datadb/compbio/cassandra/CassandraNativeConnector.java

   1 package compbio.cassandra;
   2
   3 import java.util.Calendar;
   4
   5 import org.apache.log4j.Logger;
   6 import org.springframework.dao.DataIntegrityViolationException;
   7
   8 import com.datastax.driver.core.Cluster;
   9 import com.datastax.driver.core.Configuration;
  10 import com.datastax.driver.core.Host;
  11 import com.datastax.driver.core.Metadata;
  12 import com.datastax.driver.core.MetricsOptions;
  13 import com.datastax.driver.core.PoolingOptions;
  14 import com.datastax.driver.core.ProtocolOptions;
  15 import com.datastax.driver.core.QueryOptions;
  16 import com.datastax.driver.core.ResultSet;
  17 import com.datastax.driver.core.Row;
  18 import com.datastax.driver.core.SocketOptions;
  19
  20 import com.datastax.driver.core.Session;
  21 import com.datastax.driver.core.exceptions.QueryExecutionException;
  22 import com.datastax.driver.core.exceptions.QueryValidationException;
  23 import com.datastax.driver.core.policies.Policies;
  24
  25 import compbio.engine.ProteoCachePropertyHelperManager;
  26 import compbio.util.PropertyHelper;
  27
  28 public class CassandraNativeConnector {
  29         private static Cluster cluster;
  30         private static Session session;
  31         private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
  32         private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
  33
  34         public static String CASSANDRA_HOSTNAME = "localhost";
  35
  36         public static Session getSession() {
  37                 return session;
  38         }
  39
  40         /*
  41          * connect to the cluster and look whether all tables exist
  42          */
  43         public void Connect() {
  44
  45                 String cassandrahostname = ph.getProperty("cassandra.host");
  46                 if (null != cassandrahostname) {
  47                         CASSANDRA_HOSTNAME = cassandrahostname;
  48                 }
  49
  50                 Cluster.Builder builder = Cluster.builder();
  51                 builder.addContactPoint(CASSANDRA_HOSTNAME);
  52                 // PrintClusterConfiguration( builder.getConfiguration());
  53                 cluster = builder.build();
  54
  55                 Metadata metadata = cluster.getMetadata();
  56                 System.out.printf("Connected to cluster: %s\n", metadata.getClusterName());
  57                 for (Host host : metadata.getAllHosts()) {
  58                         System.out.printf("Datatacenter: %s; Host: %s; Rack: %s\n", host.getDatacenter(), host.getAddress(), host.getRack());
  59                 }
  60                 session = cluster.connect();
  61                 CreateMainTables();
  62                 System.out.println("Cassandra connected");
  63         }
  64
  65         private void CreateMainTables() {
  66                 session.execute("CREATE KEYSPACE IF NOT EXISTS ProteinKeyspace WITH replication = {'class':'SimpleStrategy', 'replication_factor':3};");
  67                 session.execute("USE ProteinKeyspace");
  68
  69                 session.execute("CREATE TABLE IF NOT EXISTS MainParameters " + "(Name ascii, Value ascii, PRIMARY KEY(Name));");
  70
  71                 session.execute("CREATE TABLE IF NOT EXISTS ProteinRow "
  72                                 + "(Protein ascii, JobID ascii, Predictions map<ascii,ascii>, PRIMARY KEY(JobID));");
  73
  74                 session.execute("CREATE TABLE IF NOT EXISTS ProteinLog "
  75                                 + "(JobID ascii, DataBegin ascii, DataEnd ascii, ip ascii, FinalStatus ascii, "
  76                                 + "ExecutionStatus ascii, Protein ascii, ProgramName ascii, ProgramVersion ascii, PRIMARY KEY(JobID));");
  77
  78                 session.execute("CREATE TABLE IF NOT EXISTS ProteinData "
  79                                 + "(jobtime bigint, JobID ascii, ExecTime int, Protein ascii, PRIMARY KEY(jobtime, JobID));");
  80
  81                 session.execute("CREATE TABLE IF NOT EXISTS FailLog "
  82                                 + "(jobtime bigint, JobID ascii, ExecTime int, ip ascii, FinalStatus ascii, PRIMARY KEY(jobtime, JobID));");
  83
  84                 session.execute("CREATE TABLE IF NOT EXISTS JpredArchive "
  85                                 + "(JobID ascii, Protein varchar, IP ascii, StartTime bigint, ExecTime int, FinalStatus ascii, ExecutionStatus ascii, alignment map<ascii,ascii>, "
  86                                 + "predictions map<ascii,ascii>, ArchiveLink varchar, LOG varchar, ProgramName ascii, ProgramVersion ascii, PRIMARY KEY(JobID));");
  87
  88                 session.execute("CREATE TABLE IF NOT EXISTS JobDateInfo "
  89                                 + "(jobday bigint, Total bigint,  TotalOK bigint, TotalStopped bigint, TotalError bigint, TotalTimeOut bigint, Program varchar, Version varchar, PRIMARY KEY(jobday));");
  90
  91                 String com = "CREATE TABLE IF NOT EXISTS Users "
  92                                 + "(name varchar, id bigint, email varchar, password varchar, organisation varchar, position varchar, signedtolist boolean, registrationdate bigint, PRIMARY KEY(id));";
  93
  94                 // session.execute("ALTER TABLE ProteinLog ADD ProgramName ascii;");
  95                 // session.execute("ALTER TABLE ProteinLog ADD ProgramVersion ascii;");
  96                 // session.execute("ALTER TABLE JpredArchive ADD ProgramName ascii;");
  97                 // session.execute("ALTER TABLE JpredArchive ADD ProgramVersion ascii;");
  98
  99                 session.execute("CREATE INDEX IF NOT EXISTS ProteinSeq ON ProteinRow (protein);");
 100                 session.execute("CREATE INDEX IF NOT EXISTS ProteinIp ON ProteinLog (ip);");
 101                 session.execute("CREATE INDEX IF NOT EXISTS ON ProteinLog (ExecutionStatus);");
 102                 session.execute("CREATE INDEX IF NOT EXISTS ON FailLog (FinalStatus);");
 103                 session.execute("CREATE INDEX IF NOT EXISTS ON Users (email);");
 104                 // session.execute("CREATE INDEX IF NOT EXISTS JobDateStamp ON ProteinData (jobtime);");
 105         }
 106
 107         public void Closing() {
 108                 session.shutdown();
 109                 cluster.shutdown();
 110                 System.out.println("Cassandra has been shut down");
 111         }
 112
 113         /*
 114          * getting earlest date of jobs from the db
 115          */
 116         public static long getEarliestDateInDB() {
 117                 String com = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
 118                 System.out.println("Command: " + com);
 119                 ResultSet results = session.execute(com);
 120
 121                 if (!results.isExhausted()) {
 122                         Row r = results.one();
 123                         return Long.parseLong(r.getString("Value"));
 124                 }
 125                 Calendar cal = Calendar.getInstance();
 126                 return cal.getTimeInMillis();
 127         }
 128
 129         private void PrintClusterConfiguration(Configuration cc) {
 130                 Policies policies = cc.getPolicies();
 131                 SocketOptions sopt = cc.getSocketOptions();
 132                 ProtocolOptions propt = cc.getProtocolOptions();
 133                 PoolingOptions plopt = cc.getPoolingOptions();
 134                 MetricsOptions mopt = cc.getMetricsOptions();
 135                 QueryOptions qopt = cc.getQueryOptions();
 136                 System.out.println("Cluster configuration:");
 137                 System.out.println("   Policies = " + policies.toString());
 138                 System.out.println("   Socket Options = " + sopt.toString());
 139                 System.out.println("   Protocol Options: compression = " + propt.getCompression());
 140                 System.out.println("   Pooling Options = " + plopt.toString());
 141                 System.out.println("   Metrics Options = " + mopt.toString());
 142                 System.out.println("   Query Options = " + qopt.toString());
 143         }
 144
 145 }