fix(codacy): fix codacy

peregrine/resources/submission/__init__.py

@@ -136,7 +136,7 @@ def get_manifest():
     if(bag_path is None):
         return flask.jsonify({'bag_path': None, 'errors': 'bag_path is required!!!'}), 400
 
-    if peregrine.utils.contain_node_category(export_data,'data_file') == False:
+    if peregrine.utils.contain_node_with_category(export_data,'data_file') == False:
         return flask.jsonify({ 'errors': 'No data_file node'}), 400
 
 
@@ -149,6 +149,6 @@ def get_manifest():
             bag_path=bag_path,
             bag_info=bag_info,
             payload=res)
-    bag = peregrine.utils.create_bdbag(**args) # bag is a compressed file
+    peregrine.utils.create_bdbag(**args) # bag is a compressed file
 
     return flask.jsonify({'data': res}), 200

peregrine/utils/__init__.py

@@ -1,4 +1,4 @@
-from .payload import get_variables,jsonify_check_errors,parse_request_json,get_keys,contain_node_category
+from .payload import get_variables,jsonify_check_errors,parse_request_json,get_keys,contain_node_with_category
 from .pybdbag import create_bdbag
 from .scheduling import AsyncPool
 from .json2csv import flatten_obj,json2tbl

peregrine/utils/pybdbag.py

@@ -5,8 +5,8 @@
 
 
 def create_bdbag(bag_path, bag_info, payload, max_row=10000):
-    """Modify from https://github.com/BD2KGenomics/dcc-dashboard-service/blob/feature/manifest-handover/webservice.py"""
-    """Create compressed BDbag file."""
+    """Modify from https://github.com/BD2KGenomics/dcc-dashboard-service/blob/feature/manifest-handover/webservice.py
+    Create compressed BDbag file."""
 
     if len(payload) == 0:
         return
@@ -22,10 +22,9 @@ def create_bdbag(bag_path, bag_info, payload, max_row=10000):
         for k in payload[0].keys():
             k = k.replace('_data_','')
             row.append(k)
-        writer.writerow(row)
 
+        writer.writerow(row)
         nrow = 1
-
         for row_dict in payload:
             row=[]
             for (k,v) in row_dict.iteritems():
@@ -52,6 +51,6 @@ def create_bdbag(bag_path, bag_info, payload, max_row=10000):
 def zipdir(path, ziph):
     """https://github.com/BD2KGenomics/dcc-dashboard-service/blob/feature/manifest-handover/webservice.py"""
     # ziph is zipfile handle
-    for root, dirs, files in os.walk(path):
+    for root, _, files in os.walk(path):
         for file in files:
-            ziph.write(os.path.join(root, file))
+            ziph.write(os.path.join(root, file))