diff smart_toolShed/SMART/Java/ProgramLauncher.java @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/ProgramLauncher.java	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,209 @@
+/**
+ *
+ * Copyright INRA-URGI 2009-2010
+ * 
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "http://www.cecill.info".
+ * 
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ * 
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ * 
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+import java.util.*;
+import java.io.*;
+import javax.swing.SwingUtilities;
+import javax.swing.*;
+import java.util.concurrent.CountDownLatch;
+
+public class ProgramLauncher extends SwingWorker<Boolean, String>  {
+
+  String[]     command;
+  JTextArea    logArea;
+  JLabel       messageField;
+  JProgressBar progressBar;
+  JLabel       etaField;
+  int          exitValue;
+  CountDownLatch latch;
+
+  
+
+  public ProgramLauncher (LinkedList <String> c, JTextArea la, JLabel mf, JProgressBar pb, JLabel ef) {
+    command       = new String[c.size()];
+    logArea       = la;
+    messageField  = mf;
+    progressBar   = pb;
+    etaField      = ef;
+    exitValue     = -1;
+    c.toArray(command);
+    latch = new CountDownLatch(1);
+  }
+
+
+  public ProgramLauncher (String[] c, JTextArea la, JLabel mf, JProgressBar pb, JLabel ef) {
+    command       = c;
+    logArea       = la;
+    messageField  = mf;
+    progressBar   = pb;
+    etaField      = ef;
+    exitValue     = -1;
+    latch = new CountDownLatch(1);
+  }
+
+
+  @Override
+  public Boolean doInBackground() {
+    ProcessBuilder pb           = new ProcessBuilder(command);
+    Process process             = null;
+    BufferedReader outputReader = null;
+    pb                          = pb.redirectErrorStream(true);
+    Map<String, String> env     = pb.environment();
+    env.put("PYTHONPATH", System.getProperty("user.dir"));
+    env.put("SMARTPATH", System.getProperty("user.dir") + java.io.File.separator + "SMART" + java.io.File.separator + "Java" + java.io.File.separator + "Python");
+    env.put("SMARTMYSQLPATH", Global.mysqlCommand);
+    env.put("SMARTRPATH", Global.rCommand);
+    String commandJoined = Arrays.toString(command);
+
+    try {
+      publish("=== Starting command '" + commandJoined.trim() + "' ===\n");
+      process = pb.start();
+
+      BufferedInputStream outputStream = new BufferedInputStream(process.getInputStream());
+      InputStream is                   = process.getInputStream();
+      InputStreamReader isr            = new InputStreamReader(is);
+      outputReader                     = new BufferedReader(isr);
+    }
+    catch (Exception exception) {
+      publish("!Process cannot be started (command is '" + commandJoined + "')!\n");
+      exception.printStackTrace();
+      latch.countDown();
+      return Boolean.FALSE;
+    }
+    if (outputReader == null) {
+      publish("!Problem in the output of the command!\n");
+      latch.countDown();
+      return Boolean.FALSE;
+    }
+    else {
+      try {
+        String line;
+        while ((line = outputReader.readLine()) != null) {
+          publish(line + "\n");
+        }
+      }
+      catch (IOException e) {
+        e.printStackTrace();
+        publish("!Cannot get the output of the command!\n");
+        latch.countDown();
+        return Boolean.FALSE;
+      }
+    }
+    try {
+      process.waitFor();
+    }
+    catch (InterruptedException e) {
+      e.printStackTrace();
+      publish("!Cannot wait for the end of the command!\n");
+      latch.countDown();
+      return Boolean.FALSE;
+    }
+    try {
+      exitValue = process.exitValue();
+    }
+    catch (IllegalThreadStateException e) {
+      e.printStackTrace();
+      publish("!Cannot get the exit value of the command!\n");
+      latch.countDown();
+      return Boolean.FALSE;
+    }
+    if (exitValue != 0) {
+      publish("!Problem during the execution of the command '" + commandJoined + "'!\n");
+      latch.countDown();
+      return Boolean.FALSE;
+    }
+    publish("=== Ending command '" + commandJoined.trim() + "' ===\n");
+    latch.countDown();
+    return Boolean.TRUE;
+  }
+
+
+  @Override
+  protected void process(List<String> chunks) {
+    String message = "";
+    String text    = logArea.getText();
+    for (String chunk: chunks) {
+      text += chunk;
+    }
+    for (String lineSeparatedByCarriageReturn: text.split("\n")) {
+      for (String line: lineSeparatedByCarriageReturn.split("\r")) {
+        boolean progressLine = false;
+        if (line.matches(".*\\[=*\\s*\\]\\s*\\d*/\\d*\\s*")) {
+          String[] ratioElements = line.split("\\]")[1].trim().split("/");
+          int      current       = Integer.parseInt(ratioElements[0].trim());
+          int      aim           = Integer.parseInt(ratioElements[1].trim());
+          messageField.setText(line.split("\\[")[0].trim());
+          progressBar.setValue(current * 100 / aim);
+          etaField.setText("");
+          progressLine = true;
+        }
+        else if (line.matches(".*\\[=*\\s*\\]\\s*\\d*/\\d*\\s*ETA:\\s*.*")) {
+          String[] ratioElements = line.split("\\]")[1].split("E")[0].trim().split("/");
+          int      current       = Integer.parseInt(ratioElements[0].trim());
+          int      aim           = Integer.parseInt(ratioElements[1].trim());
+          String   eta           = line.split("ETA:")[1].trim();
+          messageField.setText(line.split("\\[")[0].trim());
+          progressBar.setValue(current * 100 / aim);
+          etaField.setText("ETA: " + eta);
+          progressLine = true;
+        }
+        else if (line.matches(".*\\[=*\\s*\\]\\s*\\d*\\s*completed in.*")) {
+          String nbElements = line.split("\\]")[1].split("completed")[0].trim();
+          String timeSpent  = line.split("completed in")[1].trim();
+          message          += line.split("\\[")[0].trim() + ": " + nbElements + " elements completed in " + timeSpent + "\n";
+          messageField.setText(line.split("\\[")[0].trim());
+          progressLine = true;
+        }
+        if (! progressLine) {
+          message += line + "\n";
+        }
+      }
+    }
+    String lines[]     = message.split("\n");
+    String toBeWritten = "";
+    for (int i = Math.max(0, lines.length - Global.logAreaSize); i < lines.length; i++) {
+      toBeWritten += lines[i] + "\n";
+    }
+    logArea.setText(toBeWritten);
+  }
+
+  public int getExitValue() {
+    try {
+      latch.await();
+    }
+    catch (InterruptedException e) {
+      logArea.append("Cannot wait for the end of the process!\n");
+      e.printStackTrace();
+      return -1;
+    }
+    return exitValue;
+  }
+}