X-Git-Url: http://source.jalview.org/gitweb/?p=proteocache.git;a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraReaderOld.java;fp=datadb%2Fcompbio%2Fcassandra%2FCassandraReader.java;h=f483dc1a7696e638586a5b065b8b7008f4901561;hp=81add8fedb2aeb83bda84adce7eee65554f4f404;hb=9bb6ee99ca7f738fac1087190b5481b8fe6e8d9f;hpb=2e3f6b76be585306f1003d849831840c0adb3360

diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReaderOld.java
similarity index 87%
rename from datadb/compbio/cassandra/CassandraReader.java
rename to datadb/compbio/cassandra/CassandraReaderOld.java
index 81add8f..f483dc1 100644
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReaderOld.java
@@ -11,13 +11,19 @@ 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.beans.DateBean;
+import compbio.beans.JobBean;
+import compbio.beans.ProteinBean;
+import compbio.beans.Total;
 import compbio.engine.JobStatus;
+import compbio.engine.Pair;
 
-public class CassandraReader {
+public class CassandraReaderOld {
 	private Session session;
 	private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
 
-	public CassandraReader() {
+	public CassandraReaderOld() {
 		Session inis = CassandraNativeConnector.getSession();
 		setSession(inis);
 	}
@@ -198,6 +204,38 @@ public class CassandraReader {
 	}
 
 	/*
+	 * getting protein sequence from the db ProteinRow
+	 */
+	public Map<String, String> ReadProtein() {
+		//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();
+		Map<String, String> output = new HashMap<String, String>();
+		for (Row r : rows) {
+			String protein = r.getString("Protein");
+			String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class));
+			if (protein != null && prediction != null) {
+				output.put(protein, prediction);
+			}
+		}
+		//final long endTime = System.currentTimeMillis();
+		return output;
+	}
+
+	private String findJnetpred(Map<String, String> pred) {
+		if (pred != null) {
+			if (pred.containsKey("jnetpred"))
+				return pred.get("jnetpred");
+		}
+		return null;
+	}
+
+	/*
 	 * getting protein sequences by counter
 	 */
 	public Map<String, Integer> ReadProteinSequenceByCounter() {
@@ -215,7 +253,6 @@ public class CassandraReader {
 		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
@@ -244,7 +281,6 @@ public class CassandraReader {
 		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
@@ -275,6 +311,12 @@ public class CassandraReader {
 		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");