From: Ben Soares <bsoares@dundee.ac.uk>
Date: Fri, 5 Apr 2019 16:19:07 +0000 (+0100)
Subject: JAL-3130 This commit concentrates on the Mac OS X DMG app bundle, ensuring only one... 
X-Git-Tag: Release_2_11_0~17^2~7^2~47
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=49a555c3890bc93583a5e0d8f0f237db21f5e3d3

JAL-3130 This commit concentrates on the Mac OS X DMG app bundle, ensuring only one JRE needed in the .app bundle for 1) install4j, 2) getdown, 3) jalview
---

diff --git a/build.gradle b/build.gradle
index 7b6cd6b..4a63af9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -180,6 +180,7 @@ task syncLib(type: Sync) {
 task syncResources(type: Sync) {
   from "$jalviewDir/$resourceDir"
   include "**/*.*"
+  exclude "install4j"
   into "$jalviewDir/$classesDir"
   preserve {
     include "**"
diff --git a/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar b/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
index e8eef5f..545f20b 100644
Binary files a/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar and b/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar differ
diff --git a/getdown/lib/getdown-launcher.jar b/getdown/lib/getdown-launcher.jar
index 3439ea4..f71b6ee 100644
Binary files a/getdown/lib/getdown-launcher.jar and b/getdown/lib/getdown-launcher.jar differ
diff --git a/resources/install4j/jalview_getdown.install4j b/resources/install4j/jalview_getdown.install4j
index 16aad1d..fed85e9 100644
--- a/resources/install4j/jalview_getdown.install4j
+++ b/resources/install4j/jalview_getdown.install4j
@@ -1,15 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <install4j version="7.0.9" transformSequenceNumber="7">
-  <directoryPresets config="../../resources/install4j" />
-  <application name="Jalview" distributionSourceDir="" applicationId="6595-2347-1923-0725" mediaDir="../../build/install4j" mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}" compression="6" lzmaCompression="true" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="true" shortName="Jalview" publisher="University of Dundee" publisherWeb="http://www.jalview.org/" version="DEVELOPMENT" allPathsRelative="true" backupOnSave="false" autoSave="false" convertDotsToUnderscores="true" macSignature="????" macVolumeId="5aac4968c304f65" javaMinVersion="11" javaMaxVersion="11" allowBetaVM="false" jdkMode="jdk" jdkName="JDK 11.0">
+  <directoryPresets config="libjli.dylib" />
+  <application name="Jalview" distributionSourceDir="" applicationId="6595-2347-1923-0725" mediaDir="../../build/install4j" mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}" compression="6" lzmaCompression="true" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="true" shortName="Jalview" publisher="University of Dundee" publisherWeb="http://www.jalview.org/" version="DEVELOPMENT" allPathsRelative="true" backupOnSave="false" autoSave="false" convertDotsToUnderscores="true" macSignature="????" macVolumeId="5aac4968c304f65" javaMinVersion="11" javaMaxVersion="" allowBetaVM="true" jdkMode="jdk" jdkName="JDK 11.0">
     <languages skipLanguageSelection="false" languageSelectionInPrincipalLanguage="false">
       <principalLanguage id="en" customLocalizationFile="" />
       <additionalLanguages />
     </languages>
     <searchSequence>
-      <registry />
-      <envVar name="JAVA_HOME" />
-      <envVar name="JDK_HOME" />
+      <directory location="java_vm" />
     </searchSequence>
     <variables />
     <mergedProjects />
@@ -21,13 +19,19 @@
   <files keepModificationTimes="false" missingFilesStrategy="warn" globalExcludeSuffixes="" defaultOverwriteMode="4" defaultUninstallMode="2" launcherOverwriteMode="3" defaultFileMode="644" defaultDirMode="755">
     <filesets>
       <fileset name="Full file set" id="734" customizedId="" />
+      <fileset name="Mac OS X JRE" id="880" customizedId="" />
+      <fileset name="Windows JRE" id="882" customizedId="" />
     </filesets>
     <roots>
       <root id="735" fileset="734" location="" />
+      <root id="881" fileset="880" location="" />
+      <root id="883" fileset="882" location="" />
     </roots>
     <mountPoints>
       <mountPoint id="454" root="" location="" mode="755" />
       <mountPoint id="736" root="735" location="" mode="755" />
+      <mountPoint id="884" root="881" location="" mode="755" />
+      <mountPoint id="885" root="883" location="" mode="755" />
     </mountPoints>
     <entries>
       <dirEntry mountPoint="454" file="../../getdown/files" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="direct" subDirectory="files" excludeSuffixes="" dirMode="755" overrideDirMode="false">
@@ -36,11 +40,19 @@
       <dirEntry mountPoint="736" file="../../getdown/website" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="direct" subDirectory="files" excludeSuffixes="" dirMode="755" overrideDirMode="false">
         <exclude />
       </dirEntry>
+      <dirEntry mountPoint="884" file="./jre/jre-11.0.2-macos-amd64/java_vm" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="true" entryMode="subdir" subDirectory="java_vm" excludeSuffixes="" dirMode="755" overrideDirMode="false">
+        <exclude />
+      </dirEntry>
+      <dirEntry mountPoint="885" file="./jre/jre-11.0.2-windows-amd64/java_vm" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="true" entryMode="subdir" subDirectory="java_vm" excludeSuffixes="" dirMode="755" overrideDirMode="false">
+        <exclude />
+      </dirEntry>
     </entries>
     <components>
       <component name="getdown" id="456" customizedId="" displayDescription="false" hideHelpButton="false" selected="true" changeable="true" downloadable="false" hidden="false">
         <description />
-        <include all="true" />
+        <include all="false">
+          <entry location=".i4j_fileset_" fileType="regular" />
+        </include>
         <dependencies />
       </component>
     </components>
@@ -79,7 +91,7 @@
         <file path="../../resources/images/Jalview_Logo.png" />
       </iconImageFiles>
     </launcher>
-    <launcher name="Offline Jalview Launcher" id="737" customizedId="" external="false" excludeFromMenu="false" unixMode="755" unixAutoStart="true" menuName="${compiler:sys.shortName}-${compiler:sys.version}" icnsFile="../../resources/images/jalview_logos.icns" customMacBundleIdentifier="false" macBundleIdentifier="" swtApp="false" fileset="" macBundleBinary="JavaApplicationStub" addMacEntitlements="false" macEntitlementsFile="" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:sys.shortName}" useJavaMinVersionOverride="false" javaMinVersionOverride="" useJavaMaxVersionOverride="false" javaMaxVersionOverride="" checkUpdater="false" updateExecutionMode="unattendedProgress" unattendedUpdateTitle="${i18n:updater.WindowTitle(&quot;${compiler:sys.fullName}&quot;)}">
+    <launcher name="Offline Jalview Launcher" id="737" customizedId="" external="false" excludeFromMenu="false" unixMode="755" unixAutoStart="true" menuName="${compiler:sys.shortName}-${compiler:sys.version}" icnsFile="../../resources/images/jalview_logos.icns" customMacBundleIdentifier="false" macBundleIdentifier="" swtApp="false" fileset="734" macBundleBinary="JavaApplicationStub" addMacEntitlements="false" macEntitlementsFile="" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:sys.shortName}" useJavaMinVersionOverride="false" javaMinVersionOverride="" useJavaMaxVersionOverride="false" javaMaxVersionOverride="" checkUpdater="false" updateExecutionMode="unattendedProgress" unattendedUpdateTitle="${i18n:updater.WindowTitle(&quot;${compiler:sys.fullName}&quot;)}">
       <executable name="Jalview" type="1" iconSet="true" iconFile="../../resources/images/jalview_logos.ico" executableDir="." redirectStderr="true" stderrFile="error.log" stderrMode="overwrite" redirectStdout="true" stdoutFile="output.log" stdoutMode="overwrite" failOnStderrOutput="true" executableMode="1" changeWorkingDirectory="true" workingDirectory="." singleInstance="true" serviceStartType="2" serviceDependencies="" serviceDescription="" jreLocation="" executionLevel="asInvoker" checkConsoleParameter="true" globalSingleInstance="false" singleInstanceActivate="true" dpiAware="java9+">
         <versionInfo include="false" fileVersion="" fileDescription="" legalCopyright="" internalName="" productName="" />
       </executable>
@@ -1469,7 +1481,7 @@ return console.askYesNo(message, true);
     </styles>
   </installerGui>
   <mediaSets>
-    <windows name="Windows" id="130" customizedId="" mediaFileName="" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="windows-amd64-1.8.0_202" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
+    <windows name="Windows" id="130" customizedId="" mediaFileName="" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="windows-amd64-11.0.2" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
       <excludedComponents />
       <includedDownloadableComponents />
       <excludedLaunchers>
@@ -1479,6 +1491,7 @@ return console.askYesNo(message, true);
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
       <exclude>
         <entry location=".i4j_fileset_734" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
@@ -1486,7 +1499,7 @@ return console.askYesNo(message, true);
         <customAttributes />
       </autoUpdate>
     </windows>
-    <macos name="macOS Single Bundle" id="131" customizedId="" mediaFileName="${compiler:sys.shortName}_${compiler:sys.platform}-installer_${compiler:sys.version}" installDir="${compiler:sys.fullName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="macosx-amd64-1.8.0_202_unpacked" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" requiredVmIdPrefix="" customInstallBaseDir="" contentFilesType="1" installerName="${i18n:InstallerName(${compiler:sys.fullName})}" volumeName="${compiler:sys.shortName}" compressDmg="true" launcherId="121">
+    <macos name="macOS Single Bundle Archive with Getdown JRE" id="131" customizedId="" mediaFileName="${compiler:sys.shortName}_${compiler:sys.platform}-installer_${compiler:sys.version}" installDir="${compiler:sys.fullName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="macosx-amd64-1.8.0_202_unpacked" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" requiredVmIdPrefix="" customInstallBaseDir="" contentFilesType="1" installerName="${i18n:InstallerName(${compiler:sys.fullName})}" volumeName="${compiler:sys.shortName}" compressDmg="true" launcherId="121">
       <excludedComponents />
       <includedDownloadableComponents />
       <excludedBeans />
@@ -1511,6 +1524,8 @@ return console.askYesNo(message, true);
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
       <exclude>
         <entry location=".i4j_fileset_734" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
@@ -1528,6 +1543,8 @@ return console.askYesNo(message, true);
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
       <exclude>
         <entry location=".i4j_fileset_734" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
@@ -1550,6 +1567,8 @@ return console.askYesNo(message, true);
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
       <exclude>
         <entry location=".i4j_fileset_" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
@@ -1579,6 +1598,8 @@ return console.askYesNo(message, true);
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
       <exclude>
         <entry location=".i4j_fileset_" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
@@ -1627,6 +1648,8 @@ return console.askYesNo(message, true);
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
       <exclude>
         <entry location=".i4j_fileset_" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
@@ -1637,7 +1660,7 @@ return console.askYesNo(message, true);
         <content />
       </installerScript>
     </unixInstaller>
-    <windows name="Offline Windows" id="743" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_${compiler:sys.version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="windows-amd64-1.8.0_202" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
+    <windows name="Offline Windows" id="743" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_${compiler:sys.version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="windows-amd64-11.0.2" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
       <excludedComponents />
       <includedDownloadableComponents />
       <excludedLaunchers>
@@ -1647,6 +1670,7 @@ return console.askYesNo(message, true);
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
       <exclude>
         <entry location=".i4j_fileset_" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
@@ -1654,12 +1678,34 @@ return console.askYesNo(message, true);
         <customAttributes />
       </autoUpdate>
     </windows>
+    <macosArchive name="Offline macOS Single Bundle Archive with Getdown JRE" id="878" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}-app_${compiler:sys.version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="macosx-amd64-11.0.2" manualJREEntry="false" archiveType="dmg" volumeName="${compiler:sys.shortName} Offline Installer" launcherId="737">
+      <excludedComponents />
+      <includedDownloadableComponents />
+      <excludedBeans />
+      <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
+      <exclude>
+        <entry location=".i4j_fileset_" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
+      </exclude>
+      <variables />
+      <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
+        <commentFiles />
+        <customAttributes />
+      </autoUpdate>
+      <topLevelFiles>
+        <symlink name="&quot; &quot;" target="/Applications" />
+        <file name=".background/jalview_dmg_background.png" file="../../resources/install4j/jalview_dmg_background.png" />
+        <file name=".DS_Store" file="../../resources/install4j/DS_Store" />
+        <symlink name="Jalview.app/Contents/Resources/app/java_vm" target="../jre.bundle/Contents/Home" />
+      </topLevelFiles>
+    </macosArchive>
   </mediaSets>
   <buildIds buildAll="false">
-    <mediaSet refId="130" />
-    <mediaSet refId="152" />
-    <mediaSet refId="739" />
+    <mediaSet refId="153" />
+    <mediaSet refId="570" />
     <mediaSet refId="743" />
+    <mediaSet refId="878" />
   </buildIds>
   <buildOptions verbose="true" faster="true" disableSigning="true" disableJreBundling="false" debug="false" />
 </install4j>
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index fc36047..1fed71e 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -553,7 +553,15 @@ public class Desktop extends jalview.jbgui.GDesktop
                     + System.getProperty("java.version") + "\n"
                     + System.getProperty("os.arch") + " "
                     + System.getProperty("os.name") + " "
-                    + System.getProperty("os.version"));
+                    + System.getProperty("os.version")
+                    + (jalview.bin.Cache.getProperty("VERSION").equals("DEVELOPMENT")
+                                    ? "\nJava path:"
+                                            + System.getProperty(
+                                                    "java.home")
+                                            + File.separator + "bin"
+                                            + File.separator + "java"
+                                    : "")
+            );
 
     showConsole(showjconsole);