1 package compbio.cassandra;
3 import java.util.Calendar;
5 import org.apache.log4j.Logger;
7 import com.datastax.driver.core.Cluster;
8 import com.datastax.driver.core.Configuration;
9 import com.datastax.driver.core.Host;
10 import com.datastax.driver.core.Metadata;
11 import com.datastax.driver.core.MetricsOptions;
12 import com.datastax.driver.core.PoolingOptions;
13 import com.datastax.driver.core.ProtocolOptions;
14 import com.datastax.driver.core.QueryOptions;
15 import com.datastax.driver.core.ResultSet;
16 import com.datastax.driver.core.Row;
17 import com.datastax.driver.core.SocketOptions;
19 import com.datastax.driver.core.Session;
20 import com.datastax.driver.core.policies.Policies;
22 import compbio.engine.ProteoCachePropertyHelperManager;
23 import compbio.util.PropertyHelper;
25 public class CassandraNativeConnector {
26 private static Cluster cluster;
27 private static Session session;
28 private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
29 private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
31 public static String CASSANDRA_HOSTNAME = "localhost";
33 public static Session getSession () {
38 * connect to the cluster and look whether all tables exist
40 public void Connect() {
42 String cassandrahostname = ph.getProperty("cassandra.host");
43 if (null != cassandrahostname) {
44 CASSANDRA_HOSTNAME = cassandrahostname;
47 Cluster.Builder builder = Cluster.builder();
48 builder.addContactPoint(CASSANDRA_HOSTNAME);
49 //PrintClusterConfiguration( builder.getConfiguration());
50 cluster = builder.build();
52 Metadata metadata = cluster.getMetadata();
53 System.out.printf("Connected to cluster: %s\n", metadata.getClusterName());
54 for (Host host : metadata.getAllHosts()) {
55 System.out.printf("Datatacenter: %s; Host: %s; Rack: %s\n", host.getDatacenter(), host.getAddress(), host.getRack());
57 session = cluster.connect();
59 System.out.println("Cassandra connected");
62 private void CreateMainTables() {
63 session.execute("CREATE KEYSPACE IF NOT EXISTS ProteinKeyspace WITH replication = {'class':'SimpleStrategy', 'replication_factor':3};");
64 session.execute("USE ProteinKeyspace");
66 session.execute("CREATE TABLE IF NOT EXISTS MainParameters "
67 + "(Name ascii, Value ascii, PRIMARY KEY(Name));");
69 session.execute("CREATE TABLE IF NOT EXISTS ProteinRow "
70 + "(Protein ascii, JobID ascii, Predictions map<ascii,ascii>, PRIMARY KEY(JobID));");
72 session.execute("CREATE TABLE IF NOT EXISTS ProteinLog "
73 + "(JobID ascii, DataBegin ascii, DataEnd ascii, ip ascii, FinalStatus ascii, "
74 + "ExecutionStatus ascii, Protein ascii, PRIMARY KEY(JobID));");
76 session.execute("CREATE TABLE IF NOT EXISTS ProteinData "
77 + "(jobtime bigint, JobID ascii, ExecTime int, Protein ascii, PRIMARY KEY(jobtime, JobID));");
79 session.execute("CREATE TABLE IF NOT EXISTS FailLog "
80 + "(jobtime bigint, JobID ascii, ExecTime int, ip ascii, FinalStatus ascii, PRIMARY KEY(jobtime, JobID));");
82 session.execute("CREATE TABLE IF NOT EXISTS JpredArchive "
83 + "(JobID ascii, Protein varchar, IP ascii, StartTime bigint, ExecTime int, FinalStatus ascii, ExecutionStatus ascii, alignment map<ascii,ascii>, "
84 + "predictions map<ascii,ascii>, ArchiveLink varchar, LOG varchar, PRIMARY KEY(JobID));");
86 session.execute("CREATE TABLE IF NOT EXISTS JobDateInfo "
87 + "(jobday bigint, Total bigint, TotalOK bigint, TotalStopped bigint, TotalError bigint, TotalTimeOut bigint, Program varchar, Version varchar, PRIMARY KEY(jobday));");
89 session.execute("CREATE INDEX IF NOT EXISTS ProteinSeq ON ProteinRow (protein);");
90 session.execute("CREATE INDEX IF NOT EXISTS ProteinIp ON ProteinLog (ip);");
91 // session.execute("CREATE INDEX IF NOT EXISTS JobDateStamp ON ProteinData (jobtime);");
94 public void Closing() {
97 System.out.println("Cassandra has been shut down");
101 * getting earlest date of jobs from the db
103 public static long getEarliestDateInDB() {
104 String com = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
105 System.out.println("Command: " + com);
106 ResultSet results = session.execute(com);
108 if (!results.isExhausted()) {
109 Row r = results.one();
110 return Long.parseLong(r.getString("Value"));
112 Calendar cal = Calendar.getInstance();
113 return cal.getTimeInMillis();
116 private void PrintClusterConfiguration(Configuration cc) {
117 Policies policies = cc.getPolicies();
118 SocketOptions sopt = cc.getSocketOptions();
119 ProtocolOptions propt = cc.getProtocolOptions();
120 PoolingOptions plopt = cc.getPoolingOptions();
121 MetricsOptions mopt = cc.getMetricsOptions();
122 QueryOptions qopt = cc.getQueryOptions();
123 System.out.println("Cluster configuration:");
124 System.out.println(" Policies = " + policies.toString());
125 System.out.println(" Socket Options = " + sopt.toString());
126 System.out.println(" Protocol Options: compression = " + propt.getCompression());
127 System.out.println(" Pooling Options = " + plopt.toString());
128 System.out.println(" Metrics Options = " + mopt.toString());
129 System.out.println(" Query Options = " + qopt.toString());