Merge pull request #9 from cgmeyer/develop

Develop

Author: cgmeyer

expansion/expansion.py

@@ -1324,7 +1324,7 @@ def submit_file(self, project_id, filename, chunk_size=30, row_offset=0):
 
 
 # indexd functions:
-    def get_urls(self, guids,api):
+    def get_urls(self, guids, api):
         # Get URLs for a list of GUIDs
         if isinstance(guids, str):
             guids = [guids]
@@ -1356,6 +1356,30 @@ def get_guids_for_filenames(self, file_names,api):
                 guids[file_name] = guid
         return guids
 
+    def get_record_for_url(self, url, api):
+        """ Returns the indexd record for a file's storage location URL ('urls' in indexd)
+            Example:
+                exp.get_record_for_url(url=https://icgc.bionimbus.org/index/index/?url=s3://pcawg-tcga-sarc-us/2720a2b8-3f4e-5b6e-9f74-1067a068462a, api=api)
+        """
+        indexd_endpoint = "{}/index/index/".format(api)
+        indexd_query = "{}?url={}".format(indexd_endpoint,url)
+        output = requests.get(indexd_query, auth=self._auth_provider).text
+        response = json.loads(output)
+        index_records = response['records']
+        return index_records
+
+    def get_guid_for_url(self, url, api):
+        """Return the GUID for a file's URL in indexd"""
+        index_records = self.get_record_for_url(url=url,api=api)
+        if len(index_records) == 1:
+            guid = index_records[0]['did']
+            return guid
+        else:
+            guids = []
+            for index_record in index_records:
+                guids.append(index_record['did'])
+            return guids
+
     def delete_uploaded_files(self, guids):
         """
         DELETE http://petstore.swagger.io/?url=https://raw.githubusercontent.com/uc-cdis/fence/master/openapis/swagger.yaml#/data/delete_data__file_id_