feat(streamming): support data streaming

uc-cdis · Mar 28, 2018 · c3e1ef8 · c3e1ef8
1 parent 4db6a94
commit c3e1ef8
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Showing 2 changed files with 4 additions and 8 deletions.
diff --git a/peregrine/resources/submission/__init__.py b/peregrine/resources/submission/__init__.py
@@ -98,8 +98,6 @@ def root_graphql_query():
         return data, code
 
     if export_format == 'tsv':
-        # if peregrine.utils.contain_node_with_category(data.data, 'data_file') == False:
-        #     return flask.jsonify({'errors': 'No data_file node'}), 400
         res = peregrine.utils.json2tbl(json.loads(data.data), '', "-")
         tsv = peregrine.utils.dicts2tsv(res)
         return flask.Response(tsv, mimetype='text/tab-separated-values'), 200
@@ -116,7 +114,6 @@ def root_graphql_query():
             bag_info=bag_info,
             payload=res)
         bag = peregrine.utils.create_bdbag(**args)  # bag is a compressed file
-        print('========bag=======', bag)
         return send_file(bag, attachment_filename='manifest_bag.zip')
     else:
         return return_data

diff --git a/peregrine/utils/pybdbag.py b/peregrine/utils/pybdbag.py
@@ -14,7 +14,7 @@ def create_bdbag(bag_info, payload, max_row=10000):
 
     if len(payload) == 0:
         return
-    
+
     # if not os.path.exists(bag_path):
     #     os.makedirs(bag_path)
     tmp_dir = tempfile.mkdtemp()
@@ -28,7 +28,6 @@ def create_bdbag(bag_info, payload, max_row=10000):
     #     os.makedirs(bag_path)
     # bag = bagit.make_bag(bag_path, bag_info)
 
-
     header_set = set()
 
     for dict_row in payload:
@@ -61,15 +60,15 @@ def create_bdbag(bag_info, payload, max_row=10000):
     zip_dir = bag_path
     zip_file_name = tmp_dir + '/manifest_bag.zip'
     zipf = zipfile.ZipFile(zip_file_name, 'w', zipfile.ZIP_DEFLATED)
-    print('=====zip_file_path=====', zip_dir)
     zipdir(zip_dir, zipf)
     zipf.close()
     return zip_file_name
 
 
 def zipdir(path, ziph):
-    """https://github.com/BD2KGenomics/dcc-dashboard-service/blob/feature/manifest-handover/webservice.py"""
+    length = len(path)
     # ziph is zipfile handle
     for root, _, files in os.walk(path):
+        folder = root[length:]  # path without "parent"
         for file in files:
-            ziph.write(os.path.join(root, file))
+            ziph.write(os.path.join(root, file), os.path.join(folder, file))