def store(args, syn):
#If we are storing a fileEntity we need to have id or parentId
if args.parentid is None and args.id is None and args.file is not None:
raise ValueError('synapse store requires at least either parentId or id to be specified.')
#If both args.FILE and args.file specified raise error
if args.file and args.FILE:
raise ValueError('only specify one file')
args.file = args.FILE if args.FILE is not None else args.file
args.type = 'FileEntity' if args.type == 'File' else args.type
if args.id is not None:
entity = syn.get(args.id)
else:
entity = {'concreteType': u'org.sagebionetworks.repo.model.%s' % args.type,
'name': utils.guess_file_name(args.file) if args.file and not args.name else None,
'parentId' : None,
'description' : None,
'path': args.file}
#Overide setting for parameters included in args
entity['name'] = args.name if args.name is not None else entity['name']
entity['description'] = args.description if args.description is not None else entity['description']
entity['parentId'] = args.parentid if args.parentid is not None else entity['parentId']
entity['path'] = args.file if args.file is not None else None
if utils.is_url(args.file):
entity['synapseStore'] = False
used = _convertProvenanceList(args.used, args.limitSearch, syn)
executed = _convertProvenanceList(args.executed, args.limitSearch, syn)
entity = syn.store(entity, used=used, executed=executed)
print 'Created/Updated entity: %s\t%s' %(entity['id'], entity['name'])
def store(args, syn):
#If we are storing a fileEntity we need to have id or parentId
if args.parentid is None and args.id is None and args.file is not None:
raise ValueError(
'synapse store requires at least either parentId or id to be specified.'
)
#If both args.FILE and args.file specified raise error
if args.file and args.FILE:
raise ValueError('only specify one file')
args.file = args.FILE if args.FILE is not None else args.file
args.type = 'FileEntity' if args.type == 'File' else args.type
if args.id is not None:
entity = syn.get(args.id, downloadFile=False)
else:
entity = {
'concreteType':
u'org.sagebionetworks.repo.model.%s' % args.type,
'name':
utils.guess_file_name(args.file)
if args.file and not args.name else None,
'parentId':
None,
'description':
None,
'path':
args.file
}
#Overide setting for parameters included in args
entity['name'] = args.name if args.name is not None else entity['name']
entity[
'description'] = args.description if args.description is not None else entity.get(
'description', None)
entity[
'parentId'] = args.parentid if args.parentid is not None else entity[
'parentId']
entity['path'] = args.file if args.file is not None else None
entity['synapseStore'] = not utils.is_url(args.file)
used = _convertProvenanceList(args.used, args.limitSearch, syn)
executed = _convertProvenanceList(args.executed, args.limitSearch, syn)
entity = syn.store(entity, used=used, executed=executed)
print 'Created/Updated entity: %s\t%s' % (entity['id'], entity['name'])
# After creating/updating, if there are annotations to add then
# add them
if args.annotations is not None:
# Need to override the args id parameter
setattr(args, 'id', entity['id'])
setAnnotations(args, syn)
def add(args, syn):
if args.type == 'File': args.type = 'FileEntity'
if args.file and not args.name:
args.name = utils.guess_file_name(args.file)
entity = {'name': args.name,
'parentId': args.parentid,
'description':args.description,
'concreteType': u'org.sagebionetworks.repo.model.%s' % args.type,
'path': args.file}
if utils.is_url(args.file):
entity['synapseStore'] = False
entity = syn.store(entity, used=args.used, executed=args.executed)
print 'Created/Updated entity: %s\t%s from file: %s' %(entity['id'], entity['name'], args.file)