X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=datadb%2Fcompbio%2Fcassandra%2FCassandraReader.java;h=69f7c088f639a4029552f3ef16499bfe348bfe9b;hb=574c70838a48dd41cfadda11a493b04f02de5604;hp=cb2492e1c33aa32006255eb02efaa50ba6a380fc;hpb=4458e44cf92e699159ee1257b1bea6300a9abebe;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
index cb2492e..69f7c08 100644
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -53,7 +53,7 @@ public class CassandraReader {
 	/*
 	 * getting data from the db
 	 */
-	public List<Pair<String, String>> ReadProteinData(long day) {
+	public DateBean ReadProteinData(long day, String date) {
 		final long startTime = System.currentTimeMillis();
 		String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";";
 		System.out.println("Command: " + com);
@@ -63,11 +63,10 @@ public class CassandraReader {
 		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>>();
+		DateBean res = new DateBean(date);
 		int c = 0;
 		for (Row r : rows) {
-			Pair<String, String> pair = new Pair<String, String>(r.getString("JobID"), r.getString("Protein"));
-			res.add(pair);
+			res.setJobidAndSeq(r.getString("JobID"), r.getString("Protein"));
 			++c;
 		}
 		final long endTime = System.currentTimeMillis();
@@ -77,17 +76,13 @@ public class CassandraReader {
 	/*
 	 * getting data from the db JobDateInfo
 	 */
-	public List<Long> ReadDateTable(long queryDate) {
+	public Total ReadDateTable(long queryDate) {
 		ResultSet results = session.execute("SELECT * FROM JobDateInfo WHERE jobday = " + queryDate + ";");
 		if (results.isExhausted())
 			return null;
 		Row therow = results.one();
-		List<Long> res = new ArrayList<Long>();
-		res.add(therow.getLong("Total"));
-		res.add(therow.getLong("TotalOK"));
-		res.add(therow.getLong("TotalStopped"));
-		res.add(therow.getLong("TotalError"));
-		res.add(therow.getLong("TotalTimeOut"));
+		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 ");
@@ -98,7 +93,7 @@ public class CassandraReader {
 	/*
 	 * getting whole protein sequence from the db ProteinRow
 	 */
-	public List<AnnotatedProteinSequenceBean> ReadWholeSequence(String queryProtein) {
+	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);
@@ -107,16 +102,48 @@ public class CassandraReader {
 			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<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
+		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) {
-			AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(queryProtein, r.getString("JobID"), r.getMap(
-					"Predictions", String.class, String.class));
-			res.add(structure);
+			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;
@@ -125,7 +152,7 @@ public class CassandraReader {
 	/*
 	 * getting part of protein sequence from the db ProteinRow
 	 */
-	public List<AnnotatedProteinSequenceBean> ReadPartOfSequence(String queryProtein) {
+	public List<ProteinBean> ReadPartOfSequence(String queryProtein) {
 		final long startTime = System.currentTimeMillis();
 		String com = "SELECT * FROM ProteinRow;";
 		System.out.println("Command: " + com);
@@ -136,13 +163,13 @@ public class CassandraReader {
 		List<Row> rows = results.all();
 		System.out.println("Query time is " + (queryTime - startTime) + " msec");
 		System.out.println(" rows analysed,  " + rows.size());
-		List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
+		List<ProteinBean> res = new ArrayList<ProteinBean>();
 		int c = 0;
 		for (Row r : rows) {
 			String prot = r.getString("Protein");
 			if (prot.matches("(.*)" + queryProtein + "(.*)")) {
-				AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(prot, r.getString("JobID"), r.getMap("Predictions",
-						String.class, String.class));
+				ProteinBean structure = new ProteinBean(prot,  r.getMap("Predictions", String.class, String.class));
+				structure.setJobid(r.getString("JobID"));
 				res.add(structure);
 				++c;
 			}
@@ -182,9 +209,38 @@ public class CassandraReader {
 	}
 
 	/*
+	 * 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 StructureJobLog ReadJobLog(String jobid) {
+	public JobBean ReadJobLog(String jobid) {
 		final long startTime = System.currentTimeMillis();
 		String com = "SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';";
 		System.out.println("Command: " + com);
@@ -199,7 +255,7 @@ public class CassandraReader {
 		if (results1.isExhausted())
 			return null;
 		Row row1 = results1.one();
-		StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"),
+		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();