def load_identifier_client():
token = load_tokens()['identifiers.globus.org']['access_token']
ic = IdentifierClient('Identifier',
base_url='https://identifiers.globus.org/',
app_name='My Local App',
authorizer=AccessTokenAuthorizer(token))
return ic
def mint_minid(file_info):
namespace = MINID_PROD if MINT_PROD else MINID_TEST
token = load_tokens()['identifiers.globus.org']['access_token']
# You must specify the `base_url`
ic = IdentifierClient('Identifier',
base_url='https://identifiers.globus.org/',
app_name='My Local App',
authorizer=AccessTokenAuthorizer(token))
kwargs = {
'visible_to': ['public'],
'location': [file_info['location']],
'checksums': [{
'function': 'md5',
'value': file_info['md5']
}],
'metadata': {
'Title':
'CRAM Alignment file for GTEx Sample {}.recab.cram'
''.format(file_info['id']),
'contentSize':
file_info['size']
}
}
kwargs = {k: json.dumps(v) for k, v in kwargs.items()}
minid = ic.create_identifier(namespace=namespace, **kwargs)
return minid.data['identifier']
def gen_bdbag(remote_file_manifest, title, bag_name):
tokens = load_tokens()
minid = bag_create(remote_file_manifest,
tokens[CONCIERGE_SCOPE_NAME]['access_token'],
minid_metadata={'title': title},
minid_test=(not PRODUCTION_MINIDS),
bag_name=bag_name,
# server='http://localhost:8000'
)
return minid
def ingest():
with open(SEARCH_DATA) as f:
ingest_doc = json.loads(f.read())
tokens = load_tokens()
auther = globus_sdk.AccessTokenAuthorizer(
tokens['search.api.globus.org']['access_token'])
sc = globus_sdk.SearchClient(authorizer=auther)
preview = [ent['subject'] for ent in ingest_doc['ingest_data']['gmeta']]
print('\n'.join(preview))
print('Ingest these to "{}"?'.format(
sc.get_index(INDEX).data['display_name']))
user_input = input('Y/N> ')
if user_input in ['yes', 'Y', 'y', 'yarr']:
sc.ingest(INDEX, ingest_doc)
print('Finished')
else:
print('Aborting')