Changeset 891

Timestamp:

Dec 7, 2008, 8:46:16 PM (14 years ago)

Author:

Jari Häkkinen

Message:

Changed interface and added debug code.

File:

• plugins/base2/net.sf.basedb.pluginutilities/trunk/src/net/sf/basedb/plugins/AbstractRunBinaryPlugin.java (modified) (11 diffs)

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

@@ -47 +47 @@
 import net.sf.basedb.core.plugin.Response;
 
+import java.io.BufferedInputStream;
+import java.io.FileWriter;
 import java.io.IOException;
 import java.io.PrintStream;
@@ -79 +81 @@
 
   protected AbstractRunBinaryPlugin() {
-    if (debug_output)
+    if (debug_output) {
+      debug_outputfile=(System.getProperty("java.io.tmpdir") +
+                        java.io.File.separator + debug_outputfile);
+      debug_subprocess_outputfile=(System.getProperty("java.io.tmpdir") +
+                                   java.io.File.separator +
+                                   debug_subprocess_outputfile);
       try
       {
@@ -88 +95 @@
         e.printStackTrace();
       }
+    }
   }
 
@@ -137 +145 @@
 
 
-  protected void execute(String[] cmd, ProgressReporter progress)
+  protected void execute(String[] cmd)
     throws InterruptedException, IOException
   {
@@ -143 +151 @@
     percentDone+=1;
     progress.display(percentDone,"Running " + about.getName());
+    cmd[0]=getBinaryPath(this.getClass(),cmd[0]);
     Process p = Runtime.getRuntime().exec(cmd, null, getExecDirectory());
+    if (debug_output)
+    {
+      BufferedInputStream bis=new BufferedInputStream(p.getInputStream());
+      FileWriter fw=new FileWriter(debug_subprocess_outputfile);
+      int ch;
+      while ((ch=bis.read())>-1) fw.write(ch);
+      fw.close();
+    }
     p.waitFor();
     int status=p.exitValue();
@@ -150 +167 @@
       if (debug_output) System.err.println("execute failed");
       throw new IOException("Unexpected exit of " + about.getName() +
-                            "WeNNI sub-process. Return value: " + status);
+                            " sub-process. Return value: " + status);
     }
     if (debug_output) System.err.println("execute end succesfully reached");
@@ -162 +179 @@
 
 
-  protected String getBinaryPath(Class cls, String binaryname)
+  private String getBinaryPath(Class cls, String binaryname)
   {
     if (debug_output) System.err.println("Acquiring binary path");
@@ -209 +226 @@
     if (execDirectory == null) {
       execDirectory = new java.io.File
-        (System.getProperty("java.io.tmpdir") + java.io.File.separator +
-         getAbout().getName() + java.io.File.separator + job.getId());
+        (System.getProperty("java.io.tmpdir") + java.io.File.separator +
+         job.getPluginDefinition().getName() + java.io.File.separator +
+         job.getId());
       execDirectory.mkdirs();
     }
@@ -247 +265 @@
 
   @SuppressWarnings("unchecked")
-  public void run(Request request, Response response, ProgressReporter progress)
+  public void run(Request request, Response response, ProgressReporter _progress)
   {
     if (debug_output) System.err.println("run");
+    progress=_progress;
     DbControl dc=sc.newDbControl();
     try {
       String name=(String)job.getValue("name");
       if (name==null)
-        name="New root bioassay set";
-      Experiment experiment=(Experiment)job.getValue("experiment");
-      if (experiment==null)
-        throw new InvalidUseOfNullException("experiment");
-      experiment=Experiment.getById(dc, experiment.getId());
-      List<RawBioAssay> sources=(List<RawBioAssay>)job.getValues("rawBioAssays");
-      if (sources==null || sources.size()==0)
-        throw new InvalidUseOfNullException("sources");
-      for (RawBioAssay rba : sources)
-        dc.reattachItem(rba);
-      runBinary(sources,progress);
-      storeResult(dc,experiment,sources,name,progress);
+        name="New bioassay set";
+      BioAssaySet source = getSourceBioAssaySet(dc);
+      runBinary();
+      storeResult(dc,name);
 //      dc.commit();
       response.setDone("Plug-in ended successfully");
+      if (debug_output) System.err.println("run succesful");
     }
     catch (Throwable e) {
@@ -289 +301 @@
     }
     if (debug_output) System.err.println("run end");
-  }
-
-
-  abstract protected void runBinary(List<RawBioAssay> sources,
-                         ProgressReporter progress)
+    response.setError("All is okay, just make sure that BASE produces error.",
+                      null);
+  }
+
+
+  abstract protected void runBinary()
     throws InterruptedException, IOException;
 
 
-  abstract protected void storeResult(DbControl dc, Experiment experiment,
-                                      List<RawBioAssay> sources, String name,
-                                      ProgressReporter progress);
+  abstract protected void storeResult(DbControl dc, String name);
 
 
@@ -317 +328 @@
   private java.io.File execDirectory;
   private int percentDone=0;
-
-  // debug options. Note, if debug information is on, the exec
-  // directory is not removed after plug-in execution.
-  protected Boolean debug_output=true; 
-  private String debug_outputfile="/tmp/base_debug.txt";
+  private ProgressReporter progress=null;
+
+  // debug settings. Note, if debug information is on, the exec
+  // directory is not removed after plug-in execution. The file names
+  // are modified in the constructor to contain the java temp
+  // directory, i.e. debug files are written into the java temp
+  // directory. The file names are (somewhat) arbitrarily chosen and
+  // may overwrite existing files.
+  protected Boolean debug_output=false; 
+  private String debug_outputfile="ARBPdebug.txt";
+  private String debug_subprocess_outputfile="ARBPdebug_subprocess.txt";
 }