def put(self, id, file_set_id):
parser = reqparse.RequestParser()
parser.add_argument('name', type=str, required=True, location='json')
args = parser.parse_args()
# Retrieve repository
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
# Retrieve file set and check it belongs to repository
file_set_dao = FileSetDao(self.db_session())
file_set = file_set_dao.retrieve(id=file_set_id)
if file_set is None:
return self.error_response('File set {} not found'.format(file_set_id), http.NOT_FOUND_404)
if file_set.repository != repository:
return self.error_response('File set {} not in repository {}'.format(file_set_id, id), http.BAD_REQUEST_400)
# Update file set
file_set.name = args['name']
file_set_dao.save(file_set)
return self.response(file_set.to_dict())
def delete(self, id, file_id):
# Retrieve repository
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
# Retrieve file from database and then delete it
f_dao = FileDao(self.db_session())
f = f_dao.retrieve(id=file_id)
if f is None:
return self.error_response('File {} not found'.format(file_id), http.NOT_FOUND_404)
if f.repository != repository:
return self.error_response('File {} not in repository {}'.format(file_id, id), http.BAD_REQUEST_400)
# Delete physical file on file server. This requires we get the storage ID of the
# file and append it to the STORAGE_ROOT_DIR environment variable. This variable
# must exist! It allows us to test locally. In a full Docker environment it will
# most likely point to /mnt/shared/files whereas in a local development environment
# it will point to a /files somewhere inside this project
path = os.path.join(os.getenv('STORAGE_ROOT_DIR'), f.storage_id)
path_shactx = path + '.shactx'
try:
os.remove(path)
os.remove(path_shactx)
f_dao.delete(f)
except IOError:
return self.error_response(
'File {} at path {} could not be deleted'.format(file_id, path), http.INTERNAL_SERVER_ERROR_500)
return self.response({}, http.NO_CONTENT_204)
def delete(self, id, file_set_id, file_id):
# Retrieve repository
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
# Get file set and check its part of repository
file_set_dao = FileSetDao(self.db_session())
file_set = file_set_dao.retrieve(id=file_set_id)
if file_set is None:
return self.error_response('File set {} not found'.format(file_set_id), http.NOT_FOUND_404)
# Get file and check it's also part of repository
f_dao = FileDao(self.db_session())
f = f_dao.retrieve(id=file_id)
if f is None:
return self.error_response('File {} not found'.format(file_id), http.NOT_FOUND_404)
if f.repository != repository:
return self.error_response('File {} not in repository {}'.format(file_id, id), http.BAD_REQUEST_400)
# Remove file from file set
if f in file_set.files:
file_set.remove(f)
file_set_dao.save(file_set)
return self.response(file_set.to_dict())
def get(self, id):
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
return self.response(repository.to_dict())
def post(self):
parser = reqparse.RequestParser()
parser.add_argument('name', type=str, required=True, location='json')
args = parser.parse_args()
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.create(**args)
return self.response(repository.to_dict(), http.CREATED_201)
def post(self):
r = request
# These arguments are posted by nginx-big-upload as form encoded data
parser = reqparse.RequestParser()
parser.add_argument('id', type=str, location='form')
parser.add_argument('path', type=str, location='form')
parser.add_argument('name', type=str, location='form')
parser.add_argument('size', type=int, location='form')
# These arguments have to be passed in the headers, otherwise it won't work
parser.add_argument('X-File-Type', type=int, location='headers')
parser.add_argument('X-Scan-Type', type=int, location='headers')
parser.add_argument('X-Repository-ID', type=int, location='headers')
parser.add_argument('Content-Type', type=str, location='headers')
args = parser.parse_args()
# Retrieve file type
file_type_dao = FileTypeDao(self.db_session())
file_type = file_type_dao.retrieve(id=args['X-File-Type'])
if file_type is None:
return self.error_response('File type {} not found'.format(args['X-File-Type']), http.NOT_FOUND_404)
# Retrieve scan type
scan_type_dao = ScanTypeDao(self.db_session())
scan_type = scan_type_dao.retrieve(id=args['X-Scan-Type'])
if scan_type is None:
return self.error_response('Scan type {} not found'.format(args['X-Scan-Type']), http.NOT_FOUND_404)
# Retrieve repository for this file
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=args['X-Repository-ID'])
if repository is None:
return self.error_response('Repository {} not found'.format(args['X-Repository-ID']), http.NOT_FOUND_404)
# Set content type to something generic if it was not specified
if args['Content-Type'] is None:
args['Content-Type'] = 'application/octet-stream'
# Strip file name from any path-related info
name = os.path.basename(args['name'])
# Create media link for downloading the file. The link should refer to the UI_SERVICE
# IP address because it will be used by clients.
media_link = '{}/{}'.format(self.config()['DOWNLOAD_URI'], args['id'])
# Create the file and return its dictionary info
f_dao = FileDao(self.db_session())
f = f_dao.create(
name=name, file_type=file_type, scan_type=scan_type, content_type=args['Content-Type'],
size=args['size'], storage_id=args['id'], storage_path=args['path'],
media_link=media_link, repository=repository)
return self.response(f.to_dict(), http.CREATED_201)
def get(self):
parser = reqparse.RequestParser()
parser.add_argument('name', type=str, location='args')
args = parser.parse_args()
repository_dao = RepositoryDao(self.db_session())
repositories = repository_dao.retrieve_all(**args)
result = [repository.to_dict() for repository in repositories]
return self.response(result)
def get(self, id):
# Retrieve repository
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
# Retrieve files in given repository
result = [f.to_dict() for f in repository.files]
return self.response(result)
def put(self, id):
parser = reqparse.RequestParser()
parser.add_argument('name', type=str, required=True, location='json')
args = parser.parse_args()
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
repository.name = args['name']
repository_dao.save(repository)
return self.response(repository.to_dict())
def get(self, id):
# Get optional 'name' parameter if client is searching specific file set.
parser = reqparse.RequestParser()
parser.add_argument('name', type=str, location='args')
args = parser.parse_args()
# Retrieve repository
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
# Retrieve file sets in given repository
result = [file_set.to_dict() for file_set in repository.file_sets]
return self.response(result)
def get(self, id, file_set_id):
# Retrieve repository
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
# Retrieve file set and check it's a member of repository
file_set_dao = FileSetDao(self.db_session())
file_set = file_set_dao.retrieve(id=file_set_id)
if file_set is None:
return self.error_response('File set {} not found'.format(id), http.NOT_FOUND_404)
if file_set.repository != repository:
return self.error_response('File set {} not in repository {}'.format(file_set_id, id), http.BAD_REQUEST_400)
return self.response(file_set.to_dict())
def init_tables():
# Create pre-defined file types
file_type_dao = FileTypeDao(db.session)
for name in FileType.ALL:
file_type = file_type_dao.retrieve(name=name)
if file_type is None:
file_type_dao.create(name=name)
# Create pre-defined scan types
scan_type_dao = ScanTypeDao(db.session)
for name in ScanType.ALL:
scan_type = scan_type_dao.retrieve(name=name)
if scan_type is None:
scan_type_dao.create(name=name)
# Create default repository
repository_dao = RepositoryDao(db.session)
repository = repository_dao.retrieve(name='default')
if repository is None:
repository_dao.create(name='default')
def get(self, id, file_id):
# Retrieve repository
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
# Retrieve file meta data from the database
f_dao = FileDao(self.db_session())
f = f_dao.retrieve(id=file_id)
if f is None:
return self.error_response('File {} not found'.format(file_id), http.NOT_FOUND_404)
if f.repository != repository:
return self.error_response('File {} not in repository {}'.format(file_id, id), http.BAD_REQUEST_400)
# Return file meta information
return self.response(f.to_dict())
def post(self):
parser = reqparse.RequestParser()
parser.add_argument('name', type=str, required=True, location='json')
args = parser.parse_args()
# Retrieve repository
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
args['repository'] = repository
# Create file set
file_set_dao = FileSetDao(self.db_session())
file_set = file_set_dao.create(**args)
return self.response(file_set.to_dict(), http.CREATED_201)
def delete(self, id):
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
# Check if repository has files. If not, return an error
if len(repository.files) > 0:
return self.error_response('Repository {} not empty'.format(id), http.FORBIDDEN_403)
# Check if repository has file sets. If so, return an error
if len(repository.file_sets) > 0:
return self.error_response('Repository {} not empty'.format(id), http.FORBIDDEN_403)
# Delete repository
repository_dao.delete(repository)
return self.response({}, http.NO_CONTENT_204)
def delete(self, id, file_set_id):
# Retrieve repository
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
# Retrieve file set and check it belongs to repository
file_set_dao = FileSetDao(self.db_session())
file_set = file_set_dao.retrieve(id=file_set_id)
if file_set is None:
return self.error_response('File set {} not found'.format(file_set_id), http.NOT_FOUND_404)
if file_set.repository != repository:
return self.error_response('File set {} not in repository {}'.format(file_set_id, id), http.BAD_REQUEST_400)
# Delete file set
file_set_dao.delete(file_set)
return self.response({}, http.NO_CONTENT_204)
def put(self, id, file_set_id, file_id):
# Retrieve repository
repository_dao = RepositoryDao(self.db_session())
repository = repository_dao.retrieve(id=id)
if repository is None:
return self.error_response('Repository {} not found'.format(id), http.NOT_FOUND_404)
# Get file set and check its part of repository
file_set_dao = FileSetDao(self.db_session())
file_set = file_set_dao.retrieve(id=file_set_id)
if file_set is None:
return self.error_response('File set {} not found'.format(file_set_id), http.NOT_FOUND_404)
if file_set.repository != repository:
return self.error_response('File set {} not in repository {}'.format(file_set_id, id), http.BAD_REQUEST_400)
# Get file and check it's also part of repository
f_dao = FileDao(self.db_session())
f = f_dao.retrieve(id=file_id)
if f is None:
return self.error_response('File {} not found'.format(file_id), http.NOT_FOUND_404)
if f.repository != repository:
return self.error_response('File {} not in repository {}'.format(file_id, id), http.BAD_REQUEST_400)
# Add file to file set
if f not in file_set.files:
# Verify that given file complies with file set schema. This requires that
# schema validation is enabled on the file set. The schema specification
# specifies which additional arguments should be provided for each file, e.g.,
# subject ID, session ID, etc.
# TODO: Implement file set schemas or something similar...
if file_set.schema_enabled:
pass
# Schema seems to be satisfied so add the file to the set and save.
file_set.files.append(f)
file_set_dao.save(file_set)
return self.response(file_set.to_dict())