A bash script for creating a subject / experiment in xnat

createexperiment.sh

#!/bin/bash
# creates subject / experiment ids if they dont already exist
# 1. url - xnat url
# 2. session - tomcat session_id (instead of username / password)
# 3. project - project id
# 4. subject - subject_id
# 5. experiment - experiment id
# 6. date - experiment_date
# 7. verbosity - 0 = surpress, 1 = log (default), 2 = debug

verbose_default=1
verbose=${7:-$verbose_default}
function log {
  if [[ $verbose -gt 0 ]]; then
    echo "createexperiment: $1"
  fi
}
function debug {
  if [[ $verbose -eq 2 ]]; then
    echo "createexperiment (debug): $1"
  fi
}

url="$1/data/archive/projects"
# check for correct number of arguments
if [[ "$#" -lt 6 && "$#" -gt 7 ]]; then
  echo -e "Incorrect number of arguments - expected 6/7 - found $#"
  echo "Usage: createexperiment.sh xnat_url tomcat_session_id project_id subject_id session_id session_date (verbosity)"
else
  debug "project_id: $3, subject_id: $4, experiment_id: $5, experiment_date: $6"
  project_exists=$(./XnatDataClient -c -s $2 -r $url/$3 | tail -n 1)
  if [[ $project_exists == HTTP\ status\:\ 200 ]]; then
    debug "project found: $3"
    subject_exists=$(./XnatDataClient -c -s $2 -r $url/$3/subjects/$4 | tail -n 1)
    if [[ $subject_exists == HTTP\ status\:\ 200 ]]; then
      debug "subject found: $4"
    else
      log "creating subject: $4"
      subject_created=$(./XnatDataClient -m PUT -s $2 -r $url/$3/subjects/$4)
      debug "$subject_created"
    fi
    experiment_exists=$(./XnatDataClient -c -s $2 -r $url/$3/subjects/$4/experiments/$5 | tail -n 1)
    if [[ $experiment_exists == HTTP\ status\:\ 200 ]]; then
      debug "experiment found: $5"
    else
      log "creating MR session experiment: $5 $6"
      experiment_created=$(./XnatDataClient -m PUT -s $2 -r $url/$3/subjects/$4/experiments/$5?xsiType=xnat\:mrSessionData\&xnat\:mrSessionData/date=$6)
      debug "$experiment_created"
    fi
  elif [[ $project_exists == HTTP\ status\:\ 404 ]]; then
    log "Failed: unknown project"
  else
    log "Failed: reason unknown ($project_exists)"
  fi
fi