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

Last change on this file was 6684, checked in by Nicklas Nordborg, 4 months ago

Fixes #1387: Reload reggie-config.xml

File size: 55.3 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) && !sc.isRoleInactive(admin.getId());
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.merge + .counter.done:before
142{
143  content: '/';
144  padding-right: 0;
145}
146
147span.counter.done:not(.more):after
148{
149  content: ')';
150  padding-left: 1px;
151}
152
153span.info-warning
154{
155  display: none;
156  color: #666666;
157  font-style: italic;
158  background-image: url('images/warning_small.png');
159  background-repeat: no-repeat;
160  background-position: 0 50%;
161  padding-left: 16px;
162  margin-left: 0.5em;
163}
164
165.require-permission
166{
167  color: #999999;
168  font-style: italic;
169}
170
171.snake-quote
172{
173  width: 32em;
174}
175
176.snake-quote-source
177{
178  margin-top: 0.5em;
179  float: right;
180  font-style: italic;
181}
182
183.snake-quote .notify-message
184{
185  margin: 0;
186}
187
188.snake-quote .notify-message:before
189{
190  margin: 0;
191  content: '';
192}
193
194#summary-stats
195{
196  font-variant: small-caps;
197  font-size: 125%;
198  white-space: nowrap;
199  overflow: hidden;
200}
201
202#activity-log
203{
204 
205}
206
207#activity-log .activity-day
208{
209  font-size: 1.1em;
210  font-weight: bold;
211  margin-top: 0.5em;
212}
213
214#activity-log .activity
215{
216  white-space: nowrap;
217  overflow: hidden;
218  padding: 0.15em 0;
219}
220
221#activity-log .activity.nothing-yet
222{
223  font-style: italic;
224}
225
226
227#activity-log .activity.quote-of-the-day
228{
229  font-style: italic;
230  white-space: normal;
231  text-align: center;
232  margin: 1em 1em 0.5em 0;
233  border-top-width: 1px;
234  border-top-style: dotted;
235  padding-top: 0.5em;
236}
237
238#activity-log .activity-author
239{
240  white-space: nowrap;
241}
242
243#activity-log .activity-author:before
244{
245  content: '–';
246  padding-left: 0.5em;
247  padding-right: 0.25em;
248}
249
250#activity-log .quote-of-the-day .activity-link
251{
252  text-align: right;
253  border-top-width: 1px;
254  border-top-style: dotted;
255  margin-top: 0.5em;
256}
257
258#activity-log .activity-time
259{
260  margin-right: 0.5em;
261  color: #666666;
262}
263
264#activity-log .quote-of-the-day .activity-time
265{
266  display: none;
267}
268
269#activity-log-rss
270{
271  float: right;
272  margin-right: 1em;
273}
274#counter-age-control
275{
276  position: absolute;
277  bottom: 2px;
278  right: 1rem;
279  font-size: 90%;
280}
281
282#counter-refresh, #counter-loading
283{
284  padding-left: 3px;
285  vertical-align: -2px;
286}
287
288div.counter
289{
290  display: inline-block;
291  min-width: 4em;
292  text-align: right;
293  padding-right: 0.25em;
294  font-size: 120%;
295  font-weight: bold;
296}
297
298.high-alert
299{
300  background-color: #ffff00;
301  font-weight: bold;
302  padding: 2px 0.5em;
303  margin-bottom: 0.25em;
304  margin-left: 0.5em;
305  border-width: 2px;
306  border-radius: 5px;
307}
308
309#more-boxes-are-needed::before
310{
311  content: url('images/warning.png');
312  vertical-align: top;
313  margin-right: 0.25em;
314}
315
316div.group-menu
317{
318  background-color: #F8F8F8;
319  padding: 0.5em 10px 0.5em 1em;
320  border-width: 1px;
321  margin-bottom: 1em;
322  border-radius: 6px;
323}
324
325div.group-menu:hover
326{
327  text-decoration: none;
328  border-right-width: 10px;
329  padding-right: 0;
330}
331
332div.group-menu .group-title
333{
334  font-weight: bold;
335  font-size: 125%;
336  color: #333377;
337  margin-bottom: 0.25em;
338}
339div.group-menu .group-examples span
340{
341  color: #666666;
342  font-style: italic;
343  white-space: nowrap;
344}
345
346div.group-menu .group-examples span:before
347{
348  content: '•';
349  padding-right: 0.25em;
350}
351
352#wizard[data-wizard-group="sample-processing-section"] .group-menu[data-wizard-group="sample-processing-section"],
353#wizard[data-wizard-group="rna-libprep-section"] .group-menu[data-wizard-group="rna-libprep-section"],
354#wizard[data-wizard-group="rnaseq-analysis-section"] .group-menu[data-wizard-group="rnaseq-analysis-section"],
355#wizard[data-wizard-group="mips-libprep-section"] .group-menu[data-wizard-group="mips-libprep-section"],
356#wizard[data-wizard-group="personal-information-section"] .group-menu[data-wizard-group="personal-information-section"],
357#wizard[data-wizard-group="statistics-section"] .group-menu[data-wizard-group="statistics-section"],
358#wizard[data-wizard-group="administration-section"] .group-menu[data-wizard-group="administration-section"]
359{
360  background-color: #FFFFF0;
361  border-right-width: 10px;
362  border-right-color: #2288AA;
363  padding-right: 0;
364}
365
366.wizard-group
367{
368  display: none;
369}
370
371#wizard[data-wizard-group="sample-processing-section"] #sample-processing-section,
372#wizard[data-wizard-group="rna-libprep-section"] #rna-libprep-section,
373#wizard[data-wizard-group="rnaseq-analysis-section"] #rnaseq-analysis-section,
374#wizard[data-wizard-group="mips-libprep-section"] #mips-libprep-section,
375#wizard[data-wizard-group="personal-information-section"] #personal-information-section,
376#wizard[data-wizard-group="statistics-section"] #statistics-section,
377#wizard[data-wizard-group="administration-section"] #administration-section
378{
379  display: block;
380}
381
382</style>
383</base:head>
384<base:body>
385
386  <p:path><p:pathelement title="Reggie" /></p:path>
387
388  <div class="content">
389    <form name="reggie" id="wizard" class="wizard" data-wizard-group="<%=HTML.encodeTags(lastWizardGroup)%>">
390    <div id="wizard-status" style="position: absolute; z-index: 99; left: 25%; right: 25%; top: 25%; height: auto; text-align: center;"></div>
391    <div class="absolutefull" style="width: 30%;">
392      <div class="absolutefull" style="left: 1em; right: 0.5em; ">
393       
394        <div class="group-menu link" data-wizard-group="sample-processing-section">
395          <div class="group-title">Sample processing and histology</div>
396          <div class="group-examples">
397            <span>Registration</span>
398            <span>Partitioning</span>
399            <span>Extraction</span>
400            <span>Quality control</span>
401            <span>Histology scoring</span>
402          </div>
403        </div>
404 
405        <div class="group-menu link" data-wizard-group="rna-libprep-section">
406          <div class="group-title">RNA library preparation and sequencing</div>
407          <div class="group-examples">
408            <span>Plate design</span>
409            <span>Library registration</span>
410            <span>Pooling</span>
411            <span>Sequencing</span>
412          </div>
413        </div>
414
415        <div class="group-menu link" data-wizard-group="rnaseq-analysis-section">
416          <div class="group-title">RNA-seq secondary analysis</div>
417          <div class="group-examples">
418            <span>Demux</span>
419            <span>Alignment</span>
420            <span>Variant calling</span>
421            <span>Reports</span>
422          </div>
423        </div>
424         
425        <div class="group-menu link" data-wizard-group="mips-libprep-section" style="display: none;">
426          <div class="group-title">MIPs library preparation and analysis</div>
427          <div class="group-examples">
428            <span>Aliquot import</span>
429            <span>Plate design</span>
430            <span>Library registration</span>
431            <span>Pooling</span>
432            <span>Sequencing</span>
433            <span>Secondary analysis</span>
434          </div>
435        </div>
436       
437        <div class="group-menu link" data-wizard-group="personal-information-section">
438          <div class="group-title">Personal information and sample curation</div>
439          <div class="group-examples">
440            <span>Referral forms</span>
441            <span>Retraction</span>
442            <span>INCA</span>
443            <span>Flagged items</span>
444            <span>Batch updates</span>
445            <span>Outtakes</span>
446          </div>
447        </div>
448 
449        <div class="group-menu link" data-wizard-group="statistics-section">
450          <div class="group-title">Statistics and reporting</div>
451          <div class="group-examples">
452            <span>Sample count tables</span>
453            <span>Sample processing plots</span>
454            <span>YellowLabel tracking</span>
455          </div>
456        </div>
457        <%
458        if (isAdmin)
459        {
460          %>
461          <div class="group-menu link" data-wizard-group="administration-section">
462            <div class="group-title">Server administration</div>
463            <div class="group-examples">
464              <span>Installation wizard</span>
465              <span>Configuration</span>
466              <span>Cleanup</span>
467            </div>
468          </div>
469          <%
470        }
471        %>
472      </div>
473    </div>
474   
475    <div class="absolutefull" style="width: 40%; left: 30%; right: auto;">
476      <div class="absolutefull" style="left: 0.5em; right: 0.5em;">
477     
478        <div id="sample-processing-section" class="wizard-group">
479          <h3>Sample processing wizards</h3>
480          <dl class="leftborder rightborder bottomborder has-lib-prep">
481 
482          <dt>
483            <base:icon image="<%=home+"/images/specimen.png" %>" />
484            Specimen tube registration
485          </dt>
486          <dd>
487            <ul>
488            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/specimentube.jsp?ID=<%=ID%>"
489              >Register new specimen tubes</span>.
490            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/store-paused.jsp?ID=<%=ID%>"
491              >Store paused specimen</span>
492              <span class="counter" data-counter="paused-specimen-to-store" 
493                title="Number of paused specimen that has not yet been stored"></span>
494            </ul>
495          </dd>
496 
497          <dt>
498            <base:icon image="<%=home+"/images/partition.png" %>" />
499            <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/partitionform.jsp?ID=<%=ID%>"
500              >Partition wizard</span>
501          </dt>
502          <dd>
503            <ul>
504            <li>Register new partitions of existing specimens
505              <span class="counter more" data-counter="specimen-for-partition"
506                title="Number of unpartitioned specimen"></span><span 
507              class="counter" data-counter="specimen-for-reextraction" 
508                title="Number of specimen for re-extration"></span>
509            </ul>
510          </dd>
511           
512          <dt>
513            <base:icon image="<%=home+"/images/extraction.png" %>" />
514            DNA/RNA extraction wizards
515          </dt>
516          <dd>
517            <ul>
518            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/lysate_reextraction.jsp?ID=<%=ID%>"
519              >Pick lysate for re-extraction</span> 
520              <span class="counter" data-counter="lysates-to-pick-for-reextraction" 
521                title="Number of lysates for re-extraction that must be picked from freezers"></span>
522            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/allprep_protocol.jsp?ID=<%=ID%>"
523              >Lab tracking protocol for Allprep isolation</span> 
524              <span class="counter more" data-counter="lysates-for-allprep" 
525                title="Number of unprocessed lysates"></span><span
526              class="counter" data-counter="lysates-picked-for-rextraction"
527                title="Number of lysates for re-extraction that has been picked from freezers"></span>
528 
529            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/extraction_registration.jsp?ID=<%=ID%>"
530              >DNA/RNA/FlowThrough registration</span> 
531              <span class="counter more" data-counter="lysates-for-allprep" 
532                title="Number of unprocessed lysates"></span><span
533              class="counter" data-counter="lysates-picked-for-rextraction"
534                title="Number of lysates for re-extraction that has been picked from freezers"></span>
535               
536            <li>Normalization
537              <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rna_normalization.jsp?ID=<%=ID%>"
538              >RNA</span> 
539              <span class="counter" data-counter="rna-to-normalize" title="Number of RNA not yet normalized"></span>
540              <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/dna_normalization.jsp?ID=<%=ID%>"
541              >DNA</span> 
542              <span class="counter" data-counter="dna-to-normalize" title="Number of DNA not yet normalized"></span>
543             
544            </ul>
545          </dd>
546          <dt>
547            <base:icon image="<%=home+"/images/rnaqc.png" %>" />
548            RNA quality control wizards
549          </dt>
550          <dd>
551            <ul>
552            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_aliquot.jsp?ID=<%=ID%>"
553              >Create aliquots on Bioanalyzer/Caliper plates</span> 
554              <span class="counter" data-counter="rna-without-rnaqc" 
555                title="Number of RNA waiting for QC"></span>
556           
557            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_plate_export.jsp?ID=<%=ID%>"
558              >Export Caliper sample names and run parameters</span> 
559              <span class="counter" data-counter="caliper-rnaqc-waiting" 
560                title="Number of active Caliper plates"></span>
561           
562            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_plate_import.jsp?ID=<%=ID%>"
563              >Import RQS scores from Caliper well table file</span> 
564              <span class="counter" data-counter="caliper-rnaqc-waiting"
565                title="Number of active Caliper plates"></span>
566               
567            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_baprotocol.jsp?ID=<%=ID%>"
568              >Lab protocol for BioAnalyzer plates</span> 
569              <span class="counter" data-counter="bioanalyzer-rnaqc-waiting" 
570                title="Number of active BioAnalyzer plates"></span>
571               
572            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_bioanalyzer.jsp?ID=<%=ID%>"
573              >Register RIN scores for BioAnalyzer plates</span> 
574              <span class="counter" data-counter="bioanalyzer-rnaqc-waiting" 
575                title="Number of active BioAnalyzer plates"></span>
576            </ul>
577          </dd>
578          <dt style="margin-bottom: 0.5em;">
579            <base:icon image="<%=home+"/images/box.png" %>" />
580            <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/storage-box.jsp?ID=<%=ID%>"
581              >Storage box creation wizard</span>
582              <span class="counter more" data-counter="empty-storage-boxes" 
583                title="Number of empty storage boxes"></span><span 
584              class="counter" data-counter="empty-paused-storage-boxes" 
585                title="Number of empty storage boxes for paused specimen"></span>
586              <span id="more-boxes-are-needed" class="high-alert" style="display: none;">More boxes are needed</span>
587          </dt>
588          </dl>
589       
590          <h3>Histology wizards</h3>
591          <dl class="leftborder rightborder bottomborder">     
592          <dt>
593            <base:icon image="<%=home+"/images/histology.png" %>" />
594            Embedding and staining wizards
595          </dt>
596          <dd>
597            <ul>
598            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_protocol.jsp?ID=<%=ID%>"
599              >Lab tracking protocol for FFPE/HE</span> 
600              <span class="counter" data-counter="histology-active-lists" 
601                title="Number of active histology work lists"></span>
602           
603            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_block.jsp?ID=<%=ID%>"
604              >Register paraffin blocks</span> 
605              <span class="counter" data-counter="paraffin-blocks-not-embedded"
606                title="Number of paraffin blocks waiting for registration"></span>
607 
608            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_labels.jsp?ID=<%=ID%>"
609              >Download HE glass labels</span>
610           
611            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_glass.jsp?ID=<%=ID%>"
612              >Register HE glass</span> 
613              <span class="counter" data-counter="paraffin-blocks-without-heglass" 
614                title="Number of paraffin blocks without HE glass"></span>
615            </ul>
616          </dd>
617         
618          <dt>
619            <base:icon image="<%=home+"/images/microscope.png" %>" />
620            Scoring wizard
621          </dt>
622          <dd>
623            <ul>
624            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_score.jsp?ID=<%=ID%>"
625              >Score HE glass</span> 
626              <span class="counter" data-counter="heglass-not-scored" 
627                title="Number of unscored HE glass"></span>
628            </ul>
629          </dd>
630          </dl>
631        </div>
632     
633        <div id="rna-libprep-section" class="wizard-group">
634          <h3>Library preparation wizards</h3>
635          <dl class="leftborder rightborder bottomborder">
636       
637          <dt>
638            <base:icon image="<%=home+"/images/libprep.png" %>" />
639            Library preparation design wizards <span class="counter more" data-counter="rna-without-mrna-or-lib"
640                title="Number of RNA with no child mRNA or Library"></span><span 
641              class="counter" data-counter="normalized-rna-without-mrna-or-lib" 
642                title="Number of pre-normalized RNA with no child mRNA or Library"></span>
643          </dt>
644          <dd>
645            <ul>
646            <li><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/import-external-rna.jsp?ID=<%=ID%>"
647              >Import external RNA</span>
648            <li><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/select_rna.jsp?ID=<%=ID%>&plateType=MRNA"
649              >New manual library preparation</span> 
650              (<span class="require-permission" data-role="LibraryPrep" data-link="libprep/select_rna.jsp?ID=<%=ID%>&autoDesign=1&plateType=MRNA"
651              >auto-design</span>)
652            <li><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/select_rna.jsp?ID=<%=ID%>&plateType=EXTERNAL_LIBRARY"
653              >Select RNA for external sequencing</span> 
654            </ul>
655          </dd>
656         
657          <dt>
658            <base:icon image="<%=home+"/images/pipette.png" %>" />
659            Manual library preparation wizards
660          </dt>
661          <dd>
662            <ul>
663            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_protocol.jsp?ID=<%=ID%>"
664              >Lab protocols for mRNA and cDNA preparation</span> 
665              <span class="counter" data-counter="mrna-plates-not-registered" 
666                title="Number of mRNA plates waiting for registration"></span>
667           
668            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/rna_dilution_registration.jsp?ID=<%=ID%>"
669              >RNA dilution registration</span>
670              <span class="counter" data-counter="mrna-plates-not-diluted" 
671                title="Number of mRNA plates waiting for dilution"></span>
672           
673            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_registration.jsp?ID=<%=ID%>"
674              >mRNA registration and quality control results</span> 
675              <span class="counter" data-counter="mrna-plates-diluted-not-registered" 
676                title="Number of mRNA plates waiting for registration"></span>
677           
678            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/cdna_registration.jsp?ID=<%=ID%>"
679              >cDNA registration</span> 
680              <span class="counter" data-counter="cdna-plates-not-registered" 
681                title="Number of cDNA plates waiting for registration"></span>
682           
683            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/assign_barcode.jsp?ID=<%=ID%>"
684              >Assign barcodes to cDNA plate</span> 
685              <span class="counter" data-counter="cdna-plates-for-barcoding" 
686                title="Number of cDNA plates waiting for barcode layout"></span>
687           
688            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/libprep_protocol.jsp?ID=<%=ID%>"
689              >Lab protocols and files for library preparation</span> 
690              <span class="counter" data-counter="lib-plates-for-libprep" 
691                title="Number of Lib plates waiting for registration"></span>
692           
693            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/libqc_registration.jsp?ID=<%=ID%>"
694              >Register quality control results</span> 
695              <span class="counter" data-counter="lib-plates-for-libprep" 
696                title="Number of Lib plates waiting for registration"></span>
697           
698            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/lib_registration.jsp?ID=<%=ID%>"
699              >Library registration</span> 
700              <span class="counter" data-counter="lib-plates-for-libprep"
701                title="Number of Lib plates waiting for registration"></span>
702            </ul>
703          </dd>
704         
705          <dt>
706            <base:icon image="<%=home+"/images/pool.png" %>" />
707            Pooling wizards
708          </dt>
709          <dd>
710            <ul>
711            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/create_pools.jsp?ID=<%=ID%>"
712              >Create pooled libraries</span> 
713              <span class="counter" data-counter="lib-plates-for-pooling"
714                title="Number of Lib plates waiting for pooling"></span>
715           
716            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/pool_protocol.jsp?ID=<%=ID%>"
717              >Lab protocols for pooling</span> 
718              <span class="counter" data-counter="pools-not-registered-rnaseq" 
719                title="Number of pools waiting for registration"></span>
720           
721            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/pool_registration.jsp?ID=<%=ID%>"
722              >Register pooled libraries</span> 
723              <span class="counter" data-counter="pools-not-registered-rnaseq" 
724                title="Number of pools waiting for registration"></span>
725            </ul>
726          </dd>
727          </dl>
728         
729          <h3>Sequencing wizards</h3>
730          <dl class="leftborder rightborder bottomborder">
731         
732          <dt>
733            <base:icon image="<%=home+"/images/flowcell.png" %>" />
734            Sequencing wizards
735          </dt>
736          <dd>
737            <ul>
738            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/create_flowcells.jsp?ID=<%=ID%>"
739              >Create flow cells</span> 
740              <span class="counter" data-counter="pools-not-used-rnaseq" 
741                title="Number of pools waiting for sequencing"></span>
742           
743            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/flowcell_protocol.jsp?ID=<%=ID%>"
744              >Lab protocol for sequencing</span> 
745              <span class="counter" data-counter="flow-cells-not-sequenced-rnaseq" 
746                title="Number of flow cells waiting to be sequenced"></span>
747           
748            <li><span class="require-permission" data-role="LibraryPrep" data-link="sequencing/sequencing_started.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
749              >Register sequencing started</span> 
750              <span class="counter" data-counter="flow-cells-not-sequenced-rnaseq" 
751                title="Number of flow cells waiting to be sequenced"></span>
752 
753            <li><span class="require-permission" data-role="LibraryPrep" data-link="sequencing/sequencing_ended.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
754              >Register sequencing ended</span> 
755              <span class="counter" data-counter="sequencing-runs-active-rnaseq" 
756                title="Number of active sequencing runs"></span>
757            </ul>
758          </dd>
759
760          <dt>
761            <base:icon image="<%=home+"/images/lorry.png" %>" />
762            External sequencing wizards
763          </dt>
764          <dd>
765            <ul>
766            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/external_protocol.jsp?ID=<%=ID%>"
767              >Lab protocols and files for external sequencing</span> 
768              <span class="counter" data-counter="external-plates-not-registered" 
769                title="Number of external plates waiting for registration"></span>
770     
771            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="sequencing/sequencing_external.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
772              >Register external sequencing</span> 
773              <span class="counter" data-counter="external-libs-not-sequenced" 
774                title="Number of libraries sent for external sequencing"></span>
775            </ul>
776          </dd>
777          </dl>
778        </div>
779       
780        <div id="rnaseq-analysis-section" class="wizard-group">
781          <h3>Secondary analysis wizards</h3>
782          <dl class="leftborder rightborder bottomborder">
783            <dt>
784              <base:icon image="<%=home+"/images/server.png" %>" />
785              Demux and merge wizards
786            </dt>
787            <dd>
788              <ul>
789              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="sequencing/sequencing_confirm.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
790                >Confirm sequencing completed</span> 
791                <span class="counter" data-counter="sequencing-runs-unconfirmed-rnaseq" 
792                  title="Number of ended but not confirmed sequencing runs"></span>
793             
794              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
795                >Start demux and merge</span> 
796                <span class="counter" data-counter="sequencing-runs-for-demux-rnaseq" 
797                  title="Number of confirmed sequencing runs waiting to be demuxed"></span>
798             
799              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/demux_confirm.jsp?ID=<%=ID%>"
800                >Confirm demux and merge completed</span> 
801                <span class="counter" data-counter="demux-jobs-not-confirmed-rnaseq"
802                  title="Number of demux jobs waiting for confirmation"></span>
803              </ul>
804            </dd>
805           
806            <dt>
807              <base:icon image="<%=home+"/images/lorry.png" %>" />
808              External sequencing wizards
809            </dt>
810            <dd>
811              <ul>
812              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/import_fastq.jsp?ID=<%=ID%>"
813                >Import FASTQ files</span> 
814                <span class="counter" data-counter="demuxed-sequences-for-fastq-import" 
815                  title="Number of demuxed sequences waiting for FASTQ import"></span>
816                  <span id="fastq-import-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
817 
818              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/import_confirm.jsp?ID=<%=ID%>"
819                >Confirm FASTQ import</span> 
820                <span class="counter" data-counter="merged-sequences-fastq-import-not-confirmed" 
821                  title="Number of merged sequences waiting for confirmation of FASTQ import"></span>
822              </ul>
823            </dd>
824 
825            <dt>
826              <base:icon image="<%=home+"/images/align.png" %>" />
827              Hisat and StringTie pipeline
828            </dt>
829            <dd>
830              <ul>
831              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/hisat_start.jsp?ID=<%=ID%>"
832                >Start Hisat alignment</span>
833                <span class="counter" data-counter="merged-sequences-for-hisat-alignment"
834                  title="Number of merged sequences waiting for Hisat alignment"></span>
835                <span id="hisat-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
836                 
837              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/hisat_confirm.jsp?ID=<%=ID%>"
838                >Confirm Hisat alignment</span> 
839                <span class="counter" data-counter="hisat-aligned-sequences-not-confirmed" 
840                  title="Number of Hisat aligned sequences waiting for confirmation"></span>
841             
842              <li><span id="genotype-qc" class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/genotype_qc.jsp?ID=<%=ID%>"
843                >Genotype quality control</span> 
844                <span class="counter" data-counter="alignments-for-genotype-qc" 
845                  title="Number of alignments with VCF files that has not been checked"></span>
846
847              <%
848              if (isAdmin)
849              {
850                %>
851                <li><span id="genotype-standalone-check" class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/genotype_standalone_check.jsp?ID=<%=ID%>"
852                  >Genotype check standalone VCF files</span> 
853                <%
854              }
855              %>
856              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/mbaf_start.jsp?ID=<%=ID%>"
857                >Start mBAF analysis</span> 
858                <span class="counter" data-counter="aligned-sequences-for-mbaf" 
859                  title="Number of aligned sequences waiting for mBAF analysis"></span>
860                <span id="mbaf-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
861               
862              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/stringtie_start.jsp?ID=<%=ID%>"
863                >Start StringTie</span>
864                <span class="counter" data-counter="aligned-sequences-for-stringtie"
865                  title="Number of aligned sequences waiting for StringTie"></span>
866                <span id="stringtie-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
867 
868              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/stringtie_confirm.jsp?ID=<%=ID%>"
869                >Confirm StringTie completed</span> 
870                <span class="counter" data-counter="stringtie-not-confirmed" 
871                  title="Number of StringTie jobs waiting for confirmation"></span>
872                 
873              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/ssp_start.jsp?ID=<%=ID%>"
874                >Start Single Sample Predictor analysis</span> 
875                <span class="counter" data-counter="rawbioassays-for-ssp" 
876                  title="Number of StringTie raw bioassays waiting for Single Sample predictor analysis"></span>
877                <span id="ssp-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
878               
879              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=SCANB_REPORT"
880                >SCAN-B report</span> 
881                <span class="counter" data-counter="rawbioassys-without-scanbreport" 
882                  title="Number of rawbioassays without a SCAN-B report PDF"></span>
883                  <span id="scanb-report-disabled" class="info-warning">auto-processing is disabled</span>
884             
885              </ul>
886            </dd>
887           
888            <dt>
889              <base:icon image="<%=home+"/images/variantcall.png" %>" />
890              Variant calling pipeline
891            </dt>
892           
893            <dd>
894              <ul>
895              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/vcall_start.jsp?ID=<%=ID%>"
896                >Start variant calling</span> 
897                <span class="counter" data-counter="aligned-sequences-for-variant-calling" 
898                  title="Number of aligned sequences waiting for variant calling pipeline"></span>
899                <span id="variant-calling-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
900              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/vcall_confirm.jsp?ID=<%=ID%>"
901                >Confirm variant calling</span> 
902                <span class="counter" data-counter="variantcall-not-confirmed" 
903                  title="Number of VariantCall jobs waiting for confirmation"></span>
904              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/targeted_gt_start.jsp?ID=<%=ID%>"
905                >Start targeted genotyping</span> 
906                <span class="counter" data-counter="variantcall-for-targeted-genotype" 
907                  title="Number of variant calls waiting for targeted genotyping"></span>
908                <span id="targeted-genotype-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
909              <li><span class="require-permission" data-role="Administrator" data-link="analysis/vcall_build.jsp?ID=<%=ID%>"
910                >Build SCAN-B variant database</span> 
911              <li id="variant-import-wizard"><span class="require-permission" data-role="Administrator" data-link="analysis/vcall_import.jsp?ID=<%=ID%>"
912                >Import variants for existing variant call raw bioassays</span>
913                <span class="counter" data-counter="variant-calls-needing-import" 
914                  title="Number of VariantCall item that need to import variants"></span>
915              </ul>
916            </dd>
917           
918            <dt>
919              <base:icon image="<%=home+"/images/pdffile.png" %>" />
920              Legacy Tophat and Cufflinks pipeline <span id="legacy-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
921            </dt>
922            <dd>
923              <ul>
924              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/align_start.jsp?ID=<%=ID%>"
925                >Start Tophat and Cufflinks</span> 
926                <span class="counter" data-counter="merged-sequences-for-legacy-alignment"
927                  title="Number of merged sequences waiting for Tophat alignment"></span>
928                 
929              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/cufflinks_confirm.jsp?ID=<%=ID%>"
930                >Confirm Cufflinks completed</span> 
931                <span class="counter" data-counter="cufflinks-not-confirmed" 
932                  title="Number of Cufflinks jobs waiting for confirmation"></span>
933              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=GENE_REPORT"
934                >Gene report</span> 
935                <span class="counter" data-counter="rawbioassys-without-genereport" 
936                  title="Number of rawbioassays without a Gene report PDF"></span>
937                  <span id="gene-report-disabled" class="info-warning">auto-processing is disabled</span>
938              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=PILOT_REPORT"
939                >Pilot report</span> 
940                <span class="counter" data-counter="rawbioassys-without-pilotreport" 
941                  title="Number of rawbioassays without a Pilot report PDF"></span>
942                  <span id="pilot-report-disabled" class="info-warning">auto-processing is disabled</span>
943              </ul>
944            </dd>
945           
946          </dl>     
947       
948        </div>
949       
950        <div id="mips-libprep-section" class="wizard-group">
951          <h3>Library preparation wizards</h3>
952          <dl class="leftborder rightborder bottomborder">
953       
954          <dt>
955            <base:icon image="<%=home+"/images/libprep.png" %>" />
956            MIPs plate design wizards
957          </dt>
958          <dd>
959            <ul>
960            <li><span class="require-permission" data-role="MIPsPlateDesigner" data-link="mipsprep/import_plates.jsp?ID=<%=ID%>"
961              >Import DNA aliquot plates</span>
962             
963            <li><span class="require-permission" data-role="MIPsPlateDesigner" data-link="mipsprep/design_mipsplate.jsp?ID=<%=ID%>"
964              >Design MIPs plate</span>
965              <span class="counter more" data-counter="prenormalized-designmips"
966                title="Number of aliquot plates with DNA waiting for MIPs"></span><span 
967              class="counter" data-counter="prenormalized-addaliquots"
968                title="Number of aliquot plates in the SCAN-B lab"></span>
969            </ul>
970          </dd>
971         
972          <dt>
973            <base:icon image="<%=home+"/images/pipette.png" %>" />
974            MIPs library preparation wizards
975          </dt>
976          <dd>
977            <ul>
978            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/mips_protocol.jsp?ID=<%=ID%>"
979              >Lab protocols for MIPs library preparation</span> 
980              <span class="counter" data-counter="mips-plates-for-libprep" 
981                title="Number of MIPs plates waiting for registration"></span>
982           
983            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/lib_registration.jsp?ID=<%=ID%>"
984              >MIPs library registration</span> 
985              <span class="counter" data-counter="mips-plates-for-libprep"
986                title="Number of MIPs plates waiting for registration"></span>
987           
988            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/pool_registration.jsp?ID=<%=ID%>"
989              >Register pooled libraries</span> 
990              <span class="counter" data-counter="mips-plates-for-pooling" 
991                title="Number of MIPs library plates waiting for pooling"></span>
992            </ul>
993          </dd>
994
995          </dl>
996         
997          <h3>Sequencing wizards</h3>
998          <dl class="leftborder rightborder bottomborder">
999         
1000          <dt>
1001            <base:icon image="<%=home+"/images/flowcell.png" %>" />
1002            Sequencing wizards
1003          </dt>
1004          <dd>
1005            <ul>
1006            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/create_flowcells.jsp?ID=<%=ID%>"
1007              >Create flow cells</span> 
1008              <span class="counter" data-counter="pools-not-used-mips" 
1009                title="Number of MIPs pools waiting for sequencing"></span>
1010           
1011            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/flowcell_protocol.jsp?ID=<%=ID%>"
1012              >Lab protocol for sequencing</span> 
1013              <span class="counter" data-counter="flow-cells-not-sequenced-mips" 
1014                title="Number of MIPs flow cells waiting to be sequenced"></span>
1015           
1016            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="sequencing/sequencing_started.jsp?ID=<%=ID%>&pipeline=MIPS"
1017              >Register sequencing started</span> 
1018              <span class="counter" data-counter="flow-cells-not-sequenced-mips" 
1019                title="Number of MIPs flow cells waiting to be sequenced"></span>
1020 
1021            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="sequencing/sequencing_ended.jsp?ID=<%=ID%>&pipeline=MIPS"
1022              >Register sequencing ended</span> 
1023              <span class="counter" data-counter="sequencing-runs-active-mips" 
1024                title="Number of active MIPs sequencing runs"></span>
1025            </ul>
1026          </dd>
1027         
1028          </dl>
1029         
1030          <h3>Secondary analysis wizards</h3>
1031          <dl class="leftborder rightborder bottomborder">
1032            <dt>
1033              <base:icon image="<%=home+"/images/server.png" %>" />
1034              Demux wizards
1035            </dt>
1036            <dd>
1037              <ul>
1038              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="sequencing/sequencing_confirm.jsp?ID=<%=ID%>&pipeline=MIPS"
1039                >Confirm sequencing completed</span> 
1040                <span class="counter" data-counter="sequencing-runs-unconfirmed-mips" 
1041                  title="Number of ended but not confirmed MIPs sequencing runs"></span>
1042             
1043              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/demux_start.jsp?ID=<%=ID%>&pipeline=MIPS"
1044                >Start demux</span> 
1045                <span class="counter" data-counter="sequencing-runs-for-demux-mips" 
1046                  title="Number of confirmed MIPs sequencing runs waiting to be demuxed"></span>
1047             
1048              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/demux_confirm.jsp?ID=<%=ID%>"
1049                >Confirm demux completed</span> 
1050                <span class="counter" data-counter="demux-jobs-not-confirmed-mips"
1051                  title="Number of MIPs demux jobs waiting for confirmation"></span>
1052              </ul>
1053            </dd>
1054           
1055            <dt>
1056              <base:icon image="<%=home+"/images/align.png" %>" />
1057              Alignment pipeline
1058            </dt>
1059            <dd>
1060              <ul>
1061              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/align_start.jsp?ID=<%=ID%>"
1062                >Start MIPs alignment</span>
1063                <span class="counter" data-counter="merged-sequences-for-mips-alignment"
1064                  title="Number of merged sequences waiting for MIPs alignment"></span>
1065                <span id="mips-align-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
1066
1067              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/align_confirm.jsp?ID=<%=ID%>"
1068                >Confirm MIPs alignment</span> 
1069                <span class="counter" data-counter="mips-aligned-sequences-not-confirmed" 
1070                  title="Number of MIPs aligned sequences waiting for confirmation"></span>
1071              </ul>
1072            </dd>
1073           
1074          </dl>
1075         
1076        </div>
1077       
1078        <div id="personal-information-section" class="wizard-group">
1079          <%
1080          if (isPatientCurator || isAdmin)
1081          {
1082            %>
1083            <h3>Personal information wizards</h3>
1084            <dl class="leftborder rightborder bottomborder">
1085            <dt>
1086              <base:icon image="<%=home + "/images/personal.png" %>"/>
1087              Referral form registration wizards
1088            </dt>
1089            <dd>
1090              <ul>
1091              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/persinfo.jsp?ID=<%=ID%>"
1092                >Pathology referral form registration</span>
1093                <span class="counter more" data-counter="specimen-local-without-case" 
1094                  title="Number of (local) specimen tubes not linked to a case"></span><span 
1095                  class="counter" data-counter="specimen-external-without-case" 
1096                  title="Number of (external) specimen tubes not linked to a case"></span>
1097 
1098              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodform.jsp?ID=<%=ID%>"
1099                >Blood referral forms registration</span>
1100               
1101              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodfollowupform.jsp?ID=<%=ID%>"
1102                >Follow-up blood referral form registration</span>
1103
1104              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/import_followup_blood.jsp?ID=<%=ID%>"
1105                >Batch-import follow-up blood referral forms</span>
1106 
1107              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/consentform.jsp?ID=<%=ID%>"
1108                >Consent form registration</span>
1109                <span class="counter" data-counter="case-or-blood-without-consent" 
1110                  title="Number of cases and blood samples without consent"></span>
1111              </ul>
1112            </dd>
1113           
1114            <dt>
1115              <base:icon image="<%=home+"/images/report.png" %>" />
1116              Referral forms
1117            </dt>
1118            <dd>
1119              <ul>
1120              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/generate-referral-forms.jsp?ID=<%=ID%>"
1121                >Referral ID generator</span>
1122              </ul>
1123            </dd>
1124 
1125            <dt>
1126              <base:icon image="<%=home+"/images/delete.png" %>" />
1127              Retraction wizard
1128            </dt>
1129            <dd>
1130              <ul>
1131              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/retractionform.jsp?ID=<%=ID%>"
1132                >Mark extracts for retraction</span>
1133 
1134              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/retraction_followup_form.jsp?ID=<%=ID%>"
1135                >Retraction follow-up and destruction</span>
1136                <span class="counter more" data-counter="patientitems-ready-for-retraction-followup" 
1137                  title="Number of patient items ready for retraction follow-up"></span><span 
1138                  class="counter" data-counter="patientitems-ready-for-destruction" 
1139                  title="Number of patient items ready for destruction"></span>
1140 
1141              </ul>
1142            </dd>
1143           
1144            <dt>
1145              <base:icon image="<%=home+"/images/export_import.png" %>" />
1146              Import and export wizards
1147            </dt>
1148            <dd>
1149              <ul>
1150              <li><span class="require-permission" data-role="Administrator" data-link="batch/import-external-specimen.jsp?ID=<%=ID%>"
1151                >Import externally processed samples</span>
1152                <span class="counter more merge" data-counter="import-files-json" 
1153                  title="Number JSON files waiting to be imported"></span><span
1154                  class="counter more" data-counter="import-files-fastq"
1155                  title="Number FASTQ pairs waiting to be imported"></span><span 
1156                  class="counter" data-counter="nospecimen-with-external-specimen" 
1157                  title="Number of NoSpecimen with ExternalSpecimenExists=Yes">
1158             
1159              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export-inca.jsp?ID=<%=ID%>"
1160                >INCA export</span>
1161 
1162              <li><span id="inca-import" 
1163                class="require-permission" 
1164                data-role="PatientCurator"
1165                data-link="personal/import-inca.jsp?ID=<%=ID%>"
1166                >INCA import</span>
1167 
1168              <li><span id="inca-statistics" 
1169                class="require-permission" 
1170                data-role="PatientCurator"
1171                data-link="personal/inca-statistics.jsp?ID=<%=ID%>"
1172                >INCA statistics</span>
1173 
1174              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export-monthly-oplist.jsp?ID=<%=ID%>"
1175                >Export monthly operation list</span>
1176               
1177              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_data_sample_list.jsp?ID=<%=ID%>"
1178                >Export missing data sample list</span>
1179 
1180              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_consent_data_sample_list.jsp?ID=<%=ID%>"
1181                >Export missing consent data sample list</span>
1182               
1183              <li><span class="require-permission" data-role="PatientCurator" data-link="batch/frozen-tissue-date.jsp?ID=<%=ID%>"
1184                >Import frozen tissue date</span> 
1185               
1186              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/map-external-data.jsp?ID=<%=ID%>"
1187                >Map external data to releases</span>
1188              </ul>
1189            </dd>
1190           
1191            </dl>
1192            <%
1193          }
1194          %>
1195          <h3>Sample curation and outtake wizards</h3>
1196          <dl class="leftborder rightborder bottomborder">
1197            <dt>
1198              <base:icon image="<%=home+"/images/flag.png" %>" />
1199              Re-processing wizards
1200            </dt>
1201            <dd>
1202              <ul>
1203              <li><span class="require-permission" data-role="PrepCurator" data-link="flaggedrna/search.jsp?ID=<%=ID%>"
1204                >Flagged RNA</span> 
1205                <span class="counter" data-counter="flagged-rna" 
1206                  title="Number of flagged RNA items"></span>
1207              <li><span class="require-permission" data-role="PrepCurator" data-link="flaggedalignment/search.jsp?ID=<%=ID%>"
1208                >Flagged alignment</span> 
1209                <span class="counter" data-counter="flagged-alignment" 
1210                  title="Number of flagged alignment items"></span>
1211              <li><span class="require-permission" data-role="PrepCurator" data-link="sampleproc/paused-specimen.jsp?ID=<%=ID%>"
1212                >Paused specimen</span> 
1213                <span class="counter" data-counter="paused-specimen" 
1214                  title="Number of paused+scheduled specimen items"></span>
1215              </ul>
1216            </dd>
1217 
1218            <dt>
1219              <base:icon image="<%=home+"/images/smile.png" %>" />
1220              Batch update wizards
1221            </dt>
1222            <dd>
1223              <ul>
1224              <li><span class="require-permission" data-role="PrepCurator" data-link="batch/linked-specimen.jsp?ID=<%=ID%>"
1225                >Linked specimen</span> 
1226              <li><span class="require-permission" data-role="PrepCurator" data-link="batch/reference-date.jsp?ID=<%=ID%>"
1227                >Reference date and linked cases</span> 
1228              </ul>
1229            </dd>
1230           
1231            <dt>
1232              <base:icon image="<%=home+"/images/outtake.png" %>" />
1233              Sample outtake wizards
1234            </dt>
1235            <dd>
1236              <ul>
1237              <li><span class="require-permission" data-role="PrepCurator" data-link="outtake/define.jsp?ID=<%=ID%>"
1238                >Define a new sample outtake</span>
1239              <li><span class="require-permission" data-role="SamplePrep" data-link="outtake/picklist.jsp?ID=<%=ID%>"
1240                >Protocols and labels for sample outtakes</span> 
1241                <span class="counter" data-counter="active-outtake-lists" 
1242                  title="Number of sample outtakes waiting to be processed"></span>
1243              <li><span class="require-permission" data-role="SamplePrep" data-link="outtake/register.jsp?ID=<%=ID%>"
1244                >Register sample outtake</span> 
1245                <span class="counter" data-counter="active-outtake-lists" 
1246                  title="Number of sample outtakes waiting to be processed"></span>
1247              <li><span class="require-permission" data-role="PrepCurator" data-link="outtake/delivery_export.jsp?ID=<%=ID%>"
1248                >Export delivery data file for sample outtake</span>
1249                <span class="counter" data-counter="undelivered-outtake-lists" 
1250                  title="Number of sample outtakes not delivered"></span>
1251              </ul>
1252            </dd>
1253 
1254          </dl>
1255        </div>
1256       
1257        <div id="statistics-section" class="wizard-group">
1258          <h3>Statistics and reporting wizards</h3>
1259          <dl class="leftborder rightborder bottomborder">
1260            <dt>
1261              <base:icon image="<%=home+"/images/report.png" %>" />
1262              <span class="require-permission" data-role="" data-link="reports/samplereportgenerator.jsp?ID=<%=ID%>"
1263                >Sample source report</span>
1264            </dt>
1265            <dd>
1266              <ul>
1267              <li>Sample count report</li> 
1268              <li>Consent count report</li> 
1269              <li>Patient count report</li> 
1270              <li>Overview report</li> 
1271              <li>Missing sample data report</li> 
1272              </ul>
1273            </dd>
1274            <dt>
1275              <base:icon image="<%=home+"/images/chart_bar.png" %>" />
1276              <span class="require-permission" data-role="" data-link="reports/scanbquartermonthreportgenerator.jsp?ID=<%=ID%>"
1277                >Sample processing statistics</span>
1278            </dt>       
1279            <dd>       
1280              <ul>
1281              <li>SCAN-B quarter/month report</li> 
1282              </ul>
1283            </dd>
1284            <dt style="margin-bottom: 0.5em;">
1285              <base:icon image="<%=home+"/images/yellow-label.png" %>" />
1286              <span class="require-permission" data-role="" data-link="yellowlabel/list.jsp?ID=<%=ID%>"
1287                >YellowLabel tracking and reporting</span>
1288                <span class="counter" data-counter="specimen-active-yellow-label" 
1289                  title="Number of active YellowLabel specimen"></span>
1290            </dt> 
1291          </dl>
1292        </div>
1293
1294        <div id="administration-section" class="wizard-group">
1295          <%
1296          if (isAdmin)
1297          {
1298            %>
1299            <h3>Server administrator wizards</h3>
1300            <dl class="leftborder rightborder bottomborder">
1301            <dt>
1302              <base:icon image="<%=home + "/images/install.png" %>" />
1303              <span class="require-permission" data-role="Administrator" data-link="admin/install.jsp?ID=<%=ID%>">Installation wizard</span>
1304            </dt>
1305            <dd>
1306              <ul>
1307              <li>Check that items needed by Reggie exists in BASE.
1308              <li>Create and fix items.
1309              </ul>
1310            </dd>
1311
1312            <div id="reload-config-wizard" style="display: none;">
1313              <dt class="high-alert">Reggie configuration has been modified</dt>
1314              <dd>
1315              <ul>
1316              <li><span id="reload-config" class="require-permission" data-role="Administrator"
1317                >Reload reggie-config.xml</span>
1318              </ul>
1319              </dd>
1320            </div>
1321         
1322            <dt>
1323              <base:icon image="<%=home + "/images/ogs-cluster.png"%>" />
1324              Other tasks
1325            </dt>
1326            <dd>
1327              <ul>
1328              <li><span class="require-permission" data-role="Administrator" data-link="admin/remote/list-hosts.jsp?ID=<%=ID%>"
1329                >Job scheduler hosts</span>
1330               
1331              <li><span class="require-permission" data-role="Administrator" data-link="admin/stray-files.jsp?ID=<%=ID%>"
1332                >Stray files wizard</span>
1333                <span class="counter" data-counter="stray-folders" 
1334                  title="Number of stray folders"></span>
1335                 
1336              <li><span class="require-permission" data-role="Administrator" data-link="admin/analysis-cleanup.jsp?ID=<%=ID%>"
1337                >Secondary analysis cleanup</span>
1338                <span class="counter more" data-counter="analysis-cleanup-dba"
1339                  title="Number of derived bioassay items to cleanup"></span><span 
1340                  class="counter" data-counter="analysis-cleanup-rba" 
1341                  title="Number of raw bioassay items to cleanup"></span>
1342              </ul>
1343            </dd>
1344            </dl>
1345            <%
1346          }
1347          %>
1348        </div>
1349       
1350      </div>
1351    </div>
1352   
1353    <div class="absolutefull" style="width: 30%; left: auto;">
1354      <div class="absolutefull" style="left: 0.5em; bottom: 2em;">
1355        <div class="absolutefull" style="right: 1em; height: 4em;">
1356          <b>Case summary</b><br>
1357          <input type="text" class="text auto-init" data-auto-init="focus" 
1358            name="caseName" id="caseName" title="Please enter a SCAN-B case id, personal number, release id, PAD, etc." 
1359            style="width: 15em;">
1360          <base:button id="btnCaseSummary" title="Go" image="<%=home+"/images/gonext.png"%>" />
1361        </div>
1362        <div class="absolutefull" style="top: 4em; padding-right: 0.5em;">
1363          <div id="summary-stats">
1364            <div class="counter" data-counter="patients-all" 
1365              title="Total number of patients"></div> Patients<br>
1366            <div class="counter" data-counter="specimen-all" 
1367              title="Total number of specimen tubes"></div> Specimen Tubes<br>
1368            <div class="counter" data-counter="rna-all-extracted" 
1369              title="Total number of extracted RNA"></div> Extracted Rna<br>
1370            <div class="counter" data-counter="libraries-all-aligned" 
1371              title="Total number of aligned libraries"></div> Aligned Libraries<br>
1372            <div class="counter" data-counter="rawbioassys-all-with-genereport"
1373              title="Total number of generated gene reports"></div> Gene Reports<br>
1374            <div class="counter" data-counter="stained-score-complete"
1375              title="Total number of completely scored histology samples"></div> Scored Histology Samples
1376          </div>
1377
1378          <div id="activity-log">
1379            <div id="quote-of-the-day"></div>
1380            <a id="activity-log-rss" href="<%=servletHome%>/ActivityLog.rss" 
1381              title="Get the activity log as an RSS feed"><img src="images/rss.png"></a>
1382            <div id="activity-log-entries"></div>
1383          </div>
1384        </div>
1385      </div>
1386      <div id="counter-age-control">
1387        <b>Counters last updated</b> <span id="counter-age"></span><base:icon id="counter-refresh" 
1388          image="<%=home+"/images/refresh-small.png"%>" style="display:none;" title="Force update of counters" 
1389          /><base:icon id="counter-loading" image="<%=home+"/images/loading-small.gif"%>" />
1390      </div>
1391    </div>
1392    </form>
1393   
1394  </div>
1395 
1396</base:body>
1397</base:page>
1398<%
1399}
1400finally
1401{
1402  if (dc != null) dc.close();
1403}
1404%>
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