def gen_manifest_artifact_files(file_names, collection_path, chksum_type=None):
# file_names = file_names or []
file_names = file_names or []
default_chksum_type = chksum_type or 'sha256'
for file_name in file_names:
current_chksum_type = default_chksum_type
# TODO: enum
if os.path.isfile(file_name):
ftype = 'file'
if os.path.isdir(file_name):
ftype = 'dir'
chksum = None
if ftype == 'file':
chksum = chksums.sha256sum_from_path(file_name)
else:
chksum = None
current_chksum_type = None
dest_relative_path = os.path.relpath(file_name, collection_path)
arcname = dest_relative_path
artifact_file = CollectionArtifactFile(
src_name=file_name,
# The path where the file will live inside the archive
name=arcname,
ftype=ftype,
chksum_type=current_chksum_type,
chksum_sha256=chksum)
yield artifact_file
def _publish(galaxy_context, archive_path, display_callback=None):
results = {'errors': [], 'success': True}
api = GalaxyAPI(galaxy_context)
publish_api_key = galaxy_context.server.get('api_key', None)
data = {
'sha256': chksums.sha256sum_from_path(archive_path),
}
form = multipart_form.MultiPartForm()
for key in data:
form.add_field(key, data[key])
form.add_file('file', os.path.basename(archive_path),
codecs.open(archive_path, 'rb'), 'application/octet-stream')
log.debug('form: %s', form)
log.debug("Publishing file %s with data: %s" %
(archive_path, json.dumps(data)))
try:
response_data = api.publish_file(form, publish_api_key)
log.debug('response_data: %s', response_data)
results['response_data'] = response_data
except exceptions.GalaxyError as exc:
results['success'] = False
results['errors'].append(str(exc))
return results
def validate_artifact(artifact_path, expected_chksum):
'''Check the sha256sum of file at `artifact_path` against `expected_chksum`
Raise a GalaxyArtifactChksumError if they don't match.
'''
actual = chksums.sha256sum_from_path(artifact_path)
if actual != expected_chksum:
raise exceptions.GalaxyArtifactChksumError(artifact_path=artifact_path,
expected=expected_chksum,
actual=actual)
def create_file_manifest_item(file_name, file_name_in_archive):
if os.path.isfile(file_name):
# At the moment, 'sha256' is the only supported chksum_type for files
ftype = 'file'
chksum_type = 'sha256'
chksum = chksums.sha256sum_from_path(file_name)
if os.path.isdir(file_name):
chksum = None
chksum_type = None
ftype = 'dir'
log.debug('ftype: %s file_name: %s fnia: %s', ftype, file_name,
file_name_in_archive)
artifact_file_item = CollectionArtifactFile(
src_name=file_name,
# The path where the file will live inside the archive
name=file_name_in_archive,
ftype=ftype,
chksum_type=chksum_type,
chksum_sha256=chksum)
return artifact_file_item