X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraNativeConnector.java;h=be90b059a69bf6d2256c7b9e984fdba177ca6cf2;hb=507e4c2efbc7db28b52dd00a9c35247a11dcc0b1;hp=1fb01fc3fd1b09afb25d6b37a41b26358de33800;hpb=150023cca8f1a5215e84889dc284f00963905c34;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java
index 1fb01fc..be90b05 100644
--- a/datadb/compbio/cassandra/CassandraNativeConnector.java
+++ b/datadb/compbio/cassandra/CassandraNativeConnector.java
@@ -1,25 +1,21 @@
 package compbio.cassandra;
 
 import java.io.IOException;
+import java.util.Calendar;
+import java.util.HashMap;
 import java.util.List;
+import java.util.ArrayList;
 
 import com.datastax.driver.core.Cluster;
 import com.datastax.driver.core.Host;
 import com.datastax.driver.core.Metadata;
+import com.datastax.driver.core.Row;
 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
 	 */
@@ -41,8 +37,8 @@ public class CassandraNativeConnector {
 				+ "(JobID ascii, DataBegin ascii, DataEnd ascii, ip ascii, FinalStatus ascii, ExecutionStatus ascii, Protein ascii, PRIMARY KEY(JobID));");
 		session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.ProteinData (jobtime bigint, JobID ascii, Protein ascii, PRIMARY KEY(JobID));");
 
-		session.execute("CREATE INDEX ProteinSeq ON ProteinKeyspace.ProteinRow (protein);");
-		session.execute("CREATE INDEX JobDateStamp ON ProteinKeyspace.ProteinData (jobtime);");
+		session.execute("CREATE INDEX IF NOT EXISTS ProteinSeq ON ProteinKeyspace.ProteinRow (protein);");
+		session.execute("CREATE INDEX IF NOT EXISTS JobDateStamp ON ProteinKeyspace.ProteinData (jobtime);");
 
 		System.out.println("Cassandra connected");
 	}
@@ -51,7 +47,7 @@ public class CassandraNativeConnector {
 	 * parsing data source and filling the database
 	 */
 	public void Parsing() throws IOException {
-		if (false) {
+		if (true) {
 			// if (source.equals("http")) {
 			// get data from real Jpred production server
 			System.out.println("Parsing web data source......");
@@ -60,7 +56,7 @@ public class CassandraNativeConnector {
 			JpredParserHTTP parser = new JpredParserHTTP(prefix);
 			parser.Parsing(datasrc, 4);
 		}
-		if (true) {
+		if (false) {
 			// if (source.equals("file")) {
 			// get irtifical data generated for the DB stress tests
 			System.out.println("Parsing local file data source......");
@@ -72,29 +68,27 @@ public class CassandraNativeConnector {
 	}
 
 	public void Closing() {
+		session.shutdown();
 		cluster.shutdown();
 		System.out.println("Cassandra has been shut down");
 	}
 
 	/*
-	 * prepare data for insertion into the db
+	 * inserting data 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 * 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 = "";
@@ -109,15 +103,64 @@ public class CassandraNativeConnector {
 			}
 
 			String check2 = "SELECT * FROM ProteinKeyspace.ProteinRow WHERE JobID = '" + jobid + "';";
-			//System.out.println(check2);
 			ResultSet results2 = session.execute(check2);
 			if (results2.isExhausted()) {
 				String com3 = "INSERT INTO ProteinKeyspace.ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" 
 			+ protein + "','" + jobid + "',{" + final_prediction + "});";
-				//System.out.println(com3);
 				session.execute(com3);
 			}
 		}
 	}
 
+	/*
+	 * getting data from the db
+	 */
+	public List<Pair<String, String>> ReadProteinDataTable() {
+		final long startTime = System.currentTimeMillis();
+		String com = "SELECT DataBegin,DataEnd FROM ProteinKeyspace.ProteinLog;";
+		System.out.println("Command: " + com);
+		ResultSet results = session.execute(com);
+		final long queryTime = System.currentTimeMillis();
+		List<Row> rows = results.all();
+		System.out.println ("Query time is " + (queryTime - startTime) + " msec");
+
+		List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
+		int c = 0;
+		for (Row r : rows) {
+			Pair<String, String> pair = new Pair<String, String>(r.getString("DataBegin"),r.getString("DataEnd"));
+			res.add(pair);
+			++c;
+		}
+		final long endTime = System.currentTimeMillis();
+		System.out.println (c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+
+	/*
+	 * getting earlest date of jobs from the db
+	 */
+	public long getEarliestDateInDB() {
+		final long startTime = System.currentTimeMillis();
+		String com = "SELECT jobtime FROM ProteinKeyspace.ProteinData;";
+		System.out.println("Command: " + com);
+		ResultSet results = session.execute(com);
+		final long queryTime = System.currentTimeMillis();
+		System.out.println ("Query time is " + (queryTime - startTime) + " msec");
+
+		Calendar cal = Calendar.getInstance();
+		long res = cal.getTimeInMillis();
+		int c = 0;
+		while (!results.isExhausted()) {
+			Row r = results.one();
+			long d1 = r.getLong("jobtime");
+			if (res > d1) {
+				res = d1;
+			}
+			++c;
+		}
+		final long endTime = System.currentTimeMillis();
+		System.out.println (c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+	
 }