--- /dev/null
+package compbio.cassandra;
+
+import java.io.IOException;
+import java.util.List;
+
+import com.datastax.driver.core.Cluster;
+import com.datastax.driver.core.Host;
+import com.datastax.driver.core.Metadata;
+import com.datastax.driver.core.Session;
+import com.datastax.driver.core.ResultSet;
+
+public class CassandraNativeConnector {
+ private static Cluster cluster;
+ private static Session session;
+
+ /*
+ * private static Keyspace ksp; private static Mutator<Long> mutatorLong;
+ * private static Mutator<String> mutatorString; private static
+ * Mutator<String> mutatorLog; StringSerializer ss = StringSerializer.get();
+ * LongSerializer ls = LongSerializer.get();
+ */
+
+ /*
+ * connect to the cluster and look weather the dababase has any data inside
+ */
+ public void Connect() {
+ // local cassandra cluster
+ cluster = Cluster.builder().addContactPoint("localhost").build();
+ // distributed cassandra cluster
+ /* cluster = Cluster.builder().addContactPoint("10.0.115.190").build(); */
+ Metadata metadata = cluster.getMetadata();
+ System.out.printf("Connected to cluster: %s\n", metadata.getClusterName());
+ for (Host host : metadata.getAllHosts()) {
+ System.out.printf("Datatacenter: %s; Host: %s; Rack: %s\n", host.getDatacenter(), host.getAddress(), host.getRack());
+ }
+
+ session = cluster.connect();
+ session.execute("CREATE KEYSPACE IF NOT EXISTS ProteinKeyspace WITH replication = {'class':'SimpleStrategy', 'replication_factor':3};");
+ session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.ProteinRow (Protein ascii PRIMARY KEY, Predictions map<ascii,ascii>);");
+ session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.ProteinLog "
+ + "(JobID ascii PRIMARY KEY, DataBegin ascii, DataEnd ascii, ip ascii, FinalStatus ascii, ExecutionStatus ascii, Protein ascii);");
+ session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.ProteinData (jobtime bigint PRIMARY KEY, JobID ascii, Protein ascii);");
+
+ System.out.println("Cassandra connected");
+ }
+
+ /*
+ * parsing data source and filling the database
+ */
+ public void Parsing() throws IOException {
+ if (false) {
+ // if (source.equals("http")) {
+ // get data from real Jpred production server
+ System.out.println("Parsing web data source......");
+ String datasrc = "http://www.compbio.dundee.ac.uk/www-jpred/results/usage-new/alljobs.dat";
+ String prefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
+ JpredParserHTTP parser = new JpredParserHTTP(prefix);
+ parser.Parsing(datasrc, 4);
+ }
+ if (true) {
+ // if (source.equals("file")) {
+ // get irtifical data generated for the DB stress tests
+ System.out.println("Parsing local file data source......");
+ String datasrc = "/home/asherstnev/Projects/Java.projects/proteocache/data_stress_test/data.dat";
+ String prefix = "/home/asherstnev/Projects/Java.projects/proteocache/data_stress_test/Jpreddata";
+ JpredParserLocalFile parser = new JpredParserLocalFile(prefix);
+ parser.Parsing(datasrc, 190);
+ }
+ }
+
+ public void Closing() {
+ cluster.shutdown();
+ System.out.println("Cassandra has been shut down");
+ }
+
+ /*
+ * check whether the job id exists in the DB
+ */
+ public boolean CheckID(String jobid) {
+ String com = "SELECT * FROM ProteinKeyspace.ProteinData WHERE jobid = '" + jobid + "';";
+ System.out.println(com);
+ ResultSet results = session.execute(com);
+ if (null != results) {
+ return true;
+ }
+ return false;
+ }
+
+ /*
+ * prepare data for insertion into the db
+ */
+ public void InsertData(long jobtime, String startdate, String enddate, String ip, String jobid, String statusEx, String statusFinal,
+ String protein, List<FastaSequence> predictions) {
+
+ String check1 = "SELECT count(*) FROM ProteinKeyspace.ProteinLog WHERE JobID = '" + jobid + "';";
+ //System.out.println(check1);
+ ResultSet results1 = session.execute(check1);
+ if (!results1.isExhausted()) {
+ String com1 = "INSERT INTO ProteinKeyspace.ProteinLog "
+ + "(JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein)" + " VALUES ('" + jobid + "','" + ip + "','"
+ + startdate + "','" + enddate + "','" + statusFinal + "','" + statusEx + "','" + protein + "');";
+ // System.out.println(com1);
+ session.execute(com1);
+
+ String com2 = "INSERT INTO ProteinKeyspace.ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + jobtime + ",'" + jobid
+ + "','" + protein + "');";
+ // System.out.println(com2);
+ // session.execute(com2);
+
+ String allpredictions = "";
+ for (FastaSequence pred : predictions) {
+ String predictionname = pred.getId();
+ String prediction = pred.getSequence().replaceAll("\n", "");
+ allpredictions += "'" + predictionname + "':'" + prediction + "',";
+ }
+ String final_prediction = "";
+ if (null != allpredictions) {
+ final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
+ }
+
+ String check2 = "SELECT count(*) FROM ProteinKeyspace.ProteinRow WHERE Protein = '" + protein + "';";
+ //System.out.println(check1);
+ ResultSet results2 = session.execute(check2);
+
+ if (results1.isExhausted()) {
+ String com3 = "INSERT INTO ProteinKeyspace.ProteinRow " + "(Protein, " + jobid + ")" + " VALUES ('" + protein + "'," + "{"
+ + final_prediction + "}" + ");";
+ System.out.println(com3);
+ session.execute(com3);
+ } else {
+ String com4 = "ALTER TABLE ProteinKeyspace.ProteinRow ADD " + jobid + ");";
+ System.out.println(com4);
+ session.execute(com4);
+ String com3 = "INSERT INTO ProteinKeyspace.ProteinRow " + "(" + jobid + ")" + " VALUES ({" + final_prediction + "}" + ")"
+ + " WHERE Protein = '" + protein + "';";
+ System.out.println(com3);
+ session.execute(com3);
+ }
+ }
+ }
+
+}
git://source.jalview.org / proteocache.git / blobdiff