X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=011be6702613d4704477cd3c8c4442485fd81806;hb=bc7ebbb58133e64e7a77cb83eef8e2df75faec03;hp=673cec5b4da7e6c62e11032836838504aac0e3fd;hpb=5f7b889ee04f8bae65c785c9cebc04d29e0811d5;p=jalview.git

diff --git a/build.gradle b/build.gradle
index 673cec5..011be67 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) {
@@ -1830,7 +1851,9 @@ 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 ]
   }
 
@@ -2133,12 +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"
@@ -3000,6 +3044,7 @@ task sourceDist(type: Tar) {
   into project.name
 
   def EXCLUDE_FILES=[
+    "dist/*",
     "build/*",
     "bin/*",
     "test-output/",
@@ -4260,7 +4305,7 @@ task jalviewjsLaunchTest {
   def stdout
   def stderr
   doFirst {
-    def timeoutms = Integer.valueOf(jalviewjs_chromium_timeout) * 1000
+    def timeoutms = Integer.valueOf(jalviewjs_chromium_overall_timeout) * 1000
     
     def binary = file(chromiumBinary)
     if (!binary.exists()) {
@@ -4303,6 +4348,7 @@ task jalviewjsLaunchTest {
             errorOutput = execStderr
             executable(chromiumBinary)
             args(execArgs)
+            println "COMMAND: '"+commandLine.join(" ")+"'"
           }
           executor.shutdownNow()
         }
@@ -4320,7 +4366,7 @@ task jalviewjsLaunchTest {
             executor.shutdownNow()
           }
           // if no change in stderr for 10s then also end
-          if (noChangeIterations >= 10) {
+          if (noChangeIterations >= jalviewjs_chromium_idle_timeout) {
             executor.shutdownNow()
           }
           if (stderrString.length() == noChangeBytes) {