From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 25 Nov 2013 11:35:01 +0000 (+0000)
Subject: Make all necessary changes for combining old and new servlets
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4458e44cf92e699159ee1257b1bea6300a9abebe;p=proteocache.git

Make all necessary changes for combining old and new servlets
---

diff --git a/conf/Proteocache.properties b/conf/Proteocache.properties
index 5ab8858..b1730f4 100644
--- a/conf/Proteocache.properties
+++ b/conf/Proteocache.properties
@@ -1,9 +1,8 @@
 #################################################################################
 # Cassandra host or IP
 # test server is 10.0.115.190
-#cassandra.host=localhost
-#cassandra.host=10.31.0.97
 cassandra.host=localhost
+#cassandra.host=gjb-www-1.cluster.lifesci.dundee.ac.uk
 
 cassandra.newtables.update=false
 
diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
index 6e3587b..cb2492e 100644
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -94,6 +94,7 @@ public class CassandraReader {
 		}
 		return res;
 	}
+
 	/*
 	 * getting whole protein sequence from the db ProteinRow
 	 */
@@ -113,10 +114,6 @@ public class CassandraReader {
 		for (Row r : rows) {
 			AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(queryProtein, r.getString("JobID"), r.getMap(
 					"Predictions", String.class, String.class));
-			if (structure.getPrediction().containsKey("jnetpred"))
-				structure.setJnetpred(structure.getPrediction().get("jnetpred"));
-			else
-				structure.setJnetpred("");
 			res.add(structure);
 			++c;
 		}
diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index 410a722..72ec074 100755
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -159,19 +159,49 @@ public class CassandraRequester {
 		return query;
 	}
 
+	/*
+	 * query: jobs and sequence at date
+	 */
+	public List<DataBase> readJobByDay (String date) {
+		System.out.println(date);
+		if (null == date) {
+			return null;
+		}
+		if (!isThisDateValid(date, formatDDMMYY)) {
+			System.out.println("Wrong date: point 3");
+			return null;
+		}
+		SetDateRange();
+		long day = DateParsing(date, formatDDMMYY);
+		System.out.println(day);
+		if (day < earlestDate || day > currentDate)
+			return null;	
+		List<Pair<String, String>>	res = db.ReadProteinData(day);
+		if (res == null)
+			return null;
+		query = new ArrayList<DataBase>();
+		for (Pair<String, String> entry : res) {		
+			DataBase bean = new DataBase();
+			bean.setDate(date);
+			bean.setId(entry.getElement0());
+			bean.setProt(entry.getElement1());
+			query.add(bean);
+		}
+		System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
+		return query;
+	}
+
+
 	/* 
 	 * query: protein sequence
 	 * */
 	public List<DataBase> readProteins(String protIn, String flag) {
-		if (protIn == null)
-			return null;
-		System.out.println(protIn.length());
 		query = new ArrayList<DataBase>();
 		List<AnnotatedProteinSequenceBean> res;
 		if (flag.equals("whole")) 
 			res = db.ReadWholeSequence(protIn);
 		 else 
-			 res = (protIn.length() > 0) ? db.ReadPartOfSequence(protIn) : null;
+			res = db.ReadPartOfSequence(protIn);
 		if (res == null)
 			return null;
 		for (AnnotatedProteinSequenceBean entry : res) {
@@ -186,6 +216,7 @@ public class CassandraRequester {
 		}
 		return query;
 	}
+	
 
 	/* 
 	 * query protein sequences with number of jobs