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<%@ page |
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pageEncoding="UTF-8" |
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session="false" |
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import="net.sf.basedb.core.User" |
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import="net.sf.basedb.core.DbControl" |
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import="net.sf.basedb.core.SessionControl" |
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import="net.sf.basedb.core.Application" |
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import="net.sf.basedb.core.Extract" |
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import="net.sf.basedb.core.BioMaterial" |
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import="net.sf.basedb.core.MeasuredBioMaterial" |
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import="net.sf.basedb.core.BioMaterialEventSource" |
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import="net.sf.basedb.core.BioPlate" |
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import="net.sf.basedb.core.BioWell" |
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import="net.sf.basedb.core.PermissionDeniedException" |
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import="net.sf.basedb.core.ItemQuery" |
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import="net.sf.basedb.core.query.Restrictions" |
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import="net.sf.basedb.core.query.Hql" |
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import="net.sf.basedb.util.Values" |
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import="net.sf.basedb.util.formatter.WellCoordinateFormatter" |
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import="net.sf.basedb.util.extensions.Extension" |
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import="net.sf.basedb.clients.web.Base" |
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import="net.sf.basedb.clients.web.util.HTML" |
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import="net.sf.basedb.clients.web.extensions.ExtensionsControl" |
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import="java.util.List" |
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import="java.util.ArrayList" |
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%> |
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<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %> |
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<% |
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final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true); |
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final String ID = sc.getId(); |
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final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie"); |
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final String root = request.getContextPath(); |
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DbControl dc = null; |
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try |
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{ |
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dc = sc.newDbControl(); |
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final Extension reggie = ExtensionsControl.get(dc).getExtension("net.sf.basedb.reggie"); |
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final User user = User.getById(dc, sc.getLoggedInUserId()); |
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int libPlateId = Values.getInt(request.getParameter("bioplate")); |
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String poolSchema = request.getParameter("poolSchema"); |
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String barcodeVariant = request.getParameter("barcodeVariant"); |
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|
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BioPlate plate = BioPlate.getById(dc, libPlateId); |
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int columns = plate.getColumns(); |
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int rows = plate.getRows(); |
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String view = Values.getString(request.getParameter("view"), "list"); |
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String title = "Lab protocol for " + HTML.encodeTags(plate.getName()) + " - " + (view.equals("list") ? "list" : "table"); |
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%> |
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<base:page id="protocol" type="iframe" favicon="<%=home+"/images/libprep.png"%>" title="<%=title%>" noskin="true"> |
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<base:head |
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scripts="~../reggie-2.js,~pools.js,~plate.js,~libprep_protocol.js" |
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styles="~../css/reggie-2.css,~../css/printable.css,~../css/plate.css" |
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> |
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<style> |
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table.protocolheader |
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{ |
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width: 100%; |
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border: 1px solid #000000; |
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margin-bottom: 1em; |
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border-collapse: collapse; |
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} |
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|
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table.protocolheader > tbody > tr |
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{ |
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vertical-align: top; |
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height: 1.25em; |
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} |
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|
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table.protocolheader > tbody > tr > th |
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{ |
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text-align: left; |
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font-size: 1em; |
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background-color: #F0F0F0; |
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padding: 2px; |
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} |
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|
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table.protocolheader > tbody > tr > td |
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{ |
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text-align: left; |
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font-size: 1em; |
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padding: 2px; |
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} |
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|
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#listview |
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{ |
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width: 100%; |
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font-size: 85%; |
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border-collapse: collapse; |
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border: 1px solid #000000; |
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} |
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|
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#listview tr.evencol |
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{ |
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background-color: #F0F0F0; |
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} |
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|
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#listview thead |
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{ |
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border: 1px solid #000000; |
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background-color: #F0F0F0; |
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} |
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|
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#listview tbody |
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{ |
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page-break-inside: avoid; |
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border-top: 1px solid #000000; |
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border-bottom: 1px solid #000000; |
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} |
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|
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#listview th |
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{ |
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border-left: 1px solid #000000; |
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} |
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|
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#listview td |
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{ |
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border-left: 1px solid #000000; |
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border-top: 1px dotted #666666; |
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vertical-align: middle; |
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padding: 1px; |
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} |
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|
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#listview .col-num |
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{ |
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width: 1.75em; |
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text-align: center; |
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font-size: 125%; |
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font-weight: bold; |
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vertical-align: top; |
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} |
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|
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#listview .lib |
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{ |
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width: 15em; |
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text-align: center; |
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} |
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|
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#listview .empty .lib |
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{ |
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font-style: italic; |
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color: #666666; |
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text-align: center; |
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} |
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|
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#listview .workplate, #listview .barcode |
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{ |
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width: 7em; |
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text-align: center; |
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} |
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#listview .remarks |
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{ |
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vertical-align: top; |
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padding-left: 0.25em; |
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} |
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|
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/* Divide the 12 wells across the full page */ |
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#plateview .well |
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{ |
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width: 8.2%; |
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max-width: 8.2%; |
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min-width: 8.2%; |
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padding: 4px; |
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} |
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|
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#plateview .well:hover |
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{ |
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padding: 3px; |
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} |
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|
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#plateview .rowheader |
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{ |
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width: 2em; |
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} |
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|
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#plateview .lib |
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{ |
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font-weight: bold; |
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margin-bottom: 0.25em; |
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} |
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#plateview .remarks |
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{ |
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color: #C80000; |
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font-style: italic; |
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} |
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|
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#plateview .well.primary.empty |
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{ |
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background-color: #FFFFFF; |
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} |
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|
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#plateview .yellow-specimen .if-yellow |
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{ |
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background-image: url('../images/yellow-label-small.png'); |
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background-position: 1px 50%; |
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background-repeat: no-repeat; |
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/* Grow background without shifting text position veritcally, move to right to make room for icon*/ |
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padding: 4px 4px 3px 14px; |
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margin: -4px -4px -1px -4px; |
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} |
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|
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</style> |
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</base:head> |
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<base:body> |
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<div class="paper <%=view.equals("list") ? "" : "landscape"%>"> |
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|
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<form name="reggie" id="wizard"> |
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|
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<div id="page-data" class="datacontainer" |
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data-view="<%=view%>" |
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data-libplate="<%=libPlateId%>" |
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data-schema="<%=poolSchema%>" |
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data-barcode-variant="<%=barcodeVariant%>" |
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data-rows="<%=rows%>" |
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data-columns="<%=columns%>" |
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data-home-url="<%=home%>" |
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></div> |
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|
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<div id="wizard-status"></div> |
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|
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<div id="all-protocol" style="display: none;"> |
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|
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<div id="print-instructions" class="noprint fullwidth"> |
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<base:button id="print-button" image="<%=home+"/images/print.png"%>" title="Print…" /> |
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<span id="printNote"> |
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<b>Note!</b> |
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<% |
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if (view.equals("list")) |
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{ |
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%> |
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For better printing reduce margins to about <i>5mm</i> and set page orientation |
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to <i>portrait</i>. To fit everything on a single page, scale down to <i>60-70%</i>. |
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<% |
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} |
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else |
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{ |
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%> |
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For better printing reduce margins to about <i>5mm</i> and set page orientation |
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to <i>landscape</i>. The recommended scale is <i>100%</i>. |
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<% |
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} |
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%> |
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</span> |
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<br clear="all"> |
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</div> |
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|
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|
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<h1>Lab protocol for library preparation <span class="reggie">Reggie <%=reggie.getAbout().getVersion() %></span></h1> |
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|
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<table style="width: 100%;" class="protocolheader"> |
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<tr style="border-bottom: 1px solid #000000;"> |
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<th style="width: 15%;">Work plate</th> |
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<td style="width: 30%; border-right: 1px solid #000000;"><%=HTML.encodeTags(plate.getName())%></td> |
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<th style="width: 15%;">LibPrep</th> |
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<th style="width: 20%;">Date</th> |
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<th style="width: 20%;">Operator</th> |
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</tr> |
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<tr> |
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<td rowspan="2" colspan="2" style="width: 50%; border-right: 1px solid #000000;"><%=HTML.niceFormat(plate.getDescription()) %></td> |
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<td style="border-right: 1px solid #000000;">Amplification</td> |
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<td style="border-right: 1px solid #000000;"></td> |
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<td></td> |
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</tr> |
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<tr style="border-top: 1px solid #CCCCCC;"> |
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<td style="border-right: 1px solid #000000;">Cleanup</td> |
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<td style="border-right: 1px solid #000000;"></td> |
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<td></td> |
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</tr> |
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</table> |
1814 |
30 Jan 13 |
nicklas |
269 |
|
1814 |
30 Jan 13 |
nicklas |
270 |
<% |
1814 |
30 Jan 13 |
nicklas |
271 |
if (view.equals("list")) |
1814 |
30 Jan 13 |
nicklas |
272 |
{ |
1814 |
30 Jan 13 |
nicklas |
273 |
%> |
2673 |
16 Sep 14 |
nicklas |
274 |
<div id="listviewcontainer"> |
1814 |
30 Jan 13 |
nicklas |
275 |
<table style="width: 100%;" id="listview"> |
1814 |
30 Jan 13 |
nicklas |
276 |
<thead> |
1814 |
30 Jan 13 |
nicklas |
277 |
<tr class="toprow"> |
1814 |
30 Jan 13 |
nicklas |
278 |
<th></th> |
1814 |
30 Jan 13 |
nicklas |
279 |
<th class="lib"></th> |
1814 |
30 Jan 13 |
nicklas |
280 |
<th class="workplate">Work</th> |
1814 |
30 Jan 13 |
nicklas |
281 |
<th class="barcode">TruSeq</th> |
1814 |
30 Jan 13 |
nicklas |
282 |
<th></th> |
1814 |
30 Jan 13 |
nicklas |
283 |
</tr> |
1814 |
30 Jan 13 |
nicklas |
284 |
<tr> |
1814 |
30 Jan 13 |
nicklas |
285 |
<th></th> |
1814 |
30 Jan 13 |
nicklas |
286 |
<th class="lib">Library</th> |
1814 |
30 Jan 13 |
nicklas |
287 |
<th class="workplate">plate</th> |
1814 |
30 Jan 13 |
nicklas |
288 |
<th class="barcode">index</th> |
1814 |
30 Jan 13 |
nicklas |
289 |
<th>Remarks</th> |
1814 |
30 Jan 13 |
nicklas |
290 |
</tr> |
1814 |
30 Jan 13 |
nicklas |
291 |
</thead> |
1814 |
30 Jan 13 |
nicklas |
292 |
<% |
1814 |
30 Jan 13 |
nicklas |
293 |
WellCoordinateFormatter rowF = new WellCoordinateFormatter(true); |
1814 |
30 Jan 13 |
nicklas |
294 |
WellCoordinateFormatter colF = new WellCoordinateFormatter(false); |
1814 |
30 Jan 13 |
nicklas |
295 |
for (int c = 0; c < columns; ++c) |
1814 |
30 Jan 13 |
nicklas |
296 |
{ |
1814 |
30 Jan 13 |
nicklas |
297 |
String rowClass = c % 2 == 0 ? "evencol" : "oddcol"; |
1814 |
30 Jan 13 |
nicklas |
298 |
%> |
1814 |
30 Jan 13 |
nicklas |
299 |
<tbody> |
1814 |
30 Jan 13 |
nicklas |
300 |
<% |
1814 |
30 Jan 13 |
nicklas |
301 |
for (int r = 0; r < rows; ++r) |
1814 |
30 Jan 13 |
nicklas |
302 |
{ |
1814 |
30 Jan 13 |
nicklas |
303 |
String idSuffix = c + "." + r; |
1814 |
30 Jan 13 |
nicklas |
304 |
%> |
1814 |
30 Jan 13 |
nicklas |
305 |
<tr class="<%=rowClass%> empty" id="row.<%=idSuffix%>"> |
1814 |
30 Jan 13 |
nicklas |
306 |
<% |
1814 |
30 Jan 13 |
nicklas |
307 |
if (r == 0) |
1814 |
30 Jan 13 |
nicklas |
308 |
{ |
1814 |
30 Jan 13 |
nicklas |
309 |
%> |
2218 |
10 Feb 14 |
nicklas |
310 |
<td id="col.<%=c%>" class="col-num" rowspan="<%=rows%>"><%=c+1%></td> |
1814 |
30 Jan 13 |
nicklas |
311 |
<% |
1814 |
30 Jan 13 |
nicklas |
312 |
} |
1814 |
30 Jan 13 |
nicklas |
313 |
%> |
3760 |
19 Feb 16 |
nicklas |
314 |
<td class="lib if-yellow" id="lib.<%=idSuffix%>">empty</td> |
1814 |
30 Jan 13 |
nicklas |
315 |
<td class="workplate"><%=rowF.format(r)+colF.format(c)%></td> |
1814 |
30 Jan 13 |
nicklas |
316 |
<td class="barcode" id="barcode.<%=idSuffix%>"></td> |
1814 |
30 Jan 13 |
nicklas |
317 |
<td class="remarks" id="remarks.<%=idSuffix%>"></td> |
1814 |
30 Jan 13 |
nicklas |
318 |
</tr> |
1814 |
30 Jan 13 |
nicklas |
319 |
<% |
1814 |
30 Jan 13 |
nicklas |
320 |
} |
1814 |
30 Jan 13 |
nicklas |
321 |
%> |
1814 |
30 Jan 13 |
nicklas |
322 |
</tbody> |
1814 |
30 Jan 13 |
nicklas |
323 |
<% |
1814 |
30 Jan 13 |
nicklas |
324 |
} |
1814 |
30 Jan 13 |
nicklas |
325 |
%> |
1814 |
30 Jan 13 |
nicklas |
326 |
</table> |
1933 |
17 Apr 13 |
nicklas |
327 |
</div> |
1814 |
30 Jan 13 |
nicklas |
328 |
<% |
1814 |
30 Jan 13 |
nicklas |
329 |
} |
1814 |
30 Jan 13 |
nicklas |
330 |
else |
1814 |
30 Jan 13 |
nicklas |
331 |
{ |
1814 |
30 Jan 13 |
nicklas |
332 |
%> |
2673 |
16 Sep 14 |
nicklas |
333 |
<div id="plateviewcontainer"> |
1933 |
17 Apr 13 |
nicklas |
334 |
<table class="plate" style="margin: 0em 0 0 0; width: 100%;" id="plateview"> |
1814 |
30 Jan 13 |
nicklas |
335 |
<% |
1814 |
30 Jan 13 |
nicklas |
336 |
WellCoordinateFormatter rowF = new WellCoordinateFormatter(true); |
1814 |
30 Jan 13 |
nicklas |
337 |
WellCoordinateFormatter colF = new WellCoordinateFormatter(false); |
1814 |
30 Jan 13 |
nicklas |
338 |
%> |
1814 |
30 Jan 13 |
nicklas |
339 |
<tr class="header"> |
1814 |
30 Jan 13 |
nicklas |
340 |
<th></th> |
1814 |
30 Jan 13 |
nicklas |
341 |
<% |
1814 |
30 Jan 13 |
nicklas |
342 |
for (int c = 0; c < columns; ++c) |
1814 |
30 Jan 13 |
nicklas |
343 |
{ |
1814 |
30 Jan 13 |
nicklas |
344 |
%> |
1814 |
30 Jan 13 |
nicklas |
345 |
<th id="col.<%=c%>"><%=colF.format(c)%></th> |
1814 |
30 Jan 13 |
nicklas |
346 |
<% |
1814 |
30 Jan 13 |
nicklas |
347 |
} |
1814 |
30 Jan 13 |
nicklas |
348 |
%> |
1814 |
30 Jan 13 |
nicklas |
349 |
</tr> |
1814 |
30 Jan 13 |
nicklas |
350 |
<tbody> |
1814 |
30 Jan 13 |
nicklas |
351 |
<% |
1814 |
30 Jan 13 |
nicklas |
352 |
for (int r = 0; r < rows; ++r) |
1814 |
30 Jan 13 |
nicklas |
353 |
{ |
1814 |
30 Jan 13 |
nicklas |
354 |
String row = rowF.format(r); |
1814 |
30 Jan 13 |
nicklas |
355 |
%> |
1814 |
30 Jan 13 |
nicklas |
356 |
<tr class="row-<%=r%>"> |
1814 |
30 Jan 13 |
nicklas |
357 |
<th id="row.<%=r%>" class="rowheader"><%=row%></th> |
1814 |
30 Jan 13 |
nicklas |
358 |
<% |
1814 |
30 Jan 13 |
nicklas |
359 |
for (int c = 0; c < columns; ++c) |
1814 |
30 Jan 13 |
nicklas |
360 |
{ |
1814 |
30 Jan 13 |
nicklas |
361 |
%> |
1814 |
30 Jan 13 |
nicklas |
362 |
<td class="well col-<%=c%>" id="well.<%=r%>.<%=c%>"></td> |
1814 |
30 Jan 13 |
nicklas |
363 |
<% |
1814 |
30 Jan 13 |
nicklas |
364 |
} |
1814 |
30 Jan 13 |
nicklas |
365 |
%> |
1814 |
30 Jan 13 |
nicklas |
366 |
</tr> |
1814 |
30 Jan 13 |
nicklas |
367 |
<% |
1814 |
30 Jan 13 |
nicklas |
368 |
} |
1814 |
30 Jan 13 |
nicklas |
369 |
%> |
1814 |
30 Jan 13 |
nicklas |
370 |
</tbody> |
1814 |
30 Jan 13 |
nicklas |
371 |
<tr id="pool-row"> |
1814 |
30 Jan 13 |
nicklas |
372 |
<th colspan="13"> </th> |
1814 |
30 Jan 13 |
nicklas |
373 |
</tr> |
1814 |
30 Jan 13 |
nicklas |
374 |
</table> |
1933 |
17 Apr 13 |
nicklas |
375 |
</div> |
1814 |
30 Jan 13 |
nicklas |
376 |
<% |
1814 |
30 Jan 13 |
nicklas |
377 |
} |
1814 |
30 Jan 13 |
nicklas |
378 |
%> |
2673 |
16 Sep 14 |
nicklas |
379 |
</div> |
2673 |
16 Sep 14 |
nicklas |
380 |
</form> |
2673 |
16 Sep 14 |
nicklas |
381 |
</div> |
2673 |
16 Sep 14 |
nicklas |
382 |
</base:body> |
2673 |
16 Sep 14 |
nicklas |
383 |
</base:page> |
1814 |
30 Jan 13 |
nicklas |
384 |
<% |
1814 |
30 Jan 13 |
nicklas |
385 |
} |
1814 |
30 Jan 13 |
nicklas |
386 |
finally |
1814 |
30 Jan 13 |
nicklas |
387 |
{ |
1814 |
30 Jan 13 |
nicklas |
388 |
if (dc != null) dc.close(); |
1814 |
30 Jan 13 |
nicklas |
389 |
} |
1814 |
30 Jan 13 |
nicklas |
390 |
%> |