JAL-3631 Add --updateuser and --updateinstallation to the jalview.sh script: This...

diff --git a/utils/getdown/bin/jalview.sh b/utils/getdown/bin/jalview.sh
index e2e7599..9fb7058 100755 (executable)
--- a/utils/getdown/bin/jalview.sh
+++ b/utils/getdown/bin/jalview.sh
@@ -41,6 +41,8 @@ GUI=0
 HELP=0
 DEBUG=0
 UPDATE=0
+UPDATEUSER=0
+UPDATEINSTALLATION=0
 for RAWARG in "${@}"; do
   ARG="${RAWARG%%=*}"
   case "${ARG}" in
@@ -49,6 +51,7 @@ for RAWARG in "${@}"; do
       ;;
     --help|--help-*|--version|-h)
       HELP=1
+      HEADLESS=1
       ;;
     --gui)
       GUI=1
@@ -56,24 +59,30 @@ for RAWARG in "${@}"; do
     --debug)
       DEBUG=1
       ;;
-    --update)
+    --updateinstallation)
       UPDATE=1
+      UPDATEINSTALLATION=1
+      HEADLESS=1
+      ;;
+    --updateuser)
+      UPDATE=1
+      UPDATEUSER=1
+      HEADLESS=1
       ;;
   esac
 done
 if [ "${HELP}" = 1 ]; then
   # --help takes precedence
-  HEADLESS=1
   GUI=0
 elif [ "${UPDATE}" = 1 ]; then
   # --update takes precedence over everything else, we don't run jalview!
-  HEADLESS=1
   GUI=0
 elif [ "${GUI}" = 1 ]; then
   # --gui takes precedence over --headless
   HEADLESS=0
 fi
 
+# args for the JVM
 declare -a JVMARGS=()
 
 # set vars for being inside the macos App Bundle
@@ -86,14 +95,21 @@ if [ "${ISMACOS}" = 1 ]; then
   if [ "${HEADLESS}" != 1 ]; then
    JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
   fi
+  # e.g. APPFOLDER=/Applications/Jalview.app
+  APPFOLDER="${APPDIR%%.app/*}.app"
+  VMOPTIONS="${APPFOLDER}/Contents/vmoptions.txt"
 else
 # NOT MACOS
   SCRIPT="$(readlink -f "$0")"
   DIR="$(dirname "${SCRIPT}")"
   APPDIR="${DIR%/bin}"
   JAVA="${APPDIR}/jre/bin/java"
+  # e.g. APPFOLDER=/opt/jalview
+  APPFOLDER="${APPDIR}"
+  VMOPTIONS="${APPDIR}/jalviewg.vmoptions"
 fi
 
+# headless java arguments
 if [ "${HEADLESS}" = 1 ]; then
   # not setting java.awt.headless in java invocation of running jalview due to problem with Jmol
   if [ "${HELP}" = 1 ]; then
@@ -119,21 +135,59 @@ if [ "${UPDATE}" = 1 ]; then
   # JUST RUNNING A GETDOWN INSTALLATION UPDATE, not launching Jalview
   CLASS="com.threerings.getdown.launcher.GetdownApp"
   if [ -e "${GETDOWNJAR}" ]; then
-    CLASSPATH="${APPDIR}/${GETDOWNJAR}"
-    JARPATHS=( "${JARPATHS[@]}" "${APPDIR}/${GETDOWNJAR}" )
+    CLASSPATH="${GETDOWNJAR}"
+    JARPATHS=( "${JARPATHS[@]}" "${GETDOWNJAR}" )
   else
     echo "Cannot find getdown-launcher.jar to run update" >&2
     exit 13
   fi
 
+  # user-space update
+  if [ "${UPDATEUSER}" = 1 ]; then
+    if [ -e "${VMOPTIONS}" ]; then
+      LINENUM=0
+      while IFS= read -r line; do
+        # remove comments
+        line=${line%%#*}
+        # remove trailing whitespace
+        line="${line%"${line##*[![:space:]]}"}"
+        LINENUM=$((LINENUM+1))
+
+        # add settings for user appdir
+        if [ "${line}" != "${line#-Dsetuserappdirpath=}" ]; then # starts with -Dsetuserappdirpath=
+          JVMARGS=( "${JVMARGS[@]}" "${line}" )
+        fi
+        if [ "${line}" != "${line#-Dnouserdefaultappdir=}" ]; then # starts with -Dnouserdefaultappdir=
+          # don't perform user update if user updates are disabled
+          NOUSERUPDATEVALUE="$(echo "${line#-Dnouserdefaultappdir=}" | tr '[:upper:]' '[:lower:]')"
+          if [ "${NOUSERUPDATEVALUE}" = "true" ]; then
+            echo "Cannot perform manual user-space update when user-space updates are disabled." >&2
+            echo "See line ${LINENUM} (${line}) in file '${VMOPTIONS}'." >&2
+            exit 14
+          fi
+          JVMARGS=( "${JVMARGS[@]}" "${line}" )
+        fi
+      done < "${VMOPTIONS}"
+    fi
+    JVMARGS=( "${JVMARGS[@]}" "-Duserdefaultappdir=true" )
+  fi
+
+  # installation update
+  if [ "${UPDATEINSTALLATION}" = 1 ]; then
+    JVMARGS=( "${JVMARGS[@]}" "-Dnouserdefaultappdir=true" )
+  fi
+
+  # tell getdown to update jalview withouth launching
   JVMARGS=( "${JVMARGS[@]}" "-Dsilent=true" )
-  JVMARGS=( "${JVMARGS[@]}" "-Dnouserdefaultappdir=true" )
+  JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.script=${SCRIPT}" )
+  JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.update=true" )
   JVMARGS=( "${JVMARGS[@]}" "-Dappid=jalview" )
   JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.appdir=${APPDIR}" )
 
   # resetting ARGS to just these two values
   ARGS=( "${APPDIR}" "jalview" )
-
+  # add these Just In Case although jalview shouldn't be launched
+  ARGS=( "${ARGS[@]}" "--headless" "--quit" "--nojavaconsole" "--nosplash" "--nonews" )
 else
 
   # LAUNCHING JALVIEW without getdown-launcher
@@ -166,13 +220,12 @@ else
   JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.appdir=${APPDIR}" )
   JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.appdir=${APPDIR}" )
   JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.script=${SCRIPT}" )
-
 fi
 
 # WINDOWS ONLY (Cygwin or WSL)
 # change paths for Cygwin or Windows Subsystem for Linux (WSL)
 if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
-  if [ "$(uname -o)" = "Cygwin" ]; then
+  if [ "$(uname -o)" = "Cygwin" ]; then # Cygwin
   # CYGWIN
     CLASSPATH=$(cygpath -pw "${CLASSPATH}")
     # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
@@ -184,7 +237,7 @@ if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoi
         ARGS=( "${ARGS[@]}" "${ARG}" )
       fi
     done
-  elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
+  elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then # Windows Subsystem for Linux (WSL)
   # WSL
     CLASSPATH=""
     for JARPATH in "${JARPATHS[@]}"; do
@@ -207,10 +260,10 @@ if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoi
   fi
 fi
 
-# Is there a bundled Java?  If not just try one in the PATH (do need .exe in WSL)
+# Is there a bundled Java?  If not just try one in the PATH (we need .exe in WSL, added above)
 if [ \! -e "${JAVA}" ]; then
   JAVA=$SYSJAVA
-  echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
+  echo "Cannot find bundled ${JAVA}, using system ${SYSJAVA} and hoping for the best!" >&2
 fi
 
 # This is just needed for display purposes
@@ -229,7 +282,7 @@ JVMARGSSTR=$(quotearray "${JVMARGS[@]}")
 ARGSSTR=$(quotearray "${ARGS[@]}")
 
 if [ "${DEBUG}" = 1 ]; then
- echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -cp \""${CLASSPATH}"\" "${CLASS}" ${ARGSSTR}
+ echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -cp \""${CLASSPATH}"\" \""${CLASS}"\" ${ARGSSTR} >&2
 fi
 
 "${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" "${CLASS}" "${ARGS[@]}"