Fixed ENCODE and GDC import functions

Author: sveinugu

src/unifair/modules/fairtracks/functions.py

@@ -1,9 +1,29 @@
 import requests
 
+ENCODE_HEADERS = {'accept': 'application/json'}
+ENCODE_BASE_URL = 'https://www.encodeproject.org/'
+GDC_BASE_URL = 'https://api.gdc.cancer.gov/'
+
+
+# ['experiments', 'biosample']
+def encode_api(cls, endpoint='experiments', id=None, limit=None, format='json', frame='object'):
+    api_url = ENCODE_BASE_URL + endpoint + '/' + (id if id else '@@listing') + '?' + '&'.join(
+        (['limit=' + limit] if limit else []) + (['format=' + format] if format else [])
+        + (['frame=' + frame] if frame else []))
+    print(api_url)
+    response = requests.get(api_url, headers=ENCODE_HEADERS)
+    if response.status_code == 200:
+        results = response.json()
+        if results['notification'] == 'Success':
+            graph = results['@graph']
+            return graph
+    else:
+        print('No result found')
+
 
 # ['projects', 'cases', 'files', 'annotations'], starting_point='0', size='25'
 def gdc_api(cls, object_type='projects', starting_point=None, size=None):
-    api_url = cls.GDC_BASE_URL + object_type + '/' + '?' + \
+    api_url = GDC_BASE_URL + object_type + '/' + '?' + \
               '&'.join(
                   (['from=' + starting_point] if starting_point else [])
                   + (['size=' + size] if size else [])
@@ -24,19 +44,3 @@ def gdc_api(cls, object_type='projects', starting_point=None, size=None):
 
     hits = (results['data']['hits'])
     return hits
-
-
-# ['experiments', 'biosample']
-def encode_api(cls, endpoint='experiments', id=None, limit=None, format='json', frame='object'):
-    api_url = cls.ENCODE_BASE_URL + endpoint + '/' + (id if id else '@@listing') + '?' + '&'.join(
-        (['limit=' + limit] if limit else []) + (['format=' + format] if format else [])
-        + (['frame=' + frame] if frame else []))
-    print(api_url)
-    response = requests.get(api_url, headers=cls.HEADERS)
-    if response.status_code == 200:
-        results = response.json()
-        if results['notification'] == 'Success':
-            graph = results['@graph']
-            return graph
-    else:
-        print('No result found')