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 ip = job.getIP();
  54                         String protein = job.getProtein();
  55                         String finalstatus = job.getFinalStatus();
  56                         String execstatus = job.getExecutionStatus();
  57                         String com1 = "INSERT INTO ProteinLog " + "(JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein)"
  58                                         + " VALUES ('" + id + "','" + ip + "','" + job.getStartingTimeStr() + "','" + job.getEndTimeStr() + "','" + finalstatus
  59                                         + "','" + execstatus + "','" + protein + "');";
  60                         session.execute(com1);
  61
  62                         String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + job.getStartingDate() + ",'" + id
  63                                         + "','" + 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                         String check2 = "SELECT * FROM ProteinRow WHERE JobID = '" + job.getJobID() + "';";
  79                         ResultSet results2 = session.execute(check2);
  80                         if (results2.isExhausted()) {
  81                                 String com3 = "INSERT INTO ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','" + id + "',{"
  82                                                 + final_prediction + "});";
  83                                 session.execute(com3);
  84                         }
  85
  86                         // update some internal query tables
  87                         String check3 = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
  88                         ResultSet results3 = session.execute(check3);
  89                         boolean updateparameter = true;
  90                         if (!results3.isExhausted()) {
  91                                 Row r = results3.one();
  92                                 if (job.getStartingDate() >= Long.parseLong(r.getString("Value")))
  93                                         updateparameter = false;
  94                         }
  95                         if (updateparameter) {
  96                                 String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('EarliestJobDate','" + job.getStartingDateStr()
  97                                                 + "');";
  98                                 session.execute(com);
  99                         }
 100                         String check4 = "SELECT * FROM JobDateInfo WHERE jobday = " + job.getStartingDate() + ";";
 101                         ResultSet results4 = session.execute(check4);
 102                         updateparameter = true;
 103                         int njobs = 1;
 104                         if (!results4.isExhausted()) {
 105                                 Row r = results4.one();
 106                                 njobs += r.getLong("Total");
 107                         }
 108                         String com = "INSERT INTO JobDateInfo " + "(jobday, Total)" + " VALUES (" + job.getStartingDate() + "," + njobs + ");";
 109                         session.execute(com);
 110
 111                         return 1;
 112                 }
 113                 return 0;
 114         }
 115
 116         /*
 117          * insert data from a real Jpred job: timing+IP, Execution Status, Final
 118          * status, protein sequence, predictions, alignment, LOG and tar.gz files
 119          */
 120         public int ArchiveData(JpredJob job, String archivepath) {
 121                 if (JobisNotArchived(job.getJobID())) {
 122                         String id = job.getJobID();
 123                         String log = job.getLog().replaceAll("'", "");
 124                         String com = "INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime,LOG, ArchiveLink) VALUES ('" + id + "','"
 125                                         + job.getProtein() + "','" + job.getIP() + "'," + job.getStartingTime() + "," + job.getExecutionTime() + ",'" + log
 126                                         + "','" + archivepath + "');";
 127                         session.execute(com);
 128
 129                         List<FastaSequence> predictions = job.getPredictions();
 130                         for (FastaSequence p : predictions) {
 131                                 session.execute("UPDATE JpredArchive SET predictions = predictions + {'" + p.getId() + "':'"
 132                                                 + p.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
 133                         }
 134
 135                         List<FastaSequence> seqs = job.getAlignment();
 136                         for (FastaSequence s : seqs) {
 137                                 session.execute("UPDATE JpredArchive SET alignment = alignment + {'" + s.getId() + "':'"
 138                                                 + s.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
 139                         }
 140                         return 1;
 141                 }
 142                 return 0;
 143         }
 144
 145 }