Changeset 1035

Timestamp:

Apr 8, 2009, 12:06:41 AM (14 years ago)

Author:

Jari Häkkinen

Message:

Addresses #197. Abort functionality in place in abstract class.

Location:

plugins/base2/net.sf.basedb.pluginutilities/trunk

Files:

• build.xml (modified) (1 diff)
• src/net/sf/basedb/plugins/AbstractRunBinaryPlugin.java (modified) (9 diffs)

plugins/base2/net.sf.basedb.pluginutilities/trunk/build.xml

@@ -45 +45 @@
   <property name="javac.encoding" value="UTF-8" />
   <property name="depend.jars" 
-    value="http://base2.thep.lu.se/base/jars/2.5.0" 
+    value="http://base2.thep.lu.se/base/jars/2.6.0" 
     description="The location of the BASE core JARs that we depend on"
   />

plugins/base2/net.sf.basedb.pluginutilities/trunk/src/net/sf/basedb/plugins/AbstractRunBinaryPlugin.java

@@ -38 +38 @@
 import net.sf.basedb.core.SpotBatcher;
 import net.sf.basedb.core.Transformation;
+import net.sf.basedb.core.signal.SignalException;
+import net.sf.basedb.core.signal.SignalHandler;
+import net.sf.basedb.core.signal.SignalTarget;
+import net.sf.basedb.core.signal.ThreadSignalHandler;
 import net.sf.basedb.util.Values;
 
@@ -81 +85 @@
 abstract public class AbstractRunBinaryPlugin
   extends AbstractAnalysisPlugin
-  implements InteractivePlugin 
+  implements InteractivePlugin, SignalTarget
 {
 
@@ -151 +155 @@
     throws InterruptedException, IOException
   {
-    if (debug_output) System.err.println("execute");
+    checkInterrupted();
+    if (debug_output)
+    {
+      System.err.println("executing:");
+      for (String s: cmd) System.err.print(" "+s);
+      System.err.println("");
+    }
     if (progress != null) progress.display(5, (about.getName() +
                                                " waiting for external binary."));
@@ -167 +177 @@
       bos.close();
     }
+    BufferedInputStream bis=new BufferedInputStream(p.getInputStream());
+    try
+    {
+      if (debug_output) System.err.println("waiting for binary to finish");
+      p.waitFor();
+    }
+    catch (InterruptedException se)
+    {
+      p.destroy();
+      throw new InterruptedException("Aborted by user");
+    }
     if (subprocess_stdout!=null)
     {
       if (debug_output) System.err.println("reading stdout");
-      BufferedInputStream bis=new BufferedInputStream(p.getInputStream());
       FileWriter fw=new FileWriter(getExecDirectory() + java.io.File.separator +
                                    subprocess_stdout);
@@ -177 +197 @@
       fw.close();
     }
-    p.waitFor();
     int status=p.exitValue();
     if (status>0)
@@ -293 +312 @@
 
 
+  public SignalHandler getSignalHandler()
+  {
+    signalHandler = new ThreadSignalHandler();
+    return signalHandler;
+  }
+
+
   public boolean requiresConfiguration()
   {
@@ -302 +328 @@
   {
     if (debug_output) System.err.println("ARBP: run");
+    if (signalHandler != null) signalHandler.setWorkerThread(null);
     progress=_progress;
     DbControl dc=sc.newDbControl();
@@ -309 +336 @@
       if (progress != null) progress.display(0, about.getName());
       runBinary();
+      checkInterrupted();
       if (progress != null) progress.display(90, "Storing result");
       storeResult(dc);
+      checkInterrupted();
       if (debug_output)
       {
@@ -400 +429 @@
   private java.io.File execDirectory;
   private ProgressReporter progress=null;
+  private ThreadSignalHandler signalHandler;
 
   // debug settings. Note, if debug information is on, the exec