1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
|
package compbio.ws.server;
import java.io.File;
import java.io.IOException;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
import org.apache.log4j.Logger;
import compbio.engine.client.Executable.ExecProvider;
import compbio.engine.client.EngineUtil;
import compbio.engine.conf.PropertyHelperManager;
import compbio.runner.disorder.IUPred;
import compbio.runner.msa.Muscle;
import compbio.util.SysPrefs;
/**
* Run setexecflag.sh script if executable flag is not set
*
* @author pvtroshin
*
*/
public class SetExecutableFlag implements ServletContextListener {
private final Logger log = Logger.getLogger(SetExecutableFlag.class);
@Override
public void contextDestroyed(ServletContextEvent arg0) {
// do nothing
}
/**
* This listener is designed to run only once when the web application is
* deployed to set executable flag for binaries.
*
* @param arg0
* - ignored
*/
@Override
public void contextInitialized(ServletContextEvent arg0) {
// Assume at least one of these is configured
// Do not even bother with cluster execution, sysadmins set the flag
// themselves
String command = EngineUtil.getCommand(ExecProvider.Local, Muscle.class);
if (compbio.util.Util.isEmpty(command)) {
command = EngineUtil.getCommand(ExecProvider.Local, IUPred.class);
}
boolean isExec = true;
if (!compbio.util.Util.isEmpty(command)) {
File file = new File(command);
isExec = file.canExecute();
}
String workDir = PropertyHelperManager.getLocalPath() + "binaries/src";
String script = "setexecflag.sh";
// Run only one once if not on Windows
if (!SysPrefs.isWindows && !isExec) {
// verify script exists
File scriptFile = new File(workDir, script);
if (!scriptFile.exists()) {
log.debug("Setexecflag.sh script is NOT found in " + scriptFile.getAbsolutePath());
return;
} else {
scriptFile.setExecutable(true);
log.debug("Setexecflag.sh script is found");
}
try {
log.debug("Executable flag is NOT set for the binaries - attemping to set it");
ProcessBuilder pb = new ProcessBuilder(scriptFile.getAbsolutePath());
pb.directory(new File(workDir));
Process process = pb.start();
process.waitFor();
process.destroy();
} catch (IOException e) {
log.debug("Failed to execute set executable flag script due to IOException! Please run it manually!");
log.debug(e.getMessage(), e);
} catch (InterruptedException e) {
log.debug("Failed to execute set executable flag script due to Interruption! Please run it manually!");
}
} else {
log.debug("Executable flag is already set for the binaries.");
}
}
}
|
