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)
class LabelResource(Resource):
def __init__(self):
super().__init__()
self.resourceName = 'label'
self.ann_file_name = "annotation.json"
self.coll_m = Collection()
self.file_m = File()
self.folder_m = Folder()
self.item_m = Item()
self.upload_m = Upload()
self.asset_m = Assetstore()
self.setupRoutes()
def setupRoutes(self):
self.route('GET', (), handler=self.getLabelList)
self.route('GET', (':label_id',), self.getLabel)
self.route('GET', ('meta',), self.getLabelMeta)
self.route('GET', ('create',), self.createLabelFile)
self.route('GET', ('by_name',), self.getLabelByName)
self.route('POST', (), self.postLabel)
# ############# PUBLIC METHODS ##################
@access.public
@autoDescribeRoute(
Description('Get label list').param('assign_id', 'assignment folder id'))
@rest.rawResponse
@trace
def getLabelList(self, assign_id):
files = self.folder_m.fileList(assign_id, user=self.getCurrentUser(), data=False,
includeMetadata=True, mimeFilter=['application/json'])
files = list(files)
cherrypy.response.headers["Content-Type"] = "application/json"
return dumps(files)
@access.public
@autoDescribeRoute(
Description('Create a new label file inside the label folder if it doesnt exist')
.param('assign_id', 'the parent folder id')
.param('name', 'image name for which we are creating this label file'))
@rest.rawResponse
@trace
def createLabelFile(self, assign_id, name):
p_folder = self.folder_m.load(id=assign_id,
user=self.getCurrentUser(),
level=AccessType.WRITE)
label_folder = find_folder(p_folder=p_folder,
name=name,
user=self.getCurrentUser(),
desc="Label Folder",
create=True)
file = find_file(p_folder=label_folder,
name=self.ann_file_name,
user=self.getCurrentUser(),
assetstore=self.asset_m.getCurrent(),
create=False)
if not file:
file = create_new_file(p_folder=label_folder,
name=self.ann_file_name,
user=self.getCurrentUser(),
assetstore=self.asset_m.getCurrent())
config_file = self.__find_config(assign_id)
if not config_file:
printFail("No config file found")
return errorMessage("No config file found")
else:
res = copy_file(src_file=config_file,
dest_file=file,
user=self.getCurrentUser())
return dumps({
"label_id": res['fileId']
})
return dumps({
"label_id": file['_id']
})
@access.public
@autoDescribeRoute(
Description('Get labels by file_name')
.param('name', 'label file name')
.param('assign_id', 'the assignment id'))
@rest.rawResponse
@trace
def getLabelByName(self, name, assign_id):
p_folder = self.folder_m.load(assign_id,
user=self.getCurrentUser(),
level=AccessType.READ)
label_folder = find_folder(p_folder=p_folder,
name=name,
user=self.getCurrentUser(),
desc="Label Folder",
create=True)
# this file is created in <assign_folder>/<label_folder>/assignment.json
file = find_file(p_folder=label_folder,
name=self.ann_file_name,
user=self.getCurrentUser(),
assetstore=self.asset_m.getCurrent(),
create=False)
cherrypy.response.headers["Content-Type"] = "application/json"
if file:
return self.file_m.download(file)
else:
return dumps({})
@access.public
@autoDescribeRoute(
Description('Get label file by id')
.param('label_id', 'label file id'))
@rest.rawResponse
@trace
def getLabel(self, label_id):
file = self.file_m.load(label_id, level=AccessType.READ, user=self.getCurrentUser())
printOk2(file)
cherrypy.response.headers["Content-Type"] = "application/json"
return self.file_m.download(file)
@access.public
@autoDescribeRoute(
Description('Get label meta data by id')
.param('label_id', 'label file id'))
@trace
def getLabelMeta(self, label_id):
file = self.file_m.load(label_id, level=AccessType.READ, user=self.getCurrentUser())
cherrypy.response.headers["Content-Type"] = "application/json"
return dumps(file)
@access.public
@autoDescribeRoute(
Description('Post to label file by id')
.param('label_id', 'label file id')
.param('labels', 'labels to be updated'))
@rest.rawResponse
@trace
def postLabel(self, label_id, labels):
file = self.file_m.load(label_id, level=AccessType.WRITE, user=self.getCurrentUser())
cherrypy.response.headers["Content-Type"] = "application/json"
params = {'labels': json.loads(labels)}
data = json.dumps(params, indent=2, sort_keys=True)
upload = writeData(self.getCurrentUser(), file, data)
printOk2(file)
printOk(upload)
return dumps(upload)
# ############# PRIVATE METHODS ##################
def __create_new_file(self, folder, file_name):
item = self.item_m.createItem(file_name,
creator=self.getCurrentUser(),
folder=folder,
description='label file',
reuseExisting=False)
file = self.file_m.createFile(size=0,
item=item,
name=file_name,
creator=self.getCurrentUser(),
assetstore=self.asset_m.getCurrent(),
mimeType="application/json")
return file
@staticmethod
def __get_owner_id(folder):
aclList = Folder().getFullAccessList(folder)
for acl in aclList['users']:
if acl['level'] == AccessType.ADMIN:
return str(acl['id'])
return None
def __get_config_folder(self, label_folder_id):
label_folder = Folder().load(label_folder_id,
user=self.getCurrentUser(),
level=AccessType.READ)
ownerId = self.__get_owner_id(label_folder)
config_folder = self.folder_m.load(label_folder['meta'][ownerId], level=AccessType.READ,
user=self.getCurrentUser())
return config_folder
def __find_config(self, folder_id):
folder = self.__get_config_folder(folder_id)
printOk2("Config folder {}".format(folder))
files = self.folder_m.fileList(folder, self.getCurrentUser(), data=False)
for file_path, file in files:
printOk(file)
if file['name'] == "config.json":
return file
def __findFolder(self, p_folder, name, desc="", create=False):
"""
Find folder by name. If not found create the folder
:param p_folder: parent folder
:param name: name of the folder you want to find inside the parent folder
:return: folder doc
"""
folder = list(self.folder_m.find({'folderId': p_folder['_id'], 'name': name}).limit(1))
if not folder:
# check if you are allowed to create, else return nothing
if create:
folder = self.folder_m.createFolder(parent=p_folder,
name=name,
creator=self.getCurrentUser(),
description=desc,
reuseExisting=True)
else:
return None
return folder
def __findFile(self, folder, file_name):
item = list(self.item_m.find({'folderId': folder['_id'], 'name': file_name}).limit(1))
if not item:
return None
item = item[0]
file = list(self.file_m.find({'itemId': item['_id']}).limit(1))
if not file:
return None
return file[0]
class LabelResource(Resource):
def __init__(self):
super().__init__()
self.resourceName = 'label'
self.coll_m = Collection()
self.file_m = File()
self.folder_m = Folder()
self.item_m = Item()
self.upload_m = Upload()
self.asset_m = Assetstore()
self.setupRoutes()
def setupRoutes(self):
self.route('GET', (), handler=self.getLabelList)
self.route('GET', (':label_id',), self.getLabel)
self.route('GET', ('meta',), self.getLabelMeta)
self.route('GET', ('create',), self.createLabelFile)
self.route('GET', ('by_name',), self.getLabelByName)
self.route('POST', (), self.postLabel)
def createNewFile(self, folder, file_name):
item = self.item_m.createItem(file_name,
creator=self.getCurrentUser(),
folder=folder,
description='label file',
reuseExisting=False)
file = self.file_m.createFile(size=0,
item=item,
name=file_name,
creator=self.getCurrentUser(),
assetstore=self.asset_m.getCurrent(),
mimeType="application/json")
return file
def copy(self, srcFile, destFile):
upload = self.upload_m.createUploadToFile(destFile, self.getCurrentUser(), srcFile['size'])
self.upload_m.handleChunk(upload=upload,
chunk=RequestBodyStream(self.file_m.open(srcFile), size=destFile['size']),
user=self.getCurrentUser())
return upload
@access.public
@autoDescribeRoute(
Description('Get label list'))
@rest.rawResponse
def getLabelList(self):
printOk('getLabelsList() was called!')
try:
collection = list(self.coll_m.list(user=self.getCurrentUser(), offset=0, limit=1))[0]
files = self.coll_m.fileList(collection, user=self.getCurrentUser(), data=False,
includeMetadata=True, mimeFilter=['application/json'])
files = list(files)
cherrypy.response.headers["Content-Type"] = "application/json"
return dumps(files)
except:
printFail(traceback.print_exc)
@staticmethod
def getOwnerId(folder):
aclList = Folder().getFullAccessList(folder)
for acl in aclList['users']:
if acl['level'] == AccessType.ADMIN:
return str(acl['id'])
return None
def getConfigFolder(self, label_folder_id):
label_folder = Folder().load(label_folder_id,
user=self.getCurrentUser(),
level=AccessType.READ)
ownerId = self.getOwnerId(label_folder)
config_folder = self.folder_m.load(label_folder['meta'][ownerId], level=AccessType.READ,
user=self.getCurrentUser())
return config_folder
def findConfig(self, folder_id):
folder = self.getConfigFolder(folder_id)
printOk2("Config folder {}".format(folder))
files = self.folder_m.fileList(folder, self.getCurrentUser(), data=False)
for file_path, file in files:
printOk(file)
if file['name'] == "config.json":
return file
def __findFile(self, folder, file_name):
item = list(self.item_m.find({'folderId': folder['_id'], 'name': file_name}).limit(1))
if not item:
return None
item = item[0]
file = list(self.file_m.find({'itemId': item['_id']}).limit(1))
if not file:
return None
return file[0]
@access.public
@autoDescribeRoute(
Description('Create a new label file if it doesnt exist')
.param('file_name', 'label file name').param('folder_id', 'the parent folder id'))
@rest.rawResponse
def createLabelFile(self, file_name, folder_id):
try:
folder = self.folder_m.load(folder_id, user=self.getCurrentUser(), level=AccessType.WRITE)
file = self.__findFile(folder, file_name)
if not file:
file = self.createNewFile(folder, file_name)
config_file = self.findConfig(folder_id)
if not config_file:
printFail("No config file found")
return errorMessage("No config file found")
else:
res = self.copy(config_file, file)
return dumps({
"label_id": res['fileId']
})
return dumps({
"label_id": file['_id']
})
except:
printFail(traceback.print_exc)
cherrypy.response.status = 500
@access.public
@autoDescribeRoute(
Description('Get labels by file_name')
.param('file_name', 'label file name').param('folder_id', 'the parent folder id'))
@rest.rawResponse
def getLabelByName(self, file_name, folder_id):
try:
folder = self.folder_m.load(folder_id, user=self.getCurrentUser(), level=AccessType.READ)
file = self.__findFile(folder, file_name)
cherrypy.response.headers["Content-Type"] = "application/json"
if file:
return self.file_m.download(file)
else:
return dumps({})
except:
printFail(traceback.print_exc)
cherrypy.response.status = 500
@access.public
@autoDescribeRoute(
Description('Get label by id')
.param('label_id', 'label file id'))
@rest.rawResponse
def getLabel(self, label_id):
try:
file = self.file_m.load(label_id, level=AccessType.READ, user=self.getCurrentUser())
printOk2(file)
cherrypy.response.headers["Content-Type"] = "application/json"
return self.file_m.download(file)
except:
# Unknown slug
printFail(traceback.print_exc)
cherrypy.response.status = 404
@access.public
@autoDescribeRoute(
Description('Get label by id')
.param('label_id', 'label file id'))
def getLabelMeta(self, label_id):
try:
file = self.file_m.load(label_id, level=AccessType.READ, user=self.getCurrentUser())
cherrypy.response.headers["Content-Type"] = "application/json"
return dumps(file)
except:
# Unknown slug
printFail(traceback.print_exc)
cherrypy.response.status = 404
@access.public
@autoDescribeRoute(
Description('Post label by id')
.param('label_id', 'label file id'))
@rest.rawResponse
def postLabel(self, label_id, params):
try:
file = self.file_m.load(label_id, level=AccessType.WRITE, user=self.getCurrentUser())
cherrypy.response.headers["Content-Type"] = "application/json"
params['labels'] = json.loads(params['labels'])
data = json.dumps(params, indent=2, sort_keys=True)
upload = writeData(self.getCurrentUser(), file, data)
printOk2(file)
printOk(upload)
return dumps(upload)
except:
# Unknown slug
printFail(traceback.print_exc)
cherrypy.response.status = 404
@access.public
@autoDescribeRoute(
Description('Post label by id')
.param('label_id', 'label file id'))
@rest.rawResponse
def strokeToOutline(self, strokes):
pass
