fix app paths to find resources from tests dir

patientMatcher/cli/add.py

@@ -71,6 +71,8 @@ def demodata(monarch_phenotypes):
     click.echo('Adding 50 test patients to database..')
     app_root=os.path.abspath(__file__).split('patientMatcher')[0]
     path_to_json_patients = os.path.abspath(os.path.join(app_root, 'patientMatcher', 'resources', 'benchmark_patients.json'))
+    if not os.path.isfile(path_to_json_patients): # running command from tests folder
+        path_to_json_patients = os.path.abspath(os.path.join(app_root, 'patientMatcher', 'patientMatcher', 'resources', 'benchmark_patients.json'))
     inserted_ids = load_demo(path_to_json_data=path_to_json_patients, mongo_db=current_app.db,
         host=current_app.config.get('MME_HOST') ,compute_phenotypes=monarch_phenotypes)
     click.echo('inserted {} patients into db'.format(len(inserted_ids)))

patientMatcher/server/__init__.py

@@ -19,8 +19,13 @@ def create_app():
     except:
         LOG.warning('Environment variable settings not found, configuring from instance file.')
         app_root=os.path.abspath(__file__).split('patientMatcher')[0]
-        LOG.info('app root is: {}'.format(app_root))
-        app = Flask(__name__, instance_path=os.path.join(app_root, 'patientMatcher', 'instance'), instance_relative_config=True)
+
+        # check if config file exists under ../instance:
+        instance_path = os.path.join(app_root,'patientMatcher', 'instance')
+        if not os.path.isfile(os.path.join(instance_path,'config.py')): # running app from tests
+            instance_path = os.path.join(app_root,'patientMatcher','patientMatcher','instance')
+
+        app = Flask(__name__, instance_path=instance_path, instance_relative_config=True)
         app.config.from_pyfile('config.py')
 
     client = MongoClient(app.config['DB_URI'])