Merge pull request #49 from TheJacksonLaboratory/G3-212-genes-endpoin…

…t-return-schema G3 212 genes endpoint return schema
TheJacksonLaboratory · Apr 5, 2024 · 27e7d3c · 27e7d3c
2 parents 8b0680b + d66e174
commit 27e7d3c
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Showing 7 changed files with 45 additions and 40 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.4.0a9"
+version = "0.4.0a11"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <[email protected]>",

diff --git a/src/geneweaver/api/controller/genes.py b/src/geneweaver/api/controller/genes.py
@@ -9,9 +9,11 @@
     GeneIdMappingAonReq,
     GeneIdMappingReq,
     GeneIdMappingResp,
+    GeneReturn,
 )
 from geneweaver.api.services import genes as genes_service
 from geneweaver.core.enum import GeneIdentifier, Species
+from geneweaver.core.schema.gene import Gene
 from typing_extensions import Annotated
 
 from . import message as api_message
@@ -48,7 +50,7 @@ def get_genes(
             description=api_message.OFFSET,
         ),
     ] = None,
-) -> dict:
+) -> GeneReturn:
     """Get geneweaver list of genes."""
     if limit is None:
         limit = 100
@@ -65,7 +67,7 @@ def get_gene_preferred(
         int, Path(format="int64", minimum=0, maxiumum=9223372036854775807)
     ],
     cursor: Optional[deps.Cursor] = Depends(deps.cursor),
-) -> dict:
+) -> Gene:
     """Get preferred gene for a given gene ode_id."""
     response = genes_service.get_gene_preferred(cursor, gene_id)
     return response

diff --git a/src/geneweaver/api/schemas/apimodels.py b/src/geneweaver/api/schemas/apimodels.py
@@ -3,6 +3,7 @@
 from typing import Iterable, List, Optional
 
 from geneweaver.core.enum import GeneIdentifier, Species
+from geneweaver.core.schema.gene import Gene
 from pydantic import BaseModel
 
 
@@ -35,3 +36,9 @@ class GeneIdMappingAonReq(BaseModel):
 
     source_ids: List[str]
     species: Species
+
+
+class GeneReturn(BaseModel):
+    """Model for gene endpoint return."""
+
+    data: List[Gene]
diff --git a/src/geneweaver/api/services/genes.py b/src/geneweaver/api/services/genes.py
@@ -39,7 +39,7 @@ def get_genes(
         logger.error(err)
         raise err
 
-    return {"genes": gene_list}
+    return {"data": gene_list}
 
 
 def get_gene_preferred(cursor: Cursor, gene_id: int) -> dict:
@@ -56,7 +56,7 @@ def get_gene_preferred(cursor: Cursor, gene_id: int) -> dict:
         logger.error(err)
         raise err
 
-    return {"gene": gene}
+    return gene
 
 
 def get_homolog_ids(

diff --git a/tests/controllers/test_genes.py b/tests/controllers/test_genes.py
@@ -32,7 +32,7 @@ def test_gene_id_mapping_response_post_req(mock_gene_id_mapping, client):
     response = client.post(
         url="/api/genes/homologs", data=json.dumps(gene_ids_homolog_req_1)
     )
-    print(response)
+
     assert response.status_code == 200
     assert response.json() == gene_ids_homolog_resp_1
 
@@ -47,7 +47,7 @@ def test_gene_id_mapping_invalid_url(mock_gene_id_mapping, client):
     response = client.post(
         url="/api/genes/homologous-ids", data=json.dumps(gene_ids_homolog_req_1)
     )
-    print(response)
+
     assert response.status_code == 404
 
 
@@ -98,7 +98,7 @@ def test_gene_mapping_valid_post_req(mock_gene_id_mapping, client):
     response = client.post(
         url="/api/genes/mappings", data=json.dumps(gene_id_mapping_req_1)
     )
-    print(response)
+
     assert response.status_code == 200
     assert response.json() == gene_id_mapping_resp_1
 
@@ -113,7 +113,7 @@ def test_gene_mapping_invalid_url(mock_gene_id_mapping, client):
     response = client.post(
         url="/api/genes/mapping", data=json.dumps(gene_id_mapping_req_1)
     )
-    print(response)
+
     assert response.status_code == 404
 
 
@@ -138,7 +138,7 @@ def test_gene_aon_mapping_valid_post_req(mock_gene_id_aon_mapping, client):
     response = client.post(
         url="/api/genes/mappings/aon", data=json.dumps(gene_id_aon_mapping_req_1)
     )
-    print(response)
+
     assert response.status_code == 200
     assert response.json() == gene_id_aon_mapping_resp_1
 
@@ -158,7 +158,6 @@ def test_valid_gene_get_req(mock_gene_call, client):
 
     response = client.get(url="/api/genes")
 
-    print(response)
     assert response.status_code == 200
     assert response.json() == genes_list_10
 
@@ -188,7 +187,6 @@ def test_invalid_param_gene_get_req(mock_gene_call, client):
 def test_valid_get_preferred_gene_req(mock_gene_call, client):
     """Test valid get preferred gene request."""
     mock_gene_call.return_value = gene_preferred_resp_1
-
     response = client.get(url="/api/genes/1000/preferred")
 
     assert response.status_code == 200

diff --git a/tests/data/genes.json b/tests/data/genes.json
@@ -1,96 +1,94 @@
 {
   "genes_list_10": {
-    "genes": [
+    "data": [
       {
         "id": 1,
         "reference_id": "MGI:87853",
-        "gene_database": 10,
-        "species": 1,
+        "gene_database": "MGI",
+        "species": "Mus Musculus",
         "preferred": false,
         "date": "2020-05-05"
       },
       {
         "id": 2,
         "reference_id": "MGI:87854",
-        "gene_database": 10,
-        "species": 1,
+        "gene_database": "MGI",
+        "species": "Mus Musculus",
         "preferred": false,
         "date": "2020-05-05"
       },
       {
         "id": 3,
         "reference_id": "MGI:87859",
-        "gene_database": 10,
-        "species": 1,
+        "gene_database": "MGI",
+        "species": "Mus Musculus",
         "preferred": false,
         "date": "2020-05-05"
       },
       {
         "id": 4,
         "reference_id": "MGI:87860",
-        "gene_database": 10,
-        "species": 1,
+        "gene_database": "MGI",
+        "species": "Mus Musculus",
         "preferred": false,
         "date": "2020-05-05"
       },
       {
         "id": 5,
         "reference_id": "MGI:87862",
-        "gene_database": 10,
-        "species": 1,
+        "gene_database": "MGI",
+        "species": "Mus Musculus",
         "preferred": false,
         "date": "2020-05-05"
       },
       {
         "id": 6,
         "reference_id": "MGI:87863",
-        "gene_database": 10,
-        "species": 1,
+        "gene_database": "MGI",
+        "species": "Mus Musculus",
         "preferred": false,
         "date": "2020-05-05"
       },
       {
         "id": 7,
         "reference_id": "MGI:87864",
-        "gene_database": 10,
-        "species": 1,
+        "gene_database": "MGI",
+        "species": "Mus Musculus",
         "preferred": false,
         "date": "2020-05-05"
       },
       {
         "id": 8,
         "reference_id": "MGI:87866",
-        "gene_database": 10,
-        "species": 1,
+        "gene_database": "MGI",
+        "species": "Mus Musculus",
         "preferred": false,
         "date": "2020-05-05"
       },
       {
         "id": 9,
         "reference_id": "MGI:87867",
-        "gene_database": 10,
-        "species": 1,
+        "gene_database": "MGI",
+        "species": "Mus Musculus",
         "preferred": false,
         "date": "2020-05-05"
       },
       {
         "id": 10,
         "reference_id": "MGI:87868",
-        "gene_database": 10,
-        "species": 1,
+        "gene_database": "MGI",
+        "species": "Mus Musculus",
         "preferred": false,
         "date": "2020-05-05"
       }
     ]
   },
   "gene_preferred_resp_1": {
-    "gene": {
       "id": 1000,
       "reference_id": "Il1r2",
-      "gene_database": 7,
-      "species": 1,
+      "gene_database": "Gene Symbol",
+      "species": "Mus Musculus",
       "preferred": true,
       "date": "2020-05-05"
     }
-  }
 }
diff --git a/tests/services/test_gene.py b/tests/services/test_gene.py
@@ -231,7 +231,7 @@ def test_get_gene_error(mock_db_gene):
     mock_db_gene.get.side_effect = Exception("ERROR")
 
     with pytest.raises(expected_exception=Exception):
-        genes.get(None)
+        genes.get_genes(None)
 
 
 @patch("geneweaver.api.services.genes.db_gene")
@@ -242,7 +242,7 @@ def test_get_gene(mock_db_gene):
     response = genes.get_genes(None)
 
     assert response.get("error") is None
-    assert response.get("genes") == genes_list_10
+    assert response.get("data") == genes_list_10
 
     response = genes.get_genes(
         None,
@@ -265,7 +265,7 @@ def test_get_gene_preferred(mock_db_gene):
     response = genes.get_gene_preferred(None, gene_id=1000)
 
     assert response.get("error") is None
-    assert response.get("gene") == gene_preferred_resp_1
+    assert response == gene_preferred_resp_1
 
 
 @patch("geneweaver.api.services.genes.db_gene")