datadb/compbio/cassandra/CassandraWriter.java

   1 package compbio.cassandra;
   2
   3 import java.io.IOException;
   4 import java.util.List;
   5
   6 import org.apache.log4j.Logger;
   7
   8 import com.datastax.driver.core.Row;
   9 import com.datastax.driver.core.Session;
  10 import com.datastax.driver.core.ResultSet;
  11 import com.datastax.driver.core.PreparedStatement;
  12 import com.datastax.driver.core.BoundStatement;
  13
  14 import compbio.engine.ProteoCachePropertyHelperManager;
  15 import compbio.util.PropertyHelper;
  16
  17 public class CassandraWriter {
  18         private Session session;
  19         private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
  20         private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
  21
  22         CassandraWriter() {
  23                 Session inis = CassandraNativeConnector.getSession();
  24                 setSession(inis);
  25         }
  26
  27         public void setSession(Session s) {
  28                 assert s != null;
  29                 session = s;
  30         }
  31
  32         public boolean JobisNotInsterted(String jobid) {
  33                 ResultSet results1 = session.execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
  34                 if (results1.isExhausted()) {
  35                         return true;
  36                 }
  37                 return false;
  38         }
  39
  40         public boolean JobisNotArchived(String jobid) {
  41                 ResultSet results1 = session.execute("SELECT * FROM JpredArchive WHERE JobID = '" + jobid + "';");
  42                 if (results1.isExhausted()) {
  43                         return true;
  44                 }
  45                 return false;
  46         }
  47
  48         /*
  49          * inserting data into the tables for queries
  50          */
  51         public int FormQueryTables(long jobtime, String startdate, String enddate, String ip, String jobid, String statusEx,
  52                         String statusFinal, String protein, List<FastaSequence> predictions) {
  53                 if (JobisNotInsterted(jobid)) {
  54                         String com1 = "INSERT INTO ProteinLog " + "(JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein)"
  55                                         + " VALUES ('" + jobid + "','" + ip + "','" + startdate + "','" + enddate + "','" + statusFinal + "','" + statusEx
  56                                         + "','" + protein + "');";
  57                         session.execute(com1);
  58
  59                         String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + jobtime + ",'" + jobid + "','" + protein
  60                                         + "');";
  61                         session.execute(com2);
  62
  63                         String allpredictions = "";
  64                         for (FastaSequence pred : predictions) {
  65                                 String predictionname = pred.getId();
  66                                 String prediction = pred.getSequence().replaceAll("\n", "");
  67                                 allpredictions += "'" + predictionname + "':'" + prediction + "',";
  68                         }
  69                         String final_prediction = "";
  70                         if (!allpredictions.equals("")) {
  71                                 final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
  72                         }
  73
  74                         String check2 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "';";
  75                         ResultSet results2 = session.execute(check2);
  76                         if (results2.isExhausted()) {
  77                                 String com3 = "INSERT INTO ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','" + jobid + "',{"
  78                                                 + final_prediction + "});";
  79                                 session.execute(com3);
  80                         }
  81
  82                         // update some internal query tables
  83                         String check3 = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
  84                         ResultSet results3 = session.execute(check3);
  85                         boolean updateparameter = true;
  86                         if (!results3.isExhausted()) {
  87                                 Row r = results3.one();
  88                                 if (jobtime >= Long.parseLong(r.getString("Value")))
  89                                         updateparameter = false;
  90                         }
  91                         if (updateparameter) {
  92                                 String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('EarliestJobDate','" + String.valueOf(jobtime)
  93                                                 + "');";
  94                                 session.execute(com);
  95                         }
  96                         String check4 = "SELECT * FROM JobDateInfo WHERE jobday = " + jobtime + ";";
  97                         ResultSet results4 = session.execute(check4);
  98                         updateparameter = true;
  99                         int njobs = 1;
 100                         if (!results4.isExhausted()) {
 101                                 Row r = results4.one();
 102                                 njobs += r.getLong("Total");
 103                         }
 104                         String com = "INSERT INTO JobDateInfo " + "(jobday, Total)" + " VALUES (" + jobtime + "," + njobs + ");";
 105                         session.execute(com);
 106
 107                         return 1;
 108                 }
 109                 return 0;
 110         }
 111
 112         /*
 113          * insert data from a real Jpred job: timing+IP, Execution Status, Final
 114          * status, protein sequence, predictions, alignment, LOG and tar.gz files
 115          */
 116         public int ArchiveData(long starttime, long exectime, String ip, String jobid, String statusEx, String statusFinal, String protein,
 117                         List<FastaSequence> predictions, List<FastaSequence> seqs, String LogFile, String archivepath) {
 118                 if (JobisNotArchived(jobid)) {
 119                         String log = LogFile.replaceAll("'", "");
 120                         session.execute("INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime,LOG) VALUES ('" + jobid + "','" + protein
 121                                         + "','" + ip + "'," + starttime + "," + exectime + ",'" + log + "');");
 122                         if (false) {
 123                                 PreparedStatement statement = session.prepare("INSERT INTO JpredArchive (JobID, archive) VALUES (?,?);");
 124                                 BoundStatement boundStatement = new BoundStatement(statement);
 125                                 session.execute(boundStatement.bind(jobid, archivepath));
 126                         }
 127
 128                         for (FastaSequence p : predictions) {
 129                                 session.execute("UPDATE JpredArchive SET predictions = predictions + {'" + p.getId() + "':'"
 130                                                 + p.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + jobid + "';");
 131                         }
 132
 133                         for (FastaSequence s : seqs) {
 134                                 session.execute("UPDATE JpredArchive SET alignment = alignment + {'" + s.getId() + "':'"
 135                                                 + s.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + jobid + "';");
 136                         }
 137                         return 1;
 138                 }
 139                 return 0;
 140         }
 141
 142 }