Merge pull request #45 from TheJacksonLaboratory/G3-346-client-ensemb…

…le-mouse-output

G3-346 client cli ensemble mouse output updates

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-client"
-version = "0.10.0a1"
+version = "0.10.0a2"
 description = "A Python Client for the Geneweaver API"
 authors = ["Jax Computational Sciences <[email protected]>"]
 readme = "README.md"

src/geneweaver/client/api/mapping.py

@@ -33,7 +33,10 @@ def ensembl_mouse_mapping(
     response = genesets.get_values(access_token, geneset_id, gene_id_type, in_threshold)
 
     if species == Species.MUS_MUSCULUS:
-        result = response["data"]
+        result = [
+            {"gene_id": item["symbol"], "score": item["value"]}
+            for item in response["data"]
+        ]
 
     else:
         if algorithm:
@@ -67,6 +70,6 @@ def ensembl_mouse_mapping(
             ],
         )
 
-        result = [{"symbol": k, "value": v} for k, v in ensembl_result.items()]
+        result = [{"gene_id": k, "score": v} for k, v in ensembl_result.items()]
 
     return result

src/geneweaver/client/cli/alpha/geneset.py

@@ -43,8 +43,12 @@ def get_values_as_ensembl_mouse(
         default=None, help="Ortholog mapping algorithm. Leave empty for all algorithms."
     ),
     as_csv: bool = typer.Option(False, "--csv", help="Output as CSV"),
+    csv_headers: bool = typer.Option(True, "--omit-headers", help="Omit CSV headers"),
 ) -> List[dict]:
-    """Get a Geneset's values as Ensembl Mouse Gene IDs."""
+    """Get a Geneset's values as Ensembl Mouse Gene IDs.
+
+    Optional csv output with or without headers.
+    """
     # Check Geneset Species
     token = get_access_token()
     result = mapping.ensembl_mouse_mapping(
@@ -55,7 +59,7 @@ def get_values_as_ensembl_mouse(
     )
 
     if as_csv:
-        result = format_csv(result)
+        result = format_csv(result, with_header=csv_headers)
 
     if not ctx.obj["quiet"]:
         if not as_csv:

tests/unit/api/test_mapping.py

@@ -53,13 +53,16 @@ def test_ensembl_mouse_mapping(
     assert mock_genesets_get_values.call_count == 1
 
     if species_id == 1:
-        assert result == [{"symbol": "A", "value": "1"}, {"symbol": "B", "value": "2"}]
+        assert result == [
+            {"gene_id": "A", "score": "1"},
+            {"gene_id": "B", "score": "2"},
+        ]
         expected_api_calls, expected_mapping_calls = 0, 0
 
     else:
         assert result == [
-            {"symbol": "A2", "value": "1"},
-            {"symbol": "B2", "value": "2"},
+            {"gene_id": "A2", "score": "1"},
+            {"gene_id": "B2", "score": "2"},
         ]
         expected_api_calls, expected_mapping_calls = 1, 2