Merge branch 'servlets'

diff --combined datadb/compbio/cassandra/CassandraWriter.java
index 24abd4b,521f98c..41ce8ba
--- 1/datadb/compbio/cassandra/CassandraWriter.java
--- 2/datadb/compbio/cassandra/CassandraWriter.java
+++ b/datadb/compbio/cassandra/CassandraWriter.java
@@@ -1,5 -1,8 +1,8 @@@
  package compbio.cassandra;
  
+ import java.text.ParseException;
+ import java.text.SimpleDateFormat;
+ import java.util.Date;
  import java.util.List;
  
  import org.apache.log4j.Logger;
@@@ -8,7 -11,6 +11,7 @@@ import com.datastax.driver.core.Row
  import com.datastax.driver.core.Session;
  import com.datastax.driver.core.ResultSet;
  
 +import compbio.data.sequence.FastaSequence;
  import compbio.engine.JpredJob;
  import compbio.engine.ProteoCachePropertyHelperManager;
  import compbio.util.PropertyHelper;
@@@ -49,6 -51,10 +52,10 @@@ public class CassandraWriter 
         */
        public int FormQueryTables(JpredJob job) {
                if (JobisNotInsterted(job.getJobID())) {
+                       int njobsOk = 0;
+                       int njobsStop = 0;
+                       int njobsError = 0;
+                       int njobsTimeOut = 0;
                        String id = job.getJobID();
                        String ip = job.getIP();
                        String protein = job.getProtein();
@@@ -58,42 -64,55 +65,55 @@@
                                        + " VALUES ('" + id + "','" + ip + "','" + job.getStartingTimeStr() + "','" + job.getEndTimeStr() + "','" + finalstatus
                                        + "','" + execstatus + "','" + protein + "');";
                        session.execute(com1);
- 
-                       String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + job.getStartingDate() + ",'" + id
-                                       + "','" + protein + "');";
-                       session.execute(com2);
- 
-                       String allpredictions = "";
-                       List<FastaSequence> pr = job.getPredictions();
-                       for (FastaSequence pred : pr) {
-                               String predictionname = pred.getId();
-                               String prediction = pred.getSequence().replaceAll("\n", "");
-                               allpredictions += "'" + predictionname + "':'" + prediction + "',";
-                       }
-                       String final_prediction = "";
-                       if (!allpredictions.equals("")) {
-                               final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
-                       }
- 
-                       String check2 = "SELECT * FROM ProteinRow WHERE JobID = '" + job.getJobID() + "';";
-                       ResultSet results2 = session.execute(check2);
-                       if (results2.isExhausted()) {
-                               String com3 = "INSERT INTO ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','" + id + "',{"
-                                               + final_prediction + "});";
-                               session.execute(com3);
+                       if (execstatus.equals("OK")) {
+                               String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, ExecTime, Protein)" + " VALUES (" + job.getStartingDate() + ",'" + id
+                                               + "'," + job.getExecutionTime() + ",'" + protein + "');";
+                               session.execute(com2);
+                               
+                               String allpredictions = "";
+                               List<FastaSequence> pr = job.getPredictions();
+                               for (FastaSequence pred : pr) {
+                                       String predictionname = pred.getId();
+                                       String prediction = pred.getSequence().replaceAll("\n", "");
+                                       allpredictions += "'" + predictionname + "':'" + prediction + "',";
+                               }
+                               String final_prediction = "";
+                               if (!allpredictions.equals("")) {
+                                       final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
+                               }
+ 
+                               String check2 = "SELECT * FROM ProteinRow WHERE JobID = '" + job.getJobID() + "';";
+                               ResultSet results2 = session.execute(check2);
+                               if (results2.isExhausted()) {
+                                       String com3 = "INSERT INTO ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','" + id + "',{"
+                                                       + final_prediction + "});";
+                                       session.execute(com3);
+                               }
+                               njobsOk = 1;
+                       } else {
+                               String com5 = "INSERT INTO FailLog " + "(jobtime, JobID, ExecTime, ip, FinalStatus)" + " VALUES ("
+                                               + job.getStartingDate() + ",'" + id
+                                               + "'," + job.getExecutionTime() + ",'" + ip + "', '" +  finalstatus + "');";
+                               session.execute(com5);
+                               System.out.println(com5);
+                               if (finalstatus.equals("TIMEDOUT"))
+                                       njobsTimeOut = 1;
+                               else if (finalstatus.equals("JPREDERROR"))
+                                       njobsError = 1;
+                               else if (finalstatus.equals("STOPPED"))
+                                       njobsStop = 1;
                        }
- 
                        // update some internal query tables
                        String check3 = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
                        ResultSet results3 = session.execute(check3);
                        boolean updateparameter = true;
                        if (!results3.isExhausted()) {
-                               Row r = results3.one();
+                               Row r = results3.one();         
                                if (job.getStartingDate() >= Long.parseLong(r.getString("Value")))
                                        updateparameter = false;
                        }
                        if (updateparameter) {
-                               String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('EarliestJobDate','" + job.getStartingDateStr()
+                               String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('EarliestJobDate','" + job.getStartingDate()
                                                + "');";
                                session.execute(com);
                        }
@@@ -104,10 -123,15 +124,15 @@@
                        if (!results4.isExhausted()) {
                                Row r = results4.one();
                                njobs += r.getLong("Total");
+                               njobsOk += r.getLong("TotalOK");
+                               njobsError += r.getLong("TotalError");
+                               njobsStop += r.getLong("TotalStopped");
+                               njobsTimeOut += r.getLong("TotalTimeOut");
                        }
-                       String com = "INSERT INTO JobDateInfo " + "(jobday, Total)" + " VALUES (" + job.getStartingDate() + "," + njobs + ");";
+                       String com = "INSERT INTO JobDateInfo " + "(jobday, Total, TotalOK, TotalStopped, TotalError, TotalTimeOut)" + " VALUES ("
+                                       + job.getStartingDate() + "," + njobs + "," + njobsOk + "," + njobsStop + "," + njobsError + "," + njobsTimeOut + ");";
+                       System.out.println(com);
                        session.execute(com);
- 
                        return 1;
                }
                return 0;
@@@ -121,11 -145,10 +146,10 @@@
                if (JobisNotArchived(job.getJobID())) {
                        String id = job.getJobID();
                        String log = job.getLog().replaceAll("'", "");
-                       String com = "INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime,LOG, ArchiveLink) VALUES ('" + id + "','"
-                                       + job.getProtein() + "','" + job.getIP() + "'," + job.getStartingTime() + "," + job.getExecutionTime() + ",'" + log
-                                       + "','" + archivepath + "');";
+                       String com = "INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime, FinalStatus, ExecutionStatus, LOG, ArchiveLink) VALUES ('" + id + "','"
+                                       + job.getProtein() + "','" + job.getIP() + "'," + job.getStartingTime() + "," + job.getExecutionTime() + ",'" + job.getFinalStatus() + "','"
+                                       + job.getExecutionStatus() + "','" + log + "','" + archivepath + "');";
                        session.execute(com);
- 
                        List<FastaSequence> predictions = job.getPredictions();
                        for (FastaSequence p : predictions) {
                                session.execute("UPDATE JpredArchive SET predictions = predictions + {'" + p.getId() + "':'"

diff --combined datadb/compbio/cassandra/JpredParserHTTP.java
index 2167a2d,bb2993b..129d8d1
--- 1/datadb/compbio/cassandra/JpredParserHTTP.java
--- 2/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@@ -15,8 -15,6 +15,8 @@@ import java.util.Date
  import java.util.List;
  
  import compbio.cassandra.JpredParser;
 +import compbio.data.sequence.FastaReader;
 +import compbio.data.sequence.FastaSequence;
  import compbio.engine.JpredJob;
  
  public class JpredParserHTTP implements JpredParser {
@@@ -56,8 -54,8 +56,8 @@@
        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>();
+ //            alignment = new ArrayList<FastaSequence>();
+ //            predictions = new ArrayList<FastaSequence>();
                while (fr.hasNext()) {
                        final FastaSequence fs = fr.next();
                        String seqid = fs.getId();
@@@ -86,6 -84,8 +86,8 @@@
        }
  
        private int analyseJob(String[] jobinfo) throws IOException {
+               alignment = new ArrayList<FastaSequence>();
+               predictions = new ArrayList<FastaSequence>();
                boolean running = true;
                boolean ConcisefileExists = false;
                boolean LogfileExists = false;