Merge pull request #33 from TheJacksonLaboratory/G3-197-gene-aon-mapping

G3 197 gene aon mapping

src/geneweaver/api/controller/genes.py

@@ -5,7 +5,7 @@
 from geneweaver.api import dependencies as deps
 from geneweaver.api.schemas.apimodels import (
     GeneIdHomologReq,
-    GeneIdHomologResp,
+    GeneIdMappingAonReq,
     GeneIdMappingReq,
     GeneIdMappingResp,
 )
@@ -14,11 +14,11 @@
 router = APIRouter(prefix="/genes", tags=["genes"])
 
 
-@router.post("/homologs", response_model=GeneIdHomologResp)
+@router.post("/homologs", response_model=GeneIdMappingResp)
 def get_related_gene_ids(
     gene_id_mapping: GeneIdHomologReq,
     cursor: Optional[deps.Cursor] = Depends(deps.cursor),
-) -> GeneIdHomologResp:
+) -> GeneIdMappingResp:
     """Get homologous gene ids given list of gene ids."""
     response = genes_service.get_homolog_ids(
         cursor,
@@ -30,7 +30,7 @@ def get_related_gene_ids(
     )
 
     resp_id_map = response.get("ids_map")
-    gene_id_mapping_resp = GeneIdHomologResp(gene_ids_map=resp_id_map)
+    gene_id_mapping_resp = GeneIdMappingResp(gene_ids_map=resp_id_map)
 
     return gene_id_mapping_resp
 
@@ -39,7 +39,7 @@ def get_related_gene_ids(
 def get_genes_mapping(
     gene_id_mapping: GeneIdMappingReq,
     cursor: Optional[deps.Cursor] = Depends(deps.cursor),
-) -> GeneIdHomologResp:
+) -> GeneIdMappingResp:
     """Get gene ids mapping."""
     response = genes_service.get_gene_mapping(
         cursor,
@@ -52,3 +52,19 @@ def get_genes_mapping(
     gene_id_mapping_resp = GeneIdMappingResp(gene_ids_map=resp_id_map)
 
     return gene_id_mapping_resp
+
+
+@router.post("/mapping/aon", response_model=GeneIdMappingResp)
+def get_genes_mapping_aon(
+    gene_id_mapping: GeneIdMappingAonReq,
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+) -> GeneIdMappingResp:
+    """Get gene ids mapping given list of gene ids and target gene identifier type."""
+    response = genes_service.get_gene_aon_mapping(
+        cursor, gene_id_mapping.source_ids, gene_id_mapping.species
+    )
+
+    resp_id_map = response.get("ids_map")
+    gene_id_mapping_resp = GeneIdMappingResp(gene_ids_map=resp_id_map)
+
+    return gene_id_mapping_resp

src/geneweaver/api/schemas/apimodels.py

@@ -5,8 +5,8 @@
 from pydantic import BaseModel
 
 
-class GeneIdHomologResp(BaseModel):
-    """Model for homolog gene id mapping."""
+class GeneIdMappingResp(BaseModel):
+    """Model for gene id mapping response."""
 
     gene_ids_map: list[dict]
 
@@ -21,15 +21,16 @@ class GeneIdHomologReq(BaseModel):
     source_species: Optional[Species] = None
 
 
-class GeneIdMappingResp(BaseModel):
-    """Model for gene id mapping."""
-
-    gene_ids_map: list[dict]
-
-
 class GeneIdMappingReq(BaseModel):
     """Model for gene id mapping request."""
 
     source_ids: List[str]
     target_gene_id_type: GeneIdentifier
     species: Species
+
+
+class GeneIdMappingAonReq(BaseModel):
+    """Model for AON gene id mapping request."""
+
+    source_ids: List[str]
+    species: Species

src/geneweaver/api/services/genes.py

@@ -72,3 +72,32 @@ def get_gene_mapping(
         raise err
 
     return {"ids_map": ids_map}
+
+
+def get_gene_aon_mapping(
+    cursor: Cursor,
+    source_ids: List[str],
+    species: Species,
+) -> dict:
+    """Get gene identifier AON mappings.
+
+    Get gene id mappings based on species and default gene identifier type.
+
+    @param cursor: DB Cursor
+    @param source_ids: list of gene ids to search
+    @param species: target species identifier
+    @return: dictionary with id mappings.
+    """
+    ids_map = None
+    try:
+        ids_map = db_gene.aon_mapping(
+            cursor,
+            source_ids,
+            species,
+        )
+
+    except Exception as err:
+        logger.error(err)
+        raise err
+
+    return {"ids_map": ids_map}

tests/controllers/test_genes.py

@@ -13,6 +13,8 @@
 # gene id mapping test data
 gene_id_mapping_req_1 = test_gene_mapping_data.get("gene_mapping_req_1")
 gene_id_mapping_resp_1 = test_gene_mapping_data.get("gene_mapping_resp_1")
+gene_id_aon_mapping_req_1 = test_gene_mapping_data.get("gene_aon_mapping_req_1")
+gene_id_aon_mapping_resp_1 = test_gene_mapping_data.get("gene_aon_mapping_resp_1")
 
 
 @patch("geneweaver.api.services.genes.get_homolog_ids")
@@ -119,3 +121,26 @@ def test_gene_mapping_invalid_post_data_(mock_gene_id_mapping, client):
 
     response = client.post(url="/api/genes/mapping", data=json.dumps({"test": "test"}))
     assert response.status_code == 422
+
+
+@patch("geneweaver.api.services.genes.get_gene_aon_mapping")
+def test_gene_aon_mapping_valid_post_req(mock_gene_id_aon_mapping, client):
+    """Test genes mapping ids url and post request."""
+    mock_gene_id_aon_mapping.return_value = {
+        "ids_map": gene_id_aon_mapping_resp_1.get("gene_ids_map")
+    }
+
+    response = client.post(
+        url="/api/genes/mapping/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
+
+
+def test_gene_aon_mapping_invalid_post_data_(client):
+    """Test genes ids aon mapping url and invalid post data request."""
+    response = client.post(
+        url="/api/genes/mapping/aon", data=json.dumps({"test": "test"})
+    )
+    assert response.status_code == 422

tests/data/__init__.py

@@ -72,6 +72,12 @@
     "gene_mapping_resp_2": json.loads(gene_id_mapping_json).get(
         "gene_mapping_response_2"
     ),
+    "gene_aon_mapping_req_1": json.loads(gene_id_mapping_json).get(
+        "gene_aon_mapping_request_1"
+    ),
+    "gene_aon_mapping_resp_1": json.loads(gene_id_mapping_json).get(
+        "gene_aon_mapping_response_1"
+    ),
 }
 
 # Publication test data

tests/data/gene_maping.json

@@ -39,5 +39,24 @@
         "mapped_ref_id": "KLHL13"
       }
     ]
+  },
+  "gene_aon_mapping_request_1": {
+    "source_ids": [
+      "DAB1",
+      "SLC6A9"
+    ],
+    "species": "Homo Sapiens"
+  },
+  "gene_aon_mapping_response_1": {
+    "gene_ids_map": [
+      {
+        "original_ref_id": "DAB1",
+        "mapped_ref_id": "HGNC:2661"
+      },
+      {
+        "original_ref_id": "SLC6A9",
+        "mapped_ref_id": "HGNC:11056"
+      }
+    ]
   }
 }

tests/services/test_gene.py

@@ -27,6 +27,8 @@
 gene_id_mapping_resp_1 = test_gene_mapping_data.get("gene_mapping_resp_1")
 gene_id_mapping_req_2 = test_gene_mapping_data.get("gene_mapping_req_2")
 gene_id_mapping_resp_2 = test_gene_mapping_data.get("gene_mapping_resp_2")
+gene_id_aon_mapping_req_1 = test_gene_mapping_data.get("gene_aon_mapping_req_1")
+gene_id_aon_mapping_resp_1 = test_gene_mapping_data.get("gene_aon_mapping_resp_1")
 
 
 @patch("geneweaver.api.services.genes.db_gene")
@@ -147,7 +149,7 @@ def test_get_gene_map_mouse(mock_db_gene):
     response = genes.get_gene_mapping(
         None,
         gene_id_mapping_req_1.get("source_ids"),
-        gene_id_mapping_req_1.get("target_species"),
+        gene_id_mapping_req_1.get("species"),
         gene_id_mapping_req_1.get("target_gene_id_type"),
     )
 
@@ -165,7 +167,7 @@ def test_get_gene_map_human(mock_db_gene):
     response = genes.get_gene_mapping(
         None,
         gene_id_mapping_req_2.get("source_ids"),
-        gene_id_mapping_req_2.get("target_species"),
+        gene_id_mapping_req_2.get("species"),
         gene_id_mapping_req_2.get("target_gene_id_type"),
     )
 
@@ -182,6 +184,38 @@ def test_get_gene_map_error(mock_db_gene):
         genes.get_gene_mapping(
             None,
             gene_id_mapping_req_2.get("source_ids"),
-            gene_id_mapping_req_2.get("target_species"),
+            gene_id_mapping_req_2.get("species"),
             gene_id_mapping_req_2.get("target_gene_id_type"),
         )
+
+
+@patch("geneweaver.api.services.genes.db_gene")
+def test_get_gene_aon_map(mock_db_gene):
+    """Test gene ids map by gene id type and species - Human."""
+    mock_db_gene.aon_mapping.return_value = gene_id_aon_mapping_resp_1.get(
+        "gene_ids_map"
+    )
+
+    # Request:
+    # (source_ids, target gene id type, target species)
+    response = genes.get_gene_aon_mapping(
+        None,
+        gene_id_aon_mapping_req_1.get("source_ids"),
+        gene_id_aon_mapping_req_1.get("species"),
+    )
+
+    assert response.get("error") is None
+    assert response.get("ids_map") == gene_id_aon_mapping_resp_1.get("gene_ids_map")
+
+
+@patch("geneweaver.api.services.genes.db_gene")
+def test_get_aon_gene_map_error(mock_db_gene):
+    """Test error in DB call."""
+    mock_db_gene.aon_mapping.side_effect = Exception("ERROR")
+
+    with pytest.raises(expected_exception=Exception):
+        genes.get_gene_aon_mapping(
+            None,
+            gene_id_aon_mapping_req_1.get("source_ids"),
+            gene_id_aon_mapping_req_1.get("species"),
+        )