From d4ff3d58065a0f8c7ea7c8f56be182ae39e6f20b Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 12 Dec 2019 17:11:06 +0000
Subject: [PATCH] JAL-3447 Change to install4j template version, JAL-3394
 removed redundant compiler variable. Fixed help when run in
 Eclipse and removed redundant helpDir

---
 build.gradle      |   36 +++++++++++++++++-------------------
 gradle.properties |    1 +
 2 files changed, 18 insertions(+), 19 deletions(-)

diff --git a/build.gradle b/build.gradle
index 770f3f2..87a5c69 100644
--- a/build.gradle
+++ b/build.gradle
@@ -302,8 +302,7 @@ ext {
   buildingHTML = string("${jalviewDir}/${docDir}/building.html")
   helpFile = string("${classesDir}/${help_dir}/help.jhm")
   helpParentDir = string("${jalviewDir}/${help_parent_dir}")
-  helpDir = string("${help_dir}")
-  helpSourceDir = string("${helpParentDir}/${helpDir}")
+  helpSourceDir = string("${helpParentDir}/${help_dir}")
 
 
   relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
@@ -341,11 +340,13 @@ sourceSets {
 
     resources {
       srcDirs resourceDir
+      srcDirs += helpParentDir
     }
 
     jar.destinationDir = file("${jalviewDir}/${packageDir}")
 
     compileClasspath = files(sourceSets.main.java.outputDir)
+    //compileClasspath += files(sourceSets.main.resources.srcDirs)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
@@ -454,8 +455,8 @@ eclipse {
         cp.entries.removeAll(removeTheseToo)
 
         //cp.entries += new Output("${eclipse_bin_dir}/main")
-        if (file(helpSourceDir).isDirectory()) {
-          cp.entries += new Library(fileReference(helpSourceDir))
+        if (file(helpParentDir).isDirectory()) {
+          cp.entries += new Library(fileReference(helpParentDir))
         }
         if (file(resourceDir).isDirectory()) {
           cp.entries += new Library(fileReference(resourceDir))
@@ -746,7 +747,7 @@ task syncDocs(type: Sync) {
 
 task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
-  def outputDir = "${classesDir}/${helpDir}"
+  def outputDir = "${classesDir}/${help_dir}"
   from(inputDir) {
     exclude '**/*.gif'
     exclude '**/*.jpg'
@@ -828,7 +829,7 @@ task buildIndices(type: JavaExec) {
   dependsOn copyHelp
   classpath = sourceSets.main.compileClasspath
   main = "com.sun.java.help.search.Indexer"
-  workingDir = "${classesDir}/${helpDir}"
+  workingDir = "${classesDir}/${help_dir}"
   def argDir = "html"
   args = [ argDir ]
   inputs.dir("${workingDir}/${argDir}")
@@ -864,8 +865,7 @@ task linkCheck(type: JavaExec) {
   classpath = files("${jalviewDir}/${utilsDir}")
   main = "HelpLinksChecker"
   workingDir = jalviewDir
-  def help = "${classesDir}/${helpDir}"
-  args = [ "${classesDir}/${helpDir}", "-nointernet" ]
+  args = [ "${classesDir}/${help_dir}", "-nointernet" ]
 
   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
   def errFOS = outFOS
@@ -876,13 +876,13 @@ task linkCheck(type: JavaExec) {
     outFOS,
     errorOutput)
 
-  inputs.dir("${classesDir}/${helpDir}")
+  inputs.dir("${classesDir}/${help_dir}")
   outputs.file(helpLinksCheckerOutFile)
 }
 
 // import the pubhtmlhelp target
 ant.properties.basedir = "${jalviewDir}"
-ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${helpDir}"
+ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
 ant.importBuild "${utilsDir}/publishHelp.xml"
 
 
@@ -1269,7 +1269,6 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   projectFile = install4jConfFile
 
   // create an md5 for the input files to use as version for install4j conf file
-  def install4jTemplateMd5 = ""
   def digest = MessageDigest.getInstance("MD5")
   digest.update(
     (file("${install4jDir}/${install4j_template}").text + 
@@ -1279,13 +1278,13 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   if (filesMd5.length() >= 8) {
     filesMd5 = filesMd5.substring(0,8)
   }
-  install4jTemplateMd5 += filesMd5
-  install4jTemplateMd5 += "_${gitHash}"
-  def install4jTemplateVersion = "${JALVIEW_VERSION}_${install4jTemplateMd5}"
+  def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
 
   variables = [
     'OSX_KEYSTORE': OSX_KEYSTORE,
     'JSIGN_SH': JSIGN_SH,
+    'JRE_DIR': getdown_app_dir_java,
+    'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
     'JALVIEW_VERSION': JALVIEW_VERSION,
     'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
     'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
@@ -1296,16 +1295,15 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
     'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
     'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
-    'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4j_info_plist_file_associations,
-    'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
     'COPYRIGHT_MESSAGE': install4j_copyright_message,
     'MACOS_BUNDLE_ID': install4j_macOS_bundle_id,
     'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
     'GETDOWN_DIST_DIR': getdown_app_dir,
     'GETDOWN_ALT_DIR': getdown_app_dir_alt,
     'GETDOWN_INSTALL_DIR': getdown_install_dir,
-    'INFO_PLIST_FILE_ASSOCIATIONS_FILE': "${install4j_info_plist_file_associations}",
+    'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
   ]
+
   destination = "${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}"
   buildSelected = true
 
@@ -1414,8 +1412,8 @@ task helppages {
   dependsOn copyHelp
   dependsOn pubhtmlhelp
   
-  inputs.dir("${classesDir}/${helpDir}")
-  outputs.dir("${buildDir}/distributions/${helpDir}")
+  inputs.dir("${classesDir}/${help_dir}")
+  outputs.dir("${buildDir}/distributions/${help_dir}")
 }
 
 // LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE
diff --git a/gradle.properties b/gradle.properties
index c1f3118..7337984 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -137,6 +137,7 @@ getdown_channel_base = https://www.jalview.org/getdown
 getdown_channel_name = SCRATCH-DEFAULT
 getdown_app_dir_release = release
 getdown_app_dir_alt = alt
+getdown_app_dir_java = jre
 getdown_install_dir = install
 getdown_rsync_dest = /Volumes/jalview/docroot/getdown
 reportRsyncCommand =
-- 
1.7.10.2