}
}
- def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+ def getdownWrapperScripts = [
+ getdown_bash_wrapper_script,
+ getdown_powershell_wrapper_script,
+ getdown_batch_wrapper_script,
+ getdown_bash_update_script,
+ getdown_powershell_update_script,
+ getdown_batch_update_script
+ ]
getdownWrapperScripts.each{ script ->
def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
if (s.exists()) {
'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script,
+ 'BASH_UPDATE_SCRIPT': getdown_bash_update_script,
+ 'POWERSHELL_UPDATE_SCRIPT': getdown_powershell_update_script,
+ 'BATCH_UPDATE_SCRIPT': getdown_batch_update_script,
'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
'MACOSARCHIVE_X64_NAME': install4jmacOSArchiveX64Name,
'MACOSARCHIVE_AARCH64_NAME': install4jmacOSArchiveAarch64Name,
getdown_bash_wrapper_script = jalview.sh
getdown_powershell_wrapper_script = jalview.ps1
getdown_batch_wrapper_script = jalview.bat
+getdown_bash_update_script = update.sh
+getdown_powershell_update_script = update.ps1
+getdown_batch_update_script = update.bat
OSX_KEYSTORE =
OSX_KEYPASS =
$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] $help = 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" ) {
+Switch -Regex ($args) {
+ "--help|--help-|--version|-h" {
$help = 1
$headless = 1
+ Continue
}
- if ( $args[$i] -eq "--gui" ) {
+ "--gui" {
$gui = 1
+ Continue
+ }
+ "--headless" {
+ $headless = 1
+ Continue
}
- if ( $args[$i] -eq "--debug" ) {
+ "--debug" {
$debug = 1
+ Continue
}
}
if ( $help ) {
- $gui = 0
-} elseif ( $update ) {
+ # --help takes precedence
$gui = 0
} elseif ( $gui ) {
+ # --gui takes precedence over --headless
$headless = 0
}
throw "Script or link to script must have extension .ps1"
}
+# args for the JVM
+$JVMARGS = @()
+
$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}" )
-$JVMARGS = @()
if ( $headless ) {
# not setting java.awt.headless in java invocation of running jalview due to problem with Jmol
}
$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 = $JAVAEXE
+# look for getdown.txt -- needed to create classpath
+if ( -not ( Test-Path -Path "${GETDOWNTXT}" ) ) {
+ throw "Cannot find ${GETDOWNTXT}"
}
+# launching Jalview with jalview.bin.Launcher instead of getdown-launcher.jar
$CLASS = "jalview.bin.Launcher"
-if ( $update ) {
-
- # JUST RUNNING A GETDOWN INSTALLATION UPDATE, not launching Jalview
- $CLASS = "com.threerings.getdown.launcher.GetdownApp"
-
- $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 ( $myIsWindows ) { ";" } Else { ":" } )
+# get CLASSPATH from the code= entries in getdown.txt
+$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}"
+# get console width
+$COLUMNS = $Host.UI.RawUI.WindowSize.Width
+$JVMARGS += "-DCONSOLEWIDTH=${COLUMNS}"
+$JVMARGS += "-Dgetdownappdir=${APPDIR}"
+$JVMARGS += "-Dinstaller.appdir=${APPDIR}"
+$JVMARGS += "-Dlauncher.script=${SCRIPT}"
+# look for bundled JRE. Might not be there if unix installer used in which case just invoke "java"
+if ( -not ( Test-Path -Path "${JAVA}" ) ) {
+ Write-Host "Cannot find bundled ${JAVA}. Using system ${JAVAEXE} and hoping for the best!"
+ $JAVA = $JAVAEXE
}
-# we should always have at least one JVMARGS
+# we should always have at least one JVMARGS so this is okay
$myJvmArgsString = '"' + $($JVMARGS -join '" "') + '"'
-# quote the args and the command (in case of spaces) with escape chars (`) and precede with & to indicate command not string
+# quote the args and the command (in case of spaces) with escape chars (`) and precede with & to indicate a command not string
if ( $myArgs.count -eq 0 ) {
$COMMAND = "& `"${JAVA}`" ${myJvmArgsString} -cp `"${CLASSPATH}`" $CLASS"
} else {
Invoke-Expression -Command ${COMMAND}
-# move updated getdown-launcher.jar into place
-if ( $update )
- Invoke-Expression -Command "& `"${JAVA}`" ${myJvmArgString} -cp `"${GDCOREPATH}`" jalview.bin.GetdownUpdate `"${APPDIR}`"
-fi
-
declare -a ARGS=("${@}")
-# this whole next part is because there's no readlink -f in Darwin
-function readlinkf() {
- FINDFILE="$1"
- FILE="${FINDFILE}"
- PREVFILE=""
- C=0
- MAX=100 # just in case we end up in a loop
- FOUND=0
- while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
- PREVFILE="${FILE}"
- FILE="$(readlink "${FILE}")"
- if [ -z "${FILE}" ]; then
- # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
- FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
- FOUND=1
- elif [ "${FILE#/}" = "${FILE}" ]; then
- # FILE is not an absolute path link, we need to add the relative path to the previous dir
- FILE="$(dirname "${PREVFILE}")/${FILE}"
- fi
- C=$((C+1))
- done
- if [ "${FOUND}" -ne 1 ]; then
- echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
- exit 1
- fi
- echo "${FILE}"
-}
-
ISMACOS=0
if [ "$( uname -s )" = "Darwin" ]; then
ISMACOS=1
GUI=0
HELP=0
DEBUG=0
-UPDATE=0
-UPDATEUSER=0
-UPDATEINSTALLATION=0
for RAWARG in "${@}"; do
ARG="${RAWARG%%=*}"
case "${ARG}" in
--debug)
DEBUG=1
;;
- --updateinstallation)
- UPDATE=1
- UPDATEINSTALLATION=1
- HEADLESS=1
- ;;
- --updateuser)
- UPDATE=1
- UPDATEUSER=1
- HEADLESS=1
- ;;
esac
done
if [ "${HELP}" = 1 ]; then
# --help takes precedence
GUI=0
-elif [ "${UPDATE}" = 1 ]; then
- # --update takes precedence over everything else, we don't run jalview!
- GUI=0
elif [ "${GUI}" = 1 ]; then
# --gui takes precedence over --headless
HEADLESS=0
fi
+# this whole next part is because there's no readlink -f in Darwin
+function readlinkf() {
+ FINDFILE="$1"
+ FILE="${FINDFILE}"
+ PREVFILE=""
+ C=0
+ MAX=100 # just in case we end up in a loop
+ FOUND=0
+ while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
+ PREVFILE="${FILE}"
+ FILE="$(readlink "${FILE}")"
+ if [ -z "${FILE}" ]; then
+ # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
+ FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
+ FOUND=1
+ elif [ "${FILE#/}" = "${FILE}" ]; then
+ # FILE is not an absolute path link, we need to add the relative path to the previous dir
+ FILE="$(dirname "${PREVFILE}")/${FILE}"
+ fi
+ C=$((C+1))
+ done
+ if [ "${FOUND}" -ne 1 ]; then
+ echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
+ exit 1
+ fi
+ echo "${FILE}"
+}
+
# args for the JVM
declare -a JVMARGS=()
SCRIPT="$(readlinkf "$0")"
DIR="$(dirname "${SCRIPT}")"
APPDIR="${DIR%/bin}"
- JAVA="${APPDIR}/jre/Contents/Home/bin/java"
+ JAVABIN="${APPDIR}/jre/Contents/Home/bin"
+ JAVA="${JAVABIN}/java"
if [ "${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="${APPDIR}/jalviewg.vmoptions"
+ JAVABIN="${APPDIR}/jre/bin"
+ JAVA="${JAVABIN}/java"
fi
# headless java arguments
SYSJAVA=java
GETDOWNTXT="${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// /_}"
+NAME="$( grep app_name= "${CHANNELPROPS}" | cut -d= -f2 )"
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
+# look for getdown.txt -- needed to create classpath
+if [ \! -e "${GETDOWNTXT}" ]; then
+ echo "Cannot find ${GETDOWNTXT}" >&2
exit 3
fi
-CLASS="jalview.bin.Launcher" # set as default Just In Case
-if [ "${UPDATE}" = 1 ]; then
-
- # GETDOWN UPDATE ONLY, not launching Jalview
- CLASS="com.threerings.getdown.launcher.GetdownApp"
- if [ -e "${GETDOWNJAR}" ]; then
- CLASSPATH="${GETDOWNJAR}"
- JARPATHS=( "${JARPATHS[@]}" "${GETDOWNJAR}" )
- else
- echo "Cannot find getdown-launcher.jar to run update" >&2
- exit 13
- fi
+# launching Jalview with jalview.bin.Launcher instead of getdown-launcher.jar
+CLASS="jalview.bin.Launcher"
- # 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=( "${JVMARGS[@]}" "-Duserdefaultappdir=true" )
- # resetting ARGS to just these two blank values so userappdir is determined
- ARGS=( "" "jalview" )
- fi
-
- # INSTALLATION update
- if [ "${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.update=true" )
- JVMARGS=( "${JVMARGS[@]}" "-Dappid=jalview" )
- JVMARGS=( "${JVMARGS[@]}" "-Dchannel.app_name=${NAME}" )
- JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.application_folder=${US_NAME}" )
-
- # add these Just In Case although jalview shouldn't be launched due to -Dsilent=true
- ARGS=( "${ARGS[@]}" "--headless" "--quit" "--nojavaconsole" "--nosplash" "--nonews" )
-
-else
-
- # LAUNCHING JALVIEW without getdown-launcher
- CLASS="jalview.bin.Launcher"
- JARPATHS="${APPJARPATHS[@]}"
-
- COLUMNS=80
- # get console width -- three ways to try, just in case (not needed for update)
- if command -v tput 2>&1 >/dev/null; then
- COLUMNS=$(tput cols) 2>/dev/null
- elif command -v stty 2>&1 >/dev/null; then
- COLUMNS=$(stty size | cut -d" " -f2) 2>/dev/null
- elif command -v resize 2>&1 >/dev/null; then
- COLUMNS=$(resize -u | grep COLUMNS= | sed -e 's/.*=//;s/;//') 2>/dev/null
- fi
-
- JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" )
- JVMARGS=( "${JVMARGS[@]}" "-Dgetdownappdir=${APPDIR}" )
+# get classpath from the code= entries in getdown.txt
+# 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}/${JAR}" )
+done
+COLUMNS=80
+# get console width -- three ways to try, just in case (not needed for update)
+if command -v tput 2>&1 >/dev/null; then
+ COLUMNS=$(tput cols) 2>/dev/null
+elif command -v stty 2>&1 >/dev/null; then
+ COLUMNS=$(stty size | cut -d" " -f2) 2>/dev/null
+elif command -v resize 2>&1 >/dev/null; then
+ COLUMNS=$(resize -u | grep COLUMNS= | sed -e 's/.*=//;s/;//') 2>/dev/null
fi
+JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dgetdownappdir=${APPDIR}" )
JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.script=${SCRIPT}" )
JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.appdir=${APPDIR}" )
+JAVAEXT=""
# WINDOWS ONLY in Cygwin or Windows Subsystem for Linux (WSL)
# change paths for Cygwin or WSL
if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
ARGS=( "${ARGS[@]}" "${ARG}" )
fi
done
- JAVA="${JAVA}.exe"
- SYSJAVA="java.exe"
+ JAVAEXT=".exe"
+ JAVA="${JAVA}${JAVAEXT}"
+ SYSJAVA="java${JAVAEXT}"
fi
fi
-# Is there a bundled Java? If not just try one in the PATH (we need .exe in WSL, added above)
+# look for bundled JRE. Might not be there if unix installer used in which case just invoke "java"
+if [ -e "${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
- JAVA=$SYSJAVA
+ JAVA="${SYSJAVA}"
echo "Cannot find bundled ${JAVA}, using system ${SYSJAVA} and hoping for the best!" >&2
fi
echo $QUOTEDVALS
}
+# for the debug command display
JVMARGSSTR=$(quotearray "${JVMARGS[@]}")
ARGSSTR=$(quotearray "${ARGS[@]}")
fi
"${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
--- /dev/null
+@ECHO OFF
+
+REM This is the Jalview batch script wrapper to run the powershell script of the same name.
+REM There is nothing specific to Jalview.
+
+REM ******************************************************************************
+REM If you need to set a full path to the PowerShell executable please do so here:
+SET PWSHPATH=
+REM ******************************************************************************
+
+REM This is some DOS magic to substitute the extension in the full path of this batch script with .ps1
+SET SCRIPTPATH=%~dpn0.ps1
+
+REM PowerShell script isn't where it should be!
+IF NOT EXIST "%SCRIPTPATH%" (
+ ECHO Could not find PowerShell script "%SCRIPTPATH%". Is %~nx0 in the right folder?
+ EXIT /B 1
+)
+
+REM Look for either pwsh.exe or powershell.exe if not set in PWSHPATH above.
+REM pwsh.exe is preferred as it is likely to be a newer version.
+SET PWSH=
+IF DEFINED PWSHPATH (
+ SET PWSH=%PWSHPATH%
+)
+FOR %%X IN (pwsh.exe powershell.exe) DO (
+ IF NOT DEFINED PWSH (
+ IF NOT "%%~$PATH:X" == "" (
+ REM Found a PowerShell executable in the PATH
+ SET PWSH="%%X"
+ GOTO end_looking
+ )
+ )
+)
+:end_looking
+
+IF NOT DEFINED PWSH (
+ REM No PowerShell executable found -- tell the user what to do.
+ ECHO No PowerShell found in %%PATH%%. If PowerShell is installed either
+ ECHO 1. add it to your PATH, or
+ ECHO 2. edit the PWSHPATH value at the top of this file:
+ ECHO "%~dpnx0"
+ ECHO.
+ ECHO %~n0 on the command line requires PowerShell. To install PowerShell see
+ ECHO https://docs.microsoft.com/en-us/powershell/scripting/install/installing-powershell
+ EXIT /B 2
+)
+
+REM Run the PowerShell script
+"%PWSH%" -NoProfile -ExecutionPolicy Bypass -Command "& '%SCRIPTPATH%' %*";
--- /dev/null
+#!/usr/bin/env pwsh
+
+# save args and first parameter
+$myArgs = $args.Clone()
+$myArg1 = $args[0]
+
+# setup for powershell version < 6.0
+[bool] $myIsWindows = 0
+[bool] $myIsMacOS = 0
+if ( $IsWindows -eq $null ) {
+ # for powershell version < 6.0 let's assume Windows
+ $myIsWindows = 1
+ $myIsMacOS = 0
+} else {
+ $myIsWindows = $IsWindows
+ $myIsMacOS = $IsMacOS
+}
+
+[bool] $headless = 0
+[bool] $gui = 0
+[bool] $help = 0
+[bool] $debug = 0
+Switch -Regex ($args) {
+ "--help|--help-|--version|-h" {
+ $help = 1
+ $headless = 1
+ Continue
+ }
+ "--gui" {
+ $gui = 1
+ Continue
+ }
+ "--headless" {
+ $headless = 1
+ Continue
+ }
+ "--debug" {
+ $debug = 1
+ Continue
+ }
+}
+if ( $help ) {
+ # --help takes precedence
+ $gui = 0
+} elseif ( $gui ) {
+ # --gui takes precedence over --headless
+ $headless = 0
+}
+
+# parent dir of this actual script (which should be the getdown appdir/bin). Follow all symlinks. Like GNU readlink -f
+function Readlink-f {
+ Param($Link)
+ $Return = $null
+ $c = 0
+ $max = 100 # just in case we end up in a loop
+ [bool] $found = 0
+ $file = Get-Item -Path $Link
+ $prevfile = $null
+ While ( $c -lt $max -and "${file}" -ne "${prevfile}" -and -not $found ) {
+ $prevfile = $file
+ [string] $target = ( $file ).Target
+ If ( $target -eq $null -or ( $file ).LinkType -ne "SymbolicLink" ) {
+ $Return = $file
+ $found = 1
+ } Else {
+ If ( $( Split-Path -Path $target -IsAbsolute ) ) {
+ $file = Get-Item -Path $target
+ } Else {
+# symbolic link is relative: combine previous link parent dir with the link target and resolve
+ $file = Get-Item -Path ( Join-Path -Path ( Split-Path -Path $prevfile -Parent ) -ChildPath $target -Resolve )
+ }
+ }
+ $c++
+ }
+ if ( -not $found ) {
+ throw "Could not determine path to actual file $( Split-Path -Path $Link -Leaf )"
+ }
+ $Return
+}
+
+# Avert problem with unix version of powershell and tell user the reason (Windows must always have .ps1 extension)
+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}" )
+$JVMARGS = @()
+
+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 $APPDIR -ChildPath "getdown.txt"
+
+# look for bundled JRE. Might not be there if unix installer used in which case just invoke "java"
+if ( -not ( Test-Path -Path "${JAVA}" ) ) {
+ Write-Host "Cannot find bundled ${JAVA}. Using system ${JAVAEXE} and hoping for the best!"
+ $JAVA = $JAVAEXE
+}
+
+# launching Jalview with jalview.bin.Launcher instead of getdown-launcher.jar
+$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 ( $myIsWindows ) { ";" } Else { ":" } )
+
+# get console width
+$COLUMNS = $Host.UI.RawUI.WindowSize.Width
+$JVMARGS += "-DCONSOLEWIDTH=${COLUMNS}"
+$JVMARGS += "-Dgetdownappdir=${APPDIR}"
+$JVMARGS += "-Dinstaller.appdir=${APPDIR}"
+$JVMARGS += "-Dlauncher.appdir=${APPDIR}"
+$JVMARGS += "-Dlauncher.script=${SCRIPT}"
+
+# we should always have at least one JVMARGS so this is okay
+$myJvmArgsString = '"' + $($JVMARGS -join '" "') + '"'
+
+# quote the args and the command (in case of spaces) with escape chars (`) and precede with & to indicate a command not string
+if ( $myArgs.count -eq 0 ) {
+ $COMMAND = "& `"${JAVA}`" ${myJvmArgsString} -cp `"${CLASSPATH}`" $CLASS"
+} else {
+ $myArgsString = '"' + $($myArgs -join '" "') + '"'
+ $COMMAND = "& `"${JAVA}`" ${myJvmArgsString} -cp `"${CLASSPATH}`" $CLASS ${myArgsString}"
+}
+
+if ( $debug -or $help ) {
+ Write-Error -Message "Shell running: ${COMMAND}"
+}
+
+Invoke-Expression -Command ${COMMAND}
+
--- /dev/null
+#!/usr/bin/env bash
+
+declare -a ARGS=("${@}")
+
+# this whole next part is because there's no readlink -f in Darwin
+function readlinkf() {
+ FINDFILE="$1"
+ FILE="${FINDFILE}"
+ PREVFILE=""
+ C=0
+ MAX=100 # just in case we end up in a loop
+ FOUND=0
+ while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
+ PREVFILE="${FILE}"
+ FILE="$(readlink "${FILE}")"
+ if [ -z "${FILE}" ]; then
+ # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
+ FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
+ FOUND=1
+ elif [ "${FILE#/}" = "${FILE}" ]; then
+ # FILE is not an absolute path link, we need to add the relative path to the previous dir
+ FILE="$(dirname "${PREVFILE}")/${FILE}"
+ fi
+ C=$((C+1))
+ done
+ if [ "${FOUND}" -ne 1 ]; then
+ echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
+ exit 1
+ fi
+ echo "${FILE}"
+}
+
+ISMACOS=0
+if [ "$( uname -s )" = "Darwin" ]; then
+ ISMACOS=1
+fi
+
+DEBUG=0
+USERSPACE=0
+INSTALLATION=0
+for RAWARG in "${@}"; do
+ ARG="${RAWARG%%=*}"
+ case "${ARG}" in
+ --debug)
+ DEBUG=1
+ ;;
+ --installation)
+ INSTALLATION=1
+ ;;
+ --userspace)
+ USERSPACE=1
+ ;;
+ *)
+ echo "Unkown option '${ARG}'" >&2
+ exit 2
+ esac
+done
+
+# args for the JVM
+declare -a JVMARGS=()
+
+# set vars for being inside the macos App Bundle
+if [ "${ISMACOS}" = 1 ]; then
+# MACOS ONLY
+ SCRIPT="$(readlinkf "$0")"
+ DIR="$(dirname "${SCRIPT}")"
+ APPDIR="${DIR%/bin}"
+ JAVABIN="${APPDIR}/jre/Contents/Home/bin"
+ JAVA="${JAVABIN}/java"
+ # 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}"
+ JAVABIN="${APPDIR}/jre/bin"
+ JAVA="${JAVABIN}/java"
+ # e.g. APPFOLDER=/opt/jalview
+ APPFOLDER="${APPDIR}"
+ VMOPTIONS="${APPDIR}/jalviewg.vmoptions"
+fi
+
+# headless java arguments
+JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" )
+if [ "${ISMACOS}" = 1 ]; then
+ JVMARGS=( "${JVMARGS[@]}" "-Dapple.awt.UIElement=true" )
+fi
+
+SYSJAVA=java
+GETDOWNTXT="${APPDIR}/getdown.txt"
+GETDOWNLAUNCHERJAR="${APPDIR}/getdown-launcher.jar"
+GETDOWNCOREJAR="${APPDIR}/resource/getdown-core.jar"
+CHANNELPROPS="${APPDIR}/channel.props"
+NAME="$( grep app_name= "${CHANNELPROPS}" | cut -d= -f2 )"
+echo $NAME
+US_NAME="${NAME// /_}"
+
+GDL_CLASSPATH=""
+GDC_CLASSPATH=""
+# save an array of JAR paths in case we're in WSL (see later)
+declare -a GDL_JARPATHS=()
+declare -a GDC_JARPATHS=()
+declare -a GDL_ARGS=()
+
+# getdown-launcher classpath
+if [ -e "${GETDOWNLAUNCHERJAR}" ]; then
+ GDL_CLASSPATH="${GETDOWNLAUNCHERJAR}"
+ GDL_JARPATHS=( "${GDL_JARPATHS[@]}" "${GETDOWNLAUNCHERJAR}" )
+else
+ echo "Cannot find $( basename "${GETDOWNLAUNCHERJAR}" ) to run update" >&2
+ exit 3
+fi
+
+# getdown-core classpath
+if [ -e "${GETDOWNCOREJAR}" ]; then
+ GDC_CLASSPATH="${GETDOWNCOREJAR}"
+ GDC_JARPATHS=( "${GDC_JARPATHS[@]}" "${GETDOWNCOREJAR}" )
+else
+ echo "Cannot find $( basename "${GETDOWNCOREJAR}" ) to run update" >&2
+ exit 4
+fi
+
+# USER space update
+if [ "${USERSPACE}" = 1 ]; then
+ if [ -e "${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 '${VMOPTIONS}'." >&2
+ exit 5
+ fi
+ JVMARGS=( "${JVMARGS[@]}" "${line}" )
+ fi
+ done < "${VMOPTIONS}"
+ fi
+ JVMARGS=( "${JVMARGS[@]}" "-Duserdefaultappdir=true" )
+ JVMARGS=( "${JVMARGS[@]}" "-Dnouserdefaultappdir=false" )
+ # setting the appdir arg[0] to a blank value so appDir is determined by EnvConfig.getUserAppdir()
+fi
+
+# INSTALLATION update
+if [ "${INSTALLATION}" = 1 ]; then
+ JVMARGS=( "${JVMARGS[@]}" "-Duserdefaultappdir=false" )
+ JVMARGS=( "${JVMARGS[@]}" "-Dnouserdefaultappdir=true" )
+ JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.appdir=${APPDIR}" )
+ JVMARGS=( "${JVMARGS[@]}" "-Dappdir=${APPDIR}" )
+ # set GDL_ARGS to these two values
+fi
+
+GDL_ARGS=( "" "" )
+
+# both USER and INSTALLATION updates
+JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.appdir=${APPDIR}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.application_folder=${US_NAME}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.script=${SCRIPT}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.update=true" )
+JVMARGS=( "${JVMARGS[@]}" "-Dchannel.app_name=${NAME}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dappid=jalview" )
+
+# IMPORTANT! tell getdown to update jalview withouth launching
+JVMARGS=( "${JVMARGS[@]}" "-Dsilent=true" )
+
+# add these Just In Case although jalview shouldn't be launched due to -Dsilent=true
+GDL_ARGS=( "${GDL_ARGS[@]}" "--headless" "--quit" "--nojavaconsole" "--nosplash" "--nonews" )
+
+# WINDOWS ONLY in Cygwin or Windows Subsystem for Linux (WSL)
+# change paths for Cygwin or WSL
+if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
+ if [ "$(uname -o)" = "Cygwin" ]; then
+ # CYGWIN
+ GDL_CLASSPATH=$(cygpath -pw "${GDL_CLASSPATH}")
+ elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
+ # WSL
+ GDL_CLASSPATH=""
+ for JARPATH in "${GDL_JARPATHS[@]}"; do
+ [ -n "${GDL_CLASSPATH}" ] && GDL_CLASSPATH="${GDL_CLASSPATH};"
+ GDL_CLASSPATH="${GDL_CLASSPATH}$(wslpath -aw "${JARPATH}")"
+ done
+ JAVA="${JAVA}.exe"
+ SYSJAVA="java.exe"
+ fi
+fi
+
+# 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 ${SYSJAVA} and hoping for the best!" >&2
+fi
+
+# This is just needed for display purposes
+function quotearray() {
+ QUOTEDVALS=""
+ for VAL in "${@}"; do
+ if [ \! "$QUOTEDVALS" = "" ]; then
+ QUOTEDVALS="${QUOTEDVALS} "
+ fi
+ QUOTEDVALS="${QUOTEDVALS}\"${VAL}\""
+ done
+ echo $QUOTEDVALS
+}
+
+JVMARGSSTR=$(quotearray "${JVMARGS[@]}")
+ARGSSTR=$(quotearray "${GDL_ARGS[@]}")
+
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -cp \""${GDL_CLASSPATH}"\" com.threerings.getdown.launcher.GetdownApp ${ARGSSTR} >&2
+fi
+
+"${JAVA}" "${JVMARGS[@]}" -cp "${GDL_CLASSPATH}" com.threerings.getdown.launcher.GetdownApp "${GDL_ARGS[@]}"
+
+# move updated getdown-launcher.jar into place
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -cp \""${GDC_CLASSPATH}"\" jalview.bin.GetdownLauncherUpdate >&2
+fi
+
+"${JAVA}" "${JVMARGS[@]}" -cp "${GDC_CLASSPATH}" jalview.bin.GetdownLauncherUpdate
<variable name="MACOSARCHIVE_VOLUMEICON" />
<variable name="WRAPPER_LINK" value="jalview" />
<variable name="BASH_WRAPPER_SCRIPT" value="jalview.sh" />
+ <variable name="BATCH_WRAPPER_SCRIPT" value="jalview.bat" />
+ <variable name="POWERSHELL_WRAPPER_SCRIPT" value="jalview.ps1" />
+ <variable name="BASH_UPDATE_SCRIPT" value="update.sh" />
+ <variable name="BATCH_UPDATE_SCRIPT" value="update.bat" />
+ <variable name="POWERSHELL_UPDATE_SCRIPT" value="update.ps1" />
<variable name="WRAPPER_SCRIPT_BIN_DIR" value="bin" />
<variable name="MACOSARCHIVE_X64_NAME" value="Install Jalview (Intel)" />
<variable name="MACOSARCHIVE_AARCH64_NAME" value="Install Jalview (Apple Silicon)" />
<variable name="WINDOWS_ICONS_FILE" value="jalview_logo.ico" />
<variable name="PNG_ICON_FILE" value="jalview_logo.png" />
<variable name="BACKGROUND" value="utils/channels/release/images/jalview_logo_background_fade-640x480.png" />
- <variable name="BATCH_WRAPPER_SCRIPT" value="jalview.bat" />
- <variable name="POWERSHELL_WRAPPER_SCRIPT" value="jalview.ps1" />
<variable name="WIZARD_WIDTH" value="640" description="Default/initial width of installer wizard window. Linux media types adapt this.
NOT USED" />
<variable name="WIZARD_HEIGHT" value="480" description="Default/initial width of installer wizard window. Linux media types adapt this.
NOT USED" />
<variable name="MACOSARCHIVE_X64_DMG_FILENAME" value="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-x64-java_${compiler:JAVA_INTEGER_VERSION}" />
</serializedBean>
<condition>context.getBooleanVariable("makeSymbolicLink")</condition>
</action>
- <action name="USERSPACE: Set macWrapperLinkLocation (macOS)" id="2745" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
+ <action name="USERSPACE: Set MacOSDir (macOS)" id="2745" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
<serializedBean>
<property name="script">
<object class="com.install4j.api.beans.ScriptProperty">
<property name="value" type="string">String javaHome = System.getProperty("java.home");
String appName = ((String)context.getCompilerVariable("JALVIEW_APPLICATION_NAME")) + ".app";
int i = javaHome.indexOf(appName);
-String wrapperLink = null;
+String MacOSDir = null;
if (i > -1) {
- wrapperLink = javaHome.substring(0, i) + appName + File.separator + "Contents" + File.separator + "MacOS" + File.separator + ((String)context.getCompilerVariable("WRAPPER_LINK"));
+ MacOSDir = javaHome.substring(0, i) + appName + File.separator + "Contents" + File.separator + "MacOS";
}
-return wrapperLink;
+return MacOSDir;
</property>
</object>
</property>
- <property name="variableName" type="string">macWrapperLinkLocation</property>
+ <property name="variableName" type="string">MacOSDir</property>
</serializedBean>
<condition>Util.isMacOS() && !context.getBooleanVariable("isAdmin") // Admin on macOS will add path to /etc/paths.d in Create File action</condition>
</action>
|| Util.isUnixInstaller()
|| (
( Util.isMacOS() && !Util.hasFullAdminRights() ) // Admin on macOS will add path to /etc/paths.d
- && context.getVariable("macWrapperLinkLocation") != null
+ && context.getVariable("MacOSDir") != null
)
)</visibilityScript>
</formComponent>
|| Util.isUnixInstaller()
|| (
( Util.isMacOS() && !Util.hasFullAdminRights() ) // Admin on macOS will add path to /etc/paths.d
- && context.getVariable("macWrapperLinkLocation") != null
+ && context.getVariable("MacOSDir") != null
)
)
</visibilityScript>
</serializedBean>
<condition>context.getBooleanVariable("appendToPathAction")</condition>
</action>
- <action name="USERSPACE: Create macOS symbolic link to jalview in user's local bin" id="2920" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixBinDir}">
+ <action name="USERSPACE: Create macOS symbolic link to jalview.sh" id="2920" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:MacOSDir}">
+ <serializedBean>
+ <property name="file">
+ <object class="java.io.File">
+ <string>../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}</string>
+ </object>
+ </property>
+ <property name="linkFile">
+ <object class="java.io.File">
+ <string>${installer:MacOSDir}/${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>Util.isMacOS() &&
+(
+ context.getBooleanVariable("makeSymbolicLinkAction")
+ && context.getVariable("unixBinDir") != null
+ && context.getVariable("MacOSDir") != null
+)</condition>
+ </action>
+ <action name="USERSPACE: Create macOS symbolic link to update.sh" id="3052" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:MacOSDir}">
<serializedBean>
<property name="file">
<object class="java.io.File">
- <string>${installer:macWrapperLinkLocation}</string>
+ <string>../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_UPDATE_SCRIPT}</string>
+ </object>
+ </property>
+ <property name="linkFile">
+ <object class="java.io.File">
+ <string>${installer:MacOSDir}/update_${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>Util.isMacOS() &&
+(
+ context.getBooleanVariable("makeSymbolicLinkAction")
+ && context.getVariable("unixBinDir") != null
+ && context.getVariable("MacOSDir") != null
+)</condition>
+ </action>
+ <action name="USERSPACE: Create macOS symbolic link to jalview in user's local bin" id="3048" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixBinDir}">
+ <serializedBean>
+ <property name="file">
+ <object class="java.io.File">
+ <string>${installer:MacOSDir}/${compiler:WRAPPER_LINK}</string>
</object>
</property>
<property name="linkFile">
(
context.getBooleanVariable("makeSymbolicLinkAction")
&& context.getVariable("unixBinDir") != null
- && context.getVariable("macWrapperLinkLocation") != null
+ && context.getVariable("MacOSDir") != null
+)</condition>
+ </action>
+ <action name="USERSPACE: Create macOS symbolic link to jalview_update in user's local bin" id="3049" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixBinDir}">
+ <serializedBean>
+ <property name="file">
+ <object class="java.io.File">
+ <string>${installer:MacOSDir}/update_${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ <property name="linkFile">
+ <object class="java.io.File">
+ <string>${installer:unixBinDir}/update_${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>Util.isMacOS() &&
+(
+ context.getBooleanVariable("makeSymbolicLinkAction")
+ && context.getVariable("unixBinDir") != null
+ && context.getVariable("MacOSDir") != null
)</condition>
</action>
</beans>
</group>
<group name="Windows scripts" id="2949" beanClass="com.install4j.runtime.beans.groups.ActionGroup">
<beans>
- <action name="Windows copy BAT file" id="2947" beanClass="com.install4j.runtime.beans.actions.files.CopyFileAction" rollbackBarrierExitCode="0">
+ <action name="Windows copy BAT jalview file" id="2947" beanClass="com.install4j.runtime.beans.actions.files.CopyFileAction" rollbackBarrierExitCode="0">
<serializedBean>
<property name="destinationFile">
<object class="java.io.File">
</serializedBean>
<condition>Util.isWindows() && !(((String)context.getCompilerVariable("WRAPPER_LINK")+".bat").equals((String)context.getCompilerVariable("BATCH_WRAPPER_SCRIPT")))</condition>
</action>
- <action name="Windows copy PS1 file" id="2948" beanClass="com.install4j.runtime.beans.actions.files.CopyFileAction" rollbackBarrierExitCode="0">
+ <action name="Windows copy PS1 jalview file" id="2948" beanClass="com.install4j.runtime.beans.actions.files.CopyFileAction" rollbackBarrierExitCode="0">
<serializedBean>
<property name="destinationFile">
<object class="java.io.File">
</serializedBean>
<condition>Util.isWindows() && !(((String)context.getCompilerVariable("WRAPPER_LINK")+".ps1").equals((String)context.getCompilerVariable("POWERSHELL_WRAPPER_SCRIPT")))</condition>
</action>
+ <action name="Windows copy BAT update file" id="3055" beanClass="com.install4j.runtime.beans.actions.files.CopyFileAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="destinationFile">
+ <object class="java.io.File">
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/update_${compiler:WRAPPER_LINK}.bat</string>
+ </object>
+ </property>
+ <property name="files" type="array" class="java.io.File" length="1">
+ <element index="0">
+ <object class="java.io.File">
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BATCH_UPDATE_SCRIPT}</string>
+ </object>
+ </element>
+ </property>
+ </serializedBean>
+ <condition>Util.isWindows()</condition>
+ </action>
+ <action name="Windows copy PS1 update file" id="3056" beanClass="com.install4j.runtime.beans.actions.files.CopyFileAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="destinationFile">
+ <object class="java.io.File">
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/update_${compiler:WRAPPER_LINK}.ps1</string>
+ </object>
+ </property>
+ <property name="files" type="array" class="java.io.File" length="1">
+ <element index="0">
+ <object class="java.io.File">
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:POWERSHELL_UPDATE_SCRIPT}</string>
+ </object>
+ </element>
+ </property>
+ </serializedBean>
+ <condition>Util.isWindows()</condition>
+ </action>
</beans>
</group>
<action id="3020" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
( Util.isLinux()
|| Util.isUnixInstaller()
|| ( Util.isMacOS()
- && context.getVariable("macWrapperLinkLocation") != null
+ && context.getVariable("MacOSDir") != null
)
)
&& context.getVariable("unixBinDir") != null</visibilityScript>
<file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/Jalview-File.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Jalview-File.icns" />
<file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/jvl_file.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/jvl_file.icns" />
<symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS/${compiler:WRAPPER_LINK}" target="../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}" />
+ <symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS/update_${compiler:WRAPPER_LINK}" target="../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_UPDATE_SCRIPT}" />
<symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/app/jre/Contents/Home/bin/${compiler:JALVIEW_APPLICATION_NAME}" target="java" />
<symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/app/jre/Contents/Home/bin/${compiler:JALVIEW_NAME}" target="java" />
<file name=".VolumeIcon.icns" file="${compiler:JALVIEW_DIR}/${compiler:MACOSARCHIVE_VOLUMEICON}" />
<file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/Jalview-File.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Jalview-File.icns" />
<file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/jvl_file.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/jvl_file.icns" />
<symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS/${compiler:WRAPPER_LINK}" target="../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}" />
+ <symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS/update_${compiler:WRAPPER_LINK}" target="../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_UPDATE_SCRIPT}" />
<symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/app/jre/Contents/Home/bin/${compiler:JALVIEW_APPLICATION_NAME}" target="java" />
<symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/app/jre/Contents/Home/bin/${compiler:JALVIEW_NAME}" target="java" />
<file name=".VolumeIcon.icns" file="${compiler:JALVIEW_DIR}/${compiler:MACOSARCHIVE_VOLUMEICON}" />
git://source.jalview.org / jalview.git / commitdiff