def create_auth_token():
# get server token from header (convert to str to fix weird encoding issue on production)
server_token = request.headers.get('X-Server-Token', type=str)
json_data = request.get_json()
try:
user = str(json_data.get('user'))
except AttributeError:
return return_message('Error: missing user', 400)
name = str(json_data.get('name', ''))
email = str(json_data.get('email', ''))
duration = int(json_data.get('duration', 1))
if not all([server_token, user]):
return return_message('Error: missing parameter', 400)
if user.find('/') != -1:
return return_message('Error: invalid username, must not contain "/"', 400)
try:
auth_token, expiry_date = generate_auth_token(server_token, user, name, email, duration)
return return_data({'user': user,
'transferCode': auth_token,
'expiresAt': expiry_date.strftime("%Y-%m-%dT%H:%M:%SZ")})
except InvalidServerToken:
return return_message('Error: Unauthorized', 401)
def update_upload_status(auth_token, sample_name, identifier):
auth_token = str(auth_token)
sample_name = str(sample_name)
identifier = str(identifier)
data = {
'status': request.form.get('status', type=str),
'identifier': identifier,
'sample_name': sample_name,
'auth_token': auth_token,
'total_chunks': request.form.get('flowTotalChunks', type=int),
'total_size': request.form.get('flowTotalSize', type=int),
'filename': request.form.get('flowFilename', type=str),
'file_type': request.form.get('fileType', type=str, default=''),
'readset': request.form.get('readset', type=str, default=''),
'library': request.form.get('library', type=str, default=''),
'run_type': request.form.get('runType', type=str, default=''),
'platform': request.form.get('platform', type=str, default=''),
'capture_kit': request.form.get('captureKit', type=str, default=''),
'reference': request.form.get('reference', type=str, default=''),
}
if data['status'] == 'start':
file_row = File.query.filter_by(identifier=identifier).first()
if file_row and file_row.upload_status == 'complete':
return return_message('Error: File already uploaded', 400)
get_or_create_file(data)
return return_message('Success: Upload set to ongoing in db', 200)
elif data['status'] == 'complete':
return generate_file(data)
return return_message('Error: Unexpected status', 400)
def update_db_file(identifier):
# get server token from header (convert to str to fix weird encoding issue on production)
server_token = request.headers.get('X-Server-Token', type=str)
json_data = request.get_json()
column = json_data.get('column')
value = json_data.get('value')
if not all([column, value]):
return return_message('Error: missing parameter', 400)
try:
return update_file(server_token, identifier, str(column), str(value))
except InvalidServerToken:
return return_message('Error: Unauthorized', 401)
def chunk_info(auth_token, sample_name, identifier, chunk_number):
auth_token = str(auth_token)
sample_name = str(sample_name)
identifier = str(identifier)
try:
chunk_number = int(chunk_number)
except ValueError:
return return_message('Error: invalid chunk number', 400)
temp_dir = get_tempdir(auth_token, identifier)
chunk_filename = get_chunk_filename(temp_dir, chunk_number)
if os.path.isfile(chunk_filename):
# Chunk transfer completed successfully on HTTP code 200 only
return return_message('Chunk already transferred', 200)
# Chunk transfer not complete, send chunk requires HTTP code 204 (or anything other than 200, 400s, 500, 501)
return return_message('Chunk not yet transferred', 204)
def cancel_upload(auth_token, sample_name, identifier):
auth_token = str(auth_token)
sample_name = str(sample_name)
identifier = str(identifier)
file_row = File.query.filter_by(identifier=identifier).first()
if not file_row:
return return_message('Error: Identifier does not exist', 404)
if file_row.upload_status != 'complete':
update_file_status(identifier, 'cancelled')
remove_from_uploads(get_tempdir(auth_token, identifier))
return return_message('Success: Cancel received', 200)
return return_message('Error: Upload already complete', 400)
def get_db_files():
# get server token from header (convert to str to fix weird encoding issue on production)
server_token = request.headers.get('X-Server-Token', type=str)
json_data = request.get_json()
try:
if json_data:
data = get_files(server_token, json_data)
else:
data = get_files(server_token)
return return_data(data)
except InvalidServerToken:
return return_message('Error: Unauthorized', 401)
except InvalidColumnName:
return return_message('Error: Column name does not exist', 400)
def chunk_upload(auth_token, sample_name, identifier, chunk_number):
auth_token = str(auth_token)
sample_name = str(sample_name)
identifier = str(identifier)
file = File.query.filter_by(identifier=identifier).first()
try:
chunk_number = int(chunk_number)
except ValueError:
return return_message('Error: invalid chunk number', 400)
filename = request.form.get('flowFilename', type=str)
total_chunks = request.form.get('flowTotalChunks', type=int)
current_chunk_size = request.form.get('flowCurrentChunkSize', type=int)
input_chunk = request.files['file']
if not all([filename, total_chunks, current_chunk_size]):
return return_message('Error: missing parameter', 400)
if not file or file.upload_status != 'ongoing':
return return_message('Error: Chunk refused, file status not set to ongoing', 202)
temp_dir = get_tempdir(auth_token, identifier)
chunk_filename = get_chunk_filename(temp_dir, chunk_number)
try:
make_tempdir(temp_dir)
except DirectoryCreationError:
return return_message('Error: File directory could not be created', 500)
try:
input_chunk.save(chunk_filename)
if os.path.getsize(chunk_filename) != current_chunk_size:
raise InvalidFileSize
# BAM test for integrity done here since only the prioritized last chunk is needed to determine corruption
if chunk_number == total_chunks and file.file_type == 'BAM/SAM':
validate_bam(chunk_filename)
except TruncatedBam:
remove_from_uploads(temp_dir)
update_file_status(identifier, 'corrupt')
return return_message('Error: Truncated BAM file', 415)
except InvalidFileSize:
os.remove(chunk_filename)
return return_message('Error: Chunk size on disk does not match', 500)
except:
os.remove(chunk_filename)
return return_message('Error: Chunk could not be saved', 500)
return return_message('Success: Upload of chunk complete', 200)
def bad_request(error):
app.logger.error(error)
return return_message('Bad request', 400)
def page_not_found(error):
app.logger.error(error)
return return_message('This page does not exist', 404)
def internal_server_error(error):
app.logger.error(error)
return return_message('Error: Caught an internal server error', 500)
