Facilitate ensembl id lookup for eqtl data.

  Test api endpoints for bravue issue #32

bravo_api/blueprints/eqtl/eqtl.py

@@ -74,6 +74,7 @@ def susie(gene_name: str) -> list:
     cursor = current_app.mmongo.db.genes.aggregate(pipeline)
     cursor.limit = 1
     answer = next(cursor, None)
+
     if answer is None:
         return []
     else:
@@ -100,6 +101,16 @@ def cond(gene_name: str) -> list:
         return answer['eqtls']
 
 
+def susie_ensembl(ensembl_id: str) -> list:
+    pipeline = [{'$match': {'phenotype_id': ensembl_id}}, {'$project': {'_id': False}}]
+    cursor = current_app.mmongo.db.eqtl_susie.aggregate(pipeline)
+    result = next(cursor, None)
+    if result is None:
+        return []
+    else:
+        return result
+
+
 def susie_count(ensembl_id: str) -> int:
     mongo_filter = {'phenotype_id': ensembl_id}
     result = current_app.mmongo.db.eqtl_susie.count_documents(mongo_filter)

tests/eqtl/test_eqtl.py

@@ -0,0 +1,46 @@
+from bravo_api.blueprints.eqtl import eqtl
+from flask import Flask
+
+app = Flask('dummy')
+app.register_blueprint(eqtl.bp)
+
+# Test using fixture containing  "ENSG00000239920" and "ENSG00000244734"
+# Gene names CTD-2643I7.5 and HBB respetively
+SUSIE_EXPECTED = {"ENSG00000239920": 22, "ENSG00000244734": 0}
+COND_EXPECTED = {"ENSG00000239920": 5, "ENSG00000244734": 2}
+
+
+def test_susie_count(mocker, mongodb):
+    # Mock PyMongo's database with pytest-mongo's fixtures
+    pymongo_mock = mocker.Mock()
+    pymongo_mock.db = mongodb
+    app.mmongo = pymongo_mock
+
+    # Mock the app's cache to return None (no caching)
+    cache_mock = mocker.Mock()
+    cache_mock.get = mocker.Mock(return_value=None)
+    app.cache = cache_mock
+
+    with app.test_client() as client:
+        for id in SUSIE_EXPECTED:
+            resp = client.get('/eqtl/susie_count', query_string={'ensembl': id})
+            assert(resp.content_type == 'application/json')
+            assert(resp.get_json() == SUSIE_EXPECTED[id])
+
+
+def test_cond_count(mocker, mongodb):
+    # Mock PyMongo's database with pytest-mongo's fixtures
+    pymongo_mock = mocker.Mock()
+    pymongo_mock.db = mongodb
+    app.mmongo = pymongo_mock
+
+    # Mock the app's cache to return None (no caching)
+    cache_mock = mocker.Mock()
+    cache_mock.get = mocker.Mock(return_value=None)
+    app.cache = cache_mock
+
+    with app.test_client() as client:
+        for id in COND_EXPECTED:
+            resp = client.get('/eqtl/cond_count', query_string={'ensembl': id})
+            assert(resp.content_type == 'application/json')
+            assert(resp.get_json() == COND_EXPECTED[id])