extensions/net.sf.basedb.reggie/trunk/resources/methylation/beta_start.jsp

Code
Comments
Other
Rev Date Author Line
6869 15 Nov 22 nicklas 1 <%@ page
6869 15 Nov 22 nicklas 2   pageEncoding="UTF-8"
6869 15 Nov 22 nicklas 3   session="false"
6869 15 Nov 22 nicklas 4   import="net.sf.basedb.core.User"
6869 15 Nov 22 nicklas 5   import="net.sf.basedb.core.DbControl"
6869 15 Nov 22 nicklas 6   import="net.sf.basedb.core.SessionControl"
6869 15 Nov 22 nicklas 7   import="net.sf.basedb.core.Application"
6869 15 Nov 22 nicklas 8   import="net.sf.basedb.clients.web.Base"  
6869 15 Nov 22 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
6869 15 Nov 22 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
6869 15 Nov 22 nicklas 11 %>
6869 15 Nov 22 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
6869 15 Nov 22 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
6869 15 Nov 22 nicklas 14 <%
6869 15 Nov 22 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
6869 15 Nov 22 nicklas 16 final String ID = sc.getId();
6869 15 Nov 22 nicklas 17 final float scale = Base.getScale(sc);
6869 15 Nov 22 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
6869 15 Nov 22 nicklas 19 DbControl dc = null;
6869 15 Nov 22 nicklas 20 try
6869 15 Nov 22 nicklas 21 {
6869 15 Nov 22 nicklas 22   dc = sc.newDbControl();
6869 15 Nov 22 nicklas 23   final User user = User.getById(dc, sc.getLoggedInUserId());
6869 15 Nov 22 nicklas 24 %>
6869 15 Nov 22 nicklas 25 <base:page type="default" >
6869 15 Nov 22 nicklas 26 <base:head 
6869 15 Nov 22 nicklas 27   scripts="~../reggie-2.js,~beta_start.js" 
6869 15 Nov 22 nicklas 28   styles="path.css,~../css/reggie-2.css"
6869 15 Nov 22 nicklas 29 />
6869 15 Nov 22 nicklas 30 <base:body>
6869 15 Nov 22 nicklas 31
6869 15 Nov 22 nicklas 32   <p:path><p:pathelement 
6869 15 Nov 22 nicklas 33     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
6869 15 Nov 22 nicklas 34     /><p:pathelement title="Start methylation beta-analysis" 
6869 15 Nov 22 nicklas 35     /></p:path>
6869 15 Nov 22 nicklas 36
6869 15 Nov 22 nicklas 37   <div class="content">
6869 15 Nov 22 nicklas 38   <form name="reggie" id="wizard" class="wizard">
6869 15 Nov 22 nicklas 39
6869 15 Nov 22 nicklas 40   <div class="step auto-hide" id="step-1">
6869 15 Nov 22 nicklas 41     <div class="step-no">1</div>
6869 15 Nov 22 nicklas 42     <div class="step-title">Select methylation items</div>
6869 15 Nov 22 nicklas 43     <div class="step-content">
6869 15 Nov 22 nicklas 44     
6869 15 Nov 22 nicklas 45       <table class="step-form">
6869 15 Nov 22 nicklas 46       <tr class="align-top">
6869 15 Nov 22 nicklas 47         <td class="prompt">Methylation items</td>
6869 15 Nov 22 nicklas 48         <td class="input">
6869 15 Nov 22 nicklas 49           <select class="required yellow-label-support" multiple size="30"
6869 15 Nov 22 nicklas 50             name="methylationItems" id="methylationItems"></select>
6869 15 Nov 22 nicklas 51             
6869 15 Nov 22 nicklas 52           <base:buttongroup style="margin-top: 0.5em;">
6869 15 Nov 22 nicklas 53             <base:button title="Select manually&hellip;" id="btnSelectMethylation" />
6869 15 Nov 22 nicklas 54           </base:buttongroup>
6869 15 Nov 22 nicklas 55         </td>
6869 15 Nov 22 nicklas 56         <td class="status" id="methylationItems.status"></td>
6869 15 Nov 22 nicklas 57         <td class="help"><span id="methylationItems.message" class="message"></span>
6869 15 Nov 22 nicklas 58           Select the methylation items that should be processed. 
6869 15 Nov 22 nicklas 59           The list contains items from the <b>Methylation beta-analysis</b> item list 
6869 15 Nov 22 nicklas 60           (max 250) and are sorted by BeadChip identifier and position.<br><br> 
6869 15 Nov 22 nicklas 61           
6869 15 Nov 22 nicklas 62           Items marked with <b>[R]</b> have been marked for re-processing 
6869 15 Nov 22 nicklas 63           due to a  previous failure.<br><br>
6869 15 Nov 22 nicklas 64           
6869 15 Nov 22 nicklas 65           It is possible to add more items manually as long as they belong to
6869 15 Nov 22 nicklas 66           the <b>DNA/Methylation</b> pipeline.
6869 15 Nov 22 nicklas 67         </td>
6869 15 Nov 22 nicklas 68       </tr>
6869 15 Nov 22 nicklas 69       </table>
6869 15 Nov 22 nicklas 70     </div>
6869 15 Nov 22 nicklas 71   </div>
6869 15 Nov 22 nicklas 72   
6869 15 Nov 22 nicklas 73   <div class="step" id="step-2">
6869 15 Nov 22 nicklas 74     <div class="step-no">2</div>
6869 15 Nov 22 nicklas 75     <div class="step-title">Analysis settings</div>
6869 15 Nov 22 nicklas 76     <div class="step-content">
6869 15 Nov 22 nicklas 77
6869 15 Nov 22 nicklas 78       <table class="step-form">
6869 15 Nov 22 nicklas 79       <tbody>
6869 15 Nov 22 nicklas 80         <tr>
6869 15 Nov 22 nicklas 81           <td class="prompt">Software</td>
6869 15 Nov 22 nicklas 82           <td class="input">
6869 15 Nov 22 nicklas 83             <select name="betaSoftware" id="betaSoftware"></select>
6869 15 Nov 22 nicklas 84           </td>
6869 15 Nov 22 nicklas 85           <td class="status" id="betaSoftware.status"></td>
6869 15 Nov 22 nicklas 86           <td class="help">
6869 15 Nov 22 nicklas 87             <span id="betaSoftware.message" class="message"></span>
6869 15 Nov 22 nicklas 88             Select the software to use.
6869 15 Nov 22 nicklas 89           </td>
6869 15 Nov 22 nicklas 90         </tr>
6869 15 Nov 22 nicklas 91       </tbody>
6869 15 Nov 22 nicklas 92       <tbody class="info-section">
6869 15 Nov 22 nicklas 93         <tr>
6869 15 Nov 22 nicklas 94           <td class="subprompt">Parameter set</td>
6869 15 Nov 22 nicklas 95           <td class="info" colspan="2">
6869 15 Nov 22 nicklas 96             <span id="betaSoftware.parameterSet"></span>
6869 15 Nov 22 nicklas 97             <div id="betaSoftware.description" class="item-description"></div>
6869 15 Nov 22 nicklas 98           </td>
6869 15 Nov 22 nicklas 99           <td class="help">
6869 15 Nov 22 nicklas 100             This step uses Minfi for calculating beta values. Parameters are configured in 
6869 15 Nov 22 nicklas 101             the &lt;methylation-beta&gt; section in reggie-config.xml.
6869 15 Nov 22 nicklas 102           </td>
6869 15 Nov 22 nicklas 103         </tr>
6869 15 Nov 22 nicklas 104       </tbody>
6869 15 Nov 22 nicklas 105       <tbody>
6869 15 Nov 22 nicklas 106         <tr class="section-header">
6869 15 Nov 22 nicklas 107           <td colspan="4">Job scheduler</td>
6869 15 Nov 22 nicklas 108         </tr>
6869 15 Nov 22 nicklas 109         <tr>
6869 15 Nov 22 nicklas 110           <td class="subprompt">Cluster</td>
6869 15 Nov 22 nicklas 111           <td class="input">
6869 15 Nov 22 nicklas 112             <select name="clusters" id="clusters" class="required"></select></td>
6869 15 Nov 22 nicklas 113           <td class="status" id="clusters.status"></td>
6869 15 Nov 22 nicklas 114           <td class="help">
6869 15 Nov 22 nicklas 115             <span id="clusters.message" class="message"></span>
6869 15 Nov 22 nicklas 116             Select the cluster to use for running the software.
6869 15 Nov 22 nicklas 117           </td>
6869 15 Nov 22 nicklas 118         </tr>
6869 15 Nov 22 nicklas 119         <tr id="job-priority" style="display: none;">
6869 15 Nov 22 nicklas 120           <td class="subprompt">Job priority</td>
6869 15 Nov 22 nicklas 121           <td class="input">
6869 15 Nov 22 nicklas 122             <select name="priority" id="priority"></select>
6869 15 Nov 22 nicklas 123           </td>
6869 15 Nov 22 nicklas 124           <td class="status" id="priority.status"></td>
6869 15 Nov 22 nicklas 125           <td class="help">
6869 15 Nov 22 nicklas 126             <span id="priority.message" class="message"></span>
6869 15 Nov 22 nicklas 127             Select the priority of the job.
6869 15 Nov 22 nicklas 128           </td>
6869 15 Nov 22 nicklas 129         </tr>
6980 17 Jan 23 nicklas 130         <tr id="job-partition" style="display: none;">
6980 17 Jan 23 nicklas 131           <td class="subprompt">Job partition</td>
6980 17 Jan 23 nicklas 132           <td class="input">
6980 17 Jan 23 nicklas 133             <select name="partition" id="partition"></select>
6980 17 Jan 23 nicklas 134           </td>
6980 17 Jan 23 nicklas 135           <td class="status" id="partition.status"></td>
6980 17 Jan 23 nicklas 136           <td class="help">
6980 17 Jan 23 nicklas 137             <span id="partition.message" class="message"></span>
6980 17 Jan 23 nicklas 138             Select the partition/queue that the job should be submitted to.
6980 17 Jan 23 nicklas 139           </td>
6980 17 Jan 23 nicklas 140         </tr>
6869 15 Nov 22 nicklas 141         <tr>
6869 15 Nov 22 nicklas 142           <td class="subprompt">Auto-confirm</td>
6869 15 Nov 22 nicklas 143           <td class="input"><input type="checkbox" name="autoConfirm" checked></td>
6869 15 Nov 22 nicklas 144           <td class="status" id="autoConfirm.status"></td>
6869 15 Nov 22 nicklas 145           <td class="help">
6869 15 Nov 22 nicklas 146             <span id="autoConfirm.message" class="message"></span>
6885 24 Nov 22 nicklas 147             If checked, the results are automatically confirmed unless there is
6885 24 Nov 22 nicklas 148             an error or warning.
6869 15 Nov 22 nicklas 149           </td>
6869 15 Nov 22 nicklas 150         </tr>
6869 15 Nov 22 nicklas 151         <tr>
6869 15 Nov 22 nicklas 152           <td class="subprompt">Debug</td>
6869 15 Nov 22 nicklas 153           <td class="input"><input type="checkbox" name="debug"></td>
6869 15 Nov 22 nicklas 154           <td class="status" id="debug.status"></td>
6869 15 Nov 22 nicklas 155           <td class="help">
6869 15 Nov 22 nicklas 156             <span id="debug.message" class="message"></span>
6869 15 Nov 22 nicklas 157             When running in debug mode temporary files are not removed from the
6869 15 Nov 22 nicklas 158             cluster node.
6869 15 Nov 22 nicklas 159           </td>
6869 15 Nov 22 nicklas 160         </tr>
6869 15 Nov 22 nicklas 161       </tbody>
6869 15 Nov 22 nicklas 162       </table>
6869 15 Nov 22 nicklas 163     </div>
6869 15 Nov 22 nicklas 164   </div>
6869 15 Nov 22 nicklas 165     
6869 15 Nov 22 nicklas 166     <div id="wizard-status"></div>
6869 15 Nov 22 nicklas 167   
6869 15 Nov 22 nicklas 168     <table class="navigation" id="navigation">
6869 15 Nov 22 nicklas 169     <tr>
6869 15 Nov 22 nicklas 170       <td><base:button id="gocancel" title="Cancel" /></td>
6869 15 Nov 22 nicklas 171       <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
6869 15 Nov 22 nicklas 172       <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
6869 15 Nov 22 nicklas 173       <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
6869 15 Nov 22 nicklas 174       <td id="gonext-message" class="message"></td>
6869 15 Nov 22 nicklas 175     </tr>
6869 15 Nov 22 nicklas 176     </table>
6869 15 Nov 22 nicklas 177   
6869 15 Nov 22 nicklas 178   </form>
6869 15 Nov 22 nicklas 179   </div>
6869 15 Nov 22 nicklas 180   
6869 15 Nov 22 nicklas 181 </base:body>
6869 15 Nov 22 nicklas 182 </base:page>
6869 15 Nov 22 nicklas 183 <%
6869 15 Nov 22 nicklas 184 }
6869 15 Nov 22 nicklas 185 finally
6869 15 Nov 22 nicklas 186 {
6869 15 Nov 22 nicklas 187   if (dc != null) dc.close();
6869 15 Nov 22 nicklas 188 }
6869 15 Nov 22 nicklas 189 %>

Generated on Tue Nov 21 03:31:07 2023 (UTC) by svndigest 0.11.2pre (dev build 1672)