From c3357e172e3c6cc9e257ee9e9cf87442f7d83dea Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Mon, 20 May 2019 16:33:04 +0100
Subject: [PATCH] JAL-3247 Unix shell installer and tar archive corrected --
 network and offline versions. RPM and DEB have had JRE
 dependencies added (not tested yet)

---
 gradle.properties                            |    1 -
 utils/install4j/install4j_template.install4j |   81 ++++++++++++++++++++++----
 2 files changed, 69 insertions(+), 13 deletions(-)

diff --git a/gradle.properties b/gradle.properties
index e49c3ab..de1bc8f 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -101,7 +101,6 @@ install4jTemplate = install4j_template.install4j
 install4jInfoPlistFileAssociations = file_associations_auto-Info_plist.xml
 install4jInstallerFileAssociations = file_associations_auto-install4j.xml
 install4jBuildDir = build/install4j
-install4jMediaTypes = windows,macosArchive,linuxRPM,linuxDeb,unixArchive
 install4jMediaTypes = windows,macosArchive,linuxRPM,linuxDeb,unixArchive,unixInstaller
 install4jFaster = false
 
diff --git a/utils/install4j/install4j_template.install4j b/utils/install4j/install4j_template.install4j
index 7a924e2..f8e9c98 100644
--- a/utils/install4j/install4j_template.install4j
+++ b/utils/install4j/install4j_template.install4j
@@ -8,6 +8,8 @@
     </languages>
     <searchSequence>
       <directory location="${compiler:JRE_DIR}" />
+      <registry />
+      <envVar name="JAVA_HOME" />
     </searchSequence>
     <variables>
       <variable name="OSX_KEYSTORE" value="" description="" category="" />
@@ -1666,7 +1668,7 @@ return console.askYesNo(message, true);
     </styles>
   </installerGui>
   <mediaSets>
-    <linuxDeb name="Linux Deb Archive" id="153" customizedId="" mediaFileName="" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="" bzip="true" description="Jalview Desktop" maintainerEmail="help@jalview.org" architectureSet="false" architecture="">
+    <linuxDeb name="Linux Deb Package" id="153" customizedId="" mediaFileName="" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="openjdk-8-jre" bzip="true" description="Jalview Desktop" maintainerEmail="help@jalview.org" architectureSet="false" architecture="">
       <excludedComponents>
         <component id="1155" />
         <component id="1156" />
@@ -1701,7 +1703,7 @@ return console.askYesNo(message, true);
         <content />
       </postUninstallScript>
     </linuxDeb>
-    <linuxRPM name="Linux RPM" id="570" customizedId="" mediaFileName="" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="" os="linux" arch="i386">
+    <linuxRPM name="Linux RPM Package" id="570" customizedId="" mediaFileName="" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="java-1.8.0-openjdk" os="linux" arch="noarch">
       <excludedComponents>
         <component id="1155" />
         <component id="1156" />
@@ -1736,7 +1738,7 @@ return console.askYesNo(message, true);
         <content />
       </postUninstallScript>
     </linuxRPM>
-    <windows name="Offline Windows" id="743" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" 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="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
+    <windows name="Windows Offline Installer" id="743" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" 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="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
       <excludedComponents>
         <component id="1155" />
         <component id="1156" />
@@ -1758,7 +1760,7 @@ return console.askYesNo(message, true);
         <customAttributes />
       </autoUpdate>
     </windows>
-    <macosArchive name="Offline macOS Single Bundle Archive" id="878" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}-app_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" 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="737">
+    <macosArchive name="macOS Offline DMG" id="878" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}-app_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" 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="737">
       <excludedComponents>
         <component id="1156" />
         <component id="1276" />
@@ -1784,7 +1786,7 @@ return console.askYesNo(message, true);
         <file name="Jalview.app/Contents/Resources/Jalview-Version-Locator.icns" file="Jalview-Version-Locator.icns" />
       </topLevelFiles>
     </macosArchive>
-    <macosArchive name="Network macOS Single Bundle Archive" id="1274" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}-app_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" 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="macOS Network DMG" id="1274" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}-app_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" 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">
       <excludedComponents>
         <component id="1031" />
         <component id="1156" />
@@ -1810,8 +1812,12 @@ return console.askYesNo(message, true);
         <file name="Jalview.app/Contents/Resources/Jalview-File.icns" file="Jalview-File.icns" />
       </topLevelFiles>
     </macosArchive>
-    <unixInstaller name="Unix Installer" id="1595" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_installer_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1">
-      <excludedComponents />
+    <unixInstaller name="Unix Offline Installer" id="1595" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_installer_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/opt/" contentFilesType="1">
+      <excludedComponents>
+        <component id="1155" />
+        <component id="1156" />
+        <component id="1276" />
+      </excludedComponents>
       <includedDownloadableComponents />
       <excludedLaunchers>
         <launcher id="1402" />
@@ -1819,7 +1825,7 @@ return console.askYesNo(message, true);
       <excludedBeans />
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
       <exclude>
-        <entry location=".i4j_fileset_734" fileType="regular" />
+        <entry location=".i4j_fileset_" fileType="regular" />
         <entry location=".i4j_fileset_880" fileType="regular" />
         <entry location=".i4j_fileset_882" fileType="regular" />
       </exclude>
@@ -1832,11 +1838,11 @@ return console.askYesNo(message, true);
         <content />
       </installerScript>
     </unixInstaller>
-    <unixArchive name="Unix Archive" id="1596" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_archive_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false">
+    <unixArchive name="Unix Offline Archive" id="1596" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_archive_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false">
       <excludedComponents>
-        <component id="1031" />
         <component id="1155" />
         <component id="1156" />
+        <component id="1276" />
       </excludedComponents>
       <includedDownloadableComponents />
       <excludedLaunchers>
@@ -1844,14 +1850,18 @@ return console.askYesNo(message, true);
       </excludedLaunchers>
       <excludedBeans />
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
-      <exclude />
+      <exclude>
+        <entry location=".i4j_fileset_" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
+      </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
         <commentFiles />
         <customAttributes />
       </autoUpdate>
     </unixArchive>
-    <windows name="Network Windows" id="1862" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" 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="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
+    <windows name="Windows Network Installer" id="1862" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" 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="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
       <excludedComponents>
         <component id="1031" />
         <component id="1155" />
@@ -1871,6 +1881,51 @@ return console.askYesNo(message, true);
         <customAttributes />
       </autoUpdate>
     </windows>
+    <unixInstaller name="Unix Network Installer" id="1867" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_installer_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/opt/" contentFilesType="1">
+      <excludedComponents>
+        <component id="1031" />
+        <component id="1155" />
+        <component id="1156" />
+      </excludedComponents>
+      <includedDownloadableComponents />
+      <excludedLaunchers />
+      <excludedBeans />
+      <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
+      <exclude>
+        <entry location=".i4j_fileset_734" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
+      </exclude>
+      <variables />
+      <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
+        <commentFiles />
+        <customAttributes />
+      </autoUpdate>
+      <installerScript mode="1" file="">
+        <content />
+      </installerScript>
+    </unixInstaller>
+    <unixArchive name="Unix Network Archive" id="1871" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_archive_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false">
+      <excludedComponents>
+        <component id="1031" />
+        <component id="1155" />
+        <component id="1156" />
+      </excludedComponents>
+      <includedDownloadableComponents />
+      <excludedLaunchers />
+      <excludedBeans />
+      <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="">
+        <commentFiles />
+        <customAttributes />
+      </autoUpdate>
+    </unixArchive>
   </mediaSets>
   <buildIds buildAll="true">
     <mediaSet refId="153" />
@@ -1881,6 +1936,8 @@ return console.askYesNo(message, true);
     <mediaSet refId="1595" />
     <mediaSet refId="1596" />
     <mediaSet refId="1862" />
+    <mediaSet refId="1867" />
+    <mediaSet refId="1871" />
   </buildIds>
   <buildOptions verbose="false" faster="false" disableSigning="false" disableJreBundling="false" debug="false" />
 </install4j>
-- 
1.7.10.2