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 DateBean ReadProteinData(long day, String date) {
  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                 DateBean res = new DateBean(date);
  67                 int c = 0;
  68                 for (Row r : rows) {
  69                         res.setJobidAndSeq(r.getString("JobID"), r.getString("Protein"));
  70                         ++c;
  71                 }
  72                 final long endTime = System.currentTimeMillis();
  73                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
  74                 return res;
  75         }
  76         /*
  77          * getting data from the db JobDateInfo
  78          */
  79         public Total ReadDateTable(long queryDate) {
  80                 ResultSet results = session.execute("SELECT * FROM JobDateInfo WHERE jobday = " + queryDate + ";");
  81                 if (results.isExhausted())
  82                         return null;
  83                 Row therow = results.one();
  84                 Total res = new Total(therow.getLong("Total"), therow.getLong("TotalOK"), therow.getLong("TotalStopped"),
  85                                 therow.getLong("TotalError"), therow.getLong("TotalTimeOut"));
  86                 if (!results.isExhausted()) {
  87                         Date date = new Date (queryDate);
  88                         log.warn("CassandraReader.ReadDateTable: date row for " + date.toString () + " ("+ queryDate + ") duplicated ");
  89                 }
  90                 return res;
  91         }
  92
  93         /*
  94          * getting whole protein sequence from the db ProteinRow
  95          */
  96         public List<ProteinBean> ReadWholeSequence(String queryProtein) {
  97                 final long startTime = System.currentTimeMillis();
  98                 String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
  99                 System.out.println("Command: " + com);
 100                 ResultSet results = session.execute(com);
 101                 if (results.isExhausted())
 102                         return null;
 103                 final long queryTime = System.currentTimeMillis();
 104                 List<Row> rows = results.all();
 105                 System.out.println("first size : " + rows.size());
 106                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 107                 System.out.println(" rows analysed,  " + rows.size());
 108                 List<ProteinBean> res = new ArrayList<ProteinBean>();
 109                 ProteinBean structure = new ProteinBean(queryProtein, rows.get(0).getMap(
 110                                 "Predictions", String.class, String.class));
 111                 System.out.println("second size : " + rows.size());
 112                 int c = 0;
 113                 for (Row r : rows) {
 114                         structure.setJobid(r.getString("JobID"));
 115                         ++c;
 116                 }
 117                 res.add(structure);
 118                 final long endTime = System.currentTimeMillis();
 119                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 120                 return res;
 121         }
 122
 123
 124         /*
 125          * getting jobs by ip
 126          */
 127         public Map<String, String[]> ReadIpWithJobs(String ip) {
 128                 final long startTime = System.currentTimeMillis();
 129                 String com = "SELECT JobID, Protein, FinalStatus, DataBegin FROM ProteinLog WHERE ip = '" + ip + "';";
 130                 System.out.println("Command: " + com);
 131                 ResultSet results = session.execute(com);
 132                 if (results.isExhausted())
 133                         return null;
 134                 final long queryTime = System.currentTimeMillis();
 135                 List<Row> rows = results.all();
 136                 Map<String, String[]> res = new HashMap<String, String[]>();
 137                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 138                 System.out.println(" rows analysed,  " + rows.size());
 139                 int c = 0;
 140                 for (Row r : rows) {
 141                         if (r.getString("FinalStatus").equals("OK")) {
 142                                 String date = r.getString("DataBegin");
 143                                 res.put(r.getString("JobID"), new String[] {date.substring(0, date.indexOf(":")), r.getString("Protein")});
 144                                 ++c;
 145                         }
 146                 }
 147                 final long endTime = System.currentTimeMillis();
 148                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 149                 return res;
 150         }
 151
 152         /*
 153          * getting part of protein sequence from the db ProteinRow
 154          */
 155         public List<ProteinBean> ReadPartOfSequence(String queryProtein) {
 156                 final long startTime = System.currentTimeMillis();
 157                 String com = "SELECT * FROM ProteinRow;";
 158                 System.out.println("Command: " + com);
 159                 ResultSet results = session.execute(com);
 160                 if (results.isExhausted())
 161                         return null;
 162                 final long queryTime = System.currentTimeMillis();
 163                 List<Row> rows = results.all();
 164                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 165                 System.out.println(" rows analysed,  " + rows.size());
 166                 List<ProteinBean> res = new ArrayList<ProteinBean>();
 167                 int c = 0;
 168                 for (Row r : rows) {
 169                         String prot = r.getString("Protein");
 170                         if (prot.matches("(.*)" + queryProtein + "(.*)")) {
 171                                 ProteinBean structure = new ProteinBean(prot,  r.getMap("Predictions", String.class, String.class));
 172                                 structure.setJobid(r.getString("JobID"));
 173                                 res.add(structure);
 174                                 ++c;
 175                         }
 176                 }
 177                 final long endTime = System.currentTimeMillis();
 178                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 179                 return res;
 180         }
 181
 182         /*
 183          * getting protein sequences by counter
 184          */
 185         public Map<String, Integer> ReadProteinSequenceByCounter() {
 186                 final long startTime = System.currentTimeMillis();
 187                 String com = "SELECT Protein, JobID FROM ProteinRow;";
 188                 System.out.println("Command: " + com);
 189                 ResultSet results = session.execute(com);
 190                 if (results.isExhausted())
 191                         return null;
 192                 final long queryTime = System.currentTimeMillis();
 193                 List<Row> rows = results.all();
 194                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 195                 System.out.println(" rows analysed,  " + rows.size());
 196                 Map<String, Integer> res = new HashMap<String, Integer>();
 197                 int c = 0;
 198                 for (Row r : rows) {
 199                         String protein = r.getString("Protein");
 200                         String id = r.getString("JobID");
 201                         if (res.containsKey(protein))
 202                                 res.put(protein, res.get(protein) + 1);
 203                         else
 204                                 res.put(protein, 1);
 205                 }
 206                 final long endTime = System.currentTimeMillis();
 207                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 208                 return res;
 209         }
 210
 211         /*
 212          * getting ip by counter
 213          */
 214         public Map<String, Integer> ReadIpByCounter() {
 215                 final long startTime = System.currentTimeMillis();
 216                 String com = "SELECT JobID, ip FROM ProteinLog;";
 217                 System.out.println("Command: " + com);
 218                 ResultSet results = session.execute(com);
 219                 if (results.isExhausted())
 220                         return null;
 221                 final long queryTime = System.currentTimeMillis();
 222                 List<Row> rows = results.all();
 223                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 224                 System.out.println(" rows analysed,  " + rows.size());
 225                 Map<String, Integer> res = new HashMap<String, Integer>();
 226                 int c = 0;
 227                 for (Row r : rows) {
 228                         String ip = r.getString("ip");
 229                         String id = r.getString("JobID");
 230                         if (res.containsKey(ip))
 231                                 res.put(ip, res.get(ip) + 1);
 232                         else
 233                                 res.put(ip, 1);
 234                 }
 235                 final long endTime = System.currentTimeMillis();
 236                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 237                 return res;
 238         }
 239
 240         /*
 241          * getting log info for jobid
 242          */
 243         public JobBean ReadJobLog(String jobid) {
 244                 final long startTime = System.currentTimeMillis();
 245                 String com = "SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';";
 246                 System.out.println("Command: " + com);
 247                 ResultSet results = session.execute(com);
 248                 if (results.isExhausted())
 249                         return null;
 250                 final long queryTime = System.currentTimeMillis();
 251                 Row row = results.one();
 252                 String com1 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;";
 253                 System.out.println("Command: " + com1);
 254                 ResultSet results1 = session.execute(com1);
 255                 if (results1.isExhausted())
 256                         return null;
 257                 Row row1 = results1.one();
 258                 JobBean res = new JobBean(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"),
 259                                 row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
 260                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 261                 final long endTime = System.currentTimeMillis();
 262                 System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec");
 263                 return res;
 264         }
 265 }