X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=build.gradle;h=cbd65f2f92e73ead0e39a234210adbfcecfed25c;hp=516f0a08acb4a91b592fe91ab7c9097c144f95e1;hb=HEAD;hpb=356e8509b7876a62d6bb5a9f4b7993451d5ccae8

diff --git a/build.gradle b/build.gradle
index 516f0a0..3b81404 100644
--- a/build.gradle
+++ b/build.gradle
@@ -10,6 +10,10 @@ import org.gradle.plugins.ide.eclipse.model.Output
 import org.gradle.plugins.ide.eclipse.model.Library
 import java.security.MessageDigest
 import java.util.regex.Matcher
+import java.util.concurrent.Executors
+import java.util.concurrent.Future
+import java.util.concurrent.ScheduledExecutorService
+import java.util.concurrent.TimeUnit
 import groovy.transform.ExternalizeMethods
 import groovy.util.XmlParser
 import groovy.xml.XmlUtil
@@ -48,9 +52,9 @@ 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 '2.1.0' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
+  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
 }
 
@@ -568,11 +572,16 @@ ext {
   jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
   jalviewjsJ2sProps = null
   jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
+  jalviewjsStderrLaunchFilename = "${jalviewjsSiteDir}/"+(file(jalviewjs_stderr_launch).getName())
 
   eclipseWorkspace = null
   eclipseBinary = string("")
   eclipseVersion = string("")
   eclipseDebug = false
+
+  jalviewjsChromiumUserDir = "${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}"
+  jalviewjsChromiumProfileDir = "${ext.jalviewjsChromiumUserDir}/${jalviewjs_chromium_profile_name}"
+
   // ENDEXT
 }
 
@@ -1064,7 +1073,7 @@ compileJava {
   // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
   sourceCompatibility = compile_source_compatibility
   targetCompatibility = compile_target_compatibility
-  options.compilerArgs = additional_compiler_args
+  options.compilerArgs += additional_compiler_args
   options.encoding = "UTF-8"
   doFirst {
     print ("Setting target compatibility to "+compile_target_compatibility+"\n")
@@ -1076,7 +1085,7 @@ compileJava {
 compileTestJava {
   sourceCompatibility = compile_source_compatibility
   targetCompatibility = compile_target_compatibility
-  options.compilerArgs = additional_compiler_args
+  options.compilerArgs += additional_compiler_args
   doFirst {
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
@@ -1732,35 +1741,142 @@ task prepare {
 
 compileJava.dependsOn prepare
 run.dependsOn compileJava
-//run.dependsOn prepare
+compileTestJava.dependsOn compileJava
+
 
 
-//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
-  dependsOn prepare
+  group = "Verification"
+  description = "Runs all testTaskN tasks)"
 
   if (useClover) {
     dependsOn cloverClasses
-   } else { //?
-    dependsOn compileJava //?
+  } else { //?
+    dependsOn testClasses
   }
 
+  // not running tests in this task
+  exclude "**/*"
+}
+/* testTask0 is the main test task */
+task testTask0(type: Test) {
+  group = "Verification"
+  description = "The main test task. Runs all non-testTaskN-labelled tests (unless excluded)"
   useTestNG() {
-    includeGroups testng_groups
-    excludeGroups testng_excluded_groups
+    includeGroups testng_groups.split(",")
+    excludeGroups testng_excluded_groups.split(",")
+    tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name}
     preserveOrder true
     useDefaultListeners=true
   }
+}
 
-  maxHeapSize = "2048m"
+/* separated tests */
+task testTask1(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
+  }
+}
 
-/* delete these! 
-  maxParallelForks = 1
-  forkEvery = 1
-  failFast = true
-  jvmArgs '-Xmx2048m', '-Xms2048m'
+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) {
+  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
+  }
+}
 */
 
+/*
+ * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c
+ * to summarise test results from all Test tasks
+ */
+/* START of test tasks results summary */
+import groovy.time.TimeCategory
+import org.gradle.api.tasks.testing.logging.TestExceptionFormat
+import org.gradle.api.tasks.testing.logging.TestLogEvent
+rootProject.ext.testsResults = [] // Container for tests summaries
+
+tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask ->
+
+  // from original test task
+  if (useClover) {
+    dependsOn cloverClasses
+  } else { //?
+    dependsOn testClasses //?
+  }
+
+  // run main tests first
+  if (!testTask.name.equals("testTask0"))
+    testTask.mustRunAfter "testTask0"
+
+  testTask.testLogging { logging ->
+    events TestLogEvent.FAILED
+//      TestLogEvent.SKIPPED,
+//      TestLogEvent.STANDARD_OUT,
+//      TestLogEvent.STANDARD_ERROR
+
+    exceptionFormat TestExceptionFormat.FULL
+    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
+
+  afterSuite { desc, result ->
+    if (desc.parent)
+      return // Only summarize results for whole modules
+
+    def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint]
+
+    rootProject.ext.testsResults.add(resultsInfo)
+  }
+
+  // from original test task
+  maxHeapSize = "1024m"
+
   workingDir = jalviewDir
   def testLaf = project.findProperty("test_laf")
   if (testLaf != null) {
@@ -1777,11 +1893,143 @@ test {
   jvmArgs += additional_compiler_args
 
   doFirst {
+    // this is not perfect yet -- we should only add the commandLineIncludePatterns to the
+    // testTasks that include the tests, and exclude all from the others.
+    // get --test argument
+    filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns
+    // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the
+    // commandLineIncludePatterns not matching anything.  Instead we are doing setFailOnNoMatchingTests(false) below
+
+
     if (useClover) {
       println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
     }
   }
+
+
+  /* don't fail on no matching tests (so --tests will run across all testTasks) */
+  testTask.filter.setFailOnNoMatchingTests(false)
+
+  /* ensure the "test" task dependsOn all the testTasks */
+  test.dependsOn testTask
+}
+
+gradle.buildFinished {
+    def allResults = rootProject.ext.testsResults
+
+    if (!allResults.isEmpty()) {
+        printResults allResults
+        allResults.each {r ->
+          if (r[2].resultType == TestResult.ResultType.FAILURE)
+            throw new GradleException("Failed tests!")
+        }
+    }
+}
+
+private static String colString(styler, col, colour, text) {
+  return col?"${styler[colour](text)}":text
+}
+
+private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) {
+  def colour = 'black'
+  def text = rt
+  def nocol = false
+  if (rc == 0) {
+    text = "-----"
+    nocol = true
+  } else {
+    switch(rt) {
+      case TestResult.ResultType.SUCCESS:
+        colour = 'green'
+        break;
+      case TestResult.ResultType.FAILURE:
+        colour = 'red'
+        break;
+      default:
+        nocol = true
+        break;
+    }
+  }
+  StringBuilder sb = new StringBuilder()
+  sb.append("${pn}")
+  if (tn != null)
+    sb.append(":${tn}")
+  sb.append(" results: ")
+  sb.append(colString(s, col && !nocol, colour, text))
+  sb.append(" (")
+  sb.append("${rc} tests, ")
+  sb.append(colString(s, col && rs > 0, 'green', rs))
+  sb.append(" successes, ")
+  sb.append(colString(s, col && rf > 0, 'red', rf))
+  sb.append(" failures, ")
+  sb.append("${rsk} skipped) in ${t}")
+  return sb.toString()
+}
+
+private static void printResults(allResults) {
+
+    // styler from https://stackoverflow.com/a/56139852
+    def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] }
+
+    def maxLength = 0
+    def failedTests = false
+    def summaryLines = []
+    def totalcount = 0
+    def totalsuccess = 0
+    def totalfail = 0
+    def totalskip = 0
+    def totaltime = TimeCategory.getSeconds(0)
+    // sort on project name then task name
+    allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each {
+      def projectName = it[0]
+      def taskName = it[1]
+      def result = it[2]
+      def time = it[3]
+      def report = it[4]
+      def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true)
+      def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false)
+      def reportLine = "Report file: ${report}"
+      def ls = summaryPlain.length()
+      def lr = reportLine.length()
+      def m = [ls, lr].max()
+      if (m > maxLength)
+        maxLength = m
+      def info = [ls, summaryCol, reportLine]
+      summaryLines.add(info)
+      failedTests |= result.resultType == TestResult.ResultType.FAILURE
+      totalcount += result.testCount
+      totalsuccess += result.successfulTestCount
+      totalfail += result.failedTestCount
+      totalskip += result.skippedTestCount
+      totaltime += time
+    }
+    def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true)
+    def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false)
+    def tls = totalSummaryPlain.length()
+    if (tls > maxLength)
+      maxLength = tls
+    def info = [tls, totalSummaryCol, null]
+    summaryLines.add(info)
+
+    def allSummaries = []
+    for(sInfo : summaryLines) {
+      def ls = sInfo[0]
+      def summary = sInfo[1]
+      def report = sInfo[2]
+
+      StringBuilder sb = new StringBuilder()
+      sb.append("│" + summary + " " * (maxLength - ls) + "│")
+      if (report != null) {
+        sb.append("\n│" + report + " " * (maxLength - report.length()) + "│")
+      }
+      allSummaries += sb.toString()
+    }
+
+    println "┌${"${"─" * maxLength}"}┐"
+    println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n")
+    println "└${"${"─" * maxLength}"}┘"
 }
+/* END of test tasks results summary */
 
 
 task compileLinkCheck(type: JavaCompile) {
@@ -1908,12 +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"
@@ -1971,9 +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) {
@@ -2025,8 +2294,8 @@ task getdownWebsite() {
       props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}")
       props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}")
       props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}")
-      props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}")
-      props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}")
+      props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
+      props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
     }
 
     props.put("getdown_txt_title", jalview_name)
@@ -2085,7 +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}"
       }
     }
 
@@ -2227,7 +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)
   }
@@ -2260,12 +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}"
@@ -2575,6 +2853,7 @@ task installerFiles(type: com.install4j.gradle.Install4jTask) {
     'WRAPPER_LINK': getdownWrapperLink,
     'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
     'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+    'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script,
     'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
     'INSTALLER_NAME': install4jInstallerName,
     'INSTALL4J_UTILS_DIR': install4j_utils_dir,
@@ -2774,6 +3053,7 @@ task sourceDist(type: Tar) {
   into project.name
 
   def EXCLUDE_FILES=[
+    "dist/*",
     "build/*",
     "bin/*",
     "test-output/",
@@ -3988,9 +4268,157 @@ task eclipseAutoBuildTask {
 }
 
 
+task jalviewjsCopyStderrLaunchFile(type: Copy) {
+  from file(jalviewjs_stderr_launch)
+  into jalviewjsSiteDir
+
+  inputs.file jalviewjs_stderr_launch
+  outputs.file jalviewjsStderrLaunchFilename
+}
+
+task cleanJalviewjsChromiumUserDir {
+  doFirst {
+    delete jalviewjsChromiumUserDir
+  }
+  outputs.dir jalviewjsChromiumUserDir
+  // always run when depended on
+  outputs.upToDateWhen { !file(jalviewjsChromiumUserDir).exists() }
+}
+
+task jalviewjsChromiumProfile {
+  dependsOn cleanJalviewjsChromiumUserDir
+  mustRunAfter cleanJalviewjsChromiumUserDir
+
+  def firstRun = file("${jalviewjsChromiumUserDir}/First Run")
+
+  doFirst {
+    mkdir jalviewjsChromiumProfileDir
+    firstRun.text = ""
+  }
+  outputs.file firstRun
+}
+
+task jalviewjsLaunchTest {
+  group "Test"
+  description "Check JalviewJS opens in a browser"
+  dependsOn jalviewjsBuildSite
+  dependsOn jalviewjsCopyStderrLaunchFile
+  dependsOn jalviewjsChromiumProfile
+
+  def macOS = OperatingSystem.current().isMacOsX()
+  def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary
+  if (chromiumBinary.startsWith("~/")) {
+    chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1)
+  }
+  
+  def stdout
+  def stderr
+  doFirst {
+    def timeoutms = Integer.valueOf(jalviewjs_chromium_overall_timeout) * 1000
+    
+    def binary = file(chromiumBinary)
+    if (!binary.exists()) {
+      throw new StopExecutionException("Could not find chromium binary '${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()
+        }
+      )
+
+      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 {
+            noChangeBytes = stderrString.length()
+            noChangeIterations = 0
+          }
+        },
+        1, 1, TimeUnit.SECONDS)
+
+      executor.schedule(new Runnable(){
+        public void run(){
+          f1.cancel()
+          executor.shutdownNow()
+        }
+      }, timeoutms, TimeUnit.MILLISECONDS)
+
+      executor.awaitTermination(timeoutms+10000, TimeUnit.MILLISECONDS)
+      executor.shutdownNow()
+    }
+
+  }
+  
+  doLast {
+    def found = false
+    stderr.toString().eachLine { line ->
+      if (line.contains(jalviewjs_desktop_init_string)) {
+        println("Found line '"+line+"'")
+        found = true
+        return
+      }
+    }
+    if (!found) {
+      throw new GradleException("Could not find evidence of Desktop launch in JalviewJS.")
+    }
+  }
+}
+  
+
 task jalviewjs {
   group "JalviewJS"
-  description "Build the site"
+  description "Build the JalviewJS site and run the launch test"
   dependsOn jalviewjsBuildSite
+  dependsOn jalviewjsLaunchTest
 }
-