X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraReader.java;h=00f878ad1be07fa57361208257fa89cb7f6c65ea;hb=23ef7a6a36233ee82656f6d0f602b82f009847ed;hp=c71243b26e94458b092b83107f8f2d03edc28e8d;hpb=c4aca39f2d4a49b34e7e0b564450d100f442f3bf;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
index c71243b..00f878a 100644
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -1,184 +1,39 @@
 package compbio.cassandra;
 
-import java.util.Calendar;
-import java.util.HashMap;
-import java.util.List;
-import java.util.ArrayList;
-import java.util.Map;
-
 import org.apache.log4j.Logger;
 
-import com.datastax.driver.core.Row;
-import com.datastax.driver.core.Session;
 import com.datastax.driver.core.ResultSet;
-
-import compbio.engine.ProteoCachePropertyHelperManager;
-import compbio.util.PropertyHelper;
+import com.datastax.driver.core.Session;
 
 public class CassandraReader {
+	private static long earlestDate = 0;
 	private Session session;
 	private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
 
 	public CassandraReader() {
 		Session inis = CassandraNativeConnector.getSession();
-		setSession (inis);
+		setSession(inis);
 	}
 
 	public void setSession(Session s) {
 		assert s != null;
 		session = s;
 	}
-
-	/*
-	 * getting data from the db
-	 */
-	public List<Pair<String, String>> ReadProteinDataTable() {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT DataBegin,DataEnd FROM 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 data from the db ProteinData
-	 */
-	public Integer ReadDateTable(long queryDate) {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT jobtime, JobID FROM ProteinData WHERE jobtime = " + queryDate + ";";
-		System.out.println("Command: " + com);
-		ResultSet results = session.execute(com);
-		final long queryTime = System.currentTimeMillis();
-		System.out.println("Query time is " + (queryTime - startTime) + " msec");
-		if (results.isExhausted())
-			return 0;
-		List<Row> rows = results.all();
-		final long endTime = System.currentTimeMillis();
-		System.out.println("Processing time is " + (endTime - queryTime) + " msec");
-		return rows.size();
-	}
-
-	/*
-	 * getting whole protein sequence from the db ProteinRow
-	 */
-	public List<StructureProteinPrediction> ReadWholeSequence(String queryProtein) {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
+	
+	public ResultSet CassandraQuery(String column, String table, String condition) {
+		String com = "SELECT " + column + " FROM " + table + ";";
 		System.out.println("Command: " + com);
 		ResultSet results = session.execute(com);
-		if (results.isExhausted())
-			return null;
-		final long queryTime = System.currentTimeMillis();
-		List<Row> rows = results.all();
-		System.out.println("Query time is " + (queryTime - startTime) + " msec");
-		System.out.println(" rows analysed,  " + rows.size());
-		List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
-		int c = 0;
-		for (Row r : rows) {
-			StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap(
-					"Predictions", String.class, String.class));
-			res.add(structure);
-			++c;
-		}
-		final long endTime = System.currentTimeMillis();
-		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
-		return res;
+		return results;
 	}
-
+	
 	/*
-	 * getting part of protein sequence from the db ProteinRow
+	 * find the earliest date in the database
 	 */
-	public List<StructureProteinPrediction> ReadPartOfSequence(String queryProtein) {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT * FROM ProteinRow;";
-		System.out.println("Command: " + com);
-		ResultSet results = session.execute(com);
-		if (results.isExhausted())
-			return null;
-		final long queryTime = System.currentTimeMillis();
-		List<Row> rows = results.all();
-		System.out.println("Query time is " + (queryTime - startTime) + " msec");
-		System.out.println(" rows analysed,  " + rows.size());
-		List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
-		int c = 0;
-		for (Row r : rows) {
-			String prot = r.getString("Protein");
-			if (prot.matches("(.*)" + queryProtein + "(.*)")) {
-				StructureProteinPrediction structure = new StructureProteinPrediction(prot, r.getString("JobID"), r.getMap("Predictions",
-						String.class, String.class));
-				res.add(structure);
-				++c;
-			}
-		}
-		final long endTime = System.currentTimeMillis();
-		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
-		return res;
+	public static long earliestDate() {
+		earlestDate = CassandraNativeConnector.getEarliestDateInDB();
+		return earlestDate;
 	}
 
-	/*
-	 * getting protein sequences by counter
-	 */
-	public Map<String, Integer> ReadProteinDataByCounter() {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT Protein FROM ProteinRow;";
-		System.out.println("Command: " + com);
-		ResultSet results = session.execute(com);
-		if (results.isExhausted())
-			return null;
-		final long queryTime = System.currentTimeMillis();
-		List<Row> rows = results.all();
-		System.out.println("Query time is " + (queryTime - startTime) + " msec");
-		System.out.println(" rows analysed,  " + rows.size());
-		Map<String, Integer> res = new HashMap<String, Integer>();
-		int c = 0;
-		for (Row r : rows) {
-			String protein = r.getString("Protein");
-			if (res.containsKey(protein))
-				res.put(protein, res.get(protein) + 1);
-			else
-				res.put(protein, 1);
-		}
-		final long endTime = System.currentTimeMillis();
-		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
-		return res;
-	}
-
-	/*
-	 * getting protein sequences by counter
-	 */
-	public StructureJobLog ReadJobLog(String jobid) {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';";
-		System.out.println("Command: " + com);
-		ResultSet results = session.execute(com);
-		if (results.isExhausted())
-			return null;
-		final long queryTime = System.currentTimeMillis();
-		Row row = results.one();
-		String com1 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;";
-		System.out.println("Command: " + com1);
-		ResultSet results1 = session.execute(com1);
-		if (results1.isExhausted())
-			return null;
-		Row row1 = results1.one();
-		StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"),
-				row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
-		System.out.println("Query time is " + (queryTime - startTime) + " msec");
-		final long endTime = System.currentTimeMillis();
-		System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec");
-		return res;
-	}
+	
 }