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
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
|
/* Copyright (c) 2013 Alexander Sherstnev
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.1
*
* This library is free software; you can redistribute it and/or modify it under the terms of the
* Apache License version 2 as published by the Apache Software Foundation
*
* This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
* even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* must include this copyright and license notice.
*/
package compbio.stat.collector;
import java.io.File;
import java.io.FileFilter;
import java.util.Date;
import org.apache.log4j.Logger;
import compbio.engine.Cleaner;
import compbio.engine.client.PathValidator;
import compbio.stat.collector.JobStat;
/**
* Number of runs of each WS = number of folders with name
*
* Number of successful runs = all runs with no result file
*
* Per period of time = limit per file creating time Runtime (avg/max) =
*
* started time - finished time
*
* Task & result size = result.size
*
* Abandoned runs - not collected runs
*
* Cancelled runs - cancelled
*
* Cluster vs local runs
*
* Reasons for failure = look in the err out?
*
* Metadata required:
*
* work directory for local and cluster tasks = from Helper or cmd parameter. WS
* names - enumeration. Status file names and content.
*
* @author pvtroshin
*
*/
public class DirCleaner implements Runnable {
static final int UNDEFINED = -1;
private static final Logger log = Logger.getLogger(DirCleaner.class);
final private File workDirectory;
final private int LifeSpanInHours;
/**
*
* @param workDirectory
* @param timeOutInHours
*/
public DirCleaner(String workDirectory, int LifeSpanInHours) {
log.info("Starting cleaning for directory: " + workDirectory);
log.info("Maximum allowed directory life span (h): " + LifeSpanInHours);
if (!PathValidator.isValidDirectory(workDirectory)) {
throw new IllegalArgumentException("workDirectory '" + workDirectory + "' does not exist!");
}
this.workDirectory = new File(workDirectory);
this.LifeSpanInHours = LifeSpanInHours;
}
boolean hasCompleted(JobDirectory jd) {
JobStat jstat = jd.getJobStat();
if (jstat.hasResult() || jstat.getIsCancelled() || jstat.getIsFinished()) {
return true;
}
return false;
}
boolean livesOverLifeSpan(JobDirectory jd) {
long LifeTime = (System.currentTimeMillis() - jd.jobdir.lastModified()) / (1000 * 60 * 60);
log.debug("lifetime = " + LifeTime + ", lifespan = " + LifeSpanInHours);
return LifeTime > LifeSpanInHours;
}
static FileFilter directories = new FileFilter() {
@Override
public boolean accept(File pathname) {
return pathname.isDirectory() && !pathname.getName().startsWith(".");
}
};
// TODO test!
void doCleaning() {
File[] dirs = workDirectory.listFiles(directories);
for (File dir : dirs) {
// Do not look at dirs with unfinished jobs
JobDirectory jd = new JobDirectory(dir);
Date d = new Date (dir.lastModified());
log.debug("Directory " + dir.getName() + " has timestamp: " + d);
// TODO. removed hasCompeted. Maybe it needs to be restored...
// if (hasCompleted(jd) && livesOverLifeSpan(jd)) {
if (livesOverLifeSpan(jd)) {
if (Cleaner.deleteDirectory(workDirectory.getAbsolutePath() + File.separator + dir.getName())) {
log.error("Directory " + dir.getName() + " failed to deleted...");
} else {
log.debug("Directory " + dir.getName() + " is deleted");
}
} else {
log.debug("Directory " + dir.getName() + " is too new and kept");
}
}
}
@Override
public void run() {
log.info("Started cleaning job directory at " + new Date());
log.info("For directory: " + workDirectory.getAbsolutePath());
doCleaning();
log.info("Finished cleaning job directory at " + new Date());
}
}
|
