X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=d05e8659cd9916de13661d6bb8e8e809fa946096;hb=bba78613eb93924c43c35ed7b7d090c1c9c4e466;hp=7ad6f9965e560830bad4e1a2afa2f9cf72f4cf31;hpb=06eaa901379256f8db2114acb4e1bc75002b2527;p=jalview.git

diff --git a/build.gradle b/build.gradle
index 7ad6f99..d05e865 100644
--- a/build.gradle
+++ b/build.gradle
@@ -52,7 +52,7 @@ plugins {
   id 'application'
   id 'eclipse'
   id "com.diffplug.gradle.spotless" version "3.28.0"
-  id 'com.github.johnrengelman.shadow' version '4.0.3'
+  id 'com.github.johnrengelman.shadow' version '6.0.0'
   id 'com.install4j.gradle' version '10.0.3'
   id 'com.dorongold.task-tree' version '2.1.1' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
   id 'com.palantir.git-version' version '0.13.0' apply false
@@ -1783,6 +1783,27 @@ task testTask1(type: Test) {
   }
 }
 
+task testTask2(type: Test) {
+  group = "Verification"
+  description = "Tests that need to be isolated from the main test run"
+  useTestNG() {
+    includeGroups name
+    excludeGroups testng_excluded_groups.split(",")
+    preserveOrder true
+    useDefaultListeners=true
+  }
+}
+task testTask3(type: Test) {
+  group = "Verification"
+  description = "Tests that need to be isolated from the main test run"
+  useTestNG() {
+    includeGroups name
+    excludeGroups testng_excluded_groups.split(",")
+    preserveOrder true
+    useDefaultListeners=true
+  }
+}
+
 /* insert more testTaskNs here -- change N to next digit or other string */
 /*
 task testTaskN(type: Test) {
@@ -1830,10 +1851,16 @@ tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { te
     showExceptions true
     showCauses true
     showStackTraces true
-
+    if (test_output) {
+      showStandardStreams true
+    }
     info.events = [ TestLogEvent.FAILED ]
   }
 
+  if (OperatingSystem.current().isMacOsX()) {
+    testTask.systemProperty "apple.awt.UIElement", "true"
+    testTask.environment "JAVA_TOOL_OPTIONS", "-Dapple.awt.UIElement=true"
+  }
 
 
   ignoreFailures = true // Always try to run all tests for all modules
@@ -2129,12 +2156,33 @@ shadowJar {
   if (buildDist) {
     dependsOn makeDist
   }
-  from ("${jalviewDir}/${libDistDir}") {
-    include("*.jar")
-  }
-  manifest {
-    attributes "Implementation-Version": JALVIEW_VERSION,
-    "Application-Name": applicationName
+
+  def jarFiles = fileTree(dir: "${jalviewDir}/${libDistDir}", include: "*.jar", exclude: "regex.jar").getFiles()
+  def groovyJars = jarFiles.findAll {it1 -> file(it1).getName().startsWith("groovy-swing")}
+  def otherJars = jarFiles.findAll {it2 -> !file(it2).getName().startsWith("groovy-swing")}
+  from groovyJars
+  from otherJars
+
+  // we need to include the groovy-swing Include-Package for it to run in the shadowJar
+  doFirst {
+    def jarFileManifests = []
+    groovyJars.each { jarFile ->
+      def mf = zipTree(jarFile).getFiles().find { it.getName().equals("MANIFEST.MF") }
+      if (mf != null) {
+        jarFileManifests += mf
+      }
+    }
+
+    manifest {
+      attributes "Implementation-Version": JALVIEW_VERSION, "Application-Name": applicationName
+      from (jarFileManifests) {
+        eachEntry { details ->
+          if (!details.key.equals("Import-Package")) {
+            details.exclude()
+          }
+        }
+      }
+    }
   }
 
   duplicatesStrategy "INCLUDE"
@@ -3360,7 +3408,7 @@ task jalviewjsTransferUnzipSwingJs {
 
 
 task jalviewjsTransferUnzipLib {
-  def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
+  def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip").sort()
 
   doLast {
     zipFiles.each { file_zip -> 
@@ -3377,11 +3425,13 @@ task jalviewjsTransferUnzipLib {
 
 
 task jalviewjsTransferUnzipAllLibs {
-  dependsOn jalviewjsTransferUnzipSwingJs
   dependsOn jalviewjsTransferUnzipLib
+  dependsOn jalviewjsTransferUnzipSwingJs
 }
 
 
+
+
 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
   group "JalviewJS"
   description "Create the alternative j2s file from the j2s.* properties"
@@ -3436,7 +3486,7 @@ task jalviewjsSyncAllLibs (type: Sync) {
     include "**"
   }
 
-  // should this be exclude really ?
+  // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite)
   duplicatesStrategy "INCLUDE"
 
   outputs.files outputFiles
@@ -3669,7 +3719,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
     classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
     main = "com.google.javascript.jscomp.CommandLineRunner"
     jvmArgs = [ "-Dfile.encoding=UTF-8" ]
-    args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
+    args = [ "--compilation_level", jalviewjs_closure_compiler_optimization_level, "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
     maxHeapSize = "2g"
 
     msg = "\nRunning '"+commandLine.join(' ')+"'\n"
@@ -4277,12 +4327,14 @@ task jalviewjsLaunchTest {
       execStdout = stdout
       execStderr = stderr
     }
-    def execArgs = [
+    // macOS not running properly with timeout arguments
+    def execArgs = macOS ? [] : [
+      "--virtual-time-budget=${timeoutms}",
+    ]
+    execArgs += [
       "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
       "--headless=new",
       "--disable-gpu",
-      "--timeout=${timeoutms}",
-      "--virtual-time-budget=${timeoutms}",
       "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
       "--profile-directory=${jalviewjs_chromium_profile_name}",
       "--allow-file-access-from-files",