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Temporary fix problem with wrong Jpred version
[proteocache.git]
/
datadb
/
compbio
/
cassandra
/
JpredParserHTTP.java
diff --git
a/datadb/compbio/cassandra/JpredParserHTTP.java
b/datadb/compbio/cassandra/JpredParserHTTP.java
index
1d888e4
..
c6db457
100644
(file)
--- a/
datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/
datadb/compbio/cassandra/JpredParserHTTP.java
@@
-9,6
+9,8
@@
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
@@
-35,6
+37,7
@@
public class JpredParserHTTP implements JpredParser {
private int countNoData;
private static boolean archiving = false;
private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
private int countNoData;
private static boolean archiving = false;
private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
+ static SimpleDateFormat timeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
public JpredParserHTTP() {
dirprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
public JpredParserHTTP() {
dirprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
@@
-115,7
+118,7
@@
public class JpredParserHTTP implements JpredParser {
if (null != (out = buffer.readLine()) && (out.contains("version"))) {
Matcher matcher = Pattern.compile("((\\d|\\.)+)").matcher(out);
if (matcher.find())
if (null != (out = buffer.readLine()) && (out.contains("version"))) {
Matcher matcher = Pattern.compile("((\\d|\\.)+)").matcher(out);
if (matcher.find())
- job.setVersion(matcher.group(0));
+ job.setProgramVersion(matcher.group(0));
}
while (null != (line = buffer.readLine())) {
out += line;
}
while (null != (line = buffer.readLine())) {
out += line;
@@
-131,10
+134,20
@@
public class JpredParserHTTP implements JpredParser {
boolean LogfileExists = false;
JpredJob job = new JpredJob(jobinfo[jobinfo.length - 1], jobinfo[0], jobinfo[1]);
job.setIP(jobinfo[2]);
boolean LogfileExists = false;
JpredJob job = new JpredJob(jobinfo[jobinfo.length - 1], jobinfo[0], jobinfo[1]);
job.setIP(jobinfo[2]);
+ job.setProgramName("Jpred");
+ job.setProgramVersion("3.0.1");
Date currDate = new Date();
String maindir = dirprefix + "/" + job.getJobID() + "/";
try {
Date currDate = new Date();
String maindir = dirprefix + "/" + job.getJobID() + "/";
try {
+ Date finishTime = timeformatter.parse(jobinfo[1]);
+ long delay = currDate.getTime() / 1000 - finishTime.getTime() / 1000;
+ if (delay < 120) return 0;
+ } catch (ParseException e) {
+ e.printStackTrace();
+ }
+
+ try {
URL dirurl = new URL(maindir);
HttpURLConnection httpConnection_dirurl = (HttpURLConnection) dirurl.openConnection();
if (httpConnection_dirurl.getResponseCode() < 199 || 300 <= httpConnection_dirurl.getResponseCode()) {
URL dirurl = new URL(maindir);
HttpURLConnection httpConnection_dirurl = (HttpURLConnection) dirurl.openConnection();
if (httpConnection_dirurl.getResponseCode() < 199 || 300 <= httpConnection_dirurl.getResponseCode()) {
@@
-158,10
+171,10
@@
public class JpredParserHTTP implements JpredParser {
}
if (199 < httpConnection_logurl.getResponseCode() && httpConnection_logurl.getResponseCode() < 300) {
LogfileExists = true;
}
if (199 < httpConnection_logurl.getResponseCode() && httpConnection_logurl.getResponseCode() < 300) {
LogfileExists = true;
- job.setProgrammeName("Jpred");
job.setLog(parseLogFile(logurl.openStream(), job));
} else {
// The job has not been started at all...
job.setLog(parseLogFile(logurl.openStream(), job));
} else {
// The job has not been started at all...
+ System.out.println ("WARNING! Job " + job.getJobID() + " has status FAIL/STOPPED");
job.setExecutionStatus("FAIL");
job.setFinalStatus("STOPPED");
running = false;
job.setExecutionStatus("FAIL");
job.setFinalStatus("STOPPED");
running = false;