From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 25 Apr 2019 11:47:51 +0000 (+0100)
Subject: JAL-3224 JAL-3225 To be compatible with install4j bundled JRE on windows, have change... 
X-Git-Tag: Release_2_11_0~17^2~7^2~1^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4425808d85ab0d70e4c5b7542cb4e5d3ee295b21;p=jalview.git

JAL-3224 JAL-3225 To be compatible with install4j bundled JRE on windows, have changed all the java_vm folder references to jre in getdown jars too. Install4j Windows media now bundles a JRE (into this location) so it can launch install4j installer too.  Java 11 installers working on Windows, but Java 1.8 complaining about com.sun.xml.ws.policy.Policy not found.
---

diff --git a/.classpath b/.classpath
index 7a5cc53..35bf3de 100644
--- a/.classpath
+++ b/.classpath
@@ -29,6 +29,7 @@
 	<classpathentry kind="lib" path="j11lib/javax.servlet-api-MODULE.jar"/>
 	<classpathentry kind="lib" path="j11lib/httpclient-4.0.3.jar"/>
 	<classpathentry kind="lib" path="j11lib/regex.jar"/>
+	<classpathentry kind="lib" path="j11lib/getdown-core.jar"/>
 	<classpathentry kind="lib" path="j11lib/policy.jar"/>
 	<classpathentry kind="lib" path="j11lib/jaxb-api-java9.jar"/>
 	<classpathentry kind="lib" path="j11lib/JGoogleAnalytics_0.3.jar"/>
@@ -46,7 +47,6 @@
 	<classpathentry kind="lib" path="j11lib/commons-discovery.jar"/>
 	<classpathentry kind="lib" path="j11lib/slf4j-api-1.7.7.jar"/>
 	<classpathentry kind="lib" path="j11lib/VAqua5-patch.jar"/>
-	<classpathentry kind="lib" path="j11lib/getdown-core-1.8.3-SNAPSHOT.jar"/>
 	<classpathentry kind="lib" path="j11lib/jaxws-api.jar"/>
 	<classpathentry kind="lib" path="j11lib/javax.xml.soap-api.jar"/>
 	<classpathentry kind="lib" path="j11lib/libquaqua-8.0.jnilib.jar"/>
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
index e8b0ee7..47c03b7 100644
--- a/.settings/org.eclipse.jdt.core.prefs
+++ b/.settings/org.eclipse.jdt.core.prefs
@@ -1,5 +1,5 @@
 #
-#Thu Apr 25 01:57:42 BST 2019
+#Thu Apr 25 12:37:19 BST 2019
 org.eclipse.jdt.core.formatter.insert_space_after_ellipsis=insert
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations=insert
 org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration=insert
diff --git a/build.gradle b/build.gradle
index 55d5709..4cb626d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -797,19 +797,23 @@ install4j {
 
 def install4jConf
 def macosJavaVMDir
+def macosJavaVMTgz
 def windowsJavaVMDir
+def windowsJavaVMTgz
 def install4jDir = "$jalviewDir/$install4jResourceDir"
 def install4jConfFile = "jalview-installers-java"+JAVA_VERSION+".install4j"
 install4jConf = "$install4jDir/$install4jConfFile"
   
 task copyInstall4jTemplate(type: Copy) {
-  macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/macos-jre"+JAVA_VERSION+"/java_vm"
-  windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/windows-jre"+JAVA_VERSION+"/java_vm"
+  macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/java_vm"
+  macosJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre"+JAVA_VERSION+".tar.gz"
+  windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/windows-jre"+JAVA_VERSION+"/java_vm"
+  windowsJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre"+JAVA_VERSION+".tar.gz"
   from (install4jDir) {
     include install4jTemplate
     rename (install4jTemplate, install4jConfFile)
     filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
-    filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['JAVA_VERSION': JAVA_VERSION, 'VERSION': JALVIEW_VERSION, 'MACOS_JAVA_VM_DIR': macosJavaVMDir, 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir])
+    filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['JAVA_VERSION': JAVA_VERSION, 'VERSION': JALVIEW_VERSION, 'MACOS_JAVA_VM_DIR': macosJavaVMDir, 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz])
   }
   into install4jDir
   inputs.files("$install4jDir/$install4jTemplate")
diff --git a/getdown/lib/getdown-launcher.jar b/getdown/lib/getdown-launcher.jar
index 6a73694..b52deec 100644
Binary files a/getdown/lib/getdown-launcher.jar and b/getdown/lib/getdown-launcher.jar differ
diff --git a/j11lib/getdown-core.jar b/j11lib/getdown-core.jar
new file mode 100644
index 0000000..3e811b2
Binary files /dev/null and b/j11lib/getdown-core.jar differ
diff --git a/j8lib/getdown-core.jar b/j8lib/getdown-core.jar
new file mode 100644
index 0000000..3e811b2
Binary files /dev/null and b/j8lib/getdown-core.jar differ
diff --git a/lib/getdown-core.jar b/lib/getdown-core.jar
new file mode 100644
index 0000000..3e811b2
Binary files /dev/null and b/lib/getdown-core.jar differ
diff --git a/utils/install4j/install4j_template.install4j b/utils/install4j/install4j_template.install4j
index 9261cd7..3366b72 100644
--- a/utils/install4j/install4j_template.install4j
+++ b/utils/install4j/install4j_template.install4j
@@ -1,13 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <install4j version="7.0.9" transformSequenceNumber="7">
   <directoryPresets config="../../../../../buildtools/jre/openjdk-java_vm/macos-jdk8u202-b08-jre" />
-  <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="$$VERSION$$" allPathsRelative="true" backupOnSave="false" autoSave="false" convertDotsToUnderscores="true" macSignature="????" macVolumeId="5aac4968c304f65" javaMinVersion="9999999999" javaMaxVersion="15" allowBetaVM="true" jdkMode="jdk" jdkName="JDK 11.0">
+  <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="$$VERSION$$" allPathsRelative="true" backupOnSave="false" autoSave="false" convertDotsToUnderscores="true" macSignature="????" macVolumeId="5aac4968c304f65" javaMinVersion="9999999999" javaMaxVersion="" allowBetaVM="true" jdkMode="jdk" jdkName="JDK 11.0">
     <languages skipLanguageSelection="false" languageSelectionInPrincipalLanguage="false">
       <principalLanguage id="en" customLocalizationFile="" />
       <additionalLanguages />
     </languages>
     <searchSequence>
-      <directory location="java_vm" />
+      <directory location="jre" />
     </searchSequence>
     <variables />
     <mergedProjects />
@@ -40,10 +40,10 @@
       <dirEntry mountPoint="736" file="../../getdown/website/$$JAVA_VERSION$$" 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="$$MACOS_JAVA_VM_DIR$$" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="true" entryMode="subdir" subDirectory="java_vm" excludeSuffixes="" dirMode="755" overrideDirMode="false">
+      <dirEntry mountPoint="884" file="$$MACOS_JAVA_VM_DIR$$" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="true" entryMode="subdir" subDirectory="jre" excludeSuffixes="" dirMode="755" overrideDirMode="false">
         <exclude />
       </dirEntry>
-      <dirEntry mountPoint="885" file="$$WINDOWS_JAVA_VM_DIR$$" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="true" entryMode="subdir" subDirectory="java_vm" excludeSuffixes="" dirMode="755" overrideDirMode="false">
+      <dirEntry mountPoint="885" file="$$WINDOWS_JAVA_VM_DIR$$" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="true" entryMode="subdir" subDirectory="jre" excludeSuffixes="" dirMode="755" overrideDirMode="false">
         <exclude />
       </dirEntry>
     </entries>
@@ -1574,9 +1574,10 @@ return console.askYesNo(message, true);
         <content />
       </postUninstallScript>
     </linuxRPM>
-    <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="" 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="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
       <excludedComponents>
         <component id="1155" />
+        <component id="1156" />
         <component id="1276" />
       </excludedComponents>
       <includedDownloadableComponents />
@@ -1619,10 +1620,11 @@ return console.askYesNo(message, true);
         <symlink name="Jalview.app/Contents/Resources/app/java_vm/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
       </topLevelFiles>
     </macosArchive>
-    <windows name="Network Windows" id="1272" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${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="" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
+    <windows name="Network Windows" id="1272" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${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="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
       <excludedComponents>
         <component id="1031" />
         <component id="1155" />
+        <component id="1156" />
       </excludedComponents>
       <includedDownloadableComponents />
       <excludedLaunchers>
@@ -1640,7 +1642,7 @@ return console.askYesNo(message, true);
         <customAttributes />
       </autoUpdate>
     </windows>
-    <macosArchive name="Network macOS Single Bundle Archive" id="1274" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${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="" manualJREEntry="false" archiveType="dmg" volumeName="${compiler:sys.shortName} Installer" launcherId="1402">
+    <macosArchive name="Network macOS Single Bundle Archive" id="1274" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}-app_${compiler:sys.version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" archiveType="dmg" volumeName="${compiler:sys.shortName} Installer" launcherId="1402">
       <excludedComponents>
         <component id="1031" />
         <component id="1156" />
@@ -1673,5 +1675,5 @@ return console.askYesNo(message, true);
     <mediaSet refId="1272" />
     <mediaSet refId="1274" />
   </buildIds>
-  <buildOptions verbose="false" faster="false" disableSigning="true" disableJreBundling="true" debug="false" />
+  <buildOptions verbose="false" faster="false" disableSigning="true" disableJreBundling="false" debug="false" />
 </install4j>