def findItemsByMetadata(self, key, value, limit, offset, sort): # Construct a mongo query from the parameters given. Developers should # be careful when constructing these queries to ensure that private # information is not leaked. In this example, the user could pass an # arbitrary dictionary which could involve an aggregation pipeline, so # we check that only simple types are accepted. if isinstance(value, (list, dict)): # This is a special type of exception that tells girder to respond # with an HTTP response with the given code and message. raise RestException('The value must not be a dictionary or list.', code=400) query = { 'meta': { key: value } } # This gets the logged in user who created the request. If it is an # anonymous request, this value will be `None`. user = self.getCurrentUser() # Here, item is a "model" class which is a single instance providing an # api that wraps traditional mongo queries. This API is described at: # http://girder.readthedocs.io/en/latest/api-docs.html?#models item = Item() # This runs a "find" operation on the item collection returning a mongo # cursor. cursor = item.find(query, sort=sort) # The `filterResultsByPermission` allows paged access to a mongo query # while filtering out documents that the current user doesn't have # access to. In this case, it requires the current user have read # access to the items. The return value is an iterator that begins at # `offset` and ends at `offset + limit`. response = item.filterResultsByPermission( cursor, user=user, level=AccessType.READ, limit=limit, offset=offset ) # Finally, we turn the iterator into an explicit list for return to the # user. Girder handles json encoding the response. return list(response)
def _virtualChildItems(self, event): params = event.info['params'] if 'folderId' not in params: return # This is not a child listing request user = self.getCurrentUser() folder = Folder().load(params['folderId'], user=user, level=AccessType.READ) if not folder.get('isVirtual') or 'virtualItemsQuery' not in folder: return # Parent is not a virtual folder, proceed as normal limit, offset, sort = self.getPagingParameters(params, defaultSortField='name') q = json_util.loads(folder['virtualItemsQuery']) if 'virtualItemsSort' in folder: sort = json.loads(folder['virtualItemsSort']) item = Item() # These items may reside in folders that the user cannot read, so we must filter items = item.filterResultsByPermission( item.find(q, sort=sort), user, level=AccessType.READ, limit=limit, offset=offset) event.preventDefault().addResponse([item.filter(i, user) for i in items])
class LabelResource(Resource): def __init__(self): super().__init__() self.resourceName = 'label' self.ann_file_name = "annotation.json" self.coll_m = Collection() self.file_m = File() self.folder_m = Folder() self.item_m = Item() self.upload_m = Upload() self.asset_m = Assetstore() self.setupRoutes() def setupRoutes(self): self.route('GET', (), handler=self.getLabelList) self.route('GET', (':label_id',), self.getLabel) self.route('GET', ('meta',), self.getLabelMeta) self.route('GET', ('create',), self.createLabelFile) self.route('GET', ('by_name',), self.getLabelByName) self.route('POST', (), self.postLabel) # ############# PUBLIC METHODS ################## @access.public @autoDescribeRoute( Description('Get label list').param('assign_id', 'assignment folder id')) @rest.rawResponse @trace def getLabelList(self, assign_id): files = self.folder_m.fileList(assign_id, user=self.getCurrentUser(), data=False, includeMetadata=True, mimeFilter=['application/json']) files = list(files) cherrypy.response.headers["Content-Type"] = "application/json" return dumps(files) @access.public @autoDescribeRoute( Description('Create a new label file inside the label folder if it doesnt exist') .param('assign_id', 'the parent folder id') .param('name', 'image name for which we are creating this label file')) @rest.rawResponse @trace def createLabelFile(self, assign_id, name): p_folder = self.folder_m.load(id=assign_id, user=self.getCurrentUser(), level=AccessType.WRITE) label_folder = find_folder(p_folder=p_folder, name=name, user=self.getCurrentUser(), desc="Label Folder", create=True) file = find_file(p_folder=label_folder, name=self.ann_file_name, user=self.getCurrentUser(), assetstore=self.asset_m.getCurrent(), create=False) if not file: file = create_new_file(p_folder=label_folder, name=self.ann_file_name, user=self.getCurrentUser(), assetstore=self.asset_m.getCurrent()) config_file = self.__find_config(assign_id) if not config_file: printFail("No config file found") return errorMessage("No config file found") else: res = copy_file(src_file=config_file, dest_file=file, user=self.getCurrentUser()) return dumps({ "label_id": res['fileId'] }) return dumps({ "label_id": file['_id'] }) @access.public @autoDescribeRoute( Description('Get labels by file_name') .param('name', 'label file name') .param('assign_id', 'the assignment id')) @rest.rawResponse @trace def getLabelByName(self, name, assign_id): p_folder = self.folder_m.load(assign_id, user=self.getCurrentUser(), level=AccessType.READ) label_folder = find_folder(p_folder=p_folder, name=name, user=self.getCurrentUser(), desc="Label Folder", create=True) # this file is created in <assign_folder>/<label_folder>/assignment.json file = find_file(p_folder=label_folder, name=self.ann_file_name, user=self.getCurrentUser(), assetstore=self.asset_m.getCurrent(), create=False) cherrypy.response.headers["Content-Type"] = "application/json" if file: return self.file_m.download(file) else: return dumps({}) @access.public @autoDescribeRoute( Description('Get label file by id') .param('label_id', 'label file id')) @rest.rawResponse @trace def getLabel(self, label_id): file = self.file_m.load(label_id, level=AccessType.READ, user=self.getCurrentUser()) printOk2(file) cherrypy.response.headers["Content-Type"] = "application/json" return self.file_m.download(file) @access.public @autoDescribeRoute( Description('Get label meta data by id') .param('label_id', 'label file id')) @trace def getLabelMeta(self, label_id): file = self.file_m.load(label_id, level=AccessType.READ, user=self.getCurrentUser()) cherrypy.response.headers["Content-Type"] = "application/json" return dumps(file) @access.public @autoDescribeRoute( Description('Post to label file by id') .param('label_id', 'label file id') .param('labels', 'labels to be updated')) @rest.rawResponse @trace def postLabel(self, label_id, labels): file = self.file_m.load(label_id, level=AccessType.WRITE, user=self.getCurrentUser()) cherrypy.response.headers["Content-Type"] = "application/json" params = {'labels': json.loads(labels)} data = json.dumps(params, indent=2, sort_keys=True) upload = writeData(self.getCurrentUser(), file, data) printOk2(file) printOk(upload) return dumps(upload) # ############# PRIVATE METHODS ################## def __create_new_file(self, folder, file_name): item = self.item_m.createItem(file_name, creator=self.getCurrentUser(), folder=folder, description='label file', reuseExisting=False) file = self.file_m.createFile(size=0, item=item, name=file_name, creator=self.getCurrentUser(), assetstore=self.asset_m.getCurrent(), mimeType="application/json") return file @staticmethod def __get_owner_id(folder): aclList = Folder().getFullAccessList(folder) for acl in aclList['users']: if acl['level'] == AccessType.ADMIN: return str(acl['id']) return None def __get_config_folder(self, label_folder_id): label_folder = Folder().load(label_folder_id, user=self.getCurrentUser(), level=AccessType.READ) ownerId = self.__get_owner_id(label_folder) config_folder = self.folder_m.load(label_folder['meta'][ownerId], level=AccessType.READ, user=self.getCurrentUser()) return config_folder def __find_config(self, folder_id): folder = self.__get_config_folder(folder_id) printOk2("Config folder {}".format(folder)) files = self.folder_m.fileList(folder, self.getCurrentUser(), data=False) for file_path, file in files: printOk(file) if file['name'] == "config.json": return file def __findFolder(self, p_folder, name, desc="", create=False): """ Find folder by name. If not found create the folder :param p_folder: parent folder :param name: name of the folder you want to find inside the parent folder :return: folder doc """ folder = list(self.folder_m.find({'folderId': p_folder['_id'], 'name': name}).limit(1)) if not folder: # check if you are allowed to create, else return nothing if create: folder = self.folder_m.createFolder(parent=p_folder, name=name, creator=self.getCurrentUser(), description=desc, reuseExisting=True) else: return None return folder def __findFile(self, folder, file_name): item = list(self.item_m.find({'folderId': folder['_id'], 'name': file_name}).limit(1)) if not item: return None item = item[0] file = list(self.file_m.find({'itemId': item['_id']}).limit(1)) if not file: return None return file[0]
def find(self, query=None, **kwargs): annotation_query = self._find_query_filter(query) return Item.find(self, annotation_query, **kwargs)
class LabelResource(Resource): def __init__(self): super().__init__() self.resourceName = 'label' self.coll_m = Collection() self.file_m = File() self.folder_m = Folder() self.item_m = Item() self.upload_m = Upload() self.asset_m = Assetstore() self.setupRoutes() def setupRoutes(self): self.route('GET', (), handler=self.getLabelList) self.route('GET', (':label_id',), self.getLabel) self.route('GET', ('meta',), self.getLabelMeta) self.route('GET', ('create',), self.createLabelFile) self.route('GET', ('by_name',), self.getLabelByName) self.route('POST', (), self.postLabel) def createNewFile(self, folder, file_name): item = self.item_m.createItem(file_name, creator=self.getCurrentUser(), folder=folder, description='label file', reuseExisting=False) file = self.file_m.createFile(size=0, item=item, name=file_name, creator=self.getCurrentUser(), assetstore=self.asset_m.getCurrent(), mimeType="application/json") return file def copy(self, srcFile, destFile): upload = self.upload_m.createUploadToFile(destFile, self.getCurrentUser(), srcFile['size']) self.upload_m.handleChunk(upload=upload, chunk=RequestBodyStream(self.file_m.open(srcFile), size=destFile['size']), user=self.getCurrentUser()) return upload @access.public @autoDescribeRoute( Description('Get label list')) @rest.rawResponse def getLabelList(self): printOk('getLabelsList() was called!') try: collection = list(self.coll_m.list(user=self.getCurrentUser(), offset=0, limit=1))[0] files = self.coll_m.fileList(collection, user=self.getCurrentUser(), data=False, includeMetadata=True, mimeFilter=['application/json']) files = list(files) cherrypy.response.headers["Content-Type"] = "application/json" return dumps(files) except: printFail(traceback.print_exc) @staticmethod def getOwnerId(folder): aclList = Folder().getFullAccessList(folder) for acl in aclList['users']: if acl['level'] == AccessType.ADMIN: return str(acl['id']) return None def getConfigFolder(self, label_folder_id): label_folder = Folder().load(label_folder_id, user=self.getCurrentUser(), level=AccessType.READ) ownerId = self.getOwnerId(label_folder) config_folder = self.folder_m.load(label_folder['meta'][ownerId], level=AccessType.READ, user=self.getCurrentUser()) return config_folder def findConfig(self, folder_id): folder = self.getConfigFolder(folder_id) printOk2("Config folder {}".format(folder)) files = self.folder_m.fileList(folder, self.getCurrentUser(), data=False) for file_path, file in files: printOk(file) if file['name'] == "config.json": return file def __findFile(self, folder, file_name): item = list(self.item_m.find({'folderId': folder['_id'], 'name': file_name}).limit(1)) if not item: return None item = item[0] file = list(self.file_m.find({'itemId': item['_id']}).limit(1)) if not file: return None return file[0] @access.public @autoDescribeRoute( Description('Create a new label file if it doesnt exist') .param('file_name', 'label file name').param('folder_id', 'the parent folder id')) @rest.rawResponse def createLabelFile(self, file_name, folder_id): try: folder = self.folder_m.load(folder_id, user=self.getCurrentUser(), level=AccessType.WRITE) file = self.__findFile(folder, file_name) if not file: file = self.createNewFile(folder, file_name) config_file = self.findConfig(folder_id) if not config_file: printFail("No config file found") return errorMessage("No config file found") else: res = self.copy(config_file, file) return dumps({ "label_id": res['fileId'] }) return dumps({ "label_id": file['_id'] }) except: printFail(traceback.print_exc) cherrypy.response.status = 500 @access.public @autoDescribeRoute( Description('Get labels by file_name') .param('file_name', 'label file name').param('folder_id', 'the parent folder id')) @rest.rawResponse def getLabelByName(self, file_name, folder_id): try: folder = self.folder_m.load(folder_id, user=self.getCurrentUser(), level=AccessType.READ) file = self.__findFile(folder, file_name) cherrypy.response.headers["Content-Type"] = "application/json" if file: return self.file_m.download(file) else: return dumps({}) except: printFail(traceback.print_exc) cherrypy.response.status = 500 @access.public @autoDescribeRoute( Description('Get label by id') .param('label_id', 'label file id')) @rest.rawResponse def getLabel(self, label_id): try: file = self.file_m.load(label_id, level=AccessType.READ, user=self.getCurrentUser()) printOk2(file) cherrypy.response.headers["Content-Type"] = "application/json" return self.file_m.download(file) except: # Unknown slug printFail(traceback.print_exc) cherrypy.response.status = 404 @access.public @autoDescribeRoute( Description('Get label by id') .param('label_id', 'label file id')) def getLabelMeta(self, label_id): try: file = self.file_m.load(label_id, level=AccessType.READ, user=self.getCurrentUser()) cherrypy.response.headers["Content-Type"] = "application/json" return dumps(file) except: # Unknown slug printFail(traceback.print_exc) cherrypy.response.status = 404 @access.public @autoDescribeRoute( Description('Post label by id') .param('label_id', 'label file id')) @rest.rawResponse def postLabel(self, label_id, params): try: file = self.file_m.load(label_id, level=AccessType.WRITE, user=self.getCurrentUser()) cherrypy.response.headers["Content-Type"] = "application/json" params['labels'] = json.loads(params['labels']) data = json.dumps(params, indent=2, sort_keys=True) upload = writeData(self.getCurrentUser(), file, data) printOk2(file) printOk(upload) return dumps(upload) except: # Unknown slug printFail(traceback.print_exc) cherrypy.response.status = 404 @access.public @autoDescribeRoute( Description('Post label by id') .param('label_id', 'label file id')) @rest.rawResponse def strokeToOutline(self, strokes): pass