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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.util.Values" |
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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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%> |
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<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %> |
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<%@ taglib prefix="p" uri="/WEB-INF/path.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 float scale = Base.getScale(sc); |
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final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie"); |
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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 User user = User.getById(dc, sc.getLoggedInUserId()); |
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%> |
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<base:page type="default" > |
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<base:head |
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scripts="~../reggie-2.js,~lib_registration.js" |
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styles="path.css,~../css/reggie-2.css" |
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> |
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<style> |
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.date-col |
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{ |
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width: 12em; |
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} |
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|
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.operator-col input |
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{ |
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width: 95%; |
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} |
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|
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</style> |
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|
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</base:head> |
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<base:body> |
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|
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<p:path><p:pathelement |
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title="Reggie" href="<%="../index.jsp?ID="+ID%>" |
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/><p:pathelement title="Library registration" |
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/></p:path> |
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|
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<div class="content"> |
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|
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<form name="reggie" id="wizard" class="wizard"> |
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|
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<div class="step" id="step-1"> |
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<div class="step-no">1</div> |
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<div class="step-title">Select Library bioplate</div> |
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<div class="step-content"> |
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|
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<table class="step-form"> |
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<tr> |
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<td class="prompt">Library bioplate</td> |
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<td class="input"> |
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<select class="required" name="bioplate" id="bioplate"></select> |
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</td> |
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<td class="status" id="bioplate.status"></td> |
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<td class="help"> |
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<span id="bioplate.message" class="message"></span> |
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Select an existing bioplate. The list contain all bioplates that |
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has not yet been processed (determined by the absence of a 'creation' date). |
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</td> |
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</tr> |
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<tr class="align-top"> |
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<td class="prompt">Outcome</td> |
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<td class="input"> |
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<label><input type="radio" name="outcome" id="outcomeSuccess" |
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checked>Success</label> - continue processing<br> |
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<img src="../images/joinbottom.gif"><label><input type="checkbox" |
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name="useCaliper" id="useCaliper" value="1">Register Caliper files</label><br> |
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|
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<label><input type="radio" name="outcome" id="outcomeFailed" |
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>Failure</label> - no further processing |
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</td> |
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<td class="status"></td> |
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<td class="help"> |
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Select the <b>Failure</b> option if further processing to pooled libraries is not possible. |
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Existing RNA will be flagged and added to the <b>Flagged RNA</b> list. |
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</td> |
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</tr> |
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</table> |
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</div> |
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</div> |
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|
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<div class="step" id="step-2"> |
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<div class="step-no">2</div> |
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<div class="step-title">Full plate registration</div> |
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<div class="step-content"> |
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|
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<table class="step-form"> |
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<tr> |
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<td class="prompt">Step</td> |
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<td class="date-col"><b>Date</b></td> |
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<td class="operator-col"><b>Operator</b></td> |
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<td class="status"></td> |
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<td class="help" rowspan="3"> |
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Enter date and operator for each step in the cDNA preparation. |
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(YYYYMMDD or MMDD) |
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</td> |
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</tr> |
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|
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<tbody id="manualSection"> |
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<tr> |
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<td class="subprompt">Amplification</td> |
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<td class="date-col"> |
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<input type="text" name="amplificationDate" id="amplificationDate" |
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class="auto-init" data-auto-init="focus-on-enter" data-next-focus="amplificationOperator" |
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style="width: 8em;" maxlength="10"> |
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<base:icon |
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id="amplificationDateCalendar" |
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subclass="auto-init" |
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data-auto-init="calendar" |
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data-textarea-id="amplificationDate" |
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data-date-format="yyyyMMdd" |
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data-title="Amplification date" |
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image="calendar.png" |
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tooltip="Select a date from a calendar" |
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tabindex="-1" |
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/> |
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</td> |
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<td class="operator-col"> |
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<input type="text" name="amplificationOperator" id="amplificationOperator" |
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class="auto-init" data-auto-init="focus-on-enter" data-next-focus="cleanupDate" |
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value="<%=HTML.encodeTags(user.getName())%>" maxlength="255"> |
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</td> |
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<td class="status" id="amplificationDate.status"></td> |
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<td class="help"> |
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<span id="amplificationDate.message" class="message"></span> |
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</td> |
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</tr> |
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<tr> |
2002 |
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<td class="subprompt">Cleanup</td> |
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<td class="date-col"> |
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<input type="text" name="cleanupDate" id="cleanupDate" |
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class="auto-init" data-auto-init="focus-on-enter" data-next-focus="cleanupOperator" |
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style="width: 8em;" maxlength="10"> |
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<base:icon |
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id="cleanupDateCalendar" |
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subclass="auto-init" |
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data-auto-init="calendar" |
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data-textarea-id="cleanupDate" |
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data-date-format="yyyyMMdd" |
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data-title="Cleanup date" |
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image="calendar.png" |
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tooltip="Select a date from a calendar" |
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tabindex="-1" |
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/> |
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</td> |
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<td class="operator-col"> |
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<input type="text" name="cleanupOperator" id="cleanupOperator" |
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class="auto-init" data-auto-init="focus-on-enter" data-next-focus="qubitcsv" |
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value="<%=HTML.encodeTags(user.getName())%>" maxlength="255"> |
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</td> |
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<td class="status" id="cleanupDate.status"></td> |
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<td class="help"> |
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<span id="cleanupDate.message" class="message"></span> |
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</td> |
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</tr> |
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</tbody> |
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|
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<tbody id="qubitFilesSection"> |
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<tr> |
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<td class="prompt">Qubit files</td> |
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<td class="input" colspan="2"></td> |
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<td class="status"></td> |
1968 |
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<td class="help"></td> |
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</tr> |
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<tr class="align-top"> |
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<td class="subprompt">Concenctrations (csv or xlsx)</td> |
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<td class="input" colspan="2"> |
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<table style="width: 100%;"> |
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<tr> |
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<td> |
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<input class="text required" type="text" name="qubitcsv" id="qubitcsv" |
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data-subtype="QUBIT_CSV" data-name-filter="%.csv|%.xlsx" |
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data-directory="/home/SCANB/LibPlateQC" |
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> |
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</td> |
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<td style="padding-left: 4px; width: 7em;"> |
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<base:button |
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title="Browse…" |
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id="qubitcsv.btn" |
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/> |
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</td> |
1968 |
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</tr> |
1968 |
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</table> |
1968 |
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</td> |
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<td class="status" id="qubitcsv.status"></td> |
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<td class="help"> |
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<span id="qubitcsv.message" class="message"></span> |
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Select the <b>Qubit CSV</b> or <b>Excel</b> file that contains the concentration |
1968 |
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measurements. |
1968 |
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</td> |
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</tr> |
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</tbody> |
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<tbody id="caliperFilesSection"> |
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<tr> |
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<td class="prompt">Caliper files</td> |
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<td class="input" colspan="2"></td> |
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<td class="status"></td> |
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<td class="help"></td> |
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</tr> |
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<tr class="align-top"> |
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<td class="subprompt">Well table CSV</td> |
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<td class="input" colspan="2"> |
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<table style="width: 100%;"> |
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<tr> |
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<td> |
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<input class="text required" type="text" name="welltable" id="welltable" |
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data-subtype="CALIPER_WELL_TABLE" data-name-filter="%.csv" |
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data-directory="/home/SCANB/LibPlateQC" |
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> |
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</td> |
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<td style="padding-left: 4px; width: 7em;"> |
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<base:button |
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title="Browse…" |
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id="welltable.btn" |
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/> |
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</td> |
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</tr> |
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</table> |
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</td> |
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<td class="status" id="welltable.status"></td> |
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<td class="help"> |
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<span id="welltable.message" class="message"></span> |
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Select the <b>Well Table CSV</b> file that contains the exported |
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analysis result from the Caliper software. |
1908 |
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</td> |
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</tr> |
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|
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<tr class="align-top"> |
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<td class="subprompt">GXD raw data</td> |
2002 |
29 May 13 |
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<td class="input" colspan="2"> |
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<table style="width: 100%;"> |
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<tr> |
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<td> |
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17 Sep 14 |
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<input class="text" type="text" name="calipergxd" id="calipergxd" |
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data-subtype="CALIPER_RAW_DATA" data-name-filter="%.gxd" |
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17 Sep 14 |
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data-directory="/home/SCANB/LibPlateQC" |
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17 Sep 14 |
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> |
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</td> |
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<td style="padding-left: 4px; width: 7em;"> |
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<base:button |
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19 Mar 13 |
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title="Browse…" |
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17 Sep 14 |
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id="calipergxd.btn" |
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17 Sep 14 |
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/> |
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</td> |
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19 Mar 13 |
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</tr> |
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</table> |
1908 |
19 Mar 13 |
nicklas |
260 |
</td> |
1908 |
19 Mar 13 |
nicklas |
261 |
<td class="status" id="calipergxd.status"></td> |
2675 |
17 Sep 14 |
nicklas |
262 |
<td class="help"> |
2675 |
17 Sep 14 |
nicklas |
263 |
<span id="calipergxd.message" class="message"></span> |
1908 |
19 Mar 13 |
nicklas |
264 |
Select the <b>GXD raw data file</b> from Caliper. |
1908 |
19 Mar 13 |
nicklas |
265 |
</td> |
1908 |
19 Mar 13 |
nicklas |
266 |
</tr> |
2675 |
17 Sep 14 |
nicklas |
267 |
|
2675 |
17 Sep 14 |
nicklas |
268 |
<tr class="align-top"> |
1908 |
19 Mar 13 |
nicklas |
269 |
<td class="subprompt">PDF file</td> |
2002 |
29 May 13 |
nicklas |
270 |
<td class="input" colspan="2"> |
2675 |
17 Sep 14 |
nicklas |
271 |
<table style="width: 100%;"> |
1908 |
19 Mar 13 |
nicklas |
272 |
<tr> |
2675 |
17 Sep 14 |
nicklas |
273 |
<td> |
2675 |
17 Sep 14 |
nicklas |
274 |
<input class="text" type="text" name="caliperpdf" id="caliperpdf" |
2675 |
17 Sep 14 |
nicklas |
275 |
data-subtype="CALIPER_PDF" data-name-filter="%.pdf" |
2675 |
17 Sep 14 |
nicklas |
276 |
data-directory="/home/SCANB/LibPlateQC" |
2675 |
17 Sep 14 |
nicklas |
277 |
> |
2675 |
17 Sep 14 |
nicklas |
278 |
</td> |
2675 |
17 Sep 14 |
nicklas |
279 |
<td style="padding-left: 4px; width: 7em;"> |
2675 |
17 Sep 14 |
nicklas |
280 |
<base:button |
1908 |
19 Mar 13 |
nicklas |
281 |
title="Browse…" |
2675 |
17 Sep 14 |
nicklas |
282 |
id="caliperpdf.btn" |
2675 |
17 Sep 14 |
nicklas |
283 |
/> |
1908 |
19 Mar 13 |
nicklas |
284 |
</td> |
1908 |
19 Mar 13 |
nicklas |
285 |
</tr> |
1908 |
19 Mar 13 |
nicklas |
286 |
</table> |
1908 |
19 Mar 13 |
nicklas |
287 |
</td> |
1908 |
19 Mar 13 |
nicklas |
288 |
<td class="status" id="caliperpdf.status"></td> |
2675 |
17 Sep 14 |
nicklas |
289 |
<td class="help"> |
2675 |
17 Sep 14 |
nicklas |
290 |
<span id="caliperpdf.message" class="message"></span> |
1908 |
19 Mar 13 |
nicklas |
291 |
Select the <b>PDF file</b> that contains a printout with diagrams and other |
1906 |
14 Mar 13 |
nicklas |
292 |
useful documentation. |
1906 |
14 Mar 13 |
nicklas |
293 |
</td> |
1906 |
14 Mar 13 |
nicklas |
294 |
</tr> |
1908 |
19 Mar 13 |
nicklas |
295 |
</tbody> |
2675 |
17 Sep 14 |
nicklas |
296 |
|
3834 |
11 Apr 16 |
nicklas |
297 |
<tbody id="noCaliperFilesSection"> |
3834 |
11 Apr 16 |
nicklas |
298 |
<tr> |
3834 |
11 Apr 16 |
nicklas |
299 |
<td class="prompt">Library size</td> |
3834 |
11 Apr 16 |
nicklas |
300 |
<td class="input" colspan="2"> |
3834 |
11 Apr 16 |
nicklas |
301 |
<input type="text" name="libSize" id="libSize" |
3834 |
11 Apr 16 |
nicklas |
302 |
class="auto-init required" data-auto-init="focus-on-enter" data-next-focus="libProtocol" |
3834 |
11 Apr 16 |
nicklas |
303 |
style="width: 8em;" maxlength="10" value="300" data-default-value="300" data-min-value="0"> BP |
3834 |
11 Apr 16 |
nicklas |
304 |
</td> |
3834 |
11 Apr 16 |
nicklas |
305 |
<td class="status" id="libSize.status"></td> |
3834 |
11 Apr 16 |
nicklas |
306 |
<td class="help"> |
3834 |
11 Apr 16 |
nicklas |
307 |
<span id="libSize.message" class="message"></span> |
3834 |
11 Apr 16 |
nicklas |
308 |
The size in base-pairs of the final libraries. |
3834 |
11 Apr 16 |
nicklas |
309 |
</td> |
3834 |
11 Apr 16 |
nicklas |
310 |
</tr> |
3834 |
11 Apr 16 |
nicklas |
311 |
|
3834 |
11 Apr 16 |
nicklas |
312 |
</tbody> |
3834 |
11 Apr 16 |
nicklas |
313 |
|
2675 |
17 Sep 14 |
nicklas |
314 |
<tr> |
1908 |
19 Mar 13 |
nicklas |
315 |
<td class="prompt">Protocol</td> |
2675 |
17 Sep 14 |
nicklas |
316 |
<td class="input" colspan="2"> |
2675 |
17 Sep 14 |
nicklas |
317 |
<select name="libProtocol" id="libProtocol" |
2675 |
17 Sep 14 |
nicklas |
318 |
class="auto-init" data-auto-init="focus-on-enter" data-next-focus="libComments" |
2675 |
17 Sep 14 |
nicklas |
319 |
></select> |
2675 |
17 Sep 14 |
nicklas |
320 |
</td> |
1908 |
19 Mar 13 |
nicklas |
321 |
<td class="status" id="libProtocol.status"></td> |
2675 |
17 Sep 14 |
nicklas |
322 |
<td class="help"> |
2675 |
17 Sep 14 |
nicklas |
323 |
<span id="libProtocol.message" class="message"></span> |
1908 |
19 Mar 13 |
nicklas |
324 |
Select the protocol used for library preparation. |
1908 |
19 Mar 13 |
nicklas |
325 |
</td> |
1908 |
19 Mar 13 |
nicklas |
326 |
</tr> |
2675 |
17 Sep 14 |
nicklas |
327 |
<tr class="align-top"> |
1906 |
14 Mar 13 |
nicklas |
328 |
<td class="prompt">Comments</td> |
2675 |
17 Sep 14 |
nicklas |
329 |
<td class="input" colspan="2"> |
2675 |
17 Sep 14 |
nicklas |
330 |
<textarea rows="4" name="libComments" id="libComments"></textarea> |
2675 |
17 Sep 14 |
nicklas |
331 |
</td> |
1908 |
19 Mar 13 |
nicklas |
332 |
<td class="status" id="libComments.status"></td> |
2675 |
17 Sep 14 |
nicklas |
333 |
<td class="help"> |
2675 |
17 Sep 14 |
nicklas |
334 |
<span id="libComments.message" class="message"></span> |
2675 |
17 Sep 14 |
nicklas |
335 |
Comments about the library preparation. |
2675 |
17 Sep 14 |
nicklas |
336 |
</td> |
1906 |
14 Mar 13 |
nicklas |
337 |
</tr> |
1906 |
14 Mar 13 |
nicklas |
338 |
</table> |
2675 |
17 Sep 14 |
nicklas |
339 |
</div> |
1906 |
14 Mar 13 |
nicklas |
340 |
</div> |
1906 |
14 Mar 13 |
nicklas |
341 |
|
2675 |
17 Sep 14 |
nicklas |
342 |
<div id="wizard-status"></div> |
1906 |
14 Mar 13 |
nicklas |
343 |
|
2675 |
17 Sep 14 |
nicklas |
344 |
<table class="navigation" id="navigation"> |
2675 |
17 Sep 14 |
nicklas |
345 |
<tr> |
2675 |
17 Sep 14 |
nicklas |
346 |
<td><base:button id="gocancel" title="Cancel" /></td> |
2675 |
17 Sep 14 |
nicklas |
347 |
<td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td> |
2675 |
17 Sep 14 |
nicklas |
348 |
<td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>" /></td> |
2675 |
17 Sep 14 |
nicklas |
349 |
<td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td> |
2675 |
17 Sep 14 |
nicklas |
350 |
<td id="gonext-message" class="message"></td> |
2675 |
17 Sep 14 |
nicklas |
351 |
</tr> |
1895 |
05 Mar 13 |
nicklas |
352 |
</table> |
1895 |
05 Mar 13 |
nicklas |
353 |
|
2925 |
13 Nov 14 |
nicklas |
354 |
<div id="debug-tools"> |
2925 |
13 Nov 14 |
nicklas |
355 |
<base:button |
2925 |
13 Nov 14 |
nicklas |
356 |
id="btnFakeQubit" |
2925 |
13 Nov 14 |
nicklas |
357 |
image="bug.png" |
2925 |
13 Nov 14 |
nicklas |
358 |
title="Fake Qubit file" |
2925 |
13 Nov 14 |
nicklas |
359 |
tooltip="Generate a fake Qubit file" |
2925 |
13 Nov 14 |
nicklas |
360 |
data-cmd="GenerateFakeQubitFile" |
2925 |
13 Nov 14 |
nicklas |
361 |
data-file-field="qubitcsv" |
2925 |
13 Nov 14 |
nicklas |
362 |
/> |
2925 |
13 Nov 14 |
nicklas |
363 |
<base:button |
2925 |
13 Nov 14 |
nicklas |
364 |
id="btnFakeWelltable" |
2925 |
13 Nov 14 |
nicklas |
365 |
image="bug.png" |
2925 |
13 Nov 14 |
nicklas |
366 |
title="Fake Caliper well table" |
2925 |
13 Nov 14 |
nicklas |
367 |
tooltip="Generate a fake Caliper file" |
2925 |
13 Nov 14 |
nicklas |
368 |
data-cmd="GenerateFakeCaliperFile" |
2925 |
13 Nov 14 |
nicklas |
369 |
data-file-field="welltable" |
2925 |
13 Nov 14 |
nicklas |
370 |
/> |
2925 |
13 Nov 14 |
nicklas |
371 |
</div> |
2925 |
13 Nov 14 |
nicklas |
372 |
|
1895 |
05 Mar 13 |
nicklas |
373 |
</form> |
1895 |
05 Mar 13 |
nicklas |
374 |
</div> |
1895 |
05 Mar 13 |
nicklas |
375 |
|
1895 |
05 Mar 13 |
nicklas |
376 |
</base:body> |
1895 |
05 Mar 13 |
nicklas |
377 |
</base:page> |
1895 |
05 Mar 13 |
nicklas |
378 |
<% |
1895 |
05 Mar 13 |
nicklas |
379 |
} |
1895 |
05 Mar 13 |
nicklas |
380 |
finally |
1895 |
05 Mar 13 |
nicklas |
381 |
{ |
1895 |
05 Mar 13 |
nicklas |
382 |
if (dc != null) dc.close(); |
1895 |
05 Mar 13 |
nicklas |
383 |
} |
1895 |
05 Mar 13 |
nicklas |
384 |
%> |