Merge pull request #52 from TheJacksonLaboratory/G3-230-geneset-gene-…

…values-endpoint

G3-230 geneset gene values endpoint

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.4.0a13"
+version = "0.4.0a14"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <alexander.berger@jax.org>",

src/geneweaver/api/controller/genesets.py

@@ -9,6 +9,7 @@
 from fastapi import APIRouter, Depends, HTTPException, Path, Query, Security
 from fastapi.responses import FileResponse
 from geneweaver.api import dependencies as deps
+from geneweaver.api.schemas.apimodels import GeneValueReturn
 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
@@ -140,6 +141,29 @@ def get_geneset(
     return response
 
 
+@router.get("/{geneset_id}/values")
+def get_geneset_values(
+    geneset_id: Annotated[
+        int, Path(format="int64", minimum=0, maxiumum=9223372036854775807)
+    ],
+    user: UserInternal = Security(deps.full_user),
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+) -> GeneValueReturn:
+    """Get geneset gene values by geneset ID."""
+    response = genset_service.get_geneset_gene_values(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)
+
+    if response.get("data") is None:
+        raise HTTPException(status_code=404, detail=api_message.RECORD_NOT_FOUND_ERROR)
+
+    return response
+
+
 @router.get("/{geneset_id}/file", response_class=FileResponse)
 def get_export_geneset_by_id_type(
     geneset_id: Annotated[

src/geneweaver/api/schemas/apimodels.py

@@ -4,6 +4,7 @@
 
 from geneweaver.core.enum import GeneIdentifier, Species
 from geneweaver.core.schema.gene import Gene as GeneSchema
+from geneweaver.core.schema.geneset import GeneValue as GeneValueSchema
 from geneweaver.core.schema.species import Species as SpeciesSchema
 from pydantic import AnyUrl, BaseModel
 
@@ -75,3 +76,9 @@ class SpeciesReturn(CollectionResponse):
     """Model for Species endpoint return."""
 
     data: List[SpeciesSchema]
+
+
+class GeneValueReturn(BaseModel):
+    """Model for geneset values endpoint return."""
+
+    data: List[GeneValueSchema]

src/geneweaver/api/services/geneset.py

@@ -126,13 +126,42 @@ def get_geneset(cursor: Cursor, geneset_id: int, user: User) -> dict:
         )
         geneset = results[0]
         geneset_values = db_geneset_value.by_geneset_id(cursor, geneset_id)
+
         return {"geneset": geneset, "geneset_values": geneset_values}
 
     except Exception as err:
         logger.error(err)
         raise err
 
 
+def get_geneset_gene_values(cursor: Cursor, geneset_id: int, user: User) -> dict:
+    """Get a gene values for a given geneset ID.
+
+    @param cursor: DB cursor
+    @param geneset_id: geneset identifier
+    @param user: GW user
+    @return: dictionary response (geneset and genset values).
+    """
+    try:
+        if user is None or user.id is None:
+            return {"error": True, "message": message.ACCESS_FORBIDDEN}
+
+        geneset_values = db_geneset_value.by_geneset_id(cursor, geneset_id)
+        if geneset_values is None or len(geneset_values) <= 0:
+            return {"data": None}
+
+        genes_data = []
+        for gsv in geneset_values:
+            gene_value = {"symbol": gsv["ode_ref_id"], "value": float(gsv["gsv_value"])}
+            genes_data.append(gene_value)
+
+        return {"data": genes_data}
+
+    except Exception as err:
+        logger.error(err)
+        raise err
+
+
 def get_geneset_w_gene_id_type(
     cursor: Cursor, geneset_id: int, user: User, gene_id_type: GeneIdentifier
 ) -> dict:

tests/controllers/test_genesets.py

@@ -10,6 +10,7 @@
 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")
 publication_by_id_resp = test_publication_data.get("publication_by_id")
+geneset_genes_values_resp = test_geneset_data.get("geneset_genes_values_resp_1")
 
 
 @patch("geneweaver.api.services.geneset.get_geneset")
@@ -198,3 +199,32 @@ def test_get_visible_geneset_errors(mock_get_visible_genesets, client):
 
     response = client.get("/api/genesets?gs_id=1234")
     assert response.status_code == 500
+
+
+@patch("geneweaver.api.services.geneset.get_geneset_gene_values")
+def test_get_geneset_gene_values_url_response(mock_get_geneset_gene_values, client):
+    """Test get geneset gene values data response."""
+    mock_get_geneset_gene_values.return_value = geneset_genes_values_resp
+
+    response = client.get("/api/genesets/1234/values")
+    assert response.status_code == 200
+    assert response.json() == geneset_genes_values_resp
+
+
+@patch("geneweaver.api.services.geneset.get_geneset_gene_values")
+def test_get_geneset_gene_values_errors(mock_get_geneset_gene_values, client):
+    """Test get geneset gene values error responses."""
+    mock_get_geneset_gene_values.return_value = {
+        "error": True,
+        "message": message.ACCESS_FORBIDDEN,
+    }
+    response = client.get("/api/genesets/1234/values")
+    assert response.status_code == 403
+
+    mock_get_geneset_gene_values.return_value = {"error": True, "message": "other"}
+    response = client.get("/api/genesets/1234/values")
+    assert response.status_code == 500
+
+    mock_get_geneset_gene_values.return_value = {"data": None}
+    response = client.get("/api/genesets/1234/values")
+    assert response.status_code == 404

tests/data/__init__.py

@@ -41,7 +41,12 @@
     "geneset_metadata_w_pub_info": json.loads(geneset_response_json).get(
         "geneset_with_publication_info"
     ),
-    "geneset_list_resp": json.loads(geneset_list_response_json),
+    "geneset_list_resp": json.loads(geneset_list_response_json).get(
+        "geneset_resp_1_list_10"
+    ),
+    "geneset_genes_values_resp_1": json.loads(geneset_list_response_json).get(
+        "geneset_genes_values_resp_1"
+    ),
 }
 
 # Gene homolog ids test data

tests/data/geneset.json

@@ -280,5 +280,21 @@
       "publication_year": null,
       "publication_pubmed_id": null
     }
-  ]
+  ],
+  "geneset_genes_values_resp_1": {
+    "data": [
+      {
+        "symbol": "Hs.629744",
+        "value": 1.0
+      },
+      {
+        "symbol": "Hs.517155",
+        "value": 1.0
+      },
+      {
+        "symbol": "Hs.356063",
+        "value": 1.0
+      }
+    ]
+  }
 }

tests/services/test_genset.py

@@ -14,6 +14,7 @@
 geneset_list_resp = test_geneset_data.get("geneset_list_resp")
 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")
 mock_user = User()
 mock_user.id = 1
 
@@ -176,10 +177,10 @@ def test_geneset_metadata_db_call_error(mock_db_geneset):
 @patch("geneweaver.api.services.geneset.db_geneset")
 def test_visible_geneset_response(mock_db_geneset):
     """Test general get geneset data no parameters -- default limit."""
-    mock_db_geneset.get.return_value = geneset_list_resp.get("geneset_resp_1_list_10")
+    mock_db_geneset.get.return_value = geneset_list_resp
 
     response = geneset.get_visible_genesets(None, mock_user)
-    assert response.get("data") == geneset_list_resp.get("geneset_resp_1_list_10")
+    assert response.get("data") == geneset_list_resp
 
 
 def test_visible_geneset_no_user():
@@ -196,7 +197,7 @@ def test_visible_geneset_no_user():
 @patch("geneweaver.api.services.geneset.db_geneset")
 def test_visible_geneset_all_expected_parameters(mock_db_geneset):
     """Test general get geneset data no parameters -- default limit."""
-    mock_db_geneset.get.return_value = geneset_list_resp.get("geneset_resp_1_list_10")
+    mock_db_geneset.get.return_value = geneset_list_resp
 
     response = geneset.get_visible_genesets(
         cursor=None,
@@ -215,7 +216,7 @@ def test_visible_geneset_all_expected_parameters(mock_db_geneset):
         with_publication_info=True,
     )
 
-    assert response.get("data") == geneset_list_resp.get("geneset_resp_1_list_10")
+    assert response.get("data") == geneset_list_resp
 
 
 @patch("geneweaver.api.services.geneset.db_geneset")
@@ -249,3 +250,31 @@ def test_map_geneset_homology_db_call_error(mock_db_gene):
         geneset.map_geneset_homology(
             None, geneset_by_id_resp["geneset_values"], GeneIdentifier(2)
         )
+
+
+@patch("geneweaver.api.services.geneset.db_geneset_value")
+def test_geneset_gene_value_response(mock_db_geneset_value):
+    """Test geneset gene value data response."""
+    mock_db_geneset_value.by_geneset_id.return_value = geneset_by_id_resp.get(
+        "geneset_values"
+    )
+
+    response = geneset.get_geneset_gene_values(None, user=mock_user, geneset_id=1234)
+    assert response == geneset_genes_values_resp
+
+
+@patch("geneweaver.api.services.geneset.db_geneset_value")
+def test_get_geneset_gene_values_db_errors(mock_db_geneset_value):
+    """Test error in get DB call."""
+    mock_db_geneset_value.by_geneset_id.side_effect = Exception("ERROR")
+
+    with pytest.raises(expected_exception=Exception):
+        geneset.get_geneset_gene_values(None, user=mock_user, geneset_id=1234)
+
+
+@patch("geneweaver.api.services.geneset.db_geneset_value")
+def test_get_geneset_gene_values_invalid_user(mock_db_geneset_value):
+    """Test invalid user."""
+    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