Upload mulitple dicom sessions as outlined in a spreadsheet

csvupload.sh

#!/bin/bash
# uploads dicom images for a set of subject sessions to the tng xnat instance
# takes three parameters:
# 1: csv - the filename a csv file that contains three columns:
#   a: subject_id
#   b: directory
#   c: scan date
# 2: xnat-username
# 3: xnat-password
# 4: xnat-project_id

# check for correct number of arguments
if [ "$#" -ne 4 ]; then
  echo -e "Incorrect number of arguments - expected 4"
  echo "Usage: csvupload.sh csvfilepath user password project"
else
  # check that csvfile can be found
  if [ -e $1 ]; then
    cat $1 | while read line
    do
      subject_id=$(echo $line | cut -d',' -f1)
      dir=$(echo $line | cut -d',' -f2)
      scan_date=$(echo $line | cut -d',' -f3)
      echo "subject_id: WH_$subject_id, directory: $dir, scan date: $scan_date"
      ./uploaddcmtk.sh $2 $3 $4 $dir WH_$subject_id
      # todo: check scan-dates match
    done
  else
    echo "csvfile $1 not found - no session uploaded."
  fi
fi