From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Tue, 3 Dec 2013 14:04:05 +0000 (+0000)
Subject: Add additional checks of input parameters
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8f30a2189dc9926985d82a113aba87711a91c244;p=proteocache.git

Add additional checks of input parameters
---

diff --git a/server/compbio/controllers/DailyStatisticsController.java b/server/compbio/controllers/DailyStatisticsController.java
index edfe876..c9df6be 100644
--- a/server/compbio/controllers/DailyStatisticsController.java
+++ b/server/compbio/controllers/DailyStatisticsController.java
@@ -52,6 +52,7 @@ public class DailyStatisticsController {
 		model.put("date2", date2);
 		List<DataBase> res = cr.countJobs(date1, date2);
 		model.put("result", res);
+		model.put("ndays", res.size());
 		final long endTime = System.currentTimeMillis();
 		model.put("timeExecution", (endTime - startTime));
 		model.put("option", option);
diff --git a/server/compbio/controllers/JobExecutionTimeController.java b/server/compbio/controllers/JobExecutionTimeController.java
index 191a40c..6170078 100644
--- a/server/compbio/controllers/JobExecutionTimeController.java
+++ b/server/compbio/controllers/JobExecutionTimeController.java
@@ -1,6 +1,7 @@
 package compbio.controllers;
 
 import java.util.Calendar;
+import java.util.List;
 import java.util.Map;
 
 import org.springframework.stereotype.Controller;
@@ -8,7 +9,9 @@ import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 
+
 import compbio.statistic.CassandraRequester;
+import compbio.cassandra.DataBase;
 import compbio.statistic.StatisticsProt;
 
 /**
@@ -44,7 +47,9 @@ public class JobExecutionTimeController {
 		model.put("date1", date1);
 		model.put("date2", date2);
 		model.put("option", option);
-		model.put("result", sp.extractExecutionTime(date1, date2));
+		List<DataBase> res = sp.extractExecutionTime(date1, date2);
+		model.put("result", res);
+		model.put("ndays", res.size() - 1);
 		final long endTime = System.currentTimeMillis();
 		model.put("timeExecution", (endTime - startTime));
 		return "/reportTimeExecution";
diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index 2986312..0f154d3 100644
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -2,6 +2,7 @@ package compbio.controllers;
 
 import java.util.List;
 import java.util.Map;
+import java.util.regex.Pattern;
 
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.RequestMapping;
@@ -10,14 +11,25 @@ import org.springframework.web.bind.annotation.RequestParam;
 
 import compbio.cassandra.ProteinBean;
 import compbio.cassandra.DataBase;
+import compbio.data.sequence.SequenceUtil;
 import compbio.statistic.CassandraRequester;
 
 /**
+ * Spring controller for sequence search. This version works in the servlet style.
+ * 
  * @author Alexander Sherstnev
  * @author Natasha Sherstneva
+ * 
+ * @since 0.5
+ * @version 1.0 December 2013
  */
 @Controller
 public class SequenceController {
+	
+	/**
+	 * pattern for NON-protein alphabet  symbols
+	 */
+	private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
 
 	@RequestMapping(value = "/sequence/query1", method = RequestMethod.GET)
 	public String formSequenceQuery(Map<String, Object> model) {
@@ -35,7 +47,19 @@ public class SequenceController {
 	public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map<String, Object> model) {
 		final long startTime = System.currentTimeMillis();
 
+		// input checks
 		String trimmedsequence = sequence.replaceAll("\\s", "");
+		if (trimmedsequence.equalsIgnoreCase("")) {
+			model.put("error", "The sequence cann't be empty");
+			model.put("value", sequence);
+			return "queryProteinSequence";
+		}
+		if (NONPROTEIN.matcher(trimmedsequence).find()) {
+			model.put("error", "The sequence contains symbols not from the standard protein alphabet");
+			model.put("value", sequence);
+			return "queryProteinSequence";
+		}
+
 		model.put("njobs", 0);
 		model.put("prot", trimmedsequence);
 		model.put("flag", flag);
diff --git a/webapp/view/queryProteinSequence.jsp b/webapp/view/queryProteinSequence.jsp
index a0bde5a..7feeb4e 100644
--- a/webapp/view/queryProteinSequence.jsp
+++ b/webapp/view/queryProteinSequence.jsp
@@ -1,6 +1,7 @@
 <!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 prefix="c" uri="http://java.sun.com/jsp/jstl/core" %>
 <%@ 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" %>
@@ -10,18 +11,33 @@
 <body>
 	<div class="container">
 	<jsp:include page="fragments/mainmenu.jsp" />
+	<spring:url value="/sequence/querysequence" var="query"/>
 
 	<div class="panel panel-default">
 		<div class="panel-heading">
 			<div style="font-weight:bold;">Enter protein sequence</div>
 		</div>
 		<div class="panel-body">
-			<spring:url value="/sequence/querysequence" var="formurl"/>
-			<form method="get" action="${fn:escapeXml(formurl)}">
-				<p><textarea class="form-control" rows="3" name="sequence">${value}</textarea></p>
-				<p><input type="radio" name="protein" value="whole">search for the whole sequence<br/>
-				<input type="radio" name="protein" value="part" Checked>search for partial sequence matching</p>
-				<input type="submit" name="Search" value="Search"/>
+			<form method="get" action="${query}">
+			<c:choose>
+			<c:when test="${error == null}">
+				<div class="form-group">
+					<p><textarea class="form-control" rows="3" name="sequence">${value}</textarea></p>
+					<p><input type="radio" name="protein" value="whole">search for the whole sequence<br/>
+					<input type="radio" name="protein" value="part" Checked>search for partial sequence matching</p>
+					<input type="submit" name="Search" value="Search"/>
+				</div>
+			</c:when>
+			<c:otherwise>
+				<div class="form-group has-error">
+					<p><textarea class="form-control" rows="3" name="sequence">${value}</textarea></p>
+					<p class="help-block">${error}</p>
+					<p><input type="radio" name="protein" value="whole">search for the whole sequence<br/>
+					<input type="radio" name="protein" value="part" Checked>search for partial sequence matching</p>
+					<input type="submit" name="Search" value="Search"/>
+				</div>
+			</c:otherwise>
+			</c:choose>
 			</form>
 		</div>
 	</div>
diff --git a/webapp/view/reportJobStatistics.jsp b/webapp/view/reportJobStatistics.jsp
index 5c707b7..59a0cb1 100644
--- a/webapp/view/reportJobStatistics.jsp
+++ b/webapp/view/reportJobStatistics.jsp
@@ -23,11 +23,11 @@
 	<div class="panel-heading">
 		<c:choose>
 			<c:when test="${option == 'AllDates,off'}">
-				<p style="font-weight:bold;">Jobs statistics for the whole period</p>
+				<p style="font-weight:bold;">Jobs statistics for the whole period (${ndays} days)</p>
 			</c:when>
 			<c:otherwise>
 				<p style="font-weight:bold;">
-				Jobs statistics for the time period: <c:out value="${date1}" /> to <c:out value="${date2}"/>
+				Jobs statistics for the time period: <c:out value="${date1}" /> to <c:out value="${date2}"/> (${ndays} days)
 				</p>
 			</c:otherwise>
 		</c:choose>
diff --git a/webapp/view/reportTimeExecution.jsp b/webapp/view/reportTimeExecution.jsp
index 907a578..fceb06e 100644
--- a/webapp/view/reportTimeExecution.jsp
+++ b/webapp/view/reportTimeExecution.jsp
@@ -23,10 +23,10 @@
 	<div class="panel-heading">
 		<c:choose>
 			<c:when test="${option == 'AllDates,off'}">
-				<p style="font-weight:bold;">Time execution for the whole period</p>
+				<p style="font-weight:bold;">Time execution for the whole period (${ndays} days)</p>
 			</c:when>
 			<c:otherwise>
-				<p style="font-weight:bold;">Time execution for the interval: ${date1} - ${date2}</p>
+				<p style="font-weight:bold;">Time execution for the interval: ${date1} - ${date2} (${ndays} days)</p>
 			</c:otherwise>
 		</c:choose>
 	</div>
@@ -63,7 +63,11 @@
 						<c:when test="${loop.last}">
 							<tr style="font-weight: bolder;">
 								<td style="text-align: right">Total numbers:</td>
-								<td style="text-align: right">0</td>
+								<c:set var="alldaytotal" value="0"/>
+								<c:forEach items="${res.timeTotalExec}" var="total">
+									<c:set var="alldaytotal" value="${alldaytotal + total}"/>
+								</c:forEach>
+								<td style="text-align: right">${alldaytotal}</td>
 								<c:forEach items="${res.timeTotalExec}" var="total">
 									<td style="text-align: right">${total}</td>
 								</c:forEach>
@@ -77,7 +81,11 @@
 						<c:when test="${not loop.last}">
 							<tr>
 								<td style="text-align: center">${res.date}</td>
-								<td style="text-align: right">0</td>
+								<c:set var="daytotal" value="0"/>
+								<c:forEach items="${res.timeRez}" var="time">
+									<c:set var="daytotal" value="${daytotal + time}"/>
+								</c:forEach>
+								<td style="text-align: right">${daytotal}</td>
 								<c:forEach items="${res.timeRez}" var="time">
 									<td style="text-align: right">${time}</td>
 								</c:forEach>