extensions/net.sf.basedb.reggie/trunk/resources/admin/analysis-cleanup.jsp

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4687 26 Feb 18 nicklas 1 <%@ page
4687 26 Feb 18 nicklas 2   pageEncoding="UTF-8"
4687 26 Feb 18 nicklas 3   session="false"
4687 26 Feb 18 nicklas 4   import="net.sf.basedb.core.Application"
4687 26 Feb 18 nicklas 5   import="net.sf.basedb.core.User"
4687 26 Feb 18 nicklas 6   import="net.sf.basedb.core.DbControl"
4687 26 Feb 18 nicklas 7   import="net.sf.basedb.core.SessionControl"
4687 26 Feb 18 nicklas 8   import="net.sf.basedb.clients.web.Base"
4687 26 Feb 18 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"
4687 26 Feb 18 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
4687 26 Feb 18 nicklas 11   import="net.sf.basedb.util.Values"
4687 26 Feb 18 nicklas 12 %>
4687 26 Feb 18 nicklas 13 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
4687 26 Feb 18 nicklas 14 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
4687 26 Feb 18 nicklas 15 <%
4687 26 Feb 18 nicklas 16 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
4687 26 Feb 18 nicklas 17 final String ID = sc.getId();
4687 26 Feb 18 nicklas 18 final float scale = Base.getScale(sc);
4687 26 Feb 18 nicklas 19 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
4687 26 Feb 18 nicklas 20
4687 26 Feb 18 nicklas 21 DbControl dc = null;
4687 26 Feb 18 nicklas 22 try
4687 26 Feb 18 nicklas 23 {
4687 26 Feb 18 nicklas 24   dc = sc.newDbControl();
4687 26 Feb 18 nicklas 25   final User user = User.getById(dc, sc.getLoggedInUserId());
4687 26 Feb 18 nicklas 26 %>
4687 26 Feb 18 nicklas 27 <base:page type="default" >
4687 26 Feb 18 nicklas 28 <base:head 
4687 26 Feb 18 nicklas 29   scripts="~../reggie-2.js,~analysis-cleanup.js" 
4687 26 Feb 18 nicklas 30   styles="path.css,~../css/reggie-2.css"
4687 26 Feb 18 nicklas 31 >
4687 26 Feb 18 nicklas 32 </base:head>
4687 26 Feb 18 nicklas 33 <base:body>
4687 26 Feb 18 nicklas 34
4687 26 Feb 18 nicklas 35   <p:path><p:pathelement 
4687 26 Feb 18 nicklas 36     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
4687 26 Feb 18 nicklas 37     /><p:pathelement title="Secondary analysis cleanup" 
4687 26 Feb 18 nicklas 38     /></p:path>
4687 26 Feb 18 nicklas 39
4687 26 Feb 18 nicklas 40   <div class="content">
4687 26 Feb 18 nicklas 41   <form name="reggie" id="wizard" class="wizard">
4687 26 Feb 18 nicklas 42   
4687 26 Feb 18 nicklas 43   <div class="step" id="step-1">
4687 26 Feb 18 nicklas 44     <div class="step-no">1</div>
4687 26 Feb 18 nicklas 45     <div class="step-title">Derived and raw bioassays</div>
4687 26 Feb 18 nicklas 46     <div class="step-content" style="padding: 0.5em;">
4687 26 Feb 18 nicklas 47
4687 26 Feb 18 nicklas 48       This wizard will look for derived and raw bioassays that has
4687 26 Feb 18 nicklas 49       been put in the trashcan and delete them including all child items
4687 26 Feb 18 nicklas 50       and linked files. It checks the following item types:
4687 26 Feb 18 nicklas 51       
4687 26 Feb 18 nicklas 52       <ul style="padding: 0.5em 2em;">
4687 26 Feb 18 nicklas 53       <li>Derived bioassays:
4687 26 Feb 18 nicklas 54         <ul>
4687 26 Feb 18 nicklas 55         <li>DemuxedSequences
4687 26 Feb 18 nicklas 56         <li>MergedSequences
4687 26 Feb 18 nicklas 57         <li>MaskedSequences
4687 26 Feb 18 nicklas 58         <li>AlignedSequences
7345 11 Sep 23 nicklas 59         <li>CopyNumber
7345 11 Sep 23 nicklas 60         <li>Methylation
7345 11 Sep 23 nicklas 61         <li>GenotypeCall
4687 26 Feb 18 nicklas 62         </ul>
4687 26 Feb 18 nicklas 63       <li>Raw bioassays:
4687 26 Feb 18 nicklas 64         <ul>
4687 26 Feb 18 nicklas 65         <li>Cufflinks
4687 26 Feb 18 nicklas 66         <li>StringTie
5722 13 Nov 19 nicklas 67         <li>VariantCall
4687 26 Feb 18 nicklas 68         </ul>
4687 26 Feb 18 nicklas 69       </ul>
4687 26 Feb 18 nicklas 70       
5581 21 Aug 19 nicklas 71       There are currently <b><span id="countDerivedBioAssays"></span></b> such derived
5581 21 Aug 19 nicklas 72       bioassays with <b><span id="countDerivedBioAssayChildren"></span></b> child items,  
5581 21 Aug 19 nicklas 73       <b><span id="countRawBioAssays"></span></b> raw bioassays and <b><span id="countFiles"></span></b> linked files.
4687 26 Feb 18 nicklas 74     </div>
4687 26 Feb 18 nicklas 75   </div>
4687 26 Feb 18 nicklas 76
4687 26 Feb 18 nicklas 77
4687 26 Feb 18 nicklas 78   <div id="wizard-status"></div>
4687 26 Feb 18 nicklas 79   <div id="wizard-progress"></div>
4687 26 Feb 18 nicklas 80
4687 26 Feb 18 nicklas 81     <table class="navigation" id="navigation">
4687 26 Feb 18 nicklas 82     <tr>
4687 26 Feb 18 nicklas 83       <td><base:button id="gocancel" title="Cancel" /></td>
4687 26 Feb 18 nicklas 84       <td><base:button id="goregister" title="Delete" image="<%=home+"/images/gonext.png"%>" /></td>
4687 26 Feb 18 nicklas 85       <td id="gonext-message" class="message"></td>
4687 26 Feb 18 nicklas 86     </tr>
4687 26 Feb 18 nicklas 87     </table>
4687 26 Feb 18 nicklas 88   </form>
4687 26 Feb 18 nicklas 89   </div>
4687 26 Feb 18 nicklas 90   
4687 26 Feb 18 nicklas 91 </base:body>
4687 26 Feb 18 nicklas 92 </base:page>
4687 26 Feb 18 nicklas 93 <%
4687 26 Feb 18 nicklas 94 }
4687 26 Feb 18 nicklas 95 finally
4687 26 Feb 18 nicklas 96 {
4687 26 Feb 18 nicklas 97   if (dc != null) dc.close();
4687 26 Feb 18 nicklas 98 }
4687 26 Feb 18 nicklas 99 %>

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