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