From 6097c3a4b7510ced14696c7ec98981b0cd0cea01 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 8 Nov 2013 12:11:41 +0000
Subject: [PATCH] Still not-working system for reading cassandra

---
 datadb/compbio/cassandra/CassandraReader.java      |   16 +++
 .../readers/CassandraReaderExecutionTime.java      |  104 ++++++++++++++++++++
 2 files changed, 120 insertions(+)
 create mode 100644 datadb/compbio/cassandra/CassandraReader.java
 create mode 100644 datadb/compbio/cassandra/readers/CassandraReaderExecutionTime.java

diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
new file mode 100644
index 0000000..d2d2e1b
--- /dev/null
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -0,0 +1,16 @@
+package compbio.cassandra;
+
+import com.datastax.driver.core.Session;
+
+public interface CassandraReader {
+
+	/*
+	 * Defines a source file with metainformation of Jpred Jobs
+	 **/
+	void setSession (Session s);
+	
+	/*
+	 * Makes real parsing of the source file
+	 **/
+	/*void getResults();*/
+}
diff --git a/datadb/compbio/cassandra/readers/CassandraReaderExecutionTime.java b/datadb/compbio/cassandra/readers/CassandraReaderExecutionTime.java
new file mode 100644
index 0000000..8648aeb
--- /dev/null
+++ b/datadb/compbio/cassandra/readers/CassandraReaderExecutionTime.java
@@ -0,0 +1,104 @@
+package compbio.cassandra.readers;
+
+
+import java.util.Calendar;
+import java.util.List;
+import java.util.ArrayList;
+
+import org.apache.log4j.Logger;
+
+import com.datastax.driver.core.Row;
+import com.datastax.driver.core.Session;
+import com.datastax.driver.core.ResultSet;
+import com.datastax.driver.core.PreparedStatement;
+import com.datastax.driver.core.BoundStatement;
+
+import compbio.cassandra.CassandraReader;
+import compbio.cassandra.Pair;
+import compbio.engine.ProteoCachePropertyHelperManager;
+import compbio.util.PropertyHelper;
+
+public class CassandraReaderExecutionTime implements CassandraReader {
+	private Session session;
+
+	public static String CASSANDRA_HOSTNAME = "localhost";
+	public static boolean READ_WEB_JPRED = false;
+	public static boolean READ_LOCALFILE_JPRED = false;
+
+	public void setSession(Session s) {
+		assert s != null;
+		session = s;
+	}
+
+	private void setConditions() {
+
+	}
+
+	public boolean JobisNotInsterted(String jobid) {
+		ResultSet results1 = session.execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
+		if (results1.isExhausted()) {
+			return true;
+		}
+		return false;
+	}
+
+	public boolean JobisNotArchived(String jobid) {
+		ResultSet results1 = session.execute("SELECT * FROM JpredArchive WHERE JobID = '" + jobid + "';");
+		if (results1.isExhausted()) {
+			return true;
+		}
+		return false;
+	}
+
+	/*
+	 * 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;
+	}
+
+}
-- 
1.7.10.2