datadb/compbio/cassandra/CassandraWriter.java

   1 package compbio.cassandra;
   2
   3 import java.text.ParseException;
   4 import java.text.SimpleDateFormat;
   5 import java.util.Date;
   6 import java.util.List;
   7
   8 import org.apache.log4j.Logger;
   9
  10 import com.datastax.driver.core.Row;
  11 import com.datastax.driver.core.Session;
  12 import com.datastax.driver.core.ResultSet;
  13
  14 import compbio.data.sequence.FastaSequence;
  15 import compbio.engine.JpredJob;
  16 import compbio.engine.ProteoCachePropertyHelperManager;
  17 import compbio.util.PropertyHelper;
  18
  19 public class CassandraWriter {
  20         private Session session;
  21         private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
  22         private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
  23
  24         CassandraWriter() {
  25                 Session inis = CassandraNativeConnector.getSession();
  26                 setSession(inis);
  27         }
  28
  29         public void setSession(Session s) {
  30                 assert s != null;
  31                 session = s;
  32         }
  33
  34         public boolean JobisNotInsterted(String jobid) {
  35                 ResultSet results1 = session.execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
  36                 if (results1.isExhausted()) {
  37                         return true;
  38                 }
  39                 return false;
  40         }
  41
  42         public boolean JobisNotArchived(String jobid) {
  43                 ResultSet results1 = session.execute("SELECT * FROM JpredArchive WHERE JobID = '" + jobid + "';");
  44                 if (results1.isExhausted()) {
  45                         return true;
  46                 }
  47                 return false;
  48         }
  49
  50         /*
  51          * inserting data into the tables for queries
  52          */
  53         public int FormQueryTables(JpredJob job) {
  54                 if (JobisNotInsterted(job.getJobID())) {
  55                         int njobsOk = 0;
  56                         int njobsStop = 0;
  57                         int njobsError = 0;
  58                         int njobsTimeOut = 0;
  59                         String id = job.getJobID();
  60                         String ip = job.getIP();
  61                         String protein = job.getProtein();
  62                         String finalstatus = job.getFinalStatus();
  63                         String execstatus = job.getExecutionStatus();
  64                         String com1 = "INSERT INTO ProteinLog " + "(JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein)"
  65                                         + " VALUES ('" + id + "','" + ip + "','" + job.getStartingTimeStr() + "','" + job.getEndTimeStr() + "','" + finalstatus
  66                                         + "','" + execstatus + "','" + protein + "');";
  67                         session.execute(com1);
  68                         if (execstatus.equals("OK")) {
  69                                 String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, ExecTime, Protein)" + " VALUES (" + job.getStartingDate() + ",'" + id
  70                                                 + "'," + job.getExecutionTime() + ",'" + protein + "');";
  71                                 session.execute(com2);
  72
  73                                 String allpredictions = "";
  74                                 List<FastaSequence> pr = job.getPredictions();
  75                                 for (FastaSequence pred : pr) {
  76                                         String predictionname = pred.getId();
  77                                         String prediction = pred.getSequence().replaceAll("\n", "");
  78                                         allpredictions += "'" + predictionname + "':'" + prediction + "',";
  79                                 }
  80                                 String final_prediction = "";
  81                                 if (!allpredictions.equals("")) {
  82                                         final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
  83                                 }
  84
  85                                 String check2 = "SELECT * FROM ProteinRow WHERE JobID = '" + job.getJobID() + "';";
  86                                 ResultSet results2 = session.execute(check2);
  87                                 if (results2.isExhausted()) {
  88                                         String com3 = "INSERT INTO ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','" + id + "',{"
  89                                                         + final_prediction + "});";
  90                                         session.execute(com3);
  91                                 }
  92                                 njobsOk = 1;
  93                         } else {
  94                                 String com5 = "INSERT INTO FailLog " + "(jobtime, JobID, ExecTime, ip, FinalStatus)" + " VALUES ("
  95                                                 + job.getStartingDate() + ",'" + id
  96                                                 + "'," + job.getExecutionTime() + ",'" + ip + "', '" +  finalstatus + "');";
  97                                 session.execute(com5);
  98                                 if (finalstatus.equals("TIMEDOUT"))
  99                                         njobsTimeOut = 1;
 100                                 else if (finalstatus.equals("JPREDERROR"))
 101                                         njobsError = 1;
 102                                 else if (finalstatus.equals("STOPPED"))
 103                                         njobsStop = 1;
 104                         }
 105                         // update some internal query tables
 106                         String check3 = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
 107                         ResultSet results3 = session.execute(check3);
 108                         boolean updateparameter = true;
 109                         if (!results3.isExhausted()) {
 110                                 Row r = results3.one();
 111                                 if (job.getStartingDate() >= Long.parseLong(r.getString("Value")))
 112                                         updateparameter = false;
 113                         }
 114                         if (updateparameter) {
 115                                 String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('EarliestJobDate','" + job.getStartingDate()
 116                                                 + "');";
 117                                 session.execute(com);
 118                         }
 119                         String check4 = "SELECT * FROM JobDateInfo WHERE jobday = " + job.getStartingDate() + ";";
 120                         ResultSet results4 = session.execute(check4);
 121                         updateparameter = true;
 122                         int njobs = 1;
 123                         if (!results4.isExhausted()) {
 124                                 Row r = results4.one();
 125                                 njobs += r.getLong("Total");
 126                                 njobsOk += r.getLong("TotalOK");
 127                                 njobsError += r.getLong("TotalError");
 128                                 njobsStop += r.getLong("TotalStopped");
 129                                 njobsTimeOut += r.getLong("TotalTimeOut");
 130                         }
 131                         String com = "INSERT INTO JobDateInfo " + "(jobday, Total, TotalOK, TotalStopped, TotalError, TotalTimeOut)" + " VALUES ("
 132                                         + job.getStartingDate() + "," + njobs + "," + njobsOk + "," + njobsStop + "," + njobsError + "," + njobsTimeOut + ");";
 133                         session.execute(com);
 134                         return 1;
 135                 }
 136                 return 0;
 137         }
 138
 139         /*
 140          * insert data from a real Jpred job: timing+IP, Execution Status, Final
 141          * status, protein sequence, predictions, alignment, LOG and tar.gz files
 142          */
 143         public int ArchiveData(JpredJob job, String archivepath) {
 144                 if (JobisNotArchived(job.getJobID())) {
 145                         String id = job.getJobID();
 146                         String log = job.getLog().replaceAll("'", "");
 147                         String com = "INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime, FinalStatus, ExecutionStatus, LOG, ArchiveLink) VALUES ('" + id + "','"
 148                                         + job.getProtein() + "','" + job.getIP() + "'," + job.getStartingTime() + "," + job.getExecutionTime() + ",'" + job.getFinalStatus() + "','"
 149                                         + job.getExecutionStatus() + "','" + log + "','" + archivepath + "');";
 150                         session.execute(com);
 151                         List<FastaSequence> predictions = job.getPredictions();
 152                         for (FastaSequence p : predictions) {
 153                                 session.execute("UPDATE JpredArchive SET predictions = predictions + {'" + p.getId() + "':'"
 154                                                 + p.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
 155                         }
 156
 157                         List<FastaSequence> seqs = job.getAlignment();
 158                         for (FastaSequence s : seqs) {
 159                                 session.execute("UPDATE JpredArchive SET alignment = alignment + {'" + s.getId() + "':'"
 160                                                 + s.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
 161                         }
 162                         return 1;
 163                 }
 164                 return 0;
 165         }
 166
 167 }