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 = (',', ': '))
# if no -v
else:
for item in permissions:
permission_string = item['username'] + ' '
if item['permission']['read']:
permission_string += 'r'
if item['permission']['write']:
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 file; exit if file not found
project_files = vdjpy.get_project_files(current_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 paths
extra_path = ''
if filetype == 'projectJobFile':
extra_path += str(file_metadata['value']['relativeArchivePath']) + '/'
current_path = vdjpy.build_vdj_path(current_uuid, args.file_name, filetype, extra_path)
destination_path = vdjpy.build_vdj_path(destination_uuid, args.file_name, 'projectFile', '')
# move in agave (cannot move to jobfile destination)
agave_move = my_agave.files.manage(systemId = 'data.vdjserver.org',
filePath = current_path,
body = {'action': 'move',
'path': destination_path})
# update filepath, project uuid, and remove unnecessary metadata if jobfile
file_metadata['_links']['file']['href'] = unicode('https://vdj-agave-api.tacc.utexas.edu/files/v2/media/system/data.vdjserver.org/' + destination_path)
file_metadata['value']['projectUuid'] = unicode(destination_uuid)
if filetype == 'projectJobFile':
file_metadata['name'] = 'projectFile'
del file_metadata['value']['relativeArchivePath']
del file_metadata['value']['jobName']
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()
# -n; use args.file_name if flag not used
if args.newfile_name is '':
args.newfile_name = args.file_name
elif args.newfile_name is None:
args.newfile_name = vdjpy.prompt_user('name of file once downloaded')
# if jobfile, get extra path; then build path
extra_path = ''
if filetype == 'projectJobFile':
extra_path += str(file_metadata['value']['relativeArchivePath']) + '/'
file_path = vdjpy.build_vdj_path(project_uuid, args.file_name, filetype, extra_path)
# download file
download = my_agave.files.download(systemId = 'data.vdjserver.org',
filePath = file_path)
download.raise_for_status()
# write contents to file
with open(os.path.expanduser(args.newfile_name), 'w') as download_file:
download_file.write(download.text)
print 'Successfully downloaded', args.file_name, 'as', args.newfile_name
parser.add_argument('-v', '--verbose', dest = 'verbose', action = 'store_true', help = 'verbose output')
parser.add_argument('-z', '--accesstoken', dest = 'accesstoken', nargs = '?', help = 'access token')
args = parser.parse_args()
# UPLOAD FILE SETUP
my_agave = vdjpy.make_vdj_agave(args.accesstoken)
kwargs = {}
kwargs['systemId'] = 'data.vdjserver.org'
# -p
if args.project is None:
args.project = vdjpy.prompt_user('project name')
project_uuid = vdjpy.get_uuid(args.project, my_agave)
if project_uuid is None:
sys.exit('Could not find specified project')
kwargs['filePath'] = vdjpy.build_vdj_path(project_uuid, '', 'projectFile', '')
# -f
if args.file_upload is None:
args.file_upload = vdjpy.prompt_user('file to upload')
kwargs['fileToUpload'] = open(args.file_upload)
# -n
if args.file_name is None:
args.file_name = args.file_upload
kwargs['fileName'] = args.file_name
# -w
if args.email_or_webhook is not '':
if args.email_or_webhook is None:
args.email_or_webhook = vdjpy.prompt_user('email or webhook')
