From 5a9e223e17c5b12aa876da0ddd12b63b95cd5526 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Tue, 1 Nov 2022 14:21:19 +0000
Subject: [PATCH] JAL-4064 re-added bundled macOS JREs as Filesets, which is
 the only way to get them in the DMG where we want them

---
 utils/install4j/install4j9_template.install4j |   44 ++++++++++++++++++-------
 1 file changed, 33 insertions(+), 11 deletions(-)

diff --git a/utils/install4j/install4j9_template.install4j b/utils/install4j/install4j9_template.install4j
index 9e07abd..979b1a9 100644
--- a/utils/install4j/install4j9_template.install4j
+++ b/utils/install4j/install4j9_template.install4j
@@ -37,8 +37,8 @@
       <variable name="BUNDLE_ID" value="org.jalview.jalview-desktop" />
       <variable name="INTERNAL_ID" value="Jalview" />
       <variable name="WINDOWS_APPLICATION_ID" value="6595-2347-1923-0725" />
-      <variable name="MACOS_DMG_DS_STORE" value="jalview_default_dmg_DS_Store" />
-      <variable name="MACOS_DMG_BG_IMAGE" value="jalview_default_dmg_background-72dpi.png" />
+      <variable name="MACOS_DMG_DS_STORE" value="utils/channels/default/images/jalview_default_dmg_DS_Store" />
+      <variable name="MACOS_DMG_BG_IMAGE" value="utils/channels/default/images/jalview_default_dmg_background-72dpi.png" />
       <variable name="WRAPPER_LINK" value="jalview" />
       <variable name="BASH_WRAPPER_SCRIPT" value="jalview.sh" />
       <variable name="WRAPPER_SCRIPT_BIN_DIR" value="bin" />
@@ -90,12 +90,18 @@
   <files defaultUninstallMode="2" preserveSymlinks="false">
     <filesets>
       <fileset name="Full file set" id="734" customizedId="FULL_FILE_SET" />
+      <fileset name="macOS x64 JVM" id="2801" customizedId="MACOS_X64_JVM" />
+      <fileset name="macOS aarch64 JVM" id="2803" customizedId="MACOS_AARCH64_JVM" />
     </filesets>
     <roots>
       <root id="735" fileset="734" />
+      <root id="2802" fileset="2801" />
+      <root id="2804" fileset="2803" />
     </roots>
     <mountPoints>
       <mountPoint id="736" root="735" />
+      <mountPoint id="2805" root="2802" />
+      <mountPoint id="2806" root="2804" />
     </mountPoints>
     <entries>
       <dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_CHANNEL_DIR}/${compiler:JAVA_VERSION}" uninstallMode="2" overrideOverwriteMode="true" overrideUninstallMode="true" subDirectory="files">
@@ -105,6 +111,8 @@
       </dirEntry>
       <dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/examples" overwriteMode="1" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="examples" />
       <dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_CHANNEL_DIR}/${compiler:JAVA_VERSION}/${compiler:WRAPPER_SCRIPT_BIN_DIR}" fileMode="755" overrideFileMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:WRAPPER_SCRIPT_BIN_DIR}" overrideDirMode="true" />
+      <dirEntry mountPoint="2805" file="${compiler:MACOS_X64_JAVA_VM_DIR}" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
+      <dirEntry mountPoint="2806" file="${compiler:MACOS_AARCH64_JAVA_VM_DIR}" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
     </entries>
     <components>
       <component name="jalview_getdown" id="1031">
@@ -1396,52 +1404,60 @@ ${compiler:JALVIEW_APPLICATION_NAME} will now launch.</property>
       </excludedBeans>
       <exclude>
         <entry defaultFileset="true" />
+        <entry filesetId="2801" />
+        <entry filesetId="2803" />
       </exclude>
       <jreBundle jreBundleSource="preCreated" includedJre="${compiler:WINDOWS_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
     </windows>
-    <macosArchive name="macOS x64 Disk Image" id="878" customizedId="MACOS-X64-DMG" mediaFileName="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-macOS_x64-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" volumeName="${compiler:INSTALLER_NAME}" launcherId="737" setupAppId="2746">
+    <macosArchive name="macOS x64 Disk Image" id="878" customizedId="MACOS-X64-DMG" mediaFileName="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-macOS-x64-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" volumeName="${compiler:INSTALLER_NAME}" launcherId="737" setupAppId="2746">
       <exclude>
         <entry defaultFileset="true" />
+        <entry filesetId="2803" />
       </exclude>
-      <jreBundle jreBundleSource="none" />
+      <jreBundle jreBundleSource="none" includedJre="${compiler:MACOS_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
       <topLevelFiles>
         <symlink name="&quot; &quot;" target="/Applications" />
-        <file name=".background/jalview_dmg_background.png" file="${compiler:JALVIEW_DIR}/utils/channels/default/images/${compiler:MACOS_DMG_BG_IMAGE}" />
-        <file name=".DS_Store" file="${compiler:JALVIEW_DIR}/utils/channels/default/images/${compiler:MACOS_DMG_DS_STORE}" />
+        <file name=".background/jalview_dmg_background.png" file="${compiler:JALVIEW_DIR}/${compiler:MACOS_DMG_BG_IMAGE}" />
+        <file name=".DS_Store" file="${compiler:JALVIEW_DIR}/${compiler:MACOS_DMG_DS_STORE}" />
         <file name="${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}/${compiler:BASH_WRAPPER_SCRIPT}" />
       </topLevelFiles>
     </macosArchive>
-    <macosArchive name="macOS aarch64 Disk Image" id="2796" customizedId="MACOS-AARCH64-DMG" mediaFileName="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-macOS_aarch64-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" volumeName="${compiler:INSTALLER_NAME}" architecture="aarch64" launcherId="737" setupAppId="2746">
+    <macosArchive name="macOS aarch64 Disk Image" id="2796" customizedId="MACOS-AARCH64-DMG" mediaFileName="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-macOS-aarch64-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" volumeName="${compiler:INSTALLER_NAME}" architecture="aarch64" launcherId="737" setupAppId="2746">
       <exclude>
         <entry defaultFileset="true" />
+        <entry filesetId="2801" />
       </exclude>
       <jreBundle jreBundleSource="none" />
       <topLevelFiles>
         <symlink name="&quot; &quot;" target="/Applications" />
-        <file name=".background/jalview_dmg_background.png" file="${compiler:JALVIEW_DIR}/utils/channels/default/images/${compiler:MACOS_DMG_BG_IMAGE}" />
-        <file name=".DS_Store" file="${compiler:JALVIEW_DIR}/utils/channels/default/images/${compiler:MACOS_DMG_DS_STORE}" />
+        <file name=".background/jalview_dmg_background.png" file="${compiler:JALVIEW_DIR}/${compiler:MACOS_DMG_BG_IMAGE}" />
+        <file name=".DS_Store" file="${compiler:JALVIEW_DIR}/${compiler:MACOS_DMG_DS_STORE}" />
         <file name="${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}/${compiler:BASH_WRAPPER_SCRIPT}" />
       </topLevelFiles>
     </macosArchive>
-    <unixInstaller name="Linux x64 Shell Installer" id="1595" customizedId="LINUX-X64-SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux_x64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
+    <unixInstaller name="Linux x64 Shell Installer" id="1595" customizedId="LINUX-X64-SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux-x64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
       <excludedBeans>
         <bean refId="2746" />
       </excludedBeans>
       <exclude>
         <entry defaultFileset="true" />
+        <entry filesetId="2801" />
+        <entry filesetId="2803" />
       </exclude>
       <jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
     </unixInstaller>
-    <unixInstaller name="Linux aarch64 Shell Installer" id="2782" customizedId="LINUX-AARCH64-SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux_aarch64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
+    <unixInstaller name="Linux aarch64 Shell Installer" id="2782" customizedId="LINUX-AARCH64-SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux-aarch64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
       <excludedBeans>
         <bean refId="2746" />
       </excludedBeans>
       <exclude>
         <entry defaultFileset="true" />
+        <entry filesetId="2801" />
+        <entry filesetId="2803" />
       </exclude>
       <jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_AARCH64_JAVA_VM_TGZ}" manualJreEntry="true" />
     </unixInstaller>
@@ -1451,6 +1467,8 @@ ${compiler:JALVIEW_APPLICATION_NAME} will now launch.</property>
       </excludedBeans>
       <exclude>
         <entry defaultFileset="true" />
+        <entry filesetId="2801" />
+        <entry filesetId="2803" />
       </exclude>
       <jreBundle jreBundleSource="none" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
     </unixArchive>
@@ -1460,6 +1478,8 @@ ${compiler:JALVIEW_APPLICATION_NAME} will now launch.</property>
       </excludedBeans>
       <exclude>
         <entry defaultFileset="true" />
+        <entry filesetId="2801" />
+        <entry filesetId="2803" />
       </exclude>
       <jreBundle jreBundleSource="none" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
     </unixInstaller>
@@ -1467,7 +1487,9 @@ ${compiler:JALVIEW_APPLICATION_NAME} will now launch.</property>
   <buildIds>
     <mediaSet refId="743" />
     <mediaSet refId="878" />
+    <mediaSet refId="2796" />
     <mediaSet refId="1595" />
+    <mediaSet refId="2782" />
     <mediaSet refId="1596" />
     <mediaSet refId="2639" />
   </buildIds>
-- 
1.7.10.2