Add endpoints for file object and info key editing

api/api.py

@@ -243,8 +243,9 @@ def prefix(path, routes):
                 route('/packfile',                              FileListHandler, h='packfile',       m=['POST']),
                 route('/packfile-end',                          FileListHandler, h='packfile_end'),
                 route('/<list_name:files>',                     FileListHandler,                     m=['POST']),
-                route('/<list_name:files>/<name:{fname}>',      FileListHandler,                     m=['GET', 'DELETE']),
+                route('/<list_name:files>/<name:{fname}>',      FileListHandler,                     m=['GET', 'PUT', 'DELETE']),
                 route('/<list_name:files>/<name:{fname}>/info', FileListHandler, h='get_info',       m=['GET']),
+                route('/<list_name:files>/<name:{fname}>/info', FileListHandler, h='modify_info',    m=['POST']),
 
                 route( '/analyses',                                AnalysesHandler,                  m=['POST']),
                 prefix('/analyses', [

api/config.py

@@ -159,8 +159,10 @@ def apply_env_variables(config):
     'container.json',
     'device.json',
     'file.json',
+    'file-update.json',
     'group-new.json',
     'group-update.json',
+    'info_update.json',
     'note.json',
     'packfile.json',
     'permission.json',

api/dao/liststorage.py

@@ -1,10 +1,13 @@
 import bson.errors
 import bson.objectid
 import datetime
+import pymongo
 
-from . import APIStorageException, APIConflictException
+from . import APIStorageException, APIConflictException, APINotFoundException
 from . import consistencychecker
 from .. import config
+from .. import util
+from ..jobs import rules
 from .containerstorage import SessionStorage, AcquisitionStorage
 
 log = config.log
@@ -41,7 +44,6 @@ def get_container(self, _id, query_params=None):
                 '$elemMatch': query_params
             }
             projection = {self.list_name + '.$': 1, 'permissions': 1, 'public': 1}
-        log.debug('query {}'.format(query))
         return self.dbc.find_one(query, projection)
 
     def exec_op(self, action, _id=None, query_params=None, payload=None, exclude_params=None):
@@ -67,24 +69,19 @@ def exec_op(self, action, _id=None, query_params=None, payload=None, exclude_par
         raise ValueError('action should be one of GET, POST, PUT, DELETE')
 
     def _create_el(self, _id, payload, exclude_params):
-        log.debug('payload {}'.format(payload))
         query = {'_id': _id}
         if exclude_params:
             query[self.list_name] = {'$not': {'$elemMatch': exclude_params} }
         update = {
             '$push': {self.list_name: payload},
             '$set': {'modified': datetime.datetime.utcnow()}
         }
-        log.debug('query {}'.format(query))
-        log.debug('update {}'.format(update))
         result = self.dbc.update_one(query, update)
         if result.matched_count < 1:
             raise APIConflictException('Item already exists in list.')
         return result
 
     def _update_el(self, _id, query_params, payload, exclude_params):
-        log.debug('query_params {}'.format(query_params))
-        log.debug('payload {}'.format(payload))
         mod_elem = {}
         for k,v in payload.items():
             mod_elem[self.list_name + '.$.' + k] = v
@@ -100,19 +97,14 @@ def _update_el(self, _id, query_params, payload, exclude_params):
         update = {
             '$set': mod_elem
         }
-        log.debug('query {}'.format(query))
-        log.debug('update {}'.format(update))
         return self.dbc.update_one(query, update)
 
     def _delete_el(self, _id, query_params):
-        log.debug('query_params {}'.format(query_params))
         query = {'_id': _id}
         update = {
             '$pull': {self.list_name: query_params},
             '$set': { 'modified': datetime.datetime.utcnow()}
             }
-        log.debug('query {}'.format(query))
-        log.debug('update {}'.format(update))
         result =  self.dbc.update_one(query, update)
         if self.list_name is 'files' and self.cont_name in ['sessions', 'acquisitions']:
             if self.cont_name == 'sessions':
@@ -123,16 +115,93 @@ def _delete_el(self, _id, query_params):
         return result
 
     def _get_el(self, _id, query_params):
-        log.debug('query_params {}'.format(query_params))
         query = {'_id': _id, self.list_name: {'$elemMatch': query_params}}
         projection = {self.list_name + '.$': 1}
-        log.debug('query {}'.format(query))
-        log.debug('projection {}'.format(projection))
         result = self.dbc.find_one(query, projection)
         if result and result.get(self.list_name):
             return result.get(self.list_name)[0]
 
 
+class FileStorage(ListStorage):
+
+    def __init__(self, cont_name):
+        super(FileStorage,self).__init__(cont_name, 'files', use_object_id=True)
+
+
+    def _update_el(self, _id, query_params, payload, exclude_params):
+        container_before = self.get_container(_id)
+        if not container_before:
+            raise APINotFoundException('Could not find {} {}, file not updated.'.format(
+                    _id, self.cont_name
+                ))
+
+        mod_elem = {}
+        for k,v in payload.items():
+            mod_elem[self.list_name + '.$.' + k] = v
+        query = {'_id': _id }
+        if exclude_params is None:
+            query[self.list_name] = {'$elemMatch': query_params}
+        else:
+            query['$and'] = [
+                {self.list_name: {'$elemMatch': query_params}},
+                {self.list_name: {'$not': {'$elemMatch': exclude_params} }}
+            ]
+        mod_elem['modified'] = datetime.datetime.utcnow()
+        update = {
+            '$set': mod_elem
+        }
+
+        container_after = self.dbc.find_one_and_update(query, update, return_document=pymongo.collection.ReturnDocument.AFTER)
+        if not container_after:
+            raise APINotFoundException('Could not find and modify {} {}. file not updated'.format(_id, self.cont_name))
+
+        jobs_spawned = rules.create_jobs(config.db, container_before, container_after, self.cont_name)
+
+        return {
+            'modified': 1,
+            'jobs_triggered': len(jobs_spawned)
+        }
+
+
+    def modify_info(self, _id, query_params, payload):
+        update = {}
+        set_payload = payload.get('set')
+        delete_payload = payload.get('delete')
+        replace_payload = payload.get('replace')
+
+        if (set_payload or delete_payload) and replace_payload is not None:
+            raise APIStorageException('Cannot set or delete AND replace info fields.')
+
+        if replace_payload is not None:
+            update = {
+                '$set': {
+                    self.list_name + '.$.info': util.mongo_sanitize_fields(replace_payload)
+                }
+            }
+
+        else:
+            if set_payload:
+                update['$set'] = {}
+                for k,v in set_payload.items():
+                    update['$set'][self.list_name + '.$.info.' + k] = util.mongo_sanitize_fields(v)
+            if delete_payload:
+                update['$unset'] = {}
+                for k in delete_payload:
+                    update['$unset'][self.list_name + '.$.info.' + k] = ''
+
+        if self.use_object_id:
+            _id = bson.objectid.ObjectId(_id)
+        query = {'_id': _id }
+        query[self.list_name] = {'$elemMatch': query_params}
+
+        if not update.get('$set'):
+            update['$set'] = {'modified': datetime.datetime.utcnow()}
+        else:
+            update['$set']['modified'] = datetime.datetime.utcnow()
+
+        return self.dbc.update_one(query, update)
+
+
 class StringListStorage(ListStorage):
     """
     This class provides access to string sublists of a mongodb collections elements (called containers).

api/handlers/listhandler.py

@@ -37,7 +37,7 @@ def initialize_list_configurations():
             'input_schema_file': 'tag.json'
         },
         'files': {
-            'storage': liststorage.ListStorage,
+            'storage': liststorage.FileStorage,
             'permchecker': listauth.default_sublist,
             'use_object_id': True,
             'storage_schema_file': 'file.json',
@@ -87,11 +87,14 @@ def initialize_list_configurations():
     for cont_name, cont_config in list_container_configurations.iteritems():
         for list_name, list_config in cont_config.iteritems():
             storage_class = list_config['storage']
-            storage = storage_class(
-                cont_name,
-                list_name,
-                use_object_id=list_config.get('use_object_id', False)
-            )
+            if list_name == 'files':
+                storage = storage_class(cont_name)
+            else:
+                storage = storage_class(
+                    cont_name,
+                    list_name,
+                    use_object_id=list_config.get('use_object_id', False)
+                )
             list_config['storage'] = storage
     return list_container_configurations
 
@@ -501,6 +504,25 @@ def get(self, cont_name, list_name, **kwargs):
     def get_info(self, cont_name, list_name, **kwargs):
         return super(FileListHandler,self).get(cont_name, list_name, **kwargs)
 
+    def modify_info(self, cont_name, list_name, **kwargs):
+        _id = kwargs.pop('cid')
+        permchecker, storage, _, _, _ = self._initialize_request(cont_name, list_name, _id, query_params=kwargs)
+
+        payload = self.request.json_body
+
+        validators.validate_data(payload, 'info_update.json', 'input', 'POST')
+
+        try:
+            permchecker(noop)('PUT', _id=_id, query_params=kwargs, payload=payload)
+            result = storage.modify_info(_id, kwargs, payload)
+        except APIStorageException as e:
+            self.abort(400, e.message)
+        # abort if the query of the update wasn't able to find any matching documents
+        if result.matched_count == 0:
+            self.abort(404, 'Element not updated in list {} of container {} {}'.format(storage.list_name, storage.cont_name, _id))
+        else:
+            return {'modified':result.modified_count}
+
     def post(self, cont_name, list_name, **kwargs):
         _id = kwargs.pop('cid')
 
@@ -517,6 +539,16 @@ def post(self, cont_name, list_name, **kwargs):
 
         return upload.process_upload(self.request, upload.Strategy.targeted, container_type=cont_name, id_=_id, origin=self.origin)
 
+    def put(self, cont_name, list_name, **kwargs):
+        _id = kwargs.pop('cid')
+        permchecker, storage, _, _, _ = self._initialize_request(cont_name, list_name, _id, query_params=kwargs)
+
+        payload = self.request.json_body
+        validators.validate_data(payload, 'file-update.json', 'input', 'PUT')
+
+        result = permchecker(storage.exec_op)('PUT', _id=_id, query_params=kwargs, payload=payload)
+        return result
+
     def delete(self, cont_name, list_name, **kwargs):
         # Overriding base class delete to audit action before completion
         _id = kwargs.pop('cid')

raml/schemas/definitions/file.json

@@ -43,6 +43,15 @@
           },
           "additionalProperties": false
         },
+        "file-update":{
+            "type": "object",
+            "properties": {
+              "type":           {"$ref":"#/definitions/file-type"},
+              "modality":       {"$ref":"#/definitions/modality"},
+              "measurements":   {"$ref":"#/definitions/measurements"}
+          },
+          "additionalProperties": false
+        },
         "file-output":{
             "type": "object",
             "properties": {

raml/schemas/input/file-update.json

@@ -0,0 +1,4 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "allOf":[{"$ref":"../definitions/file.json#/definitions/file-update"}]
+}

raml/schemas/input/info_update.json

@@ -0,0 +1,25 @@
+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "description": "Helper endpoint for editing an object's info key",
+    "type": "object",
+    "oneOf": [
+        {
+            "properties": {
+                "set":      {"type": "object", "minProperties": 1},
+                "delete":   {
+                    "type": "array",
+                    "uniqueItems": true,
+                    "minItems": 1,
+                    "items": {
+                        "type": "string"
+                    }
+                }
+            }, "additionalProperties": false
+        },
+        {
+            "properties": {
+                "replace":      {"type": "object"}
+            }, "additionalProperties": false
+        }
+    ]
+}