oops bring back deleted file

Author: baxpr

copy_subject.sh

@@ -0,0 +1,97 @@
+#!/bin/bash
+#
+# Copy certain DICOMs of a subject from one project to another on XNAT
+#
+# A DAX installation is required, and its python venv must be active.
+
+# Default options
+skipvars="no"
+
+# Parse options
+while [[ $# -gt 0 ]]
+do
+	key="${1}"
+	case "${key}" in
+		--source_project)
+			source_project="${2}"; shift; shift ;;
+		--dest_project)
+			dest_project="${2}"; shift; shift ;;
+		--subjects)
+			subjects="${2}"; shift; shift ;;
+		--scan_types)
+			scan_types="${2}"; shift; shift ;;
+		--skipvars)
+			skipvars="yes"; shift ;;
+		*)
+			echo Unknown input "${1}"; shift ;;
+	esac
+done
+
+# Check for params
+if [ -z "${source_project}" ] \
+	|| [ -z "${dest_project}" ] \
+	|| [ -z "${subjects}" ] \
+	|| [ -z "${scan_types}" ] ; then
+	cat << HERE
+Usage example:
+    ${0} \\
+      --source_project SOURCE_PROJ \\
+      --dest_project DESTINATION_PROJ \\
+      --subjects 123456,234567,345678 \\
+      --scan_types "T1,Rest"
+HERE
+	exit 0
+fi
+	
+
+# Where are our scripts? We need to find the python code
+function realpath() {
+    if ! pushd $1 &> /dev/null; then 
+        pushd ${1##*/} &> /dev/null
+        echo $( pwd -P )/${1%/*}
+    else
+        pwd -P
+    fi
+    popd > /dev/null
+}
+script_dir=$(realpath $(dirname "${0}"))
+
+
+# Check for subjects already present in dest project
+echo "Checking subject list ${subjects}"
+subjlist=$(echo ${subjects} | tr ',' ' ')
+for subj in ${subjlist} ; do
+	python "${script_dir}"/check_for_subject.py "${dest_project}" "${subj}" \
+	|| exit 1
+done
+
+
+# Make temporary directory
+tmp_dir=$(mktemp -d copy_subject.XXXXXX) || exit 1
+
+# Download
+Xnatdownload -p "${source_project}" -d "${tmp_dir}" --subj "${subjects}" -s "${scan_types}" --rs DICOM
+
+# Replace project name in download report CSV
+cat "${tmp_dir}"/download_report.csv | \
+	sed s/^scan,${source_project}/scan,${dest_project}/ > \
+	"${tmp_dir}"/upload.csv
+
+# Upload. Note, if target resource already exists, Xnatupload prints a warning and does
+# not do the upload.
+Xnatupload --csv "${tmp_dir}"/upload.csv
+
+# Clean up
+if [ -d "${tmp_dir}" ] ; then
+	rm -fr "${tmp_dir}"
+fi
+
+
+# Set subject and session variables
+if [[ "${skipvars}" == "no" ]]; then
+	subjlist=$(echo ${subjects} | tr ',' ' ')
+	for subj in ${subjlist} ; do
+		echo "Copying subject and session vars for ${subj}"
+		python "${script_dir}"/set_vars.py "${source_project}" "${dest_project}" "${subj}"
+	done
+fi