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<AnnotatedProteinSequenceBean> 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("Query time is " + (queryTime - startTime) + " msec");
 111                 System.out.println(" rows analysed,  " + rows.size());
 112                 List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
 113                 int c = 0;
 114                 for (Row r : rows) {
 115                         AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(queryProtein, r.getString("JobID"), r.getMap(
 116                                         "Predictions", String.class, String.class));
 117                         res.add(structure);
 118                         ++c;
 119                 }
 120                 final long endTime = System.currentTimeMillis();
 121                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 122                 return res;
 123         }
 124
 125
 126         /*
 127          * getting jobs by ip
 128          */
 129         public List<Pair<String, String>> ReadIpWithJobs(String ip) {
 130                 final long startTime = System.currentTimeMillis();
 131                 String com = "SELECT JobID, Protein, FinalStatus FROM ProteinLog WHERE ip = '" + ip + "';";
 132                 System.out.println("Command: " + com);
 133                 ResultSet results = session.execute(com);
 134                 if (results.isExhausted())
 135                         return null;
 136                 final long queryTime = System.currentTimeMillis();
 137                 List<Row> rows = results.all();
 138                 List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
 139                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 140                 System.out.println(" rows analysed,  " + rows.size());
 141                 int c = 0;
 142                 for (Row r : rows) {
 143                         if (r.getString("FinalStatus").equals("OK")) {
 144                                 Pair<String, String> pair = new Pair<String, String>(r.getString("JobID"), r.getString("Protein"));
 145                                 System.out.println(pair.getElement0());
 146                                 System.out.println(pair.getElement1());
 147                                 res.add(pair);
 148                                 ++c;
 149                         }
 150                 }
 151                 final long endTime = System.currentTimeMillis();
 152                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 153                 return res;
 154         }
 155
 156         /*
 157          * getting part of protein sequence from the db ProteinRow
 158          */
 159         public List<AnnotatedProteinSequenceBean> ReadPartOfSequence(String queryProtein) {
 160                 final long startTime = System.currentTimeMillis();
 161                 String com = "SELECT * FROM ProteinRow;";
 162                 System.out.println("Command: " + com);
 163                 ResultSet results = session.execute(com);
 164                 if (results.isExhausted())
 165                         return null;
 166                 final long queryTime = System.currentTimeMillis();
 167                 List<Row> rows = results.all();
 168                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 169                 System.out.println(" rows analysed,  " + rows.size());
 170                 List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
 171                 int c = 0;
 172                 for (Row r : rows) {
 173                         String prot = r.getString("Protein");
 174                         if (prot.matches("(.*)" + queryProtein + "(.*)")) {
 175                                 AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(prot, r.getString("JobID"), r.getMap("Predictions",
 176                                                 String.class, String.class));
 177                                 res.add(structure);
 178                                 ++c;
 179                         }
 180                 }
 181                 final long endTime = System.currentTimeMillis();
 182                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 183                 return res;
 184         }
 185
 186         /*
 187          * getting protein sequences by counter
 188          */
 189         public Map<String, Integer> ReadProteinSequenceByCounter() {
 190                 final long startTime = System.currentTimeMillis();
 191                 String com = "SELECT Protein, JobID FROM ProteinRow;";
 192                 System.out.println("Command: " + com);
 193                 ResultSet results = session.execute(com);
 194                 if (results.isExhausted())
 195                         return null;
 196                 final long queryTime = System.currentTimeMillis();
 197                 List<Row> rows = results.all();
 198                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 199                 System.out.println(" rows analysed,  " + rows.size());
 200                 Map<String, Integer> res = new HashMap<String, Integer>();
 201                 int c = 0;
 202                 for (Row r : rows) {
 203                         String protein = r.getString("Protein");
 204                         String id = r.getString("JobID");
 205                         if (res.containsKey(protein))
 206                                 res.put(protein, res.get(protein) + 1);
 207                         else
 208                                 res.put(protein, 1);
 209                 }
 210                 final long endTime = System.currentTimeMillis();
 211                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 212                 return res;
 213         }
 214
 215         /*
 216          * getting ip by counter
 217          */
 218         public Map<String, Integer> ReadIpByCounter() {
 219                 final long startTime = System.currentTimeMillis();
 220                 String com = "SELECT JobID, ip FROM ProteinLog;";
 221                 System.out.println("Command: " + com);
 222                 ResultSet results = session.execute(com);
 223                 if (results.isExhausted())
 224                         return null;
 225                 final long queryTime = System.currentTimeMillis();
 226                 List<Row> rows = results.all();
 227                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 228                 System.out.println(" rows analysed,  " + rows.size());
 229                 Map<String, Integer> res = new HashMap<String, Integer>();
 230                 int c = 0;
 231                 for (Row r : rows) {
 232                         String protein = r.getString("ip");
 233                         String id = r.getString("JobID");
 234                         if (res.containsKey(protein))
 235                                 res.put(protein, res.get(protein) + 1);
 236                         else
 237                                 res.put(protein, 1);
 238                 }
 239                 final long endTime = System.currentTimeMillis();
 240                 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
 241                 return res;
 242         }
 243
 244         /*
 245          * getting log info for jobid
 246          */
 247         public StructureJobLog ReadJobLog(String jobid) {
 248                 final long startTime = System.currentTimeMillis();
 249                 String com = "SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';";
 250                 System.out.println("Command: " + com);
 251                 ResultSet results = session.execute(com);
 252                 if (results.isExhausted())
 253                         return null;
 254                 final long queryTime = System.currentTimeMillis();
 255                 Row row = results.one();
 256                 String com1 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;";
 257                 System.out.println("Command: " + com1);
 258                 ResultSet results1 = session.execute(com1);
 259                 if (results1.isExhausted())
 260                         return null;
 261                 Row row1 = results1.one();
 262                 StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"),
 263                                 row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
 264                 System.out.println("Query time is " + (queryTime - startTime) + " msec");
 265                 final long endTime = System.currentTimeMillis();
 266                 System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec");
 267                 return res;
 268         }
 269 }