From c15dbff6d660ba14d41407bebeceda4414f45068 Mon Sep 17 00:00:00 2001
From: Natasha Sherstneva <n.shertneva@gmail.com>
Date: Mon, 16 Dec 2013 09:37:19 +0000
Subject: [PATCH 1/1] created features report

---
 conf/Proteocache.properties                        |    2 +-
 datadb/compbio/cassandra/CassandraReader.java      |   35 ++++++++
 datadb/compbio/cassandra/ProteinBean.java          |   16 ++++
 .../compbio/controllers/SSFeaturesController.java  |   86 ++++++++++++++++++++
 server/compbio/statistic/CassandraRequester.java   |   19 +++++
 webapp/view/fragments/mainmenu.jsp                 |    1 +
 webapp/view/query/SSFeatures.jsp                   |   56 +++++++++++++
 webapp/view/reportSSFeatures.jsp                   |   62 ++++++++++++++
 8 files changed, 276 insertions(+), 1 deletion(-)
 create mode 100644 server/compbio/controllers/SSFeaturesController.java
 create mode 100644 webapp/view/query/SSFeatures.jsp
 create mode 100644 webapp/view/reportSSFeatures.jsp

diff --git a/conf/Proteocache.properties b/conf/Proteocache.properties
index b1730f4..8851680 100644
--- a/conf/Proteocache.properties
+++ b/conf/Proteocache.properties
@@ -9,7 +9,7 @@ cassandra.newtables.update=false
 #################################################################################
 # Jpred sources
 # real Jpred web-server
-cassandra.jpred.web.update=true
+cassandra.jpred.web.update=false
 cassandra.jpred.web.inidelay=0
 cassandra.jpred.web.updaterate=30
 
diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
index 00a9f27..1720c48 100644
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -11,6 +11,7 @@ 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.engine.JobStatus;
 
 public class CassandraReader {
@@ -198,6 +199,40 @@ 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();
+		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;
+		for (Row r : rows) {
+			String prot = r.getString("Protein");
+			String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class));
+			if (prot != null || prediction != null)	
+				res.put(prot, prediction);
+		}
+		final long endTime = System.currentTimeMillis();
+		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+
+	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() {
diff --git a/datadb/compbio/cassandra/ProteinBean.java b/datadb/compbio/cassandra/ProteinBean.java
index 80f111b..d5e700b 100644
--- a/datadb/compbio/cassandra/ProteinBean.java
+++ b/datadb/compbio/cassandra/ProteinBean.java
@@ -7,6 +7,7 @@ import java.util.Map;
 
 public class ProteinBean implements PredictionIndex{
 	private String sequence;
+	private String jnetpred;
 	private List<String> jobid;
 	private LinkedHashMap<String,String> predictions;
 	private List<String> subProt;		// protein sequence divided by several parts for highlighting the particular part
@@ -19,6 +20,10 @@ public class ProteinBean implements PredictionIndex{
 		setPredictions(pred);
 	}
 	
+	public void setSequence (String seq) {
+		this.sequence = seq;
+	}
+	
 	public void setPredictions(Map<String,String> pred) {
 		if (predictions == null)
 			predictions = new LinkedHashMap<String,String>();	
@@ -32,6 +37,17 @@ public class ProteinBean implements PredictionIndex{
 		return sequence;
 	}
 	
+	public String getJnetpred () {
+		return jnetpred;
+	}
+	
+	public void setJnetpred (Map<String,String> pred) {
+		if (pred != null) {
+			if (pred.containsKey("jnetpred")) 
+				jnetpred = pred.get("jnetpred");
+		}
+	}
+	
 	public List<String> getJobid () {
 		return jobid;
 	}
diff --git a/server/compbio/controllers/SSFeaturesController.java b/server/compbio/controllers/SSFeaturesController.java
new file mode 100644
index 0000000..27015bb
--- /dev/null
+++ b/server/compbio/controllers/SSFeaturesController.java
@@ -0,0 +1,86 @@
+package compbio.controllers;
+
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+
+import compbio.cassandra.ProteinBean;
+import compbio.cassandra.TotalByCounterBean;
+import compbio.statistic.CassandraRequester;
+
+/**
+ * Spring controller for sequence queries. This version works in the servlet
+ * style.
+ * 
+ * @author Alexander Sherstnev
+ * @author Natasha Sherstneva
+ * 
+ * @since 0.5
+ * @version 1.0 December 2013
+ */
+@Controller
+@RequestMapping("/features")
+public class SSFeaturesController extends BasicController {
+
+		@RequestMapping(value = "query", method = RequestMethod.GET)
+		public String formCounterQuery(Map<String, Object> model) {
+			model.put("username", getPrincipalName());
+			model.put("type", 'E');
+			model.put("value", 80);
+			return "query/SSFeatures";
+		}
+			
+		@RequestMapping(value = "features/results", method = RequestMethod.GET)
+		public String countSequences(@RequestParam("TypeFeatures") String typeFeature, @RequestParam("Percent") String percent,Map<String, Object> model) {
+			model.put("username", getPrincipalName());
+			final long startTime = System.currentTimeMillis();
+
+			if (percent.equals("")) {
+				model.put("error", "The value must not be empty");
+				model.put("type", typeFeature);
+				model.put("value", percent);
+				return "query/SSFeatures";
+			}
+
+			int realpercent;
+			try {
+				realpercent = Integer.parseInt(percent.trim());
+			} catch (NumberFormatException e) {
+				model.put("error", "The value must be an integer number");
+				model.put("value", percent);
+				return "query/SSFeatures";
+			}
+
+			if (realpercent < 1) {
+				model.put("error", "The value must be greater than 0");
+				model.put("value", percent);
+				return "query/SSFeatures";
+			}
+			
+			if (realpercent > 100) {
+				model.put("error", "The value must be less than 100");
+				model.put("value", percent);
+				return "query/SSFeatures";
+			}
+
+			CassandraRequester cr = new CassandraRequester();
+			Map<String, String> r = cr.readProteinsPrediction(typeFeature, realpercent);
+			model.put("results", r);
+			model.put("njobs", 0);
+			if (null != r) {
+				model.put("njobs", r.size());
+			}
+			final long endTime = System.currentTimeMillis();
+			model.put("timeExecution", (endTime - startTime));
+			model.put("feature", typeFeature);
+			model.put("percent", realpercent);
+			return "reportSSFeatures";
+		}
+
+	
+
+}
diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index 1bb0050..f2336e7 100755
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -5,6 +5,7 @@ import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.Date;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -200,6 +201,24 @@ public class CassandraRequester {
 		}
 		return result;
 	}
+	
+	/*
+	 * query: protein feature
+	 */
+	public Map<String, String> readProteinsPrediction(String feature, int percent) {
+		Map<String, String> result = db.ReadProtein();;
+		if (result == null)
+			return null;
+		Map<String, String> query = new HashMap<String, String>();
+		for (Map.Entry<String, String> entry : result.entrySet()) {
+			String pred = entry.getValue();			
+			if (pred.replaceAll("[^"+feature+"]", "").length() > pred.length() * percent / 100 && (!entry.getKey().equals(""))) {
+			//	if (!entry.getKey().equals(""))
+					query.put(entry.getKey(), pred);
+			}	
+		}
+		return query;
+	}
 
 	/*
 	 * query protein sequences with number of jobs
diff --git a/webapp/view/fragments/mainmenu.jsp b/webapp/view/fragments/mainmenu.jsp
index f310fbf..8f8e403 100644
--- a/webapp/view/fragments/mainmenu.jsp
+++ b/webapp/view/fragments/mainmenu.jsp
@@ -24,6 +24,7 @@
 					<li><a href="<spring:url value="/stat/exectime/query" htmlEscape="true" />">Job Time Execution</a></li>
 					<li><a href="<spring:url value="/admin/ip/counts/query" htmlEscape="true" />">IPs by Job count</a></li>
 					<li><a href="<spring:url value="/sequence/counts/query" htmlEscape="true" />">Proteins by Job count</a></li>
+					<li><a href="<spring:url value="/features/query" htmlEscape="true" />">Proteins by SS Features</a></li>
 				</ul>
 			</li>
 <sec:authorize access="hasRole('ROLE_ADMIN')">
diff --git a/webapp/view/query/SSFeatures.jsp b/webapp/view/query/SSFeatures.jsp
new file mode 100644
index 0000000..59cdc1c
--- /dev/null
+++ b/webapp/view/query/SSFeatures.jsp
@@ -0,0 +1,56 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%@ taglib prefix="spring" uri="http://www.springframework.org/tags"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
+<%@ taglib prefix="fmt" uri="http://java.sun.com/jsp/jstl/fmt"%>
+<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions" %>
+<%@ taglib prefix="form" uri="http://www.springframework.org/tags/form" %>
+
+<html>
+<jsp:include page="../fragments/header.jsp" />
+<body>
+	<div class="container">
+	<jsp:include page="../fragments/mainmenu.jsp" />
+	<spring:url value="/features/features/results" var="query"/>
+
+	<div class="panel panel-default">
+		<div class="panel-heading">
+			<div style="font-weight:bold;">Proteins with features</div>
+		</div>
+		<div class="panel-body">
+			<form method="get" action="${query}">
+			<div class="col-xs-2"> <!-- make the field shorter -->
+			<c:choose>
+			<c:when test="${error == null}">
+			<div class="form-group">
+				<label for="TypeFeatures">Type of SS feature </label>
+				<select name = TypeFeatures>
+ 					 <option value="H">H</option>
+ 					 <option value="E">E</option>
+				</select>	
+				<label for="SSFeatureValue">Percent of SS feature </label>
+				<input class="form-control" type="text" name="Percent" value ="${value}" id="SSFeatureValue">
+			</div>
+			</c:when>
+			<c:otherwise>
+			<div class="form-group has-error">
+				<label for="SSFeature">Type of SS feature </label>
+				<select name = TypeFeatures>
+ 					 <option value="H">H</option>
+ 					 <option value="E">E</option>
+				</select>	
+				<label for="SSFeatureValue">Percent of SS feature </label>
+				<input class="form-control" type="text" name="Percent" value ="${value}" id="SSFeatureValue">
+				<p class="help-block">${error}</p>
+			</div>
+			</c:otherwise>
+			</c:choose>
+			<input type="submit" name="Search" value="Search"/>
+			</div>
+			</form>
+		</div>
+	</div>
+	<jsp:include page="../fragments/footer.jsp"/>
+	</div>
+</body>
+</html>
diff --git a/webapp/view/reportSSFeatures.jsp b/webapp/view/reportSSFeatures.jsp
new file mode 100644
index 0000000..2d885f7
--- /dev/null
+++ b/webapp/view/reportSSFeatures.jsp
@@ -0,0 +1,62 @@
+<%@ page language="java" contentType="text/html; charset=UTF-8"
+	pageEncoding="UTF-8"%>
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%@ taglib uri="http://www.springframework.org/tags" prefix="spring"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
+<%@page import="java.util.ArrayList"%>
+
+<html>
+<jsp:include page="fragments/header.jsp" />
+<body>
+	<div class="container">
+		<jsp:include page="fragments/mainmenu.jsp" />
+		<spring:url value="/sequence/sequence/results" var="sequence_query" />
+
+	<div class="panel panel-default">
+	<div class="panel-heading">
+		<div style="font-weight:bold;">Jobs Statistics</div>
+	</div>
+	<div class="panel-body">
+
+		<c:choose>
+		<c:when test="${njobs == 0}">
+			<p>No proteins with features ${feature} more then ${percent} % found</p>
+		</c:when>
+		<c:otherwise>
+			<p>${njobs} proteins with features ${feature} more then ${percent} % found</p>
+			<div class="table-responsive">
+			<table class="table table-striped table-hover table-bordered">
+			<thead>
+				<tr>
+					<th style="text-align: centre">N</th>
+					<th style="text-align: left">Protein/Prediction</th>
+				</tr>
+			</thead>
+			<tbody>
+				<c:set var="count" value="0" scope="page" />
+				<c:forEach items="${results}" var="res">
+					<c:set var="count" value="${count + 1}" scope="page"/>
+					<tr>
+						<td rowspan = 2>${count}
+						<td style="text-align: left; border-buttom: dotted; font-family: monospace">
+						<a title="Click to view all jobs" href="${sequence_query}?sequence=${res.key}&searchtype=whole">${res.key}</a></td>
+					</tr>
+					<tr>
+						<td style="text-align: left; border-buttom: dotted; font-family: monospace">${res.value}</td>
+					</tr>
+				</c:forEach>
+			</tbody>
+			</table>
+			</div>
+		</c:otherwise>
+		</c:choose>
+	</div>
+	</div>
+
+	<jsp:include page="fragments/footer.jsp" />
+	</div>
+</body>
+</html>
\ No newline at end of file
-- 
1.7.10.2