From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 12 Mar 2021 18:26:29 +0000 (+0000)
Subject: JAL-3830 improved bash scripts. Added powershell script. Needs testing
X-Git-Tag: Release_2_11_2_0~64
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=9038c9b054cee6232692f51d9370ad707a0efceb

JAL-3830 improved bash scripts. Added powershell script. Needs testing
---

diff --git a/build.gradle b/build.gradle
index 4930f94..0a27370 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1573,7 +1573,7 @@ task getdownWebsite() {
       }
     }
     
-    def getdownWrapperScripts = [ getdown_mac_wrapper_script, getdown_unix_wrapper_script ]
+    def getdownWrapperScripts = [ getdown_mac_wrapper_script, getdown_unix_wrapper_script, getdown_windows_wrapper_script ]
     getdownWrapperScripts.each{ script ->
       def s = file( "${jalviewDir}/utils/getdown/${script}" )
       if (s.exists()) {
diff --git a/gradle.properties b/gradle.properties
index 8157012..c4e9422 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -136,6 +136,7 @@ install4j_dmg_ds_store = jalview_dmg_DS_Store
 install4j_dmg_wrapper_link = jalviewc
 getdown_mac_wrapper_script = jalviewc-macos
 getdown_unix_wrapper_script = jalviewc
+getdown_windows_wrapper_script = jalviewc.ps1
 
 OSX_KEYSTORE =
 OSX_KEYPASS =
diff --git a/utils/getdown/jalviewc b/utils/getdown/jalviewc
index a3fa66b..4792a9c 100755
--- a/utils/getdown/jalviewc
+++ b/utils/getdown/jalviewc
@@ -1,12 +1,11 @@
 #!/usr/bin/env bash
 
 ARG1=$1
-WDIR="$( pwd )"
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+DIR="$(dirname "$(readlink -f "$0")")"
 
 # check to see if $1 is set and is not start of other cli set args
 OPEN=""
-if [ -n "$ARG1" -a "$ARG1" = "${ARG1#-}" -a \! "$ARG1" = "open" ]; then
+if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
  # first argument exists and does not start with a "-" and is not "open"
  OPEN="-open"
 fi
@@ -14,15 +13,21 @@ fi
 APPDIR="${DIR}"
 JAVA="${APPDIR}/jre/bin/java"
 GETDOWNTXT="${APPDIR}/getdown.txt"
-if [ -e "$GETDOWNTXT" ]; then
-  CLASSPATH=""
-  for x in $(grep -e 'code = ' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
-    [ -n "$CLASSPATH" ] && CLASSPATH="${CLASSPATH}:"
-    CLASSPATH="${CLASSPATH}${APPDIR}/${x}"
+CLASSPATH=""
+if [ -e "${GETDOWNTXT}" ]; then
+  for JAR in $(grep -e '^code\s*=\s*' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
+    [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
+    CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
   done
 else
   echo "Cannot find getdown.txt" >&2
-  exit 1
+  exit 3
 fi
 
-"$JAVA" -cp "$CLASSPATH" jalview.bin.Launcher $OPEN "$@"
+if [ \! -e "${JAVA}" ]; then
+  echo "Cannot find bundled java, using system and hoping for the best!" >&2
+  JAVA=java
+fi
+
+# don't quote $OPEN
+"${JAVA}" -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "$@"
diff --git a/utils/getdown/jalviewc-macos b/utils/getdown/jalviewc-macos
index 32748cb..e34685d 100755
--- a/utils/getdown/jalviewc-macos
+++ b/utils/getdown/jalviewc-macos
@@ -1,17 +1,46 @@
 #!/usr/bin/env bash
 
-ARG1=$1
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
-APP=${DIR%/Contents/*}
+ARG1="$1"
+
+# 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}"
+}
+
+DIR="$(dirname "$(readlinkf "$0")")"
+APP="${DIR%.app/Contents/*}".app
 
 if [ "${APP}" = "${APP%.app}" ]; then
-  echo "Could not find .app dir" >&2
-  exit 1
+  echo "Could not find Jalview.app dir" >&2
+  exit 2
 fi
 
 # check to see if $1 is set and is not start of other cli set args
 OPEN=""
-if [ -n "$ARG1" -a "$ARG1" = "${ARG1#-}" -a \! "$ARG1" = "open" ]; then
+if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
  # first argument exists and does not start with a "-" and is not "open"
  OPEN="-open"
 fi
@@ -19,16 +48,22 @@ fi
 APPDIR="${APP}/Contents/Resources/app"
 JAVA="${APPDIR}/jre/Contents/Home/bin/java"
 GETDOWNTXT="${APPDIR}/getdown.txt"
-# always check grep and sed regexes on macOS -- they're not the same
-if [ -e "$GETDOWNTXT" ]; then
-  CLASSPATH=""
-  for x in $(grep -e 'code = ' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
-    [ -n "$CLASSPATH" ] && CLASSPATH="${CLASSPATH}:"
-    CLASSPATH="${CLASSPATH}${APPDIR}/${x}"
+CLASSPATH=""
+if [ -e "${GETDOWNTXT}" ]; then
+  # always check grep and sed regexes on macOS -- they're not the same
+  for JAR in $(grep -e '^code\s*=\s*' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
+    [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
+    CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
   done
 else
   echo "Cannot find getdown.txt" >&2
-  exit 1
+  exit 3
+fi
+
+if [ \! -e "${JAVA}" ]; then
+  echo "Cannot find bundled java, using system and hoping for the best!" >&2
+  JAVA=java
 fi
 
-"$JAVA" -cp "$CLASSPATH" jalview.bin.Launcher $OPEN "$@"
+# don't quote $OPEN
+"${JAVA}" -Xdock:icon="${APPDIR}"/resource/jalview_logo.png -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "$@"
diff --git a/utils/getdown/jalviewc.ps1 b/utils/getdown/jalviewc.ps1
new file mode 100644
index 0000000..ff4d6d8
--- /dev/null
+++ b/utils/getdown/jalviewc.ps1
@@ -0,0 +1,28 @@
+# save first parameter
+$ARGS = $args
+$ARG1 = $args[0]
+# parent dir of this script (should be the getdown app dir)
+$DIR = Split-Path $MyInvocation.MyCommand.Path -Parent
+
+# insert an "-open" parameter to Jalview's ARGS if ARG1 is non-zero-length, and not "open" or starts with a "-"
+if ( $ARG1.length -gt 0 -and (-not $ARG1.StartsWith("-")) -and $ARG1 -ne "open" ) {
+  $ARGS = "-open " + $ARGS
+}
+
+$APPDIR = $DIR
+$JAVA = "${APPDIR}/jre/bin/java.exe"
+$GETDOWNTXT = "${APPDIR}/getdown.txt"
+
+if (-not (Test-Path -Path "${GETDOWNTXT}")) {
+  throw "Cannot find getdown.txt"
+}
+
+if (-not (Test-Path -Path "${JAVA}")) {
+  Write-Host "Cannot find bundled java.exe. Using system and hoping for the best!"
+  $JAVA = "java.exe"
+}
+
+$CLASSPATH = (Select-String -Path "${GETDOWNTXT}" -AllMatches -Pattern "code\s*=\s*(.*)$" | foreach { "$DIR/$($_.Matches.Groups[1].Value)" }) -join ":"
+
+Invoke-Expression -Command "${JAVA} -cp ${CLASSPATH} jalview.bin.Launcher $ARGS"
+