def fetch_image(self, id):
dataset = DatasetModel().load(id,
user=self.getCurrentUser(),
level=AccessType.READ)
if 'imageFileId' in dataset:
file_model = File()
file = file_model.load(dataset['imageFileId'], force=True)
return File().download(file, contentDisposition='inline')
return None
def removeThumbnails(event):
"""
When a resource containing thumbnails is about to be deleted, we delete
all of the thumbnails that are attached to it.
"""
thumbs = event.info.get('_thumbnails', ())
fileModel = File()
for fileId in thumbs:
file = fileModel.load(fileId, force=True)
if file:
fileModel.remove(file)
def removeThumbnails(event):
"""
When a resource containing thumbnails is about to be deleted, we delete
all of the thumbnails that are attached to it.
"""
thumbs = event.info.get('_thumbnails', ())
fileModel = File()
for fileId in thumbs:
file = fileModel.load(fileId, force=True)
if file:
fileModel.remove(file)
def fetch_reconstruction(self, id, reconstruction, format,
contentDisposition):
supported_formats = ['emd', 'tiff']
if format not in supported_formats:
raise RestException('"%s" is not a supported format.')
file_model = File()
emd_file = file_model.load(reconstruction['emdFileId'], force=True)
if format == 'emd':
return File().download(emd_file,
contentDisposition=contentDisposition)
elif format == 'tiff':
self._set_content_disposition('%s.tiff' % emd_file['name'],
contentDisposition, 'image/tiff')
return self._to_tiff(reconstruction['emdFileId'])
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]
def createThumbnail(width, height, crop, fileId, attachToType, attachToId):
"""
Creates the thumbnail. Validation and access control must be done prior
to the invocation of this method.
"""
fileModel = File()
file = fileModel.load(fileId, force=True)
streamFn = functools.partial(fileModel.download, file, headers=False)
event = events.trigger('thumbnails.create',
info={
'file': file,
'width': width,
'height': height,
'crop': crop,
'attachToType': attachToType,
'attachToId': attachToId,
'streamFn': streamFn
})
if len(event.responses):
resp = event.responses[-1]
newFile = resp['file']
if event.defaultPrevented:
if resp.get('attach', True):
newFile = attachThumbnail(file, newFile, attachToType,
attachToId, width, height)
return newFile
else:
file = newFile
streamFn = functools.partial(fileModel.download,
file,
headers=False)
if 'assetstoreId' not in file:
# TODO we could thumbnail link files if we really wanted.
raise Exception('File %s has no assetstore.' % fileId)
stream = streamFn()
data = b''.join(stream())
image = _getImage(file['mimeType'], file['exts'], data)
if not width:
width = int(height * image.size[0] / image.size[1])
elif not height:
height = int(width * image.size[1] / image.size[0])
elif crop:
x1 = y1 = 0
x2, y2 = image.size
wr = float(image.size[0]) / width
hr = float(image.size[1]) / height
if hr > wr:
y1 = int(y2 / 2 - height * wr / 2)
y2 = int(y2 / 2 + height * wr / 2)
else:
x1 = int(x2 / 2 - width * hr / 2)
x2 = int(x2 / 2 + width * hr / 2)
image = image.crop((x1, y1, x2, y2))
image.thumbnail((width, height), Image.ANTIALIAS)
out = six.BytesIO()
image.convert('RGB').save(out, 'JPEG', quality=85)
size = out.tell()
out.seek(0)
thumbnail = Upload().uploadFromFile(out,
size=size,
name='_thumb.jpg',
parentType=attachToType,
parent={'_id': ObjectId(attachToId)},
user=None,
mimeType='image/jpeg',
attachParent=True)
return attachThumbnail(file, thumbnail, attachToType, attachToId, width,
height)
def createThumbnail(width, height, crop, fileId, attachToType, attachToId):
"""
Creates the thumbnail. Validation and access control must be done prior
to the invocation of this method.
"""
fileModel = File()
file = fileModel.load(fileId, force=True)
streamFn = functools.partial(fileModel.download, file, headers=False)
event = events.trigger('thumbnails.create', info={
'file': file,
'width': width,
'height': height,
'crop': crop,
'attachToType': attachToType,
'attachToId': attachToId,
'streamFn': streamFn
})
if len(event.responses):
resp = event.responses[-1]
newFile = resp['file']
if event.defaultPrevented:
if resp.get('attach', True):
newFile = attachThumbnail(file, newFile, attachToType, attachToId, width, height)
return newFile
else:
file = newFile
streamFn = functools.partial(
fileModel.download, file, headers=False)
if 'assetstoreId' not in file:
# TODO we could thumbnail link files if we really wanted.
raise Exception('File %s has no assetstore.' % fileId)
stream = streamFn()
data = b''.join(stream())
image = _getImage(file['mimeType'], file['exts'], data)
if not width:
width = int(height * image.size[0] / image.size[1])
elif not height:
height = int(width * image.size[1] / image.size[0])
elif crop:
x1 = y1 = 0
x2, y2 = image.size
wr = float(image.size[0]) / width
hr = float(image.size[1]) / height
if hr > wr:
y1 = int(y2 / 2 - height * wr / 2)
y2 = int(y2 / 2 + height * wr / 2)
else:
x1 = int(x2 / 2 - width * hr / 2)
x2 = int(x2 / 2 + width * hr / 2)
image = image.crop((x1, y1, x2, y2))
image.thumbnail((width, height), Image.ANTIALIAS)
out = six.BytesIO()
image.convert('RGB').save(out, 'JPEG', quality=85)
size = out.tell()
out.seek(0)
thumbnail = Upload().uploadFromFile(
out, size=size, name='_thumb.jpg', parentType=attachToType,
parent={'_id': ObjectId(attachToId)}, user=None, mimeType='image/jpeg',
attachParent=True)
return attachThumbnail(file, thumbnail, attachToType, attachToId, width, height)
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
