Merge pull request #95 from TheJacksonLaboratory/G3-428-api-get-gense…

…t-by-multiple-score-type

G3-428 get geneset endpoint modification to support multiple score types

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.8.1a0"
+version = "0.8.1a1"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <alexander.berger@jax.org>",
@@ -20,7 +20,7 @@ python = "^3.9"
 geneweaver-core = "^0.10.0a3"
 fastapi = {extras = ["all"], version = "^0.111.0"}
 uvicorn = {extras = ["standard"], version = "^0.30.0"}
-geneweaver-db = "0.5.0a16"
+geneweaver-db = "0.5.0a17"
 psycopg-pool = "^3.1.7"
 requests = "^2.32.3"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}

src/geneweaver/api/controller/genesets.py

@@ -69,7 +69,7 @@ def get_visible_genesets(
     with_publication_info: Annotated[
         bool, Query(description=api_message.ONLY_MY_GS)
     ] = True,
-    score_type: Optional[ScoreType] = None,
+    score_type: Annotated[Optional[Set[ScoreType]], Query()] = None,
     size_less_than: Annotated[
         Optional[int],
         Query(

src/geneweaver/api/services/geneset.py

@@ -92,7 +92,7 @@ def get_visible_genesets(
     search_text: Optional[str] = None,
     ontology_term: Optional[str] = None,
     with_publication_info: bool = True,
-    score_type: Optional[ScoreType] = None,
+    score_type: Optional[Set[ScoreType]] = None,
     lte_count: Optional[int] = None,
     gte_count: Optional[int] = None,
     created_after: Optional[date] = None,
@@ -118,7 +118,7 @@ def get_visible_genesets(
     :param search_text: Return genesets that match this search text (using PostgreSQL
                         full-text search).
     :param ontology_term: Show only results associated with this ontology term.
-    :param score_type: Show only results with given score type.
+    :param score_type: Show only results for given score type(s).
     :param lte_count: less than or equal geneset count.
     :param gte_count: greater than or equal geneset count.
     :param updated_before: Show only results updated before this date.

tests/controllers/test_genesets.py

@@ -401,17 +401,45 @@ def test_delete_geneset_ontology_terms_errors(mock_delete_genenset_onto_terms, c
     assert response.status_code == 404
 
 
-@pytest.mark.parametrize("score_type", ["1", "binary"])
+@pytest.mark.parametrize(
+    "score_type",
+    [
+        "score_type=p-value",
+        "score_type=q-value",
+        "score_type=effect",
+        "score_type=correlation",
+        "score_type=binary",
+        "score_type=p-value&score_type=q-value",
+        "score_type=p-value&score_type=q-value&score_type=effect",
+        "score_type=p-value&score_type=q-value&score_type=effect&score_type=correlation",
+        "score_type=p-value&score_type=q-value&score_type=effect&score_type=correlation&score_type=binary",
+    ],
+)
 @patch("geneweaver.api.services.geneset.get_visible_genesets")
 def test_get_geneset_by_score_type(mock_get_visible_genesets, score_type, client):
     """Test get geneset  data response."""
     mock_get_visible_genesets.return_value = geneset_by_id_resp.get("geneset")
 
-    response = client.get("/api/genesets?score_type=" + score_type)
+    response = client.get("/api/genesets?" + score_type)
     assert response.status_code == 200
     assert response.json() == geneset_by_id_resp.get("geneset")
 
 
+@pytest.mark.parametrize(
+    "score_type",
+    ["score_type=1233", "score_type=test", "score_type=p-value&score_type=test"],
+)
+@patch("geneweaver.api.services.geneset.get_visible_genesets")
+def test_get_geneset_by_invalid_score_type(
+    mock_get_visible_genesets, score_type, client
+):
+    """Test get geneset  data response."""
+    mock_get_visible_genesets.return_value = geneset_by_id_resp.get("geneset")
+
+    response = client.get("/api/genesets?" + score_type)
+    assert response.status_code == 422
+
+
 @patch("geneweaver.api.services.geneset.get_visible_genesets")
 def test_get_geneset_by_create_date(mock_get_visible_genesets, client):
     """Test get geneset  data response."""
@@ -436,13 +464,6 @@ def test_get_geneset_by_update_date(mock_get_visible_genesets, client):
     assert response.json() == geneset_by_id_resp.get("geneset")
 
 
-@pytest.mark.parametrize("score_type", ["2342", "test"])
-def test_invalid_score_type(score_type, client):
-    """Test general get geneset data no parameters -- default limit."""
-    response = client.get("/api/genesets?score_type=" + score_type)
-    assert response.status_code == 422
-
-
 @pytest.mark.parametrize("created_before", ["20-23-20", "08-01-2023", "80/01/2022"])
 @pytest.mark.parametrize("created_after", ["20-23-20", "08-01-2023", "80/01/2022"])
 def test_invalid_create_date_params(created_before, created_after, client):

tests/services/test_genset.py

@@ -259,7 +259,7 @@ def test_visible_geneset_all_expected_parameters(mock_db_geneset):
         abbreviation="test",
         publication_id=123,
         pubmed_id="p123",
-        score_type=ScoreType("p-value"),
+        score_type={ScoreType("p-value"), ScoreType("q-value")},
         lte_count=50,
         gte_count=5,
         gene_id_type=GeneIdentifier(5),
@@ -636,3 +636,30 @@ def test_delete_geneset_ontology_term_errors(mock_db_ontology, mock_db_geneset):
         geneset.delete_geneset_ontology_term(
             cursor=None, user=mock_user, geneset_id=1234, term_ref_id="D001921"
         )
+
+
+@patch("geneweaver.api.services.geneset.db_geneset")
+@pytest.mark.parametrize(
+    "score_type",
+    [
+        None,
+        {ScoreType.P_VALUE},
+        {ScoreType.P_VALUE, ScoreType.Q_VALUE},
+        {ScoreType.P_VALUE, ScoreType.Q_VALUE, ScoreType.EFFECT},
+        {ScoreType.P_VALUE, ScoreType.Q_VALUE, ScoreType.EFFECT, ScoreType.CORRELATION},
+        {
+            ScoreType.P_VALUE,
+            ScoreType.Q_VALUE,
+            ScoreType.EFFECT,
+            ScoreType.CORRELATION,
+            ScoreType.BINARY,
+        },
+    ],
+)
+def test_get_geneset_by_score_type(mock_db_geneset, score_type):
+    """Test get geneset by score type."""
+    mock_db_geneset.get.return_value = geneset_list_resp
+
+    response = geneset.get_visible_genesets(None, mock_user, score_type=score_type)
+
+    assert response.get("data") == geneset_list_resp