Merge pull request #70 from TheJacksonLaboratory/G3-251-geneset-value…

…-w-gene-id-type

G3-251 geneset value enpoint with gene id type

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.6.0a3"
+version = "0.6.0a4"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <[email protected]>",

src/geneweaver/api/controller/genesets.py

@@ -151,9 +151,12 @@ def get_geneset_values(
     ],
     user: UserInternal = Security(deps.full_user),
     cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+    gene_id_type: Optional[GeneIdentifier] = None,
 ) -> GeneValueReturn:
     """Get geneset gene values by geneset ID."""
-    response = genset_service.get_geneset_gene_values(cursor, geneset_id, user)
+    response = genset_service.get_geneset_gene_values(
+        cursor=cursor, geneset_id=geneset_id, user=user, gene_id_type=gene_id_type
+    )
 
     if "error" in response:
         if response.get("message") == api_message.ACCESS_FORBIDDEN:

src/geneweaver/api/services/geneset.py

@@ -197,19 +197,39 @@ def get_geneset(cursor: Cursor, geneset_id: int, user: User) -> dict:
         raise err
 
 
-def get_geneset_gene_values(cursor: Cursor, geneset_id: int, user: User) -> dict:
+def get_geneset_gene_values(
+    cursor: Cursor, geneset_id: int, user: User, gene_id_type: GeneIdentifier = None
+) -> dict:
     """Get a gene values for a given geneset ID.
 
     @param cursor: DB cursor
     @param geneset_id: geneset identifier
     @param user: GW user
+    @param gene_id_type: gene identifier type object
     @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 gene id type is given, check gene species homology to
+        # construct proper gene species mapping
+        if gene_id_type is not None:
+            results = db_geneset.get(
+                cursor,
+                gs_id=geneset_id,
+                with_publication_info=False,
+            )
+            if len(results) <= 0:
+                return {"data": None}
+
+            geneset = results[0]
+            geneset_values = get_gsv_w_gene_homology_update(
+                cursor=cursor, geneset=geneset, gene_id_type=gene_id_type
+            )
+        else:
+            geneset_values = db_geneset_value.by_geneset_id(cursor, geneset_id)
+
         if geneset_values is None or len(geneset_values) <= 0:
             return {"data": None}
 
@@ -247,26 +267,10 @@ def get_geneset_w_gene_id_type(
             with_publication_info=False,
         )
         geneset = results[0]
-
-        mapping_across_species = False
-        original_gene_id_type = gene_id_type
-        genedb_sp_id = db_gene.gene_database_by_id(cursor, gene_id_type)[0]["sp_id"]
-
-        if genedb_sp_id != 0 and geneset["species_id"] != genedb_sp_id:
-            mapping_across_species = True
-            gene_id_type = GeneIdentifier(7)
-
-        geneset_values = db_geneset_value.by_geneset_id(
-            cursor, geneset_id, gene_id_type
+        geneset_values = get_gsv_w_gene_homology_update(
+            cursor=cursor, geneset=geneset, gene_id_type=gene_id_type
         )
 
-        if mapping_across_species:
-            geneset_values = map_geneset_homology(
-                cursor, geneset_values, original_gene_id_type
-            )
-
-            gene_id_type = original_gene_id_type
-
         return {
             "gene_identifier_type": gene_id_type.name,
             "geneset": geneset,
@@ -278,6 +282,35 @@ def get_geneset_w_gene_id_type(
         raise err
 
 
+def get_gsv_w_gene_homology_update(
+    cursor: Cursor, geneset: dict, gene_id_type: GeneIdentifier
+) -> Iterable[dict]:
+    """Check gene homology mapping and update it.
+
+    @param cursor: DB cursor
+    @param gene_id_type: geneset identifier
+    @return: geneset value
+    """
+    mapping_across_species = False
+    original_gene_id_type = gene_id_type
+    genedb_sp_id = db_gene.gene_database_by_id(cursor, gene_id_type)[0]["sp_id"]
+
+    if genedb_sp_id != 0 and geneset["species_id"] != genedb_sp_id:
+        mapping_across_species = True
+        gene_id_type = GeneIdentifier(7)
+
+    geneset_values = db_geneset_value.by_geneset_id(
+        cursor, geneset.get("id"), gene_id_type
+    )
+
+    if mapping_across_species:
+        geneset_values = map_geneset_homology(
+            cursor, geneset_values, original_gene_id_type
+        )
+
+    return geneset_values
+
+
 def map_geneset_homology(
     cursor: Cursor, geneset_value: Iterable[dict], gene_id_type: GeneIdentifier
 ) -> Iterable[dict]:

tests/controllers/test_genesets.py

@@ -232,6 +232,16 @@ def test_get_geneset_gene_values_errors(mock_get_geneset_gene_values, client):
     assert response.status_code == 404
 
 
+@patch("geneweaver.api.services.geneset.get_geneset_gene_values")
+def test_get_geneset_gene_values_w_gs_id_type(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?gene_id_type=2")
+    assert response.status_code == 200
+    assert response.json() == geneset_genes_values_resp
+
+
 @patch("geneweaver.api.services.geneset.update_geneset_threshold")
 def test_set_geneset_endpoint_response(mock_update_geneset_threshold, client):
     """Test set geneset threshold endpoint."""

tests/services/test_genset.py

@@ -302,7 +302,9 @@ def test_geneset_gene_value_response(mock_db_geneset_value):
         "geneset_values"
     )
 
-    response = geneset.get_geneset_gene_values(None, user=mock_user, geneset_id=1234)
+    response = geneset.get_geneset_gene_values(
+        None, user=mock_user, geneset_id=1234, gene_id_type=None
+    )
     assert response == geneset_genes_values_resp
 
 
@@ -312,13 +314,17 @@ def test_get_geneset_gene_values_db_errors(mock_db_geneset_value):
     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)
+        geneset.get_geneset_gene_values(
+            None, user=mock_user, geneset_id=1234, gene_id_type=None
+        )
 
 
 @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)
+    response = geneset.get_geneset_gene_values(
+        None, user=None, geneset_id=1234, gene_id_type=None
+    )
     assert response.get("error") is True
     assert response.get("message") == message.ACCESS_FORBIDDEN
 
@@ -369,3 +375,49 @@ def test_geneset_thershold_update_errors(mock_db_threshold, mock_db_geneset):
             geneset_id=1234,
             geneset_score=geneset_threshold,
         )
+
+
+@patch("geneweaver.api.services.geneset.db_geneset")
+@patch("geneweaver.api.services.geneset.db_gene")
+@patch("geneweaver.api.services.geneset.db_geneset_value")
+def test_geneset_gene_value_w_gene_id_type(
+    mock_db_geneset_value, mock_db_gene, mock_db_geneset
+):
+    """Test geneset gene value data response."""
+    mock_db_geneset.get.return_value = [geneset_by_id_resp.get("geneset")]
+    mock_db_gene.gene_database_by_id.return_value = [{"sp_id": 0}]
+    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, gene_id_type=GeneIdentifier(2)
+    )
+    assert response == geneset_genes_values_resp
+
+
+@patch("geneweaver.api.services.geneset.db_geneset")
+@patch("geneweaver.api.services.geneset.db_gene")
+@patch("geneweaver.api.services.geneset.db_geneset_value")
+def test_geneset_gene_value_w_gene_id_type_none_resp(
+    mock_db_geneset_value, mock_db_gene, mock_db_geneset
+):
+    """Test geneset gene value data empty response."""
+    mock_db_geneset.get.return_value = [geneset_by_id_resp.get("geneset")]
+    mock_db_gene.gene_database_by_id.return_value = [{"sp_id": 0}]
+    mock_db_geneset_value.by_geneset_id.return_value = None
+    response = geneset.get_geneset_gene_values(
+        None, user=mock_user, geneset_id=1234, gene_id_type=GeneIdentifier(2)
+    )
+    assert response == {"data": None}
+
+
+@patch("geneweaver.api.services.geneset.db_geneset")
+def test_geneset_gene_value_w_gene_id_type_none_resp2(mock_db_geneset):
+    """Test geneset gene value data empty response."""
+    mock_db_geneset.get.return_value = []
+
+    response = geneset.get_geneset_gene_values(
+        None, user=mock_user, geneset_id=1234, gene_id_type=GeneIdentifier(2)
+    )
+    assert response == {"data": None}