X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FJpredParserHTTP.java;h=453f01f73e9728d8691a01e8a5e87bb429c31226;hb=429ba39df7f7dbf7c7f940bafd5126cfab9fca61;hp=ac9ed4f8bd8919c1cbb59447987d0534bf7b244b;hpb=43a2a57fb10f89d0130960f43d136cff1fd56c59;p=proteocache.git

diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index ac9ed4f..453f01f 100644
--- a/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@ -93,6 +93,17 @@ public class JpredParserHTTP implements JpredParser {
 		}
 		return protein;
 	}
+	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) throws IOException {
 		String out = "";
@@ -170,9 +181,22 @@ public class JpredParserHTTP implements JpredParser {
 		}
 
 		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);
+
 			// archiving the job
 			if (archiving) {
 				ArchivedJob ajob = new ArchivedJob(job.getJobID());