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 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)