chore(cleanup): clean up the code

peregrine/resources/submission/__init__.py

@@ -102,28 +102,8 @@ def root_graphql_query():
             # 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),'', "_" )
-            tsv = """# omw_id	ili_id	projects\n"""
-            row = []
-            for k in sorted(res[0]):
-                k = k.replace('_data_','')
-                tsv = tsv + "{}\t".format(k)
-            tsv = tsv[:-1] + "\n"
-
-            nrow = 0
-            for row_dict in res:
-                row=[]
-                for k in sorted(row_dict):
-                    if row_dict[k]:
-                        tsv = tsv + "{}\t".format(row_dict[k])
-                    else:
-                        tsv = tsv + "None\t"      
-                tsv = tsv[:-1] + "\n"     
-                nrow = nrow + 1
-                if nrow >= 1000:
-                    break
-
-            return flask.Response(tsv, mimetype='text/tab-separated-values')
-
+            tsv = peregrine.utils.dicts2tsv(res)
+            return flask.Response(tsv, mimetype='text/tab-separated-values'), code
         else:
             return data, code
     else:
@@ -157,63 +137,37 @@ def root_graphql_schema_query():
         )
     )
 
-# @peregrine.blueprints.blueprint.route('/export', methods=['POST'])
-# def get_manifest():
-#     """
-#     Creates and returns a manifest based on the filters pased on
-#     to this endpoint
-#     parameters:
-#         - name: filters
-#           in: graphql result in json format
-#           description: Filters to be applied when generating the manifest
-#     :return: A manifest that the user can use to download the files in there
-#     """
-#     payload = peregrine.utils.parse_request_json()
-#     export_data = payload.get('export_data')
-#     bag_path = payload.get('bag_path')
-
-#     if(bag_path is None):
-#         return flask.jsonify({'bag_path': None, 'errors': 'bag_path is required!!!'}), 400
-
-#     if peregrine.utils.contain_node_with_category(export_data,'data_file') == False:
-#         return flask.jsonify({ 'errors': 'No data_file node'}), 400
-
-
-#     res = peregrine.utils.json2tbl(export_data,'', "_" )
-
-#     import pdb; pdb.set_trace()
-
-#     tsv = """# omw_id	ili_id	projects\n"""
-#     row = []
-#     for k in sorted(res[0]):
-#         k = k.replace('_data_','')
-#         tsv = tsv + "{}\t".format(k)
-#     tsv = tsv[:-1] + "\n"
-
-#     nrow = 0
-#     for row_dict in res:
-#         row=[]
-#         for k in sorted(row_dict):
-#             if row_dict[k]:
-#                 tsv = tsv + "{}\t".format(row_dict[k])
-#             else:
-#                 tsv = tsv + "None\t"
-
-#         tsv = tsv[:-1] + "\n"
-
-#         nrow = nrow + 1
-#         if nrow >= 1000:
-#             break
-
-#     import pdb; pdb.set_trace()
-
-#     # bag_info = {'organization': 'CDIS',
-#     #             'data_type': 'TOPMed',
-#     #             'date_created': datetime.date.today().isoformat()}
-#     # args = dict(
-#     #         bag_path=bag_path,
-#     #         bag_info=bag_info,
-#     #         payload=res)
-#     # peregrine.utils.create_bdbag(**args) # bag is a compressed file
-
-#     return flask.jsonify({'data': res}), 200
+@peregrine.blueprints.blueprint.route('/export', methods=['POST'])
+def get_manifest():
+    """
+    Creates and returns a manifest based on the filters pased on
+    to this endpoint
+    parameters:
+        - name: filters
+          in: graphql result in json format
+          description: Filters to be applied when generating the manifest
+    :return: A manifest that the user can use to download the files in there
+    """
+    payload = peregrine.utils.parse_request_json()
+    export_data = payload.get('export_data')
+    bag_path = payload.get('bag_path')
+
+    if(bag_path is None):
+        return flask.jsonify({'bag_path': None, 'errors': 'bag_path is required!!!'}), 400
+
+    if peregrine.utils.contain_node_with_category(export_data,'data_file') == False:
+        return flask.jsonify({ 'errors': 'No data_file node'}), 400
+
+    res = peregrine.utils.json2tbl(export_data,'', "_" )
+    tsv = peregrine.utils.dicts2tsv(res)
+
+    # bag_info = {'organization': 'CDIS',
+    #             'data_type': 'TOPMed',
+    #             'date_created': datetime.date.today().isoformat()}
+    # args = dict(
+    #         bag_path=bag_path,
+    #         bag_info=bag_info,
+    #         payload=res)
+    # peregrine.utils.create_bdbag(**args) # bag is a compressed file
+
+    return flask.jsonify({'data': res}), 200

peregrine/utils/__init__.py

@@ -1,5 +1,5 @@
 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, to_csv
-from .response import format_response
+from .json2csv import flatten_obj,json2tbl, dicts2tsv
+from .response import format_response

peregrine/utils/json2csv.py

@@ -49,6 +49,37 @@ def to_csv(hits, dialect='excel'):
     return s.getvalue()
 
 
+def dicts2tsv(dict_list):
+    """
+    Convert the list of dictionary to tsv format.
+    Each element of the list represent a row in tsv
+    Args:
+        dict_list: list of dictionary
+    Return:
+        output string
+    """
+    tsv = ""
+    row = []
+    for k in sorted(dict_list[0]):
+        k = k.replace('_data_','')
+        tsv = tsv + "{}\t".format(k)
+    tsv = tsv[:-1] + "\n"
+
+    nrow = 0
+    for dict_row in dict_list:
+        row=[]
+        for k in sorted(dict_row):
+            if dict_row[k]:
+                tsv = tsv + "{}\t".format(dict_row[k])
+            else:
+                tsv = tsv + "None\t"      
+        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
@@ -95,5 +126,3 @@ def json2tbl(json,prefix,delem):
     else:
         L.append({prefix: json})
     return L
-
-

peregrine/utils/payload.py

@@ -260,13 +260,13 @@ def contain_node_with_category(json, category):
     get_keys(json, keys_list)
     ns_field = get_fields()
 
-    dic = {}
+    category_map = {}
     for (k,v) in ns_field.iteritems():
-        dic[v] = k._dictionary['category']
+        category_map[v] = k._dictionary['category']
 
     for key in keys_list:
         try:
-            if dic[key] == category:
+            if category_map[key] == category:
                 return True
         except KeyError:
             pass