Merge pull request #41 from TheJacksonLaboratory/G3-195-gene-endpoint

G3 195 gene endpoint

README.md

@@ -46,7 +46,7 @@ such as DB, Webserver, or APIs. Create appropriate mocks for external resources
 
 To execute tests, from the command line run:
 
-    pytest 
+    pytest tests --cov=geneweaver.api --cov-report term  --cov-report html 
 
 ### Continuous Integration & Deployment
 When a PR is crated in GitHub, it will automatically trigger a workflow that will run 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.4.0a3"
+version = "0.4.0a4"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <alexander.berger@jax.org>",

src/geneweaver/api/controller/genes.py

@@ -1,7 +1,7 @@
 """Endpoints related to genes."""
 from typing import Optional
 
-from fastapi import APIRouter, Depends, Query
+from fastapi import APIRouter, Depends, Path, Query
 from geneweaver.api import dependencies as deps
 from geneweaver.api.schemas.apimodels import (
     GeneIdHomologReq,
@@ -34,7 +34,7 @@ def get_genes(
         Query(
             format="int64",
             minimum=0,
-            maxiumum=9223372036854775807,
+            maxiumum=1000,
             description=api_message.LIMIT,
         ),
     ] = None,
@@ -58,6 +58,18 @@ def get_genes(
     return response
 
 
+@router.get("/{gene_id}/preferred")
+def get_gene_preferred(
+    gene_id: Annotated[
+        int, Path(format="int64", minimum=0, maxiumum=9223372036854775807)
+    ],
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+) -> dict:
+    """Get preferred gene for a given gene ode_id."""
+    response = genes_service.get_gene_preferred(cursor, gene_id)
+    return response
+
+
 @router.post("/homologs", response_model=GeneIdMappingResp)
 def get_related_gene_ids(
     gene_id_mapping: GeneIdHomologReq,

src/geneweaver/api/services/genes.py

@@ -42,6 +42,23 @@ def get_genes(
     return {"genes": gene_list}
 
 
+def get_gene_preferred(cursor: Cursor, gene_id: int) -> dict:
+    """Get preferred gene from DB.
+
+    :param cursor: The database cursor.
+    :param gene_id: The id of the gene to get.
+    @return: dictionary with gene.
+    """
+    try:
+        gene = db_gene.get_preferred(cursor, gene_id)
+
+    except Exception as err:
+        logger.error(err)
+        raise err
+
+    return {"gene": gene}
+
+
 def get_homolog_ids(
     cursor: Cursor,
     gene_id_list: Iterable,

tests/controllers/test_genes.py

@@ -6,6 +6,7 @@
 
 # genes
 genes_list_10 = test_genes_data.get("genes_list_10")
+gene_preferred_resp_1 = test_genes_data.get("gene_preferred_resp_1")
 
 # gene homolog ids test data
 gene_ids_homolog_req_1 = test_gene_homolog_data.get(
@@ -180,3 +181,14 @@ def test_invalid_param_gene_get_req(mock_gene_call, client):
     assert response.status_code == 422
     response = client.get(url="/api/genes?preferred=abc")
     assert response.status_code == 422
+
+
+@patch("geneweaver.api.services.genes.get_gene_preferred")
+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
+    assert response.json() == gene_preferred_resp_1

tests/data/__init__.py

@@ -115,8 +115,10 @@
 ## geneweaver genes test data
 test_genes_data = {
     "genes_list_10": json.loads(genes_json).get("genes_list_10"),
+    "gene_preferred_resp_1": json.loads(genes_json).get("gene_preferred_resp_1"),
 }
 
+
 def get_species_db_resp(species_data: dict) -> dict:
     """Get species data as returned by DB."""
     species = species_data.get("species")
@@ -128,4 +130,3 @@ def get_species_db_resp(species_data: dict) -> dict:
             ).as_int()
 
     return species
-

tests/data/genes.json

@@ -82,5 +82,15 @@
         "date": "2020-05-05"
       }
     ]
+  },
+  "gene_preferred_resp_1": {
+    "gene": {
+      "id": 1000,
+      "reference_id": "Il1r2",
+      "gene_database": 7,
+      "species": 1,
+      "preferred": true,
+      "date": "2020-05-05"
+    }
   }
 }

tests/services/test_gene.py

@@ -9,6 +9,7 @@
 
 # genes
 genes_list_10 = test_genes_data.get("genes_list_10")
+gene_preferred_resp_1 = test_genes_data.get("gene_preferred_resp_1")
 
 # gene homolog ids test data
 gene_ids_homolog_req_1 = test_gene_homolog_data.get(
@@ -235,7 +236,7 @@ def test_get_gene_error(mock_db_gene):
 
 @patch("geneweaver.api.services.genes.db_gene")
 def test_get_gene(mock_db_gene):
-    """Test error in DB call."""
+    """Test get gene."""
     mock_db_gene.get.return_value = genes_list_10
 
     response = genes.get_genes(None)
@@ -254,3 +255,23 @@ def test_get_gene(mock_db_gene):
     )
 
     assert response.get("error") is None
+
+
+@patch("geneweaver.api.services.genes.db_gene")
+def test_get_gene_preferred(mock_db_gene):
+    """Test get gene preferred."""
+    mock_db_gene.get_preferred.return_value = gene_preferred_resp_1
+
+    response = genes.get_gene_preferred(None, gene_id=1000)
+
+    assert response.get("error") is None
+    assert response.get("gene") == gene_preferred_resp_1
+
+
+@patch("geneweaver.api.services.genes.db_gene")
+def test_get_gene_preferred_error(mock_db_gene):
+    """Test error in DB call gene_preferred."""
+    mock_db_gene.get_preferred.side_effect = Exception("ERROR")
+
+    with pytest.raises(expected_exception=Exception):
+        genes.get_gene_preferred(None, gene_id=1000)