refactored worker and made the launch work on OSX/16G machine

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index f776b27..062a22a 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -39,6 +39,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.Worker;
 import jalview.ws.jws2.Jws2Discoverer;
 
 import java.io.BufferedReader;
@@ -57,7 +58,10 @@ import java.security.CodeSource;
 import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
+import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
@@ -188,15 +192,62 @@ public class Jalview
     float ONE_MB = 1048576f;
     Runtime runtime = Runtime.getRuntime();
     float maxMemory = runtime.maxMemory() / ONE_MB;
-    if (maxMemory < 1024 * 15)
+    boolean is9or10 = System.getProperty("java.version").startsWith("10.")
+            || System.getProperty("java.version").startsWith("9.")
+            || System.getProperty("java.version").startsWith("10.")
+            || System.getProperty("java.version").startsWith("1.10.")
+            || System.getProperty("java.version").startsWith("1.9.");
+    if (maxMemory < 1024 * 14)
     {
-      System.exit();
+      String cmd = "";
+      for (String r : args)
+      {
+        cmd += (cmd.length() == 0) ? r : " " + r;
+      }
+      if (cmd.indexOf("-Xmx") == -1)
+      {
+        cmd = "-Xmx15G " + cmd;
+        System.err.println("relaunching with 15G: " + cmd);
+        Worker worker = Worker.jalviewDesktopRunner(false, cmd, 0,
+                "-Xmx15G"
+                        + (is9or10 ? " --add-modules=\"java.se.ee\"" : ""));
+        worker.doEcho();
+        try
+        {
+        while (worker.getExitValue() == null)
+        {
+          try
+          {
+          Thread.sleep(2000);
+          } catch (Exception q)
+          {
+          }
+          ;
+        }
+        } catch (Exception q)
+        {
+        }
+        ;
+
+        System.exit(worker.getExitValue());
+      }
     }
 
-    if (System.ge)
+    List<String> rgs = new ArrayList();
+    rgs.addAll(Arrays.asList(args));
+    int i = 0;
+    while (i < rgs.size())
     {
-      instance = new Jalview();
+      if (rgs.get(i).indexOf("-Xmx") > -1)
+      {
+        rgs.remove(i);
+      }
+      else
+      {
+        i++;
+      }
     }
+    instance = new Jalview();
     instance.doMain(args);
   }
 

diff --git a/src/jalview/util/Worker.java b/src/jalview/util/Worker.java
new file mode 100644 (file)
index 0000000..68f4174
--- /dev/null
+++ b/src/jalview/util/Worker.java
@@ -0,0 +1,193 @@
+package jalview.util;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PrintStream;
+
+import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ScanResult;
+
+/***
+ * from
+ * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
+ * -using-javas-runtime-exec
+ * 
+ * @author jimp
+ * 
+ */
+public class Worker extends Thread
+{
+  final Process process;
+
+  private BufferedReader outputReader;
+
+  private BufferedReader errorReader;
+
+  Integer exit;
+
+  public Worker(Process process)
+  {
+    this.process = process;
+  }
+
+  @Override
+  public void run()
+  {
+    try
+    {
+      exit = process.waitFor();
+    } catch (InterruptedException ignore)
+    {
+      return;
+    }
+  }
+
+  public BufferedReader getOutputReader()
+  {
+    return outputReader;
+  }
+
+  public void setOutputReader(BufferedReader outputReader)
+  {
+    this.outputReader = outputReader;
+  }
+
+  public BufferedReader getErrorReader()
+  {
+    return errorReader;
+  }
+
+  public void setErrorReader(BufferedReader errorReader)
+  {
+    this.errorReader = errorReader;
+  }
+
+  /**
+   * 
+   * @return null or process exit code
+   */
+  public Integer getExitValue()
+  {
+    return exit;
+  }
+
+  /**
+   * terminate with prejudice
+   */
+  public void destroyProcess()
+  {
+    interrupt();
+    currentThread().interrupt();
+    process.destroy();
+  }
+
+  private static ClassGraph scanner = null;
+
+  private static String classpath = null;
+
+  public synchronized static String getClassPath()
+  {
+    if (scanner == null)
+    {
+      scanner = new ClassGraph();
+      ScanResult scan = scanner.scan();
+      classpath = scan.getClasspath();
+    }
+    while (classpath == null)
+    {
+      try
+      {
+        Thread.sleep(10);
+      } catch (InterruptedException x)
+      {
+
+      }
+    }
+    return classpath;
+  }
+
+  public static Worker jalviewDesktopRunner(boolean withAwt, String cmd,
+          int timeout)
+  {
+    return jalviewDesktopRunner(withAwt, cmd, timeout, "");
+  }
+
+  public static Worker jalviewDesktopRunner(boolean withAwt, String cmd,
+          int timeout, String javaArgs)
+  {
+    // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
+    // not expanded by the shell
+    String classpath = getClassPath();
+    String _cmd = "java " + (withAwt ? "-Djava.awt.headless=true" : "")
+            + " -classpath " + classpath + " " + javaArgs
+            + " jalview.bin.Jalview ";
+    Process ls2_proc = null;
+    Worker worker = null;
+    try
+    {
+      ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
+    } catch (IOException e1)
+    {
+      e1.printStackTrace();
+    }
+    if (ls2_proc != null)
+    {
+      BufferedReader outputReader = new BufferedReader(
+              new InputStreamReader(ls2_proc.getInputStream()));
+      BufferedReader errorReader = new BufferedReader(
+              new InputStreamReader(ls2_proc.getErrorStream()));
+      worker = new Worker(ls2_proc);
+      worker.start();
+      try
+      {
+        worker.join(timeout);
+      } catch (InterruptedException e)
+      {
+        // e.printStackTrace();
+      }
+      worker.setOutputReader(outputReader);
+      worker.setErrorReader(errorReader);
+    }
+    return worker;
+  }
+
+  class Echo
+  {
+    public Echo(final PrintStream out, final BufferedReader source)
+    {
+      try
+      {
+        new Thread(new Runnable()
+        {
+          @Override
+          public void run()
+          {
+            String line;
+            try
+            {
+              while ((line = source.readLine()) != null)
+              {
+                out.print(line);
+              }
+            } catch (IOException q)
+            {
+            }
+            ;
+          };
+        }).start();
+      } catch (Exception ex)
+      {
+      }
+      ;
+
+    }
+
+  }
+
+  public void doEcho()
+  {
+    new Echo(System.out, getOutputReader());
+    new Echo(System.err, getErrorReader());
+  }
+}
\ No newline at end of file

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index b3e6af9..a6c3bea 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -21,7 +21,7 @@
 package jalview.bin;
 
 import jalview.gui.JvOptionPane;
-import jalview.ws.utils.Worker;
+import jalview.util.Worker;
 
 import java.io.File;
 import java.io.IOException;