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.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import compbio.cassandra.JpredParser;
import compbio.data.sequence.FastaReader;
import compbio.data.sequence.FastaSequence;
import compbio.engine.JpredJob;
+import compbio.engine.ProteoCachePropertyHelperManager;
+import compbio.engine.archive.Archive;
+import compbio.engine.archive.ArchivedJob;
+import compbio.util.PropertyHelper;
+import compbio.util.Util;
public class JpredParserHTTP implements JpredParser {
private CassandraWriter cw = new CassandraWriter();
+ private static Archive archive;
private String dirprefix;
private List<FastaSequence> alignment;
private List<FastaSequence> predictions;
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";
dirprefix = newsourceprefix;
}
+ private boolean initBooleanValue(String key) {
+ assert key != null;
+ String status = ph.getProperty(key);
+ if (Util.isEmpty(status)) {
+ return false;
+ }
+ return new Boolean(status.trim()).booleanValue();
+ }
+
public void Parsing(String source, int nDays) throws IOException {
Calendar cal = Calendar.getInstance();
cal.add(Calendar.DATE, -nDays);
+ archiving = initBooleanValue("archive.enable");
+ if (archiving) {
+ archive = new Archive();
+ }
for (int i = 0; i < nDays; ++i) {
cal.add(Calendar.DATE, 1);
String date = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DATE);
- ParsingForDate(source, date);
+ ParsingOneDay(source, date);
}
}
private String parsePredictions(final InputStream stream, String jobid) throws FileNotFoundException {
final FastaReader fr = new FastaReader(stream);
String protein = "";
- alignment = new ArrayList<FastaSequence>();
- predictions = new ArrayList<FastaSequence>();
while (fr.hasNext()) {
final FastaSequence fs = fr.next();
String seqid = fs.getId();
return protein;
}
- private String parseLogFile(final InputStream stream) throws IOException {
+ private String parseSeqFile(final InputStream stream, String jobid) throws FileNotFoundException {
+ final FastaReader fr = new FastaReader(stream);
+ String protein = "";
+ final FastaSequence fs = fr.next();
+ protein = fs.getSequence().replaceAll("\n", "");
+ if (fr.hasNext()) {
+ // this is an aligment job...
+ return "alignment";
+ }
+ return protein;
+ }
+
+ private String parseLogFile(final InputStream stream, JpredJob job) throws IOException {
String out = "";
BufferedReader buffer = new BufferedReader(new InputStreamReader(stream));
String line;
+ if (null != (out = buffer.readLine()) && (out.contains("version"))) {
+ Matcher matcher = Pattern.compile("((\\d|\\.)+)").matcher(out);
+ if (matcher.find())
+ job.setProgramVersion(matcher.group(0));
+ }
while (null != (line = buffer.readLine())) {
- out += line;
+ out += line;
}
return out;
}
private int analyseJob(String[] jobinfo) throws IOException {
+ alignment = new ArrayList<FastaSequence>();
+ predictions = new ArrayList<FastaSequence>();
boolean running = true;
boolean ConcisefileExists = false;
boolean LogfileExists = false;
- JpredJob job = new JpredJob (jobinfo[jobinfo.length - 1], jobinfo[0], jobinfo[1]);
+ JpredJob job = new JpredJob(jobinfo[jobinfo.length - 1], jobinfo[0], jobinfo[1]);
job.setIP(jobinfo[2]);
+ job.setProgramName("Jpred");
Date currDate = new Date();
String maindir = dirprefix + "/" + job.getJobID() + "/";
- //System.out.println("analyzing job " + 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();
return 0;
}
URL conciseurl = new URL(maindir + job.getJobID() + ".concise.fasta");
- URL archiveurl = new URL(maindir + job.getJobID() + ".tar.gz");
URL logurl = new URL(maindir + "LOG");
HttpURLConnection httpConnection_conciseurl = (HttpURLConnection) conciseurl.openConnection();
HttpURLConnection httpConnection_logurl = (HttpURLConnection) logurl.openConnection();
- HttpURLConnection httpConnection_archiveurl = (HttpURLConnection) archiveurl.openConnection();
if (199 < httpConnection_conciseurl.getResponseCode() && httpConnection_conciseurl.getResponseCode() < 300) {
ConcisefileExists = true;
running = false;
- try {
+ try {
job.setProtein(parsePredictions(conciseurl.openStream(), job.getJobID()));
} catch (IOException e) {
e.printStackTrace();
}
if (199 < httpConnection_logurl.getResponseCode() && httpConnection_logurl.getResponseCode() < 300) {
LogfileExists = true;
- job.setLog(parseLogFile(logurl.openStream()));
+ 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;
httpConnection_conciseurl.disconnect();
httpConnection_logurl.disconnect();
- httpConnection_archiveurl.disconnect();
} catch (MalformedURLException e) {
e.printStackTrace();
}
if (!running) {
+ // logging the job
job.setAlignment(alignment);
job.setPredictions(predictions);
+ if (job.getExecutionStatus().equals("FAIL")) {
+ URL sequrl = new URL(maindir + job.getJobID() + ".seq");
+ HttpURLConnection httpConnection_sequrl = (HttpURLConnection) sequrl.openConnection();
+ if (199 < httpConnection_sequrl.getResponseCode() && httpConnection_sequrl.getResponseCode() < 300) {
+ try {
+ job.setProtein(parseSeqFile(sequrl.openStream(), job.getJobID()));
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
cw.FormQueryTables(job);
- cw.ArchiveData(job, "undefined");
+
+ // archiving the job
+ if (archiving) {
+ ArchivedJob ajob = new ArchivedJob(job.getJobID());
+ String arlink = archive.createJob(job.getJobID());
+ if (job.getFinalStatus().equals("OK")) {
+ ajob.setArchivePath(arlink);
+ ajob.copyArchiveFromWeb(maindir + job.getJobID() + ".tar.gz");
+ cw.ArchiveData(job, arlink);
+ } else {
+ cw.ArchiveData(job, "undefined");
+ }
+ }
return 1;
}
return 0;
}
- private void ParsingForDate(String input, String date) {
+ private void ParsingOneDay(String input, String date) {
int totalcount = 0;
int countinsertions = 0;
int countinserted = 0;
}
;
}
-}
+};
git://source.jalview.org / proteocache.git / blobdiff