def importDocument(self, doc, **kwargs):
"""Promote a Girder core document to a TCGA model."""
self.setTCGA(doc)
self.save(doc)
if doc.get('_modelType') == 'item':
fileModel = File()
files = Item().childFiles(doc)
for file in files:
if self.setMimeType(file):
fileModel.save(file)
return doc
def importDocument(self, doc, image, **kwargs):
"""Promote the item document to an aperio type."""
tag = kwargs.get('tag')
meta = doc.setdefault('aperio', {})
meta['image'] = image['_id']
self.setTag(doc, tag)
fileModel = File()
files = Item().childFiles(doc)
for file in files:
if TCGAModel.setMimeType(file):
fileModel.save(file)
return doc
class HdfsAssetstoreResource(Resource):
def __init__(self):
super(HdfsAssetstoreResource, self).__init__()
self.resourceName = 'hdfs_assetstore'
self.route('PUT', (':id', 'import'), self.importData)
self.folderModel = Folder() # Save to avoid many lookups
self.itemModel = Item()
self.fileModel = File()
def _importFile(self, parent, name, user, assetstore, node):
item = self.itemModel.findOne({
'folderId': parent['_id'],
'name': name
})
if item is None:
item = self.itemModel.createItem(
name=name, creator=user, folder=parent)
file = self.fileModel.findOne({
'name': name,
'itemId': item['_id']
})
if file is None:
file = self.fileModel.createFile(
creator=user, item=item, name=name, size=node['length'],
assetstore=assetstore, mimeType=None, saveFile=False)
file['hdfs'] = {
'imported': True,
'path': node['path']
}
self.fileModel.save(file)
def _importData(self, parentType, parent, assetstore, client, path, ctx,
user):
for node in client.ls([path]):
ctx.update(message='Importing ' + node['path'])
name = posixpath.basename(node['path'])
if node['file_type'] == 'd':
folder = self.folderModel.findOne({
'parentId': parent['_id'],
'name': name,
'parentCollection': parentType
})
if folder is None:
folder = self.folderModel.createFolder(
parent, name, parentType=parentType, creator=user)
self._importData('folder', folder, assetstore, client,
node['path'], ctx, user)
elif node['file_type'] == 'f' and parentType == 'folder':
self._importFile(parent, name, user, assetstore, node)
@access.admin
@loadmodel(model='assetstore')
@describeRoute(
Description('Import a data hierarchy from an HDFS instance.')
.notes('Only site administrators may use this endpoint.')
.param('id', 'The ID of the assetstore representing the HDFS instance.',
paramType='path')
.param('parentId', 'The ID of the parent object in the Girder data '
'hierarchy under which to import the files.')
.param('parentType', 'The type of the parent object to import into.',
enum=('folder', 'user', 'collection'), required=False)
.param('path', 'Root of the directory structure (relative to the root '
'of the HDFS) to import.')
.param('progress', 'Whether to record progress on this operation ('
'default=False)', required=False, dataType='boolean')
.errorResponse()
.errorResponse('You are not an administrator.', 403)
)
def importData(self, assetstore, params):
self.requireParams(('parentId', 'path'), params)
user = self.getCurrentUser()
parentType = params.get('parentType', 'folder')
if parentType not in ('user', 'collection', 'folder'):
raise RestException('Invalid parentType.')
parent = self.model(parentType).load(params['parentId'], force=True, exc=True)
progress = self.boolParam('progress', params, default=False)
client = HdfsClient(
host=assetstore['hdfs']['host'], port=assetstore['hdfs']['port'], use_trash=False)
path = params['path']
with ProgressContext(progress, user=user, title='Importing data from HDFS') as ctx:
try:
self._importData(parentType, parent, assetstore, client, path, ctx, user)
except FileNotFoundException:
raise RestException('File not found: %s.' % path)
