source: extensions/net.sf.basedb.reggie/trunk/resources/index.jsp @ 6010

Last change on this file since 6010 was 6010, checked in by Nicklas Nordborg, 13 months ago

Merged Reggie 4.27.4 to the trunk.

File size: 51.7 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
221#activity-log .activity.quote-of-the-day
222{
223  font-style: italic;
224  white-space: normal;
225  text-align: center;
226  margin: 1em 1em 0.5em 0;
227  border-top-width: 1px;
228  border-top-style: dotted;
229  padding-top: 0.5em;
230}
231
232#activity-log .activity-author
233{
234  white-space: nowrap;
235}
236
237#activity-log .activity-author:before
238{
239  content: '–';
240  padding-left: 0.5em;
241  padding-right: 0.25em;
242}
243
244#activity-log .quote-of-the-day .activity-link
245{
246  text-align: right;
247  border-top-width: 1px;
248  border-top-style: dotted;
249  margin-top: 0.5em;
250}
251
252#activity-log .activity-time
253{
254  margin-right: 0.5em;
255  color: #666666;
256}
257
258#activity-log .quote-of-the-day .activity-time
259{
260  display: none;
261}
262
263#activity-log-rss
264{
265  float: right;
266  margin-right: 1em;
267}
268#counter-age-control
269{
270  position: absolute;
271  bottom: 2px;
272  right: 1rem;
273  font-size: 90%;
274}
275
276#counter-refresh, #counter-loading
277{
278  padding-left: 3px;
279  vertical-align: -2px;
280}
281
282div.counter
283{
284  display: inline-block;
285  min-width: 4em;
286  text-align: right;
287  padding-right: 0.25em;
288  font-size: 120%;
289  font-weight: bold;
290}
291
292#more-boxes-are-needed
293{
294  display: none;
295  background-color: #ffff00;
296  font-weight: bold;
297  padding: 2px 0.5em;
298  margin-bottom: 0.25em;
299  margin-left: 0.5em;
300  border-width: 2px;
301  border-radius: 5px;
302}
303
304#more-boxes-are-needed::before
305{
306  content: url('images/warning.png');
307  vertical-align: top;
308  margin-right: 0.25em;
309}
310
311div.group-menu
312{
313  background-color: #F8F8F8;
314  padding: 0.5em 10px 0.5em 1em;
315  border-width: 1px;
316  margin-bottom: 1em;
317  border-radius: 6px;
318}
319
320div.group-menu:hover
321{
322  text-decoration: none;
323  border-right-width: 10px;
324  padding-right: 0;
325}
326
327div.group-menu .group-title
328{
329  font-weight: bold;
330  font-size: 125%;
331  color: #333377;
332  margin-bottom: 0.25em;
333}
334div.group-menu .group-examples span
335{
336  color: #666666;
337  font-style: italic;
338  white-space: nowrap;
339}
340
341div.group-menu .group-examples span:before
342{
343  content: '•';
344  padding-right: 0.25em;
345}
346
347#wizard[data-wizard-group="sample-processing-section"] .group-menu[data-wizard-group="sample-processing-section"],
348#wizard[data-wizard-group="rna-libprep-section"] .group-menu[data-wizard-group="rna-libprep-section"],
349#wizard[data-wizard-group="mips-libprep-section"] .group-menu[data-wizard-group="mips-libprep-section"],
350#wizard[data-wizard-group="personal-information-section"] .group-menu[data-wizard-group="personal-information-section"],
351#wizard[data-wizard-group="statistics-section"] .group-menu[data-wizard-group="statistics-section"],
352#wizard[data-wizard-group="administration-section"] .group-menu[data-wizard-group="administration-section"]
353{
354  background-color: #FFFFF0;
355  border-right-width: 10px;
356  border-right-color: #2288AA;
357  padding-right: 0;
358}
359
360.wizard-group
361{
362  display: none;
363}
364
365#wizard[data-wizard-group="sample-processing-section"] #sample-processing-section,
366#wizard[data-wizard-group="rna-libprep-section"] #rna-libprep-section,
367#wizard[data-wizard-group="mips-libprep-section"] #mips-libprep-section,
368#wizard[data-wizard-group="personal-information-section"] #personal-information-section,
369#wizard[data-wizard-group="statistics-section"] #statistics-section,
370#wizard[data-wizard-group="administration-section"] #administration-section
371{
372  display: block;
373}
374
375</style>
376</base:head>
377<base:body>
378
379  <p:path><p:pathelement title="Reggie" /></p:path>
380
381  <div class="content">
382    <form name="reggie" id="wizard" class="wizard" data-wizard-group="<%=HTML.encodeTags(lastWizardGroup)%>">
383    <div id="wizard-status" style="position: absolute; z-index: 99; left: 25%; right: 25%; top: 25%; height: auto; text-align: center;"></div>
384    <div class="absolutefull" style="width: 30%;">
385      <div class="absolutefull" style="left: 1em; right: 0.5em; ">
386       
387        <div class="group-menu link" data-wizard-group="sample-processing-section">
388          <div class="group-title">Sample processing and histology</div>
389          <div class="group-examples">
390            <span>Registration</span>
391            <span>Partitioning</span>
392            <span>Extraction</span>
393            <span>Quality control</span>
394            <span>Histology scoring</span>
395          </div>
396        </div>
397 
398        <div class="group-menu link" data-wizard-group="rna-libprep-section">
399          <div class="group-title">RNA library preparation and analysis</div>
400          <div class="group-examples">
401            <span>Plate design</span>
402            <span>Library registration</span>
403            <span>Pooling</span>
404            <span>Sequencing</span>
405            <span>Secondary analysis</span>
406          </div>
407        </div>
408         
409        <div class="group-menu link" data-wizard-group="mips-libprep-section">
410          <div class="group-title">MIPs library preparation and analysis</div>
411          <div class="group-examples">
412            <span>Aliquot import</span>
413            <span>Plate design</span>
414            <span>Library registration</span>
415            <span>Pooling</span>
416            <span>Sequencing</span>
417            <span>Secondary analysis</span>
418          </div>
419        </div>
420       
421        <div class="group-menu link" data-wizard-group="personal-information-section">
422          <div class="group-title">Personal information and sample curation</div>
423          <div class="group-examples">
424            <span>Referral forms</span>
425            <span>Retraction</span>
426            <span>INCA</span>
427            <span>Flagged items</span>
428            <span>Batch updates</span>
429            <span>Outtakes</span>
430          </div>
431        </div>
432 
433        <div class="group-menu link" data-wizard-group="statistics-section">
434          <div class="group-title">Statistics and reporting</div>
435          <div class="group-examples">
436            <span>Sample count tables</span>
437            <span>Sample processing plots</span>
438            <span>YellowLabel tracking</span>
439          </div>
440        </div>
441        <%
442        if (isAdmin)
443        {
444          %>
445          <div class="group-menu link" data-wizard-group="administration-section">
446            <div class="group-title">Server administration</div>
447            <div class="group-examples">
448              <span>Installation wizard</span>
449              <span>Configuration</span>
450              <span>Cleanup</span>
451            </div>
452          </div>
453          <%
454        }
455        %>
456      </div>
457    </div>
458   
459    <div class="absolutefull" style="width: 40%; left: 30%; right: auto;">
460      <div class="absolutefull" style="left: 0.5em; right: 0.5em;">
461     
462        <div id="sample-processing-section" class="wizard-group">
463          <h3>Sample processing wizards</h3>
464          <dl class="leftborder rightborder bottomborder has-lib-prep">
465 
466          <dt>
467            <base:icon image="<%=home+"/images/specimen.png" %>" />
468            Specimen tube registration
469          </dt>
470          <dd>
471            <ul>
472            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/specimentube.jsp?ID=<%=ID%>"
473              >Register new specimen tubes</span>.
474            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/store-paused.jsp?ID=<%=ID%>"
475              >Store paused specimen</span>
476              <span class="counter" data-counter="paused-specimen-to-store" 
477                title="Number of paused specimen that has not yet been stored"></span>
478            </ul>
479          </dd>
480 
481          <dt>
482            <base:icon image="<%=home+"/images/partition.png" %>" />
483            <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/partitionform.jsp?ID=<%=ID%>"
484              >Partition wizard</span>
485          </dt>
486          <dd>
487            <ul>
488            <li>Register new partitions of existing specimens
489              <span class="counter more" data-counter="specimen-for-partition"
490                title="Number of unpartitioned specimen"></span><span 
491              class="counter" data-counter="specimen-for-reextraction" 
492                title="Number of specimen for re-extration"></span>
493            </ul>
494          </dd>
495           
496          <dt>
497            <base:icon image="<%=home+"/images/extraction.png" %>" />
498            DNA/RNA extraction wizards
499          </dt>
500          <dd>
501            <ul>
502            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/lysate_reextraction.jsp?ID=<%=ID%>"
503              >Pick lysate for re-extraction</span> 
504              <span class="counter" data-counter="lysates-to-pick-for-reextraction" 
505                title="Number of lysates for re-extraction that must be picked from freezers"></span>
506            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/allprep_protocol.jsp?ID=<%=ID%>"
507              >Lab tracking protocol for Allprep isolation</span> 
508              <span class="counter more" data-counter="lysates-for-allprep" 
509                title="Number of unprocessed lysates"></span><span
510              class="counter" data-counter="lysates-picked-for-rextraction"
511                title="Number of lysates for re-extraction that has been picked from freezers"></span>
512 
513            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/extraction_registration.jsp?ID=<%=ID%>"
514              >DNA/RNA/FlowThrough registration</span> 
515              <span class="counter more" data-counter="lysates-for-allprep" 
516                title="Number of unprocessed lysates"></span><span
517              class="counter" data-counter="lysates-picked-for-rextraction"
518                title="Number of lysates for re-extraction that has been picked from freezers"></span>
519               
520            <li>Normalization
521              <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rna_normalization.jsp?ID=<%=ID%>"
522              >RNA</span> 
523              <span class="counter" data-counter="rna-to-normalize" title="Number of RNA not yet normalized"></span>
524              <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/dna_normalization.jsp?ID=<%=ID%>"
525              >DNA</span> 
526              <span class="counter" data-counter="dna-to-normalize" title="Number of DNA not yet normalized"></span>
527             
528            </ul>
529          </dd>
530          <dt>
531            <base:icon image="<%=home+"/images/rnaqc.png" %>" />
532            RNA quality control wizards
533          </dt>
534          <dd>
535            <ul>
536            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_aliquot.jsp?ID=<%=ID%>"
537              >Create aliquots on Bioanalyzer/Caliper plates</span> 
538              <span class="counter" data-counter="rna-without-rnaqc" 
539                title="Number of RNA waiting for QC"></span>
540           
541            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_plate_export.jsp?ID=<%=ID%>"
542              >Export Caliper sample names and run parameters</span> 
543              <span class="counter" data-counter="caliper-rnaqc-waiting" 
544                title="Number of active Caliper plates"></span>
545           
546            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_plate_import.jsp?ID=<%=ID%>"
547              >Import RQS scores from Caliper well table file</span> 
548              <span class="counter" data-counter="caliper-rnaqc-waiting"
549                title="Number of active Caliper plates"></span>
550               
551            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_baprotocol.jsp?ID=<%=ID%>"
552              >Lab protocol for BioAnalyzer plates</span> 
553              <span class="counter" data-counter="bioanalyzer-rnaqc-waiting" 
554                title="Number of active BioAnalyzer plates"></span>
555               
556            <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_bioanalyzer.jsp?ID=<%=ID%>"
557              >Register RIN scores for BioAnalyzer plates</span> 
558              <span class="counter" data-counter="bioanalyzer-rnaqc-waiting" 
559                title="Number of active BioAnalyzer plates"></span>
560            </ul>
561          </dd>
562          <dt style="margin-bottom: 0.5em;">
563            <base:icon image="<%=home+"/images/box.png" %>" />
564            <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/storage-box.jsp?ID=<%=ID%>"
565              >Storage box creation wizard</span>
566              <span class="counter more" data-counter="empty-storage-boxes" 
567                title="Number of empty storage boxes"></span><span 
568              class="counter" data-counter="empty-paused-storage-boxes" 
569                title="Number of empty storage boxes for paused specimen"></span>
570              <span id="more-boxes-are-needed">More boxes are needed</span>
571          </dt>
572          </dl>
573       
574          <h3>Histology wizards</h3>
575          <dl class="leftborder rightborder bottomborder">     
576          <dt>
577            <base:icon image="<%=home+"/images/histology.png" %>" />
578            Embedding and staining wizards
579          </dt>
580          <dd>
581            <ul>
582            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_protocol.jsp?ID=<%=ID%>"
583              >Lab tracking protocol for FFPE/HE</span> 
584              <span class="counter" data-counter="histology-active-lists" 
585                title="Number of active histology work lists"></span>
586           
587            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_block.jsp?ID=<%=ID%>"
588              >Register paraffin blocks</span> 
589              <span class="counter" data-counter="paraffin-blocks-not-embedded"
590                title="Number of paraffin blocks waiting for registration"></span>
591 
592            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_labels.jsp?ID=<%=ID%>"
593              >Download HE glass labels</span>
594           
595            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_glass.jsp?ID=<%=ID%>"
596              >Register HE glass</span> 
597              <span class="counter" data-counter="paraffin-blocks-without-heglass" 
598                title="Number of paraffin blocks without HE glass"></span>
599            </ul>
600          </dd>
601         
602          <dt>
603            <base:icon image="<%=home+"/images/microscope.png" %>" />
604            Scoring wizard
605          </dt>
606          <dd>
607            <ul>
608            <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_score.jsp?ID=<%=ID%>"
609              >Score HE glass</span> 
610              <span class="counter" data-counter="heglass-not-scored" 
611                title="Number of unscored HE glass"></span>
612            </ul>
613          </dd>
614          </dl>
615        </div>
616     
617        <div id="rna-libprep-section" class="wizard-group">
618          <h3>Library preparation wizards</h3>
619          <dl class="leftborder rightborder bottomborder">
620       
621          <dt>
622            <base:icon image="<%=home+"/images/libprep.png" %>" />
623            Library preparation design wizards <span class="counter more" data-counter="rna-without-mrna-or-lib"
624                title="Number of RNA with no child mRNA or Library"></span><span 
625              class="counter" data-counter="normalized-rna-without-mrna-or-lib" 
626                title="Number of pre-normalized RNA with no child mRNA or Library"></span>
627          </dt>
628          <dd>
629            <ul>
630            <li><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/import-external-rna.jsp?ID=<%=ID%>"
631              >Import external RNA</span>
632            <li><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/select_rna.jsp?ID=<%=ID%>&plateType=MRNA"
633              >New manual library preparation</span> 
634              (<span class="require-permission" data-role="LibraryPrep" data-link="libprep/select_rna.jsp?ID=<%=ID%>&autoDesign=1&plateType=MRNA"
635              >auto-design</span>)
636            <li><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/select_rna.jsp?ID=<%=ID%>&plateType=EXTERNAL_LIBRARY"
637              >Select RNA for external sequencing</span> 
638            </ul>
639          </dd>
640         
641          <dt>
642            <base:icon image="<%=home+"/images/pipette.png" %>" />
643            Manual library preparation wizards
644          </dt>
645          <dd>
646            <ul>
647            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_protocol.jsp?ID=<%=ID%>"
648              >Lab protocols for mRNA and cDNA preparation</span> 
649              <span class="counter" data-counter="mrna-plates-not-registered" 
650                title="Number of mRNA plates waiting for registration"></span>
651           
652            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/rna_dilution_registration.jsp?ID=<%=ID%>"
653              >RNA dilution registration</span>
654              <span class="counter" data-counter="mrna-plates-not-diluted" 
655                title="Number of mRNA plates waiting for dilution"></span>
656           
657            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_registration.jsp?ID=<%=ID%>"
658              >mRNA registration and quality control results</span> 
659              <span class="counter" data-counter="mrna-plates-diluted-not-registered" 
660                title="Number of mRNA plates waiting for registration"></span>
661           
662            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/cdna_registration.jsp?ID=<%=ID%>"
663              >cDNA registration</span> 
664              <span class="counter" data-counter="cdna-plates-not-registered" 
665                title="Number of cDNA plates waiting for registration"></span>
666           
667            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/assign_barcode.jsp?ID=<%=ID%>"
668              >Assign barcodes to cDNA plate</span> 
669              <span class="counter" data-counter="cdna-plates-for-barcoding" 
670                title="Number of cDNA plates waiting for barcode layout"></span>
671           
672            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/libprep_protocol.jsp?ID=<%=ID%>"
673              >Lab protocols and files for library preparation</span> 
674              <span class="counter" data-counter="lib-plates-for-libprep" 
675                title="Number of Lib plates waiting for registration"></span>
676           
677            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/libqc_registration.jsp?ID=<%=ID%>"
678              >Register quality control results</span> 
679              <span class="counter" data-counter="lib-plates-for-libprep" 
680                title="Number of Lib plates waiting for registration"></span>
681           
682            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/lib_registration.jsp?ID=<%=ID%>"
683              >Library registration</span> 
684              <span class="counter" data-counter="lib-plates-for-libprep"
685                title="Number of Lib plates waiting for registration"></span>
686            </ul>
687          </dd>
688         
689          <dt>
690            <base:icon image="<%=home+"/images/pool.png" %>" />
691            Pooling wizards
692          </dt>
693          <dd>
694            <ul>
695            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/create_pools.jsp?ID=<%=ID%>"
696              >Create pooled libraries</span> 
697              <span class="counter" data-counter="lib-plates-for-pooling"
698                title="Number of Lib plates waiting for pooling"></span>
699           
700            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/pool_protocol.jsp?ID=<%=ID%>"
701              >Lab protocols for pooling</span> 
702              <span class="counter" data-counter="pools-not-registered-rnaseq" 
703                title="Number of pools waiting for registration"></span>
704           
705            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/pool_registration.jsp?ID=<%=ID%>"
706              >Register pooled libraries</span> 
707              <span class="counter" data-counter="pools-not-registered-rnaseq" 
708                title="Number of pools waiting for registration"></span>
709            </ul>
710          </dd>
711          </dl>
712         
713          <h3>Sequencing wizards</h3>
714          <dl class="leftborder rightborder bottomborder">
715         
716          <dt>
717            <base:icon image="<%=home+"/images/flowcell.png" %>" />
718            Sequencing wizards
719          </dt>
720          <dd>
721            <ul>
722            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/create_flowcells.jsp?ID=<%=ID%>"
723              >Create flow cells</span> 
724              <span class="counter" data-counter="pools-not-used-rnaseq" 
725                title="Number of pools waiting for sequencing"></span>
726           
727            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/flowcell_protocol.jsp?ID=<%=ID%>"
728              >Lab protocol for sequencing</span> 
729              <span class="counter" data-counter="flow-cells-not-sequenced-rnaseq" 
730                title="Number of flow cells waiting to be sequenced"></span>
731           
732            <li><span class="require-permission" data-role="LibraryPrep" data-link="sequencing/sequencing_started.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
733              >Register sequencing started</span> 
734              <span class="counter" data-counter="flow-cells-not-sequenced-rnaseq" 
735                title="Number of flow cells waiting to be sequenced"></span>
736 
737            <li><span class="require-permission" data-role="LibraryPrep" data-link="sequencing/sequencing_ended.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
738              >Register sequencing ended</span> 
739              <span class="counter" data-counter="sequencing-runs-active-rnaseq" 
740                title="Number of active sequencing runs"></span>
741            </ul>
742          </dd>
743
744          <dt>
745            <base:icon image="<%=home+"/images/lorry.png" %>" />
746            External sequencing wizards
747          </dt>
748          <dd>
749            <ul>
750            <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/external_protocol.jsp?ID=<%=ID%>"
751              >Lab protocols and files for external sequencing</span> 
752              <span class="counter" data-counter="external-plates-not-registered" 
753                title="Number of external plates waiting for registration"></span>
754     
755            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="sequencing/sequencing_external.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
756              >Register external sequencing</span> 
757              <span class="counter" data-counter="external-libs-not-sequenced" 
758                title="Number of libraries sent for external sequencing"></span>
759            </ul>
760          </dd>
761
762         
763          </dl>
764       
765          <h3>Secondary analysis wizards</h3>
766          <dl class="leftborder rightborder bottomborder">
767            <dt>
768              <base:icon image="<%=home+"/images/server.png" %>" />
769              Demux and merge wizards
770            </dt>
771            <dd>
772              <ul>
773              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="sequencing/sequencing_confirm.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
774                >Confirm sequencing completed</span> 
775                <span class="counter" data-counter="sequencing-runs-unconfirmed-rnaseq" 
776                  title="Number of ended but not confirmed sequencing runs"></span>
777             
778              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>&pipeline=RNA_SEQ"
779                >Start demux and merge</span> 
780                <span class="counter" data-counter="sequencing-runs-for-demux-rnaseq" 
781                  title="Number of confirmed sequencing runs waiting to be demuxed"></span>
782             
783              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/demux_confirm.jsp?ID=<%=ID%>"
784                >Confirm demux and merge completed</span> 
785                <span class="counter" data-counter="demux-jobs-not-confirmed-rnaseq"
786                  title="Number of demux jobs waiting for confirmation"></span>
787              </ul>
788            </dd>
789 
790            <dt>
791              <base:icon image="<%=home+"/images/align.png" %>" />
792              Hisat and StringTie pipeline
793            </dt>
794            <dd>
795              <ul>
796              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/hisat_start.jsp?ID=<%=ID%>"
797                >Start Hisat alignment</span>
798                <span class="counter" data-counter="merged-sequences-for-hisat-alignment"
799                  title="Number of merged sequences waiting for Hisat alignment"></span>
800                <span id="hisat-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
801                 
802              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/hisat_confirm.jsp?ID=<%=ID%>"
803                >Confirm Hisat alignment</span> 
804                <span class="counter" data-counter="hisat-aligned-sequences-not-confirmed" 
805                  title="Number of Hisat aligned sequences waiting for confirmation"></span>
806             
807              <li><span id="genotype-qc" class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/genotype_qc.jsp?ID=<%=ID%>"
808                >Genotype quality control</span> 
809                <span class="counter" data-counter="alignments-for-genotype-qc" 
810                  title="Number of alignments with VCF files that has not been checked"></span>
811 
812              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/mbaf_start.jsp?ID=<%=ID%>"
813                >Start mBAF analysis</span> 
814                <span class="counter" data-counter="aligned-sequences-for-mbaf" 
815                  title="Number of aligned sequences waiting for mBAF analysis"></span>
816                <span id="mbaf-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
817               
818              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/stringtie_start.jsp?ID=<%=ID%>"
819                >Start StringTie</span>
820                <span class="counter" data-counter="aligned-sequences-for-stringtie"
821                  title="Number of aligned sequences waiting for StringTie"></span>
822                <span id="stringtie-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
823 
824              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/stringtie_confirm.jsp?ID=<%=ID%>"
825                >Confirm StringTie completed</span> 
826                <span class="counter" data-counter="stringtie-not-confirmed" 
827                  title="Number of StringTie jobs waiting for confirmation"></span>
828                 
829              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/ssp_start.jsp?ID=<%=ID%>"
830                >Start Single Sample Predictor analysis</span> 
831                <span class="counter" data-counter="rawbioassays-for-ssp" 
832                  title="Number of StringTie raw bioassays waiting for Single Sample predictor analysis"></span>
833                <span id="ssp-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
834               
835              <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=SCANB_REPORT"
836                >SCAN-B report</span> 
837                <span class="counter" data-counter="rawbioassys-without-scanbreport" 
838                  title="Number of rawbioassays without a SCAN-B report PDF"></span>
839             
840              <li id="prepde-wizard" style="display: none;"><span class="require-permission" data-role="Administrator" data-link="analysis/prepde.jsp?ID=<%=ID%>"
841                >Run prepDE.py</span>
842                <span class="counter" data-counter="stringtie-without-prepde" 
843                  title="Number of StringTie rawbioassays that is missing prepDE data"></span>
844             
845              </ul>
846            </dd>
847           
848            <dt>
849              <base:icon image="<%=home+"/images/variantcall.png" %>" />
850              Variant calling pipeline
851            </dt>
852           
853            <dd>
854              <ul>
855              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/vcall_start.jsp?ID=<%=ID%>"
856                >Start variant calling</span> 
857                <span class="counter" data-counter="aligned-sequences-for-variant-calling" 
858                  title="Number of aligned sequences waiting for variant calling pipeline"></span>
859                <span id="variant-calling-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
860              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/vcall_confirm.jsp?ID=<%=ID%>"
861                >Confirm variant calling</span> 
862                <span class="counter" data-counter="variantcall-not-confirmed" 
863                  title="Number of VariantCall jobs waiting for confirmation"></span>
864              <li><span class="require-permission" data-role="Administrator" data-link="analysis/vcall_build.jsp?ID=<%=ID%>"
865                >Build SCAN-B variant database</span> 
866              <li id="variant-import-wizard"><span class="require-permission" data-role="Administrator" data-link="analysis/vcall_import.jsp?ID=<%=ID%>"
867                >Import variants for existing variant call raw bioassays</span>
868                <span class="counter" data-counter="variant-calls-needing-import" 
869                  title="Number of VariantCall item that need to import variants"></span>
870              </ul>
871            </dd>
872           
873            <dt>
874              <base:icon image="<%=home+"/images/pdffile.png" %>" />
875              Legacy Tophat and Cufflinks pipeline <span id="legacy-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
876            </dt>
877            <dd>
878              <ul>
879              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/align_start.jsp?ID=<%=ID%>"
880                >Start Tophat and Cufflinks</span> 
881                <span class="counter" data-counter="merged-sequences-for-legacy-alignment"
882                  title="Number of merged sequences waiting for Tophat alignment"></span>
883                 
884              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/cufflinks_confirm.jsp?ID=<%=ID%>"
885                >Confirm Cufflinks completed</span> 
886                <span class="counter" data-counter="cufflinks-not-confirmed" 
887                  title="Number of Cufflinks jobs waiting for confirmation"></span>
888              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=GENE_REPORT"
889                >Gene report</span> 
890                <span class="counter" data-counter="rawbioassys-without-genereport" 
891                  title="Number of rawbioassays without a Gene report PDF"></span>
892              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=PILOT_REPORT"
893                >Pilot report</span> 
894                <span class="counter" data-counter="rawbioassys-without-pilotreport" 
895                  title="Number of rawbioassays without a Pilot report PDF"></span>
896              </ul>
897            </dd>
898           
899          </dl>     
900        </div>
901       
902        <div id="mips-libprep-section" class="wizard-group">
903          <h3>Library preparation wizards</h3>
904          <dl class="leftborder rightborder bottomborder">
905       
906          <dt>
907            <base:icon image="<%=home+"/images/libprep.png" %>" />
908            MIPs plate design wizards
909          </dt>
910          <dd>
911            <ul>
912            <li><span class="require-permission" data-role="MIPsPlateDesigner" data-link="mipsprep/import_plates.jsp?ID=<%=ID%>"
913              >Import DNA aliquot plates</span>
914             
915            <li><span class="require-permission" data-role="MIPsPlateDesigner" data-link="mipsprep/design_mipsplate.jsp?ID=<%=ID%>"
916              >Design MIPs plate</span>
917              <span class="counter more" data-counter="prenormalized-designmips"
918                title="Number of aliquot plates with DNA waiting for MIPs"></span><span 
919              class="counter" data-counter="prenormalized-addaliquots"
920                title="Number of aliquot plates in the SCAN-B lab"></span>
921            </ul>
922          </dd>
923         
924          <dt>
925            <base:icon image="<%=home+"/images/pipette.png" %>" />
926            MIPs library preparation wizards
927          </dt>
928          <dd>
929            <ul>
930            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/mips_protocol.jsp?ID=<%=ID%>"
931              >Lab protocols for MIPs library preparation</span> 
932              <span class="counter" data-counter="mips-plates-for-libprep" 
933                title="Number of MIPs plates waiting for registration"></span>
934           
935            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/lib_registration.jsp?ID=<%=ID%>"
936              >MIPs library registration</span> 
937              <span class="counter" data-counter="mips-plates-for-libprep"
938                title="Number of MIPs plates waiting for registration"></span>
939           
940            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/pool_registration.jsp?ID=<%=ID%>"
941              >Register pooled libraries</span> 
942              <span class="counter" data-counter="mips-plates-for-pooling" 
943                title="Number of MIPs library plates waiting for pooling"></span>
944            </ul>
945          </dd>
946
947          </dl>
948         
949          <h3>Sequencing wizards</h3>
950          <dl class="leftborder rightborder bottomborder">
951         
952          <dt>
953            <base:icon image="<%=home+"/images/flowcell.png" %>" />
954            Sequencing wizards
955          </dt>
956          <dd>
957            <ul>
958            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/create_flowcells.jsp?ID=<%=ID%>"
959              >Create flow cells</span> 
960              <span class="counter" data-counter="pools-not-used-mips" 
961                title="Number of MIPs pools waiting for sequencing"></span>
962           
963            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="mipsprep/flowcell_protocol.jsp?ID=<%=ID%>"
964              >Lab protocol for sequencing</span> 
965              <span class="counter" data-counter="flow-cells-not-sequenced-mips" 
966                title="Number of MIPs flow cells waiting to be sequenced"></span>
967           
968            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="sequencing/sequencing_started.jsp?ID=<%=ID%>&pipeline=MIPS"
969              >Register sequencing started</span> 
970              <span class="counter" data-counter="flow-cells-not-sequenced-mips" 
971                title="Number of MIPs flow cells waiting to be sequenced"></span>
972 
973            <li><span class="require-permission" data-role="MIPsLibraryPrep" data-link="sequencing/sequencing_ended.jsp?ID=<%=ID%>&pipeline=MIPS"
974              >Register sequencing ended</span> 
975              <span class="counter" data-counter="sequencing-runs-active-mips" 
976                title="Number of active MIPs sequencing runs"></span>
977            </ul>
978          </dd>
979         
980          </dl>
981         
982          <h3>Secondary analysis wizards</h3>
983          <dl class="leftborder rightborder bottomborder">
984            <dt>
985              <base:icon image="<%=home+"/images/server.png" %>" />
986              Demux wizards
987            </dt>
988            <dd>
989              <ul>
990              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="sequencing/sequencing_confirm.jsp?ID=<%=ID%>&pipeline=MIPS"
991                >Confirm sequencing completed</span> 
992                <span class="counter" data-counter="sequencing-runs-unconfirmed-mips" 
993                  title="Number of ended but not confirmed MIPs sequencing runs"></span>
994             
995              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/demux_start.jsp?ID=<%=ID%>&pipeline=MIPS"
996                >Start demux</span> 
997                <span class="counter" data-counter="sequencing-runs-for-demux-mips" 
998                  title="Number of confirmed MIPs sequencing runs waiting to be demuxed"></span>
999             
1000              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/demux_confirm.jsp?ID=<%=ID%>"
1001                >Confirm demux completed</span> 
1002                <span class="counter" data-counter="demux-jobs-not-confirmed-mips"
1003                  title="Number of MIPs demux jobs waiting for confirmation"></span>
1004              </ul>
1005            </dd>
1006           
1007            <dt>
1008              <base:icon image="<%=home+"/images/align.png" %>" />
1009              Alignment pipeline
1010            </dt>
1011            <dd>
1012              <ul>
1013              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/align_start.jsp?ID=<%=ID%>"
1014                >Start MIPs alignment</span>
1015                <span class="counter" data-counter="merged-sequences-for-mips-alignment"
1016                  title="Number of merged sequences waiting for MIPs alignment"></span>
1017                <span id="mips-align-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
1018
1019              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/align_confirm.jsp?ID=<%=ID%>"
1020                >Confirm MIPs alignment</span> 
1021                <span class="counter" data-counter="mips-aligned-sequences-not-confirmed" 
1022                  title="Number of MIPs aligned sequences waiting for confirmation"></span>
1023              </ul>
1024            </dd>
1025           
1026          </dl>
1027         
1028        </div>
1029       
1030        <div id="personal-information-section" class="wizard-group">
1031          <%
1032          if (isPatientCurator || isAdmin)
1033          {
1034            %>
1035            <h3>Personal information wizards</h3>
1036            <dl class="leftborder rightborder bottomborder">
1037            <dt>
1038              <base:icon image="<%=home + "/images/personal.png" %>"/>
1039              Referral form registration wizards
1040            </dt>
1041            <dd>
1042              <ul>
1043              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/persinfo.jsp?ID=<%=ID%>"
1044                >Pathology referral form registration</span>
1045 
1046              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodform.jsp?ID=<%=ID%>"
1047                >Blood referral forms registration</span>
1048               
1049              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodfollowupform.jsp?ID=<%=ID%>"
1050                >Follow-up blood referral form registration</span>
1051
1052              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/import_followup_blood.jsp?ID=<%=ID%>"
1053                >Batch-import follow-up blood referral forms</span>
1054 
1055              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/consentform.jsp?ID=<%=ID%>"
1056                >Consent form registration</span>
1057                <span class="counter" data-counter="case-or-blood-without-consent" 
1058                  title="Number of cases and blood samples without consent"></span>
1059              </ul>
1060            </dd>
1061           
1062            <dt>
1063              <base:icon image="<%=home+"/images/report.png" %>" />
1064              Referral forms
1065            </dt>
1066            <dd>
1067              <ul>
1068              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/generate-referral-forms.jsp?ID=<%=ID%>"
1069                >Generate referral forms</span>
1070              </ul>
1071            </dd>
1072 
1073            <dt>
1074              <base:icon image="<%=home+"/images/delete.png" %>" />
1075              Retraction wizard
1076            </dt>
1077            <dd>
1078              <ul>
1079              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/retractionform.jsp?ID=<%=ID%>"
1080                >Mark extracts for retraction</span>
1081 
1082              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/retraction_followup_form.jsp?ID=<%=ID%>"
1083                >Retraction follow-up and destruction</span>
1084                <span class="counter more" data-counter="patientitems-ready-for-retraction-followup" 
1085                  title="Number of patient items ready for retraction follow-up"></span><span 
1086                  class="counter" data-counter="patientitems-ready-for-destruction" 
1087                  title="Number of patient items ready for destruction"></span>
1088 
1089              </ul>
1090            </dd>
1091           
1092            <dt>
1093              <base:icon image="<%=home+"/images/export_import.png" %>" />
1094              Import and export wizards
1095            </dt>
1096            <dd>
1097              <ul>
1098              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export-inca.jsp?ID=<%=ID%>"
1099                >INCA export</span>
1100 
1101              <li><span id="inca-import" 
1102                class="require-permission" 
1103                data-role="PatientCurator"
1104                data-link="personal/import-inca.jsp?ID=<%=ID%>"
1105                >INCA import</span>
1106 
1107              <li><span id="inca-statistics" 
1108                class="require-permission" 
1109                data-role="PatientCurator"
1110                data-link="personal/inca-statistics.jsp?ID=<%=ID%>"
1111                >INCA statistics</span>
1112 
1113              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export-monthly-oplist.jsp?ID=<%=ID%>"
1114                >Export monthly operation list</span>
1115               
1116              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_data_sample_list.jsp?ID=<%=ID%>"
1117                >Export missing data sample list</span>
1118 
1119              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_consent_data_sample_list.jsp?ID=<%=ID%>"
1120                >Export missing consent data sample list</span>
1121               
1122              <li><span class="require-permission" data-role="PatientCurator" data-link="batch/frozen-tissue-date.jsp?ID=<%=ID%>"
1123                >Import frozen tissue date</span> 
1124               
1125              <li><span class="require-permission" data-role="PatientCurator" data-link="personal/map-external-data.jsp?ID=<%=ID%>"
1126                >Map external data to releases</span>
1127              </ul>
1128            </dd>
1129           
1130            </dl>
1131            <%
1132          }
1133          %>
1134          <h3>Sample curation and outtake wizards</h3>
1135          <dl class="leftborder rightborder bottomborder">
1136            <dt>
1137              <base:icon image="<%=home+"/images/flag.png" %>" />
1138              Re-processing wizards
1139            </dt>
1140            <dd>
1141              <ul>
1142              <li><span class="require-permission" data-role="PrepCurator" data-link="flaggedrna/search.jsp?ID=<%=ID%>"
1143                >Flagged RNA</span> 
1144                <span class="counter" data-counter="flagged-rna" 
1145                  title="Number of flagged RNA items"></span>
1146              <li><span class="require-permission" data-role="PrepCurator" data-link="flaggedalignment/search.jsp?ID=<%=ID%>"
1147                >Flagged alignment</span> 
1148                <span class="counter" data-counter="flagged-alignment" 
1149                  title="Number of flagged alignment items"></span>
1150              <li><span class="require-permission" data-role="PrepCurator" data-link="sampleproc/paused-specimen.jsp?ID=<%=ID%>"
1151                >Paused specimen</span> 
1152                <span class="counter" data-counter="paused-specimen" 
1153                  title="Number of paused+scheduled specimen items"></span>
1154              </ul>
1155            </dd>
1156 
1157            <dt>
1158              <base:icon image="<%=home+"/images/smile.png" %>" />
1159              Batch update wizards
1160            </dt>
1161            <dd>
1162              <ul>
1163              <li><span class="require-permission" data-role="PrepCurator" data-link="batch/linked-specimen.jsp?ID=<%=ID%>"
1164                >Linked specimen</span> 
1165              <li><span class="require-permission" data-role="PrepCurator" data-link="batch/reference-date.jsp?ID=<%=ID%>"
1166                >Reference date on case items</span> 
1167              </ul>
1168            </dd>
1169           
1170            <dt>
1171              <base:icon image="<%=home+"/images/outtake.png" %>" />
1172              Sample outtake wizards
1173            </dt>
1174            <dd>
1175              <ul>
1176              <li><span class="require-permission" data-role="PrepCurator" data-link="outtake/define.jsp?ID=<%=ID%>"
1177                >Define a new sample outtake</span>
1178              <li><span class="require-permission" data-role="SamplePrep" data-link="outtake/picklist.jsp?ID=<%=ID%>"
1179                >Protocols and labels for sample outtakes</span> 
1180                <span class="counter" data-counter="active-outtake-lists" 
1181                  title="Number of sample outtakes waiting to be processed"></span>
1182              <li><span class="require-permission" data-role="SamplePrep" data-link="outtake/register.jsp?ID=<%=ID%>"
1183                >Register sample outtake</span> 
1184                <span class="counter" data-counter="active-outtake-lists" 
1185                  title="Number of sample outtakes waiting to be processed"></span>
1186              <li><span class="require-permission" data-role="PrepCurator" data-link="outtake/delivery_export.jsp?ID=<%=ID%>"
1187                >Export delivery data file for sample outtake</span>
1188                <span class="counter" data-counter="undelivered-outtake-lists" 
1189                  title="Number of sample outtakes not delivered"></span>
1190              </ul>
1191            </dd>
1192 
1193          </dl>
1194        </div>
1195       
1196        <div id="statistics-section" class="wizard-group">
1197          <h3>Statistics and reporting wizards</h3>
1198          <dl class="leftborder rightborder bottomborder">
1199            <dt>
1200              <base:icon image="<%=home+"/images/report.png" %>" />
1201              <span class="require-permission" data-role="" data-link="reports/samplereportgenerator.jsp?ID=<%=ID%>"
1202                >Sample source report</span>
1203            </dt>
1204            <dd>
1205              <ul>
1206              <li>Sample count report</li> 
1207              <li>Consent count report</li> 
1208              <li>Patient count report</li> 
1209              <li>Overview report</li> 
1210              <li>Missing sample data report</li> 
1211              </ul>
1212            </dd>
1213            <dt>
1214              <base:icon image="<%=home+"/images/chart_bar.png" %>" />
1215              <span class="require-permission" data-role="" data-link="reports/scanbquartermonthreportgenerator.jsp?ID=<%=ID%>"
1216                >Sample processing statistics</span>
1217            </dt>       
1218            <dd>       
1219              <ul>
1220              <li>SCAN-B quarter/month report</li> 
1221              </ul>
1222            </dd>
1223            <dt style="margin-bottom: 0.5em;">
1224              <base:icon image="<%=home+"/images/yellow-label.png" %>" />
1225              <span class="require-permission" data-role="" data-link="yellowlabel/list.jsp?ID=<%=ID%>"
1226                >YellowLabel tracking and reporting</span>
1227                <span class="counter" data-counter="specimen-active-yellow-label" 
1228                  title="Number of active YellowLabel specimen"></span>
1229            </dt> 
1230          </dl>
1231        </div>
1232
1233        <div id="administration-section" class="wizard-group">
1234          <%
1235          if (isAdmin)
1236          {
1237            %>
1238            <h3>Server administrator wizards</h3>
1239            <dl class="leftborder rightborder bottomborder">
1240            <dt>
1241              <base:icon image="<%=home + "/images/install.png" %>" />
1242              <span class="require-permission" data-role="Administrator" data-link="admin/install.jsp?ID=<%=ID%>">Installation wizard</span>
1243            </dt>
1244            <dd>
1245              <ul>
1246              <li>Check that items needed by Reggie exists in BASE.
1247              <li>Create and fix items.
1248              </ul>
1249            </dd>
1250            <dt>
1251              <base:icon image="<%=home + "/images/ogs-cluster.png"%>" />
1252              Other tasks
1253            </dt>
1254            <dd>
1255              <ul>
1256              <li><span class="require-permission" data-role="Administrator" data-link="admin/remote/list-hosts.jsp?ID=<%=ID%>"
1257                >Open Grid Scheduler hosts</span>
1258               
1259              <li><span class="require-permission" data-role="Administrator" data-link="admin/stray-files.jsp?ID=<%=ID%>"
1260                >Stray files wizard</span>
1261                <span class="counter" data-counter="stray-folders" 
1262                  title="Number of stray folders"></span>
1263                 
1264              <li><span class="require-permission" data-role="Administrator" data-link="admin/analysis-cleanup.jsp?ID=<%=ID%>"
1265                >Secondary analysis cleanup</span>
1266                <span class="counter more" data-counter="analysis-cleanup-dba"
1267                  title="Number of derived bioassay items to cleanup"></span><span 
1268                  class="counter" data-counter="analysis-cleanup-rba" 
1269                  title="Number of raw bioassay items to cleanup"></span>
1270              </ul>
1271            </dd>
1272            </dl>
1273            <%
1274          }
1275          %>
1276        </div>
1277       
1278      </div>
1279    </div>
1280   
1281    <div class="absolutefull" style="width: 30%; left: auto;">
1282      <div class="absolutefull" style="left: 0.5em; bottom: 2em;">
1283        <div class="absolutefull" style="right: 1em; height: 4em;">
1284          <b>Case summary</b><br>
1285          <input type="text" class="text auto-init" data-auto-init="focus" 
1286            name="caseName" id="caseName" title="Please enter a SCAN-B case id, personal number, release id, PAD, etc." 
1287            style="width: 15em;">
1288          <base:button id="btnCaseSummary" title="Go" image="<%=home+"/images/gonext.png"%>" />
1289        </div>
1290        <div class="absolutefull" style="top: 4em; padding-right: 0.5em;">
1291          <div id="summary-stats">
1292            <div class="counter" data-counter="patients-all" 
1293              title="Total number of patients"></div> Patients<br>
1294            <div class="counter" data-counter="specimen-all" 
1295              title="Total number of specimen tubes"></div> Specimen Tubes<br>
1296            <div class="counter" data-counter="rna-all-extracted" 
1297              title="Total number of extracted RNA"></div> Extracted Rna<br>
1298            <div class="counter" data-counter="libraries-all-aligned" 
1299              title="Total number of aligned libraries"></div> Aligned Libraries<br>
1300            <div class="counter" data-counter="rawbioassys-all-with-genereport"
1301              title="Total number of generated gene reports"></div> Gene Reports<br>
1302            <div class="counter" data-counter="stained-score-complete"
1303              title="Total number of completely scored histology samples"></div> Scored Histology Samples
1304          </div>
1305
1306          <div id="activity-log">
1307            <div id="quote-of-the-day"></div>
1308            <a id="activity-log-rss" href="<%=servletHome%>/ActivityLog.rss" 
1309              title="Get the activity log as an RSS feed"><img src="images/rss.png"></a>
1310            <div id="activity-log-entries"></div>
1311          </div>
1312        </div>
1313      </div>
1314      <div id="counter-age-control">
1315        <b>Counters last updated</b> <span id="counter-age"></span><base:icon id="counter-refresh" 
1316          image="<%=home+"/images/refresh-small.png"%>" style="display:none;" title="Force update of counters" 
1317          /><base:icon id="counter-loading" image="<%=home+"/images/loading-small.gif"%>" />
1318      </div>
1319    </div>
1320    </form>
1321   
1322  </div>
1323 
1324</base:body>
1325</base:page>
1326<%
1327}
1328finally
1329{
1330  if (dc != null) dc.close();
1331}
1332%>
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