X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraNativeConnector.java;h=55935949aec565ec07da86022ed01afc374ca750;hb=5d7a3018a6bee66bac0e3a915198a9886a091880;hp=b03845700fd4c11819437bc3a712ad3c8abc21e2;hpb=0ff63241ef7b33b89eb72fde7e0d1ab9c9eb32a5;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java
index b038457..5593594 100644
--- a/datadb/compbio/cassandra/CassandraNativeConnector.java
+++ b/datadb/compbio/cassandra/CassandraNativeConnector.java
@@ -79,7 +79,6 @@ public class CassandraNativeConnector {
 	 */
 	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 + "';";
 		ResultSet results1 = session.execute(check1);
 		if (results1.isExhausted()) {
@@ -87,11 +86,9 @@ public class CassandraNativeConnector {
 					+ "(JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein)" + " VALUES ('" + jobid + "','" + ip + "','"
 					+ startdate + "','" + enddate + "','" + statusFinal + "','" + statusEx + "','" + protein + "');";
 			session.execute(com1);
-
 			String com2 = "INSERT INTO ProteinKeyspace.ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + jobtime + ",'" + jobid
 					+ "','" + protein + "');";
 			session.execute(com2);
-
 			String allpredictions = "";
 			for (FastaSequence pred : predictions) {
 				String predictionname = pred.getId();
@@ -102,14 +99,14 @@ public class CassandraNativeConnector {
 			if (null != allpredictions) {
 				final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
 			}
-
-			String check2 = "SELECT * FROM ProteinKeyspace.ProteinRow WHERE JobID = '" + jobid + "';";
+			String check2 = "SELECT * FROM ProteinKeyspace.ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;";
 			ResultSet results2 = session.execute(check2);
 			if (results2.isExhausted()) {
 				String com3 = "INSERT INTO ProteinKeyspace.ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" 
 			+ protein + "','" + jobid + "',{" + final_prediction + "});";
 				session.execute(com3);
 			}
+			String check3 = "SELECT * FROM ProteinKeyspace.ProteinRow WHERE JobID = '" + jobid + "';";
 		}
 	}
 
@@ -212,9 +209,9 @@ public class CassandraNativeConnector {
 	/*
 	 * getting protein sequences by counter
 	 */
-	public List<Pair<String, Integer>>  ReadProteinDataByCounter(int counter) {
+	public Map<String, Integer>  ReadProteinDataByCounter() {
 		final long startTime = System.currentTimeMillis();
-		String com = "SELECT DISTINCT Protein FROM ProteinKeyspace.ProteinRow;";
+		String com = "SELECT Protein FROM ProteinKeyspace.ProteinRow;";
 		System.out.println("Command: " + com);
 		ResultSet results = session.execute(com);
 		if (results.isExhausted())
@@ -223,17 +220,46 @@ public class CassandraNativeConnector {
 		List<Row> rows = results.all();
 		System.out.println ("Query time is " + (queryTime - startTime) + " msec");   
 		System.out.println (" rows analysed,  " + rows.size());
-		List<Pair<String, Integer>>  res = new ArrayList<Pair<String, Integer>>();
+		Map<String, Integer> res = new HashMap<String, Integer>();
 		int c = 0;
 		for (Row r : rows) {
-			String prot = r.getString("Protein");
-			
+			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 ProteinKeyspace.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 ProteinKeyspace.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;
+	}
+	
 	/*
 	 * getting earlest date of jobs from the db
 	 */