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.