#!/bin/bash
#
# Script that moves DICOM/PDF/CSV data from the harddrive into XNat
# (Hauke Bartsch, hbartsch@ucsd.edu)
# requires: dcmtk, curl
# add your user name, password and server name
#

if [ $# -ne 4 ]
then
  echo "Usage: provide <project id>, <subject id>, <visit id> and <data directory>"
  echo "       Data in the directory is scanned for DICOM data, all other files are uploaded as binary."
  exit;
fi
echo "done"

subject=$2
session=$3
directory=$4
USER=<me>
PASSWORD=<mypasswd>
PROJECT=$1
XNAT=https://<myserver>:<myport>/xnat

dir=`pwd`
if [ ! -d $directory ]; then
  echo "Error: subject directory ($directory) does not exist"
  exit;
fi

# Create a session cookie, we want to re-use that session instead of providing
# login information every time. Number of sessions might be limited otherwise to 1000.
cookie=`curl -k -u $USER:$PASSWORD -X POST $XNAT/data/JSESSION`
echo "Session ID is: $cookie"

# create subject in case it does not exist
echo "create subject $c"
c=`curl --cookie JSESSIONID=$cookie -k -X PUT $XNAT/data/archive/projects/$PROJECT/subjects/$subject`
# create session in case it does not exist
echo "create session $c"
c=`curl --cookie JSESSIONID=$cookie -k -X PUT $XNAT/data/archive/projects/$PROJECT/subjects/$subject/experiments/$session?xsiType=xnat:mrSessionData`

timestamps=( )
for u in `find $directory -type f -print`
do 
  # check if the file is a DICOM
  /usr/local/bin/dcmftest $u > /dev/null; if test $? -eq 0; 
  then 
     # move file over using REST API
     c=`curl  --cookie JSESSIONID=$cookie -s -k -H 'Content-Type: application/dicom' -X POST "$XNAT/data/services/import?inbody=true&PROJECT_ID=$PROJECT&SUBJECT_ID=$subject&EXPT_LABEL=$session&prearchive=true&overwrite=append&format=DICOM&content=T1_RAW" --data-binary @$u | tr -d [:cntrl:]`
     echo -n "."
     timestamp=`echo $c | cut -d'/' -f6`
     # is timestamp new?
     found="0"
     for f in "${timestamps[@]}"; do
        if [ "$f" = "$timestamp" ]; then
           found="1"
        fi
     done
     # add to array
     if [ $found = "0" ]; then
        timestamps+=($timestamp)
        echo "found a new series $timestamp"
     fi
  else 
     echo "found non-DICOM file"; 
     # what is the file extension?
     ext=${u##*.}
     case $ext in
     "pdf")
       echo file $u is a pdf;
       args="-k -X PUT  --cookie JSESSIONID=$cookie"
       url="$XNAT/data/archive/projects/$PROJECT/subjects/$subject/experiments/$session/files/$u?inbody=true&format=PDF"
       curl $args "$url" --data-binary @$u
       ;;
     "csv")
       echo file $u is a csv;
       args="-k -X PUT  --cookie JSESSIONID=$cookie"
       url="$XNAT/data/archive/projects/$PROJECT/subjects/$subject/experiments/$session/files/$u?inbody=true&format=CSV"
       curl $args "$url" --data-binary @$u
       ;;
     *)
       echo unknown file type $ext for file $u
       ;;
     esac
  fi;
done
echo "done sending files... (c=$c)"

# DICOM files have to be moved from the pre-archive to the archive to be visible
# for this we do build and commit for each session.
# Limitation: If you have more than one session the above part will upload using a
# single session id provided on the command line. The part below will fail 
# because each session needs to be unique. Provide a single session as input
# only!
for ids in "${timestamps[@]}"; do

  #timestamp=`echo $c | cut -d'/' -f6`
  timesteamp=$ids
  echo "timestamp is: $timestamp"

  args=" --cookie JSESSIONID=$cookie -k -X POST"
  url=$XNAT${c}?action=build
  echo "CALLING URL: $url ($args)"
  /usr/bin/curl $args $url

  echo "CALLING: commit action"
  url=$XNAT${c}?action=commit
  /usr/bin/curl $args $url

  url="$XNAT/data/services/archive?overwrite=delete&src=${c}&dest=/archive/projects/$PROJECT/subjects/$subject"
  echo "Move to archive..."
  /usr/bin/curl $args $url
done

echo "$subject $session done"