# SET UP FILETYPE
# -f
if args.projectfile is not '' and args.jobfile is '':
filetype = 'projectFile'
# -j
elif args.jobfile is not '' and args.projectfile is '':
filetype = 'projectJobFile'
else:
filetype = None
# get files for metadata
files = vdjpy.get_project_files(project_uuid, filetype, kwargs, my_agave)
# filter to one file if name specified; quit if file not found
if filetype == 'projectFile' and args.projectfile is not None:
files = vdjpy.get_file_metadata(files, args.projectfile)
elif filetype == 'projectJobFile' and args.jobfile is not None:
files = vdjpy.get_file_metadata(files, args.jobfile)
if files is None:
sys.exit()
# if -v or specific file given
if args.verbose is True or type(files) is not list:
print json.dumps(files, default = vdjpy.json_serial, sort_keys = True, indent = 4, separators = (',', ': '))
# if no -v and files is a list
else:
for item in files:
print item['value']['name']
# SET UP FILETYPE AND GET FILE NAME IN ARGS.FILE_NAME
# -f (default)
if args.file_name is not '' or args.jobfile_name is '':
if args.file_name is None or '':
args.file_name = vdjpy.prompt_user('file name')
filetype = 'projectFile'
# -j (only if flag given)
else:
if args.jobfile_name is None:
args.jobfile_name = vdjpy.prompt_user('jobfile name')
filetype = 'projectJobFile'
args.file_name = args.jobfile_name
# get metadata for extra path; exit if file not found
project_files = vdjpy.get_project_files(project_uuid, filetype, {}, my_agave)
file_metadata = vdjpy.get_file_metadata(project_files, args.file_name)
if file_metadata is None:
sys.exit()
# if jobfile, get extra path; then build file path
extra_path = ''
if filetype == 'projectJobFile':
extra_path += str(file_metadata['value']['relativeArchivePath']) + '/'
kwargs['filePath'] = vdjpy.build_vdj_path(project_uuid, args.file_name, filetype, extra_path)
# list permissions
permissions = my_agave.files.listPermissions(**kwargs)
# if -v
if args.verbose:
print json.dumps(permissions, default = vdjpy.json_serial, sort_keys = True, indent = 4, separators = (',', ': '))
# -f (default file type; used if -j not called)
if args.file_to_delete is not '' or args.jobfile_to_delete is '':
if args.file_to_delete is None:
args.file_to_delete = vdjpy.prompt_user('file to delete')
filetype = 'projectFile'
# -j (only used if specified)
else:
if args.jobfile_to_delete is None:
args.jobfile_to_delte = vdjpy.prompt_user('jobfile to delete')
filetype = 'projectJobFile'
# consolidate file name to args.file_to_delete no matter file type
args.file_to_delete = args.jobfile_to_delete
# get file_to_delete metadata
files = vdjpy.get_project_files(project_uuid, filetype, {}, my_agave)
file_metadata = vdjpy.get_file_metadata(files, args.file_to_delete)
if file_metadata is None:
sys.exit()
# change isDeleted to true
file_metadata['value']['isDeleted'] = True
# delete file via metadata update
delete_resp = my_agave.meta.updateMetadata(uuid = file_metadata['uuid'],
body = json.dumps(file_metadata))
# if -v
if args.verbose:
print json.dumps(delete_resp, default = vdjpy.json_serial, sort_keys = True, indent = 4, separators = (',', ': '))
# if no -v
