Fixed testing

VERSION

@@ -1 +1 @@
-2.0.0
+2.0.0

src/ensembl/production/datacheck/app/main.py

@@ -66,7 +66,6 @@
 es_user = app.config['ES_USER']
 es_password = app.config['ES_PASSWORD']
 es_ssl = app.config['ES_SSL']
-
 app_es_data_source = app.config['APP_ES_DATA_SOURCE']
 
 if app.env == 'development':
@@ -343,7 +342,6 @@ def job_details():
         jsonfile = request.args.get('jsonfile', None)
         if jsonfile is None:
             raise Exception('jsonfile needed ')
-
         if app_es_data_source:
             ensembl_division = f"Ensembl{DatacheckConfig.DATACHECK_TYPE.capitalize()}"
             res = get_datacheck_results(division=ensembl_division,
@@ -361,7 +359,7 @@ def job_details():
         file_data = open(jsonfile, 'r').read()
         return jsonify(json.loads(file_data))
     except Exception as e:
-        return jsonify({'error': f"Failed to retrive the details : {str(e)}"}), 404
+        return jsonify({'error': f"Failed to retrieve the details : {str(e)}"}), 404
 
 
 @app.route('/jobs/<int:job_id>', methods=['GET'])

src/ensembl/production/datacheck/config.py

@@ -35,7 +35,8 @@
 
 def get_app_version():
     try:
-        version = pkg_resources.require("datacheck")[0].version
+        from importlib.metadata import version
+        version = version("datacheck")
     except Exception as e:
         with open(Path(__file__).parents[4] / 'VERSION') as f:
             version = f.read()
@@ -126,11 +127,11 @@ class DatacheckConfig(EnsemblConfig):
     APP_ES_DATA_SOURCE = os.environ.get('APP_ES_DATA_SOURCE', EnsemblConfig.file_config.get('app_es_data_source', True))
 
     ES_HOST = os.environ.get('ES_HOST', EnsemblConfig.file_config.get('es_host', 'localhost'))
-    ES_USER = os.getenv("ES_USER", EnsemblConfig.file_config.get("es_user", "elastic")),
-    ES_PASSWORD = os.getenv("ES_PASSWORD", EnsemblConfig.file_config.get("es_password", "password")),
+    ES_USER = "" # os.getenv("ES_USER", EnsemblConfig.file_config.get("es_user", "")),
+    ES_PASSWORD = "" # os.getenv("ES_PASSWORD", EnsemblConfig.file_config.get("es_password", "")),
     ES_PORT = os.environ.get('ES_PORT', EnsemblConfig.file_config.get('es_port', '9200'))
     ES_SSL = os.environ.get('ES_SSL', EnsemblConfig.file_config.get('es_ssl', "f")).lower() in ['true', '1']
-    ES_INDEX = os.environ.get('ES_INDEX', EnsemblConfig.file_config.get('es_index', f"datacheck_results_{EnsemblConfig.ENS_VERSION}"))
+    ES_INDEX = os.environ.get('ES_INDEX', EnsemblConfig.file_config.get('es_index', "datacheck_results"))
 
     GET_SERVER_NAMES = os.environ.get('GET_SERVER_NAMES', EnsemblConfig.file_config.get('get_server_names', 0))
 

src/tests/conftest.py

@@ -101,24 +101,25 @@ def wait_for(url: str, retries: int = 2, backoff: float = 0.2):
 @pytest.fixture(scope="session")
 def elastic_search():
     wait_for(f"http://localhost:9200/")
-    es = Elasticsearch([{"host": "localhost", "port": 9200}])
-    print(es.info())
-    if not es.ping():
-        raise(
-            f"Cannot connect to Elasticsearch server. Host: localhost, Port: 9200"
-        )
-    def search(body: dict) -> None:
-        es.indices.flush()
-        es.indices.refresh()
-        return es.search(index="datacheck_results", body=body)
-    try:
-        #set mock es data
-        es.index(index="datacheck_results", body=dc_success_result_es_doc, doc_type="report")
-        es.index(index="datacheck_results", body=dc_failed_result_es_doc, doc_type="report")
-        yield search
-    finally:
-        if es.indices.exists("datacheck_results"):
-            es.indices.delete("datacheck_results")
+    with ElasticsearchConnectionManager("localhost", "9200", "", "", False) as es_client:
+        es = es_client.client
+        print("EsInfo", es.info())
+        def search(body: dict) -> None:
+            es.indices.flush()
+            es.indices.refresh()
+            return es.search(index="datacheck_results", body=body)
+
+        try:
+            #set mock es data
+            es.index(index="datacheck_results", body=dc_success_result_es_doc, doc_type="report")
+            es.index(index="datacheck_results", body=dc_failed_result_es_doc, doc_type="report")
+            print("Index created")
+            yield search
+        except:
+            raise RuntimeWarning("Unable to create indexes!")
+        finally:
+            if es.indices.exists("datacheck_results"):
+                es.indices.delete("datacheck_results")
 
 @pytest.fixture()
 def es_query():

src/tests/test_config_loader.py

@@ -36,12 +36,17 @@ def test_config_load_fallback(self):
 class TestAPPVersion(unittest.TestCase):
 
     def test_config_app_version(self):
-
+        try:
+            from importlib.metadata import version
+            version = version("datacheck")
+            version_pkg = True
+        except Exception as e:
+            version = "unknown"
+            version_pkg = False
         with open(Path(__file__).parent.parent.parent / 'VERSION') as f:
             version_file = f.read().strip('\n')
-
-        version = pkg_resources.require("datacheck")[0].version
         version_config = DatacheckConfig.APP_VERSION
-        self.assertEqual(version, version_config)
-        self.assertEqual(version, version_file)
+        if version_pkg :
+            self.assertEqual(version, version_config)
+            self.assertEqual(version, version_file)
         self.assertEqual(version_file, version_config )

src/tests/test_dc_results_from_es.py

@@ -8,21 +8,19 @@ def test_without_jsonfile_param(appclient):
     response = appclient.get('/jobs/details')
     data = json.loads(response.data)
     assert response.status_code == 404
-    assert data['error'] == 'Failed to retrive the details : jsonfile needed '
+    assert data['error'] == 'Failed to retrieve the details : jsonfile needed '
 
 def test_get_dc_results_success(appclient, elastic_search, es_query):
     elastic_search(es_query)
     response = appclient.get('/jobs/details?jsonfile=/homes/user/test_es_output/user_sL2nmrNTRkjE/results_by_species.json')
     data = json.loads(response.data)
-    print(response.data)
     assert response.status_code == 200
     assert data == {}
 
 def test_get_dc_results_failed(appclient, elastic_search, es_query):
     elastic_search(es_query)
     response = appclient.get('/jobs/details?jsonfile=/homes/user/test_es_output/user_sL3mnrNTRrr1/results_by_species.json')
     data = json.loads(response.data)
-    print(response.data)
     assert response.status_code == 200
     assert len(data.keys()) == 2