X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=3b81404290f0068e6827038e1b74f157cd43822b;hb=HEAD;hp=4aa019c9815eacbe0f1c1f8e8de3c7cec29c8fc9;hpb=469dc5a0e6d06a2c8a27f27b712ccfdbe3314ee4;p=jalview.git

diff --git a/build.gradle b/build.gradle
index 4aa019c..437c43a 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
@@ -1769,6 +1769,7 @@ task testTask0(type: Test) {
     preserveOrder true
     useDefaultListeners=true
   }
+  timeout = Duration.ofMinutes(15)
 }
 
 /* separated tests */
@@ -1781,6 +1782,7 @@ task testTask1(type: Test) {
     preserveOrder true
     useDefaultListeners=true
   }
+  timeout = Duration.ofMinutes(5)
 }
 
 task testTask2(type: Test) {
@@ -1792,6 +1794,7 @@ task testTask2(type: Test) {
     preserveOrder true
     useDefaultListeners=true
   }
+  timeout = Duration.ofMinutes(5)
 }
 task testTask3(type: Test) {
   group = "Verification"
@@ -1802,6 +1805,7 @@ task testTask3(type: Test) {
     preserveOrder true
     useDefaultListeners=true
   }
+  timeout = Duration.ofMinutes(5)
 }
 
 /* insert more testTaskNs here -- change N to next digit or other string */
@@ -1818,6 +1822,7 @@ task testTaskN(type: Test) {
 }
 */
 
+
 /*
  * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
  * to summarise test results from all Test tasks
@@ -1851,8 +1856,9 @@ tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { te
     showExceptions true
     showCauses true
     showStackTraces true
-    showStandardStreams true
-
+    if (test_output) {
+      showStandardStreams true
+    }
     info.events = [ TestLogEvent.FAILED ]
   }
 
@@ -2149,22 +2155,56 @@ task cleanDist {
 }
 
 
+task launcherJar(type: Jar) {
+  manifest {
+      attributes (
+        "Main-Class": shadow_jar_main_class,
+        "Implementation-Version": JALVIEW_VERSION,
+        "Application-Name": applicationName
+      )
+  }
+}
+
 shadowJar {
   group = "distribution"
   description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
   if (buildDist) {
     dependsOn makeDist
   }
-  from ("${jalviewDir}/${libDistDir}") {
-    include("*.jar")
-  }
+
+  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
+
   manifest {
-    attributes "Implementation-Version": JALVIEW_VERSION,
-    "Application-Name": applicationName
+    // shadowJar manifest must inheritFrom another Jar task.  Can't set attributes here.
+    inheritFrom(project.tasks.launcherJar.manifest)
+  }
+  // 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 {
+      from (jarFileManifests) {
+        eachEntry { details ->
+          if (!details.key.equals("Import-Package")) {
+            details.exclude()
+          }
+        }
+      }
+    }
   }
 
   duplicatesStrategy "INCLUDE"
 
+  // this mainClassName is mandatory but gets ignored due to manifest created in doFirst{}. Set the Main-Class as an attribute in launcherJar instead
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
@@ -2218,9 +2258,9 @@ 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) {
@@ -2332,7 +2372,7 @@ task getdownWebsite() {
           from s
           into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
         }
-        getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
+        getdownTextLines += "xresource = ${getdown_wrapper_script_dir}/${script}"
       }
     }
 
@@ -2474,7 +2514,9 @@ task getdownDigestDir(type: JavaExec) {
 task getdownDigest(type: JavaExec) {
   group = "distribution"
   description = "Digest the getdown website folder"
-  dependsOn getdownWebsite
+
+  dependsOn getdownWebsiteBuild
+
   doFirst {
     classpath = files(getdownLauncher)
   }
@@ -2507,12 +2549,19 @@ 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}"
@@ -2559,6 +2608,14 @@ task getdownArchiveBuild() {
       }
     }
 
+    // the wrapper scripts dir
+    if ( file("${getdownAppBaseDir}/${getdown_wrapper_script_dir}").exists() ) {
+      copy {
+        from "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
+        into "${getdownFullArchiveDir}/${getdown_wrapper_script_dir}"
+      }
+    }
+
     getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
 
     def vLaunchJvl = file(getdownVersionLaunchJvl)
@@ -3022,6 +3079,7 @@ task sourceDist(type: Tar) {
   into project.name
 
   def EXCLUDE_FILES=[
+    "dist/*",
     "build/*",
     "bin/*",
     "test-output/",