Database improvements

This patch series fixes bugs in the database API and improve the tools to set them up.

beat/web/databases/api.py

@@ -25,6 +25,9 @@
 #                                                                             #
 ###############################################################################
 
+import os
+import json
+
 from django.http import HttpResponse
 from django.core.urlresolvers import reverse
 
@@ -93,6 +96,20 @@ def database_to_json(database, request_user, fields_to_return,
     return result
 
 
+def clean_paths(declaration):
+    pseudo_path = '/path_to_db_folder'
+    json_data = json.loads(declaration)
+    root_folder = json_data['root_folder']
+    cleaned_folder = os.path.basename(os.path.normpath(root_folder))
+    json_data['root_folder'] = os.path.join(pseudo_path, cleaned_folder)
+    for protocol in json_data['protocols']:
+        for set_ in protocol['sets']:
+            if 'parameters' in set_ and 'annotations' in set_['parameters']:
+                annotations_folder = set_['parameters']['annotations']
+                cleaned_folder = annotations_folder.split('/')[-2:]
+                set_['parameters']['annotations'] = os.path.join(pseudo_path, *cleaned_folder)
+    return json.dumps(json_data)
+
 #----------------------------------------------------------
 
 
@@ -227,11 +244,12 @@ class RetrieveDatabaseView(views.APIView):
             # Retrieve the code
             if 'declaration' in fields_to_return:
                 try:
-                    result['declaration'] = database.declaration_file.read()
+                    declaration = database.declaration_file.read()
                 except:
                     logger.error(traceback.format_exc())
                     return HttpResponse(status=500)
 
+                result['declaration'] = clean_paths(declaration)
 
             # Retrieve the source code
             if 'code' in fields_to_return: