genestack-uploader¶
genestack-uploader
is installed with the Python Client Library and can be accessed from a terminal by typing genestack-uploader
.
Usage¶
usage: __main__.py [-h] [-H <host>] [-u <user>] [-p <password>] [--token <api-token>] [--debug] [--show-logs] [-n] [-F <name> | --upload-to <accession>] <paths> [<paths> ...] Upload raw files to server and try to auto recognize them as genestack files. - Collecting files: Application can handle files and folder (will recursively collect all files). All paths must be valid. There is not limit to number of files. - Uploading: Files are stored in subfolder of 'Raw uploads'; subfolder name corresponds to user local time. Files are uploaded one by one, each in multiple threads. In case of network errors application attempts to retry until number of retries exceeded (5 by default), in which case application exits with error code. Uploaded data is not lost though and you can continue uploading this file from the point you stop. ATTENTION: When you upload multiple files from the command line, be sure to remove successfully uploaded files from the arguments when before re-running uploader, because otherwise all of them will be uploaded to the server again. - Recognition: Recognition done only if all files were uploaded successfully. It works over all files. Files that were not recognized are linked to subfolder 'Unrecognized files'. ATTENTION: Recognition of big number of files may cause server timeouts. Split uploading with recognition into relatively small iterations to prevent timeout failures. optional arguments: -h, --help show this help message and exit connection: -H <host>, --host <host> server host -u <user>, --user <user> user alias from settings or email -p <password>, --password <password> user password --token <api-token> API token to be used instead of the login and password --debug include server stacktrace into error messages (implies --show-logs) --show-logs print application logs received from server to stdout command arguments: <paths> path to files or folders -n, --no-recognition don't try to recognize files -F <name>, --folder_name <name> name of the upload folder, if name is not specified it will be generated --upload-to <accession> accession of the upload folder
genestack-uploader
exits with 0
return code in case of success, 1
if
recognition failed, and 13
if server requires newer Python Client version.