From a770e3a56aaa5da7e6e88faa199ae9882339489a Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Fri, 24 Jan 2020 17:11:10 +0000
Subject: [PATCH] JAL-3394 Removed libjli.dylib symbolic link from embedded
 macOS JRE, works in 8 and 11. Preparation for non-linked
 Uninstall.app in DMG

---
 build.gradle                                             |    2 ++
 utils/install4j/DMG_creation_README.md                   |    4 +++-
 utils/install4j/DS_Store_no_link                         |  Bin 0 -> 12292 bytes
 utils/install4j/dmg_nolink_install4j8_template.install4j |   11 +++++++++++
 utils/install4j/install4j8_template.install4j            |   12 +++++++-----
 5 files changed, 23 insertions(+), 6 deletions(-)
 create mode 100644 utils/install4j/DS_Store_no_link
 create mode 100644 utils/install4j/dmg_nolink_install4j8_template.install4j

diff --git a/build.gradle b/build.gradle
index ad49dfc..810eb57 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1299,6 +1299,7 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
 
   variables = [
+    'JALVIEW_DIR': "../..",
     'OSX_KEYSTORE': OSX_KEYSTORE,
     'JSIGN_SH': JSIGN_SH,
     'JRE_DIR': getdown_app_dir_java,
@@ -1317,6 +1318,7 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
     'COPYRIGHT_MESSAGE': install4j_copyright_message,
     'MACOS_BUNDLE_ID': install4j_macOS_bundle_id,
+    'INSTALL4J_UTILS_DIR': install4j_utils_dir,
     'GETDOWN_WEBSITE_DIR': getdown_website_dir,
     'GETDOWN_FILES_DIR': getdown_files_dir,
     'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
diff --git a/utils/install4j/DMG_creation_README.md b/utils/install4j/DMG_creation_README.md
index c923557..eeb10d4 100644
--- a/utils/install4j/DMG_creation_README.md
+++ b/utils/install4j/DMG_creation_README.md
@@ -2,7 +2,7 @@
 
 ## How to make the DS_Store file needed for the DMG prettification
 
-> ALSO SEE https://www.ej-technologies.com/resources/install4j/help/doc/#install4j.concepts.dmgStyling
+> ALSO SEE https://www.ej-technologies.com/resources/install4j/help/doc/concepts/dmgStyling.html
 
 ```
 cp ../../build/install4j/11/Jalview-OFFLINE_macos-app_DEVELOPMENT-j11.dmg ./temp.dmg
@@ -15,6 +15,8 @@ NEWSIZE=$(( CURSIZE + 20000))
 
 hdiutil resize -sectors $NEWSIZE temp_rw.dmg
 
+open temp_rw.dmg
+
 open /Volumes/Jalview\ Installer
 ```
 
diff --git a/utils/install4j/DS_Store_no_link b/utils/install4j/DS_Store_no_link
new file mode 100644
index 0000000000000000000000000000000000000000..afa9a350084eb7122de759f7a3ed93d975dfe941
GIT binary patch
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diff --git a/utils/install4j/dmg_nolink_install4j8_template.install4j b/utils/install4j/dmg_nolink_install4j8_template.install4j
new file mode 100644
index 0000000..74f3839
--- /dev/null
+++ b/utils/install4j/dmg_nolink_install4j8_template.install4j
@@ -0,0 +1,11 @@
+        <symlink name="Uninstall Old Jalview (optional).app" target="Jalview.app/Contents/Resources/app/Uninstall Old Jalview.app" />
+        <!--
+        <file name="Uninstall Old Jalview (optional).app/Contents/_CodeSignature/CodeResources" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Uninstall Old Jalview.app/Contents/_CodeSignature/CodeResources" />
+        <file name="Uninstall Old Jalview (optional).app/Contents/MacOS/applet" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Uninstall Old Jalview.app/Contents/MacOS/applet" />
+        <file name="Uninstall Old Jalview (optional).app/Contents/Resources/applet.rsrc" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Uninstall Old Jalview.app/Contents/Resources/applet.rsrc" />
+        <file name="Uninstall Old Jalview (optional).app/Contents/Resources/description.rtfd/TXT.rtf" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf" />
+        <file name="Uninstall Old Jalview (optional).app/Contents/Resources/Scripts/main.scpt" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt" />
+        <file name="Uninstall Old Jalview (optional).app/Contents/Resources/applet.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Uninstall Old Jalview.app/Contents/Resources/applet.icns" />
+        <file name="Uninstall Old Jalview (optional).app/Contents/Info.plist" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Uninstall Old Jalview.app/Contents/Info.plist" />
+        <file name="Uninstall Old Jalview (optional).app/Contents/PkgInfo" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Uninstall Old Jalview.app/Contents/PkgInfo" />
+        -->
diff --git a/utils/install4j/install4j8_template.install4j b/utils/install4j/install4j8_template.install4j
index 08dd02e..477e428 100644
--- a/utils/install4j/install4j8_template.install4j
+++ b/utils/install4j/install4j8_template.install4j
@@ -28,6 +28,7 @@
       <variable name="LINUX_JAVA_VM_TGZ" value="~/buildtools/jre/tgz/jre-${compiler:JAVA_INTEGER_VERSION}-linux-x64.tar.gz" />
       <variable name="COPYRIGHT_MESSAGE" value="..." />
       <variable name="MACOS_BUNDLE_ID" value="org.jalview.jalview-desktop" />
+      <variable name="INSTALL4J_UTILS_DIR" value="utils/install4j" />
       <variable name="GETDOWN_WEBSITE_DIR" value="getdown/website" />
       <variable name="GETDOWN_FILES_DIR" value="getdown/files" />
       <variable name="GETDOWN_RESOURCE_DIR" value="resource" />
@@ -1117,6 +1118,7 @@ return console.askYesNo(message, true);
         <entry filesetId="880" />
         <entry filesetId="882" />
         <entry filesetId="1873" />
+        <entry filesetId="2105" />
       </exclude>
       <jreBundle jreBundleSource="preCreated" includedJre="${compiler:WINDOWS_JAVA_VM_TGZ}" manualJreEntry="true" />
     </windows>
@@ -1133,6 +1135,7 @@ return console.askYesNo(message, true);
         <entry filesetId="880" />
         <entry filesetId="882" />
         <entry filesetId="1873" />
+        <entry filesetId="2105" />
       </exclude>
       <jreBundle jreBundleSource="preCreated" includedJre="${compiler:WINDOWS_JAVA_VM_TGZ}" manualJreEntry="true" />
     </windows>
@@ -1149,11 +1152,10 @@ return console.askYesNo(message, true);
       </exclude>
       <topLevelFiles>
         <symlink name="&quot; &quot;" target="/Applications" />
-        <file name=".background/jalview_dmg_background.png" file="./jalview_dmg_background.png" />
-        <file name=".DS_Store" file="./DS_Store" />
-        <symlink name="Jalview.app/Contents/Resources/app/${compiler:JRE_DIR}/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
-        <file name="Jalview.app/Contents/Resources/Jalview-File.icns" file="./Jalview-File.icns" />
-        <file name="Jalview.app/Contents/Resources/Jalview-Launch.icns" file="Jalview-Launch.icns" />
+        <file name=".background/jalview_dmg_background.png" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/jalview_dmg_background.png" />
+        <file name=".DS_Store" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/DS_Store" />
+        <file name="Jalview.app/Contents/Resources/Jalview-File.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Jalview-File.icns" />
+        <file name="Jalview.app/Contents/Resources/Jalview-Launch.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Jalview-Launch.icns" />
         <symlink name="Uninstall Old Jalview (optional).app" target="Jalview.app/Contents/Resources/app/Uninstall Old Jalview.app" />
       </topLevelFiles>
     </macosArchive>
-- 
1.7.10.2