Commit f281d7d5 authored by Marco Guimaräes's avatar Marco Guimaräes

undo unwanted push of dynamic content

parent 9d58ca9f
This diff is collapsed.
<?xml version="1.0" encoding="UTF-8"?>
<Configuration status="WARN">
<Appenders>
<File name="MyDebugFile" fileName="dnaanalyze.log">
<File name="FileOutput" fileName="dnaanalyze.log">
<PatternLayout>
<Pattern>%d %p %c{1.} [%t] %m%n</Pattern>
</PatternLayout>
</File>
<Console name="ConsoleOutput" target="SYSTEM_OUT">
<PatternLayout pattern="%d{HH:mm:ss.SSS} [%t] %-5level %logger{36} - %msg%n" />
</Console>
</Appenders>
<Loggers>
<Root level="debug">
<AppenderRef ref="MyDebugFile"/>
<AppenderRef ref="FileOutput"/>
<AppenderRef ref="ConsoleOutput" />
</Root>
</Loggers>
</Configuration>
\ No newline at end of file
......@@ -3,17 +3,80 @@
<head>
<meta charset="UTF-8">
<title>DNA Analyzer Application</title>
<style>
body {
text-align:center;
}
</style>
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css" />
<script type="text/javascript" src="https://code.jquery.com/jquery-3.5.1.min.js"></script>
<script type="text/javascript" src="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.min.js"></script>
</head>
<body>
<!--
<h1>DNA Analysis</h1>
<form method="post" action="startApp" id="startApp" name="startApp">
<input type="submit" value="Start Application">
</form>
<h2>Resources</h2>
<button onclick="location.href='http://www.ncbi.nlm.nih.gov'" type="button">Visit NCBI page</button>
-->
<div class="container-md">
<div class="page-header">
<h1>
<img src = "images/fhnw_logo.png" class = "img-rounded" width="60">
MSC Medical Informatics
<br/><img src = "images/dna_icon.jpg" class = "img-rounded" width="60">
<small>DNA Analysis Application</small>
</h1>
</div>
<p class="text-justify">
This web application has been developed during the software engineering
lectures for the master medical informatics degree course.
</p>
<p class="h2">
<form method="post" action="startApp" id="startApp" name="startApp">
<button type="submit" class="btn btn-primary">Start Application</button>
</form>
</p>
<p class="h2">
Resources
</p>
<p class="text-justify">
<ul class="list-group">
<li class="list-group-item list-group-item-primary">National Center for Biotechnology Information (<a href="https://www.ncbi.nlm.nih.gov/" target="_new">https://www.ncbi.nlm.nih.gov/</a>)</li>
<li class="list-group-item list-group-item-secondary">Ensembl (<a href="https://www.ensembl.org/" target="_new">https://www.ensembl.org/</a>)</li>
</ul>
</p>
<p class="h2">
Technologies
</p>
<p class="text-justify">
<ul class="list-group">
<li class="list-group-item list-group-item-primary">Java (Programming Language) (<a href="https://www.oracle.com/java/" target="_new">https://www.oracle.com/java/</a>)</li>
<li class="list-group-item list-group-item-secondary">Apache ANT (Build Tool) (<a href="https://ant.apache.org/" target="_new">https://ant.apache.org/</a>)</li>
<li class="list-group-item list-group-item-primary">Apache Maven (Build Tool) (<a href="https://maven.apache.org/" target="_new">https://maven.apache.org/</a>)</li>
<li class="list-group-item list-group-item-secondary">Apache Tomcat (Application Server) (<a href="https://tomcat.apache.org/" target="_new">https://tomcat.apache.org/</a>)</li>
<li class="list-group-item list-group-item-primary">JUnit (Testing Tool) (<a href="https://junit.org/" target="_new">https://junit.org/</a>)</li>
<li class="list-group-item list-group-item-secondary">IntelliJ (Development Environment) (<a href="https://www.jetbrains.com/de-de/idea/" target="_new">https://www.jetbrains.com/de-de/idea/</a>)</li>
<li class="list-group-item list-group-item-primary">Eclipse (Development Environment) (<a href="https://www.eclipse.org/" target="_new">https://www.eclipse.org/</a>)</li>
<li class="list-group-item list-group-item-secondary">Git (Version Control) (<a href="https://git-scm.com/" target="_new">https://git-scm.com/</a>)</li>
<li class="list-group-item list-group-item-primary">Bootstrap (HTML Library) (<a href="https://getbootstrap.com/" target="_new">https://getbootstrap.com/</a>)</li>
<li class="list-group-item list-group-item-secondary">JQuery (Javascript Library) (<a href="https://jquery.com/" target="_new">https://jquery.com/</a>)</li>
<li class="list-group-item list-group-item-primary">Unified Modeling Language (UML) (<a href="https://www.uml.org/" target="_new">https://www.uml.org/</a>)</li>
<li class="list-group-item list-group-item-secondary">Apache Log4J 2 (Logging Library) (<a href="https://logging.apache.org/log4j/2.x/" target="_new">https://logging.apache.org/log4j/2.x/</a>)</li>
<li class="list-group-item list-group-item-primary">Jenkins (Continuous Integration) (<a href="https://www.jenkins.io/" target="_new">https://www.jenkins.io/</a>)</li>
<li class="list-group-item list-group-item-secondary">Apache JMeter (Testing Tool) (<a href="https://jmeter.apache.org/" target="_new">https://jmeter.apache.org/</a>)</li>
<li class="list-group-item list-group-item-primary">BioJava (<a href="https://biojava.org/" target="_new">https://biojava.org/</a>)</li>
</ul>
</p>
<p class="h2">
Source Code
</p>
<p class="text-justify">
The source code for this application is available on Git:<br/>
<a href="https://gitlab.fhnw.ch/david.herzig/dnaanalyzerwa" target="_new">https://gitlab.fhnw.ch/david.herzig/dnaanalyzerwa</a><br/>
<code>git clone https://gitlab.fhnw.ch/david.herzig/dnaanalyzerwa.git</code>
</p>
</div>
</body>
</html>
\ No newline at end of file
<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %>
<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt" %>
<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn" %>
<%@ page import ="java.util.*,ch.fhnw.model.*,ch.fhnw.util.*" %>
<!DOCTYPE html>
<html>
<head>
<title>DNA Analyzer Application</title>
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css" />
<script type="text/javascript" src="https://code.jquery.com/jquery-3.5.1.min.js"></script>
<script type="text/javascript" src="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.min.js"></script>
<!--
<link rel="stylesheet" href='<c:url value="/scripts/bootstrap.min.css"/>' />
<script type="text/javascript" src='<c:url value="/scripts/jquery-3.5.1.min.js"/>'></script>
<script type="text/javascript" src='<c:url value="/scripts/bootstrap.min.js"/>'></script>
-->
<style>
body {
text-align:center;
}
.modal-body{
word-break: break-all;
}
</style>
</head>
<body>
<h1>
DNA Analysis
</h1>
Enter DNA Sequence<br/>
<textarea rows="20" cols="200" name="dnasequence" form="addform"></textarea><br/>
Window Size<br/>
<input type="text" value="100" name="windowsize" form="addform"></input>
<br/><br/>
<form method="post" action="AnalyzeDNA" id="addform">
<input type="submit" value="Analyse"><br/>
</form>
<div class="container-md">
<div class="page-header">
<h1>
<img src = "images/fhnw_logo.png" class = "img-rounded" width="60">
MSC Medical Informatics
<br/><img src = "images/dna_icon.jpg" class = "img-rounded" width="60">
<small>DNA Analysis Application</small>
</h1>
</div>
<p class="text-justify">
<textarea placeholder="Place DNA sequence here..." form="addform" name="dnasequence" class="form-control rounded-0" id="exampleFormControlTextarea1" rows="10"></textarea>
</p>
<p class="text-justify">
Window Size<br/>
<input class="form-control" name="windowsize" type="text" value="100" form="addform"></input>
</p>
<p class="text-justify">
<form method="post" action="AnalyzeDNA" id="addform">
<button type="submit" class="btn btn-primary">Analyse</button>
</form>
</p>
<br/><br/>
<br/>
<% if (!request.getAttribute("informationStr").toString().isEmpty()) { %>
<div class="alert alert-dark" role="alert">
<% out.println(request.getAttribute("informationStr")); %>
</div>
<% } %>
<br/>
<% out.println(request.getAttribute("header")); %>
<div>
<br/><br/>
<br/><br/>
<h2 font-size = "32px"; >
<% out.println(request.getAttribute("header")); %>
</h2>
<br/><br/>
<%
List result= (List) request.getAttribute("analyzeresult");
Iterator it = result.iterator();
long reqTime = 0;
if (!result.isEmpty()){
Information info = (Information)result.get(result.size()-1);
reqTime = info.getReqTime();
out.println("Required time for analysis: " + reqTime + " miliseconds");
}else {
out.println("Start analyzing today!");
}
%>
<table>
<% if (it.hasNext()) { %>
<jsp:useBean id="counter" class="ch.fhnw.model.Counter" />
<jsp:setProperty name="counter" property="value" value="1"/>
<table class="table">
<thead class="thead-dark">
<tr>
<th>Start Index</th>
<th>A</th>
<th>C</th>
<th>G</th>
<th>T</th>
<th>Sequence</th>
</tr>
<% if (it.hasNext()) { %>
<th scope="col">Start Index</th>
<th scope="col">A</th>
<th scope="col">C</th>
<th scope="col">G</th>
<th scope="col">T</th>
<th scope="col">Sequence</th>
<% } %>
</tr>
</thead>
<tbody>
<%
while(it.hasNext()){
Information obj = (Information)it.next();
out.println("<tr>");
out.println("<td>" + obj.getIndex() + "</th>");
out.println("<td>" + obj.getSeq().count("A") + "</th>");
out.println("<td>" + obj.getSeq().count("C") + "</th>");
out.println("<td>" + obj.getSeq().count("G") + "</th>");
out.println("<td>" + obj.getSeq().count("T") + "</th>");
out.println("<td>" + obj.getColoredDNA() + "</th>");
out.println("<th scope=\"row\">" + obj.getIndex() + "</th>");
out.println("<td>" + obj.getSeq().count("A") + "</td>");
out.println("<td>" + obj.getSeq().count("C") + "</td>");
out.println("<td>" + obj.getSeq().count("G") + "</td>");
out.println("<td>" + obj.getSeq().count("T") + "</td>");
%>
<td>
<button type="button" class="btn btn-primary" data-toggle="modal" data-target="#sequenceDialog_${counter.valueAndIncrease}">Sequence</button>
<div class="modal fade" id="sequenceDialog_${counter.value}" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title" id="exampleModalLabel">Sequence</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">&times;</span>
</button>
</div>
<div class="modal-body">
<% out.println(obj.getColoredDNA()); %>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
</td>
<%
out.println("</tr>");
}
%>
</tbody>
</table>
<!-- Modal -->
</body>
</html>
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<?xml version="1.0" encoding="UTF-8"?>
<Configuration status="WARN">
<Appenders>
<File name="MyDebugFile" fileName="dnaanalyze.log">
<File name="FileOutput" fileName="dnaanalyze.log">
<PatternLayout>
<Pattern>%d %p %c{1.} [%t] %m%n</Pattern>
</PatternLayout>
</File>
<Console name="ConsoleOutput" target="SYSTEM_OUT">
<PatternLayout pattern="%d{HH:mm:ss.SSS} [%t] %-5level %logger{36} - %msg%n" />
</Console>
</Appenders>
<Loggers>
<Root level="debug">
<AppenderRef ref="MyDebugFile"/>
<AppenderRef ref="FileOutput"/>
<AppenderRef ref="ConsoleOutput" />
</Root>
</Loggers>
</Configuration>
\ No newline at end of file
#Generated by Maven
#Fri Apr 24 16:04:17 CEST 2020
#Thu Jun 18 09:54:09 CEST 2020
groupId=ch.fhnw
artifactId=DNAAnalysis_MES
version=0.1-SNAPSHO
ch/fhnw/AnalyzeDNAServlet.class
ch/fhnw/model/Information.class
ch/fhnw/DNAService.class
ch/fhnw/model/Sequence.class
ch/fhnw/util/SequenceValidator.class
ch/fhnw/model/Counter.class
ch/fhnw/AnalyzeDNAServlet.class
ch/fhnw/model/Information.class
ch/fhnw/util/DNAUtil.class
/Users/marcopereira/dnaanalyzerwa/src/main/java/ch/fhnw/util/DNAUtil.java
/Users/marcopereira/dnaanalyzerwa/src/main/java/ch/fhnw/model/Sequence.java
/Users/marcopereira/dnaanalyzerwa/src/main/java/ch/fhnw/model/Counter.java
/Users/marcopereira/dnaanalyzerwa/src/main/java/ch/fhnw/util/SequenceValidator.java
/Users/marcopereira/dnaanalyzerwa/src/main/java/ch/fhnw/model/Information.java
/Users/marcopereira/dnaanalyzerwa/src/main/java/ch/fhnw/AnalyzeDNAServlet.java
/Users/marcopereira/dnaanalyzerwa/src/main/java/ch/fhnw/DNAService.java
<?xml version="1.0" encoding="UTF-8" ?>
<testsuite tests="2" failures="0" name="ch.fhnw.model.SequenceTest" time="0.003" errors="0" skipped="0">
<testsuite tests="2" failures="0" name="ch.fhnw.model.SequenceTest" time="0.004" errors="0" skipped="0">
<properties>
<property name="java.runtime.name" value="Java(TM) SE Runtime Environment"/>
<property name="java.vm.version" value="13+33"/>
......@@ -41,7 +41,7 @@
<property name="java.class.path" value="/usr/local/Cellar/maven/3.6.2/libexec/boot/plexus-classworlds-2.6.0.jar"/>
<property name="java.vm.specification.version" value="13"/>
<property name="sun.arch.data.model" value="64"/>
<property name="sun.java.command" value="org.codehaus.plexus.classworlds.launcher.Launcher clean package"/>
<property name="sun.java.command" value="org.codehaus.plexus.classworlds.launcher.Launcher clean package cargo:undeploy cargo:deploy"/>
<property name="java.home" value="/Library/Java/JavaVirtualMachines/jdk-13.jdk/Contents/Home"/>
<property name="user.language" value="en"/>
<property name="java.specification.vendor" value="Oracle Corporation"/>
......@@ -57,6 +57,6 @@
<property name="socksNonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/>
<property name="ftp.nonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/>
</properties>
<testcase classname="ch.fhnw.model.SequenceTest" name="testCount" time="0.003"/>
<testcase classname="ch.fhnw.model.SequenceTest" name="testCount" time="0.004"/>
<testcase classname="ch.fhnw.model.SequenceTest" name="testCountAll" time="0"/>
</testsuite>
\ No newline at end of file
-------------------------------------------------------------------------------
Test set: ch.fhnw.model.SequenceTest
-------------------------------------------------------------------------------
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 sec
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.124 sec
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