The garjus command-line interface is implemented with the click python package. Like docker or other similar packages, garjus uses sub-commands. Each sub-command has it's own set of options and arguments.
Usage: garjus [OPTIONS] COMMAND [ARGS]...
Options:
--debug / --no-debug
--quiet / --no-quiet
--help Show this message and exit.
Commands:
activity
analyses
compare
copyscan
copysess
dashboard
delete
download
export
finish
getinputs
getoutputs
image03csv
image03download
importdicom
importnifti
issues
orphans
pdf
processing
progress
quicktest
report
retry
run
setsesstype
setsite
stats
statshot
subjects
switch
tasks
update
You can get help for each subcommand.
garjus stats --help
Usage: garjus stats [OPTIONS] CSV
Options:
-p, --projects TEXT [required]
-t, --types TEXT
-s, --sesstypes TEXT
-a, --analysis TEXT
--persubject
-e, --sessions TEXT
--help Show this message and exit.
...
Use garjus delete to remove assessors from XNAT by project and processing type with optional filters for statuses.
garjus delete --help
Usage: garjus delete [OPTIONS]
Options:
-p, --project TEXT [required]
-t, --type TEXT [required]
-s, --procstatus TEXT
-q, --qcstatus TEXT
--help Show this message and exit.
This method of deleting is often useful when testing a pipeline and want to quickly purge any test assessor data for the new type.
At times, you will want to apply some or all updates immediately. For example, automations can be run manually to extract a recently uploaded file.
garjus update automations -p REMBRANDT -t etl_nihtoolbox
stats can be synchronized manually to copy stats from XNAT to REDCap so it's visible in the dashboard.
garjus update stats -p REMBRANDT