datadb/compbio/cassandra/CassandraReader.java

   1 package compbio.cassandra;
   2
   3 import java.util.Date;
   4 import java.util.HashMap;
   5 import java.util.List;
   6 import java.util.ArrayList;
   7 import java.util.Map;
   8
   9 import org.apache.log4j.Logger;
  10
  11 import com.datastax.driver.core.Row;
  12 import com.datastax.driver.core.Session;
  13 import com.datastax.driver.core.ResultSet;
  14
  15 public class CassandraReader {
  16         private Session session;
  17         private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
  18
  19         public CassandraReader() {
  20                 Session inis = CassandraNativeConnector.getSession();
  21                 setSession (inis);
  22         }
  23
  24         public void setSession(Session s) {
  25                 assert s != null;
  26                 session = s;
  27         }
  28
  29         /*
  30          * getting data from the db
  31          */
  32         public List<Pair<String, String>> ReadProteinDataTable() {
  33                 final long startTime = System.currentTimeMillis();
  34                 String com = "SELECT DataBegin,DataEnd FROM ProteinLog;";
  35                 System.out.println("Command: " + com);
  36                 ResultSet results = session.execute(com);
  37                 final long queryTime = System.currentTimeMillis();
  38                 List<Row> rows = results.all();
  39                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
  40
  41                 List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
  42                 int c = 0;
  43                 for (Row r : rows) {
  44                         Pair<String, String> pair = new Pair<String, String>(r.getString("DataBegin"), r.getString("DataEnd"));
  45                         res.add(pair);
  46                         ++c;
  47                 }
  48                 final long endTime = System.currentTimeMillis();
  49                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
  50                 return res;
  51         }
  52
  53         /*
  54          * getting data from the db
  55          */
  56         public List<Pair<String, String>> ReadProteinData(long day) {
  57                 final long startTime = System.currentTimeMillis();
  58                 String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";";
  59                 System.out.println("Command: " + com);
  60                 ResultSet results = session.execute(com);
  61                 if (results.isExhausted())
  62                         return null;
  63                 final long queryTime = System.currentTimeMillis();
  64                 List<Row> rows = results.all();
  65                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
  66                 List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
  67                 int c = 0;
  68                 for (Row r : rows) {
  69                         Pair<String, String> pair = new Pair<String, String>(r.getString("JobID"), r.getString("Protein"));
  70                         res.add(pair);
  71                         ++c;
  72                 }
  73                 final long endTime = System.currentTimeMillis();
  74                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
  75                 return res;
  76         }
  77         /*
  78          * getting data from the db JobDateInfo
  79          */
  80         public List<Long> ReadDateTable(long queryDate) {
  81                 ResultSet results = session.execute("SELECT * FROM JobDateInfo WHERE jobday = " + queryDate + ";");
  82                 if (results.isExhausted())
  83                         return null;
  84                 Row therow = results.one();
  85                 List<Long> res = new ArrayList<Long>();
  86                 res.add(therow.getLong("Total"));
  87                 res.add(therow.getLong("TotalOK"));
  88                 res.add(therow.getLong("TotalStopped"));
  89                 res.add(therow.getLong("TotalError"));
  90                 res.add(therow.getLong("TotalTimeOut"));
  91                 if (!results.isExhausted()) {
  92                         Date date = new Date (queryDate);
  93                         log.warn("CassandraReader.ReadDateTable: date row for " + date.toString () + " ("+ queryDate + ") duplicated ");
  94                 }
  95                 return res;
  96         }
  97
  98         /*
  99          * getting whole protein sequence from the db ProteinRow
 100          */
 101         public List<ProteinBean> ReadWholeSequence(String queryProtein) {
 102                 final long startTime = System.currentTimeMillis();
 103                 String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
 104                 System.out.println("Command: " + com);
 105                 ResultSet results = session.execute(com);
 106                 if (results.isExhausted())
 107                         return null;
 108                 final long queryTime = System.currentTimeMillis();
 109                 List<Row> rows = results.all();
 110                 System.out.println("first size : " + rows.size());
 111                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 112                 System.out.println(" rows analysed,  " + rows.size());
 113                 List<ProteinBean> res = new ArrayList<ProteinBean>();
 114                 ProteinBean structure = new ProteinBean(queryProtein, rows.get(0).getMap(
 115                                 "Predictions", String.class, String.class));
 116                 System.out.println("second size : " + rows.size());
 117                 int c = 0;
 118                 for (Row r : rows) {
 119                         structure.setJobid(r.getString("JobID"));
 120                         ++c;
 121                 }
 122                 res.add(structure);
 123                 final long endTime = System.currentTimeMillis();
 124                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 125                 return res;
 126         }
 127
 128
 129         /*
 130          * getting jobs by ip
 131          */
 132         public List<Pair<String, String>> ReadIpWithJobs(String ip) {
 133                 final long startTime = System.currentTimeMillis();
 134                 String com = "SELECT JobID, Protein, FinalStatus FROM ProteinLog WHERE ip = '" + ip + "';";
 135                 System.out.println("Command: " + com);
 136                 ResultSet results = session.execute(com);
 137                 if (results.isExhausted())
 138                         return null;
 139                 final long queryTime = System.currentTimeMillis();
 140                 List<Row> rows = results.all();
 141                 List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
 142                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 143                 System.out.println(" rows analysed,  " + rows.size());
 144                 int c = 0;
 145                 for (Row r : rows) {
 146                         if (r.getString("FinalStatus").equals("OK")) {
 147                                 Pair<String, String> pair = new Pair<String, String>(r.getString("JobID"), r.getString("Protein"));
 148                                 System.out.println(pair.getElement0());
 149                                 System.out.println(pair.getElement1());
 150                                 res.add(pair);
 151                                 ++c;
 152                         }
 153                 }
 154                 final long endTime = System.currentTimeMillis();
 155                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 156                 return res;
 157         }
 158
 159         /*
 160          * getting part of protein sequence from the db ProteinRow
 161          */
 162         public List<ProteinBean> ReadPartOfSequence(String queryProtein) {
 163                 final long startTime = System.currentTimeMillis();
 164                 String com = "SELECT * FROM ProteinRow;";
 165                 System.out.println("Command: " + com);
 166                 ResultSet results = session.execute(com);
 167                 if (results.isExhausted())
 168                         return null;
 169                 final long queryTime = System.currentTimeMillis();
 170                 List<Row> rows = results.all();
 171                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 172                 System.out.println(" rows analysed,  " + rows.size());
 173                 List<ProteinBean> res = new ArrayList<ProteinBean>();
 174                 int c = 0;
 175                 for (Row r : rows) {
 176                         String prot = r.getString("Protein");
 177                         if (prot.matches("(.*)" + queryProtein + "(.*)")) {
 178                                 ProteinBean structure = new ProteinBean(prot,  r.getMap("Predictions", String.class, String.class));
 179                                 structure.setJobid(r.getString("JobID"));
 180                                 res.add(structure);
 181                                 ++c;
 182                         }
 183                 }
 184                 final long endTime = System.currentTimeMillis();
 185                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 186                 return res;
 187         }
 188
 189         /*
 190          * getting protein sequences by counter
 191          */
 192         public Map<String, Integer> ReadProteinSequenceByCounter() {
 193                 final long startTime = System.currentTimeMillis();
 194                 String com = "SELECT Protein, JobID FROM ProteinRow;";
 195                 System.out.println("Command: " + com);
 196                 ResultSet results = session.execute(com);
 197                 if (results.isExhausted())
 198                         return null;
 199                 final long queryTime = System.currentTimeMillis();
 200                 List<Row> rows = results.all();
 201                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 202                 System.out.println(" rows analysed,  " + rows.size());
 203                 Map<String, Integer> res = new HashMap<String, Integer>();
 204                 int c = 0;
 205                 for (Row r : rows) {
 206                         String protein = r.getString("Protein");
 207                         String id = r.getString("JobID");
 208                         if (res.containsKey(protein))
 209                                 res.put(protein, res.get(protein) + 1);
 210                         else
 211                                 res.put(protein, 1);
 212                 }
 213                 final long endTime = System.currentTimeMillis();
 214                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 215                 return res;
 216         }
 217
 218         /*
 219          * getting ip by counter
 220          */
 221         public Map<String, Integer> ReadIpByCounter() {
 222                 final long startTime = System.currentTimeMillis();
 223                 String com = "SELECT JobID, ip FROM ProteinLog;";
 224                 System.out.println("Command: " + com);
 225                 ResultSet results = session.execute(com);
 226                 if (results.isExhausted())
 227                         return null;
 228                 final long queryTime = System.currentTimeMillis();
 229                 List<Row> rows = results.all();
 230                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 231                 System.out.println(" rows analysed,  " + rows.size());
 232                 Map<String, Integer> res = new HashMap<String, Integer>();
 233                 int c = 0;
 234                 for (Row r : rows) {
 235                         String protein = r.getString("ip");
 236                         String id = r.getString("JobID");
 237                         if (res.containsKey(protein))
 238                                 res.put(protein, res.get(protein) + 1);
 239                         else
 240                                 res.put(protein, 1);
 241                 }
 242                 final long endTime = System.currentTimeMillis();
 243                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 244                 return res;
 245         }
 246
 247         /*
 248          * getting log info for jobid
 249          */
 250         public StructureJobLog ReadJobLog(String jobid) {
 251                 final long startTime = System.currentTimeMillis();
 252                 String com = "SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';";
 253                 System.out.println("Command: " + com);
 254                 ResultSet results = session.execute(com);
 255                 if (results.isExhausted())
 256                         return null;
 257                 final long queryTime = System.currentTimeMillis();
 258                 Row row = results.one();
 259                 String com1 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;";
 260                 System.out.println("Command: " + com1);
 261                 ResultSet results1 = session.execute(com1);
 262                 if (results1.isExhausted())
 263                         return null;
 264                 Row row1 = results1.one();
 265                 StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"),
 266                                 row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
 267                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 268                 final long endTime = System.currentTimeMillis();
 269                 System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec");
 270                 return res;
 271         }
 272 }