inserted 2 columns: version and pragramme name

[proteocache.git] / datadb / compbio / cassandra / JpredParserHTTP.java

diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index ac9ed4f..1d888e4 100644 (file)
--- a/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@ -13,6 +13,8 @@ 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;
@@ -94,12 +96,29 @@ public class JpredParserHTTP implements JpredParser {
                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.setVersion(matcher.group(0));
+               }
                while (null != (line = buffer.readLine())) {
-                       out += line;
+                       out += line;            
                }
                return out;
        }
@@ -128,7 +147,7 @@ public class JpredParserHTTP implements JpredParser {
                        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();
@@ -139,7 +158,8 @@ public class JpredParserHTTP implements JpredParser {
                        }
                        if (199 < httpConnection_logurl.getResponseCode() && httpConnection_logurl.getResponseCode() < 300) {
                                LogfileExists = true;
-                               job.setLog(parseLogFile(logurl.openStream()));
+                               job.setProgrammeName("Jpred");
+                               job.setLog(parseLogFile(logurl.openStream(), job));
                        } else {
                                // The job has not been started at all...
                                job.setExecutionStatus("FAIL");
@@ -170,9 +190,22 @@ 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());