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 profile'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)
"""
from girderformindlogger.models.item import Item
itemModel = Item()
if subpath:
path = os.path.join(path, doc['name'])
metadataFile = 'girder-folder-metadata.json'
# Eagerly evaluate this list, as the MongoDB cursor can time out on long requests
childFolders = list(
self.childFolders(parentType='profile',
parent=doc,
user=user,
fields=['name'] +
(['meta'] if includeMetadata else [])))
for sub in childFolders:
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)
# Eagerly evaluate this list, as the MongoDB cursor can time out on long requests
childItems = list(
self.childItems(folder=doc,
fields=['name'] +
(['meta'] if includeMetadata else [])))
for item in childItems:
if item['name'] == metadataFile:
metadataFile = None
for (filepath, file) in itemModel.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)
class Item(Resource):
def __init__(self):
super(Item, self).__init__()
self.resourceName = 'item'
self._model = ItemModel()
self.route('DELETE', (':id', ), self.deleteItem)
self.route('GET', (), self.find)
self.route('GET', (':id', ), self.getItem)
self.route('GET', (':id', 'files'), self.getFiles)
self.route('GET', (':id', 'download'), self.download)
self.route('GET', (':id', 'rootpath'), self.rootpath)
self.route('POST', (), self.createItem)
self.route('PUT', (':id', ), self.updateItem)
self.route('POST', (':id', 'copy'), self.copyItem)
self.route('PUT', (':id', 'metadata'), self.setMetadata)
self.route('DELETE', (':id', 'metadata'), self.deleteMetadata)
self.route('PUT', ('templates', ), self.upsertTemplates)
self.route('GET', ('templates', ), self.getTemplates)
@access.user(scope=TokenScope.DATA_WRITE)
@autoDescribeRoute(
Description('Insert/Update template.').notes(
'This endpoint will be used for inserting/updating template for item data for existing account'
).jsonParam('templateInfo',
'template data',
paramType='form',
required=False).errorResponse(
'Write access was denied to the account.', 403))
def upsertTemplates(self, templateInfo):
from girderformindlogger.utility import jsonld_expander
thisUser = self.getCurrentUser()
profile = self.getAccountProfile()
if not profile or (
thisUser['accountId'] != profile['accountId']
and not len(profile.get('applets', {}).get('editor', []))):
raise AccessException(
'You don\'t have enough permission to update template on this account'
)
templateFolder = Folder().findOne({
'accountId': profile['accountId'],
'meta.contentType': 'templates'
})
if not templateFolder:
owner = User().findOne({'accountId': profile['accountId']})
templateFolder = User().createTemplatesFolder(owner)
templates = templateInfo.get('templates', [])
for template in templates:
expanded = jsonld_expander._fixUpFormat(
jsonld_expander.expandObj(templateInfo.get('contexts', {}),
template))
prefName = self._model.preferredName(expanded)
prefName = '{} template'.format(
'item' if not prefName else prefName)
item = None
if '_id' in template:
try:
item = self._model.load(template['_id'], force=True)
except Exception as e:
print('wrong item id', template['_id'])
if not item:
item = self._model.createItem(name=prefName,
creator=thisUser,
folder=templateFolder,
reuseExisting=False)
expanded['_id'] = item['_id']
item['content'] = json_util.dumps(expanded)
self._model.save(item)
deleted = templateInfo.get('removed', [])
self._model.removeWithQuery(
{'_id': {
'$in': [ObjectId(itemId) for itemId in deleted]
}})
templates = list(self._model.find({'folderId': templateFolder['_id']}))
return [json_util.loads(template['content']) for template in templates]
@access.user(scope=TokenScope.DATA_READ)
@autoDescribeRoute(
Description('Insert/Update template.').notes(
'This endpoint will be used for inserting/updating template for item data for existing account'
).errorResponse('Write access was denied to the account.', 403))
def getTemplates(self):
from girderformindlogger.utility import jsonld_expander
thisUser = self.getCurrentUser()
profile = self.getAccountProfile()
if not profile or (
thisUser['accountId'] != profile['accountId']
and not len(profile.get('applets', {}).get('editor', []))):
raise AccessException(
'You don\'t have enough permission to update template on this account'
)
templateFolder = Folder().findOne({
'accountId': profile['accountId'],
'meta.contentType': 'templates'
})
if not templateFolder:
return []
templates = list(self._model.find({'folderId': templateFolder['_id']}))
return [json_util.loads(template['content']) for template in templates]
@access.public(scope=TokenScope.DATA_READ)
@filtermodel(model=ItemModel)
@autoDescribeRoute(
Description('List or search for items.').notes(
'You must pass either a "itemId" or "text" field '
'to specify how you are searching for items. '
'If you omit one of these parameters the request will fail and respond : '
'"Invalid search mode."').responseClass('Item', array=True).param(
'folderId',
'Pass this to list all items in a folder.',
required=False).param(
'text',
'Pass this to perform a full text search for items.',
required=False).param(
'name',
'Pass to lookup an item by exact name match. Must '
'pass folderId as well when using this.',
required=False).pagingParams(defaultSort='lowerName').
errorResponse().errorResponse(
'Read access was denied on the parent folder.', 403))
def find(self, folderId, text, name, limit, offset, sort):
"""
Get a list of items with given search parameters. Currently accepted
search modes are:
1. Searching by folderId, with optional additional filtering by the name
field (exact match) or using full text search within a single parent
folder. Pass a "name" parameter or "text" parameter to invoke these
additional filters.
2. Searching with full text search across all items in the system.
Simply pass a "text" parameter for this mode.
"""
user = self.getCurrentUser()
if folderId:
folder = Folder().load(id=folderId,
user=user,
level=AccessType.READ,
exc=True)
filters = {}
if text:
filters['$text'] = {'$search': text}
if name:
filters['name'] = name
return Folder().childItems(folder=folder,
limit=limit,
offset=offset,
sort=sort,
filters=filters)
elif text is not None:
return self._model.textSearch(text,
user=user,
limit=limit,
offset=offset,
sort=sort)
else:
raise RestException('Invalid search mode.')
@access.public(scope=TokenScope.DATA_READ)
@filtermodel(model=ItemModel)
@autoDescribeRoute(
Description('Get an item by ID.').responseClass('Item').modelParam(
'id', model=ItemModel, level=AccessType.READ).errorResponse(
'ID was invalid.').errorResponse(
'Read access was denied for the item.', 403))
def getItem(self, item):
return item
@access.user(scope=TokenScope.DATA_WRITE)
@filtermodel(model=ItemModel)
@autoDescribeRoute(
Description('Create a new item.').responseClass('Item').modelParam(
'folderId',
'The ID of the parent folder.',
model=Folder,
level=AccessType.WRITE,
paramType='query').param('name', 'Name for the item.', strip=True).
param('description',
'Description for the item.',
required=False,
default='',
strip=True).param(
'reuseExisting',
'Return existing item (by name) if it exists.',
required=False,
dataType='boolean',
default=False).jsonParam(
'metadata',
'A JSON object containing the metadata keys to add',
paramType='form',
requireObject=True,
required=False).errorResponse().errorResponse(
'Write access was denied on the parent folder.',
403))
def createItem(self, folder, name, description, reuseExisting, metadata):
newItem = self._model.createItem(folder=folder,
name=name,
creator=self.getCurrentUser(),
description=description,
reuseExisting=reuseExisting)
if metadata:
newItem = self._model.setMetadata(newItem, metadata)
return newItem
@access.user(scope=TokenScope.DATA_WRITE)
@filtermodel(model=ItemModel)
@autoDescribeRoute(
Description('Edit an item or move it to another folder.'
).responseClass('Item').modelParam(
'id', model=ItemModel, level=AccessType.WRITE).param(
'name',
'Name for the item.',
required=False,
strip=True).param('description',
'Description for the item.',
required=False).
modelParam(
'folderId',
'Pass this to move the item to a new folder.',
model=Folder,
required=False,
paramType='query',
level=AccessType.WRITE).jsonParam(
'metadata',
'A JSON object containing the metadata keys to add',
paramType='form',
requireObject=True,
required=False).errorResponse('ID was invalid.').errorResponse(
'Write access was denied for the item or folder.', 403))
def updateItem(self, item, name, description, folder, metadata):
if name is not None:
item['name'] = name
if description is not None:
item['description'] = description
self._model.updateItem(item)
if folder and folder['_id'] != item['folderId']:
self._model.move(item, folder)
if metadata:
item = self._model.setMetadata(item, metadata)
return item
@access.user(scope=TokenScope.DATA_WRITE)
@filtermodel(model=ItemModel)
@autoDescribeRoute(
Description('Set metadata fields on an item.').responseClass('Item').
notes(
'Set metadata fields to null in order to delete them.').modelParam(
'id', model=ItemModel, level=AccessType.WRITE).jsonParam(
'metadata',
'A JSON object containing the metadata keys to add',
paramType='body',
requireObject=True).param(
'allowNull',
'Whether "null" is allowed as a metadata value.',
required=False,
dataType='boolean',
default=False).errorResponse(
('ID was invalid.',
'Invalid JSON passed in request body.',
'Metadata key name was invalid.')).errorResponse(
'Write access was denied for the item.', 403))
def setMetadata(self, item, metadata, allowNull):
return self._model.setMetadata(item, metadata, allowNull=allowNull)
@access.user(scope=TokenScope.DATA_WRITE)
@filtermodel(ItemModel)
@autoDescribeRoute(
Description('Delete metadata fields on an item.').responseClass(
'Item').modelParam(
'id', model=ItemModel, level=AccessType.WRITE).jsonParam(
'fields',
'A JSON list containing the metadata fields to delete',
paramType='body',
schema={
'type': 'array',
'items': {
'type': 'string'
}
}).errorResponse(
('ID was invalid.',
'Invalid JSON passed in request body.',
'Metadata key name was invalid.')).errorResponse(
'Write access was denied for the item.', 403))
def deleteMetadata(self, item, fields):
return self._model.deleteMetadata(item, fields)
def _downloadMultifileItem(self, item, user):
setResponseHeader('Content-Type', 'application/zip')
setContentDisposition(item['name'] + '.zip')
def stream():
zip = ziputil.ZipGenerator(item['name'])
for (path, file) in self._model.fileList(item, subpath=False):
for data in zip.addFile(file, path):
yield data
yield zip.footer()
return stream
@access.public(scope=TokenScope.DATA_READ)
@filtermodel(model=File)
@autoDescribeRoute(
Description('Get the files within an item.').responseClass('File',
array=True).
modelParam('id', model=ItemModel, level=AccessType.READ).pagingParams(
defaultSort='name').errorResponse('ID was invalid.').errorResponse(
'Read access was denied for the item.', 403))
def getFiles(self, item, limit, offset, sort):
return self._model.childFiles(item=item,
limit=limit,
offset=offset,
sort=sort)
@access.public(scope=TokenScope.DATA_READ, cookie=True)
@autoDescribeRoute(
Description('Download the contents of an item.').modelParam(
'id', model=ItemModel, level=AccessType.READ).param(
'offset',
'Byte offset into the file.',
dataType='int',
required=False,
default=0).param(
'format',
'If unspecified, items with one file are downloaded '
'as that file, and other items are downloaded as a zip '
"archive. If 'zip', a zip archive is always sent.",
required=False).
param('contentDisposition', 'Specify the Content-Disposition response '
'header disposition-type value, only applied for single file '
'items.',
required=False,
enum=['inline', 'attachment'],
default='attachment').param(
'extraParameters', 'Arbitrary data to send along with the '
'download request, only applied for single file '
'items.',
required=False)
# single file items could produce other types, too.
.produces(['application/zip', 'application/octet-stream'
]).errorResponse('ID was invalid.').errorResponse(
'Read access was denied for the item.', 403))
def download(self, item, offset, format, contentDisposition,
extraParameters):
user = self.getCurrentUser()
files = list(self._model.childFiles(item=item, limit=2))
if format not in (None, '', 'zip'):
raise RestException('Unsupported format: %s.' % format)
if len(files) == 1 and format != 'zip':
if contentDisposition not in {None, 'inline', 'attachment'}:
raise RestException('Unallowed contentDisposition type "%s".' %
contentDisposition)
return File().download(files[0],
offset,
contentDisposition=contentDisposition,
extraParameters=extraParameters)
else:
return self._downloadMultifileItem(item, user)
@access.user(scope=TokenScope.DATA_WRITE)
@autoDescribeRoute(
Description('Delete an item by ID.').modelParam(
'id', model=ItemModel, level=AccessType.WRITE).errorResponse(
'ID was invalid.').errorResponse(
'Write access was denied for the item.', 403))
def deleteItem(self, item):
self._model.remove(item)
return {'message': 'Deleted item %s.' % item['name']}
@access.public(scope=TokenScope.DATA_READ)
@autoDescribeRoute(
Description(
"Get the path to the root of the item's hierarchy.").modelParam(
'id', model=ItemModel, level=AccessType.READ).errorResponse(
'ID was invalid.').errorResponse(
'Read access was denied for the item.', 403))
def rootpath(self, item):
return self._model.parentsToRoot(item, self.getCurrentUser())
@access.user(scope=TokenScope.DATA_WRITE)
@filtermodel(model=ItemModel)
@autoDescribeRoute(
Description('Copy an item.').notes(
'If no folderId parameter is specified, creates a copy of the item in '
'its current containing folder.').responseClass('Item').modelParam(
'id',
'The ID of the original item.',
model=ItemModel,
level=AccessType.READ).modelParam(
'folderId',
'The ID of the parent folder.',
required=False,
model=Folder,
level=AccessType.WRITE,
paramType='query').param('name',
'Name for the new item.',
required=False,
strip=True).
param('description',
'Description for the new item.',
required=False,
strip=True).errorResponse(
('A parameter was invalid.',
'ID was invalid.')).errorResponse(
'Read access was denied on the original item.\n\n'
'Write access was denied on the parent folder.', 403))
def copyItem(self, item, folder, name, description):
user = self.getCurrentUser()
if folder is None:
folder = Folder().load(id=item['folderId'],
user=user,
level=AccessType.WRITE,
exc=True)
return self._model.copyItem(item,
creator=user,
name=name,
folder=folder,
description=description)