X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraReader.java;h=00f878ad1be07fa57361208257fa89cb7f6c65ea;hb=429ba39df7f7dbf7c7f940bafd5126cfab9fca61;hp=00a9f27f265667b3eaea9de2331f345111cea3f2;hpb=bf5e83e2959a3b88963cb9a8da68fc50ce4329af;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
index 00a9f27..00f878a 100644
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -1,19 +1,12 @@
 package compbio.cassandra;
 
-import java.util.Date;
-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.JobStatus;
+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);
 
@@ -26,258 +19,21 @@ public class CassandraReader {
 		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;";
+	
+	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);
-		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;
+		return results;
 	}
-
+	
 	/*
-	 * getting data from the db
+	 * find the earliest date in the database
 	 */
-	public DateBean ReadProteinData(long day, String date) {
-		String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";";
-		System.out.println("Command: " + com);
-		ResultSet results = session.execute(com);
-		if (results.isExhausted())
-			return null;
-		List<Row> rows = results.all();
-		DateBean res = new DateBean(date);
-		for (Row r : rows) {
-			res.setJobidAndSeq(r.getString("JobID"), r.getString("Protein"));
-		}
-		return res;
-	}
-
-	/**
-	 * getting data from the db
-	 */
-	public DateBean ReadFailedJobs(long day, String date, JobStatus status) {
-		// FailLog (jobtime, JobID, ExecTime, ip, FinalStatus)
-		String com = "SELECT JobID FROM FailLog WHERE jobtime = " + day + " and FinalStatus = '" + status.name() + "';";
-		ResultSet results = session.execute(com);
-		if (results.isExhausted())
-			return null;
-		List<Row> rows = results.all();
-		DateBean res = new DateBean(date);
-		for (Row r : rows) {
-			String jobid = r.getString("JobID");
-			String com1 = "SELECT Protein FROM ProteinLog WHERE JobID = '" + jobid + "';";
-			System.out.println("Command: " + com1);
-			ResultSet results2 = session.execute(com1);
-			List<Row> jrows = results2.all();
-			if (1 == jrows.size()) {
-				String protein = jrows.get(0).getString("Protein");
-				res.setJobidAndSeq(jobid, protein);
-			}
-		}
-		return res;
+	public static long earliestDate() {
+		earlestDate = CassandraNativeConnector.getEarliestDateInDB();
+		return earlestDate;
 	}
 
-	/*
-	 * getting data from the db JobDateInfo
-	 */
-	public Total ReadDateTable(long queryDate) {
-		ResultSet results = session.execute("SELECT * FROM JobDateInfo WHERE jobday = " + queryDate + ";");
-		if (results.isExhausted())
-			return null;
-		Row therow = results.one();
-		Total res = new Total(therow.getLong("Total"), therow.getLong("TotalOK"), therow.getLong("TotalStopped"),
-				therow.getLong("TotalError"), therow.getLong("TotalTimeOut"));
-		if (!results.isExhausted()) {
-			Date date = new Date(queryDate);
-			log.warn("CassandraReader.ReadDateTable: date row for " + date.toString() + " (" + queryDate + ") duplicated ");
-		}
-		return res;
-	}
-
-	/*
-	 * getting whole protein sequence from the db ProteinRow
-	 */
-	public List<ProteinBean> ReadWholeSequence(String queryProtein) {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
-		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("first size : " + rows.size());
-		System.out.println("Query time is " + (queryTime - startTime) + " msec");
-		System.out.println(" rows analysed,  " + rows.size());
-		List<ProteinBean> res = new ArrayList<ProteinBean>();
-		ProteinBean structure = new ProteinBean(queryProtein, rows.get(0).getMap("Predictions", String.class, String.class));
-		System.out.println("second size : " + rows.size());
-		int c = 0;
-		for (Row r : rows) {
-			structure.setJobid(r.getString("JobID"));
-			++c;
-		}
-		res.add(structure);
-		final long endTime = System.currentTimeMillis();
-		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
-		return res;
-	}
-
-	/*
-	 * getting jobs by ip
-	 */
-	public Map<String, String[]> ReadIpWithJobs(String ip) {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT JobID, Protein, FinalStatus, DataBegin FROM ProteinLog WHERE ip = '" + ip + "';";
-		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();
-		Map<String, String[]> res = new HashMap<String, String[]>();
-		System.out.println("Query time is " + (queryTime - startTime) + " msec");
-		System.out.println(" rows analysed,  " + rows.size());
-		int c = 0;
-		for (Row r : rows) {
-			if (r.getString("FinalStatus").equals("OK")) {
-				String date = r.getString("DataBegin");
-				res.put(r.getString("JobID"), new String[] { date.substring(0, date.indexOf(":")), r.getString("Protein") });
-				++c;
-			}
-		}
-		final long endTime = System.currentTimeMillis();
-		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
-		return res;
-	}
-
-	/*
-	 * getting part of protein sequence from the db ProteinRow
-	 */
-	public List<ProteinBean> 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<ProteinBean> res = new ArrayList<ProteinBean>();
-		int c = 0;
-		for (Row r : rows) {
-			String prot = r.getString("Protein");
-			if (prot.matches("(.*)" + queryProtein + "(.*)")) {
-				ProteinBean structure = new ProteinBean(prot, r.getMap("Predictions", String.class, String.class));
-				structure.setJobid(r.getString("JobID"));
-				res.add(structure);
-				++c;
-			}
-		}
-		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 Map<String, Integer> ReadProteinSequenceByCounter() {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT Protein, JobID 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");
-			String id = r.getString("JobID");
-			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 ip by counter
-	 */
-	public Map<String, Integer> ReadIpByCounter() {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT JobID, ip FROM ProteinLog;";
-		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 ip = r.getString("ip");
-			String id = r.getString("JobID");
-			if (res.containsKey(ip))
-				res.put(ip, res.get(ip) + 1);
-			else
-				res.put(ip, 1);
-		}
-		final long endTime = System.currentTimeMillis();
-		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
-		return res;
-	}
-
-	/*
-	 * getting log info for jobid
-	 */
-	public JobBean 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();
-		JobBean res = new JobBean(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;
-	}
+	
 }