uploadnifti.sh

#!/bin/bash
# upload pre-processed niftii images to xnat 1.6.5
# 1. xnat - xnat url, e.g. https://central.xnat.org
# 2. username - xnat username
# 3. password - xnat password
# 4. project - project id
# 5. subject - subject id
# 6. session - session id
# 7. scan - scan id
# 8. nifti - filepath of nifti image

verbose=1
function log {
  if [[ $verbose == 1 ]]; then
    echo "uploadnifti: $1"
  fi
}

# check for correct number of arguments
if [ "$#" -ne 8 ]; then
  echo -e "Incorrect number of arguments - expected 8"
  echo "Usage: uploadnifti.sh xnat-url xnat-username xnat-password project_id subject_id session_id scan_id filepath"
else
  url="$1/data/archive/projects"
  log "project_id: $4, subject_id: $5, session_id: $6, scan_id: $7, filepath: $8"
  resources_exist=$(curl -silent -I -u $2:$3 $url/$4/subjects/$5/experiments/$6/scans/$7/resources)
  if [[ $resources_exist == HTTP/1.1\ 200* ]]; then
    resources=$(curl -sb -H -u $2:$3 $url/$4/subjects/$5/experiments/$6/scans/$7/resources?format=csv)
    # create NIFTI resource type if not already present
    if [[ $(echo "$resources" | grep "NIFTI" | wc -l) == 0 ]]; then
      curl -X PUT -u $2:$3 $url/$4/subjects/$5/experiments/$6/scans/$7/resources/NIFTI
      log "NIFTI resource folder created for subject $5, session $6, scan $7"
    fi
    filename=$(basename $8)
    nifti_exists=$(curl -silent -I -u $2:$3 $url/$4/subjects/$5/experiments/$6/scans/$7/resources/NIFTI/files/$filename)
    if [[ $nifti_exists == HTTP/1.1\ 200* ]]; then
      log "Nifti file already exists: IGNORED"
    else
      curl -u $2:$3 -X PUT --data-binary "@$8" "$url/$4/subjects/$5/experiments/$6/scans/$7/resources/NIFTI/files/$filename?format=NIFTI&inbody=true"
      log "Nifti file uploaded: $filename"
    fi
  else
    # something is amiss in the first seven parameters, lets debug...
    project_exists=$(curl -silent -I -u $2:$3 $url/$4)
    if [[ $project_exists == HTTP/1.1\ 200* ]]; then
      subject_exists=$(curl -silent -I -u $2:$3 $url/$4/subjects/$5)
      if [[ $subject_exists == HTTP/1.1\ 200* ]]; then
        session_exists=$(curl -silent -I -u $2:$3 $url/$4/subjects/$5/experiments/$6)
        if [[ $session_exists == HTTP/1.1\ 200* ]]; then
          scan_exists=$(curl -silent -I -u $2:$3 $url/$4/subjects/$5/experiments/$6/scans/$7)
          if [[ $scan_exists == HTTP/1.1\ 200* ]]; then
            echo "Failed: Reason unknown! (project,subject,session and scan are all present)"
          else
            echo "Failed: unknown scan"
          fi
        else
          echo "Failed: unknown session"
        fi
      else
        echo "Failed: unknown subject"
      fi
    else
      # todo: check that credentials work at all?
      echo "Failed: unknown project $project_exists"
    fi
  fi
fi