From b3aa009895567ae6c7131c2c09aefb7def40fc7a Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 19 Aug 2024 17:08:12 +0100
Subject: [PATCH] JAL-3631 Change macos-install-jalview.sh to use ditto
 instead of rsync. Localise function vars.

---
 utils/install4j/macos-install-jalview.sh |   39 ++++++++++++++++++++----------
 1 file changed, 26 insertions(+), 13 deletions(-)

diff --git a/utils/install4j/macos-install-jalview.sh b/utils/install4j/macos-install-jalview.sh
index aa9f0fd..9b40271 100755
--- a/utils/install4j/macos-install-jalview.sh
+++ b/utils/install4j/macos-install-jalview.sh
@@ -232,35 +232,48 @@ hdiutil attach ${HDIUTILOPT} -mountpoint "${VOLUMEDIR}" "${DMGFILE}"
 VOLUMEFILES=$( ls -1 ${VOLUMEDIR} )
 while IFS= read -r VOLUMEFILE; do
   FILE=$( basename "${VOLUMEFILE}" )
-  if [ "${FILE}" != "${FILE#Jalview}" -a "${FILE}" != "${FILE%.app}" ]; then
-    APP="${FILE}"
+  if [ "$FILE" != "${FILE#Jalview}" -a "$FILE" != "${FILE%.app}" ]; then
+    APP="$FILE"
     break
   fi
 done <<< "$VOLUMEFILES"
-[ -z "${APP}" ] && echo "Could not find Jalview\*.app in the volume '${VOLUMEDIR}'" && exit 10
+[ -z "$APP" ] && echo "Could not find Jalview\*.app in the volume '${VOLUMEDIR}'" && exit 10
 
 APPNAME=$( basename "$APP" )
 
 # ensure no trailing slash on APPNAME or APPLICATIONFOLDER (important for rsync)
-while [ "${APPLICATIONFOLDER}" != "${APPLICATIONFOLDER%/}" -a "${APPLICATIONFOLDER}" != "/" ]; do
+while [ "${APPLICATIONFOLDER}" != "/" ]; do
   APPLICATIONFOLDER=${APPLICATIONFOLDER%/}
 done
 while [ "${APPNAME}" != "${APPNAME%/}" ]; do
   APPNAME=${APPNAME%/}
 done
-[ -z "${APPNAME}" ] && echo "Could not find suitable Jalview\*.app in the volume '${VOLUMEDIR}'" && exit 11
-
-# rsync .app from mounted volume to application folder
-myecho "Rsyncing '${VOLUMEDIR}/${APPNAME}' to '${APPLICATIONFOLDER}/${APPNAME}'"
-rsync ${RSYNCOPT} -ah --delete "${VOLUMEDIR}/${APPNAME}" "${APPLICATIONFOLDER}/"
-[ $? != 0 ] && echo "Possible problem when rsyncing '${APP}' to '${APPLICATIONFOLDER}'" && exit 12
-myecho "Finished rsync"
+[ -z "$APPNAME" -o "${APPNAME%.app}" = "$APPNAME" ] && echo "Could not find suitable Jalview\*.app in the volume '${VOLUMEDIR}'" && exit 11
+
+## rsync .app from mounted volume to application folder
+#myecho "Rsyncing '${VOLUMEDIR}/${APPNAME}' to '${APPLICATIONFOLDER}/${APPNAME}'"
+#rsync ${RSYNCOPT} -ah --delete "${VOLUMEDIR}/${APPNAME}" "${APPLICATIONFOLDER}/"
+#[ $? != 0 ] && echo "Possible problem when rsyncing '${APP}' to '${APPLICATIONFOLDER}'" && exit 12
+#myecho "Finished rsync"
+
+# using ditto
+APPPATH="${APPLICATIONFOLDER}/${APPNAME}"
+OLDAPPPATH="${APPPATH}.old"
+myecho "Copying '${VOLUMEDIR}/${APPNAME}' to '${APPPATH}'"
+if [ -e "$APPPATH" ]; then
+  if [ -e "$OLDAPPPATH" ]; then
+    rm -Rf "$OLDAPPPATH"
+  fi
+  mv "$APPPATH" "$OLDAPPPATH"
+fi
+ditto "${VOLUMEDIR}/${APPNAME}" "$APPPATH" && [ -e "$OLDAPPPATH" ] && rm -Rf "$OLDAPPPATH"
+myecho "Finished copying '${APPNAME}'"
 
 EXIT=0
 declare -a WARNINGS=()
 addwarning() {
-  W=$1
-  N=$2
+  local W=$1
+  local N=$2
   myecho "${W}"
   WARNINGS=( "${WARNINGS[@]}" "${W}" )
   # exit with the first warning value
-- 
1.7.10.2