Source code for girder.models.item

#!/usr/bin/env python
# -*- coding: utf-8 -*-

#  Copyright 2013 Kitware Inc.
#  Licensed under the Apache License, Version 2.0 ( the "License" );
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  See the License for the specific language governing permissions and
#  limitations under the License.

import copy
import datetime
import json
import os
import six

from bson.objectid import ObjectId
from .model_base import Model, ValidationException, GirderException
from girder import events
from girder import logger
from girder.constants import AccessType
from girder.utility import acl_mixin
from girder.utility.progress import setResponseTimeLimit

[docs]class Item(acl_mixin.AccessControlMixin, Model): """ Items are leaves in the data hierarchy. They can contain 0 or more files within them, and can also contain arbitrary metadata. """ def initialize(self): = 'item' self.ensureIndices(('folderId', 'name', 'lowerName', ([('folderId', 1), ('name', 1)], {}))) self.ensureTextIndex({ 'name': 10, 'description': 1 }) self.resourceColl = 'folder' self.resourceParent = 'folderId' self.exposeFields(level=AccessType.READ, fields=( '_id', 'size', 'updated', 'description', 'created', 'meta', 'creatorId', 'folderId', 'name', 'baseParentType', 'baseParentId'))
[docs] def filter(self, *args, **kwargs): """ Preserved override for kwarg backwards compatibility. Prior to the refactor for centralizing model filtering, this method's first formal parameter was called "item", whereas the centralized version's first parameter is called "doc". This override simply detects someone using the old kwarg and converts it to the new form. """ if 'item' in kwargs: args = [kwargs.pop('item')] + list(args) return Model.filter(self, *args, **kwargs)
def _validateString(self, value): """ Make sure a value is a string and is stripped of whitespace. :param value: the value to coerce into a string if it isn't already. :returns: the string version of the value. """ if value is None: value = '' if not isinstance(value, six.string_types): value = str(value) return value.strip() def validate(self, doc): doc['name'] = self._validateString(doc.get('name', '')) doc['description'] = self._validateString(doc.get('description', '')) if not doc['name']: raise ValidationException('Item name must not be empty.', 'name') # Ensure unique name among sibling items and folders. If the desired # name collides with an existing item or folder, we will append (n) # onto the end of the name, incrementing n until the name is unique. name = doc['name'] n = 0 while True: q = { 'name': name, 'folderId': doc['folderId'] } if '_id' in doc: q['_id'] = {'$ne': doc['_id']} dupItem = self.findOne(q, fields=['_id']) q = { 'parentId': doc['folderId'], 'name': name, 'parentCollection': 'folder' } dupFolder = self.model('folder').findOne(q, fields=['_id']) if dupItem is None and dupFolder is None: doc['name'] = name break else: n += 1 name = '%s (%d)' % (doc['name'], n) doc['lowerName'] = doc['name'].lower() return doc
[docs] def load(self, id, level=AccessType.ADMIN, user=None, objectId=True, force=False, fields=None, exc=False): """ Calls AccessControlMixin.load while doing some auto-correction. Takes the same parameters as :py:func:`girder.models.model_base.AccessControlledMixin.load`. """ doc = super(Item, self).load(id, level, user, objectId, force, fields, exc) if doc is not None and 'baseParentType' not in doc: pathFromRoot = self.parentsToRoot(doc, user=user, force=True) baseParent = pathFromRoot[0] doc['baseParentId'] = baseParent['object']['_id'] doc['baseParentType'] = baseParent['type'], triggerEvents=False) if doc is not None and 'lowerName' not in doc:, triggerEvents=False) return doc
[docs] def move(self, item, folder): """ Move the given item from its current folder into another folder. :param item: The item to move. :type item: dict :param folder: The folder to move the item into. :type folder: dict. """ self.propagateSizeChange(item, -item['size']) item['folderId'] = folder['_id'] item['baseParentType'] = folder['baseParentType'] item['baseParentId'] = folder['baseParentId'] self.propagateSizeChange(item, item['size']) return
def propagateSizeChange(self, item, inc): self.model('folder').increment(query={ '_id': item['folderId'] }, field='size', amount=inc, multi=False) self.model(item['baseParentType']).increment(query={ '_id': item['baseParentId'] }, field='size', amount=inc, multi=False)
[docs] def recalculateSize(self, item): """ Recalculate the item size based on the files that are in it. If this is different than the recorded size, propagate the changes. :param item: The item to recalculate the size of. :returns: the recalculated size in bytes """ size = 0 for file in self.childFiles(item): # We could add a recalculateSize to the file model, in which case # this would be: # size += self.model('file').recalculateSize(file) size += file.get('size', 0) delta = size-item.get('size', 0) if delta:'Item %s was wrong size: was %d, is %d' % ( item['_id'], item['size'], size)) item['size'] = size self.update({'_id': item['_id']}, update={'$set': {'size': size}}) self.propagateSizeChange(item, delta) return size
[docs] def childFiles(self, item, limit=0, offset=0, sort=None, **kwargs): """ Returns child files of the item. Passes any kwargs to the find function. :param item: The parent item. :param limit: Result limit. :param offset: Result offset. :param sort: The sort structure to pass to pymongo. """ q = { 'itemId': item['_id'] } return self.model('file').find( q, limit=limit, offset=offset, sort=sort, **kwargs)
[docs] def remove(self, item, **kwargs): """ Delete an item, and all references to it in the database. :param item: The item document to delete. :type item: dict """ # Delete all files in this item files = self.model('file').find({ 'itemId': item['_id'] }) for file in files: fileKwargs = kwargs.copy() fileKwargs.pop('updateItemSize', None) self.model('file').remove(file, updateItemSize=False, **fileKwargs) # Delete pending uploads into this item uploads = self.model('upload').find({ 'parentId': item['_id'], 'parentType': 'item' }) for upload in uploads: self.model('upload').remove(upload, **kwargs) # Delete the item itself Model.remove(self, item)
[docs] def createItem(self, name, creator, folder, description='', reuseExisting=False): """ Create a new item. The creator will be given admin access to it. :param name: The name of the item. :type name: str :param description: Description for the item. :type description: str :param folder: The parent folder of the item. :param creator: User document representing the creator of the item. :type creator: dict :param reuseExisting: If an item with the given name already exists under the given folder, return that item rather than creating a new one. :type reuseExisting: bool :returns: The item document that was created. """ if reuseExisting: existing = self.findOne({ 'folderId': folder['_id'], 'name': name }) if existing: return existing now = datetime.datetime.utcnow() if not type(creator) is dict or '_id' not in creator: # Internal error -- this shouldn't be called without a user. raise GirderException('Creator must be a user.', 'girder.models.item.creator-not-user') if 'baseParentType' not in folder: pathFromRoot = self.parentsToRoot({'folderId': folder['_id']}, creator, force=True) folder['baseParentType'] = pathFromRoot[0]['type'] folder['baseParentId'] = pathFromRoot[0]['object']['_id'] return{ 'name': self._validateString(name), 'description': self._validateString(description), 'folderId': ObjectId(folder['_id']), 'creatorId': creator['_id'], 'baseParentType': folder['baseParentType'], 'baseParentId': folder['baseParentId'], 'created': now, 'updated': now, 'size': 0 })
[docs] def updateItem(self, item): """ Updates an item. :param item: The item document to update :type item: dict :returns: The item document that was edited. """ item['updated'] = datetime.datetime.utcnow() # Validate and save the item return
[docs] def setMetadata(self, item, metadata): """ Set metadata on an item. A `ValidationException` is thrown in the cases where the metadata JSON object is badly formed, or if any of the metadata keys contains a period ('.'). :param item: The item to set the metadata on. :type item: dict :param metadata: A dictionary containing key-value pairs to add to the items meta field :type metadata: dict :returns: the item document """ if 'meta' not in item: item['meta'] = {} # Add new metadata to existing metadata item['meta'].update(six.viewitems(metadata)) # Remove metadata fields that were set to null (use items in py3) toDelete = [k for k, v in six.viewitems(item['meta']) if v is None] for key in toDelete: del item['meta'][key] item['updated'] = datetime.datetime.utcnow() # Validate and save the item return
[docs] def parentsToRoot(self, item, user=None, force=False): """ Get the path to traverse to a root of the hierarchy. :param item: The item whose root to find :type item: dict :param user: The user making the request (not required if force=True). :type user: dict or None :param force: Set to True to skip permission checking. If False, the returned models will be filtered. :type force: bool :returns: an ordered list of dictionaries from root to the current item """ curFolder = self.model('folder').load( item['folderId'], user=user, level=AccessType.READ, force=force) folderIdsToRoot = self.model('folder').parentsToRoot( curFolder, user=user, level=AccessType.READ, force=force) if force: folderIdsToRoot.append({'type': 'folder', 'object': curFolder}) else: filteredFolder = self.model('folder').filter(curFolder, user) folderIdsToRoot.append({'type': 'folder', 'object': filteredFolder}) return folderIdsToRoot
[docs] def copyItem(self, srcItem, creator, name=None, folder=None, description=None): """ Copy an item, including duplicating files and metadata. :param srcItem: the item to copy. :type srcItem: dict :param creator: the user who will own the copied item. :param name: The name of the new item. None to copy the original name. :type name: str :param folder: The parent folder of the new item. None to store in the same folder as the original item. :param description: Description for the new item. None to copy the original description. :type description: str :returns: the new item. """ if name is None: name = srcItem['name'] if folder is None: folder = self.model('folder').load(srcItem['folderId'], force=True) if description is None: description = srcItem['description'] newItem = self.createItem( folder=folder, name=name, creator=creator, description=description) # copy metadata and other extension values filteredItem = self.filter(newItem, creator) updated = False for key in srcItem: if key not in filteredItem and key not in newItem: newItem[key] = copy.deepcopy(srcItem[key]) updated = True if updated:, triggerEvents=False) # Give listeners a chance to change things events.trigger('model.item.copy.prepare', (srcItem, newItem)) # copy files for file in self.childFiles(item=srcItem): self.model('file').copyFile(file, creator=creator, item=newItem) events.trigger('model.item.copy.after', newItem) return newItem
[docs] def fileList(self, doc, user=None, path='', includeMetadata=False, subpath=True): """ Generate a list of files within this item. :param doc: The item to list. :param user: A user used to validate data that is returned. This isn't used, but is present to be consistent across all model implementations of fileList. :param path: A path prefix to add to the results. :type path: str :param includeMetadata: If True and there is any metadata, include a result which is the JSON string of the metadata. This is given a name of metadata[-(number).json that is distinct from any file within the item. :type includeMetadata: bool :param subpath: If True and the item has more than one file, any metadata, or the sole file is not named the same as the item, then the returned paths include the item name. :type subpath: bool :returns: Iterable over files in this item, where each element is a tuple of (path name of the file, stream function with file data). :rtype: generator(str, func) """ if subpath: files = list(self.childFiles(item=doc, limit=2)) if (len(files) != 1 or files[0]['name'] != doc['name'] or (includeMetadata and doc.get('meta', {}))): path = os.path.join(path, doc['name']) metadataFile = "girder-item-metadata.json" for file in self.childFiles(item=doc): if file['name'] == metadataFile: metadataFile = None yield (os.path.join(path, file['name']), self.model('file').download(file, headers=False)) if includeMetadata and metadataFile and len(doc.get('meta', {})): def stream(): yield json.dumps(doc['meta'], default=str) yield (os.path.join(path, metadataFile), stream)
[docs] def checkConsistency(self, stage, progress=None): """ Check all of the items and make sure they are valid. This operates in stages, since some actions should be done before other models that rely on items and some need to be done after. The stages are: * count - count how many items need to be checked. * remove - remove lost items * verify - verify and fix existing items :param stage: which stage of the check to run. See above. :param progress: an optional progress context to update. :returns: numItems: number of items to check or processed, numChanged: number of items changed. """ if stage == 'count': numItems = self.find(limit=1).count() return numItems, 0 elif stage == 'remove': # Check that all items are in existing folders. Any that are not # can be deleted. Perhaps we should put them in a lost+found # instead folderIds = self.model('folder').collection.distinct('_id') lostItems = self.find({ '$or': [{'folderId': {'$nin': folderIds}}, {'folderId': {'$exists': False}}]}) numItems = itemsLeft = lostItems.count() if numItems: if progress is not None: progress.update(message='Removing orphaned items') for item in lostItems: setResponseTimeLimit() self.collection.delete_one({'_id': item['_id']}) if progress is not None: itemsLeft -= 1 progress.update(increment=1, message='Removing ' 'orphaned items (%d left)' % itemsLeft) return numItems, numItems elif stage == 'verify': # Check items sizes items = self.find() numItems = itemsLeft = items.count() itemsCorrected = 0 if progress is not None: progress.update(message='Checking items') for item in items: itemCorrected = False setResponseTimeLimit() oldSize = item.get('size', 0) newSize = self.recalculateSize(item) if newSize != oldSize: itemCorrected = True newBaseParent = self.parentsToRoot(item, force=True)[0] if item['baseParentType'] != newBaseParent['type'] or \ item['baseParentId'] != newBaseParent['object']['_id']: self.update( {'_id': item['_id']}, update={'$set': { 'baseParentType': newBaseParent['type'], 'baseParentId': newBaseParent['object']['_id'] }}) itemCorrected = True if itemCorrected: itemsCorrected += 1 if progress is not None: itemsLeft -= 1 progress.update(increment=1, message='Checking items (%d ' 'left)' % itemsLeft) return numItems, itemsCorrected