pyopencga 4.0.1.dev0__tar.gz → 4.1.0.dev0__tar.gz

{pyopencga-4.0.1.dev0 → pyopencga-4.1.0.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyopencga
-Version: 4.0.1.dev0
+Version: 4.1.0.dev0
 Summary: A REST client for OpenCGA REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyopencga-4.0.1.dev0 → pyopencga-4.1.0.dev0}/pyopencga/commons.py

@@ -176,23 +176,28 @@ def _fetch(config, sid, category, resource, method, subcategory=None, query_id=N
             raise OpencgaInvalidToken(r.content)
         elif r.status_code == 403:
             raise OpencgaAuthorisationError(r.content)
-
         elif r.status_code != 200:
             raise Exception(r.content)
 
-        try:
-            response = r.json()
-
-            # TODO Remove deprecated response and result in future release. Added for backwards compatibility
-            if 'response' in response:
-                response['responses'] = response['response']
-            for query_result in response['responses']:
-                if 'result' in query_result:
-                    query_result['results'] = query_result['result']
-
-        except ValueError:
-            msg = 'Bad JSON format retrieved from server'
-            raise ValueError(msg)
+        if r.headers['Content-Type'] == 'application/json':
+            try:
+                response = r.json()
+
+                # TODO Remove deprecated response and result in future release. Added for backwards compatibility
+                if 'response' in response:
+                    response['responses'] = response['response']
+                for query_result in response['responses']:
+                    if 'result' in query_result:
+                        query_result['results'] = query_result['result']
+
+            except ValueError:
+                raise ValueError('Bad JSON format retrieved from server')
+        elif r.headers['Content-Type'] == 'application/octet-stream':
+            return r.content
+        else:
+            raise ValueError('Unexpected content type retrieved from server ("{}"): "{}"'.format(
+                r.headers['Content-Type'], r.content)
+            )
 
         # Setting up final_response
         if final_response is None:
@@ -324,7 +329,7 @@ def execute(config, sid, category, resource, method, subcategory=None, query_id=
                                          'options': options})
             # Setting threads as "daemon" allows main program to exit eventually
             # even if these do not finish correctly
-            t.setDaemon(True)
+            t.daemon = True
             t.start()
 
         # Loading up the queue with index and id batches for each job

{pyopencga-4.0.1.dev0 → pyopencga-4.1.0.dev0}/pyopencga/rest_clients/_parent_rest_clients.py

@@ -1,3 +1,5 @@
+import json
+
 from pyopencga.commons import execute
 from pyopencga.rest_response import RestResponse
 from pyopencga.retry import retry
@@ -67,7 +69,11 @@ class _ParentRestClient(object):
 
         if self.auto_refresh:
             self._refresh_token_client()
-        return RestResponse(response)
+
+        if isinstance(response, dict):
+            return RestResponse(response)
+        else:  # Not a JSON (e.g. /{apiVersion}/files/{file}/download)
+            return response
 
     def _get(self, category, resource, query_id=None, subcategory=None,
              second_query_id=None, **options):

{pyopencga-4.0.1.dev0 → pyopencga-4.1.0.dev0}/pyopencga.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyopencga
-Version: 4.0.1.dev0
+Version: 4.1.0.dev0
 Summary: A REST client for OpenCGA REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyopencga-4.0.1.dev0 → pyopencga-4.1.0.dev0}/setup.py

@@ -14,7 +14,7 @@ with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
 
 setup(
     name='pyopencga',
-    version='4.0.1.dev0',
+    version='4.1.0.dev0',
     description='A REST client for OpenCGA REST web services',
     long_description=long_description,
     long_description_content_type='text/x-rst',