Use args[] form of System.exec in order to resolve path to java on osx that may inclu...

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 062a22a..8203663 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -199,18 +199,35 @@ public class Jalview
             || System.getProperty("java.version").startsWith("1.9.");
     if (maxMemory < 1024 * 14)
     {
-      String cmd = "";
+      ArrayList<String> cmd = new ArrayList();
+      
+      boolean dontspawn=false;
       for (String r : args)
       {
-        cmd += (cmd.length() == 0) ? r : " " + r;
+        cmd.add(r);
+        if (r.indexOf("-Xmx")>-1) {
+          dontspawn=true;
+          break;
+        }
       }
-      if (cmd.indexOf("-Xmx") == -1)
+      if (!dontspawn)
       {
-        cmd = "-Xmx15G " + cmd;
-        System.err.println("relaunching with 15G: " + cmd);
-        Worker worker = Worker.jalviewDesktopRunner(false, cmd, 0,
-                "-Xmx15G"
-                        + (is9or10 ? " --add-modules=\"java.se.ee\"" : ""));
+        cmd.add("-Xmx15G");
+        String[] javargs=new String[1];
+        if (is9or10) {
+          javargs = new String[2];
+          javargs[1] = "--add-modules=java.se.ee";
+        }
+        javargs[0]="-Xmx15G";
+        
+        System.err.print("relaunching with 15G: ");
+        for (String r : cmd)
+        {
+          System.err.print(r + " ");
+        }
+        System.err.println("");
+        Worker worker = Worker.jalviewDesktopRunner(false,
+                cmd.toArray(new String[0]), 0, javargs);
         worker.doEcho();
         try
         {

diff --git a/src/jalview/util/Worker.java b/src/jalview/util/Worker.java
index ff7f0a9..b5297e1 100644 (file)
--- a/src/jalview/util/Worker.java
+++ b/src/jalview/util/Worker.java
@@ -5,6 +5,8 @@ import java.io.File;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
 
 import io.github.classgraph.ClassGraph;
 import io.github.classgraph.ScanResult;
@@ -121,8 +123,21 @@ public class Worker extends Thread
     // not expanded by the shell
     String classpath = getClassPath();
     String javahome = System.getProperty("java.home");
-
-    String _cmd = javahome + File.pathSeparator + "java "
+    File java = new File(javahome + File.separator + "bin"
+            + File.separator + "java");
+    if (!java.exists())
+    {
+      System.err.println("Can't find " + java.getAbsolutePath());
+      java = new File(javahome + File.separator + "bin"
+              + File.separator + "java.exe");
+      if (!java.exists())
+      {
+        System.err.println("Can't find " + java.getAbsolutePath());
+        throw new Error(
+                "Can't locate java in JAVA_HOME/bin/java or JAVA_HOME/bin/java.exe");
+      }
+    }
+    String _cmd = "\"" + javahome + "\" "
             + (withAwt ? "-Djava.awt.headless=true" : "")
             + " -classpath " + classpath + " " + javaArgs
             + " jalview.bin.Jalview ";
@@ -156,6 +171,69 @@ public class Worker extends Thread
     return worker;
   }
 
+  public static Worker jalviewDesktopRunner(boolean withAwt, String[] args,
+          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 javahome = System.getProperty("java.home");
+    File java = new File(
+            javahome + File.separator + "bin" + File.separator + "java");
+    if (!java.exists())
+    {
+      System.err.println("Can't find " + java.getAbsolutePath());
+      java = new File(javahome + File.separator + "bin" + File.separator
+              + "java.exe");
+      if (!java.exists())
+      {
+        System.err.println("Can't find " + java.getAbsolutePath());
+        throw new Error(
+                "Can't locate java in JAVA_HOME/bin/java or JAVA_HOME/bin/java.exe");
+      }
+    }
+    ArrayList<String> _cmd = new ArrayList();
+    _cmd.add(java.getAbsolutePath());
+    if (withAwt)
+    {
+      _cmd.add("-Djava.awt.headless=true");
+    }
+    _cmd.add("-classpath");
+    _cmd.add(classpath);
+    _cmd.addAll(Arrays.asList(javaArgs));
+    _cmd.add("jalview.bin.Jalview");
+    _cmd.addAll(Arrays.asList(args));
+    Process ls2_proc = null;
+    Worker worker = null;
+    try
+    {
+      ls2_proc = Runtime.getRuntime()
+              .exec(_cmd.toArray(new String[_cmd.size()]));
+    } 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)