Source code for girder.models.folder

#!/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 AccessControlledModel, ValidationException, \
from girder import events
from girder.constants import AccessType
from girder.utility.progress import noProgress, setResponseTimeLimit

[docs]class Folder(AccessControlledModel): """ Folders are used to store items and can also store other folders in a hierarchical way, like a directory on a filesystem. Every folder has its own set of access control policies, but by default the access control list is inherited from the folder's parent folder, if it has one. Top-level folders are ones whose parent is a user or a collection. """ def initialize(self): = 'folder' self.ensureIndices(('parentId', 'name', 'lowerName', ([('parentId', 1), ('name', 1)], {}))) self.ensureTextIndex({ 'name': 10, 'description': 1 }) self.exposeFields(level=AccessType.READ, fields=( '_id', 'name', 'public', 'publicFlags', 'description', 'created', 'updated', 'size', 'meta', 'parentId', 'parentCollection', 'creatorId', 'baseParentType', 'baseParentId'))
[docs] def validate(self, doc, allowRename=False): """ Validate the name and description of the folder, ensure that it is associated with a valid parent and that it has a unique name. :param doc: the folder document to validate. :param allowRename: if True and a folder or item exists with the same name, rename the folder so that it is unique. :returns: the validated folder document. """ doc['name'] = doc['name'].strip() doc['lowerName'] = doc['name'].lower() doc['description'] = doc['description'].strip() if not doc['name']: raise ValidationException('Folder name must not be empty.', 'name') if not doc['parentCollection'] in ('folder', 'user', 'collection'): # Internal error; this shouldn't happen raise GirderException('Invalid folder parent type: %s.' % doc['parentCollection'], 'girder.models.folder.invalid-parent-type') name = doc['name'] n = 0 while True: q = { 'parentId': doc['parentId'], 'name': name, 'parentCollection': doc['parentCollection'] } if '_id' in doc: q['_id'] = {'$ne': doc['_id']} dupFolder = self.findOne(q, fields=['_id']) if doc['parentCollection'] == 'folder': q = { 'folderId': doc['parentId'], 'name': name } dupItem = self.model('item').findOne(q, fields=['_id']) else: dupItem = None if dupItem is None and dupFolder is None: doc['name'] = name break if not allowRename: if dupFolder: raise ValidationException('A folder with that name ' 'already exists here.', 'name') raise ValidationException('An item with that name already ' 'exists here.', 'name') n += 1 name = '%s (%d)' % (doc['name'], n) return doc
[docs] def load(self, id, level=AccessType.ADMIN, user=None, objectId=True, force=False, fields=None, exc=False): """ We override load in order to ensure the folder has certain fields within it, and if not, we add them lazily at read time. :param id: The id of the resource. :type id: string or ObjectId :param user: The user to check access against. :type user: dict or None :param level: The required access type for the object. :type level: AccessType :param force: If you explicitly want to circumvent access checking on this resource, set this to True. :type force: bool """ doc = AccessControlledModel.load( self, id=id, objectId=objectId, level=level, fields=fields, exc=exc, force=force, user=user) 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'] doc =, triggerEvents=False) if doc is not None and 'lowerName' not in doc: doc =, triggerEvents=False) return doc
[docs] def getSizeRecursive(self, folder): """ Calculate the total size of the folder by recursing into all of its descendant folders. """ size = folder['size'] q = { 'parentId': folder['_id'], 'parentCollection': 'folder' } for child in self.find(q): size += self.getSizeRecursive(child) return size
[docs] def setMetadata(self, folder, metadata): """ Set metadata on a folder. 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 folder: The folder to set the metadata on. :type folder: dict :param metadata: A dictionary containing key-value pairs to add to the folder's meta field :type metadata: dict :returns: the folder document """ if 'meta' not in folder: folder['meta'] = {} # Add new metadata to existing metadata folder['meta'].update(six.viewitems(metadata)) # Remove metadata fields that were set to null (use items in py3) folder['meta'] = {k: v for k, v in six.viewitems(folder['meta']) if v is not None} folder['updated'] = datetime.datetime.utcnow() # Validate and save the item return
def _updateDescendants(self, folderId, updateQuery): """ This helper is used to update all items and folders underneath a folder. This is expensive, so think carefully before using it. :param folderId: The _id of the folder at the root of the subtree. :param updateQuery: The mongo query to apply to all of the children of the folder. :type updateQuery: dict """ self.update(query={ 'parentId': folderId, 'parentCollection': 'folder' }, update=updateQuery, multi=True) self.model('item').update(query={ 'folderId': folderId, }, update=updateQuery, multi=True) q = { 'parentId': folderId, 'parentCollection': 'folder' } for child in self.find(q): self._updateDescendants( child['_id'], updateQuery) def _isAncestor(self, ancestor, descendant): """ Returns whether folder "ancestor" is an ancestor of folder "descendant", or if they are the same folder. :param ancestor: The folder to test as an ancestor. :type ancestor: folder :param descendant: The folder to test as a descendant. :type descendant: folder """ if ancestor['_id'] == descendant['_id']: return True if descendant['parentCollection'] != 'folder': return False descendant = self.load(descendant['parentId'], force=True) if descendant is None: return False return self._isAncestor(ancestor, descendant)
[docs] def move(self, folder, parent, parentType): """ Move the given folder from its current parent to another parent object. Raises an exception if folder is an ancestor of parent. :param folder: The folder to move. :type folder: dict :param parent: The new parent object. :param parentType: The type of the new parent object (user, collection, or folder). :type parentType: str """ if (parentType == 'folder' and (self._isAncestor(folder, parent) or folder['_id'] == parent['_id'])): raise ValidationException( 'You may not move a folder underneath itself.') folder['parentId'] = parent['_id'] folder['parentCollection'] = parentType if parentType == 'folder': rootType, rootId = parent['baseParentType'], parent['baseParentId'] else: rootType, rootId = parentType, parent['_id'] if (folder['baseParentType'], folder['baseParentId']) !=\ (rootType, rootId): def propagateSizeChange(folder, inc): self.model(folder['baseParentType']).increment(query={ '_id': folder['baseParentId'] }, field='size', amount=inc, multi=False) totalSize = self.getSizeRecursive(folder) propagateSizeChange(folder, -totalSize) folder['baseParentType'] = rootType folder['baseParentId'] = rootId propagateSizeChange(folder, totalSize) self._updateDescendants(folder['_id'], { '$set': { 'baseParentType': rootType, 'baseParentId': rootId } }) return
[docs] def clean(self, folder, progress=None, **kwargs): """ Delete all contents underneath a folder recursively, but leave the folder itself. :param folder: The folder document to delete. :type folder: dict :param progress: A progress context to record progress on. :type progress: girder.utility.progress.ProgressContext or None. """ setResponseTimeLimit() # Delete all child items items = self.model('item').find({ 'folderId': folder['_id'] }) for item in items: setResponseTimeLimit() self.model('item').remove(item, progress=progress, **kwargs) if progress: progress.update(increment=1, message='Deleted item %s' % item['name']) # subsequent operations take a long time, so free the cursor's resources items.close() # Delete all child folders folders = self.find({ 'parentId': folder['_id'], 'parentCollection': 'folder' }) for subfolder in folders: self.remove(subfolder, progress=progress, **kwargs) folders.close()
[docs] def remove(self, folder, progress=None, **kwargs): """ Delete a folder recursively. :param folder: The folder document to delete. :type folder: dict :param progress: A progress context to record progress on. :type progress: girder.utility.progress.ProgressContext or None. """ # Remove the contents underneath this folder recursively. self.clean(folder, progress, **kwargs) # Delete pending uploads into this folder uploads = self.model('upload').find({ 'parentId': folder['_id'], 'parentType': 'folder' }) for upload in uploads: self.model('upload').remove(upload, progress=progress, **kwargs) uploads.close() # Delete this folder AccessControlledModel.remove(self, folder, progress=progress, **kwargs) if progress: progress.update(increment=1, message='Deleted folder %s' % folder['name'])
[docs] def childItems(self, folder, limit=0, offset=0, sort=None, filters=None, **kwargs): """ Generator function that yields child items in a folder. Passes any kwargs to the find function. :param folder: The parent folder. :param limit: Result limit. :param offset: Result offset. :param sort: The sort structure to pass to pymongo. :param filters: Additional query operators. """ q = { 'folderId': folder['_id'] } q.update(filters or {}) return self.model('item').find( q, limit=limit, offset=offset, sort=sort, **kwargs)
[docs] def childFolders(self, parent, parentType, user=None, limit=0, offset=0, sort=None, filters=None, **kwargs): """ This generator will yield child folders of a user, collection, or folder, with access policy filtering. Passes any kwargs to the find function. :param parent: The parent object. :type parentType: Type of the parent object. :param parentType: The parent type. :type parentType: 'user', 'folder', or 'collection' :param user: The user running the query. Only returns folders that this user can see. :param limit: Result limit. :param offset: Result offset. :param sort: The sort structure to pass to pymongo. :param filters: Additional query operators. """ if not filters: filters = {} parentType = parentType.lower() if parentType not in ('folder', 'user', 'collection'): raise ValidationException('The parentType must be folder, ' 'collection, or user.') q = { 'parentId': parent['_id'], 'parentCollection': parentType } q.update(filters) # Perform the find; we'll do access-based filtering of the result set # afterward. cursor = self.find(q, sort=sort, **kwargs) return self.filterResultsByPermission( cursor=cursor, user=user, level=AccessType.READ, limit=limit, offset=offset)
[docs] def createFolder(self, parent, name, description='', parentType='folder', public=None, creator=None, allowRename=False, reuseExisting=False): """ Create a new folder under the given parent. :param parent: The parent document. Should be a folder, user, or collection. :type parent: dict :param name: The name of the folder. :type name: str :param description: Description for the folder. :type description: str :param parentType: What type the parent is: ('folder' | 'user' | 'collection') :type parentType: str :param public: Public read access flag. :type public: bool or None to inherit from parent :param creator: User document representing the creator of this folder. :type creator: dict :param allowRename: if True and a folder or item of this name exists, automatically rename the folder. :type allowRename: bool :param reuseExisting: If a folder with the given name already exists under the given parent, return that folder rather than creating a new one. :type reuseExisting: bool :returns: The folder document that was created. """ if reuseExisting: existing = self.findOne({ 'parentId': parent['_id'], 'name': name, 'parentCollection': parentType }) if existing: return existing parentType = parentType.lower() if parentType not in ('folder', 'user', 'collection'): raise ValidationException('The parentType must be folder, ' 'collection, or user.') if parentType == 'folder': if 'baseParentId' not in parent: pathFromRoot = self.parentsToRoot( parent, user=creator, force=True) parent['baseParentId'] = pathFromRoot[0]['object']['_id'] parent['baseParentType'] = pathFromRoot[0]['type'] else: parent['baseParentId'] = parent['_id'] parent['baseParentType'] = parentType now = datetime.datetime.utcnow() if creator is None: creatorId = None else: creatorId = creator.get('_id', None) folder = { 'name': name, 'description': description, 'parentCollection': parentType, 'baseParentId': parent['baseParentId'], 'baseParentType': parent['baseParentType'], 'parentId': ObjectId(parent['_id']), 'creatorId': creatorId, 'created': now, 'updated': now, 'size': 0 } if parentType in ('folder', 'collection'): self.copyAccessPolicies(src=parent, dest=folder, save=False) if creator is not None: self.setUserAccess(folder, user=creator, level=AccessType.ADMIN, save=False) # Allow explicit public flag override if it's set. if public is not None and isinstance(public, bool): self.setPublic(folder, public, save=False) if allowRename: self.validate(folder, allowRename=True) # Now validate and save the folder. return
[docs] def updateFolder(self, folder): """ Updates a folder. :param folder: The folder document to update :type folder: dict :returns: The folder document that was edited. """ folder['updated'] = datetime.datetime.utcnow() # Validate and save the folder return
[docs] def parentsToRoot(self, folder, curPath=None, user=None, force=False, level=AccessType.READ): """ Get the path to traverse to a root of the hierarchy. :param folder: The folder whose root to find :type folder: dict :returns: an ordered list of dictionaries from root to the current folder """ if not curPath: curPath = [] curParentId = folder['parentId'] curParentType = folder['parentCollection'] if curParentType == 'user' or curParentType == 'collection': curParentObject = self.model(curParentType).load( curParentId, user=user, level=level, force=force) if not force: parentFiltered = \ self.model(curParentType).filter(curParentObject, user) else: parentFiltered = curParentObject return [{'type': curParentType, 'object': parentFiltered}] + curPath else: curParentObject = self.load( curParentId, user=user, level=level, force=force) if not force: curPath = \ [{'type': curParentType, 'object': self.filter(curParentObject, user)}] + curPath else: curPath = [{'type': curParentType, 'object': curParentObject}] + curPath return self.parentsToRoot(curParentObject, curPath, user=user, force=force)
[docs] def countItems(self, folder): """ Returns the number of items within the given folder. """ return self.childItems(folder, fields=()).count()
[docs] def countFolders(self, folder, user=None, level=None): """ Returns the number of subfolders within the given folder. Access checking is optional; to circumvent access checks, pass ``level=None``. :param folder: The parent folder. :type folder: dict :param user: If performing access checks, the user to check against. :type user: dict or None :param level: The required access level, or None to return the raw subfolder count. """ fields = () if level is None else ('access', 'public') folders = self.find({ 'parentId': folder['_id'], 'parentCollection': 'folder' }, fields=fields) if level is None: return folders.count() else: return sum(1 for _ in self.filterResultsByPermission( cursor=folders, user=user, level=level))
[docs] def subtreeCount(self, folder, includeItems=True, user=None, level=None): """ Return the size of the subtree rooted at the given folder. Includes the root folder in the count. :param folder: The root of the subtree. :type folder: dict :param includeItems: Whether to include items in the subtree count, or just folders. :type includeItems: bool :param user: If filtering by permission, the user to filter against. :param level: If filtering by permission, the required permission level. :type level: AccessLevel """ count = 1 if includeItems: count += self.countItems(folder) folders = self.find({ 'parentId': folder['_id'], 'parentCollection': 'folder' }, fields=('access',)) if level is not None: folders = self.filterResultsByPermission( cursor=folders, user=user, level=level) count += sum(self.subtreeCount(subfolder, includeItems=includeItems, user=user, level=level) for subfolder in folders) return count
[docs] def fileList(self, doc, user=None, path='', includeMetadata=False, subpath=True, mimeFilter=None, data=True): """ This function generates a list of 2-tuples whose first element is the relative path to the file from the folder's root and whose second element depends on the value of the `data` flag. If `data=True`, the second element will be a generator that will generate the bytes of the file data as stored in the assetstore. If `data=False`, the second element is the file document itself. :param doc: The folder to list. :param user: The user used for access. :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 folder. :type includeMetadata: bool :param subpath: if True, add the folder's name to the path. :type subpath: bool :param mimeFilter: Optional list of MIME types to filter by. Set to None to include all files. :type mimeFilter: list or tuple :param data: If True return raw content of each file as stored in the assetstore, otherwise return file document. :type data: bool :returns: Iterable over files in this folder, where each element is a tuple of (path name of the file, stream function with file data or file object). :rtype: generator(str, func) """ if subpath: path = os.path.join(path, doc['name']) metadataFile = 'girder-folder-metadata.json' for sub in self.childFolders(parentType='folder', parent=doc, user=user): if sub['name'] == metadataFile: metadataFile = None for (filepath, file) in self.fileList( sub, user, path, includeMetadata, subpath=True, mimeFilter=mimeFilter, data=data): yield (filepath, file) for item in self.childItems(folder=doc): if item['name'] == metadataFile: metadataFile = None for (filepath, file) in self.model('item').fileList( item, user, path, includeMetadata, mimeFilter=mimeFilter, data=data): yield (filepath, file) if includeMetadata and metadataFile and doc.get('meta', {}): def stream(): yield json.dumps(doc['meta'], default=str) yield (os.path.join(path, metadataFile), stream)
[docs] def copyFolder(self, srcFolder, parent=None, name=None, description=None, parentType=None, public=None, creator=None, progress=None, firstFolder=None): """ Copy a folder, including all child items and child folders. :param srcFolder: the folder to copy. :type srcFolder: dict :param parent: The parent document. Must be a folder, user, or collection. :type parent: dict :param name: The name of the new folder. None to copy the original name. :type name: str :param description: Description for the new folder. None to copy the original description. :type description: str :param parentType: What type the parent is: ('folder' | 'user' | 'collection') :type parentType: str :param public: Public read access flag. None to inherit from parent, 'original' to inherit from original folder. :type public: bool, None, or 'original'. :param creator: user representing the creator of the new folder. :type creator: dict :param progress: a progress context to record process on. :type progress: girder.utility.progress.ProgressContext or None. :param firstFolder: if not None, the first folder copied in a tree of folders. :returns: the new folder document. """ setResponseTimeLimit() if parentType is None: parentType = srcFolder['parentCollection'] parentType = parentType.lower() if parentType not in ('folder', 'user', 'collection'): raise ValidationException('The parentType must be folder, ' 'collection, or user.') if parent is None: parent = self.model(parentType).load(srcFolder['parentId'], force=True) if name is None: name = srcFolder['name'] if description is None: description = srcFolder['description'] if public == 'original': public = srcFolder.get('public', None) newFolder = self.createFolder( parentType=parentType, parent=parent, name=name, description=description, public=public, creator=creator, allowRename=True) if firstFolder is None: firstFolder = newFolder return self.copyFolderComponents( srcFolder, newFolder, creator, progress, firstFolder)
[docs] def copyFolderComponents(self, srcFolder, newFolder, creator, progress, firstFolder=None): """ Copy the items, subfolders, and extended data of a folder that was just copied. :param srcFolder: the original folder. :type srcFolder: dict :param newFolder: the new folder. :type newFolder: dict :param creator: user representing the creator of the new folder. :type creator: dict :param progress: a progress context to record process on. :type progress: girder.utility.progress.ProgressContext or None. :param firstFolder: if not None, the first folder copied in a tree of folders. :returns: the new folder document. """ # copy metadata and other extension values filteredFolder = self.filter(newFolder, creator) updated = False for key in srcFolder: if key not in filteredFolder and key not in newFolder: newFolder[key] = copy.deepcopy(srcFolder[key]) updated = True if updated: newFolder =, triggerEvents=False) # Give listeners a chance to change things events.trigger('model.folder.copy.prepare', (srcFolder, newFolder)) # copy items for item in self.childItems(folder=srcFolder): setResponseTimeLimit() self.model('item').copyItem(item, creator, folder=newFolder) if progress: progress.update(increment=1, message='Copied item ' + item['name']) # copy subfolders for sub in self.childFolders(parentType='folder', parent=srcFolder, user=creator): if firstFolder and firstFolder['_id'] == sub['_id']: continue self.copyFolder(sub, parent=newFolder, parentType='folder', creator=creator, progress=progress) events.trigger('model.folder.copy.after', newFolder) if progress: progress.update(increment=1, message='Copied folder ' + newFolder['name']) # Reload to get updated size value return self.load(newFolder['_id'], force=True)
[docs] def setAccessList(self, doc, access, save=False, recurse=False, user=None, progress=noProgress, setPublic=None, publicFlags=None, force=False): """ Overrides AccessControlledModel.setAccessList to add a recursive option. When `recurse=True`, this will set the access list on all subfolders to which the given user has ADMIN access level. Any subfolders that the given user does not have ADMIN access on will be skipped. :param doc: The folder to set access settings on. :type doc: folder :param access: The access control list. :type access: dict :param save: Whether the changes should be saved to the database. :type save: bool :param recurse: Whether this access list should be propagated to all subfolders underneath this folder. :type recurse: bool :param user: The current user (for recursive mode filtering). :param progress: Progress context to update. :type progress: :py:class:`girder.utility.progress.ProgressContext` :param setPublic: Pass this if you wish to set the public flag on the resources being updated. :type setPublic: bool or None :param publicFlags: Pass this if you wish to set the public flag list on resources being updated. :type publicFlags: flag identifier str, or list/set/tuple of them, or None :param force: Set this to True to set the flags regardless of the passed in user's permissions. :type force: bool """ progress.update(increment=1, message='Updating ' + doc['name']) if setPublic is not None: self.setPublic(doc, setPublic, save=False) if publicFlags is not None: doc = self.setPublicFlags(doc, publicFlags, user=user, save=False, force=force) doc = AccessControlledModel.setAccessList( self, doc, access, user=user, save=save, force=force) if recurse: cursor = self.find({ 'parentId': doc['_id'], 'parentCollection': 'folder' }) subfolders = self.filterResultsByPermission( cursor=cursor, user=user, level=AccessType.ADMIN) for folder in subfolders: self.setAccessList( folder, access, save=True, recurse=True, user=user, progress=progress, setPublic=setPublic, publicFlags=publicFlags, force=force) return doc
[docs] def isOrphan(self, folder): """ Returns True if this folder is orphaned (its parent is missing). :param folder: The folder to check. :type folder: dict """ return not self.model(folder.get('parentCollection')).load( folder.get('parentId'), force=True)
[docs] def updateSize(self, doc): """ Recursively recomputes the size of this folder and its underlying folders and fixes the sizes as needed. :param doc: The folder. :type doc: dict """ size = 0 fixes = 0 # recursively fix child folders but don't include their size children = self.model('folder').find({ 'parentId': doc['_id'], 'parentCollection': 'folder' }) for child in children: _, f = self.model('folder').updateSize(child) fixes += f # get correct size from child items for item in self.childItems(doc): s, f = self.model('item').updateSize(item) size += s fixes += f # fix value if incorrect if size != doc.get('size'): self.update({'_id': doc['_id']}, update={'$set': {'size': size}}) fixes += 1 return size, fixes