Get resource files from XNAT dataset collection

get-resources.sh

#!/usr/bin/env bash

showHelp() {
    echo
    echo "Usage: ${0} --server <URL> --username <USER> --password <PASSWORD> --project <PROJECT> --collection <COLLECTION_ID>"
    echo
    echo "Note: all options are required, with the exception of --password. If --password"
    echo "      is omitted, you must enter your password when the script runs."
    echo
    exit 255
}

pause() {
    read -n 1 -p "Press any key to continue > "
    echo
}

while [ ! -z ${1} ]; do
    case ${1} in
        --collection|-c)
            COLLECTION="${2}"
            shift 2
            ;;
        --password|-p)
            PASSWORD="${2}"
            shift 2
            ;;
        --project|-P)
            PROJECT="${2}"
            shift 2
            ;;
        --server|-s)
            SERVER="${2}"
            shift 2
            ;;
        --username|-u)
            USERNAME="${2}"
            shift 2
            ;;
        *)
            echo "Unknown option: ${1}"
            showHelp
            ;;
    esac
done

[[ -z ${COLLECTION} || -z ${PROJECT} || -z ${SERVER} || -z ${USERNAME} ]] && { echo "You must specify a value for all script options other than \"--password\""; showHelp; }
[[ -z ${PASSWORD} ]] && {
    stty -echo
    printf "Enter password for user ${USERNAME} on server ${SERVER}: "
    read PASSWORD
    stty echo
}

[[ -z ${PASSWORD} ]] && { echo "No password entered!"; showHelp; }

echo "Server:     ${SERVER}"
echo "Username:   ${USERNAME}"
echo "Project:    ${PROJECT}"
echo "Collection: ${COLLECTION}"

SESSION="$(http --auth=${USERNAME}:${PASSWORD} --session=${USERNAME} --pretty=format --check-status --body ${SERVER}/data/JSESSION)"
[[ ${?} == 0 ]] && { echo "Authenticated with session ID ${SESSION}, beginning"; } || { echo "Failed to authenticate"; exit 1; }


# Get IDs of all collections in project
# http --session=${USERNAME} --pretty=format --body ${SERVER}/xapi/sets/collections/projects/${PROJECT} | jq '.[] | .id' | sort | tr -d '"'

# Select a collection
# Could select from the list returned by the call above. For now, collection is a required input parameter.

# Get a list of files in the collection: commented call below is plain call to render full collection object, second renders just the file paths, third extracts experiment label. Format of path is something like:
#
#    /data/xnat/archive/AbdomenCT-RSNA2019/arc001/48/SCANS/1/NIFTI/input_IMAGES_20191025163500_1.nii
#
# http --session=${USERNAME} --pretty=format --body ${SERVER}/xapi/sets/collections/${COLLECTION} format==json
# http --session=${USERNAME} --pretty=format --body ${SERVER}/xapi/sets/collections/${COLLECTION} format==json | jq '.files | .[] | .image, .label' | sort | tr -d '"'

# Validate collection ID

http --session=${USERNAME} --pretty=format --check-status --body ${SERVER}/xapi/sets/collections/${COLLECTION} format==json &> /dev/null
[[ ${?} != 0 ]] && { echo "The collection ID ${COLLECTION} doesn't appear to be a valid ID. Please check the ID and try again."; exit 3; }

http --session=${USERNAME} --pretty=format --body ${SERVER}/xapi/sets/collections/${COLLECTION} format==json | jq '.files | .[] | .image, .label' | sort | tr -d '"' | while read DATA_PATH; do
    EXPERIMENT="$(echo ${DATA_PATH} | sed -E "s#^.*/${PROJECT}/arc[0-9]+/([^/]+)/.*#\1#")"
    EXPT_ID="$(http --session=${USERNAME} --pretty=format --ignore-stdin ${SERVER}/data/projects/${PROJECT}/experiments/${EXPERIMENT} format==json | jq '.items | .[] | .data_fields.ID' | tr -d '"')"
    SCAN="$(echo ${DATA_PATH} | sed -E "s#^.*/${PROJECT}/arc[0-9]+/${EXPERIMENT}/SCANS/([^/]+)/.*#\1#")"
    RESOURCE="$(echo ${DATA_PATH} | sed -E "s#^.*/${PROJECT}/arc[0-9]+/${EXPERIMENT}/SCANS/${SCAN}/([^/]+)/.*#\1#")"
    FILE="$(echo ${DATA_PATH} | sed -E "s#^.*/${PROJECT}/arc[0-9]+/${EXPERIMENT}/SCANS/${SCAN}/${RESOURCE}/(.*)#\1#")"
    OUTPUT_FOLDER="${PROJECT}/${SUBJECT}/${EXPERIMENT}/${SCAN}/${RESOURCE}"
    echo "Downloading file ${FILE} to ${OUTPUT_FOLDER}"
    mkdir -p ${OUTPUT_FOLDER}
    http --session=${USERNAME} --pretty=format --download --output=${OUTPUT_FOLDER}/${FILE} --ignore-stdin --body ${SERVER}/data/experiments/${EXPT_ID}/scans/${SCAN}/resources/${RESOURCE}/files/${FILE}
done

# Close session
http --session=${USERNAME} --pretty=format --check-status --body DELETE ${SERVER}/data/JSESSION