Source code for girder.models.upload

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

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#  Copyright 2013 Kitware Inc.
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#  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
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#    http://www.apache.org/licenses/LICENSE-2.0
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#  distributed under the License is distributed on an "AS IS" BASIS,
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import datetime
import six
from bson.objectid import ObjectId

from girder import events, logger
from girder.api import rest
from girder.constants import SettingKey
from .model_base import Model
from girder.exceptions import GirderException, ValidationException
from girder.utility import RequestBodyStream
from girder.utility.progress import noProgress


[docs]class Upload(Model): """ This model stores temporary records for uploads that have been approved but are not yet complete, so that they can be uploaded in chunks of arbitrary size. The chunks must be uploaded in order. """
[docs] def initialize(self): self.name = 'upload' self.ensureIndex('sha512')
def _getChunkSize(self, minSize=32 * 1024**2): """ Return a chunk size to use in file uploads. This is the maximum of the setting for minimum upload chunk size and the specified size. :param minSize: the minimum size to return. :return: chunk size to use for file uploads. """ from .setting import Setting minChunkSize = Setting().get(SettingKey.UPLOAD_MINIMUM_CHUNK_SIZE) return max(minChunkSize, minSize)
[docs] def uploadFromFile(self, obj, size, name, parentType=None, parent=None, user=None, mimeType=None, reference=None, assetstore=None, attachParent=False): """ This method wraps the entire upload process into a single function to facilitate "internal" uploads from a file-like object. Example: .. code-block:: python size = os.path.getsize(filename) with open(filename, 'rb') as f: Upload().uploadFromFile(f, size, filename, 'item', parentItem, user) :param obj: The object representing the content to upload. :type obj: file-like :param size: The total size of the file. :type size: int :param name: The name of the file to create. :type name: str :param parentType: The type of the parent: "folder" or "item". :type parentType: str :param parent: The parent (item or folder) to upload into. :type parent: dict :param user: The user who is creating the file. :type user: dict :param mimeType: MIME type of the file. :type mimeType: str :param reference: An optional reference string that will be sent to the data.process event. :param assetstore: An optional assetstore to use to store the file. If unspecified, the current assetstore is used. :type reference: str :param attachParent: if True, instead of creating an item within the parent or giving the file an itemId, set itemId to None and set attachedToType and attachedToId instead (using the values passed in parentType and parent). This is intended for files that shouldn't appear as direct children of the parent, but are still associated with it. :type attachParent: boolean """ upload = self.createUpload( user=user, name=name, parentType=parentType, parent=parent, size=size, mimeType=mimeType, reference=reference, assetstore=assetstore, attachParent=attachParent) # The greater of 32 MB or the the upload minimum chunk size. chunkSize = self._getChunkSize() while True: data = obj.read(chunkSize) if not data: break upload = self.handleChunk(upload, RequestBodyStream(six.BytesIO(data), size)) return upload
[docs] def validate(self, doc): if doc['size'] < 0: raise ValidationException('File size must not be negative.') if doc['received'] > doc['size']: raise ValidationException('Received too many bytes.') doc['updated'] = datetime.datetime.utcnow() return doc
[docs] def handleChunk(self, upload, chunk, filter=False, user=None): """ When a chunk is uploaded, this should be called to process the chunk. If this is the final chunk of the upload, this method will finalize the upload automatically. This method will return EITHER an upload or a file document. If this is the final chunk of the upload, the upload is finalized and the created file document is returned. Otherwise, it returns the upload document with the relevant fields modified. :param upload: The upload document to update. :type upload: dict :param chunk: The file object representing the chunk that was uploaded. :type chunk: file :param filter: Whether the model should be filtered. Only affects behavior when returning a file model, not the upload model. :type filter: bool :param user: The current user. Only affects behavior if filter=True. :type user: dict or None """ from .assetstore import Assetstore from .file import File from girder.utility import assetstore_utilities assetstore = Assetstore().load(upload['assetstoreId']) adapter = assetstore_utilities.getAssetstoreAdapter(assetstore) upload = adapter.uploadChunk(upload, chunk) if '_id' in upload or upload['received'] != upload['size']: upload = self.save(upload) # If upload is finished, we finalize it if upload['received'] == upload['size']: file = self.finalizeUpload(upload, assetstore) if filter: return File().filter(file, user=user) else: return file else: return upload
[docs] def requestOffset(self, upload): """ Requests the offset that should be used to resume uploading. This makes the request from the assetstore adapter. """ from .assetstore import Assetstore from girder.utility import assetstore_utilities assetstore = Assetstore().load(upload['assetstoreId']) adapter = assetstore_utilities.getAssetstoreAdapter(assetstore) return adapter.requestOffset(upload)
[docs] def finalizeUpload(self, upload, assetstore=None): """ This should only be called manually in the case of creating an empty file, i.e. one that has no chunks. :param upload: The upload document. :type upload: dict :param assetstore: If known, the containing assetstore for the upload. :type assetstore: dict :returns: The file object that was created. """ from .assetstore import Assetstore from .file import File from .item import Item from girder.utility import assetstore_utilities events.trigger('model.upload.finalize', upload) if assetstore is None: assetstore = Assetstore().load(upload['assetstoreId']) if 'fileId' in upload: # Updating an existing file's contents file = File().load(upload['fileId'], force=True) # Delete the previous file contents from the containing assetstore assetstore_utilities.getAssetstoreAdapter( Assetstore().load(file['assetstoreId'])).deleteFile(file) item = Item().load(file['itemId'], force=True) File().propagateSizeChange(item, upload['size'] - file['size']) # Update file info file['creatorId'] = upload['userId'] file['created'] = datetime.datetime.utcnow() file['assetstoreId'] = assetstore['_id'] file['size'] = upload['size'] # If the file was previously imported, it is no longer. if file.get('imported'): file['imported'] = False else: # Creating a new file record if upload.get('attachParent'): item = None elif upload['parentType'] == 'folder': # Create a new item with the name of the file. item = Item().createItem( name=upload['name'], creator={'_id': upload['userId']}, folder={'_id': upload['parentId']}) elif upload['parentType'] == 'item': item = Item().load(id=upload['parentId'], force=True) else: item = None file = File().createFile( item=item, name=upload['name'], size=upload['size'], creator={'_id': upload['userId']}, assetstore=assetstore, mimeType=upload['mimeType'], saveFile=False) if upload.get('attachParent'): if upload['parentType'] and upload['parentId']: file['attachedToType'] = upload['parentType'] file['attachedToId'] = upload['parentId'] adapter = assetstore_utilities.getAssetstoreAdapter(assetstore) file = adapter.finalizeUpload(upload, file) event_document = {'file': file, 'upload': upload} events.trigger('model.file.finalizeUpload.before', event_document) file = File().save(file) events.trigger('model.file.finalizeUpload.after', event_document) if '_id' in upload: self.remove(upload) logger.info('Upload complete. Upload=%s File=%s User=%s' % ( upload['_id'], file['_id'], upload['userId'])) # Add an async event for handlers that wish to process this file. eventParams = { 'file': file, 'assetstore': assetstore, 'currentToken': rest.getCurrentToken(), 'currentUser': rest.getCurrentUser() } if 'reference' in upload: eventParams['reference'] = upload['reference'] events.daemon.trigger('data.process', eventParams) return file
[docs] def getTargetAssetstore(self, modelType, resource, assetstore=None): """ Get the assetstore for a particular target resource, i.e. where new data within the resource should be stored. In Girder core, this is always just the current assetstore, but plugins may override this behavior to allow for more granular assetstore selection. :param modelType: the type of the resource that will be stored. :param resource: the resource to be stored. :param assetstore: if specified, the preferred assetstore where the resource should be located. This may be overridden. :returns: the selected assetstore. """ from .assetstore import Assetstore eventParams = {'model': modelType, 'resource': resource} event = events.trigger('model.upload.assetstore', eventParams) if event.responses: assetstore = event.responses[-1] elif not assetstore: assetstore = Assetstore().getCurrent() return assetstore
[docs] def createUploadToFile(self, file, user, size, reference=None, assetstore=None): """ Creates a new upload record into a file that already exists. This should be used when updating the contents of a file. Deletes any previous file content from the assetstore it was in. This will upload into the current assetstore rather than assetstore the file was previously contained in. :param file: The file record to update. :param user: The user performing this upload. :param size: The size of the new file contents. :param reference: An optional reference string that will be sent to the data.process event. :type reference: str :param assetstore: An optional assetstore to use to store the file. If unspecified, the current assetstore is used. """ from girder.utility import assetstore_utilities assetstore = self.getTargetAssetstore('file', file, assetstore) adapter = assetstore_utilities.getAssetstoreAdapter(assetstore) now = datetime.datetime.utcnow() upload = { 'created': now, 'updated': now, 'userId': user['_id'], 'fileId': file['_id'], 'assetstoreId': assetstore['_id'], 'size': size, 'name': file['name'], 'mimeType': file['mimeType'], 'received': 0 } if reference is not None: upload['reference'] = reference upload = adapter.initUpload(upload) return self.save(upload)
[docs] def createUpload(self, user, name, parentType, parent, size, mimeType=None, reference=None, assetstore=None, attachParent=False, save=True): """ Creates a new upload record, and creates its temporary file that the chunks will be written into. Chunks should then be sent in order using the _id of the upload document generated by this method. :param user: The user performing the upload. :type user: dict :param name: The name of the file being uploaded. :type name: str :param parentType: The type of the parent being uploaded into. :type parentType: str ('folder' or 'item') :param parent: The document representing the parent. :type parent: dict. :param size: Total size in bytes of the whole file. :type size: int :param mimeType: The mimeType of the file. :type mimeType: str :param reference: An optional reference string that will be sent to the data.process event. :type reference: str :param assetstore: An optional assetstore to use to store the file. If unspecified, the current assetstore is used. :param attachParent: if True, instead of creating an item within the parent or giving the file an itemId, set itemId to None and set attachedToType and attachedToId instead (using the values passed in parentType and parent). This is intended for files that shouldn't appear as direct children of the parent, but are still associated with it. :type attachParent: boolean :param save: if True, save the document after it is created. :type save: boolean :returns: The upload document that was created. """ from girder.utility import assetstore_utilities assetstore = self.getTargetAssetstore(parentType, parent, assetstore) adapter = assetstore_utilities.getAssetstoreAdapter(assetstore) now = datetime.datetime.utcnow() if not mimeType: mimeType = 'application/octet-stream' upload = { 'created': now, 'updated': now, 'assetstoreId': assetstore['_id'], 'size': size, 'name': name, 'mimeType': mimeType, 'received': 0 } if reference is not None: upload['reference'] = reference if parentType and parent: upload['parentType'] = parentType.lower() upload['parentId'] = parent['_id'] else: upload['parentType'] = None upload['parentId'] = None if attachParent: upload['attachParent'] = attachParent if user: upload['userId'] = user['_id'] else: upload['userId'] = None upload = adapter.initUpload(upload) if save: upload = self.save(upload) return upload
[docs] def moveFileToAssetstore(self, file, user, assetstore, progress=noProgress): """ Move a file from whatever assetstore it is located in to a different assetstore. This is done by downloading and re-uploading the file. :param file: the file to move. :param user: the user that is authorizing the move. :param assetstore: the destination assetstore. :param progress: optional progress context. :returns: the original file if it is not moved, or the newly 'uploaded' file if it is. """ from .file import File if file['assetstoreId'] == assetstore['_id']: return file # Allow an event to cancel the move. This could be done, for instance, # on files that could change dynamically. event = events.trigger('model.upload.movefile', { 'file': file, 'assetstore': assetstore}) if event.defaultPrevented: raise GirderException( 'The file %s could not be moved to assetstore %s' % ( file['_id'], assetstore['_id'])) # Create a new upload record into the existing file upload = self.createUploadToFile( file=file, user=user, size=int(file['size']), assetstore=assetstore) if file['size'] == 0: return File().filter(self.finalizeUpload(upload), user) # Uploads need to be chunked for some assetstores chunkSize = self._getChunkSize() chunk = None for data in File().download(file, headers=False)(): if chunk is not None: chunk += data else: chunk = data if len(chunk) >= chunkSize: upload = self.handleChunk(upload, RequestBodyStream(six.BytesIO(chunk), len(chunk))) progress.update(increment=len(chunk)) chunk = None if chunk is not None: upload = self.handleChunk(upload, RequestBodyStream(six.BytesIO(chunk), len(chunk))) progress.update(increment=len(chunk)) return upload
[docs] def list(self, limit=0, offset=0, sort=None, filters=None): """ Search for uploads or simply list all visible uploads. :param limit: Result set size limit. :param offset: Offset into the results. :param sort: The sort direction. :param filters: if not None, a dictionary that can contain ids that must match the uploads, plus an minimumAge value. """ query = {} if filters: for key in ('uploadId', 'userId', 'parentId', 'assetstoreId'): if key in filters: id = filters[key] if id and not isinstance(id, ObjectId): id = ObjectId(id) if id: if key == 'uploadId': query['_id'] = id else: query[key] = id if 'minimumAge' in filters: query['updated'] = { '$lte': datetime.datetime.utcnow() - datetime.timedelta(days=float(filters['minimumAge'])) } # Perform the find; we'll do access-based filtering of the result # set afterward. return self.find(query, limit=limit, sort=sort, offset=offset)
[docs] def cancelUpload(self, upload): """ Discard an upload that is in progress. This asks the assetstore to discard the data, then removes the item from the upload database. :param upload: The upload document to remove. :type upload: dict """ from .assetstore import Assetstore from girder.utility import assetstore_utilities assetstore = Assetstore().load(upload['assetstoreId']) # If the assetstore was deleted, the upload may still be in our # database if assetstore: adapter = assetstore_utilities.getAssetstoreAdapter(assetstore) try: adapter.cancelUpload(upload) except ValidationException: # this assetstore is currently unreachable, so skip it pass if '_id' in upload: self.remove(upload)
[docs] def untrackedUploads(self, action='list', assetstoreId=None): """ List or discard any uploads that an assetstore knows about but that our database doesn't have in it. :param action: 'delete' to discard the untracked uploads, anything else to just return with a list of them. :type action: str :param assetstoreId: if present, only include untracked items from the specified assetstore. :type assetstoreId: str :returns: a list of items that were removed or could be removed. """ from .assetstore import Assetstore from girder.utility import assetstore_utilities results = [] knownUploads = list(self.list()) # Iterate through all assetstores for assetstore in Assetstore().list(): if assetstoreId and assetstoreId != assetstore['_id']: continue adapter = assetstore_utilities.getAssetstoreAdapter(assetstore) try: results.extend(adapter.untrackedUploads( knownUploads, delete=(action == 'delete'))) except ValidationException: # this assetstore is currently unreachable, so skip it pass return results