Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4

diff --git a/build.gradle b/build.gradle
index ca599a8..a47a7fd 100644 (file)
--- 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
@@ -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
 }
 
@@ -4201,9 +4210,156 @@ 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("${jalviewjsChromiumUserDir}/First Run")
+
+  doFirst {
+    mkdir jalviewjsChromiumProfileDir
+    firstRun.text = ""
+  }
+  outputs.file firstRun
+}
+
+task jalviewjsLaunchTest {
+  group "Test"
+  description "Check JalviewJS opens in a browser"
+  dependsOn jalviewjsBuildSite
+  dependsOn jalviewjsCopyStderrLaunchFile
+  dependsOn jalviewjsChromiumProfile
+
+  def macOS = OperatingSystem.current().isMacOsX()
+  def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary
+  if (chromiumBinary.startsWith("~/")) {
+    chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1)
+  }
+  
+  def stdout
+  def stderr
+  doFirst {
+    def timeoutms = Integer.valueOf(jalviewjs_chromium_timeout) * 1000
+    
+    def binary = file(chromiumBinary)
+    if (!binary.exists()) {
+      throw new StopExecutionException("Could not find chromium binary '${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)
+          }
+          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 >= 10) {
+            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
 }
-

diff --git a/gradle.properties b/gradle.properties
index 7b3a031..75231f3 100644 (file)
--- a/gradle.properties
+++ b/gradle.properties
@@ -260,5 +260,13 @@ jalviewjs_j2s_to_console = true
 jalviewjs_closure_compiler = tools/closure_compiler.jar
 jalviewjs_j2s_closure_stdout = j2s-closure.out
 
+# for checking jalviewjs launches okay
+jalviewjs_chromium_binary = ~/buildtools/chromium/chrome
+jalviewjs_macos_chromium_binary = /Applications/Chromium.app/Contents/MacOS/Chromium
+jalviewjs_chromium_user_dir = chromium
+jalviewjs_chromium_timeout = 30
+jalviewjs_chromium_profile_name = BUILD
+jalviewjs_stderr_launch = utils/jalviewjs/chromium_test/jalview_bin_Jalview-stderr.html
+jalviewjs_desktop_init_string = JALVIEWJS: CREATED DESKTOP
 
 testp=gradle.properties

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index cfc56b2..99c394b 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -626,6 +626,12 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
     });
     desktop.addMouseListener(ma);
+
+    if (Platform.isJS())
+    {
+      // used for jalviewjsTest
+      jalview.bin.Console.info("JALVIEWJS: CREATED DESKTOP");
+    }
   }
 
   /**
@@ -3159,10 +3165,14 @@ public class Desktop extends jalview.jbgui.GDesktop
     String title = "View of desktop";
     ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
             title);
-    try {
+    try
+    {
       exporter.doExport(of, this, width, height, title);
-    } catch (ImageOutputException ioex) {
-      jalview.bin.Console.error("Unexpected error whilst writing Jalview desktop snapshot as EPS",ioex);
+    } catch (ImageOutputException ioex)
+    {
+      jalview.bin.Console.error(
+              "Unexpected error whilst writing Jalview desktop snapshot as EPS",
+              ioex);
     }
   }
 
@@ -3609,7 +3619,8 @@ public class Desktop extends jalview.jbgui.GDesktop
    */
   public static void closeDesktop()
   {
-    if (Desktop.instance != null) {
+    if (Desktop.instance != null)
+    {
       Desktop.instance.closeAll_actionPerformed(null);
       Desktop.instance.setVisible(false);
       Desktop.instance.dispose();

diff --git a/utils/jalviewjs/chromium_test/jalview_bin_Jalview-stderr.html b/utils/jalviewjs/chromium_test/jalview_bin_Jalview-stderr.html
new file mode 100644 (file)
index 0000000..bf7a678
--- /dev/null
+++ b/utils/jalviewjs/chromium_test/jalview_bin_Jalview-stderr.html
@@ -0,0 +1,36 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>SwingJS test Jalview</title><meta charset="utf-8" />
+<script src="swingjs/swingjs2.js"></script>
+<script>
+if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href)
+Info = {
+  code: null,
+  main: "jalview.bin.Jalview",
+  core: "NONE",
+       width: 850,
+       height: 550,
+  readyFunction: null,
+       serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
+       j2sPath: 'swingjs/j2s',
+       console: window.console,
+       allowjavascript: true
+}
+</script>
+</head>
+<body>
+<script>
+// we define console.err because swingjs2.js calls it instead of console.error
+window.console.err = function() {
+       this.error.apply(this,arguments);
+}
+SwingJS.getApplet('testApplet', Info)
+getClassList = function(){J2S._saveFile('_j2sclasslist.txt', Clazz.ClassFilesLoaded.sort().join('\n'))}
+</script>
+<div style="position:absolute;left:900px;top:30px;width:600px;height:300px;">
+<div id="sysoutdiv" contentEditable="true" style="border:1px solid green;width:100%;height:95%;overflow:auto"></div>
+This is System.out. <a href="javascript:testApplet._clearConsole()">clear it</a> <br>Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files <br><a href="javascript:getClassList()">get _j2sClassList.txt</a>
+</div>
+</body>
+</html>