fix(bug): fix bugs

uc-cdis · Mar 27, 2018 · 17b1984 · 17b1984
1 parent e282e1a
commit 17b1984
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Showing 3 changed files with 17 additions and 19 deletions.
diff --git a/peregrine/resources/submission/__init__.py b/peregrine/resources/submission/__init__.py
@@ -88,7 +88,6 @@ def root_graphql_query():
     payload = peregrine.utils.parse_request_json()
     query = payload.get('query')
     export_format = payload.get('format')
-    bag_path = payload.get('path')
     variables, errors = peregrine.utils.get_variables(payload)
     if errors:
         return flask.jsonify({'data': None, 'errors': errors}), 400
@@ -98,9 +97,9 @@ def root_graphql_query():
     if export_format == 'bdbag':
         data, code = return_data
         if code == 200:
-            if peregrine.utils.contain_node_with_category(data.json, 'data_file') == False:
-                return flask.jsonify({'errors': 'No data_file node'}), 400
-            res = peregrine.utils.json2tbl(json.loads(data.data), '', "_")
+            # 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'), code
         else:

diff --git a/peregrine/utils/json2csv.py b/peregrine/utils/json2csv.py
@@ -59,30 +59,31 @@ def dicts2tsv(dict_list):
         output string
     """
     tsv = ""
-    
+
     header_set = set()
 
     for dict_row in dict_list:
         header_set.update(dict_row.keys())
 
-    for h in sorted(header_set):
-        words = h.split('_')
+    for h in header_set:
+        words = h.split('-')
         tsv = tsv + "{}\t".format(words[-1])
+    tsv = tsv[:-1] + "\n"
 
     nrow = 0
     for dict_row in dict_list:
-        row = []
-        for h in sorted(header_set):
+        for h in header_set:
             if dict_row[h]:
                 tsv = tsv + "{}\t".format(dict_row[h])
             else:
                 tsv = tsv + "None\t"
-            tsv = tsv[:-1] + "\n"
-            nrow = nrow + 1
-            if nrow >= 1000:
-                break
+        tsv = tsv[:-1] + "\n"
+        nrow = nrow + 1
+        if nrow >= 1000:
+            break
     return tsv
 
+
 def join(table_list, L, index, row):
     '''
     Join sub tables to generate a big table

diff --git a/peregrine/utils/pybdbag.py b/peregrine/utils/pybdbag.py
@@ -18,18 +18,16 @@ def create_bdbag(bag_path, bag_info, payload, max_row=10000):
 
     with open(bag_path + '/data/manifest.tsv', 'w') as tsvfile:
         writer = csv.writer(tsvfile, delimiter='\t')
-        #write header
+        # write header
         row = []
         for k in payload[0].keys():
-            k = k.replace('_data_','')
+            k = k.replace('_data_', '')
             row.append(k)
         header = copy.deepcopy(row)
         writer.writerow(row)
         nrow = 1
-        print('==============header==========')
-        print(header)
         for row_dict in payload:
-            row=[]
+            row = []
             print(row_dict)
             for h in header:
                 if row_dict.get('_data_'+h):
@@ -40,7 +38,7 @@ def create_bdbag(bag_path, bag_info, payload, max_row=10000):
             nrow = nrow + 1
             if nrow >= max_row:
                 break
-        
+
     bag.save(manifests=True)  # creates checksum manifests
     # Compress bag.
     zip_file_path = os.path.basename(os.path.normpath(str(bag)))