source: extensions/net.sf.basedb.reggie/trunk/resources/index.jsp @ 5685

Last change on this file since 5685 was 5685, checked in by Nicklas Nordborg, 3 years ago

References #1199: Implement Variant calling pipeline

Added wizard for starting variant calling jobs. It is more or less the same structure as in the mBAF wizard.

File size: 48.4 KB
Line 
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/vcall_start.jsp?ID=<%=ID%>"
784                >Start variant calling</span> 
785                <span class="counter" data-counter="aligned-sequences-for-variant-calling" 
786                  title="Number of aligned sequences waiting for variant calling pipeline"></span>
787                <span id="variant-calling-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
788 
789              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/stringtie_start.jsp?ID=<%=ID%>"
790                >Start StringTie</span>
791                <span class="counter" data-counter="aligned-sequences-for-stringtie"
792                  title="Number of aligned sequences waiting for StringTie"></span>
793                <span id="stringtie-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
794 
795              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/stringtie_confirm.jsp?ID=<%=ID%>"
796                >Confirm StringTie completed</span> 
797                <span class="counter" data-counter="stringtie-not-confirmed" 
798                  title="Number of StringTie jobs waiting for confirmation"></span>
799              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=SCANB_REPORT"
800                >SCAN-B report</span> 
801                <span class="counter" data-counter="rawbioassys-without-scanbreport" 
802                  title="Number of rawbioassays without a SCAN-B report PDF"></span>
803              </ul>
804            </dd>
805           
806            <dt>
807              <base:icon image="<%=home+"/images/pdffile.png" %>" />
808              Legacy Tophat and Cufflinks pipeline <span id="legacy-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
809            </dt>
810            <dd>
811              <ul>
812              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/align_start.jsp?ID=<%=ID%>"
813                >Start Tophat and Cufflinks</span> 
814                <span class="counter" data-counter="merged-sequences-for-legacy-alignment"
815                  title="Number of merged sequences waiting for Tophat alignment"></span>
816                 
817              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/cufflinks_confirm.jsp?ID=<%=ID%>"
818                >Confirm Cufflinks completed</span> 
819                <span class="counter" data-counter="cufflinks-not-confirmed" 
820                  title="Number of Cufflinks jobs waiting for confirmation"></span>
821              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=GENE_REPORT"
822                >Gene report</span> 
823                <span class="counter" data-counter="rawbioassys-without-genereport" 
824                  title="Number of rawbioassays without a Gene report PDF"></span>
825              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=PILOT_REPORT"
826                >Pilot report</span> 
827                <span class="counter" data-counter="rawbioassys-without-pilotreport" 
828                  title="Number of rawbioassays without a Pilot report PDF"></span>
829              </ul>
830            </dd>
831           
832          </dl>     
833        </div>
834       
835        <div id="mips-libprep-section" class="wizard-group">
836          <h3>Library preparation wizards</h3>
837          <dl class="leftborder rightborder bottomborder">
838       
839          <dt>
840            <base:icon image="<%=home+"/images/libprep.png" %>" />
841            MIPs plate design wizards
842          </dt>
843          <dd>
844            <ul>
845            <li><span class="require-permission" data-role="MIPsPlateDesigner" data-link="mipsprep/import_plates.jsp?ID=<%=ID%>"
846              >Import DNA aliquot plates</span>
847             
848            <li><span class="require-permission" data-role="MIPsPlateDesigner" data-link="mipsprep/design_mipsplate.jsp?ID=<%=ID%>"
849              >Design MIPs plate</span>
850              <span class="counter more" data-counter="prenormalized-designmips"
851                title="Number of aliquot plates with DNA waiting for MIPs"></span><span 
852              class="counter" data-counter="prenormalized-addaliquots"
853                title="Number of aliquot plates in the SCAN-B lab"></span>
854            </ul>
855          </dd>
856         
857          <dt>
858            <base:icon image="<%=home+"/images/pipette.png" %>" />
859            MIPs library preparation wizards
860          </dt>
861          <dd>
862            <ul>
863            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/mips_protocol.jsp?ID=<%=ID%>"
864              >Lab protocols for MIPs library preparation</span> 
865              <span class="counter" data-counter="mips-plates-for-libprep" 
866                title="Number of MIPs plates waiting for registration"></span>
867           
868            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/lib_registration.jsp?ID=<%=ID%>"
869              >MIPs library registration</span> 
870              <span class="counter" data-counter="mips-plates-for-libprep"
871                title="Number of MIPs plates waiting for registration"></span>
872           
873            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/pool_registration.jsp?ID=<%=ID%>"
874              >Register pooled libraries</span> 
875              <span class="counter" data-counter="mips-plates-for-pooling" 
876                title="Number of MIPs library plates waiting for pooling"></span>
877            </ul>
878          </dd>
879
880          </dl>
881         
882          <h3>Sequencing wizards</h3>
883          <dl class="leftborder rightborder bottomborder">
884         
885          <dt>
886            <base:icon image="<%=home+"/images/flowcell.png" %>" />
887            Sequencing wizards
888          </dt>
889          <dd>
890            <ul>
891            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/create_flowcells.jsp?ID=<%=ID%>"
892              >Create flow cells</span> 
893              <span class="counter" data-counter="pools-not-used-mips" 
894                title="Number of MIPs pools waiting for sequencing"></span>
895           
896            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/flowcell_protocol.jsp?ID=<%=ID%>"
897              >Lab protocol for sequencing</span> 
898              <span class="counter" data-counter="flow-cells-not-sequenced-mips" 
899                title="Number of MIPs flow cells waiting to be sequenced"></span>
900           
901            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="sequencing/sequencing_started.jsp?ID=<%=ID%>&pipeline=MIPS"
902              >Register sequencing started</span> 
903              <span class="counter" data-counter="flow-cells-not-sequenced-mips" 
904                title="Number of MIPs flow cells waiting to be sequenced"></span>
905 
906            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="sequencing/sequencing_ended.jsp?ID=<%=ID%>&pipeline=MIPS"
907              >Register sequencing ended</span> 
908              <span class="counter" data-counter="sequencing-runs-active-mips" 
909                title="Number of active MIPs sequencing runs"></span>
910            </ul>
911          </dd>
912         
913          </dl>
914         
915          <h3>Secondary analysis wizards</h3>
916          <dl class="leftborder rightborder bottomborder">
917            <dt>
918              <base:icon image="<%=home+"/images/server.png" %>" />
919              Demux and merge wizards
920            </dt>
921            <dd>
922              <ul>
923              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="sequencing/sequencing_confirm.jsp?ID=<%=ID%>&pipeline=MIPS"
924                >Confirm sequencing completed</span> 
925                <span class="counter" data-counter="sequencing-runs-unconfirmed-mips" 
926                  title="Number of ended but not confirmed MIPs sequencing runs"></span>
927             
928              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>&pipeline=MIPS"
929                >Start demux and merge</span> 
930                <span class="counter" data-counter="sequencing-runs-for-demux-mips" 
931                  title="Number of confirmed MIPs sequencing runs waiting to be demuxed"></span>
932             
933              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/demux_confirm.jsp?ID=<%=ID%>"
934                >Confirm demux and merge completed</span> 
935                <span class="counter" data-counter="demux-jobs-not-confirmed-mips"
936                  title="Number of MIPs demux jobs waiting for confirmation"></span>
937              </ul>
938            </dd>
939          </dl>
940         
941        </div>
942       
943        <div id="personal-information-section" class="wizard-group">
944          <%
945          if (isPatientCurator || isAdmin)
946          {
947            %>
948            <h3>Personal information wizards</h3>
949            <dl class="leftborder rightborder bottomborder">
950            <dt>
951              <base:icon image="<%=home + "/images/personal.png" %>"/>
952              Referral form registration wizards
953            </dt>
954            <dd>
955              <ul>
956              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/persinfo.jsp?ID=<%=ID%>"
957                >Pathology referral form registration</span>
958 
959              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodform.jsp?ID=<%=ID%>"
960                >Blood referral forms registration</span>
961               
962              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodfollowupform.jsp?ID=<%=ID%>"
963                >Follow-up blood referral form registration</span>
964 
965              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/consentform.jsp?ID=<%=ID%>"
966                >Consent form registration</span>
967                <span class="counter" data-counter="case-or-blood-without-consent" 
968                  title="Number of cases and blood samples without consent"></span>
969              </ul>
970            </dd>
971           
972            <dt>
973              <base:icon image="<%=home+"/images/report.png" %>" />
974              Referral forms
975            </dt>
976            <dd>
977              <ul>
978              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/generate-referral-forms.jsp?ID=<%=ID%>"
979                >Generate referral forms</span>
980              </ul>
981            </dd>
982 
983            <dt>
984              <base:icon image="<%=home+"/images/delete.png" %>" />
985              Retraction wizard
986            </dt>
987            <dd>
988              <ul>
989              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/retractionform.jsp?ID=<%=ID%>"
990                >Mark extracts for retraction</span>
991 
992              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/retraction_followup_form.jsp?ID=<%=ID%>"
993                >Retraction follow-up and destruction</span>
994                <span class="counter more" data-counter="patientitems-ready-for-retraction-followup" 
995                  title="Number of patient items ready for retraction follow-up"></span><span 
996                  class="counter" data-counter="patientitems-ready-for-destruction" 
997                  title="Number of patient items ready for destruction"></span>
998 
999              </ul>
1000            </dd>
1001           
1002            <dt>
1003              <base:icon image="<%=home+"/images/export_import.png" %>" />
1004              Import and export wizards
1005            </dt>
1006            <dd>
1007              <ul>
1008              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export-inca.jsp?ID=<%=ID%>"
1009                >INCA export</span>
1010 
1011              <li><span id="inca-import" 
1012                class="require-permission" 
1013                data-role="PatientCurator"
1014                data-link="personal/import-inca.jsp?ID=<%=ID%>"
1015                >INCA import</span>
1016 
1017              <li><span id="inca-statistics" 
1018                class="require-permission" 
1019                data-role="PatientCurator"
1020                data-link="personal/inca-statistics.jsp?ID=<%=ID%>"
1021                >INCA statistics</span>
1022 
1023              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export-monthly-oplist.jsp?ID=<%=ID%>"
1024                >Export monthly operation list</span>
1025               
1026              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_data_sample_list.jsp?ID=<%=ID%>"
1027                >Export missing data sample list</span>
1028 
1029              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_consent_data_sample_list.jsp?ID=<%=ID%>"
1030                >Export missing consent data sample list</span>
1031               
1032              <li><span class="require-permission" data-role="PatientCurator" data-link="batch/frozen-tissue-date.jsp?ID=<%=ID%>"
1033                >Import frozen tissue date</span> 
1034               
1035              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/map-external-data.jsp?ID=<%=ID%>"
1036                >Map external data to releases</span>
1037              </ul>
1038            </dd>
1039           
1040            </dl>
1041            <%
1042          }
1043          %>
1044          <h3>Sample curation and outtake wizards</h3>
1045          <dl class="leftborder rightborder bottomborder">
1046            <dt>
1047              <base:icon image="<%=home+"/images/flag.png" %>" />
1048              Re-processing wizards
1049            </dt>
1050            <dd>
1051              <ul>
1052              <li><span class="require-permission" data-role="PrepCurator" data-link="flaggedrna/search.jsp?ID=<%=ID%>"
1053                >Flagged RNA</span> 
1054                <span class="counter" data-counter="flagged-rna" 
1055                  title="Number of flagged RNA items"></span>
1056              <li><span class="require-permission" data-role="PrepCurator" data-link="flaggedalignment/search.jsp?ID=<%=ID%>"
1057                >Flagged alignment</span> 
1058                <span class="counter" data-counter="flagged-alignment" 
1059                  title="Number of flagged alignment items"></span>
1060              <li><span class="require-permission" data-role="PrepCurator" data-link="sampleproc/paused-specimen.jsp?ID=<%=ID%>"
1061                >Paused specimen</span> 
1062                <span class="counter" data-counter="paused-specimen" 
1063                  title="Number of paused+scheduled specimen items"></span>
1064              </ul>
1065            </dd>
1066 
1067            <dt>
1068              <base:icon image="<%=home+"/images/smile.png" %>" />
1069              Batch update wizards
1070            </dt>
1071            <dd>
1072              <ul>
1073              <li><span class="require-permission" data-role="PrepCurator" data-link="batch/linked-specimen.jsp?ID=<%=ID%>"
1074                >Linked specimen</span> 
1075              <li><span class="require-permission" data-role="PrepCurator" data-link="batch/reference-date.jsp?ID=<%=ID%>"
1076                >Reference date on case items</span> 
1077              </ul>
1078            </dd>
1079           
1080            <dt>
1081              <base:icon image="<%=home+"/images/outtake.png" %>" />
1082              Sample outtake wizards
1083            </dt>
1084            <dd>
1085              <ul>
1086              <li><span class="require-permission" data-role="PrepCurator" data-link="outtake/define.jsp?ID=<%=ID%>"
1087                >Define a new sample outtake</span>
1088              <li><span class="require-permission" data-role="SamplePrep" data-link="outtake/picklist.jsp?ID=<%=ID%>"
1089                >Protocols and labels for sample outtakes</span> 
1090                <span class="counter" data-counter="active-outtake-lists" 
1091                  title="Number of sample outtakes waiting to be processed"></span>
1092              <li><span class="require-permission" data-role="SamplePrep" data-link="outtake/register.jsp?ID=<%=ID%>"
1093                >Register sample outtake</span> 
1094                <span class="counter" data-counter="active-outtake-lists" 
1095                  title="Number of sample outtakes waiting to be processed"></span>
1096              <li><span class="require-permission" data-role="PrepCurator" data-link="outtake/delivery_export.jsp?ID=<%=ID%>"
1097                >Export delivery data file for sample outtake</span>
1098                <span class="counter" data-counter="undelivered-outtake-lists" 
1099                  title="Number of sample outtakes not delivered"></span>
1100              </ul>
1101            </dd>
1102 
1103          </dl>
1104        </div>
1105       
1106        <div id="statistics-section" class="wizard-group">
1107          <h3>Statistics and reporting wizards</h3>
1108          <dl class="leftborder rightborder bottomborder">
1109            <dt>
1110              <base:icon image="<%=home+"/images/report.png" %>" />
1111              <span class="require-permission" data-role="" data-link="reports/samplereportgenerator.jsp?ID=<%=ID%>"
1112                >Sample source report</span>
1113            </dt>
1114            <dd>
1115              <ul>
1116              <li>Sample count report</li> 
1117              <li>Consent count report</li> 
1118              <li>Patient count report</li> 
1119              <li>Overview report</li> 
1120              <li>Missing sample data report</li> 
1121              </ul>
1122            </dd>
1123            <dt>
1124              <base:icon image="<%=home+"/images/chart_bar.png" %>" />
1125              <span class="require-permission" data-role="" data-link="reports/scanbquartermonthreportgenerator.jsp?ID=<%=ID%>"
1126                >Sample processing statistics</span>
1127            </dt>       
1128            <dd>       
1129              <ul>
1130              <li>SCAN-B quarter/month report</li> 
1131              </ul>
1132            </dd>
1133            <dt style="margin-bottom: 0.5em;">
1134              <base:icon image="<%=home+"/images/yellow-label.png" %>" />
1135              <span class="require-permission" data-role="" data-link="yellowlabel/list.jsp?ID=<%=ID%>"
1136                >YellowLabel tracking and reporting</span>
1137                <span class="counter" data-counter="specimen-active-yellow-label" 
1138                  title="Number of active YellowLabel specimen"></span>
1139            </dt> 
1140          </dl>
1141        </div>
1142
1143        <div id="administration-section" class="wizard-group">
1144          <%
1145          if (isAdmin)
1146          {
1147            %>
1148            <h3>Server administrator wizards</h3>
1149            <dl class="leftborder rightborder bottomborder">
1150            <dt>
1151              <base:icon image="<%=home + "/images/install.png" %>" />
1152              <span class="require-permission" data-role="Administrator" data-link="admin/install.jsp?ID=<%=ID%>">Installation wizard</span>
1153            </dt>
1154            <dd>
1155              <ul>
1156              <li>Check that items needed by Reggie exists in BASE.
1157              <li>Create and fix items.
1158              </ul>
1159            </dd>
1160            <dt>
1161              <base:icon image="<%=home + "/images/ogs-cluster.png"%>" />
1162              Other tasks
1163            </dt>
1164            <dd>
1165              <ul>
1166              <li><span class="require-permission" data-role="Administrator" data-link="admin/remote/list-hosts.jsp?ID=<%=ID%>"
1167                >Open Grid Scheduler hosts</span>
1168               
1169              <li><span class="require-permission" data-role="Administrator" data-link="admin/stray-files.jsp?ID=<%=ID%>"
1170                >Stray files wizard</span>
1171                <span class="counter" data-counter="stray-folders" 
1172                  title="Number of stray folders"></span>
1173                 
1174              <li><span class="require-permission" data-role="Administrator" data-link="admin/analysis-cleanup.jsp?ID=<%=ID%>"
1175                >Secondary analysis cleanup</span>
1176                <span class="counter more" data-counter="analysis-cleanup-dba"
1177                  title="Number of derived bioassay items to cleanup"></span><span 
1178                  class="counter" data-counter="analysis-cleanup-rba" 
1179                  title="Number of raw bioassay items to cleanup"></span>
1180              </ul>
1181            </dd>
1182            </dl>
1183            <%
1184          }
1185          %>
1186        </div>
1187       
1188      </div>
1189    </div>
1190   
1191    <div class="absolutefull" style="width: 30%; left: auto;">
1192      <div class="absolutefull" style="left: 0.5em; bottom: 2em;">
1193        <div class="absolutefull" style="right: 1em; height: 4em;">
1194          <b>Case summary</b><br>
1195          <input type="text" class="text auto-init" data-auto-init="focus" 
1196            name="caseName" id="caseName" title="Please enter a SCAN-B case id, personal number, release id, PAD, etc." 
1197            style="width: 15em;">
1198          <base:button id="btnCaseSummary" title="Go" image="<%=home+"/images/gonext.png"%>" />
1199        </div>
1200        <div class="absolutefull" style="top: 4em; padding-right: 0.5em;">
1201          <div id="summary-stats">
1202            <div class="counter" data-counter="patients-all" 
1203              title="Total number of patients"></div> Patients<br>
1204            <div class="counter" data-counter="specimen-all" 
1205              title="Total number of specimen tubes"></div> Specimen Tubes<br>
1206            <div class="counter" data-counter="rna-all-extracted" 
1207              title="Total number of extracted RNA"></div> Extracted Rna<br>
1208            <div class="counter" data-counter="libraries-all-aligned" 
1209              title="Total number of aligned libraries"></div> Aligned Libraries<br>
1210            <div class="counter" data-counter="rawbioassys-all-with-genereport"
1211              title="Total number of generated gene reports"></div> Gene Reports<br>
1212            <div class="counter" data-counter="stained-score-complete"
1213              title="Total number of completely scored histology samples"></div> Scored Histology Samples
1214          </div>
1215
1216          <div id="activity-log">
1217            <a id="activity-log-rss" href="<%=servletHome%>/ActivityLog.rss" 
1218              title="Get the activity log as an RSS feed"><img src="images/rss.png"></a>
1219            <div id="activity-log-entries"></div>
1220          </div>
1221        </div>
1222      </div>
1223      <div id="counter-age-control">
1224        <b>Counters last updated</b> <span id="counter-age"></span><base:icon id="counter-refresh" 
1225          image="<%=home+"/images/refresh-small.png"%>" style="display:none;" title="Force update of counters" 
1226          /><base:icon id="counter-loading" image="<%=home+"/images/loading-small.gif"%>" />
1227      </div>
1228    </div>
1229    </form>
1230   
1231  </div>
1232 
1233</base:body>
1234</base:page>
1235<%
1236}
1237finally
1238{
1239  if (dc != null) dc.close();
1240}
1241%>
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