From 87ab843ae2e9afa891535b885d49d16ce6d1fce5 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 26 Aug 2024 17:44:30 +0100
Subject: [PATCH] JAL-3631 When appdir/jre can't be found, look for the
 installer.appdir found in installer.properties (if it
 exists) and use jre dir in installer.appdir

---
 utils/getdown/bin/jalview.sh |   36 +++++++++++++++++++++++++++---------
 1 file changed, 27 insertions(+), 9 deletions(-)

diff --git a/utils/getdown/bin/jalview.sh b/utils/getdown/bin/jalview.sh
index 95e6fae..04a9144 100755
--- a/utils/getdown/bin/jalview.sh
+++ b/utils/getdown/bin/jalview.sh
@@ -69,25 +69,43 @@ function readlinkf() {
 # args for the JVM
 declare -a JVMARGS=()
 
+JAVABIN=""
 # set vars for being inside the macos App Bundle
 if [ "${ISMACOS}" = 1 ]; then
 # MACOS ONLY
   SCRIPT="$(readlinkf "$0")"
   DIR="$(dirname "${SCRIPT}")"
   APPDIR="${DIR%/bin}"
-  JAVABIN="${APPDIR}/jre/Contents/Home/bin"
-  JAVA="${JAVABIN}/java"
+
+  if [ -d "${APPDIR}/jre" ]; then
+    JREDIR="${APPDIR}/jre"
+  elif [ -e "${APPDIR}/installer.properties" ]; then
+    INSTALLERAPPDIR="$( grep -E '^installer.appdir[[:space:]]*=[[:space:]]*' '${APPDIR}/installer.properties' | sed -E 's/^installer.appdir[[:space:]]*=[[:space:]]*//' )"
+    if [ -d "${INSTALLERAPPDIR}/jre" ]; then
+      JREDIR="${INSTALLERAPPDIR}/jre"
+    fi
+  fi
+  if [ ! -z "$JREDIR" ]; then
+    JAVABIN="${JREDIR}/Contents/Home/bin"
+  fi
   if [ "${HEADLESS}" != 1 ]; then
-   JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
+    JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
   fi
 else
 # NOT MACOS
   SCRIPT="$(readlink -f "$0")"
   DIR="$(dirname "${SCRIPT}")"
   APPDIR="${DIR%/bin}"
-  JAVABIN="${APPDIR}/jre/bin"
-  JAVA="${JAVABIN}/java"
+  if [ -d "${APPDIR}/jre" ]; then
+    JAVABIN="${APPDIR}/jre/bin"
+  elif [ -e "${APPDIR}/installer.properties" ]; then
+    INSTALLERAPPDIR="$( grep -E "^installer.appdir[[:space:]]*=[[:space:]]*" "${APPDIR}/installer.properties" | sed -E 's/^installer.appdir[[:space:]]*=[[:space:]]*//' )"
+    if [ ! -z "$INSTALLERAPPDIR" -a -d "${INSTALLERAPPDIR}/jre" ]; then
+      JAVABIN="${INSTALLERAPPDIR}/jre/bin"
+    fi
+  fi
 fi
+JAVA="${JAVABIN}/java"
 
 # headless java arguments
 if [ "${HEADLESS}" = 1 ]; then
@@ -111,7 +129,7 @@ CLASSPATH=""
 declare -a JARPATHS=()
 
 # look for getdown.txt -- needed to create classpath
-if [ \! -e "${GETDOWNTXT}" ]; then
+if [ ! -e "${GETDOWNTXT}" ]; then
   echo "Cannot find ${GETDOWNTXT}" >&2
   exit 3
 fi
@@ -183,11 +201,11 @@ if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoi
 fi
 
 # look for bundled JRE. Might not be there if unix installer used in which case just invoke "java"
-if [ -e "${JAVABIN}/${NAME}${JAVAEXT}" ]; then
+if [ ! -z "${JAVABIN}" -a -e "${JAVABIN}/${NAME}${JAVAEXT}" ]; then
   JAVA="${JAVABIN}/${NAME}${JAVAEXT}"
 fi
 # If not just try one in the PATH (we need .exe in WSL, added above)
-if [ \! -e "${JAVA}" ]; then
+if [ -z "${JAVABIN}" -o ! -e "${JAVA}" ]; then
   JAVA="${SYSJAVA}"
   echo "Cannot find bundled ${JAVA}, using system ${SYSJAVA} and hoping for the best!" >&2
 fi
@@ -196,7 +214,7 @@ fi
 function quotearray() {
   QUOTEDVALS=""
   for VAL in "${@}"; do
-    if [ \! "$QUOTEDVALS" = "" ]; then
+    if [ ! "$QUOTEDVALS" = "" ]; then
       QUOTEDVALS="${QUOTEDVALS} "
     fi
     QUOTEDVALS="${QUOTEDVALS}\"${VAL}\""
-- 
1.7.10.2