Mercurial > repos > yufei-luo > s_mart

comparison smart_toolShed/SMART/Java/Sav/ProgramLauncher.java @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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1 /**
2 *
3 * Copyright INRA-URGI 2009-2010
4 *
5 * This software is governed by the CeCILL license under French law and
6 * abiding by the rules of distribution of free software. You can use,
7 * modify and/ or redistribute the software under the terms of the CeCILL
8 * license as circulated by CEA, CNRS and INRIA at the following URL
9 * "http://www.cecill.info".
10 *
11 * As a counterpart to the access to the source code and rights to copy,
12 * modify and redistribute granted by the license, users are provided only
13 * with a limited warranty and the software's author, the holder of the
14 * economic rights, and the successive licensors have only limited
15 * liability.
16 *
17 * In this respect, the user's attention is drawn to the risks associated
18 * with loading, using, modifying and/or developing or reproducing the
19 * software by the user in light of its specific status of free software,
20 * that may mean that it is complicated to manipulate, and that also
21 * therefore means that it is reserved for developers and experienced
22 * professionals having in-depth computer knowledge. Users are therefore
23 * encouraged to load and test the software's suitability as regards their
24 * requirements in conditions enabling the security of their systems and/or
25 * data to be ensured and, more generally, to use and operate it in the
26 * same conditions as regards security.
27 *
28 * The fact that you are presently reading this means that you have had
29 * knowledge of the CeCILL license and that you accept its terms.
30 *
31 */
32 import java.util.*;
33 import java.io.*;
34 import javax.swing.SwingUtilities;
35 import javax.swing.*;
36 import java.util.concurrent.CountDownLatch;
37
38 public class ProgramLauncher extends SwingWorker<Boolean, String> {
39
40 String[] command;
41 JTextArea logArea;
42 JLabel messageField;
43 JProgressBar progressBar;
44 JLabel etaField;
45 int exitValue;
46
47
48 public ProgramLauncher (LinkedList <String> c, JTextArea la, JLabel mf, JProgressBar pb, JLabel ef) {
49 command = new String[c.size()];
50 logArea = la;
51 messageField = mf;
52 progressBar = pb;
53 etaField = ef;
54 exitValue = -1;
55 c.toArray(command);
56 }
57
58
59 public ProgramLauncher (String[] c, JTextArea la, JLabel mf, JProgressBar pb, JLabel ef) {
60 command = c;
61 logArea = la;
62 messageField = mf;
63 progressBar = pb;
64 etaField = ef;
65 exitValue = -1;
66 }
67
68
69 @Override
70 public Boolean doInBackground() {
71 ProcessBuilder pb = new ProcessBuilder(command);
72 Process process = null;
73 BufferedReader outputReader = null;
74 pb = pb.redirectErrorStream(true);
75 Map<String, String> env = pb.environment();
76 env.put("PYTHONPATH", System.getProperty("user.dir") + java.io.File.separator + "Python");
77 env.put("SMARTPATH", System.getProperty("user.dir") + java.io.File.separator + "Python");
78 env.put("SMARTMYSQLPATH", Global.mysqlCommand);
79 env.put("SMARTRPATH", Global.rCommand);
80 String commandJoined = Arrays.toString(command);
81
82 try {
83 publish("=== Starting command '" + commandJoined.trim() + "' ===\n");
84 process = pb.start();
85
86 BufferedInputStream outputStream = new BufferedInputStream(process.getInputStream());
87 InputStream is = process.getInputStream();
88 InputStreamReader isr = new InputStreamReader(is);
89 outputReader = new BufferedReader(isr);
90 }
91 catch (Exception exception) {
92 publish("!Process cannot be started (command is '" + commandJoined + "')!\n");
93 exception.printStackTrace();
94 return Boolean.FALSE;
95 }
96 if (outputReader == null) {
97 publish("!Problem in the output of the command!\n");
98 return Boolean.FALSE;
99 }
100 else {
101 try {
102 String line;
103 while ((line = outputReader.readLine()) != null) {
104 publish(line + "\n");
105 }
106 }
107 catch (IOException e) {
108 e.printStackTrace();
109 publish("!Cannot get the output of the command!\n");
110 return Boolean.FALSE;
111 }
112 }
113 try {
114 process.waitFor();
115 }
116 catch (InterruptedException e) {
117 e.printStackTrace();
118 publish("!Cannot wait for the end of the command!\n");
119 return Boolean.FALSE;
120 }
121 try {
122 exitValue = process.exitValue();
123 System.out.println(exitValue);
124 }
125 catch (IllegalThreadStateException e) {
126 e.printStackTrace();
127 publish("!Cannot get the exit value of the command!\n");
128 return Boolean.FALSE;
129 }
130 if (exitValue != 0) {
131 publish("!Problem during the execution of the command '" + commandJoined + "'!\n");
132 return Boolean.FALSE;
133 }
134 publish("=== Ending command '" + commandJoined.trim() + "' ===\n");
135 return Boolean.TRUE;
136 }
137
138
139 @Override
140 protected void process(List<String> chunks) {
141 String message = "";
142 String text = logArea.getText();
143 for (String chunk: chunks) {
144 text += chunk;
145 }
146 for (String lineSeparatedByCarriageReturn: text.split("\n")) {
147 for (String line: lineSeparatedByCarriageReturn.split("\r")) {
148 boolean progressLine = false;
149 if (line.matches(".*\\[=*\\s*\\]\\s*\\d*/\\d*\\s*")) {
150 String[] ratioElements = line.split("\\]")[1].trim().split("/");
151 int current = Integer.parseInt(ratioElements[0].trim());
152 int aim = Integer.parseInt(ratioElements[1].trim());
153 messageField.setText(line.split("\\[")[0].trim());
154 progressBar.setValue(current * 100 / aim);
155 etaField.setText("");
156 progressLine = true;
157 }
158 else if (line.matches(".*\\[=*\\s*\\]\\s*\\d*/\\d*\\s*ETA:\\s*.*")) {
159 String[] ratioElements = line.split("\\]")[1].split("E")[0].trim().split("/");
160 int current = Integer.parseInt(ratioElements[0].trim());
161 int aim = Integer.parseInt(ratioElements[1].trim());
162 String eta = line.split("ETA:")[1].trim();
163 messageField.setText(line.split("\\[")[0].trim());
164 progressBar.setValue(current * 100 / aim);
165 etaField.setText("ETA: " + eta);
166 progressLine = true;
167 }
168 else if (line.matches(".*\\[=*\\s*\\]\\s*\\d*\\s*completed in.*")) {
169 String nbElements = line.split("\\]")[1].split("completed")[0].trim();
170 String timeSpent = line.split("completed in")[1].trim();
171 message += line.split("\\[")[0].trim() + ": " + nbElements + " elements completed in " + timeSpent + "\n";
172 messageField.setText(line.split("\\[")[0].trim());
173 progressLine = true;
174 }
175 if (! progressLine) {
176 message += line + "\n";
177 }
178 }
179 }
180 String lines[] = message.split("\n");
181 String toBeWritten = "";
182 for (int i = Math.max(0, lines.length - Global.logAreaSize); i < lines.length; i++) {
183 toBeWritten += lines[i] + "\n";
184 }
185 logArea.setText(toBeWritten);
186 }
187
188 public int getExitValue() {
189 return exitValue;
190 }
191 }