Merge pull request #38 from TheJacksonLaboratory/G3-194-gene-list-end…

…point

G3 194 gene list endpoint

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.3.0a01"
+version = "0.3.0a02"
 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
+from fastapi import APIRouter, Depends, Query
 from geneweaver.api import dependencies as deps
 from geneweaver.api.schemas.apimodels import (
     GeneIdHomologReq,
@@ -10,10 +10,54 @@
     GeneIdMappingResp,
 )
 from geneweaver.api.services import genes as genes_service
+from geneweaver.core.enum import GeneIdentifier, Species
+from typing_extensions import Annotated
+
+from . import message as api_message
 
 router = APIRouter(prefix="/genes", tags=["genes"])
 
 
+@router.get("")
+def get_genes(
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+    reference_id: Annotated[
+        Optional[str], Query(description=api_message.GENE_REFERENCE)
+    ] = None,
+    gene_database: Optional[GeneIdentifier] = None,
+    species: Optional[Species] = None,
+    preferred: Annotated[
+        Optional[bool], Query(description=api_message.GENE_PREFERRED)
+    ] = None,
+    limit: Annotated[
+        Optional[int],
+        Query(
+            format="int64",
+            minimum=0,
+            maxiumum=9223372036854775807,
+            description=api_message.LIMIT,
+        ),
+    ] = None,
+    offset: Annotated[
+        Optional[int],
+        Query(
+            format="int64",
+            minimum=0,
+            maxiumum=9223372036854775807,
+            description=api_message.OFFSET,
+        ),
+    ] = None,
+) -> dict:
+    """Get geneweaver list of genes."""
+    if limit is None:
+        limit = 100
+
+    response = genes_service.get_genes(
+        cursor, reference_id, gene_database, species, preferred, limit, offset
+    )
+    return response
+
+
 @router.post("/homologs", response_model=GeneIdMappingResp)
 def get_related_gene_ids(
     gene_id_mapping: GeneIdHomologReq,

src/geneweaver/api/controller/message.py

@@ -6,3 +6,9 @@
 UNEXPECTED_ERROR = "Unexpected Error"
 GENE_IDENTIFIER_TYPE_VALUE_ERROR = "Invalid gene identifier type"
 RECORD_NOT_FOUND_ERROR = "Record not found"
+
+##FORM field descriptions
+GENE_REFERENCE = "The reference id to search for"
+GENE_PREFERRED = "Whether to search for preferred genes"
+LIMIT = "The limit of results to return"
+OFFSET = "The offset of results to return"

src/geneweaver/api/services/genes.py

@@ -8,6 +8,40 @@
 from psycopg import Cursor
 
 
+def get_genes(
+    cursor: Cursor,
+    reference_id: Optional[str] = None,
+    gene_database: Optional[GeneIdentifier] = None,
+    species: Optional[Species] = None,
+    preferred: Optional[bool] = None,
+    limit: Optional[int] = None,
+    offset: Optional[int] = None,
+) -> dict:
+    """Get geneweaver genes from DB.
+
+    :param cursor: The database cursor.
+    :param reference_id: The reference id to search for.
+    :param gene_database: The gene database to search for.
+    :param species: The species to search for.
+    :param preferred: Whether to search for preferred genes.
+    :param limit: The limit of results to return.
+    :param offset: The offset of results to return.
+    """
+    if limit is None:
+        limit = 100
+
+    try:
+        gene_list = db_gene.get(
+            cursor, reference_id, gene_database, species, preferred, limit, offset
+        )
+
+    except Exception as err:
+        logger.error(err)
+        raise err
+
+    return {"genes": gene_list}
+
+
 def get_homolog_ids(
     cursor: Cursor,
     gene_id_list: Iterable,

tests/controllers/test_genes.py

@@ -2,7 +2,10 @@
 import json
 from unittest.mock import patch
 
-from tests.data import test_gene_homolog_data, test_gene_mapping_data
+from tests.data import test_gene_homolog_data, test_gene_mapping_data, test_genes_data
+
+# genes
+genes_list_10 = test_genes_data.get("genes_list_10")
 
 # gene homolog ids test data
 gene_ids_homolog_req_1 = test_gene_homolog_data.get(
@@ -144,3 +147,36 @@ def test_gene_aon_mapping_invalid_post_data_(client):
         url="/api/genes/mapping/aon", data=json.dumps({"test": "test"})
     )
     assert response.status_code == 422
+
+
+@patch("geneweaver.api.services.genes.get_genes")
+def test_valid_gene_get_req(mock_gene_call, client):
+    """Test valid get genes request."""
+    mock_gene_call.return_value = genes_list_10
+
+    response = client.get(url="/api/genes")
+
+    print(response)
+    assert response.status_code == 200
+    assert response.json() == genes_list_10
+
+    response = client.get(url="/api/genes?limit=10")
+    assert response.status_code == 200
+    assert response.json() == genes_list_10
+
+
+@patch("geneweaver.api.services.genes.get_genes")
+def test_invalid_param_gene_get_req(mock_gene_call, client):
+    """Test invalid get genes request parameters."""
+    mock_gene_call.return_value = genes_list_10
+
+    response = client.get(url="/api/genes?limit=abc")
+    assert response.status_code == 422
+    response = client.get(url="/api/genes?offset=abc")
+    assert response.status_code == 422
+    response = client.get(url="/api/genes?gene_database=abc")
+    assert response.status_code == 422
+    response = client.get(url="/api/genes?species=abc")
+    assert response.status_code == 422
+    response = client.get(url="/api/genes?preferred=abc")
+    assert response.status_code == 422

tests/data/__init__.py

@@ -28,6 +28,8 @@
 
 species_json = importlib.resources.read_text("tests.data", "species.json")
 
+genes_json = importlib.resources.read_text("tests.data", "genes.json")
+
 ## laod and returns JSON string as a dictionary
 
 # geneset test data
@@ -91,7 +93,7 @@
     ),
 }
 
-# Json web token keys data =
+# Json web token keys data
 test_jwt_keys_data = {
     "test_private_key": json.loads(jwt_test_keys_json).get("private_key"),
     "test_public_key": json.loads(jwt_test_keys_json).get("public_key"),
@@ -110,6 +112,11 @@
 }
 
 
+## geneweaver genes test data
+test_genes_data = {
+    "genes_list_10": json.loads(genes_json).get("genes_list_10"),
+}
+
 def get_species_db_resp(species_data: dict) -> dict:
     """Get species data as returned by DB."""
     species = species_data.get("species")
@@ -121,3 +128,4 @@ def get_species_db_resp(species_data: dict) -> dict:
             ).as_int()
 
     return species
+

tests/data/genes.json

@@ -0,0 +1,86 @@
+{
+  "genes_list_10": {
+    "genes": [
+      {
+        "id": 1,
+        "reference_id": "MGI:87853",
+        "gene_database": 10,
+        "species": 1,
+        "preferred": false,
+        "date": "2020-05-05"
+      },
+      {
+        "id": 2,
+        "reference_id": "MGI:87854",
+        "gene_database": 10,
+        "species": 1,
+        "preferred": false,
+        "date": "2020-05-05"
+      },
+      {
+        "id": 3,
+        "reference_id": "MGI:87859",
+        "gene_database": 10,
+        "species": 1,
+        "preferred": false,
+        "date": "2020-05-05"
+      },
+      {
+        "id": 4,
+        "reference_id": "MGI:87860",
+        "gene_database": 10,
+        "species": 1,
+        "preferred": false,
+        "date": "2020-05-05"
+      },
+      {
+        "id": 5,
+        "reference_id": "MGI:87862",
+        "gene_database": 10,
+        "species": 1,
+        "preferred": false,
+        "date": "2020-05-05"
+      },
+      {
+        "id": 6,
+        "reference_id": "MGI:87863",
+        "gene_database": 10,
+        "species": 1,
+        "preferred": false,
+        "date": "2020-05-05"
+      },
+      {
+        "id": 7,
+        "reference_id": "MGI:87864",
+        "gene_database": 10,
+        "species": 1,
+        "preferred": false,
+        "date": "2020-05-05"
+      },
+      {
+        "id": 8,
+        "reference_id": "MGI:87866",
+        "gene_database": 10,
+        "species": 1,
+        "preferred": false,
+        "date": "2020-05-05"
+      },
+      {
+        "id": 9,
+        "reference_id": "MGI:87867",
+        "gene_database": 10,
+        "species": 1,
+        "preferred": false,
+        "date": "2020-05-05"
+      },
+      {
+        "id": 10,
+        "reference_id": "MGI:87868",
+        "gene_database": 10,
+        "species": 1,
+        "preferred": false,
+        "date": "2020-05-05"
+      }
+    ]
+  }
+}

tests/services/test_gene.py

@@ -5,7 +5,10 @@
 import pytest
 from geneweaver.api.services import genes
 
-from tests.data import test_gene_homolog_data, test_gene_mapping_data
+from tests.data import test_gene_homolog_data, test_gene_mapping_data, test_genes_data
+
+# genes
+genes_list_10 = test_genes_data.get("genes_list_10")
 
 # gene homolog ids test data
 gene_ids_homolog_req_1 = test_gene_homolog_data.get(
@@ -219,3 +222,35 @@ def test_get_aon_gene_map_error(mock_db_gene):
             gene_id_aon_mapping_req_1.get("source_ids"),
             gene_id_aon_mapping_req_1.get("species"),
         )
+
+
+@patch("geneweaver.api.services.genes.db_gene")
+def test_get_gene_error(mock_db_gene):
+    """Test error in DB call."""
+    mock_db_gene.get.side_effect = Exception("ERROR")
+
+    with pytest.raises(expected_exception=Exception):
+        genes.get(None)
+
+
+@patch("geneweaver.api.services.genes.db_gene")
+def test_get_gene(mock_db_gene):
+    """Test error in DB call."""
+    mock_db_gene.get.return_value = genes_list_10
+
+    response = genes.get_genes(None)
+
+    assert response.get("error") is None
+    assert response.get("genes") == genes_list_10
+
+    response = genes.get_genes(
+        None,
+        gene_database=10,
+        species=1,
+        preferred=False,
+        reference_id="MGI:87853",
+        limit=10,
+        offset=10,
+    )
+
+    assert response.get("error") is None