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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.Application" |
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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.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="net.sf.basedb.util.Values" |
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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 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,~import-external-specimen.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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|
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|
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#importItemsTable |
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{ |
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width: 100%; |
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border-collapse: collapse; |
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} |
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|
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#importItemsTable tr.highlight |
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{ |
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border-top-width: 1px; |
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border-top-style: dotted; |
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} |
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|
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#importItemsTable tr.newflowcell |
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{ |
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border-top-width: 1px; |
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border-top-style: solid; |
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border-top-color: black; |
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} |
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|
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#importItemsTable tr.evenflowcell |
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{ |
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background-color: #F8F8F8; |
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} |
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|
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|
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#importItemsTable thead |
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{ |
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border-top-width: 1px; |
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border-bottom-width: 1px; |
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} |
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|
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#importItemsTable th |
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{ |
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padding: 4px; |
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} |
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|
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#importItemsTable td |
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{ |
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text-align: center; |
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min-width: 4.5em; |
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} |
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|
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#importItemsTable tbody td |
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{ |
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padding: 2px 4px; |
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} |
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|
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#importItemsTable td.icon |
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{ |
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width: 20px; |
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min-width: 20px; |
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vertical-align: baseline; |
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} |
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|
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#importItemsTable td.valid |
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{ |
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text-align: left; |
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} |
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|
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.file-data |
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{ |
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font-style: italic; |
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opacity: 0.5; |
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} |
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|
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.action |
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{ |
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padding: 0.5em; |
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display: inline-block; |
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} |
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|
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.notes |
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{ |
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background-image: url('../images/info.png'); |
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background-repeat: no-repeat; |
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background-position: 2px 0; |
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padding-left: 20px; |
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margin: 0 0 0.5em 0.5em; |
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} |
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|
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.messagecontainer.minimal |
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{ |
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max-height: 5.5em; |
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overflow: auto; |
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} |
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|
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.messagecontainer.allvisible |
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{ |
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max-height: initial; |
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} |
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|
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.morewarnings |
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{ |
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font-weight: bold; |
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font-style: italic; |
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font-size: 90%; |
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margin-left: 1em; |
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margin-bottom: 0.25em; |
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display: inline-block; |
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} |
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.morewarnings:before |
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{ |
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content: '►'; |
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} |
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|
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.morewarnings.allvisible |
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{ |
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display: none; |
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} |
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|
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.less-messages .messagecontainer.minimal |
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{ |
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display: none; |
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} |
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|
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.less-messages .morewarnings |
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{ |
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display: initial; |
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} |
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|
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.fully-validate |
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{ |
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font-weight: bold; |
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font-style: italic; |
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margin-left: 1em; |
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} |
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|
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.fully-validate:before |
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{ |
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content: '►'; |
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} |
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|
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img.case-summary |
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{ |
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margin-left: 0.25em; |
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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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|
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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="Import externally processed samples" |
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/></p:path> |
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|
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<div class="content"> |
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<form name="reggie" id="wizard" class="wizard"> |
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|
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<div class="step auto-hide" id="step-1"> |
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<div class="step-no">1</div> |
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<div class="step-title">Select items to import</div> |
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<div class="step-content"> |
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<div style="padding: 0.5em 2em;"> |
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<li>Found <span id="num-json-files">?</span> JSON files, <span id="num-validated-files">?</span> has been fully validated |
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<span id="validate-all" class="fully-validate link" style="display: none;">Validate all!</span> |
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<li><span id="num-importable">?</span> files can be imported, <span id="num-importable-with-warnings">?</span> with warnings |
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<li><span id="num-importable-convert">?</span> existing NoSpecimen are converted to Specimen |
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<li><span id="num-importable-new">?</span> new Specimen items are created |
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<li><span id="num-importable-merge">?</span> existing Specimen are merged with data from JSON |
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<li><span id="num-no-json-files">?</span> existing NoSpecimen with no JSON match |
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<li><span id="num-stray-fastq-files">?</span> FASTQ files could not be matched to any JSON file |
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</div> |
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<div> |
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<table id="importItemsTable"> |
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<thead class="bg-filled-100"> |
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<tr> |
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<th>##</th> |
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<th class="dottedleft">Item</th> |
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<th class="dottedleft">Case</th> |
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<th class="dottedleft">JSON file</th> |
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<th>FlowCell</th> |
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<th>Reads</th> |
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<th>FASTQ files</th> |
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<th class="icon"></th> |
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<th class="valid dottedleft" style="text-align: left;">Messages/Actions |
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<label><input type="checkbox" id="lessMessages" name="lessMessages" |
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title="Show less of warnings and error messages">Show less</label> |
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</th> |
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</tr> |
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</thead> |
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<tbody id="itemTable"> |
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</tbody> |
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</table> |
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</div> |
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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">Import options</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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<tbody> |
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<tr> |
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<td class="prompt">Operator</td> |
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<td class="input"> |
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<select name="operator" id="operator"> |
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<option value="CMD">CMD |
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<option value="">- Use JSON - |
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</option> |
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</td> |
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<td class="status" id="operator.status"></td> |
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<td class="help"> |
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<span id="operator.message" class="message"></span> |
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The external operator. If the <i>Use JSON</i> option is selected |
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the operator information is taken from the JSON file. |
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</td> |
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</tr> |
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</tbody> |
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<tbody> |
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<tr class="section-header"> |
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<td colspan="4">FASTQ Import</td> |
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246 |
</tr> |
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247 |
<tr> |
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<td class="subprompt">Auto-analyze</td> |
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<td class="input"> |
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14 Apr 21 |
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<label><input type="radio" name="autoAnalyze" id="autoAnalyzeYes" disabled>Yes</label> |
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<label><input type="radio" name="autoAnalyze" id="autoAnalyzeNo" disabled>No</label> |
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</td> |
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<td class="status" id="autoAnalyze.status"></td> |
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<td class="help"> |
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<span id="autoAnalyze.message" class="message"></span> |
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If the auto-analyze option is enabled, Reggie will automatically start |
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importing the FASTQ files after a successful JSON import. |
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</td> |
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259 |
</tr> |
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260 |
<tr> |
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14 Apr 21 |
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<td class="subprompt">Protocol</td> |
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<td class="input"> |
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14 Apr 21 |
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<select name="mergeProtocol" id="mergeProtocol" disabled></select> |
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264 |
</td> |
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14 Apr 21 |
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<td class="status" id="mergeProtocol.status"></td> |
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<td class="help"> |
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<span id="mergeProtocol.message" class="message"></span> |
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14 Apr 21 |
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Select the protocol used for merging. |
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14 Apr 21 |
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</td> |
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270 |
</tr> |
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271 |
<tr> |
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14 Apr 21 |
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<td class="subprompt">Software</td> |
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14 Apr 21 |
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273 |
<td class="input"> |
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274 |
<select name="mergeSoftware" id="mergeSoftware" disabled></select> |
6211 |
14 Apr 21 |
nicklas |
275 |
</td> |
6211 |
14 Apr 21 |
nicklas |
276 |
<td class="status" id="mergeSoftware.status"></td> |
6211 |
14 Apr 21 |
nicklas |
277 |
<td class="help"> |
6211 |
14 Apr 21 |
nicklas |
278 |
<span id="mergeSoftware.message" class="message"></span> |
6211 |
14 Apr 21 |
nicklas |
279 |
Select the software to use for merging the FASTQ files. |
6211 |
14 Apr 21 |
nicklas |
280 |
</td> |
6211 |
14 Apr 21 |
nicklas |
281 |
</tr> |
6211 |
14 Apr 21 |
nicklas |
282 |
</tbody> |
6211 |
14 Apr 21 |
nicklas |
283 |
<tbody> |
6178 |
23 Mar 21 |
nicklas |
284 |
<tr class="section-header"> |
6735 |
09 May 22 |
nicklas |
285 |
<td colspan="4">Job scheduler</td> |
6178 |
23 Mar 21 |
nicklas |
286 |
</tr> |
6178 |
23 Mar 21 |
nicklas |
287 |
<tr> |
6735 |
09 May 22 |
nicklas |
288 |
<td class="subprompt">Cluster</td> |
6178 |
23 Mar 21 |
nicklas |
289 |
<td class="input"> |
6211 |
14 Apr 21 |
nicklas |
290 |
<select name="clusters" id="clusters" class="required" disabled></select> |
6211 |
14 Apr 21 |
nicklas |
291 |
</td> |
6178 |
23 Mar 21 |
nicklas |
292 |
<td class="status" id="clusters.status"></td> |
6178 |
23 Mar 21 |
nicklas |
293 |
<td class="help"> |
6178 |
23 Mar 21 |
nicklas |
294 |
<span id="clusters.message" class="message"></span> |
6211 |
14 Apr 21 |
nicklas |
295 |
Select the cluster to use for running the analysis. |
6178 |
23 Mar 21 |
nicklas |
296 |
</td> |
6178 |
23 Mar 21 |
nicklas |
297 |
</tr> |
6980 |
17 Jan 23 |
nicklas |
298 |
<tr id="job-priority" style="display: none;"> |
6178 |
23 Mar 21 |
nicklas |
299 |
<td class="subprompt">Job priority</td> |
6178 |
23 Mar 21 |
nicklas |
300 |
<td class="input"> |
6211 |
14 Apr 21 |
nicklas |
301 |
<select name="priority" id="priority" disabled></select> |
6178 |
23 Mar 21 |
nicklas |
302 |
</td> |
6178 |
23 Mar 21 |
nicklas |
303 |
<td class="status" id="priority.status"></td> |
6178 |
23 Mar 21 |
nicklas |
304 |
<td class="help"> |
6178 |
23 Mar 21 |
nicklas |
305 |
<span id="priority.message" class="message"></span> |
6211 |
14 Apr 21 |
nicklas |
306 |
Select the priority of the analysis jobs. |
6178 |
23 Mar 21 |
nicklas |
307 |
</td> |
6178 |
23 Mar 21 |
nicklas |
308 |
</tr> |
6980 |
17 Jan 23 |
nicklas |
309 |
<tr id="job-partition" style="display: none;"> |
6980 |
17 Jan 23 |
nicklas |
310 |
<td class="subprompt">Job partition</td> |
6980 |
17 Jan 23 |
nicklas |
311 |
<td class="input"> |
6980 |
17 Jan 23 |
nicklas |
312 |
<select name="partition" id="partition"></select> |
6980 |
17 Jan 23 |
nicklas |
313 |
</td> |
6980 |
17 Jan 23 |
nicklas |
314 |
<td class="status" id="partition.status"></td> |
6980 |
17 Jan 23 |
nicklas |
315 |
<td class="help"> |
6980 |
17 Jan 23 |
nicklas |
316 |
<span id="partition.message" class="message"></span> |
6980 |
17 Jan 23 |
nicklas |
317 |
Select the partition/queue that the job should be submitted to. |
6980 |
17 Jan 23 |
nicklas |
318 |
</td> |
6980 |
17 Jan 23 |
nicklas |
319 |
</tr> |
6178 |
23 Mar 21 |
nicklas |
320 |
<tr> |
6178 |
23 Mar 21 |
nicklas |
321 |
<td class="subprompt">Auto-confirm</td> |
6211 |
14 Apr 21 |
nicklas |
322 |
<td class="input"><input type="checkbox" name="autoConfirm" checked disabled></td> |
6178 |
23 Mar 21 |
nicklas |
323 |
<td class="status" id="autoConfirm.status"></td> |
6178 |
23 Mar 21 |
nicklas |
324 |
<td class="help"> |
6178 |
23 Mar 21 |
nicklas |
325 |
<span id="autoConfirm.message" class="message"></span> |
6211 |
14 Apr 21 |
nicklas |
326 |
If the FASTQ analysis is successful, with at least 10M reads |
6211 |
14 Apr 21 |
nicklas |
327 |
after trimmomatic and valid fragment size values, it is |
6211 |
14 Apr 21 |
nicklas |
328 |
automatically confirmed and alignment is started. |
6178 |
23 Mar 21 |
nicklas |
329 |
</td> |
6178 |
23 Mar 21 |
nicklas |
330 |
</tr> |
6178 |
23 Mar 21 |
nicklas |
331 |
<tr> |
6178 |
23 Mar 21 |
nicklas |
332 |
<td class="subprompt">Debug</td> |
6211 |
14 Apr 21 |
nicklas |
333 |
<td class="input"><input type="checkbox" name="debug" disabled></td> |
6178 |
23 Mar 21 |
nicklas |
334 |
<td class="status" id="debug.status"></td> |
6178 |
23 Mar 21 |
nicklas |
335 |
<td class="help"> |
6178 |
23 Mar 21 |
nicklas |
336 |
<span id="debug.message" class="message"></span> |
6211 |
14 Apr 21 |
nicklas |
337 |
When running in debug mode only part of the sequenced data is used and |
6211 |
14 Apr 21 |
nicklas |
338 |
temporary files are not removed from the cluster nodes. |
6178 |
23 Mar 21 |
nicklas |
339 |
</td> |
6178 |
23 Mar 21 |
nicklas |
340 |
</tr> |
6178 |
23 Mar 21 |
nicklas |
341 |
</tbody> |
6178 |
23 Mar 21 |
nicklas |
342 |
</table> |
6178 |
23 Mar 21 |
nicklas |
343 |
</div> |
6178 |
23 Mar 21 |
nicklas |
344 |
</div> |
6178 |
23 Mar 21 |
nicklas |
345 |
|
6178 |
23 Mar 21 |
nicklas |
346 |
<div id="wizard-status"></div> |
6178 |
23 Mar 21 |
nicklas |
347 |
<div id="wizard-progress"></div> |
6178 |
23 Mar 21 |
nicklas |
348 |
|
6178 |
23 Mar 21 |
nicklas |
349 |
<table class="navigation" id="navigation"> |
6178 |
23 Mar 21 |
nicklas |
350 |
<tr> |
6178 |
23 Mar 21 |
nicklas |
351 |
<td><base:button id="gocancel" title="Cancel" /></td> |
6178 |
23 Mar 21 |
nicklas |
352 |
<td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td> |
6178 |
23 Mar 21 |
nicklas |
353 |
<td><base:button id="goregister" title="Register" image="<%=home+"/images/gonext.png"%>" /></td> |
6178 |
23 Mar 21 |
nicklas |
354 |
<td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td> |
6178 |
23 Mar 21 |
nicklas |
355 |
<td id="gonext-message" class="message"></td> |
6178 |
23 Mar 21 |
nicklas |
356 |
</tr> |
6178 |
23 Mar 21 |
nicklas |
357 |
</table> |
6178 |
23 Mar 21 |
nicklas |
358 |
</form> |
6178 |
23 Mar 21 |
nicklas |
359 |
</div> |
6178 |
23 Mar 21 |
nicklas |
360 |
|
6178 |
23 Mar 21 |
nicklas |
361 |
</base:body> |
6178 |
23 Mar 21 |
nicklas |
362 |
</base:page> |
6178 |
23 Mar 21 |
nicklas |
363 |
<% |
6178 |
23 Mar 21 |
nicklas |
364 |
} |
6178 |
23 Mar 21 |
nicklas |
365 |
finally |
6178 |
23 Mar 21 |
nicklas |
366 |
{ |
6178 |
23 Mar 21 |
nicklas |
367 |
if (dc != null) dc.close(); |
6178 |
23 Mar 21 |
nicklas |
368 |
} |
6178 |
23 Mar 21 |
nicklas |
369 |
%> |