extensions/net.sf.basedb.reggie/trunk/resources/mipsanalysis/align_start.jsp

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5844 26 Feb 20 nicklas 1 <%@ page
5844 26 Feb 20 nicklas 2   pageEncoding="UTF-8"
5844 26 Feb 20 nicklas 3   session="false"
5844 26 Feb 20 nicklas 4   import="net.sf.basedb.core.User"
5844 26 Feb 20 nicklas 5   import="net.sf.basedb.core.DbControl"
5844 26 Feb 20 nicklas 6   import="net.sf.basedb.core.SessionControl"
5844 26 Feb 20 nicklas 7   import="net.sf.basedb.core.Application"
5844 26 Feb 20 nicklas 8   import="net.sf.basedb.clients.web.Base"  
5844 26 Feb 20 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
5844 26 Feb 20 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
5844 26 Feb 20 nicklas 11 %>
5844 26 Feb 20 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
5844 26 Feb 20 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
5844 26 Feb 20 nicklas 14 <%
5844 26 Feb 20 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
5844 26 Feb 20 nicklas 16 final String ID = sc.getId();
5844 26 Feb 20 nicklas 17 final float scale = Base.getScale(sc);
5844 26 Feb 20 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
5844 26 Feb 20 nicklas 19 DbControl dc = null;
5844 26 Feb 20 nicklas 20 try
5844 26 Feb 20 nicklas 21 {
5844 26 Feb 20 nicklas 22   dc = sc.newDbControl();
5844 26 Feb 20 nicklas 23   final User user = User.getById(dc, sc.getLoggedInUserId());
5844 26 Feb 20 nicklas 24 %>
5844 26 Feb 20 nicklas 25 <base:page type="default" >
5844 26 Feb 20 nicklas 26 <base:head 
5844 26 Feb 20 nicklas 27   scripts="~../reggie-2.js,~align_start.js" 
5844 26 Feb 20 nicklas 28   styles="path.css,~../css/reggie-2.css"
5844 26 Feb 20 nicklas 29 />
5844 26 Feb 20 nicklas 30 <base:body>
5844 26 Feb 20 nicklas 31
5844 26 Feb 20 nicklas 32   <p:path><p:pathelement 
5844 26 Feb 20 nicklas 33     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
5844 26 Feb 20 nicklas 34     /><p:pathelement title="Start MIPs alignment" 
5844 26 Feb 20 nicklas 35     /></p:path>
5844 26 Feb 20 nicklas 36
5844 26 Feb 20 nicklas 37   <div class="content">
5844 26 Feb 20 nicklas 38   <form name="reggie" id="wizard" class="wizard">
5844 26 Feb 20 nicklas 39
5844 26 Feb 20 nicklas 40   <div class="step auto-hide" id="step-1">
5844 26 Feb 20 nicklas 41     <div class="step-no">1</div>
5844 26 Feb 20 nicklas 42     <div class="step-title">Select demuxed sequences</div>
5844 26 Feb 20 nicklas 43     <div class="step-content">
5844 26 Feb 20 nicklas 44     
5844 26 Feb 20 nicklas 45       <table class="step-form">
5844 26 Feb 20 nicklas 46       <tr class="align-top">
5844 26 Feb 20 nicklas 47         <td class="prompt">Demuxed sequences</td>
5844 26 Feb 20 nicklas 48         <td class="input">
5844 26 Feb 20 nicklas 49           <select class="required yellow-label-support" multiple size="30"
5844 26 Feb 20 nicklas 50             name="mergedSequences" id="mergedSequences"></select>
5844 26 Feb 20 nicklas 51             
5844 26 Feb 20 nicklas 52           <base:buttongroup style="margin-top: 0.5em;">
5844 26 Feb 20 nicklas 53             <base:button title="Select manually&hellip;" id="btnSelectMergedSequences" />
5844 26 Feb 20 nicklas 54           </base:buttongroup>
5844 26 Feb 20 nicklas 55         </td>
5844 26 Feb 20 nicklas 56         <td class="status" id="mergedSequences.status"></td>
5844 26 Feb 20 nicklas 57         <td class="help"><span id="mergedSequences.message" class="message"></span>
5844 26 Feb 20 nicklas 58           Select the sequences that should be aligned. The list contains merged sequences 
5844 26 Feb 20 nicklas 59           from the <b>MIPs alignment pipeline</b> item list (max 250).<br><br>
5844 26 Feb 20 nicklas 60           Items marked with <b>[R]</b> have been marked for re-alignment due to a failure of
5844 26 Feb 20 nicklas 61           a previous alignment.
5844 26 Feb 20 nicklas 62         </td>
5844 26 Feb 20 nicklas 63       </tr>
5844 26 Feb 20 nicklas 64       </table>
5844 26 Feb 20 nicklas 65
5844 26 Feb 20 nicklas 66     </div>
5844 26 Feb 20 nicklas 67   </div>
5844 26 Feb 20 nicklas 68   
5844 26 Feb 20 nicklas 69   
5844 26 Feb 20 nicklas 70   <div class="step" id="step-2">
5844 26 Feb 20 nicklas 71     <div class="step-no">2</div>
5844 26 Feb 20 nicklas 72     <div class="step-title">Alignment information</div>
5844 26 Feb 20 nicklas 73     <div class="step-content">
5844 26 Feb 20 nicklas 74
5844 26 Feb 20 nicklas 75       <table class="step-form">
5844 26 Feb 20 nicklas 76       <tbody>
5844 26 Feb 20 nicklas 77         <tr class="section-header">
5844 26 Feb 20 nicklas 78           <td colspan="4">Align</td>
5844 26 Feb 20 nicklas 79         </tr>
5844 26 Feb 20 nicklas 80         <tr valign="top">
5844 26 Feb 20 nicklas 81           <td class="subprompt">Protocol</td>
5844 26 Feb 20 nicklas 82           <td class="input">
5844 26 Feb 20 nicklas 83             <select name="alignProtocol" id="alignProtocol"></select>
5844 26 Feb 20 nicklas 84           </td>
5844 26 Feb 20 nicklas 85           <td class="status" id="alignProtocol.status"></td>
5844 26 Feb 20 nicklas 86           <td class="help">
5844 26 Feb 20 nicklas 87             <span id="alignProtocol.message" class="message"></span>
5844 26 Feb 20 nicklas 88             Select the protocol used for alignment.
5844 26 Feb 20 nicklas 89           </td>
5844 26 Feb 20 nicklas 90         </tr>
5844 26 Feb 20 nicklas 91         <tr>
5844 26 Feb 20 nicklas 92           <td class="subprompt">Software</td>
5844 26 Feb 20 nicklas 93           <td class="input">
5844 26 Feb 20 nicklas 94             <select name="alignSoftware" id="alignSoftware"></select>
5844 26 Feb 20 nicklas 95           </td>
5844 26 Feb 20 nicklas 96           <td class="status" id="alignSoftware.status"></td>
5844 26 Feb 20 nicklas 97           <td class="help">
5844 26 Feb 20 nicklas 98             <span id="alignSoftware.message" class="message"></span>
5844 26 Feb 20 nicklas 99             Select the software to use for alignment.
5844 26 Feb 20 nicklas 100           </td>
5844 26 Feb 20 nicklas 101         </tr>
5844 26 Feb 20 nicklas 102       </tbody>
5844 26 Feb 20 nicklas 103       <tbody class="info-section">
5844 26 Feb 20 nicklas 104         <tr>
5844 26 Feb 20 nicklas 105           <td class="subprompt">Parameter set</td>
5844 26 Feb 20 nicklas 106           <td class="info" colspan="2">
5844 26 Feb 20 nicklas 107             <span id="alignSoftware.parameterSet"></span>
5844 26 Feb 20 nicklas 108             <div id="alignSoftware.description" class="item-description"></div>
5844 26 Feb 20 nicklas 109           </td>
5844 26 Feb 20 nicklas 110           <td class="help">
5846 26 Feb 20 nicklas 111             This step uses novoalign for for aligning sequences. Parameters are 
5846 26 Feb 20 nicklas 112             configured in &lt;align-mips&gt; section in reggie-config.xml.
5844 26 Feb 20 nicklas 113           </td>
5844 26 Feb 20 nicklas 114         </tr>
5844 26 Feb 20 nicklas 115       </tbody>
5844 26 Feb 20 nicklas 116       <tbody>
5844 26 Feb 20 nicklas 117         <tr class="section-header">
6735 09 May 22 nicklas 118           <td colspan="4">Job scheduler</td>
5844 26 Feb 20 nicklas 119         </tr>
5844 26 Feb 20 nicklas 120         <tr>
5844 26 Feb 20 nicklas 121           <td class="subprompt">Cluster</td>
5844 26 Feb 20 nicklas 122           <td class="input">
5844 26 Feb 20 nicklas 123             <select name="clusters" id="clusters" class="required"></select></td>
5844 26 Feb 20 nicklas 124           <td class="status" id="clusters.status"></td>
5844 26 Feb 20 nicklas 125           <td class="help">
5844 26 Feb 20 nicklas 126             <span id="clusters.message" class="message"></span>
5844 26 Feb 20 nicklas 127             Select the cluster to use for running the software.
5844 26 Feb 20 nicklas 128           </td>
5844 26 Feb 20 nicklas 129         </tr>
5844 26 Feb 20 nicklas 130         <tr id="job-priority" style="display: none;">
5844 26 Feb 20 nicklas 131           <td class="subprompt">Job priority</td>
5844 26 Feb 20 nicklas 132           <td class="input">
5844 26 Feb 20 nicklas 133             <select name="priority" id="priority"></select>
5844 26 Feb 20 nicklas 134           </td>
5844 26 Feb 20 nicklas 135           <td class="status" id="priority.status"></td>
5844 26 Feb 20 nicklas 136           <td class="help">
5844 26 Feb 20 nicklas 137             <span id="priority.message" class="message"></span>
5844 26 Feb 20 nicklas 138             Select the priority of the job.
5844 26 Feb 20 nicklas 139           </td>
5844 26 Feb 20 nicklas 140         </tr>
5844 26 Feb 20 nicklas 141         <tr>
5844 26 Feb 20 nicklas 142           <td class="subprompt">Auto-confirm</td>
5844 26 Feb 20 nicklas 143           <td class="input"><input type="checkbox" name="autoConfirm" checked></td>
5844 26 Feb 20 nicklas 144           <td class="status" id="autoConfirm.status"></td>
5844 26 Feb 20 nicklas 145           <td class="help">
5844 26 Feb 20 nicklas 146             <span id="autoConfirm.message" class="message"></span>
5844 26 Feb 20 nicklas 147             TODO -- 
5846 26 Feb 20 nicklas 148             If the alignment is successful the next step is automatically
5846 26 Feb 20 nicklas 149             started. 
5844 26 Feb 20 nicklas 150           </td>
5844 26 Feb 20 nicklas 151         </tr>
5844 26 Feb 20 nicklas 152         <tr>
5844 26 Feb 20 nicklas 153           <td class="subprompt">Debug</td>
5844 26 Feb 20 nicklas 154           <td class="input"><input type="checkbox" name="debug"></td>
5844 26 Feb 20 nicklas 155           <td class="status" id="debug.status"></td>
5844 26 Feb 20 nicklas 156           <td class="help">
5844 26 Feb 20 nicklas 157             <span id="debug.message" class="message"></span>
5844 26 Feb 20 nicklas 158             When running in debug mode temporary files are not removed from the
5844 26 Feb 20 nicklas 159             cluster node.
5844 26 Feb 20 nicklas 160           </td>
5844 26 Feb 20 nicklas 161         </tr>
5844 26 Feb 20 nicklas 162       </tbody>
5844 26 Feb 20 nicklas 163       </table>
5844 26 Feb 20 nicklas 164     </div>
5844 26 Feb 20 nicklas 165   </div>
5844 26 Feb 20 nicklas 166     
5844 26 Feb 20 nicklas 167     <div id="wizard-status"></div>
5844 26 Feb 20 nicklas 168   
5844 26 Feb 20 nicklas 169     <table class="navigation" id="navigation">
5844 26 Feb 20 nicklas 170     <tr>
5844 26 Feb 20 nicklas 171       <td><base:button id="gocancel" title="Cancel" /></td>
5844 26 Feb 20 nicklas 172       <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
5844 26 Feb 20 nicklas 173       <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
5844 26 Feb 20 nicklas 174       <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
5844 26 Feb 20 nicklas 175       <td id="gonext-message" class="message"></td>
5844 26 Feb 20 nicklas 176     </tr>
5844 26 Feb 20 nicklas 177     </table>
5844 26 Feb 20 nicklas 178   
5844 26 Feb 20 nicklas 179   </form>
5844 26 Feb 20 nicklas 180   </div>
5844 26 Feb 20 nicklas 181   
5844 26 Feb 20 nicklas 182 </base:body>
5844 26 Feb 20 nicklas 183 </base:page>
5844 26 Feb 20 nicklas 184 <%
5844 26 Feb 20 nicklas 185 }
5844 26 Feb 20 nicklas 186 finally
5844 26 Feb 20 nicklas 187 {
5844 26 Feb 20 nicklas 188   if (dc != null) dc.close();
5844 26 Feb 20 nicklas 189 }
5844 26 Feb 20 nicklas 190 %>

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