gistfile1.txt

#!/bin/bash
#
# 2021 ddrucker

set -o errexit

if [ $# -lt 2 ]; then
    echo "Usage: $0 xnat_username accessionid [accessionid accessionid ...]"
    echo "accessionid can be the MGB-generated one, which (typically) starts with E,"
    echo "OR the XNAT-generated one, which starts with XNAT_E."
    exit 1
fi

cleanup() { rm -f "${ACC}.zip"; }
trap cleanup INT

URL=https://image-test.mclean.harvard.edu
WHO=$1
shift

## auth to xnat
echo "Please enter your XNAT password."
JSESSIONID=$(curl -s -u $WHO "$URL/data/JSESSION")
if [[ "$JSESSIONID" == *"Unauthorized"* ]]; then
    echo "Login failed."
    exit 1
fi

## retrieve each one
for ACC in $@; do
    echo "Retrieving $ACC ..."

    if [[ $ACC == XNAT_S* ]]; then
	echo "$ACC is an XNAT Subject ID, not a Session id."
	echo "Session IDs start with XNAT_E."
	continue
    fi

    if [[ $ACC == XNAT_E* ]]; then
	SESSIONID=$ACC
    else
	SESSIONID=$(curl -s -b JSESSIONID=$JSESSIONID "$URL/data/experiments?format=json&label=$ACC" | jq -r '.ResultSet.Result[0].ID' )
	if [[ $SESSIONID == null ]]; then
	    echo "Something went wrong trying to get $ACC."
	    continue
	fi
    fi

    curl -b JSESSIONID=$JSESSIONID  "$URL/data/experiments/$SESSIONID/scans/ALL/files?format=zip" -o $ACC.zip 
    7z x $ACC.zip
    rm -f $ACC.zip
done