refactor to use unittest instead of assert directly

app/routers/bioentity.py

@@ -28,6 +28,15 @@
 
 
 class RelationshipType(str, Enum):
+
+    """
+    Enumeration for Gene Ontology relationship types used for filtering associations.
+
+    :param INVOLVED_IN: The 'involved_in' relationship type.
+    :param ACTS_UPSTREAM_OF_OR_WITHIN: The 'acts_upstream_of_or_within' relationship type.
+    :param INVOLVED_IN_REGULATION_OF: The 'involved_in_regulation_of' relationship type.
+    """
+
     INVOLVED_IN = INVOLVED_IN
     ACTS_UPSTREAM_OF_OR_WITHIN = ACTS_UPSTREAM_OF_OR_WITHIN
     INVOLVED_IN_REGULATION_OF = INVOLVED_IN_REGULATION_OF
@@ -67,7 +76,6 @@ async def get_bioentity_by_id(
           'start' determines the starting index for fetching results, and 'rows' specifies
           the number of results to be retrieved per page.
     """
-
     # special case MGI, sigh
     if id.startswith("MGI:"):
         id = id.replace("MGI:", "MGI:MGI:")
@@ -97,7 +105,8 @@ async def get_annotations_by_goterm_id(
     start: int = 0,
     rows: int = 100,
 ):
-    """Returns annotations using the provided GO term.
+    """
+    Returns annotations using the provided GO term.
 
     Retrieves annotations based on the provided Gene Ontology (GO) term identifier.
     The GO term identifier should be represented in CURIE format (e.g., GO:0044598).
@@ -175,7 +184,8 @@ async def get_genes_by_goterm_id(
     start: int = 0,
     rows: int = 100,
 ):
-    """Returns genes annotated to the provided GO Term.
+    """
+    Returns genes annotated to the provided GO Term.
 
     Retrieves genes annotated to the provided Gene Ontology (GO) term. The GO term should be
     represented in CURIE format (e.g., GO:0044598).
@@ -261,7 +271,8 @@ async def get_taxon_by_goterm_id(
     start: int = 0,
     rows: int = 100,
 ):
-    """Returns taxon information for genes annotated to the provided GO term.
+    """
+    Returns taxon information for genes annotated to the provided GO term.
 
     Retrieves taxon information for genes annotated to the provided Gene Ontology (GO) term.
     The GO term should be represented in CURIE format (e.g., GO:0044598).

tests/unit/test_models_endpoints.py

@@ -1,101 +1,125 @@
 import logging
-
-import pytest
+import unittest
 from fastapi.testclient import TestClient
-
 from app.main import app
 
 test_client = TestClient(app)
 
 gene_ids = ["ZFIN:ZDB-GENE-980526-388", "ZFIN:ZDB-GENE-990415-8", "MGI:3588192"]
-go_ids = ["GO:0008150"]
-subsets = ["goslim_agr"]
-shared_ancestors = [("GO:0006259", "GO:0046483")]
-uris = ["http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0008150"]
-
-logger = logging.getLogger(__name__)
-
-
-def test_gometadata_by_model_ids():
-    data = {"gocams": ["59a6110e00000067", "SYNGO_369"]}
-    response = test_client.get("/api/models/go", params=data)
-    assert response.status_code == 200
-    assert len(response.json()) == 2
-
-
-def test_geneproductmetadata_by_model_ids():
-    data = {"gocams": ["59a6110e00000067", "SYNGO_369"]}
-    response = test_client.get("/api/models/gp", params=data)
-    assert response.status_code == 200
-    assert len(response.json()) == 2
-
-
-def test_pubmedmetadata_by_model_ids():
-    data = {"gocams": ["59a6110e00000067", "SYNGO_369"]}
-    response = test_client.get("/api/models/pmid", params=data)
-    assert response.status_code == 200
-    assert len(response.json()) == 2
-
-
-@pytest.mark.parametrize("id", gene_ids)
-def test_bioenty_id_endpoints(id):
-    response = test_client.get(f"/api/bioentity/{id}")
-    assert response.status_code == 200
-
-
-def test_gocam_by_model_ids():
-    response = test_client.get("/api/models/581e072c00000820")
-    assert len(response.json()) > 125
-    assert response.status_code == 200
-
-
-def test_models_size_endpoint():
-    data = {
-        "start": "32",
-        "size": "10",
-    }
-    response = test_client.get("/api/models", params=data)
-    for record in response.json():
-        assert type(record.get("orcids")) == list
-    assert response.status_code == 200
-
-
-def test_userlist():
-    response = test_client.get("/api/users")
-    assert len(response.json()) > 100
-    assert response.status_code == 200
-
-
-def test_grouplist():
-    response = test_client.get("/api/groups")
-    assert len(response.json()) > 15
-    assert response.status_code == 200
-
-
-def test_groups_by_name():
-    response = test_client.get("/api/groups/MGI")
-    assert len(response.json()) > 10
-    assert response.status_code == 200
-
-
-def test_get_modelid_by_pmid():
-    response = test_client.get("/api/pmid/15314168/models")
-    assert len(response.json()) == 1
-    assert response.status_code == 200
-
 
-def test_get_go_term_detail_by_go_id():
-    response = test_client.get("/api/go/GO_0008150")
-    assert "goid" in response.json()
-    assert "label" in response.json()
-    assert response.json().get("goid") == "http://purl.obolibrary.org/obo/GO_0008150"
-    assert response.json().get("label") == "biological_process"
-    assert type(response.json()) == dict
-    assert response.status_code == 200
 
+class TestApp(unittest.TestCase):
+
+    def test_gometadata_by_model_ids(self):
+        """
+        Test the endpoint to retrieve GO metadata by model IDs.
+        """
+        data = {"gocams": ["59a6110e00000067", "SYNGO_369"]}
+        response = test_client.get("/api/models/go", params=data)
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(len(response.json()), 2)
+
+    def test_geneproductmetadata_by_model_ids(self):
+        """
+        Test the endpoint to retrieve gene product metadata by model IDs.
+        """
+        data = {"gocams": ["59a6110e00000067", "SYNGO_369"]}
+        response = test_client.get("/api/models/gp", params=data)
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(len(response.json()), 2)
+
+    def test_pubmedmetadata_by_model_ids(self):
+        """
+        Test the endpoint to retrieve PubMed metadata by model IDs.
+        """
+        data = {"gocams": ["59a6110e00000067", "SYNGO_369"]}
+        response = test_client.get("/api/models/pmid", params=data)
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(len(response.json()), 2)
+
+    def test_bioenty_id_endpoints(self):
+        """
+        Test the bioentity endpoint for each given ID.
+        """
+        for id in gene_ids:
+            response = test_client.get(f"/api/bioentity/{id}")
+            self.assertEqual(response.status_code, 200)
+
+    def test_gocam_by_model_ids(self):
+        """
+        Test the endpoint to retrieve GO-CAMs by model IDs.
+        """
+        response = test_client.get("/api/models/581e072c00000820")
+        self.assertGreater(len(response.json()), 125)
+        self.assertEqual(response.status_code, 200)
+
+    def test_models_size_endpoint(self):
+        """
+        Test the endpoint to retrieve models with specified size.
+        """
+        data = {
+            "start": "32",
+            "size": "10",
+        }
+        response = test_client.get("/api/models", params=data)
+        for record in response.json():
+            self.assertIsInstance(record.get("orcids"), list)
+        self.assertEqual(response.status_code, 200)
+
+    def test_userlist(self):
+        """
+        Test the endpoint to retrieve the list of users.
+        """
+        response = test_client.get("/api/users")
+        self.assertGreater(len(response.json()), 100)
+        self.assertEqual(response.status_code, 200)
+
+    def test_grouplist(self):
+        """
+        Test the endpoint to retrieve the list of groups.
+        """
+        response = test_client.get("/api/groups")
+        self.assertGreater(len(response.json()), 15)
+        self.assertEqual(response.status_code, 200)
+
+    def test_groups_by_name(self):
+        """
+        Test the endpoint to retrieve groups by name.
+        """
+        response = test_client.get("/api/groups/MGI")
+        self.assertGreater(len(response.json()), 10)
+        self.assertEqual(response.status_code, 200)
+
+    def test_get_modelid_by_pmid(self):
+        """
+        Test the endpoint to retrieve model IDs by PubMed ID.
+        """
+        response = test_client.get("/api/pmid/15314168/models")
+        self.assertEqual(len(response.json()), 1)
+        self.assertEqual(response.status_code, 200)
+
+    def test_get_go_term_detail_by_go_id(self):
+        """
+        Test the endpoint to retrieve GO term details by GO ID.
+        """
+        response = test_client.get("/api/go/GO_0008150")
+        self.assertIn("goid", response.json())
+        self.assertIn("label", response.json())
+        self.assertEqual(response.json()["goid"], "http://purl.obolibrary.org/obo/GO_0008150")
+        self.assertEqual(response.json()["label"], "biological_process")
+        self.assertIsInstance(response.json(), dict)
+        self.assertEqual(response.status_code, 200)
+
+    def test_get_gocam_models_by_go_id(self):
+        """
+        Test the endpoint to retrieve GO-CAM models by GO ID.
+        """
+        id = "GO:0008150"
+        response = test_client.get(f"/api/go/{id}/models")
+        self.assertGreater(len(response.json()), 100)
+        self.assertEqual(response.status_code, 200)
+
+
+if __name__ == '__main__':
+    unittest.main()
 
-def test_get_gocam_models_by_go_id():
-    id = "GO:0008150"
-    response = test_client.get(f"/api/go/{id}/models")
-    assert len(response.json()) > 100
-    assert response.status_code == 200