X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraReaderOld.java;h=ccd13edd66fc49b1023f1bcb28bce81c716cf0a7;hb=58c9b97523e2273a316a947d977ca7ddd8b1356a;hp=852beb04003787b1743892470cf888a0c7ab3509;hpb=e8b88c0c8e432f8bc1aefdbd81df81e9ef706242;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraReaderOld.java b/datadb/compbio/cassandra/CassandraReaderOld.java
index 852beb0..ccd13ed 100644
--- a/datadb/compbio/cassandra/CassandraReaderOld.java
+++ b/datadb/compbio/cassandra/CassandraReaderOld.java
@@ -17,6 +17,7 @@ import compbio.beans.JobBean;
 import compbio.beans.ProteinBean;
 import compbio.beans.Total;
 import compbio.engine.JobStatus;
+import compbio.engine.Pair;
 
 public class CassandraReaderOld {
 	private Session session;
@@ -206,36 +207,34 @@ public class CassandraReaderOld {
 	 * getting protein sequence from the db ProteinRow
 	 */
 	public Map<String, String> ReadProtein() {
-		final long startTime = System.currentTimeMillis();
+		//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();
+		//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, String> res = new HashMap<String, String>();
-		int c = 0;
+		Map<String, String> output = new HashMap<String, String>();
 		for (Row r : rows) {
-			String prot = r.getString("Protein");
+			String protein = r.getString("Protein");
 			String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class));
-			if (prot != null || prediction != null)	
-				res.put(prot, prediction);
+			if (protein != null && prediction != null) {
+				output.put(protein, prediction);
+			}
 		}
-		final long endTime = System.currentTimeMillis();
-		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
-		return res;
+		//final long endTime = System.currentTimeMillis();
+		return output;
 	}
 
-	private String findJnetpred (Map<String,String> pred) {
+	private String findJnetpred(Map<String, String> pred) {
 		if (pred != null) {
-			if (pred.containsKey("jnetpred")) 
+			if (pred.containsKey("jnetpred"))
 				return pred.get("jnetpred");
 		}
 		return null;
 	}
+
 	/*
 	 * getting protein sequences by counter
 	 */
@@ -254,7 +253,6 @@ public class CassandraReaderOld {
 		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
@@ -283,7 +281,6 @@ public class CassandraReaderOld {
 		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
@@ -314,6 +311,12 @@ public class CassandraReaderOld {
 		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));
+		String program = row.getString("ProgramName");
+		String version = row.getString("ProgramVersion");
+		if (null != program && null != version) {
+			res.setProgramName(program);
+			res.setProgramVersion(version);
+		}
 		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");