datadb/compbio/cassandra/CassandraWriter.java

   1 package compbio.cassandra;
   2
   3 import java.util.List;
   4
   5 import org.apache.log4j.Logger;
   6
   7 import com.datastax.driver.core.Row;
   8 import com.datastax.driver.core.Session;
   9 import com.datastax.driver.core.ResultSet;
  10
  11 import compbio.data.sequence.FastaSequence;
  12 import compbio.engine.JpredJob;
  13 import compbio.engine.ProteoCachePropertyHelperManager;
  14 import compbio.util.PropertyHelper;
  15
  16 public class CassandraWriter {
  17         private Session session;
  18         private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
  19         private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
  20
  21         CassandraWriter() {
  22                 Session inis = CassandraNativeConnector.getSession();
  23                 setSession(inis);
  24         }
  25
  26         public void setSession(Session s) {
  27                 assert s != null;
  28                 session = s;
  29         }
  30
  31         public boolean JobisNotInsterted(String jobid) {
  32                 ResultSet results1 = session.execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
  33                 if (results1.isExhausted()) {
  34                         return true;
  35                 }
  36                 return false;
  37         }
  38
  39         public boolean JobisNotArchived(String jobid) {
  40                 ResultSet results1 = session.execute("SELECT * FROM JpredArchive WHERE JobID = '" + jobid + "';");
  41                 if (results1.isExhausted()) {
  42                         return true;
  43                 }
  44                 return false;
  45         }
  46
  47         /*
  48          * inserting data into the tables for queries
  49          */
  50         public int FormQueryTables(JpredJob job) {
  51                 if (JobisNotInsterted(job.getJobID())) {
  52                         String id = job.getJobID();
  53                         String protein = job.getProtein();
  54                         String finalstatus = job.getFinalStatus();
  55                         String execstatus = job.getExecutionStatus();
  56
  57                         String com1 = "INSERT INTO ProteinLog (JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein) VALUES ('" + id
  58                                         + "','" + job.getIP() + "','" + job.getStartingTimeStr() + "','" + job.getEndTimeStr() + "','" + finalstatus + "','"
  59                                         + execstatus + "','" + protein + "');";
  60                         session.execute(com1);
  61                         if (finalstatus.equals("OK")) {
  62                                 String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, ExecTime, Protein)" + " VALUES (" + job.getStartingDate()
  63                                                 + ",'" + id + "'," + job.getExecutionTime() + ",'" + protein + "');";
  64                                 session.execute(com2);
  65
  66                                 String allpredictions = "";
  67                                 List<FastaSequence> pr = job.getPredictions();
  68                                 for (FastaSequence pred : pr) {
  69                                         String predictionname = pred.getId();
  70                                         String prediction = pred.getSequence().replaceAll("\n", "");
  71                                         allpredictions += "'" + predictionname + "':'" + prediction + "',";
  72                                 }
  73                                 String final_prediction = "";
  74                                 if (!allpredictions.equals("")) {
  75                                         final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
  76                                 }
  77
  78                                 ResultSet results2 = session.execute("SELECT * FROM ProteinRow WHERE JobID = '" + job.getJobID() + "';");
  79                                 if (results2.isExhausted()) {
  80                                         String com3 = "INSERT INTO ProteinRow (Protein, JobID, Predictions) VALUES ('" + protein + "','" + id + "',{"
  81                                                         + final_prediction + "});";
  82                                         session.execute(com3);
  83                                 }
  84                         } else {
  85                                 String com5 = "INSERT INTO FailLog (jobtime, JobID, ExecTime, ip, FinalStatus) VALUES (" + job.getStartingDate() + ",'"
  86                                                 + id + "'," + job.getExecutionTime() + ",'" + job.getIP() + "', '" + finalstatus + "');";
  87                                 session.execute(com5);
  88                         }
  89
  90                         // update Main parameters if the job is the earliest job so far
  91                         ResultSet results3 = session.execute("SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';");
  92                         boolean updateparameter = true;
  93                         if (!results3.isExhausted()) {
  94                                 Row r = results3.one();
  95                                 if (job.getStartingDate() >= Long.parseLong(r.getString("Value")))
  96                                         updateparameter = false;
  97                         }
  98                         if (updateparameter) {
  99                                 session.execute("INSERT INTO MainParameters (Name, Value) VALUES ('EarliestJobDate','" + job.getStartingDate() + "');");
 100                         }
 101
 102                         // update internal job counts (used by the Daily Statistics
 103                         // requests)
 104                         //TODO I don't like the bit of code. There should not be so many counters...
 105                         int njobsTotal = 1;
 106                         int njobsOk = 0;
 107                         int njobsStop = 0;
 108                         int njobsError = 0;
 109                         int njobsTimeOut = 0;
 110                         if (finalstatus.equals("OK"))
 111                                 njobsOk = 1;
 112                         else if (finalstatus.equals("TIMEDOUT"))
 113                                 njobsTimeOut = 1;
 114                         else if (finalstatus.equals("JPREDERROR"))
 115                                 njobsError = 1;
 116                         else if (finalstatus.equals("STOPPED"))
 117                                 njobsStop = 1;
 118                         ResultSet results4 = session.execute("SELECT * FROM JobDateInfo WHERE jobday = " + job.getStartingDate() + ";");
 119                         if (!results4.isExhausted()) {
 120                                 Row r = results4.one();
 121                                 njobsTotal += r.getLong("Total");
 122                                 njobsOk += r.getLong("TotalOK");
 123                                 njobsError += r.getLong("TotalError");
 124                                 njobsStop += r.getLong("TotalStopped");
 125                                 njobsTimeOut += r.getLong("TotalTimeOut");
 126                         }
 127                         String com = "INSERT INTO JobDateInfo " + "(jobday, Total, TotalOK, TotalStopped, TotalError, TotalTimeOut)" + " VALUES ("
 128                                         + job.getStartingDate() + "," + njobsTotal + "," + njobsOk + "," + njobsStop + "," + njobsError + "," + njobsTimeOut
 129                                         + ");";
 130                         session.execute(com);
 131                         return 1;
 132                 }
 133                 return 0;
 134         }
 135
 136         /*
 137          * insert data from a real Jpred job: timing+IP, Execution Status, Final
 138          * status, protein sequence, predictions, alignment, LOG and tar.gz files
 139          */
 140         public int ArchiveData(JpredJob job, String archivepath) {
 141                 if (JobisNotArchived(job.getJobID())) {
 142                         String id = job.getJobID();
 143                         String log = job.getLog().replaceAll("'", "");
 144                         String com = "INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime, FinalStatus, ExecutionStatus, LOG, ArchiveLink) VALUES ('"
 145                                         + id
 146                                         + "','"
 147                                         + job.getProtein()
 148                                         + "','"
 149                                         + job.getIP()
 150                                         + "',"
 151                                         + job.getStartingTime()
 152                                         + ","
 153                                         + job.getExecutionTime()
 154                                         + ",'" + job.getFinalStatus() + "','" + job.getExecutionStatus() + "','" + log + "','" + archivepath + "');";
 155                         session.execute(com);
 156                         List<FastaSequence> predictions = job.getPredictions();
 157                         for (FastaSequence p : predictions) {
 158                                 session.execute("UPDATE JpredArchive SET predictions = predictions + {'" + p.getId() + "':'"
 159                                                 + p.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
 160                         }
 161
 162                         List<FastaSequence> seqs = job.getAlignment();
 163                         for (FastaSequence s : seqs) {
 164                                 session.execute("UPDATE JpredArchive SET alignment = alignment + {'" + s.getId() + "':'"
 165                                                 + s.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
 166                         }
 167                         return 1;
 168                 }
 169                 return 0;
 170         }
 171
 172 }