From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 8 Nov 2013 13:28:29 +0000 (+0000)
Subject: Fix problems with Natasha's code
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c0a1ee97e2126b8be6e8cbaeeee2315d52090f14;p=proteocache.git

Fix problems with Natasha's code
---

diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java
index 8e86624..4ba9377 100644
--- a/datadb/compbio/cassandra/CassandraNativeConnector.java
+++ b/datadb/compbio/cassandra/CassandraNativeConnector.java
@@ -268,121 +268,6 @@ public class CassandraNativeConnector {
 	}
 
 	/*
-	 * getting data from the db ProteinData
-	 */
-	public Integer ReadDateTable(long queryDate) {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT jobtime, JobID FROM ProteinKeyspace.ProteinData WHERE jobtime = " + queryDate + ";";
-		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");
-		return rows.size();
-	}
-
-	/*
-	 * getting part of protein sequence from the db ProteinRow
-	 */
-	public List<StructureProteinPrediction>  ReadPartOfSequence(String queryProtein) {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT * FROM ProteinKeyspace.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<StructureProteinPrediction>  res = new ArrayList<StructureProteinPrediction>();
-		int c = 0;
-		for (Row r : rows) {
-			String prot = r.getString("Protein");
-			if (prot.matches("(.*)" + queryProtein + "(.*)")) {
-				StructureProteinPrediction structure = new StructureProteinPrediction(prot, r.getString("JobID"), r.getMap("Predictions", String.class, String.class));		
-				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>  ReadProteinDataByCounter() {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT Protein FROM ProteinKeyspace.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");
-			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 data from the db ProteinData
-	 */
-	public Integer ReadDateTable(long queryDate) {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT jobtime, JobID FROM ProteinKeyspace.ProteinData WHERE jobtime = " + queryDate + ";";
-		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");        
-		return rows.size();
-	}
-
-	/*
-	 * getting whole protein sequence from the db ProteinRow
-	 */
-	public List<StructureProteinPrediction> ReadWholeSequence(String queryProtein) {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT JobID, Predictions FROM ProteinKeyspace.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 ("Query time is " + (queryTime - startTime) + " msec");   
-		System.out.println (" rows analysed,  " + rows.size());
-		List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
-		int c = 0;
-		for (Row r : rows) {
-			StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap("Predictions", String.class, String.class));		
-			res.add(structure);
-			++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<StructureProteinPrediction>  ReadPartOfSequence(String queryProtein) {
@@ -464,7 +349,7 @@ public class CassandraNativeConnector {
 		return res;
 	}
 
-
+	/*
 	 * getting earlest date of jobs from the db
 	 */
 	public long getEarliestDateInDB() {
diff --git a/datadb/compbio/cassandra/StructureJobLog.java b/datadb/compbio/cassandra/StructureJobLog.java
new file mode 100644
index 0000000..4f2414b
--- /dev/null
+++ b/datadb/compbio/cassandra/StructureJobLog.java
@@ -0,0 +1,45 @@
+package compbio.cassandra;
+
+import java.util.Map;
+
+public class StructureJobLog {
+	private String jobid;
+	private String dateStart;
+	private String dateEnd;
+	private String sequence;
+	private String ip;	
+	private Map<String,String> prediction;
+	
+	public StructureJobLog (String seq, String id, String  dateStart, String  dateEnd, String ip, Map<String,String> pred) {
+		this.sequence = seq;
+		this.jobid = id;
+		this.dateStart = dateStart;
+		this.dateEnd = dateEnd;
+		this.ip = ip;
+		this.prediction = pred;
+	}
+	
+	public String getSequence () {
+		return sequence;
+	}
+	
+	public String getJobid () {
+		return jobid;
+	}
+	
+	public String getDateStart () {
+		return dateStart;
+	}
+	
+	public String getDateEnd () {
+		return dateEnd;
+	}
+	
+	public String getIP () {
+		return ip;
+	}
+	
+	public Map<String,String> getPrediction () {
+		return prediction;
+	}
+}