source: extensions/net.sf.basedb.reggie/trunk/resources/index.jsp @ 5724

Last change on this file since 5724 was 5724, checked in by Nicklas Nordborg, 3 years ago

References #1199: Implement Variant calling pipeline

Auto-confirmation for the full variant calling should now be implemented. This will behave more like the confirmation for StringTie and Cufflinks which means that we also need a manual confirmation wizard to set the AnalysisResult annotation for the raw bioassays in case there is a problem. The index page has been prepared for this but the wizard is not yet implemented.

File size: 48.9 KB
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1<%@ page
2  pageEncoding="UTF-8"
3  session="false"
4  import="net.sf.basedb.core.Application"
5  import="net.sf.basedb.core.User"
6  import="net.sf.basedb.core.Role"
7  import="net.sf.basedb.core.Group"
8  import="net.sf.basedb.core.DbControl"
9  import="net.sf.basedb.core.Item"
10  import="net.sf.basedb.core.Permission"
11  import="net.sf.basedb.core.SessionControl"
12  import="net.sf.basedb.core.SystemItems"
13  import="net.sf.basedb.core.ItemQuery"
14  import="net.sf.basedb.core.query.Expressions"
15  import="net.sf.basedb.core.query.Hql"
16  import="net.sf.basedb.core.query.Restrictions"
17  import="net.sf.basedb.clients.web.Base"
18  import="net.sf.basedb.clients.web.util.HTML"
19  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
20  import="net.sf.basedb.util.Values"
21  import="java.util.List"
22%>
23<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
24<%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
25<%
26final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
27
28final String ID = sc.getId();
29final float scale = Base.getScale(sc);
30final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
31final String servletHome = ExtensionsControl.getServletUrl("net.sf.basedb.reggie", "Session");
32DbControl dc = null;
33try
34{
35  dc = sc.newDbControl();
36  final User user = User.getById(dc, sc.getLoggedInUserId());
37  final String lastWizardGroup = Values.getString(sc.getUserClientSetting("reggie.lastWizardGroup"), "sample-processing-section");
38 
39  boolean isAdmin = user.getId() == SystemItems.getId(User.ROOT);
40  boolean isPatientCurator = false;
41  if (!isAdmin)
42  {
43    try
44    {
45      Role admin = Role.getById(dc, SystemItems.getId(Role.ADMINISTRATOR));
46      isAdmin = sc.isMemberOf(admin);
47    }
48    catch (RuntimeException ex)
49    {}
50  }
51  try
52  {
53    ItemQuery<Group> query = Group.getQuery();
54    query.restrict(Restrictions.eq(Hql.property("name"), Expressions.string("PatientCurator")));
55    List<Group> result = query.list(dc);
56    if (result.size() == 1)
57    {
58      isPatientCurator = sc.isMemberOf(result.get(0));
59    }
60  }
61  catch (RuntimeException ex)
62  {}
63%>
64<base:page type="default" >
65<base:head styles="path.css,~css/reggie-2.css" scripts="~index.js,~reggie-2.js">
66<style>
67dl
68{
69  margin-top: 0px;
70  margin-bottom: 1em;
71  padding: 3px;
72}
73dt
74{
75  margin-top: 0.5em;
76  margin-left: 0.5em;
77}
78dd
79{
80  margin-left: 0.5em;
81  margin-bottom: 0.5em;
82  padding-left: 3em;
83}
84ul
85{
86  margin-top: 0px;
87  margin-bottom: 0px;
88  margin-left: 0em;
89  padding-left: 0em;
90}
91li
92{
93  margin-left: 0em;
94}
95img
96{
97  vertical-align: text-bottom;
98}
99.default h3
100{
101  color: #333377;
102  background-color: #E8E8E8;
103  font-weight: bold;
104  margin: 0;
105  padding: 3px 6px 3px 6px;
106  border-width: 1px;
107  font-size: 1.1em;
108}
109.not-implemented
110{
111  filter: url(css/filters.svg#grayscale); /* Firfox, etc */
112  filter: gray; /* IE */
113  opacity: 0.75;
114  pointer-events: none;
115}
116
117.not-implemented:after
118{
119  content: ' -- coming soon';
120}
121
122span.counter
123{
124  color: #666666;
125  font-style: italic;
126}
127
128span.counter.done:before
129{
130  content: '(';
131  padding-right: 1px;
132}
133
134span.counter + .counter.done:before
135{
136  content: '+';
137  padding-left: 2px;
138  padding-right: 2px;
139}
140
141span.counter.done:not(.more):after
142{
143  content: ')';
144  padding-left: 1px;
145}
146
147span.info-warning
148{
149  display: none;
150  color: #666666;
151  font-style: italic;
152  background-image: url('images/warning_small.png');
153  background-repeat: no-repeat;
154  background-position: 0 50%;
155  padding-left: 16px;
156  margin-left: 0.5em;
157}
158
159.require-permission
160{
161  color: #999999;
162  font-style: italic;
163}
164
165.snake-quote
166{
167  width: 32em;
168}
169
170.snake-quote-source
171{
172  margin-top: 0.5em;
173  float: right;
174  font-style: italic;
175}
176
177.snake-quote .notify-message
178{
179  margin: 0;
180}
181
182.snake-quote .notify-message:before
183{
184  margin: 0;
185  content: '';
186}
187
188#summary-stats
189{
190  font-variant: small-caps;
191  font-size: 125%;
192  white-space: nowrap;
193  overflow: hidden;
194}
195
196#activity-log
197{
198 
199}
200
201#activity-log .activity-day
202{
203  font-size: 1.1em;
204  font-weight: bold;
205  margin-top: 0.5em;
206}
207
208#activity-log .activity
209{
210  white-space: nowrap;
211  overflow: hidden;
212  padding: 0.15em 0;
213}
214
215#activity-log .activity.nothing-yet
216{
217  font-style: italic;
218}
219
220#activity-log .activity-time
221{
222  margin-right: 0.5em;
223  color: #666666;
224}
225#activity-log-rss
226{
227  float: right;
228  margin-right: 1em;
229}
230#counter-age-control
231{
232  position: absolute;
233  bottom: 2px;
234  right: 1rem;
235  font-size: 90%;
236}
237
238#counter-refresh, #counter-loading
239{
240  padding-left: 3px;
241  vertical-align: -2px;
242}
243
244div.counter
245{
246  display: inline-block;
247  min-width: 4em;
248  text-align: right;
249  padding-right: 0.25em;
250  font-size: 120%;
251  font-weight: bold;
252}
253
254#more-boxes-are-needed
255{
256  display: none;
257  background-color: #ffff00;
258  font-weight: bold;
259  padding: 2px 0.5em;
260  margin-bottom: 0.25em;
261  margin-left: 0.5em;
262  border-width: 2px;
263  border-radius: 5px;
264}
265
266#more-boxes-are-needed::before
267{
268  content: url('images/warning.png');
269  vertical-align: top;
270  margin-right: 0.25em;
271}
272
273div.group-menu
274{
275  background-color: #F8F8F8;
276  padding: 0.5em 10px 0.5em 1em;
277  border-width: 1px;
278  margin-bottom: 1em;
279  border-radius: 6px;
280}
281
282div.group-menu:hover
283{
284  text-decoration: none;
285  border-right-width: 10px;
286  padding-right: 0;
287}
288
289div.group-menu .group-title
290{
291  font-weight: bold;
292  font-size: 125%;
293  color: #333377;
294  margin-bottom: 0.25em;
295}
296div.group-menu .group-examples span
297{
298  color: #666666;
299  font-style: italic;
300  white-space: nowrap;
301}
302
303div.group-menu .group-examples span:before
304{
305  content: '•';
306  padding-right: 0.25em;
307}
308
309#wizard[data-wizard-group="sample-processing-section"] .group-menu[data-wizard-group="sample-processing-section"],
310#wizard[data-wizard-group="rna-libprep-section"] .group-menu[data-wizard-group="rna-libprep-section"],
311#wizard[data-wizard-group="mips-libprep-section"] .group-menu[data-wizard-group="mips-libprep-section"],
312#wizard[data-wizard-group="personal-information-section"] .group-menu[data-wizard-group="personal-information-section"],
313#wizard[data-wizard-group="statistics-section"] .group-menu[data-wizard-group="statistics-section"],
314#wizard[data-wizard-group="administration-section"] .group-menu[data-wizard-group="administration-section"]
315{
316  background-color: #FFFFF0;
317  border-right-width: 10px;
318  border-right-color: #2288AA;
319  padding-right: 0;
320}
321
322.wizard-group
323{
324  display: none;
325}
326
327#wizard[data-wizard-group="sample-processing-section"] #sample-processing-section,
328#wizard[data-wizard-group="rna-libprep-section"] #rna-libprep-section,
329#wizard[data-wizard-group="mips-libprep-section"] #mips-libprep-section,
330#wizard[data-wizard-group="personal-information-section"] #personal-information-section,
331#wizard[data-wizard-group="statistics-section"] #statistics-section,
332#wizard[data-wizard-group="administration-section"] #administration-section
333{
334  display: block;
335}
336
337</style>
338</base:head>
339<base:body>
340
341  <p:path><p:pathelement title="Reggie" /></p:path>
342
343  <div class="content">
344    <form name="reggie" id="wizard" class="wizard" data-wizard-group="<%=HTML.encodeTags(lastWizardGroup)%>">
345    <div id="wizard-status" style="position: absolute; z-index: 99; left: 25%; right: 25%; top: 25%; height: auto; text-align: center;"></div>
346    <div class="absolutefull" style="width: 30%;">
347      <div class="absolutefull" style="left: 1em; right: 0.5em; ">
348       
349        <div class="group-menu link" data-wizard-group="sample-processing-section">
350          <div class="group-title">Sample processing and histology</div>
351          <div class="group-examples">
352            <span>Registration</span>
353            <span>Partitioning</span>
354            <span>Extraction</span>
355            <span>Quality control</span>
356            <span>Histology scoring</span>
357          </div>
358        </div>
359 
360        <div class="group-menu link" data-wizard-group="rna-libprep-section">
361          <div class="group-title">RNA library preparation and analysis</div>
362          <div class="group-examples">
363            <span>Plate design</span>
364            <span>Library registration</span>
365            <span>Pooling</span>
366            <span>Sequencing</span>
367            <span>Secondary analysis</span>
368          </div>
369        </div>
370         
371        <div class="group-menu link" data-wizard-group="mips-libprep-section">
372          <div class="group-title">MIPs library preparation and analysis</div>
373          <div class="group-examples">
374            <span>Aliquot import</span>
375            <span>Plate design</span>
376            <span>Library registration</span>
377            <span>Pooling</span>
378            <span>Sequencing</span>
379            <span>Secondary analysis</span>
380          </div>
381        </div>
382       
383        <div class="group-menu link" data-wizard-group="personal-information-section">
384          <div class="group-title">Personal information and sample curation</div>
385          <div class="group-examples">
386            <span>Referral forms</span>
387            <span>Retraction</span>
388            <span>INCA</span>
389            <span>Flagged items</span>
390            <span>Batch updates</span>
391            <span>Outtakes</span>
392          </div>
393        </div>
394 
395        <div class="group-menu link" data-wizard-group="statistics-section">
396          <div class="group-title">Statistics and reporting</div>
397          <div class="group-examples">
398            <span>Sample count tables</span>
399            <span>Sample processing plots</span>
400            <span>YellowLabel tracking</span>
401          </div>
402        </div>
403        <%
404        if (isAdmin)
405        {
406          %>
407          <div class="group-menu link" data-wizard-group="administration-section">
408            <div class="group-title">Server administration</div>
409            <div class="group-examples">
410              <span>Installation wizard</span>
411              <span>Configuration</span>
412              <span>Cleanup</span>
413            </div>
414          </div>
415          <%
416        }
417        %>
418      </div>
419    </div>
420   
421    <div class="absolutefull" style="width: 40%; left: 30%; right: auto;">
422      <div class="absolutefull" style="left: 0.5em; right: 0.5em;">
423     
424        <div id="sample-processing-section" class="wizard-group">
425          <h3>Sample processing wizards</h3>
426          <dl class="leftborder rightborder bottomborder has-lib-prep">
427 
428          <dt>
429            <base:icon image="<%=home+"/images/specimen.png" %>" />
430            Specimen tube registration
431          </dt>
432          <dd>
433            <ul>
434            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/specimentube.jsp?ID=<%=ID%>"
435              >Register new specimen tubes</span>.
436            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/store-paused.jsp?ID=<%=ID%>"
437              >Store paused specimen</span>
438              <span class="counter" data-counter="paused-specimen-to-store" 
439                title="Number of paused specimen that has not yet been stored"></span>
440            </ul>
441          </dd>
442 
443          <dt>
444            <base:icon image="<%=home+"/images/partition.png" %>" />
445            <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/partitionform.jsp?ID=<%=ID%>"
446              >Partition wizard</span>
447          </dt>
448          <dd>
449            <ul>
450            <li>Register new partitions of existing specimens
451              <span class="counter more" data-counter="specimen-for-partition"
452                title="Number of unpartitioned specimen"></span><span 
453              class="counter" data-counter="specimen-for-reextraction" 
454                title="Number of specimen for re-extration"></span>
455            </ul>
456          </dd>
457           
458          <dt>
459            <base:icon image="<%=home+"/images/extraction.png" %>" />
460            DNA/RNA extraction wizards
461          </dt>
462          <dd>
463            <ul>
464            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/lysate_reextraction.jsp?ID=<%=ID%>"
465              >Pick lysate for re-extraction</span> 
466              <span class="counter" data-counter="lysates-to-pick-for-reextraction" 
467                title="Number of lysates for re-extraction that must be picked from freezers"></span>
468            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/allprep_protocol.jsp?ID=<%=ID%>"
469              >Lab tracking protocol for Allprep isolation</span> 
470              <span class="counter more" data-counter="lysates-for-allprep" 
471                title="Number of unprocessed lysates"></span><span
472              class="counter" data-counter="lysates-picked-for-rextraction"
473                title="Number of lysates for re-extraction that has been picked from freezers"></span>
474 
475            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/extraction_registration.jsp?ID=<%=ID%>"
476              >DNA/RNA/FlowThrough registration</span> 
477              <span class="counter more" data-counter="lysates-for-allprep" 
478                title="Number of unprocessed lysates"></span><span
479              class="counter" data-counter="lysates-picked-for-rextraction"
480                title="Number of lysates for re-extraction that has been picked from freezers"></span>
481               
482            <li>Normalization
483              <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rna_normalization.jsp?ID=<%=ID%>"
484              >RNA</span> 
485              <span class="counter" data-counter="rna-to-normalize" title="Number of RNA not yet normalized"></span>
486              <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/dna_normalization.jsp?ID=<%=ID%>"
487              >DNA</span> 
488              <span class="counter" data-counter="dna-to-normalize" title="Number of DNA not yet normalized"></span>
489             
490            </ul>
491          </dd>
492          <dt>
493            <base:icon image="<%=home+"/images/rnaqc.png" %>" />
494            RNA quality control wizards
495          </dt>
496          <dd>
497            <ul>
498            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_aliquot.jsp?ID=<%=ID%>"
499              >Create aliquots on Bioanalyzer/Caliper plates</span> 
500              <span class="counter" data-counter="rna-without-rnaqc" 
501                title="Number of RNA waiting for QC"></span>
502           
503            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_plate_export.jsp?ID=<%=ID%>"
504              >Export Caliper sample names and run parameters</span> 
505              <span class="counter" data-counter="caliper-rnaqc-waiting" 
506                title="Number of active Caliper plates"></span>
507           
508            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_plate_import.jsp?ID=<%=ID%>"
509              >Import RQS scores from Caliper well table file</span> 
510              <span class="counter" data-counter="caliper-rnaqc-waiting"
511                title="Number of active Caliper plates"></span>
512               
513            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_baprotocol.jsp?ID=<%=ID%>"
514              >Lab protocol for BioAnalyzer plates</span> 
515              <span class="counter" data-counter="bioanalyzer-rnaqc-waiting" 
516                title="Number of active BioAnalyzer plates"></span>
517               
518            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_bioanalyzer.jsp?ID=<%=ID%>"
519              >Register RIN scores for BioAnalyzer plates</span> 
520              <span class="counter" data-counter="bioanalyzer-rnaqc-waiting" 
521                title="Number of active BioAnalyzer plates"></span>
522            </ul>
523          </dd>
524          <dt style="margin-bottom: 0.5em;">
525            <base:icon image="<%=home+"/images/box.png" %>" />
526            <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/storage-box.jsp?ID=<%=ID%>"
527              >Storage box creation wizard</span>
528              <span class="counter more" data-counter="empty-storage-boxes" 
529                title="Number of empty storage boxes"></span><span 
530              class="counter" data-counter="empty-paused-storage-boxes" 
531                title="Number of empty storage boxes for paused specimen"></span>
532              <span id="more-boxes-are-needed">More boxes are needed</span>
533          </dt>
534          </dl>
535       
536          <h3>Histology wizards</h3>
537          <dl class="leftborder rightborder bottomborder">     
538          <dt>
539            <base:icon image="<%=home+"/images/histology.png" %>" />
540            Embedding and staining wizards
541          </dt>
542          <dd>
543            <ul>
544            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_protocol.jsp?ID=<%=ID%>"
545              >Lab tracking protocol for FFPE/HE</span> 
546              <span class="counter" data-counter="histology-active-lists" 
547                title="Number of active histology work lists"></span>
548           
549            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_block.jsp?ID=<%=ID%>"
550              >Register paraffin blocks</span> 
551              <span class="counter" data-counter="paraffin-blocks-not-embedded"
552                title="Number of paraffin blocks waiting for registration"></span>
553 
554            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_labels.jsp?ID=<%=ID%>"
555              >Download HE glass labels</span>
556           
557            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_glass.jsp?ID=<%=ID%>"
558              >Register HE glass</span> 
559              <span class="counter" data-counter="paraffin-blocks-without-heglass" 
560                title="Number of paraffin blocks without HE glass"></span>
561            </ul>
562          </dd>
563         
564          <dt>
565            <base:icon image="<%=home+"/images/microscope.png" %>" />
566            Scoring wizard
567          </dt>
568          <dd>
569            <ul>
570            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_score.jsp?ID=<%=ID%>"
571              >Score HE glass</span> 
572              <span class="counter" data-counter="heglass-not-scored" 
573                title="Number of unscored HE glass"></span>
574            </ul>
575          </dd>
576          </dl>
577        </div>
578     
579        <div id="rna-libprep-section" class="wizard-group">
580          <h3>Library preparation wizards</h3>
581          <dl class="leftborder rightborder bottomborder">
582       
583          <dt>
584            <base:icon image="<%=home+"/images/libprep.png" %>" />
585            Library preparation design wizards <span class="counter more" data-counter="rna-without-mrna-or-lib"
586                title="Number of RNA with no child mRNA or Library"></span><span 
587              class="counter" data-counter="normalized-rna-without-mrna-or-lib" 
588                title="Number of pre-normalized RNA with no child mRNA or Library"></span>
589          </dt>
590          <dd>
591            <ul>
592            <li><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/import-external-rna.jsp?ID=<%=ID%>"
593              >Import external RNA</span>
594            <li><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/select_rna.jsp?ID=<%=ID%>"
595              >New manual library preparation</span> 
596              (<span class="require-permission" data-role="LibraryPrep" data-link="libprep/select_rna.jsp?ID=<%=ID%>&autoDesign=1"
597              >auto-design</span>)
598            <li style="display: none;"><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/select_rna.jsp?ID=<%=ID%>&neoprep=1"
599              >New NeoPrep library preparation</span> 
600              (<span class="require-permission" data-role="LibraryPrep" data-link="libprep/select_rna.jsp?ID=<%=ID%>&neoprep=1&autoDesign=1"
601              >auto-design</span>)
602            </ul>
603          </dd>
604         
605          <dt>
606            <base:icon image="<%=home+"/images/pipette.png" %>" />
607            Manual library preparation wizards
608          </dt>
609          <dd>
610            <ul>
611            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_protocol.jsp?ID=<%=ID%>"
612              >Lab protocols for mRNA and cDNA preparation</span> 
613              <span class="counter" data-counter="mrna-plates-not-registered" 
614                title="Number of mRNA plates waiting for registration"></span>
615           
616            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/rna_dilution_registration.jsp?ID=<%=ID%>"
617              >RNA dilution registration</span>
618              <span class="counter" data-counter="mrna-plates-not-diluted" 
619                title="Number of mRNA plates waiting for dilution"></span>
620           
621            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_registration.jsp?ID=<%=ID%>"
622              >mRNA registration and quality control results</span> 
623              <span class="counter" data-counter="mrna-plates-diluted-not-registered" 
624                title="Number of mRNA plates waiting for registration"></span>
625           
626            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/cdna_registration.jsp?ID=<%=ID%>"
627              >cDNA registration</span> 
628              <span class="counter" data-counter="cdna-plates-not-registered" 
629                title="Number of cDNA plates waiting for registration"></span>
630           
631            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/assign_barcode.jsp?ID=<%=ID%>"
632              >Assign barcodes to cDNA plate</span> 
633              <span class="counter" data-counter="cdna-plates-for-barcoding" 
634                title="Number of cDNA plates waiting for barcode layout"></span>
635           
636            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/libprep_protocol.jsp?ID=<%=ID%>"
637              >Lab protocols and files for library preparation</span> 
638              <span class="counter" data-counter="lib-plates-for-libprep" 
639                title="Number of Lib plates waiting for registration"></span>
640           
641            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/libqc_registration.jsp?ID=<%=ID%>"
642              >Register quality control results</span> 
643              <span class="counter" data-counter="lib-plates-for-libprep" 
644                title="Number of Lib plates waiting for registration"></span>
645           
646            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/lib_registration.jsp?ID=<%=ID%>"
647              >Library registration</span> 
648              <span class="counter" data-counter="lib-plates-for-libprep"
649                title="Number of Lib plates waiting for registration"></span>
650            </ul>
651          </dd>
652         
653          <dt style="display: none;">
654            <base:icon image="<%=home+"/images/neoprep.png" %>" />
655            NeoPrep library preparation wizards
656          </dt>
657          <dd style="display: none;">
658            <ul>
659            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/neoprep_protocol.jsp?ID=<%=ID%>"
660              >Lab protocols for NeoPrep library preparation</span> 
661              <span class="counter" data-counter="neoprep-plates-for-libprep" 
662                title="Number of NeoPrep plates waiting for registration"></span>
663           
664            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/lib_registration.jsp?ID=<%=ID%>&neoprep=1"
665              >NeoPrep library registration</span> 
666              <span class="counter" data-counter="neoprep-plates-for-libprep"
667                title="Number of NeoPrep plates waiting for registration"></span>
668            </ul>
669          </dd>
670         
671          <dt>
672            <base:icon image="<%=home+"/images/pool.png" %>" />
673            Pooling wizards
674          </dt>
675          <dd>
676            <ul>
677            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/create_pools.jsp?ID=<%=ID%>"
678              >Create pooled libraries</span> 
679              <span class="counter more" data-counter="lib-plates-for-pooling"
680                title="Number of Lib plates waiting for pooling"></span><span 
681              class="counter" data-counter="neoprep-plates-for-pooling"
682                title="Number of NeoPrep plates waiting for registration"></span>
683           
684            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/pool_protocol.jsp?ID=<%=ID%>"
685              >Lab protocols for pooling</span> 
686              <span class="counter" data-counter="pools-not-registered-rnaseq" 
687                title="Number of pools waiting for registration"></span>
688           
689            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/pool_registration.jsp?ID=<%=ID%>"
690              >Register pooled libraries</span> 
691              <span class="counter" data-counter="pools-not-registered-rnaseq" 
692                title="Number of pools waiting for registration"></span>
693            </ul>
694          </dd>
695          </dl>
696         
697          <h3>Sequencing wizards</h3>
698          <dl class="leftborder rightborder bottomborder">
699         
700          <dt>
701            <base:icon image="<%=home+"/images/flowcell.png" %>" />
702            Clustering and sequencing wizards
703          </dt>
704          <dd>
705            <ul>
706            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/create_flowcells.jsp?ID=<%=ID%>"
707              >Create flow cells</span> 
708              <span class="counter" data-counter="pools-not-used-rnaseq" 
709                title="Number of pools waiting for sequencing"></span>
710           
711            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/flowcell_protocol.jsp?ID=<%=ID%>"
712              >Lab protocol for sequencing</span> 
713              <span class="counter" data-counter="flow-cells-not-sequenced-rnaseq" 
714                title="Number of flow cells waiting to be sequenced"></span>
715           
716            <li><span class="require-permission" data-role="LibraryPrep" data-link="sequencing/sequencing_started.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
717              >Register sequencing started</span> 
718              <span class="counter" data-counter="flow-cells-not-sequenced-rnaseq" 
719                title="Number of flow cells waiting to be sequenced"></span>
720 
721            <li><span class="require-permission" data-role="LibraryPrep" data-link="sequencing/sequencing_ended.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
722              >Register sequencing ended</span> 
723              <span class="counter" data-counter="sequencing-runs-active-rnaseq" 
724                title="Number of active sequencing runs"></span>
725            </ul>
726          </dd>
727         
728          </dl>
729       
730          <h3>Secondary analysis wizards</h3>
731          <dl class="leftborder rightborder bottomborder">
732            <dt>
733              <base:icon image="<%=home+"/images/server.png" %>" />
734              Demux and merge wizards
735            </dt>
736            <dd>
737              <ul>
738              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="sequencing/sequencing_confirm.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
739                >Confirm sequencing completed</span> 
740                <span class="counter" data-counter="sequencing-runs-unconfirmed-rnaseq" 
741                  title="Number of ended but not confirmed sequencing runs"></span>
742             
743              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
744                >Start demux and merge</span> 
745                <span class="counter" data-counter="sequencing-runs-for-demux-rnaseq" 
746                  title="Number of confirmed sequencing runs waiting to be demuxed"></span>
747             
748              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/demux_confirm.jsp?ID=<%=ID%>"
749                >Confirm demux and merge completed</span> 
750                <span class="counter" data-counter="demux-jobs-not-confirmed-rnaseq"
751                  title="Number of demux jobs waiting for confirmation"></span>
752              </ul>
753            </dd>
754 
755            <dt>
756              <base:icon image="<%=home+"/images/align.png" %>" />
757              Hisat and StringTie pipeline
758            </dt>
759            <dd>
760              <ul>
761              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/hisat_start.jsp?ID=<%=ID%>"
762                >Start Hisat alignment</span>
763                <span class="counter" data-counter="merged-sequences-for-hisat-alignment"
764                  title="Number of merged sequences waiting for Hisat alignment"></span>
765                <span id="hisat-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
766                 
767              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/hisat_confirm.jsp?ID=<%=ID%>"
768                >Confirm Hisat alignment</span> 
769                <span class="counter" data-counter="hisat-aligned-sequences-not-confirmed" 
770                  title="Number of Hisat aligned sequences waiting for confirmation"></span>
771             
772              <li><span id="genotype-qc" class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/genotype_qc.jsp?ID=<%=ID%>"
773                >Genotype quality control</span> 
774                <span class="counter" data-counter="alignments-for-genotype-qc" 
775                  title="Number of alignments with VCF files that has not been checked"></span>
776 
777              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/mbaf_start.jsp?ID=<%=ID%>"
778                >Start mBAF analysis</span> 
779                <span class="counter" data-counter="aligned-sequences-for-mbaf" 
780                  title="Number of aligned sequences waiting for mBAF analysis"></span>
781                <span id="mbaf-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
782               
783              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/stringtie_start.jsp?ID=<%=ID%>"
784                >Start StringTie</span>
785                <span class="counter" data-counter="aligned-sequences-for-stringtie"
786                  title="Number of aligned sequences waiting for StringTie"></span>
787                <span id="stringtie-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
788 
789              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/stringtie_confirm.jsp?ID=<%=ID%>"
790                >Confirm StringTie completed</span> 
791                <span class="counter" data-counter="stringtie-not-confirmed" 
792                  title="Number of StringTie jobs waiting for confirmation"></span>
793              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=SCANB_REPORT"
794                >SCAN-B report</span> 
795                <span class="counter" data-counter="rawbioassys-without-scanbreport" 
796                  title="Number of rawbioassays without a SCAN-B report PDF"></span>
797              </ul>
798            </dd>
799           
800            <dt>
801              <base:icon image="<%=home+"/images/variantcall.png" %>" />
802              Variant calling pipeline
803            </dt>
804           
805            <dd>
806              <ul>
807              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/vcall_start.jsp?ID=<%=ID%>"
808                >Start variant calling</span> 
809                <span class="counter" data-counter="aligned-sequences-for-variant-calling" 
810                  title="Number of aligned sequences waiting for variant calling pipeline"></span>
811                <span id="variant-calling-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
812              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/vcall_confirm.jsp?ID=<%=ID%>"
813                >Confirm variant calling</span> 
814                <span class="counter" data-counter="variantcall-not-confirmed" 
815                  title="Number of VariantCall jobs waiting for confirmation"></span>
816              </ul>
817            </dd>
818           
819            <dt>
820              <base:icon image="<%=home+"/images/pdffile.png" %>" />
821              Legacy Tophat and Cufflinks pipeline <span id="legacy-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
822            </dt>
823            <dd>
824              <ul>
825              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/align_start.jsp?ID=<%=ID%>"
826                >Start Tophat and Cufflinks</span> 
827                <span class="counter" data-counter="merged-sequences-for-legacy-alignment"
828                  title="Number of merged sequences waiting for Tophat alignment"></span>
829                 
830              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/cufflinks_confirm.jsp?ID=<%=ID%>"
831                >Confirm Cufflinks completed</span> 
832                <span class="counter" data-counter="cufflinks-not-confirmed" 
833                  title="Number of Cufflinks jobs waiting for confirmation"></span>
834              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=GENE_REPORT"
835                >Gene report</span> 
836                <span class="counter" data-counter="rawbioassys-without-genereport" 
837                  title="Number of rawbioassays without a Gene report PDF"></span>
838              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=PILOT_REPORT"
839                >Pilot report</span> 
840                <span class="counter" data-counter="rawbioassys-without-pilotreport" 
841                  title="Number of rawbioassays without a Pilot report PDF"></span>
842              </ul>
843            </dd>
844           
845          </dl>     
846        </div>
847       
848        <div id="mips-libprep-section" class="wizard-group">
849          <h3>Library preparation wizards</h3>
850          <dl class="leftborder rightborder bottomborder">
851       
852          <dt>
853            <base:icon image="<%=home+"/images/libprep.png" %>" />
854            MIPs plate design wizards
855          </dt>
856          <dd>
857            <ul>
858            <li><span class="require-permission" data-role="MIPsPlateDesigner" data-link="mipsprep/import_plates.jsp?ID=<%=ID%>"
859              >Import DNA aliquot plates</span>
860             
861            <li><span class="require-permission" data-role="MIPsPlateDesigner" data-link="mipsprep/design_mipsplate.jsp?ID=<%=ID%>"
862              >Design MIPs plate</span>
863              <span class="counter more" data-counter="prenormalized-designmips"
864                title="Number of aliquot plates with DNA waiting for MIPs"></span><span 
865              class="counter" data-counter="prenormalized-addaliquots"
866                title="Number of aliquot plates in the SCAN-B lab"></span>
867            </ul>
868          </dd>
869         
870          <dt>
871            <base:icon image="<%=home+"/images/pipette.png" %>" />
872            MIPs library preparation wizards
873          </dt>
874          <dd>
875            <ul>
876            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/mips_protocol.jsp?ID=<%=ID%>"
877              >Lab protocols for MIPs library preparation</span> 
878              <span class="counter" data-counter="mips-plates-for-libprep" 
879                title="Number of MIPs plates waiting for registration"></span>
880           
881            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/lib_registration.jsp?ID=<%=ID%>"
882              >MIPs library registration</span> 
883              <span class="counter" data-counter="mips-plates-for-libprep"
884                title="Number of MIPs plates waiting for registration"></span>
885           
886            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/pool_registration.jsp?ID=<%=ID%>"
887              >Register pooled libraries</span> 
888              <span class="counter" data-counter="mips-plates-for-pooling" 
889                title="Number of MIPs library plates waiting for pooling"></span>
890            </ul>
891          </dd>
892
893          </dl>
894         
895          <h3>Sequencing wizards</h3>
896          <dl class="leftborder rightborder bottomborder">
897         
898          <dt>
899            <base:icon image="<%=home+"/images/flowcell.png" %>" />
900            Sequencing wizards
901          </dt>
902          <dd>
903            <ul>
904            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/create_flowcells.jsp?ID=<%=ID%>"
905              >Create flow cells</span> 
906              <span class="counter" data-counter="pools-not-used-mips" 
907                title="Number of MIPs pools waiting for sequencing"></span>
908           
909            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/flowcell_protocol.jsp?ID=<%=ID%>"
910              >Lab protocol for sequencing</span> 
911              <span class="counter" data-counter="flow-cells-not-sequenced-mips" 
912                title="Number of MIPs flow cells waiting to be sequenced"></span>
913           
914            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="sequencing/sequencing_started.jsp?ID=<%=ID%>&pipeline=MIPS"
915              >Register sequencing started</span> 
916              <span class="counter" data-counter="flow-cells-not-sequenced-mips" 
917                title="Number of MIPs flow cells waiting to be sequenced"></span>
918 
919            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="sequencing/sequencing_ended.jsp?ID=<%=ID%>&pipeline=MIPS"
920              >Register sequencing ended</span> 
921              <span class="counter" data-counter="sequencing-runs-active-mips" 
922                title="Number of active MIPs sequencing runs"></span>
923            </ul>
924          </dd>
925         
926          </dl>
927         
928          <h3>Secondary analysis wizards</h3>
929          <dl class="leftborder rightborder bottomborder">
930            <dt>
931              <base:icon image="<%=home+"/images/server.png" %>" />
932              Demux and merge wizards
933            </dt>
934            <dd>
935              <ul>
936              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="sequencing/sequencing_confirm.jsp?ID=<%=ID%>&pipeline=MIPS"
937                >Confirm sequencing completed</span> 
938                <span class="counter" data-counter="sequencing-runs-unconfirmed-mips" 
939                  title="Number of ended but not confirmed MIPs sequencing runs"></span>
940             
941              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>&pipeline=MIPS"
942                >Start demux and merge</span> 
943                <span class="counter" data-counter="sequencing-runs-for-demux-mips" 
944                  title="Number of confirmed MIPs sequencing runs waiting to be demuxed"></span>
945             
946              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/demux_confirm.jsp?ID=<%=ID%>"
947                >Confirm demux and merge completed</span> 
948                <span class="counter" data-counter="demux-jobs-not-confirmed-mips"
949                  title="Number of MIPs demux jobs waiting for confirmation"></span>
950              </ul>
951            </dd>
952          </dl>
953         
954        </div>
955       
956        <div id="personal-information-section" class="wizard-group">
957          <%
958          if (isPatientCurator || isAdmin)
959          {
960            %>
961            <h3>Personal information wizards</h3>
962            <dl class="leftborder rightborder bottomborder">
963            <dt>
964              <base:icon image="<%=home + "/images/personal.png" %>"/>
965              Referral form registration wizards
966            </dt>
967            <dd>
968              <ul>
969              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/persinfo.jsp?ID=<%=ID%>"
970                >Pathology referral form registration</span>
971 
972              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodform.jsp?ID=<%=ID%>"
973                >Blood referral forms registration</span>
974               
975              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodfollowupform.jsp?ID=<%=ID%>"
976                >Follow-up blood referral form registration</span>
977 
978              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/consentform.jsp?ID=<%=ID%>"
979                >Consent form registration</span>
980                <span class="counter" data-counter="case-or-blood-without-consent" 
981                  title="Number of cases and blood samples without consent"></span>
982              </ul>
983            </dd>
984           
985            <dt>
986              <base:icon image="<%=home+"/images/report.png" %>" />
987              Referral forms
988            </dt>
989            <dd>
990              <ul>
991              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/generate-referral-forms.jsp?ID=<%=ID%>"
992                >Generate referral forms</span>
993              </ul>
994            </dd>
995 
996            <dt>
997              <base:icon image="<%=home+"/images/delete.png" %>" />
998              Retraction wizard
999            </dt>
1000            <dd>
1001              <ul>
1002              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/retractionform.jsp?ID=<%=ID%>"
1003                >Mark extracts for retraction</span>
1004 
1005              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/retraction_followup_form.jsp?ID=<%=ID%>"
1006                >Retraction follow-up and destruction</span>
1007                <span class="counter more" data-counter="patientitems-ready-for-retraction-followup" 
1008                  title="Number of patient items ready for retraction follow-up"></span><span 
1009                  class="counter" data-counter="patientitems-ready-for-destruction" 
1010                  title="Number of patient items ready for destruction"></span>
1011 
1012              </ul>
1013            </dd>
1014           
1015            <dt>
1016              <base:icon image="<%=home+"/images/export_import.png" %>" />
1017              Import and export wizards
1018            </dt>
1019            <dd>
1020              <ul>
1021              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export-inca.jsp?ID=<%=ID%>"
1022                >INCA export</span>
1023 
1024              <li><span id="inca-import" 
1025                class="require-permission" 
1026                data-role="PatientCurator"
1027                data-link="personal/import-inca.jsp?ID=<%=ID%>"
1028                >INCA import</span>
1029 
1030              <li><span id="inca-statistics" 
1031                class="require-permission" 
1032                data-role="PatientCurator"
1033                data-link="personal/inca-statistics.jsp?ID=<%=ID%>"
1034                >INCA statistics</span>
1035 
1036              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export-monthly-oplist.jsp?ID=<%=ID%>"
1037                >Export monthly operation list</span>
1038               
1039              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_data_sample_list.jsp?ID=<%=ID%>"
1040                >Export missing data sample list</span>
1041 
1042              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_consent_data_sample_list.jsp?ID=<%=ID%>"
1043                >Export missing consent data sample list</span>
1044               
1045              <li><span class="require-permission" data-role="PatientCurator" data-link="batch/frozen-tissue-date.jsp?ID=<%=ID%>"
1046                >Import frozen tissue date</span> 
1047               
1048              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/map-external-data.jsp?ID=<%=ID%>"
1049                >Map external data to releases</span>
1050              </ul>
1051            </dd>
1052           
1053            </dl>
1054            <%
1055          }
1056          %>
1057          <h3>Sample curation and outtake wizards</h3>
1058          <dl class="leftborder rightborder bottomborder">
1059            <dt>
1060              <base:icon image="<%=home+"/images/flag.png" %>" />
1061              Re-processing wizards
1062            </dt>
1063            <dd>
1064              <ul>
1065              <li><span class="require-permission" data-role="PrepCurator" data-link="flaggedrna/search.jsp?ID=<%=ID%>"
1066                >Flagged RNA</span> 
1067                <span class="counter" data-counter="flagged-rna" 
1068                  title="Number of flagged RNA items"></span>
1069              <li><span class="require-permission" data-role="PrepCurator" data-link="flaggedalignment/search.jsp?ID=<%=ID%>"
1070                >Flagged alignment</span> 
1071                <span class="counter" data-counter="flagged-alignment" 
1072                  title="Number of flagged alignment items"></span>
1073              <li><span class="require-permission" data-role="PrepCurator" data-link="sampleproc/paused-specimen.jsp?ID=<%=ID%>"
1074                >Paused specimen</span> 
1075                <span class="counter" data-counter="paused-specimen" 
1076                  title="Number of paused+scheduled specimen items"></span>
1077              </ul>
1078            </dd>
1079 
1080            <dt>
1081              <base:icon image="<%=home+"/images/smile.png" %>" />
1082              Batch update wizards
1083            </dt>
1084            <dd>
1085              <ul>
1086              <li><span class="require-permission" data-role="PrepCurator" data-link="batch/linked-specimen.jsp?ID=<%=ID%>"
1087                >Linked specimen</span> 
1088              <li><span class="require-permission" data-role="PrepCurator" data-link="batch/reference-date.jsp?ID=<%=ID%>"
1089                >Reference date on case items</span> 
1090              </ul>
1091            </dd>
1092           
1093            <dt>
1094              <base:icon image="<%=home+"/images/outtake.png" %>" />
1095              Sample outtake wizards
1096            </dt>
1097            <dd>
1098              <ul>
1099              <li><span class="require-permission" data-role="PrepCurator" data-link="outtake/define.jsp?ID=<%=ID%>"
1100                >Define a new sample outtake</span>
1101              <li><span class="require-permission" data-role="SamplePrep" data-link="outtake/picklist.jsp?ID=<%=ID%>"
1102                >Protocols and labels for sample outtakes</span> 
1103                <span class="counter" data-counter="active-outtake-lists" 
1104                  title="Number of sample outtakes waiting to be processed"></span>
1105              <li><span class="require-permission" data-role="SamplePrep" data-link="outtake/register.jsp?ID=<%=ID%>"
1106                >Register sample outtake</span> 
1107                <span class="counter" data-counter="active-outtake-lists" 
1108                  title="Number of sample outtakes waiting to be processed"></span>
1109              <li><span class="require-permission" data-role="PrepCurator" data-link="outtake/delivery_export.jsp?ID=<%=ID%>"
1110                >Export delivery data file for sample outtake</span>
1111                <span class="counter" data-counter="undelivered-outtake-lists" 
1112                  title="Number of sample outtakes not delivered"></span>
1113              </ul>
1114            </dd>
1115 
1116          </dl>
1117        </div>
1118       
1119        <div id="statistics-section" class="wizard-group">
1120          <h3>Statistics and reporting wizards</h3>
1121          <dl class="leftborder rightborder bottomborder">
1122            <dt>
1123              <base:icon image="<%=home+"/images/report.png" %>" />
1124              <span class="require-permission" data-role="" data-link="reports/samplereportgenerator.jsp?ID=<%=ID%>"
1125                >Sample source report</span>
1126            </dt>
1127            <dd>
1128              <ul>
1129              <li>Sample count report</li> 
1130              <li>Consent count report</li> 
1131              <li>Patient count report</li> 
1132              <li>Overview report</li> 
1133              <li>Missing sample data report</li> 
1134              </ul>
1135            </dd>
1136            <dt>
1137              <base:icon image="<%=home+"/images/chart_bar.png" %>" />
1138              <span class="require-permission" data-role="" data-link="reports/scanbquartermonthreportgenerator.jsp?ID=<%=ID%>"
1139                >Sample processing statistics</span>
1140            </dt>       
1141            <dd>       
1142              <ul>
1143              <li>SCAN-B quarter/month report</li> 
1144              </ul>
1145            </dd>
1146            <dt style="margin-bottom: 0.5em;">
1147              <base:icon image="<%=home+"/images/yellow-label.png" %>" />
1148              <span class="require-permission" data-role="" data-link="yellowlabel/list.jsp?ID=<%=ID%>"
1149                >YellowLabel tracking and reporting</span>
1150                <span class="counter" data-counter="specimen-active-yellow-label" 
1151                  title="Number of active YellowLabel specimen"></span>
1152            </dt> 
1153          </dl>
1154        </div>
1155
1156        <div id="administration-section" class="wizard-group">
1157          <%
1158          if (isAdmin)
1159          {
1160            %>
1161            <h3>Server administrator wizards</h3>
1162            <dl class="leftborder rightborder bottomborder">
1163            <dt>
1164              <base:icon image="<%=home + "/images/install.png" %>" />
1165              <span class="require-permission" data-role="Administrator" data-link="admin/install.jsp?ID=<%=ID%>">Installation wizard</span>
1166            </dt>
1167            <dd>
1168              <ul>
1169              <li>Check that items needed by Reggie exists in BASE.
1170              <li>Create and fix items.
1171              </ul>
1172            </dd>
1173            <dt>
1174              <base:icon image="<%=home + "/images/ogs-cluster.png"%>" />
1175              Other tasks
1176            </dt>
1177            <dd>
1178              <ul>
1179              <li><span class="require-permission" data-role="Administrator" data-link="admin/remote/list-hosts.jsp?ID=<%=ID%>"
1180                >Open Grid Scheduler hosts</span>
1181               
1182              <li><span class="require-permission" data-role="Administrator" data-link="admin/stray-files.jsp?ID=<%=ID%>"
1183                >Stray files wizard</span>
1184                <span class="counter" data-counter="stray-folders" 
1185                  title="Number of stray folders"></span>
1186                 
1187              <li><span class="require-permission" data-role="Administrator" data-link="admin/analysis-cleanup.jsp?ID=<%=ID%>"
1188                >Secondary analysis cleanup</span>
1189                <span class="counter more" data-counter="analysis-cleanup-dba"
1190                  title="Number of derived bioassay items to cleanup"></span><span 
1191                  class="counter" data-counter="analysis-cleanup-rba" 
1192                  title="Number of raw bioassay items to cleanup"></span>
1193              </ul>
1194            </dd>
1195            </dl>
1196            <%
1197          }
1198          %>
1199        </div>
1200       
1201      </div>
1202    </div>
1203   
1204    <div class="absolutefull" style="width: 30%; left: auto;">
1205      <div class="absolutefull" style="left: 0.5em; bottom: 2em;">
1206        <div class="absolutefull" style="right: 1em; height: 4em;">
1207          <b>Case summary</b><br>
1208          <input type="text" class="text auto-init" data-auto-init="focus" 
1209            name="caseName" id="caseName" title="Please enter a SCAN-B case id, personal number, release id, PAD, etc." 
1210            style="width: 15em;">
1211          <base:button id="btnCaseSummary" title="Go" image="<%=home+"/images/gonext.png"%>" />
1212        </div>
1213        <div class="absolutefull" style="top: 4em; padding-right: 0.5em;">
1214          <div id="summary-stats">
1215            <div class="counter" data-counter="patients-all" 
1216              title="Total number of patients"></div> Patients<br>
1217            <div class="counter" data-counter="specimen-all" 
1218              title="Total number of specimen tubes"></div> Specimen Tubes<br>
1219            <div class="counter" data-counter="rna-all-extracted" 
1220              title="Total number of extracted RNA"></div> Extracted Rna<br>
1221            <div class="counter" data-counter="libraries-all-aligned" 
1222              title="Total number of aligned libraries"></div> Aligned Libraries<br>
1223            <div class="counter" data-counter="rawbioassys-all-with-genereport"
1224              title="Total number of generated gene reports"></div> Gene Reports<br>
1225            <div class="counter" data-counter="stained-score-complete"
1226              title="Total number of completely scored histology samples"></div> Scored Histology Samples
1227          </div>
1228
1229          <div id="activity-log">
1230            <a id="activity-log-rss" href="<%=servletHome%>/ActivityLog.rss" 
1231              title="Get the activity log as an RSS feed"><img src="images/rss.png"></a>
1232            <div id="activity-log-entries"></div>
1233          </div>
1234        </div>
1235      </div>
1236      <div id="counter-age-control">
1237        <b>Counters last updated</b> <span id="counter-age"></span><base:icon id="counter-refresh" 
1238          image="<%=home+"/images/refresh-small.png"%>" style="display:none;" title="Force update of counters" 
1239          /><base:icon id="counter-loading" image="<%=home+"/images/loading-small.gif"%>" />
1240      </div>
1241    </div>
1242    </form>
1243   
1244  </div>
1245 
1246</base:body>
1247</base:page>
1248<%
1249}
1250finally
1251{
1252  if (dc != null) dc.close();
1253}
1254%>
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