Merge pull request #271 from scitran/replace-metadata

Add ability to replace metadata fields in API

api/auth/containerauth.py

@@ -15,7 +15,7 @@ def default_container(handler, container=None, target_parent_container=None):
     on the container before actually executing this method.
     """
     def g(exec_op):
-        def f(method, _id=None, payload=None, recursive=False):
+        def f(method, _id=None, payload=None, recursive=False, r_payload=None, replace_metadata=False):
             projection = None
             if method == 'GET' and container.get('public', False):
                 has_access = True
@@ -48,8 +48,10 @@ def default_container(handler, container=None, target_parent_container=None):
 
             if has_access and projection:
                 return exec_op(method, _id=_id, payload=payload, projection=projection)
+            if has_access and recursive:
+                return exec_op(method, _id=_id, payload=payload, recursive=recursive, r_payload=r_payload, replace_metadata=replace_metadata)
             elif has_access:
-                return exec_op(method, _id=_id, payload=payload)
+                return exec_op(method, _id=_id, payload=payload, replace_metadata=replace_metadata)
             else:
                 handler.abort(403, 'user not authorized to perform a {} operation on the container'.format(method))
         return f

api/dao/containerstorage.py

@@ -25,11 +25,13 @@ class ContainerStorage(object):
         return self._get_el(_id)
 
     def exec_op(self, action, _id=None, payload=None, query=None, user=None,
-                public=False, projection=None, recursive=False):
+                public=False, projection=None, recursive=False, r_payload=None,
+                replace_metadata=False):
         """
         Generic method to exec an operation.
         The request is dispatched to the corresponding private methods.
         """
+
         check = consistencychecker.get_container_storage_checker(action, self.cont_name)
         data_op = payload or {'_id': _id}
         check(data_op)
@@ -40,7 +42,7 @@ class ContainerStorage(object):
         if action == 'DELETE':
             return self._delete_el(_id)
         if action == 'PUT':
-            return self._update_el(_id, payload, recursive)
+            return self._update_el(_id, payload, recursive, r_payload, replace_metadata)
         if action == 'POST':
             return self._create_el(payload)
         raise ValueError('action should be one of GET, POST, PUT, DELETE')
@@ -49,17 +51,28 @@ class ContainerStorage(object):
         log.debug(payload)
         return self.dbc.insert_one(payload)
 
-    def _update_el(self, _id, payload, recursive=False):
+    def _update_el(self, _id, payload, recursive=False, r_payload=None, replace_metadata=False):
+        replace = None
+        if replace_metadata:
+            replace = {}
+            if payload.get('metadata') is not None:
+                replace['metadata'] = util.mongo_sanitize_fields(payload.pop('metadata'))
+            if payload.get('subject') is not None and payload['subject'].get('metadata') is not None:
+                    replace['subject.metadata'] = util.mongo_sanitize_fields(payload['subject'].pop('metadata'))
+
         update = {
             '$set': util.mongo_dict(payload)
         }
+        if replace is not None:
+            update['$set'].update(replace)
+
         if self.use_object_id:
             try:
                 _id = bson.objectid.ObjectId(_id)
             except bson.errors.InvalidId as e:
                 raise APIStorageException(e.message)
-        if recursive:
-            self._propagate_changes(_id, update)
+        if recursive and r_payload is not None:
+            self._propagate_changes(_id, {'$set': util.mongo_dict(r_payload)})
         return self.dbc.update_one({'_id': _id}, update)
 
     def _propagate_changes(self, _id, update):

api/handlers/containerhandler.py

@@ -305,13 +305,16 @@ class ContainerHandler(base.RequestHandler):
 
         payload = self.request.json_body
         payload_validator(payload, 'PUT')
-        # Check if any payload keys are a propogated property, ensure they all are
+
+        # Check if any payload keys are any propogated property, add to r_payload
         rec = False
-        if set(payload.keys()).intersection(set(self.config.get('propagated_properties', []))):
-            if not set(payload.keys()).issubset(set(self.config['propagated_properties'])):
-                self.abort(400, 'Cannot update propagated properties together with unpropagated properties')
-            else:
-                rec = True  # Mark PUT request for propogation
+        r_payload = {}
+        prop_keys = set(payload.keys()).intersection(set(self.config.get('propagated_properties', [])))
+        if prop_keys:
+            rec = True
+            for key in prop_keys:
+                r_payload[key] = payload[key]
+
         # Check if we are updating the parent container of the element (ie we are moving the container)
         # In this case, we will check permissions on it.
         target_parent_container, parent_id_property = self._get_parent_container(payload)
@@ -331,10 +334,14 @@ class ContainerHandler(base.RequestHandler):
                 # Ensure subject id is a bson object
                 payload['subject']['_id'] = bson.ObjectId(str(payload['subject']['_id']))
         permchecker = self._get_permchecker(container, target_parent_container)
+
+        # Specifies wether the metadata fields should be replaced or patched with payload value
+        replace_metadata = self.get_param('replace_metadata', default=False)
         try:
             # This line exec the actual request validating the payload that will update the container
             # and checking permissions using respectively the two decorators, mongo_validator and permchecker
-            result = mongo_validator(permchecker(self.storage.exec_op))('PUT', _id=_id, payload=payload, recursive=rec)
+            result = mongo_validator(permchecker(self.storage.exec_op))('PUT',
+                        _id=_id, payload=payload, recursive=rec, r_payload=r_payload, replace_metadata=replace_metadata)
         except APIStorageException as e:
             self.abort(400, e.message)
 

api/util.py

@@ -48,6 +48,26 @@ def mongo_dict(d):
         )
     return dict(_mongo_list(d))
 
+def mongo_sanitize_fields(d):
+    """
+    Sanitize keys of arbitrarily structured map without flattening into dot notation
+
+    Adapted from http://stackoverflow.com/questions/8429318/how-to-use-dot-in-field-name
+    """
+
+    if isinstance(d, dict):
+        return {mongo_sanitize_fields(str(key)): value if isinstance(value, str) else mongo_sanitize_fields(value) for key,value in d.iteritems()}
+    elif isinstance(d, list):
+        return [mongo_sanitize_fields(element) for element in i]
+    elif isinstance(d, str):
+        # not allowing dots nor dollar signs in fieldnames
+        d = d.replace('.','_')
+        d = d.replace('$', '-')
+        return d
+    else:
+        return d
+
+
 
 def user_perm(permissions, _id, site=None):
     for perm in permissions: