X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FJpredParserHTTP.java;fp=datadb%2Fcompbio%2Fcassandra%2FJpredParserHTTP.java;h=ac9ed4f8bd8919c1cbb59447987d0534bf7b244b;hb=43a2a57fb10f89d0130960f43d136cff1fd56c59;hp=129d8d122cb5669caf95ea8ddcff899e239ce70f;hpb=ecbf46c1d769d120b2dc5ba57325f1d9e9d3c6b9;p=proteocache.git

diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index 129d8d1..ac9ed4f 100644
--- a/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@ -18,13 +18,21 @@ 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();
 
 	public JpredParserHTTP() {
 		dirprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
@@ -38,13 +46,26 @@ public class JpredParserHTTP implements JpredParser {
 		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);
 		}
 	}
 
@@ -56,8 +77,6 @@ public class JpredParserHTTP implements JpredParser {
 	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();
@@ -91,12 +110,11 @@ public class JpredParserHTTP implements JpredParser {
 		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]);
 		Date currDate = new Date();
 		String maindir = dirprefix + "/" + job.getJobID() + "/";
 
-		//System.out.println("analyzing job " + job.getJobID());
 		try {
 			URL dirurl = new URL(maindir);
 			HttpURLConnection httpConnection_dirurl = (HttpURLConnection) dirurl.openConnection();
@@ -104,11 +122,9 @@ public class JpredParserHTTP implements JpredParser {
 				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;
@@ -149,7 +165,6 @@ public class JpredParserHTTP implements JpredParser {
 
 			httpConnection_conciseurl.disconnect();
 			httpConnection_logurl.disconnect();
-			httpConnection_archiveurl.disconnect();
 		} catch (MalformedURLException e) {
 			e.printStackTrace();
 		}
@@ -158,14 +173,25 @@ public class JpredParserHTTP implements JpredParser {
 			job.setAlignment(alignment);
 			job.setPredictions(predictions);
 			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;
@@ -206,4 +232,4 @@ public class JpredParserHTTP implements JpredParser {
 		}
 		;
 	}
-}
+};