def _makeitso_():
assert (self.annotations
is not None) and (len(self.annotations) > 0)
stage = m.add_sample_stage(
sample.obfuscated_id, self.method.obfuscated_id,
';'.join(map(str, self.annotations)),
m.get_sample_stages(sample.obfuscated_id)[1])
for datafile in self.datafiles:
m.add_file(os.path.relpath(datafile.path, config.UPLOAD_PATH),
stage.obfuscated_id)
return stage
def _makeitso_():
assert (self.annotations is not None) and (len(self.annotations) > 0)
stage = m.add_sample_stage(
sample.obfuscated_id,
self.method.obfuscated_id,
';'.join(map(str, self.annotations)),
m.get_sample_stages(sample.obfuscated_id)[1])
for datafile in self.datafiles:
m.add_file(
os.path.relpath(datafile.path, config.UPLOAD_PATH),
stage.obfuscated_id)
return stage
def complete_file_upload():
request_data = json.loads(request.data)
file_identifier = request_data['upload-id']
file_name = secure_filename(request_data['file-name'])
project = request_data['project']
sample = request_data['sample']
sample_stage = as_id(request_data['sample-stage'])
req_checksum_value = request_data['checksum-value']
req_checksum_method = request_data['checksum-method']
part_upload_dir = upload_dir(file_identifier)
reconstituted_file_name = os.path.join(part_upload_dir, file_name)
parts = sorted(glob.glob(os.path.join(part_upload_dir, '*.part')))
part_digester = checksum.get_digester(req_checksum_method)
with open(reconstituted_file_name, 'w') as target:
def consume_part(data):
target.write(data)
part_digester.update(data)
for part_name in parts:
file.FileProcessor(part_name, consume_part).process()
computed_checksum_value = part_digester.hexdigest()
if computed_checksum_value != req_checksum_value:
raise checksum.ChecksumMismatch(reconstituted_file_name,
req_checksum_method,
req_checksum_value,
computed_checksum_value)
with open('.'.join([reconstituted_file_name, CHECKSUM_EXT]), 'w') as cf:
json.dump({
'method': req_checksum_method,
'value': req_checksum_value
}, cf)
logmsg = 'Successfully reconsitituted file: %s (%s=%s)' \
% (reconstituted_file_name, req_checksum_method, req_checksum_value)
app.logger.info(logmsg)
models.add_file(
os.path.relpath(reconstituted_file_name, app.config['UPLOAD_PATH']),
sample_stage)
return (json.dumps({
'identifier': file_identifier,
'file-name': file_name
}), http.HTTP_202_ACCEPTED)
def test_add_file(storepath, sample_with_stages):
ssf = models.add_file('source-file', sample_with_stages['stages'][0].obfuscated_id)
assert 1 == ssf.id
assert 'w4Kbn' == ssf.obfuscated_id
assert models.FileStatus.staged == ssf.status
assert models.FileStatus.staged.value == ssf._status
assert sample_with_stages['stages'][0].id == ssf._sample_stage_id
def test_add_file(storepath, sample_with_stages):
ssf = models.add_file('source-file',
sample_with_stages['stages'][0].obfuscated_id)
assert 1 == ssf.id
assert 'w4Kbn' == ssf.obfuscated_id
assert models.FileStatus.staged == ssf.status
assert models.FileStatus.staged.value == ssf._status
assert sample_with_stages['stages'][0].id == ssf._sample_stage_id
def stage_file(storepath, sample_with_stages):
parts_dir = ''.join([random.choice('0123456789ABCDEF') for i in range(3)])
ssf = models.add_file(os.path.join(parts_dir, 'uploaded-file'),
sample_with_stages['stages'][0].obfuscated_id)
src_fname = os.path.join(sagittariidae.app.app.config['UPLOAD_PATH'],
ssf.relative_source_path)
tgt_fname = os.path.join(sagittariidae.app.app.config['STORE_PATH'],
ssf.relative_target_path)
return {'model': ssf, 'source': src_fname, 'target': tgt_fname}
def stage_file(storepath, sample_with_stages):
parts_dir = ''.join([random.choice('0123456789ABCDEF') for i in range(3)])
ssf = models.add_file(
os.path.join(parts_dir, 'uploaded-file'),
sample_with_stages['stages'][0].obfuscated_id)
src_fname = os.path.join(
sagittariidae.app.app.config['UPLOAD_PATH'],
ssf.relative_source_path)
tgt_fname = os.path.join(
sagittariidae.app.app.config['STORE_PATH'], ssf.relative_target_path)
return {'model' : ssf,
'source' : src_fname,
'target' : tgt_fname}
def test_complete_file(sample_with_stages):
ssf = models.add_file('source-file',
sample_with_stages['stages'][0].obfuscated_id)
assert models.FileStatus.staged == ssf.status
def test_complete_file(sample_with_stages):
ssf = models.add_file('source-file', sample_with_stages['stages'][0].obfuscated_id)
assert models.FileStatus.staged == ssf.status