X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FJpredParserHTTP.java;h=e53ddd8da7f1bbf43db2969963ad804a0a62d7d5;hb=52edb573d0491d34b3951c18bced4c3e00a58d13;hp=bf4c46085021e3bb08037e9c5327296ec7f948fa;hpb=5b33e8d273539ac860bb2db853b47b5e7de0280e;p=proteocache.git

diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index bf4c460..e53ddd8 100644
--- a/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@ -1,8 +1,6 @@
 package compbio.cassandra;
 
 import java.io.BufferedReader;
-import java.io.DataInputStream;
-import java.io.EOFException;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
@@ -11,14 +9,13 @@ import java.net.HttpURLConnection;
 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 compbio.cassandra.JpredParser;
+import compbio.engine.JpredJob;
 
 public class JpredParserHTTP implements JpredParser {
 	private CassandraWriter cw = new CassandraWriter();
@@ -44,10 +41,7 @@ public class JpredParserHTTP implements JpredParser {
 		cal.add(Calendar.DATE, -nDays);
 		for (int i = 0; i < nDays; ++i) {
 			cal.add(Calendar.DATE, 1);
-			int month = cal.get(Calendar.MONTH) + 1;
-			int year = cal.get(Calendar.YEAR);
-			int day = cal.get(Calendar.DATE);
-			String date = year + "/" + month + "/" + day;
+			String date = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DATE);
 			ParsingForDate(source, date);
 		}
 	}
@@ -89,59 +83,25 @@ public class JpredParserHTTP implements JpredParser {
 		return out;
 	}
 
-	private List<Byte> parseArchiveFile(final InputStream stream) throws IOException {
-		DataInputStream data_in = new DataInputStream(stream);
-		List<Byte> out = new ArrayList<Byte>();
-		while (true) {
-			try {
-				out.add(data_in.readByte());
-			} catch (EOFException eof) {
-				break;
-			}
-		}
-		return out;
-	}
-
-	private int analyseJob(String[] job) throws IOException {
+	private int analyseJob(String[] jobinfo) throws IOException {
 		boolean running = true;
 		boolean ConcisefileExists = false;
 		boolean LogfileExists = false;
-		String id = job[job.length - 1];
-		String startdatestring = job[0].substring(0, job[0].indexOf(":"));
-		Date startdate = new Date(0);
-		Date starttime = new Date(0);
-		Date endtime = new Date(0);
+		JpredJob job = new JpredJob (jobinfo[jobinfo.length - 1], jobinfo[0], jobinfo[1]);
+		job.setIP(jobinfo[2]);
 		Date currDate = new Date();
-		String ip = job[2];
-		String execstatus = "OK";
-		String finalstatus = "OK";
-		String protein = "";
-		long exectime = 0;
-		String log = "";
-		String maindir = dirprefix + "/" + id + "/";
-		String concisefile = dirprefix + "/" + id + "/" + id + ".concise.fasta";
-		String archivefile = dirprefix + "/" + id + "/" + id + ".tar.gz";
-		String logfile = dirprefix + "/" + id + "/LOG";
-		SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
-		SimpleDateFormat timeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
-		try {
-			startdate = dateformatter.parse(startdatestring);
-			starttime = timeformatter.parse(job[0]);
-			endtime = timeformatter.parse(job[1]);
-			exectime = (endtime.getTime() - starttime.getTime()) / 1000;
-		} catch (ParseException e) {
-			e.printStackTrace();
-		}
+		String maindir = dirprefix + "/" + job.getJobID() + "/";
 
+		//System.out.println("analyzing job " + job.getJobID());
 		try {
 			URL dirurl = new URL(maindir);
 			HttpURLConnection httpConnection_dirurl = (HttpURLConnection) dirurl.openConnection();
 			if (httpConnection_dirurl.getResponseCode() < 199 || 300 <= httpConnection_dirurl.getResponseCode()) {
 				return 0;
 			}
-			URL conciseurl = new URL(concisefile);
-			URL archiveurl = new URL(archivefile);
-			URL logurl = new URL(logfile);
+			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();
@@ -149,39 +109,37 @@ public class JpredParserHTTP implements JpredParser {
 				ConcisefileExists = true;
 				running = false;
 				try {
-					protein = parsePredictions(conciseurl.openStream(), id);
+					job.setProtein(parsePredictions(conciseurl.openStream(), job.getJobID()));
 				} catch (IOException e) {
 					e.printStackTrace();
 				}
 			} else {
 				// The job still can be running of failed...
 				++countNoData;
-				alignment = new ArrayList<FastaSequence>();
-				predictions = new ArrayList<FastaSequence>();
 			}
 			if (199 < httpConnection_logurl.getResponseCode() && httpConnection_logurl.getResponseCode() < 300) {
 				LogfileExists = true;
-				log = parseLogFile(logurl.openStream());
+				job.setLog(parseLogFile(logurl.openStream()));
 			} else {
 				// The job has not been started at all...
-				execstatus = "FAIL";
-				finalstatus = "STOPPED";
+				job.setExecutionStatus("FAIL");
+				job.setFinalStatus("STOPPED");
 				running = false;
 			}
-			if (log.matches("(.*)TIMEOUT\\syour\\sjob\\stimed\\sout(.*)")) {
+			if (job.getLog().matches("(.*)TIMEOUT\\syour\\sjob\\stimed\\sout(.*)")) {
 				// blast job was too long (more than 3600 secs by default)...
-				execstatus = "FAIL";
-				finalstatus = "TIMEDOUT";
+				job.setExecutionStatus("FAIL");
+				job.setFinalStatus("TIMEDOUT");
 				running = false;
-			} else if (log.matches("(.*)Jpred\\serror:\\sDied\\sat(.*)")) {
+			} else if (job.getLog().matches("(.*)Jpred\\serror:\\sDied\\sat(.*)")) {
 				// an internal Jpred error...
-				execstatus = "FAIL";
-				finalstatus = "JPREDERROR";
+				job.setExecutionStatus("FAIL");
+				job.setFinalStatus("JPREDERROR");
 				running = false;
-			} else if ((currDate.getTime() - endtime.getTime()) / 1000 > 3601 && LogfileExists && !ConcisefileExists) {
+			} else if ((currDate.getTime() - job.getEndTime()) / 1000 > 3601 && LogfileExists && !ConcisefileExists) {
 				// the job was stopped with unknown reason...
-				execstatus = "FAIL";
-				finalstatus = "STOPPED";
+				job.setExecutionStatus("FAIL");
+				job.setFinalStatus("STOPPED");
 				running = false;
 			}
 
@@ -193,12 +151,12 @@ public class JpredParserHTTP implements JpredParser {
 		}
 
 		if (!running) {
-			long t = startdate.getTime();
-			cw.FormQueryTables(t, job[0], job[1], ip, id, execstatus, finalstatus, protein, predictions);
-			cw.ArchiveData(t, exectime, ip, id, execstatus, finalstatus, protein, predictions, alignment, log, archivefile);
+			job.setAlignment(alignment);
+			job.setPredictions(predictions);
+			cw.FormQueryTables(job);
+			cw.ArchiveData(job, "undefined");
 			return 1;
-		} else
-			System.out.println("job " + id + " is running");
+		}
 
 		return 0;
 	}