From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 31 Jul 2024 15:38:42 +0000 (+0100)
Subject: JAL-3631 Changes to bash launcher to allow headless updates to user-space or installa... 
X-Git-Tag: Release_2_11_4_0~17^2~3^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ba6b59f8f3995f6161b0bd9518773e60a1ebcf16;p=jalview.git

JAL-3631 Changes to bash launcher to allow headless updates to user-space or installation. Added some of this functionality to Powershell (work in progress).  The update functionality is to be separated out to update.sh.
---

diff --git a/utils/getdown/bin/jalview.ps1 b/utils/getdown/bin/jalview.ps1
index 1098010..d57b1de 100755
--- a/utils/getdown/bin/jalview.ps1
+++ b/utils/getdown/bin/jalview.ps1
@@ -16,6 +16,44 @@ if ( $IsWindows -eq $null ) {
   $myIsMacOS = $IsMacOS
 }
 
+# are we running an update
+[bool] $update = 0
+[bool] $updateuser = 0
+[bool] $updateinstallation = 0
+[bool] $headless = 0
+[bool] $help = 0
+[bool] $gui = 0
+[bool] $debug = 0
+for ( $i = 0; $i -lt $args.count; $i++ ) {
+  if ( $args[$i] -eq "--updateuser" ) {
+    $update = 1
+    $updateuser = 1
+    $headless = 1
+  }
+  if ( $args[$i] -eq "--updateinstallation" ) {
+    $update = 1
+    $updateinstallation = 1
+    $headless = 1
+  }
+  if ( $args[$i] -eq "--help" -or $args[$i].StartsWith("--help-") -or $args[$i] -eq "--version" -or $args[$i] -eq "-h" ) {
+    $help = 1
+    $headless = 1
+  }
+  if ( $args[$i] -eq "--gui" ) {
+    $gui = 1
+  }
+  if ( $args[$i] -eq "--debug" ) {
+    $debug = 1
+  }
+}
+if ( $help ) {
+  $gui = 0
+} elseif ( $update ) {
+  $gui = 0
+} elseif ( $gui ) {
+  $headless = 0
+}
+
 # parent dir of this actual script (which should be the getdown appdir/bin). Follow all symlinks.  Like GNU readlink -f
 function Readlink-f {
   Param($Link)
@@ -52,37 +90,100 @@ if ( $MyInvocation.MyCommand.Path -eq $null ) {
   throw "Script or link to script must have extension .ps1"
 }
 
-
 $CMDPATH = ( Get-Item $MyInvocation.MyCommand.Path )
 $SCRIPTPATH = Readlink-f -Link $CMDPATH
+$SCRIPT = $SCRIPTPATH
 $DIR = Split-Path -Path $SCRIPTPATH -Parent
 
 $APPDIR = If ( ( Split-Path -Path $DIR -Leaf ) -eq "bin" ) { Split-Path -Path $DIR -Parent } Else { $DIR }
 $JAVAEXE = If ( $myIsWindows ) { "java.exe" } Else { "java" }
 $JAVA = Join-Path -Path $APPDIR -ChildPath ( "jre/" + $( If ( $myIsMacOS ) { "Contents/Home/" } Else { "" } ) + "bin/${JAVAEXE}" )
-$GETDOWNTXT = Join-Path -Path $APPDIR -ChildPath "getdown.txt"
+$JVMARGS = @()
 
-# look for getdown.txt -- needed to create classpath
-if ( -not ( Test-Path -Path "${GETDOWNTXT}" ) ) {
-  throw "Cannot find ${GETDOWNTXT}"
+if ( $headless ) {
+  # not setting java.awt.headless in java invocation of running jalview due to problem with Jmol
+  if ( $help ) {
+    $JVMARGS += "-Djava.awt.headless=true"
+  }
+  # this suppresses the Java icon appearing in the macOS Dock
+  if ( $myIsMacOS ) {
+    $JVMARGS += "-Dapple.awt.UIElement=true"
+  }
 }
 
+$GETDOWNTXT = Join-Path -Path $APPDIR -ChildPath "getdown.txt"
+$GETDOWNJAR = Join-Path -Path $APPDIR -ChildPath "getdown-launcher.jar"
+
 # look for bundled JRE. Might not be there if unix installer used in which case just invoke "java"
 if ( -not ( Test-Path -Path "${JAVA}" ) ) {
   Write-Host "Cannot find bundled ${JAVAEXE}. Using system ${JAVAEXE} and hoping for the best!"
   $JAVA = $JAVAEXE
 }
 
-$CLASSPATH = ( Select-String -Path "${GETDOWNTXT}" -AllMatches -Pattern "code\s*=\s*(.*)$" | foreach { Join-Path -Path $APPDIR -ChildPath $($_.Matches.Groups[1].Value ) } ) -join $( If ( $myIsWindows ) { ";" } Else { ":" } )
+$CLASS = "jalview.bin.Launcher"
+if ( $update ) {
+
+  # JUST RUNNING A GETDOWN INSTALLATION UPDATE, not launching Jalview
+  $CLASS = "com.threerings.getdown.launcher.GetdownApp"
 
-# get console width
-$CONSOLEWIDTH = $Host.UI.RawUI.WindowSize.Width
+  $CLASSPATH = $GETDOWNJAR
+
+  # installation update
+  if ( $updateinstallation ) {
+    $JVMARGS += "-Dnouserdefaultappdir=true"
+  }
+
+  # tell getdown to update jalview without launching
+  $JVMARGS += "-Dsilent=true"
+  $JVMARGS += "-Dlauncher.script=${SCRIPT}"
+  $JVMARGS += "-Dlauncher.update=true"
+  $JVMARGS += "-Dappid=jalview"
+  $JVMARGS += "-Dinstaller.appdir=${APPDIR}"
+  # resetting ARGS to just these two values
+  $myArgs = @("${APPDIR}", "jalview")
+  # add these Just In Case although jalview shouldn't be launched
+  $myArgs += "--headless", "--quit", "--nojavaconsole", "--nosplash", "--nonews"
+
+} else {
+
+  # LAUNCHING JALVIEW without getdown-launcher
+  $CLASS = "jalview.bin.Launcher"
+  # look for getdown.txt -- needed to create classpath
+  if ( -not ( Test-Path -Path "${GETDOWNTXT}" ) ) {
+    throw "Cannot find ${GETDOWNTXT}"
+  }
+  # get CLASSPATH from the code= entries in getdown.txt
+  $CLASSPATH = ( Select-String -Path "${GETDOWNTXT}" -AllMatches -Pattern "code\s*=\s*(.*)$" | foreach { Join-Path -Path $APPDIR -ChildPath $($_.Matches.Groups[1].Value ) } ) -join $( If ( $myIsWindows ) { ";" } Else { ":" } )
+
+  # get console width
+  $CONSOLEWIDTH = $Host.UI.RawUI.WindowSize.Width
+  $JVMARGS += "-DCONSOLEWIDTH=${CONSOLEWIDTH}"
+  $JVMARGS += "-Dgetdownappdir=${APPDIR}"
+  $JVMARGS += "-Dinstaller.appdir=${APPDIR}"
+  $JVMARGS += "-Dlauncher.appdir=${APPDIR}"
+  $JVMARGS += "-Dlauncher.script=${SCRIPT}"
+
+}
+
+# we should always have at least one JVMARGS
+$myJvmArgsString = '"' + $($JVMARGS -join '" "') + '"'
 
 # quote the args and the command (in case of spaces) with escape chars (`) and precede with & to indicate command not string
 if ( $myArgs.count -eq 0 ) {
-  Invoke-Expression -Command "& `"${JAVA}`" `"-DCONSOLEWIDTH=${CONSOLEWIDTH}`" `"-Dgetdownappdir=${APPDIR}`" -cp `"${CLASSPATH}`" jalview.bin.Launcher"
+  $COMMAND = "& `"${JAVA}`" ${myJvmArgsString} -cp `"${CLASSPATH}`" $CLASS"
 } else {
   $myArgsString = '"' + $($myArgs -join '" "') + '"'
-  Invoke-Expression -Command "& `"${JAVA}`" `"-DCONSOLEWIDTH=${CONSOLEWIDTH}`" `"-Dgetdownappdir=${APPDIR}`" -cp `"${CLASSPATH}`" jalview.bin.Launcher ${myArgsString}"
+  $COMMAND = "& `"${JAVA}`" ${myJvmArgsString} -cp `"${CLASSPATH}`" $CLASS ${myArgsString}"
 }
 
+if ( $debug -or $help ) {
+  Write-Error -Message "Shell running: ${COMMAND}"
+}
+
+Invoke-Expression -Command ${COMMAND}
+
+# move updated getdown-launcher.jar into place
+if ( $update )
+  Invoke-Expression -Command "& `"${JAVA}`" ${myJvmArgString} -cp `"${GDCOREPATH}`" jalview.bin.GetdownUpdate `"${APPDIR}`"
+fi
+
diff --git a/utils/getdown/bin/jalview.sh b/utils/getdown/bin/jalview.sh
index 9fb7058..58a13d8 100755
--- a/utils/getdown/bin/jalview.sh
+++ b/utils/getdown/bin/jalview.sh
@@ -124,15 +124,37 @@ fi
 SYSJAVA=java
 GETDOWNTXT="${APPDIR}/getdown.txt"
 GETDOWNJAR="${APPDIR}/getdown-launcher.jar"
+CHANNELPROPS="${APPDIR}/channel.props"
+NAME="$( grep app_name= App/channel.props | cut -d= -f2 )"
+US_NAME="${NAME// /_}"
 
 CLASSPATH=""
 # save an array of JAR paths in case we're in WSL (see later)
 declare -a JARPATHS=()
+declare -a APPJARPATHS=()
+GDCOREPATH="${APPDIR}/resource/getdown-core.jar"
+
+# get classpath from getdown.txt
+if [ -e "${GETDOWNTXT}" ]; then
+  # always check grep and sed regexes on macos -- they're not the same
+  for JAR in $(grep -e '^code[[:space:]]*=[[:space:]]*' "${GETDOWNTXT}" | while read -r line; do echo $line | sed -E -e 's/code[[:space:]]*=[[:space:]]*//;'; done);
+  do
+    [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
+    CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
+    APPJARPATHS=( "${APPJARPATHS[@]}" "${APPDIR}/${JAR}" )
+    if [ "${JAR}" != "${JAR%getdown-core.jar}" -a \! -e "${GDCOREPATH}" ]; then
+      GDCOREPATH="${APPDIR}/${JAR}"
+    fi
+  done
+else
+  echo "Cannot find getdown.txt" >&2
+  exit 3
+fi
 
 CLASS="jalview.bin.Launcher" # set as default Just In Case
 if [ "${UPDATE}" = 1 ]; then
 
-  # JUST RUNNING A GETDOWN INSTALLATION UPDATE, not launching Jalview
+  # GETDOWN UPDATE ONLY, not launching Jalview
   CLASS="com.threerings.getdown.launcher.GetdownApp"
   if [ -e "${GETDOWNJAR}" ]; then
     CLASSPATH="${GETDOWNJAR}"
@@ -142,7 +164,7 @@ if [ "${UPDATE}" = 1 ]; then
     exit 13
   fi
 
-  # user-space update
+  # USER space update
   if [ "${UPDATEUSER}" = 1 ]; then
     if [ -e "${VMOPTIONS}" ]; then
       LINENUM=0
@@ -170,40 +192,37 @@ if [ "${UPDATE}" = 1 ]; then
       done < "${VMOPTIONS}"
     fi
     JVMARGS=( "${JVMARGS[@]}" "-Duserdefaultappdir=true" )
+    # resetting ARGS to just these two blank values so userappdir is determined
+    ARGS=( "" "jalview" )
   fi
 
-  # installation update
+  # INSTALLATION update
   if [ "${UPDATEINSTALLATION}" = 1 ]; then
     JVMARGS=( "${JVMARGS[@]}" "-Dnouserdefaultappdir=true" )
+    JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.appdir=${APPDIR}" )
+    # resetting ARGS to just these two values
+    ARGS=( "${APPDIR}" "jalview" )
   fi
 
+  # both USER and INSTALLATION updates
+  JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.appdir=${APPDIR}" )
+
   # tell getdown to update jalview withouth launching
   JVMARGS=( "${JVMARGS[@]}" "-Dsilent=true" )
-  JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.script=${SCRIPT}" )
+
   JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.update=true" )
   JVMARGS=( "${JVMARGS[@]}" "-Dappid=jalview" )
-  JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.appdir=${APPDIR}" )
+  JVMARGS=( "${JVMARGS[@]}" "-Dchannel.app_name=${NAME}" )
+  JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.application_folder=${US_NAME}" )
 
-  # resetting ARGS to just these two values
-  ARGS=( "${APPDIR}" "jalview" )
-  # add these Just In Case although jalview shouldn't be launched
+  # add these Just In Case although jalview shouldn't be launched due to -Dsilent=true
   ARGS=( "${ARGS[@]}" "--headless" "--quit" "--nojavaconsole" "--nosplash" "--nonews" )
+
 else
 
   # LAUNCHING JALVIEW without getdown-launcher
   CLASS="jalview.bin.Launcher"
-  if [ -e "${GETDOWNTXT}" ]; then
-    # always check grep and sed regexes on macos -- they're not the same
-    for JAR in $(grep -e '^code[[:space:]]*=[[:space:]]*' "${GETDOWNTXT}" | while read -r line; do echo $line | sed -E -e 's/code[[:space:]]*=[[:space:]]*//;'; done);
-    do
-      [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
-      CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
-      JARPATHS=( "${JARPATHS[@]}" "${APPDIR}/${JAR}" )
-    done
-  else
-    echo "Cannot find getdown.txt" >&2
-    exit 3
-  fi
+  JARPATHS="${APPJARPATHS[@]}"
 
   COLUMNS=80
   # get console width -- three ways to try, just in case (not needed for update)
@@ -217,13 +236,13 @@ else
 
   JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" )
   JVMARGS=( "${JVMARGS[@]}" "-Dgetdownappdir=${APPDIR}" )
-  JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.appdir=${APPDIR}" )
-  JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.appdir=${APPDIR}" )
-  JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.script=${SCRIPT}" )
+
 fi
+JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.script=${SCRIPT}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.appdir=${APPDIR}" )
 
-# WINDOWS ONLY (Cygwin or WSL)
-# change paths for Cygwin or Windows Subsystem for Linux (WSL)
+# WINDOWS ONLY in Cygwin or Windows Subsystem for Linux (WSL)
+# change paths for Cygwin or WSL
 if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
   if [ "$(uname -o)" = "Cygwin" ]; then # Cygwin
   # CYGWIN
@@ -237,7 +256,7 @@ if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoi
         ARGS=( "${ARGS[@]}" "${ARG}" )
       fi
     done
-  elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then # Windows Subsystem for Linux (WSL)
+  elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then # WSL
   # WSL
     CLASSPATH=""
     for JARPATH in "${JARPATHS[@]}"; do
@@ -286,3 +305,11 @@ if [ "${DEBUG}" = 1 ]; then
 fi
 
 "${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" "${CLASS}" "${ARGS[@]}"
+
+# move updated getdown-launcher.jar into place
+if [ "${DEBUG}" = 1 ]; then
+  echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -cp \""${GDCOREPATH}"\" jalview.bin.GetdownLauncherUpdate >&2
+fi
+if [ "${UPDATE}" = 1 ]; then
+  "${JAVA}" "${JVMARGS[@]}" -cp "${GDCOREPATH}" jalview.bin.GetdownLauncherUpdate
+fi