 # Gene homolog ids test data

tests/data/geneset.json

@@ -296,5 +296,10 @@
         "value": 1.0
       }
     ]
+  },
+  "geneset_threshold_update_req": {
+    "score_type": "p-value",
+    "threshold_low": 0,
+    "threshold": 0.05
   }
 }

tests/services/test_genset.py

@@ -7,6 +7,7 @@
 from geneweaver.api.schemas.auth import User
 from geneweaver.api.services import geneset
 from geneweaver.core.enum import GeneIdentifier, GenesetTier, Species
+from geneweaver.core.schema.score import GenesetScoreType
 
 from tests.data import test_geneset_data
 
@@ -15,6 +16,7 @@
 geneset_w_gene_id_type_resp = test_geneset_data.get("geneset_w_gene_id_type_resp")
 geneset_metadata_w_pub_info = test_geneset_data.get("geneset_metadata_w_pub_info")
 geneset_genes_values_resp = test_geneset_data.get("geneset_genes_values_resp_1")
+geneset_threshold_update_req = test_geneset_data.get("geneset_threshold_update_req")
 mock_user = User()
 mock_user.id = 1
 
@@ -278,3 +280,51 @@ def test_get_geneset_gene_values_invalid_user(mock_db_geneset_value):
     response = geneset.get_geneset_gene_values(None, user=None, geneset_id=1234)
     assert response.get("error") is True
     assert response.get("message") == message.ACCESS_FORBIDDEN
+
+
+@patch("geneweaver.api.services.geneset.db_geneset")
+@patch("geneweaver.api.services.geneset.db_threshold")
+def test_geneset_thershold_update(mock_db_threshold, mock_db_geneset):
+    """Test geneset gene value data response."""
+    mock_db_threshold.set_geneset_threshold.return_value = None
+    mock_db_geneset.user_is_owner.return_value = True
+    geneset_threshold = GenesetScoreType(**geneset_threshold_update_req)
+
+    response = geneset.update_geneset_threshold(
+        cursor=None, user=mock_user, geneset_id=1234, geneset_score=geneset_threshold
+    )
+    assert response == {}
+
+
+@patch("geneweaver.api.services.geneset.db_geneset")
+@patch("geneweaver.api.services.geneset.db_threshold")
+def test_geneset_thershold_update_errors(mock_db_threshold, mock_db_geneset):
+    """Test geneset gene value data response."""
+    mock_db_threshold.set_geneset_threshold.return_value = None
+    mock_db_geneset.user_is_owner.return_value = False
+    geneset_threshold = GenesetScoreType(**geneset_threshold_update_req)
+
+    # user is not the geneset owner
+    response = geneset.update_geneset_threshold(
+        cursor=None, user=mock_user, geneset_id=1234, geneset_score=geneset_threshold
+    )
+    assert response.get("error") is True
+    assert response.get("message") == message.ACCESS_FORBIDDEN
+
+    # user is not logged-in
+    response = geneset.update_geneset_threshold(
+        cursor=None, user=None, geneset_id=1234, geneset_score=geneset_threshold
+    )
+    assert response.get("error") is True
+    assert response.get("message") == message.ACCESS_FORBIDDEN
+
+    # db error
+    mock_db_geneset.user_is_owner.return_value = True
+    mock_db_threshold.set_geneset_threshold.side_effect = Exception("ERROR")
+    with pytest.raises(expected_exception=Exception):
+        geneset.update_geneset_threshold(
+            cursor=None,
+            user=mock_user,
+            geneset_id=1234,
+            geneset_score=geneset_threshold,
+        )