extensions/net.sf.basedb.reggie/trunk/resources/libprep/mrna_registration.jsp

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1758 30 Nov 12 nicklas 1 <%@ page
1758 30 Nov 12 nicklas 2   pageEncoding="UTF-8"
1758 30 Nov 12 nicklas 3   session="false"
1758 30 Nov 12 nicklas 4   import="net.sf.basedb.core.User"
1758 30 Nov 12 nicklas 5   import="net.sf.basedb.core.DbControl"
1758 30 Nov 12 nicklas 6   import="net.sf.basedb.core.SessionControl"
1758 30 Nov 12 nicklas 7   import="net.sf.basedb.core.Application"
1758 30 Nov 12 nicklas 8   import="net.sf.basedb.clients.web.Base"  
1758 30 Nov 12 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
1758 30 Nov 12 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
1758 30 Nov 12 nicklas 11 %>
1758 30 Nov 12 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
1758 30 Nov 12 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
1758 30 Nov 12 nicklas 14 <%
3976 26 May 16 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
1758 30 Nov 12 nicklas 16 final String ID = sc.getId();
1758 30 Nov 12 nicklas 17 final float scale = Base.getScale(sc);
1758 30 Nov 12 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
1758 30 Nov 12 nicklas 19 DbControl dc = null;
1758 30 Nov 12 nicklas 20 try
1758 30 Nov 12 nicklas 21 {
1758 30 Nov 12 nicklas 22   dc = sc.newDbControl();
1758 30 Nov 12 nicklas 23   final User user = User.getById(dc, sc.getLoggedInUserId());
1758 30 Nov 12 nicklas 24 %>
1758 30 Nov 12 nicklas 25 <base:page type="default" >
2666 15 Sep 14 nicklas 26 <base:head 
2666 15 Sep 14 nicklas 27   scripts="~../reggie-2.js,~mrna_registration.js" 
2666 15 Sep 14 nicklas 28   styles="path.css,~../css/reggie-2.css"
2666 15 Sep 14 nicklas 29   >
2666 15 Sep 14 nicklas 30 <style>
2666 15 Sep 14 nicklas 31 .date-col
1758 30 Nov 12 nicklas 32 {
2666 15 Sep 14 nicklas 33   width: 12em;
1758 30 Nov 12 nicklas 34 }
1758 30 Nov 12 nicklas 35
2666 15 Sep 14 nicklas 36 .operator-col input
1889 27 Feb 13 nicklas 37 {
3026 11 Dec 14 nicklas 38   width: 95%;
1889 27 Feb 13 nicklas 39 }
2666 15 Sep 14 nicklas 40 </style>
1758 30 Nov 12 nicklas 41 </base:head>
2666 15 Sep 14 nicklas 42 <base:body>
1758 30 Nov 12 nicklas 43
1758 30 Nov 12 nicklas 44   <p:path><p:pathelement 
1758 30 Nov 12 nicklas 45     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
1792 17 Dec 12 nicklas 46     /><p:pathelement title="mRNA registration and quality control results" 
1758 30 Nov 12 nicklas 47     /></p:path>
1758 30 Nov 12 nicklas 48
1758 30 Nov 12 nicklas 49   <div class="content">
1758 30 Nov 12 nicklas 50
2666 15 Sep 14 nicklas 51   <form name="reggie" id="wizard" class="wizard">
2666 15 Sep 14 nicklas 52
2666 15 Sep 14 nicklas 53   <div class="step" id="step-1">
2666 15 Sep 14 nicklas 54     <div class="step-no">1</div>
2666 15 Sep 14 nicklas 55     <div class="step-title">Select mRNA bioplate</div>
2666 15 Sep 14 nicklas 56     <div class="step-content">
1758 30 Nov 12 nicklas 57   
2666 15 Sep 14 nicklas 58       <table class="step-form">
2666 15 Sep 14 nicklas 59       <tr>
1758 30 Nov 12 nicklas 60         <td class="prompt">mRNA bioplate</td>
2666 15 Sep 14 nicklas 61         <td class="input">
2666 15 Sep 14 nicklas 62           <select class="required" name="bioplate" id="bioplate"></select>
1758 30 Nov 12 nicklas 63         </td>
1758 30 Nov 12 nicklas 64         <td class="status" id="bioplate.status"></td>
2666 15 Sep 14 nicklas 65         <td class="help">
2666 15 Sep 14 nicklas 66           <span id="bioplate.message" class="message"></span>
1758 30 Nov 12 nicklas 67           Select an existing mRNA bioplate. The list contain all mRNA bioplates that
2509 16 Jun 14 nicklas 68           has been diluted, but not yet registered as completed (determined by the absence of a 
2509 16 Jun 14 nicklas 69           'creation' date).
1758 30 Nov 12 nicklas 70         </td>
1758 30 Nov 12 nicklas 71       </tr>
3282 29 Apr 15 nicklas 72       <tbody class="info-section">
2666 15 Sep 14 nicklas 73       <tr>
3282 29 Apr 15 nicklas 74         <td class="prompt">Comments</td>
3282 29 Apr 15 nicklas 75         <td class="info" id="comments-info"></td>
3282 29 Apr 15 nicklas 76         <td class="status"></td>
3282 29 Apr 15 nicklas 77         <td class="help"></td>
3282 29 Apr 15 nicklas 78       </tr>
3282 29 Apr 15 nicklas 79       </tbody>
3282 29 Apr 15 nicklas 80       <tr>
1889 27 Feb 13 nicklas 81         <td class="prompt">Outcome</td>
1758 30 Nov 12 nicklas 82         <td class="input">
2666 15 Sep 14 nicklas 83           <label><input type="radio" name="outcome" id="outcomeSuccess" 
2666 15 Sep 14 nicklas 84             checked>Success</label> - continue processing to cDNA<br>
2666 15 Sep 14 nicklas 85           <label><input type="radio" name="outcome" id="outcomeFailed" 
2666 15 Sep 14 nicklas 86             >Failure</label> - no further processing to cDNA
1758 30 Nov 12 nicklas 87         </td>
1889 27 Feb 13 nicklas 88         <td class="status"></td>
1889 27 Feb 13 nicklas 89         <td class="help">
1889 27 Feb 13 nicklas 90           Select the <b>Failure</b> option if further processing to cDNA is not possible.
1889 27 Feb 13 nicklas 91           No child cDNA plate will be created and existing RNA will be flagged and added
1889 27 Feb 13 nicklas 92           to the <b>Flagged RNA</b> list.
1758 30 Nov 12 nicklas 93         </td>
1758 30 Nov 12 nicklas 94       </tr>
1889 27 Feb 13 nicklas 95       </table>
2666 15 Sep 14 nicklas 96     </div>
1889 27 Feb 13 nicklas 97   </div>
1889 27 Feb 13 nicklas 98   
2666 15 Sep 14 nicklas 99   <div class="step" id="step-2">
2666 15 Sep 14 nicklas 100     <div class="step-no">2</div>
2666 15 Sep 14 nicklas 101     <div class="step-title">mRNA preparation information</div>
2666 15 Sep 14 nicklas 102     <div class="step-content">
2666 15 Sep 14 nicklas 103     
2666 15 Sep 14 nicklas 104       <table class="step-form">
2666 15 Sep 14 nicklas 105       <tr>
1998 29 May 13 nicklas 106         <td class="prompt">Step</td>
2666 15 Sep 14 nicklas 107         <td class="date-col"><b>Date</b></td>
2666 15 Sep 14 nicklas 108         <td class="operator-col"><b>Operator</b></td>
1998 29 May 13 nicklas 109         <td class="status"></td>
2509 16 Jun 14 nicklas 110         <td class="help" rowspan="4">
1998 29 May 13 nicklas 111           Enter date and operator for each step in the mRNA preparation.
1998 29 May 13 nicklas 112           (YYYYMMDD or MMDD)
1758 30 Nov 12 nicklas 113         </td>
1998 29 May 13 nicklas 114       </tr>
1998 29 May 13 nicklas 115       <tr>
1998 29 May 13 nicklas 116         <td class="subprompt">Purification</td>
2666 15 Sep 14 nicklas 117         <td class="date-col">
2666 15 Sep 14 nicklas 118           <input type="text" name="purificationDate" id="purificationDate"
2666 15 Sep 14 nicklas 119             class="auto-init" data-auto-init="focus-on-enter" data-next-focus="purificationOperator"
2666 15 Sep 14 nicklas 120             style="width: 8em;" maxlength="10">
1998 29 May 13 nicklas 121             <base:icon 
2666 15 Sep 14 nicklas 122               id="purificationDateCalendar"
2666 15 Sep 14 nicklas 123               subclass="auto-init"
2666 15 Sep 14 nicklas 124               data-auto-init="calendar"
2666 15 Sep 14 nicklas 125               data-textarea-id="purificationDate"
2666 15 Sep 14 nicklas 126               data-date-format="yyyyMMdd"
2666 15 Sep 14 nicklas 127               data-title="Purification date"
1998 29 May 13 nicklas 128               image="calendar.png" 
1998 29 May 13 nicklas 129               tooltip="Select a date from a calendar" 
1998 29 May 13 nicklas 130               tabindex="-1"
1998 29 May 13 nicklas 131             />
1998 29 May 13 nicklas 132         </td>
2666 15 Sep 14 nicklas 133         <td class="operator-col">
2666 15 Sep 14 nicklas 134           <input type="text" name="purificationOperator" id="purificationOperator" 
2666 15 Sep 14 nicklas 135             class="auto-init" data-auto-init="focus-on-enter" data-next-focus="fragmentationDate"
2666 15 Sep 14 nicklas 136             value="<%=HTML.encodeTags(user.getName())%>" maxlength="255">
1998 29 May 13 nicklas 137         </td>
1998 29 May 13 nicklas 138         <td class="status" id="purificationDate.status"></td>
1998 29 May 13 nicklas 139       </tr>
1998 29 May 13 nicklas 140       <tr>
1998 29 May 13 nicklas 141         <td class="subprompt">Fragmentation</td>
2666 15 Sep 14 nicklas 142         <td class="date-col">
2666 15 Sep 14 nicklas 143           <input type="text" name="fragmentationDate" id="fragmentationDate"
2666 15 Sep 14 nicklas 144             class="auto-init" data-auto-init="focus-on-enter" data-next-focus="fragmentationOperator"
2666 15 Sep 14 nicklas 145             style="width: 8em;" maxlength="10">
1998 29 May 13 nicklas 146             <base:icon 
2666 15 Sep 14 nicklas 147               id="fragmentationDateCalendar"
2666 15 Sep 14 nicklas 148               subclass="auto-init"
2666 15 Sep 14 nicklas 149               data-auto-init="calendar"
2666 15 Sep 14 nicklas 150               data-textarea-id="fragmentationDate"
2666 15 Sep 14 nicklas 151               data-date-format="yyyyMMdd"
2666 15 Sep 14 nicklas 152               data-title="Fragmentation date"
1998 29 May 13 nicklas 153               image="calendar.png" 
1998 29 May 13 nicklas 154               tooltip="Select a date from a calendar" 
1998 29 May 13 nicklas 155               tabindex="-1"
1998 29 May 13 nicklas 156             />
1998 29 May 13 nicklas 157         </td>
2666 15 Sep 14 nicklas 158         <td class="operator-col">
2666 15 Sep 14 nicklas 159           <input type="text" name="fragmentationOperator" id="fragmentationOperator"
2666 15 Sep 14 nicklas 160             class="auto-init" data-auto-init="focus-on-enter" data-next-focus="cleanupOperator"
2666 15 Sep 14 nicklas 161             value="<%=HTML.encodeTags(user.getName())%>" maxlength="255">
1998 29 May 13 nicklas 162         </td>
1998 29 May 13 nicklas 163         <td class="status" id="fragmentationDate.status"></td>
1998 29 May 13 nicklas 164       </tr>
1998 29 May 13 nicklas 165       <tr>
1998 29 May 13 nicklas 166         <td class="subprompt">Cleanup</td>
2666 15 Sep 14 nicklas 167         <td class="date-col">
2666 15 Sep 14 nicklas 168           <input type="text" name="cleanupDate" id="cleanupDate"
2666 15 Sep 14 nicklas 169             class="auto-init" data-auto-init="focus-on-enter" data-next-focus="cleanupOperator"
2666 15 Sep 14 nicklas 170             style="width: 8em;" maxlength="10">
1998 29 May 13 nicklas 171             <base:icon 
2666 15 Sep 14 nicklas 172               id="cleanupDateCalendar"
2666 15 Sep 14 nicklas 173               subclass="auto-init"
2666 15 Sep 14 nicklas 174               data-auto-init="calendar"
2666 15 Sep 14 nicklas 175               data-textarea-id="cleanupDate"
2666 15 Sep 14 nicklas 176               data-date-format="yyyyMMdd"
2666 15 Sep 14 nicklas 177               data-title="Cleanup date"
1998 29 May 13 nicklas 178               image="calendar.png" 
1998 29 May 13 nicklas 179               tooltip="Select a date from a calendar" 
1998 29 May 13 nicklas 180               tabindex="-1"
1998 29 May 13 nicklas 181             />
1998 29 May 13 nicklas 182         </td>
2666 15 Sep 14 nicklas 183         <td class="operator-col">
2666 15 Sep 14 nicklas 184           <input type="text" name="cleanupOperator" id="cleanupOperator" 
2666 15 Sep 14 nicklas 185             class="auto-init" data-auto-init="focus-on-enter" data-next-focus="pdf"
2666 15 Sep 14 nicklas 186             value="<%=HTML.encodeTags(user.getName())%>" maxlength="255">
1998 29 May 13 nicklas 187         </td>
1998 29 May 13 nicklas 188         <td class="status" id="cleanupDate.status"></td>
1998 29 May 13 nicklas 189       </tr>
2666 15 Sep 14 nicklas 190       <tr class="align-top">
1998 29 May 13 nicklas 191         <td class="prompt">BA PDF file</td>
1998 29 May 13 nicklas 192         <td class="input" colspan="2">
2666 15 Sep 14 nicklas 193           <table style="width: 100%;">
1889 27 Feb 13 nicklas 194           <tr>
2666 15 Sep 14 nicklas 195           <td>
4426 27 Mar 17 nicklas 196             <input class="text" type="text" name="pdf" id="pdf" 
2666 15 Sep 14 nicklas 197               data-subtype="BIOANALYZER_PDF" data-name-filter="%.pdf"
2666 15 Sep 14 nicklas 198               data-directory="/home/SCANB/MRnaPlateQC"
2666 15 Sep 14 nicklas 199             >
2666 15 Sep 14 nicklas 200           </td>
2666 15 Sep 14 nicklas 201           <td style="padding-left: 4px; width: 7em;">
2666 15 Sep 14 nicklas 202             <base:button 
1889 27 Feb 13 nicklas 203               title="Browse&hellip;"
2666 15 Sep 14 nicklas 204               id="pdf.btn"
2666 15 Sep 14 nicklas 205             />
1889 27 Feb 13 nicklas 206           </td>
1889 27 Feb 13 nicklas 207           </tr>
1889 27 Feb 13 nicklas 208           </table>
1889 27 Feb 13 nicklas 209         </td>
1889 27 Feb 13 nicklas 210         <td class="status" id="pdf.status"></td>
2666 15 Sep 14 nicklas 211         <td class="help"><span id="pdf.message" class="message"></span>
1998 29 May 13 nicklas 212           Select the <b>BioAnalyzer PDF file</b> that contains a printout with diagrams and other
1889 27 Feb 13 nicklas 213           useful documentation.
1889 27 Feb 13 nicklas 214         </td>
1889 27 Feb 13 nicklas 215       </tr>
2666 15 Sep 14 nicklas 216       <tr>
1758 30 Nov 12 nicklas 217         <td class="prompt">Protocol</td>
2666 15 Sep 14 nicklas 218         <td class="input" colspan="2">
2666 15 Sep 14 nicklas 219           <select name="mrnaProtocol" id="mrnaProtocol" 
2666 15 Sep 14 nicklas 220             class="auto-init" data-auto-init="focus-on-enter" data-next-focus="comments"
2666 15 Sep 14 nicklas 221             ></select>
2666 15 Sep 14 nicklas 222         </td>
1758 30 Nov 12 nicklas 223         <td class="status" id="mrnaProtocol.status"></td>
2666 15 Sep 14 nicklas 224         <td class="help">
2666 15 Sep 14 nicklas 225           <span id="mrnaProtocol.message" class="message"></span>
1998 29 May 13 nicklas 226           Select the protocol which was used in the mRNA preparation.
1758 30 Nov 12 nicklas 227         </td>
1758 30 Nov 12 nicklas 228       </tr>
2666 15 Sep 14 nicklas 229       <tr class="align-top">
1758 30 Nov 12 nicklas 230         <td class="prompt">Comments</td>
2666 15 Sep 14 nicklas 231         <td class="input" colspan="2">
2666 15 Sep 14 nicklas 232           <textarea rows="4" name="comments" id="comments"></textarea></td>
1890 01 Mar 13 nicklas 233         <td class="status" id="comments.status"></td>
2666 15 Sep 14 nicklas 234         <td class="help">
2666 15 Sep 14 nicklas 235           <span id="comments.message" class="message"></span>
2666 15 Sep 14 nicklas 236           Comments about the mRNA processing.
2666 15 Sep 14 nicklas 237         </td>
1758 30 Nov 12 nicklas 238       </tr>
1758 30 Nov 12 nicklas 239       </table>
2666 15 Sep 14 nicklas 240     </div>
1889 27 Feb 13 nicklas 241   </div>
1758 30 Nov 12 nicklas 242   
2666 15 Sep 14 nicklas 243   <div id="wizard-status"></div>
1758 30 Nov 12 nicklas 244   
2666 15 Sep 14 nicklas 245   <table class="navigation" id="navigation">
2666 15 Sep 14 nicklas 246   <tr>
2666 15 Sep 14 nicklas 247     <td><base:button id="gocancel" title="Cancel" /></td>
2666 15 Sep 14 nicklas 248     <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
2666 15 Sep 14 nicklas 249     <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
2666 15 Sep 14 nicklas 250     <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
2666 15 Sep 14 nicklas 251     <td id="gonext-message" class="message"></td>
2666 15 Sep 14 nicklas 252   </tr>
1758 30 Nov 12 nicklas 253   </table>
1758 30 Nov 12 nicklas 254   
1758 30 Nov 12 nicklas 255   </form>
1758 30 Nov 12 nicklas 256   </div>
1758 30 Nov 12 nicklas 257   
1758 30 Nov 12 nicklas 258 </base:body>
1758 30 Nov 12 nicklas 259 </base:page>
1758 30 Nov 12 nicklas 260 <%
1758 30 Nov 12 nicklas 261 }
1758 30 Nov 12 nicklas 262 finally
1758 30 Nov 12 nicklas 263 {
1758 30 Nov 12 nicklas 264   if (dc != null) dc.close();
1758 30 Nov 12 nicklas 265 }
1758 30 Nov 12 nicklas 266 %>

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