Bash script for uploading a directory of dicom images to xnat 1.6.4

upload.sh

#!/bin/bash
# uploads dicom images for a particular subject session to the tng xnat instance
# takes five parameters:
# 1: username - xnat username
# 2: password - xnat password
# 3: project - project id
# 4: scan date - session date e.g. '01/02/14'
# 5: directory - the subdirectory that contains the session files
#
# Assumptions!
# 1. The directory name is composed of ${PID}_${SUBJECTNO} and the subject ID can be
# constructed as WH_${SUBJECTNO}.  In this script the PID is assumed to be 11 chars long.
# 2. There is a set of sub-directories under the specified directory each
# corresponding to a separate scan and that the dicom image files are all in
# those scan sub-directories.
#url="https://tng.psych.ox.ac.uk/xnat/data/archive/projects/$3"
url="http://192.168.50.50:8080/xnat/data/archive/projects/$3"

function mapType {
  if [[ "$1" == DTI_*]]; then
		type='DTI'
  elif [[ "$1" == ep-moco-nav-set* ]]; then
    type='Navigator'
  elif [[ "$1" == fieldmap_* ]]; then
    type='FieldMap'
  elif [[ "$1" == gre_0.8inplane_5mm_* ]]; then
    type='T2*'
  elif [[ "$1" == localizer_* ]]; then
    type='Localizer'
  elif [[ "$1" == mb6_hcp_2mmiso_TR1300__* ]]; then
    type='Resting-state'
  elif [[ "$1" == t2_tirm_tra_dark-fluid_3mm_9_1 ]]; then
    type='FLAIR'
  elif [[ "$1" == tfl-multiecho-epinav-711_NoMoCo_* ]]; then
    type='T1'
  elif [[ "$1" == to_PCASL_perf_ep2d_bold_BGS_inc_PLD* ]]; then
    type='ASL'
	else
    # default to directory name without the trailing slash
		type="${1%/}"
	fi
}

# step 1 - check for directory
if [ -d $5 ]; then
	cd $5
	# step 2 - check for project
	project_exists=$(curl -I -u $1:$2 $url)
	if [[ $project_exists == HTTP/1.1\ 200* ]]; then
		echo "Confirmed project $3"
    subject_id="WH_${5:12}"
		# step 3 - check for subject and create if it doesnt exist
		subject_exists=$(curl -I -u $1:$2 $url/subjects/$subject_id)
		if [[ $subject_exists == HTTP/1.1\ 200* ]]; then
			echo "Using existing subject $subject_id"
		else
			echo "Creating subject $subject_id"
			curl -X PUT -u $1:$2 $url/subjects/$subject_id
		fi

		# step 4 - create session
		session=$(curl -X PUT -u $1:$2 $url/subjects/$subject_id/experiments/$5?xnat:mrSessionData/date=$4)
		echo "Created session $session"

		# step 5 - iterate through scans
		for d in */ ; do
			cd $d
			# assign $type
			mapType $d
			echo "mapped type: $type from directory $d"
			scan=${d%/}
			curl -X PUT -u $1:$2 $url/subjects/$subject_id/experiments/$5/scans/$scan?xsiType=xnat:mrScanData\&xnat:mrScanData/type=$type
			# create resource
			curl -X PUT -u $1:$2 $url/subjects/$subject_id/experiments/$5/scans/$scan/resources/DICOM?format=DICOM\&content=${type}_RAW
			echo "Created scan $scan from directory $5/$d"
			for f in * ; do
				curl -X PUT -u $1:$2 $url/subjects/$subject_id/experiments/$5/scans/$scan/resources/DICOM/files/$f -F "$f=@./$f"
				echo "Upload file $f"
			done
			cd ..
		done
		cd ..
	else
		echo "project $3 not found - do the passed credentials have access to it?"
	fi
else
	echo "unable to find directory $5"
fi