Changeset 906

Timestamp:

Dec 8, 2008, 10:01:51 PM (14 years ago)

Author:

Jari Häkkinen

Message:

Some external binary will output result to stdout ... optionally writing output to file.

File:

• plugins/base2/net.sf.basedb.pluginutilities/trunk/src/net/sf/basedb/plugins/AbstractRunBinaryPlugin.java (modified) (8 diffs)

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

@@ -84 +84 @@
       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
       {
@@ -124 +121 @@
         DbControl dc = sc.newDbControl();
         try {
-          BioAssaySet source = getSourceBioAssaySet(dc);
-          int nofAssays = source.getBioAssays().list(dc).size();
+          sourceBAS = getSourceBioAssaySet(dc);
+          int nofAssays = sourceBAS.getBioAssays().list(dc).size();
           if (nofAssays>10 && nofAssays<30)
             execTime = Job.ExecutionTime.MEDIUM;
@@ -153 +150 @@
     cmd[0]=getBinaryPath(this.getClass(),cmd[0]);
     Process p = Runtime.getRuntime().exec(cmd, null, getExecDirectory());
-    if (debug_output)
+    if (subprocess_stdout!=null)
     {
       BufferedInputStream bis=new BufferedInputStream(p.getInputStream());
-      FileWriter fw=new FileWriter(debug_subprocess_outputfile);
+      FileWriter fw=new FileWriter(getExecDirectory() + java.io.File.separator +
+                                   subprocess_stdout);
       int ch;
       while ((ch=bis.read())>-1) fw.write(ch);
@@ -274 +272 @@
       if (name==null)
         name="New bioassay set";
-      BioAssaySet source = getSourceBioAssaySet(dc);
+      if (sourceBAS==null)
+        sourceBAS = getSourceBioAssaySet(dc);
       runBinary();
       storeResult(dc,name);
@@ -280 +279 @@
       response.setDone("Plug-in ended successfully");
       if (debug_output) System.err.println("run succesful");
+      response.setError("All is okay, just make sure that BASE produces error.",
+                        null);
     }
     catch (Throwable e) {
@@ -301 +302 @@
     }
     if (debug_output) System.err.println("run end");
-    response.setError("All is okay, just make sure that BASE produces error.",
-                      null);
   }
 
@@ -323 +322 @@
   protected Set<Permissions> permissions = new HashSet<Permissions>();
   protected Plugin.MainType plugin_maintype=null;
+  protected BioAssaySet sourceBAS = null;
+  protected String subprocess_stdout=null;
 
   private String binaryPath=null;
@@ -331 +332 @@
 
   // 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; 
+  // directory is not removed after plug-in execution. The file name
+  // is modified in the constructor to contain the java temp
+  // directory, i.e. debug file is written into the java temp
+  // directory. The file name is (somewhat) arbitrarily chosen and may
+  // overwrite existing file.
+  protected Boolean debug_output=true; 
   private String debug_outputfile="ARBPdebug.txt";
-  private String debug_subprocess_outputfile="ARBPdebug_subprocess.txt";
 }