JAL-3299 Fixed gitHash and gitBranch definitions in build.gradle
[jalview.git] / build.gradle
index adaf54d..0ae4e5c 100644 (file)
@@ -1,10 +1,15 @@
 import org.apache.tools.ant.filters.ReplaceTokens
+//import org.apache.tools.ant.filters.ReplaceRegexp
 import org.gradle.internal.os.OperatingSystem
+import org.gradle.plugins.ide.eclipse.model.*
+
+
+import groovy.transform.ExternalizeMethods
 
 buildscript {
   dependencies {
-        classpath 'org.openclover:clover:4.3.1'
-        classpath 'org.apache.commons:commons-compress:1.18'
+    classpath 'org.openclover:clover:4.3.1'
+    classpath 'org.apache.commons:commons-compress:1.18'
   }
 }
 
@@ -46,30 +51,29 @@ def compile_source_compatibility
 def compile_target_compatibility
 
 ext {
-  // where the getdown channel will be built. 
-  // TODO: consider allowing this expression to  be overrriden by -P arg
-  getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION + '/'
+  // where the getdown channel will be built.
+  // TODO: consider allowing this expression to  be overridden by -P arg
+  getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
   getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
   getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
   getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
   getdownLauncher = jalviewDir + '/' + getdown_launcher
-  getdownFilesDir = jalviewDir + '/' + getdown_files_dir
-  getdownLib1 = jalviewDir + '/' + getdown_lib1
-  def getdownChannel = getdown_channel_name
-  if (getdown_channel_name.equals("COMMIT")) {
-    getdownChannel = getGitHash()
-  }
-  getdown_app_base = getdown_channel_base+"/"+getdownChannel+"/"+JAVA_VERSION+"/"
+  getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
+  getdown_app_base = getdown_channel_base+"/"+getdown_channel_name+"/"+JAVA_VERSION+"/"
   modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"])
   modules_runtimeClasspath = modules_compileClasspath
+  gitHash = ""
+  gitBranch = ""
 }
 
+def JAVA_INTEGER_VERSION
 def additional_compiler_args = []
-// these are getdown.txt properties defined dependent on the JAVA_VERSION 
+// these are getdown.txt properties defined dependent on the JAVA_VERSION
 def getdown_alt_java_min_version
 // this property is assigned below and expanded to multiple lines in the getdown task
 def getdown_alt_multi_java_location
 if (JAVA_VERSION.equals("1.8")) {
+  JAVA_INTEGER_VERSION = "8"
   libDir = j11libDir
   libDistDir = j8libDir
   compile_source_compatibility = 1.8
@@ -77,6 +81,7 @@ if (JAVA_VERSION.equals("1.8")) {
   getdown_alt_java_min_version = getdown_alt_java8_min_version
   getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
 } else if (JAVA_VERSION.equals("11")) {
+  JAVA_INTEGER_VERSION = "11"
   libDir = j11libDir
   libDistDir = j11libDir
   compile_source_compatibility = 11
@@ -113,10 +118,10 @@ sourceSets {
   }
   clover {
     java {
-        srcDirs = [ cloverInstrDir ]
-        outputDir = file("${buildDir}/${cloverClassesDir}")
+      srcDirs = [ cloverInstrDir ]
+      outputDir = file("${buildDir}/${cloverClassesDir}")
     }
-    
+
     resources {
       srcDirs = sourceSets.main.resources.srcDirs
     }
@@ -128,7 +133,7 @@ sourceSets {
 
     runtimeClasspath = compileClasspath
   }
-  
+
   test {
     java {
       srcDirs "$jalviewDir/$testSourceDir"
@@ -139,15 +144,15 @@ sourceSets {
       srcDirs = sourceSets.main.resources.srcDirs
     }
 
-    compileClasspath = files( sourceSets.test.java.outputDir ) 
+    compileClasspath = files( sourceSets.test.java.outputDir )
 
     if (use_clover) {
       compileClasspath += sourceSets.clover.compileClasspath
     } else {
       compileClasspath += files(sourceSets.main.java.outputDir)
     }
-    compileClasspath += sourceSets.main.compileClasspath
-    compileClasspath += files( sourceSets.main.resources.srcDirs)
+    //compileClasspath += sourceSets.main.compileClasspath
+    //compileClasspath += files( sourceSets.main.resources.srcDirs)
     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
 
@@ -164,8 +169,8 @@ dependencies {
 }
 
 configurations {
-    cloverRuntime
-    cloverRuntime.extendsFrom cloverCompile
+  cloverRuntime
+  cloverRuntime.extendsFrom cloverCompile
 }
 
 eclipse {
@@ -187,8 +192,7 @@ eclipse {
         removeThese += it
       }
     }
-    containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
-    
+
     minusConfigurations += removeThese
     plusConfigurations = [ ]
     file {
@@ -198,7 +202,7 @@ eclipse {
         HashMap<String, Boolean> addedSrcPath = new HashMap<>();
         cp.entries.each { entry ->
           if (entry.kind == 'src') {
-            if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test" || entry.path == "resources")) {
+            if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) {
               removeTheseToo += entry
             } else {
               addedSrcPath.putAt(entry.path, true)
@@ -206,29 +210,11 @@ eclipse {
           }
         }
         cp.entries.removeAll(removeTheseToo)
-      }
-      
-      withXml {
-        def node = it.asNode()
-        def srcTestAttributes
-        node.children().each{ cpe ->
-          def attributes = cpe.attributes()
-          if (attributes.get("kind") == "src" && attributes.get("path") == "test") {
-            srcTestAttributes = cpe.find { a -> a.name() == "attributes" }
-            return
-          }
-        }
-        def addTestAttribute = true
-        srcTestAttributes.each{a ->
-          if (a.name() == "attribute" && a.attributes().getAt("name") == "test") {
-            addTestAttribute = false
-          }
-        }
-        if (addTestAttribute) {
-          srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"]))
-        }
         
-        node.appendNode('classpathentry', [kind:"output", path:"bin/main"])
+        cp.entries += new Output("bin/main")
+        cp.entries += new Library(fileReference(helpParentDir))
+        cp.entries += new Library(fileReference(resourceDir))
+        
         HashMap<String, Boolean> addedLibPath = new HashMap<>();
         def allPaths = sourceSets.test.compileClasspath + sourceSets.main.compileClasspath
         sourceSets.main.compileClasspath.each{
@@ -236,7 +222,6 @@ eclipse {
           //no longer want to add outputDir as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
             // don't add dirs to classpath
-            //println("Not adding directory "+it)
             return
           }
           def itPath = it.toString()
@@ -247,36 +232,69 @@ eclipse {
             //println("Not adding duplicate entry "+itPath)
           } else {
             //println("Adding entry "+itPath)
-            node.appendNode('classpathentry', [kind:"lib", path:itPath])
+            cp.entries += new Library(fileReference(itPath))
             addedLibPath.put(itPath, true)
           }
         }
+
         sourceSets.test.compileClasspath.each{
           //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
           //no longer want to add outputDir as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
             // don't add dirs to classpath
-            //println("Not adding directory "+it)
-            return
+            return false // groovy "break" in .each loop
           }
           def itPath = it.toString()
           if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
             itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
           }
           if (addedLibPath.get(itPath)) {
-            //println("Not adding duplicate entry "+itPath)
+            // don't duplicate
           } else {
-            //println("Adding entry "+itPath)
-            node.appendNode('classpathentry', [kind:"lib", path:itPath])
-              .appendNode('attributes')
-                .appendNode('attribute', [name:"test", value:"true"])
+            def lib = new Library(fileReference(itPath))
+            // this doesn't work... yet.  Adding test=true attribute using withXml below
+            //def attrs = new Node(null, 'attributes', ["test":"true"])
+            //lib.appendNode(attrs) //
+            cp.entries += lib
             addedLibPath.put(itPath, true)
           }
         }
-      }
+      }  
 
-    }
-  }
+      // withXml changes ignored by buildship, these add the "test=true" attribute
+      withXml {
+        def node = it.asNode()
+        
+        def srcTestAttributes
+        node.children().each{ cpe ->
+          def attributes = cpe.attributes()
+          if (attributes.get("kind") == "src" && attributes.get("path") == "test") {
+            srcTestAttributes = cpe.find { a -> a.name() == "attributes" }
+            return
+          }
+        }
+        def addTestAttribute = true
+        srcTestAttributes.each{a ->
+          if (a.name() == "attribute" && a.attributes().getAt("name") == "test") {
+            addTestAttribute = false
+          }
+        }
+        if (addTestAttribute) {
+          srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"]))
+        }
+
+        node.children().each{ cpe ->
+          def attributes = cpe.attributes()
+          if (attributes.get("kind") == "lib" && attributes.get("path").startsWith("utils/")) {
+            cpe.appendNode('attributes')
+                .appendNode('attribute', [name:"test", value:"true"])
+          }
+        }
+      } // withXML
+    } // file
+
+    containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+  } // classpath
 
   jdt {
     // for the IDE, use java 11 compatibility
@@ -287,58 +305,60 @@ eclipse {
     file {
       withProperties { props ->
         def jalview_prefs = new Properties()
-               def ins = new FileInputStream(eclipse_extra_jdt_prefs_file)
-               jalview_prefs.load(ins)
-               ins.close()
-               jalview_prefs.forEach { t, v ->
-                       if (props.getAt(t) == null) {
-                               props.putAt(t, v)
-                       }
-               }
+        def ins = new FileInputStream(jalviewDirAbsolutePath+"/"+eclipse_extra_jdt_prefs_file)
+        jalview_prefs.load(ins)
+        ins.close()
+        jalview_prefs.forEach { t, v ->
+          if (props.getAt(t) == null) {
+            props.putAt(t, v)
+          }
+        }
       }
     }
   }
-
-}
+  
+  //synchronizationTasks eclipseClasspath
+  //autoBuildTasks eclipseClasspath
+} 
 
 task cloverInstr() {
   // only instrument source, we build test classes as normal
-    inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
-    outputs.dir cloverInstrDir
-
-    doFirst {
-        delete cloverInstrDir
-        def argsList = ["--initstring", "${buildDir}/clover/clover.db",
-                        "-d", "${buildDir}/${cloverSourcesInstrDir}"]
-        argsList.addAll(inputs.files.files.collect({ file ->
-            file.absolutePath
-        }))
-        String[] args = argsList.toArray()
-        println("About to instrument "+args.length +" files")
-        com.atlassian.clover.CloverInstr.mainImpl(args)
-    }
+  inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
+  outputs.dir cloverInstrDir
+
+  doFirst {
+    delete cloverInstrDir
+    def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+      "-d", "${buildDir}/${cloverSourcesInstrDir}"]
+    argsList.addAll(inputs.files.files.collect({ file ->
+      file.absolutePath
+    }))
+    String[] args = argsList.toArray()
+    println("About to instrument "+args.length +" files")
+    com.atlassian.clover.CloverInstr.mainImpl(args)
+  }
 }
+  
 
 task cloverReport {
-       group = "Verification"
-       description = "Createst the Clover report"
-    inputs.dir "${buildDir}/clover"
-    outputs.dir "${reportsDir}/clover"
-    onlyIf {
-        file("${buildDir}/clover/clover.db").exists()
-    }
-    doFirst {
-        def argsList = ["--initstring", "${buildDir}/clover/clover.db",
-                        "-o", "${reportsDir}/clover"]
-        String[] args = argsList.toArray()
-        com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
-        
-        // and generate ${reportsDir}/clover/clover.xml
-        args = ["--initstring", "${buildDir}/clover/clover.db",
-                        "-o", "${reportsDir}/clover/clover.xml"].toArray()
-        com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
-    }
+  group = "Verification"
+  description = "Createst the Clover report"
+  inputs.dir "${buildDir}/clover"
+  outputs.dir "${reportsDir}/clover"
+  onlyIf {
+    file("${buildDir}/clover/clover.db").exists()
+  }
+  doFirst {
+    def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+      "-o", "${reportsDir}/clover"]
+    String[] args = argsList.toArray()
+    com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
+
+    // and generate ${reportsDir}/clover/clover.xml
+    args = ["--initstring", "${buildDir}/clover/clover.db",
+      "-o", "${reportsDir}/clover/clover.xml"].toArray()
+    com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+  }
 }
 
 // end clover bits
@@ -397,41 +417,74 @@ def getDate(format) {
   return date.format(format)
 }
 
-def getGitHash() {
-  def stdout = new ByteArrayOutputStream()
+task setGitVals {
+  def hashStdOut = new ByteArrayOutputStream()
   exec {
     commandLine "git", "rev-parse", "--short", "HEAD"
-    standardOutput = stdout
-    workingDir = jalviewDir
+    standardOutput = hashStdOut
   }
-  return stdout.toString().trim()
-}
 
-def getGitBranch() {
-  def stdout = new ByteArrayOutputStream()
+  def branchStdOut = new ByteArrayOutputStream()
   exec {
     commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
-    standardOutput = stdout
-    workingDir = jalviewDir
+    standardOutput = branchStdOut
   }
-  return stdout.toString().trim()
+
+  project.ext.gitHash = hashStdOut.toString().trim()
+  project.ext.gitBranch = branchStdOut.toString().trim()
+
+  outputs.upToDateWhen { false }
 }
 
 task createBuildProperties(type: WriteProperties) {
+  dependsOn setGitVals
   inputs.dir("$jalviewDir/$sourceDir")
+  inputs.dir("$classes")
   inputs.dir("$jalviewDir/$resourceDir")
   outputFile "$classes/$buildPropertiesFile"
-  /* taking time/date specific comment out to allow better incremental builds */
+  // taking time specific comment out to allow better incremental builds
   //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
   comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
   property "BUILD_DATE", getDate("dd MMMM yyyy")
   property "VERSION", JALVIEW_VERSION
-  property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
+  property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
   outputs.file(outputFile)
-  outputs.dir("$classes")
+}
+
+def buildingHTML = "$jalviewDir/$docDir/building.html"
+task deleteBuildingHTML(type: Delete) {
+  delete buildingHTML
+}
+
+task convertBuildingMD(type: Exec) {
+  dependsOn deleteBuildingHTML
+  def buildingMD = "$jalviewDir/$docDir/building.md"
+  def css = "$jalviewDir/$docDir/github.css"
+
+  def pandoc = pandoc_exec
+  def hostname = "hostname".execute().text.trim()
+  if (! file(pandoc).exists() && hostname.equals("jv-bamboo")) {
+    pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
+  }
+
+  if (file(pandoc).exists()) {
+    commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
+  } else {
+    commandLine "true"
+  }
+
+  ignoreExitValue true
+
+  inputs.file(buildingMD)
+  inputs.file(css)
+  outputs.file(buildingHTML)
+}
+clean {
+  delete buildingHTML
 }
 
 task syncDocs(type: Sync) {
+  dependsOn convertBuildingMD
   def syncDir = "$classes/$docDir"
   from fileTree("$jalviewDir/$docDir")
   into syncDir
@@ -439,21 +492,23 @@ task syncDocs(type: Sync) {
 }
 
 def helpFile = "$classes/$helpDir/help.jhm"
-task syncHelp(type: Sync) {
-  inputs.files("$jalviewDir/$helpDir")
-  outputs.files(helpFile)
-
-  def syncDir = "$classes/$helpDir"
-  from fileTree("$jalviewDir/$helpDir")
-  into syncDir
-}
 
 task copyHelp(type: Copy) {
-  def inputDir = "$jalviewDir/$helpDir"
+  def inputDir = "$jalviewDir/$helpParentDir/$helpDir"
   def outputDir = "$classes/$helpDir"
-  from inputDir
+  from(inputDir) {
+    exclude '**/*.gif'
+    exclude '**/*.jpg'
+    exclude '**/*.png'
+    filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION])
+  }
+  from(inputDir) {
+    include '**/*.gif'
+    include '**/*.jpg'
+    include '**/*.png'
+  }
   into outputDir
-  filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': "USING_FILTER"])
+
   inputs.dir(inputDir)
   outputs.files(helpFile)
   outputs.dir(outputDir)
@@ -490,14 +545,14 @@ test {
     dependsOn cloverInstr
   }
 
-  print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n") 
-  
+  print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+
   useTestNG() {
     includeGroups testngGroups
     preserveOrder true
     useDefaultListeners=true
   }
-  
+
   workingDir = jalviewDir
   //systemProperties 'clover.jar' System.properties.clover.jar
   sourceCompatibility = compile_source_compatibility
@@ -531,6 +586,8 @@ task compileLinkCheck(type: JavaCompile) {
   destinationDir = file("$jalviewDir/$utilsDir")
   source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
 
+  inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
+  inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
   outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class")
   outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
 }
@@ -543,7 +600,6 @@ task linkCheck(type: JavaExec) {
   workingDir = jalviewDir
   def help = "$classes/$helpDir"
   args = [ "$classes/$helpDir", "-nointernet" ]
-  //args = [ "$classesDir/$helpDir", "-nointernet" ]
 
   doFirst {
     helplinkscheckeroutputfile.createNewFile()
@@ -615,9 +671,10 @@ task cleanDist {
 }
 
 shadowJar {
+  group = "distribution"
   dependsOn makeDist
   from ("$jalviewDir/$libDistDir") {
-      include("*.jar")
+    include("*.jar")
   }
   mainClassName = shadowJarMainClass
   mergeServiceFiles()
@@ -639,7 +696,10 @@ task getdownWebsite() {
     def props = project.properties.sort { it.key }
     props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
     props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
-    
+
+    if (getdown_local == "true") {
+      getdown_app_base = file(getdownWebsiteDir).toURI().toString()
+    }
     props.put("getdown_txt_appbase", getdown_app_base)
     props.each{ prop, val ->
       if (prop.startsWith("getdown_txt_") && val != null) {
@@ -700,19 +760,24 @@ task getdownWebsite() {
       }
     }
 
-    if (JAVA_VERSION.equals("11")) {
-      def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
-      j11libFiles.sort().each{f ->
-        def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
-        getdownTextString += line
-        copy {
-          from f.getPath()
-          into project.ext.getdownJ11libDir
-        }
-      }
-    }
-
-    getdownTextString += "code = " + file(getdownLauncher).getName() + "\n"
+    // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
+    /*
+     if (JAVA_VERSION.equals("11")) {
+     def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
+     j11libFiles.sort().each{f ->
+     def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
+     getdownTextString += line
+     copy {
+     from f.getPath()
+     into project.ext.getdownJ11libDir
+     }
+     }
+     }
+     */
+
+    // getdown-launcher.jar should not be in main application class path so the main application can move it when updated.  Listed as a resource so it gets updated.
+    //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
+    getdownTextString += "resource = " + file(getdownLauncher).getName() + "\n"
     getdownTextString += "class = " + mainClass + "\n"
 
     def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt")
@@ -725,21 +790,11 @@ task getdownWebsite() {
 
     copy {
       from getdownLauncher
-      into project.ext.getdownWebsiteDir
-    }
-
-    copy {
-      from getdownLauncher
-      into project.ext.getdownFilesDir
-    }
-
-    copy {
-      from getdownLib1
       into project.ext.getdownFilesDir
     }
 
     copy {
-      from getdownLib1
+      from getdownLauncher
       into project.ext.getdownWebsiteDir
     }
 
@@ -749,7 +804,7 @@ task getdownWebsite() {
       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.progress_image')
       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.icon')
       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.mac_dock_icon')
-      into project.ext.getdownFilesDir + '/' + getdown_resource_dir 
+      into project.ext.getdownFilesDir + '/' + getdown_resource_dir
     }
   }
 
@@ -762,10 +817,10 @@ task getdownDigest(type: JavaExec) {
   group = "distribution"
   description = "Digest the getdown website folder"
   dependsOn getdownWebsite
-  classpath = files(jalviewDir + '/' + getdown_core)
-  classpath file(jalviewDir + '/' + getdown_lib1)
+  classpath = files(jalviewDir + '/' + getdown_core, jalviewDir+'/'+getdown_launcher)
   main = "com.threerings.getdown.tools.Digester"
   args project.ext.getdownWebsiteDir
+  inputs.dir(project.ext.getdownWebsiteDir)
   outputs.file(project.ext.getdownWebsiteDir + '/' + "digest2.txt")
 }
 
@@ -795,27 +850,73 @@ install4j {
   }
   installDir = file(install4jHomeDir)
   mediaTypes = Arrays.asList(install4jMediaTypes.split(","))
+  if (install4jFaster.equals("true")) {
+    faster = true
+  }
 }
 
 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+"/jre"
+  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+"/jre"
+  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: ['VERSION': JALVIEW_VERSION, 'MACOS_JAVA_VM_DIR': macosJavaVMDir, 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir])
+    filter(ReplaceTokens, beginToken: '$$', endToken: '$$',
+      tokens: [
+        'JAVA_VERSION': JAVA_VERSION,
+        'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+        'VERSION': JALVIEW_VERSION,
+        'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+        'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+        'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+        'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+        'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
+        'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
+        'MACOS_BUNDLE_ID': install4jMacOSBundleId
+      ]
+    )
+    if (OSX_KEYPASS=="") {
+      filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"'])
+      filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor'])
+    }
   }
   into install4jDir
-  inputs.files("$install4jDir/$install4jTemplate")
   outputs.files(install4jConf)
+
+  doLast {
+    // include file associations in installer
+    def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text
+    ant.replaceregexp(
+      byline: false,
+      flags: "s",
+      match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
+      replace: installerFileAssociationsXml,
+      file: install4jConf
+    )
+    /*
+    // include uninstaller applescript app files in dmg
+    def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text
+    ant.replaceregexp(
+      byline: false,
+      flags: "s",
+      match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
+      replace: installerDMGUninstallerXml,
+      file: install4jConf
+    )
+    */
+  }
 }
 
 task installers(type: com.install4j.gradle.Install4jTask) {
@@ -825,9 +926,15 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   dependsOn copyInstall4jTemplate
   projectFile = file(install4jConf)
   println("Using projectFile "+projectFile)
-  variables = [majorVersion: version.substring(2, 11), build: 001]
+  variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
   destination = "$jalviewDir/$install4jBuildDir/$JAVA_VERSION"
   buildSelected = true
+
+  if (OSX_KEYPASS) {
+    macKeystorePassword=OSX_KEYPASS
+    
+  }
+  
   inputs.dir(project.ext.getdownWebsiteDir)
   inputs.file(install4jConf)
   inputs.dir(macosJavaVMDir)