X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=build.gradle;h=cbd65f2f92e73ead0e39a234210adbfcecfed25c;hp=9b173d7b5549e55c26fae5442a526a300f893edf;hb=HEAD;hpb=20d8cc2bb3e2fab2b7f637a3d523c90ceb58903d

diff --git a/build.gradle b/build.gradle
index 9b173d7..3b81404 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"
@@ -2192,9 +2240,9 @@ task getdownImages() {
   dependsOn getdownImagesProcess
 }
 
-task getdownWebsite() {
+task getdownWebsiteBuild() {
   group = "distribution"
-  description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
+  description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer. No digest is created."
 
   dependsOn getdownImages
   if (buildDist) {
@@ -2306,7 +2354,7 @@ task getdownWebsite() {
           from s
           into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
         }
-        getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
+        getdownTextLines += "xresource = ${getdown_wrapper_script_dir}/${script}"
       }
     }
 
@@ -2448,7 +2496,9 @@ task getdownDigestDir(type: JavaExec) {
 task getdownDigest(type: JavaExec) {
   group = "distribution"
   description = "Digest the getdown website folder"
-  dependsOn getdownWebsite
+
+  dependsOn getdownWebsiteBuild
+
   doFirst {
     classpath = files(getdownLauncher)
   }
@@ -2481,12 +2531,19 @@ task getdown() {
   }
 }
 
+task getdownWebsite {
+  group = "distribution"
+  description = "A task to create the whole getdown channel website dir including digest file"
+
+  dependsOn getdownWebsiteBuild
+  dependsOn getdownDigest
+}
 
 task getdownArchiveBuild() {
   group = "distribution"
   description = "Put files in the archive dir to go on the website"
 
-  dependsOn getdownWebsite
+  dependsOn getdownWebsiteBuild
 
   def v = "v${JALVIEW_VERSION_UNDERSCORES}"
   def vDir = "${getdownArchiveDir}/${v}"
@@ -2996,6 +3053,7 @@ task sourceDist(type: Tar) {
   into project.name
 
   def EXCLUDE_FILES=[
+    "dist/*",
     "build/*",
     "bin/*",
     "test-output/",
@@ -4243,7 +4301,7 @@ task jalviewjsChromiumProfile {
 task jalviewjsLaunchTest {
   group "Test"
   description "Check JalviewJS opens in a browser"
-//  dependsOn jalviewjsBuildSite
+  dependsOn jalviewjsBuildSite
   dependsOn jalviewjsCopyStderrLaunchFile
   dependsOn jalviewjsChromiumProfile
 
@@ -4256,68 +4314,89 @@ task jalviewjsLaunchTest {
   def stdout
   def stderr
   doFirst {
-    def timeoutms = Integer.valueOf(jalviewjs_chromium_timeout) * 1000
-
-    ScheduledExecutorService executor = Executors.newScheduledThreadPool(3);
-    final Future handler = executor.submit(
-      () -> {
-
-        exec {
-          def binary = file(chromiumBinary)
-          if (!binary.exists()) {
-            throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
+    def timeoutms = Integer.valueOf(jalviewjs_chromium_overall_timeout) * 1000
+    
+    def binary = file(chromiumBinary)
+    if (!binary.exists()) {
+      throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.")
+    }
+    stdout = new ByteArrayOutputStream()
+    stderr = new ByteArrayOutputStream()
+    def execStdout
+    def execStderr
+    if (jalviewjs_j2s_to_console.equals("true")) {
+      execStdout = new org.apache.tools.ant.util.TeeOutputStream(
+        stdout,
+        System.out)
+      execStderr = new org.apache.tools.ant.util.TeeOutputStream(
+        stderr,
+        System.err)
+    } else {
+      execStdout = stdout
+      execStderr = stderr
+    }
+    def execArgs = [
+      "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER
+      "--headless=new",
+      "--disable-gpu",
+      "--timeout=${timeoutms}",
+      "--virtual-time-budget=${timeoutms}",
+      "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}",
+      "--profile-directory=${jalviewjs_chromium_profile_name}",
+      "--allow-file-access-from-files",
+      "--enable-logging=stderr",
+      "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}"
+    ]
+    
+    if (true || macOS) {
+      ScheduledExecutorService executor = Executors.newScheduledThreadPool(3);
+      Future f1 = executor.submit(
+        () -> {
+          exec {
+            standardOutput = execStdout
+            errorOutput = execStderr
+            executable(chromiumBinary)
+            args(execArgs)
+            println "COMMAND: '"+commandLine.join(" ")+"'"
           }
+          executor.shutdownNow()
+        }
+      )
 
-          stdout = new ByteArrayOutputStream()
-          stderr = new ByteArrayOutputStream()
-          if (jalviewjs_j2s_to_console.equals("true")) {
-            standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
-              stdout,
-              System.out)
-            errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
-              stderr,
-              System.err)
+      def noChangeBytes = 0
+      def noChangeIterations = 0
+      executor.scheduleAtFixedRate(
+        () -> {
+          String stderrString = stderr.toString()
+          // shutdown the task if we have a success string
+          if (stderrString.contains(jalviewjs_desktop_init_string)) {
+            f1.cancel()
+            Thread.sleep(1000)
+            executor.shutdownNow()
+          }
+          // if no change in stderr for 10s then also end
+          if (noChangeIterations >= jalviewjs_chromium_idle_timeout) {
+            executor.shutdownNow()
+          }
+          if (stderrString.length() == noChangeBytes) {
+            noChangeIterations++
           } else {
-            standardOutput = stdout
-            errorOutput = stderr
+            noChangeBytes = stderrString.length()
+            noChangeIterations = 0
           }
+        },
+        1, 1, TimeUnit.SECONDS)
 
-
-          executable(chromiumBinary)
-          args([
-            "--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",
-            "--enable-logging=stderr",
-            "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}"
-          ])
-        }
-
-      }
-
-    )
-
-    executor.schedule(new Runnable(){
-      public void run(){
-         executor.shutdownNow()
-      }
-    }, timeoutms, TimeUnit.MILLISECONDS);
-
-    executor.scheduleAtFixedRate(
-      () -> {
-        if (stderr.toString().contains(jalviewjs_desktop_init_string)) {
-          Thread.sleep(1000)
+      executor.schedule(new Runnable(){
+        public void run(){
+          f1.cancel()
           executor.shutdownNow()
         }
-      },
-      1, 1, TimeUnit.SECONDS)
+      }, timeoutms, TimeUnit.MILLISECONDS)
 
-    executor.awaitTermination(timeoutms, TimeUnit.MILLISECONDS)
+      executor.awaitTermination(timeoutms+10000, TimeUnit.MILLISECONDS)
+      executor.shutdownNow()
+    }
 
   }