source: extensions/net.sf.basedb.reggie/trunk/resources/index.jsp @ 3847

Last change on this file since 3847 was 3847, checked in by Nicklas Nordborg, 6 years ago

Fixes #877: Add counter for consent forms

File size: 29.6 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, true);
27final String ID = sc.getId();
28final float scale = Base.getScale(sc);
29final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
30DbControl dc = null;
31try
32{
33  dc = sc.newDbControl();
34  final User user = User.getById(dc, sc.getLoggedInUserId());
35 
36  boolean isAdmin = user.getId() == SystemItems.getId(User.ROOT);
37  boolean isPatientCurator = false;
38  if (!isAdmin)
39  {
40    try
41    {
42      Role admin = Role.getById(dc, SystemItems.getId(Role.ADMINISTRATOR));
43      isAdmin = sc.isMemberOf(admin);
44    }
45    catch (RuntimeException ex)
46    {}
47  }
48  try
49  {
50    ItemQuery<Group> query = Group.getQuery();
51    query.restrict(Restrictions.eq(Hql.property("name"), Expressions.string("PatientCurator")));
52    List<Group> result = query.list(dc);
53    if (result.size() == 1)
54    {
55      isPatientCurator = sc.isMemberOf(result.get(0));
56    }
57  }
58  catch (RuntimeException ex)
59  {}
60%>
61<base:page type="default" >
62<base:head styles="path.css,~css/reggie-2.css" scripts="~index.js,~reggie-2.js">
63<style>
64dl
65{
66  margin-top: 0px;
67  margin-bottom: 1em;
68  padding: 3px;
69}
70dt
71{
72  margin-top: 0.5em;
73  margin-left: 0.5em;
74}
75dd
76{
77  margin-left: 0.5em;
78  margin-bottom: 0.5em;
79  padding-left: 3em;
80}
81ul
82{
83  margin-top: 0px;
84  margin-bottom: 0px;
85  margin-left: 0em;
86  padding-left: 0em;
87}
88li
89{
90  margin-left: 0em;
91}
92img
93{
94  vertical-align: text-bottom;
95}
96.default h3
97{
98  color: #333377;
99  background-color: #E8E8E8;
100  font-weight: bold;
101  margin: 0;
102  padding: 1px 4px 1px 4px;
103  border-width: 1px;
104  font-size: 1em;
105}
106.not-implemented
107{
108  filter: url(css/filters.svg#grayscale); /* Firfox, etc */
109  filter: gray; /* IE */
110  opacity: 0.75;
111  pointer-events: none;
112}
113
114.not-implemented:after
115{
116  content: ' -- coming soon';
117}
118
119span.counter
120{
121  color: #666666;
122  font-style: italic;
123}
124
125span.counter.done:before
126{
127  content: '(';
128  padding-right: 1px;
129}
130
131span.counter + .counter.done:before
132{
133  content: '+';
134  padding-left: 2px;
135  padding-right: 2px;
136}
137
138span.counter.done:not(.more):after
139{
140  content: ')';
141  padding-left: 1px;
142}
143
144.require-permission
145{
146  color: #999999;
147  font-style: italic;
148}
149
150.snake-quote
151{
152  width: 32em;
153}
154
155.snake-quote-source
156{
157  margin-top: 0.5em;
158  float: right;
159  font-style: italic;
160}
161
162.snake-quote .notify-message
163{
164  margin: 0;
165}
166
167.snake-quote .notify-message:before
168{
169  margin: 0;
170  content: '';
171}
172
173#summary-stats
174{
175  margin-top: 1em;
176  margin-bottom: 1.5em;
177  margin-left: auto;
178  margin-right: auto;
179  display: table;
180  font-variant: small-caps;
181  font-size: 125%;
182  border-top-width: 2px;
183  border-bottom-width: 2px;
184  padding: 0.5em;
185}
186
187
188#counter-age
189{
190  position: absolute;
191  bottom: 2px;
192  right: 1rem;
193  font-size: 90%;
194}
195
196#force-update-counters
197{
198  padding-left: 3px;
199  vertical-align: -4px;
200}
201
202div.counter
203{
204  display: inline-block;
205  min-width: 4em;
206  text-align: right;
207  padding-right: 0.25em;
208  font-size: 120%;
209  font-weight: bold;
210}
211
212</style>
213</base:head>
214<base:body>
215
216  <p:path><p:pathelement title="Reggie" /></p:path>
217
218  <div class="content">
219    <form name="reggie" id="wizard" class="wizard">
220    <div id="wizard-status" style="position: absolute; z-index: 99; left: 25%; right: 25%; top: 25%; height: auto; text-align: center;"></div>
221    <div class="absolutefull" style="width: 33%;">
222      <div class="absolutefull" style="left: 1em; right: 0.5em; ">
223     
224        <div id="summary-stats">
225          <div class="counter" data-counter="patients-all" 
226            title="Total number of patients"></div> Patients<br>
227          <div class="counter" data-counter="specimen-all" 
228            title="Total number of specimen tubes"></div> Specimen Tubes<br>
229          <div class="counter" data-counter="rna-all-extracted" 
230            title="Total number of extracted RNA"></div> Extracted Rna<br>
231          <div class="counter" data-counter="libraries-all-aligned" 
232            title="Total number of aligned libraries"></div> Aligned Libraries<br>
233          <div class="counter" data-counter="rawbioassys-all-with-genereport"
234            title="Total number of generated gene reports"></div> Gene Reports<br>
235          <div class="counter" data-counter="stained-score-complete"
236            title="Total number of completely scored histology samples"></div> Scored Histology Samples
237        </div>
238     
239        <h3>Statistics and reporting wizards</h3>
240        <dl class="leftborder rightborder bottomborder">
241          <dt>
242            <base:icon image="<%=home+"/images/case_summary.png" %>" />
243            Case summary
244          </dt>
245          <dd>
246            <table>
247            <tr>
248              <td><input type="text" class="text" 
249                name="caseName" id="caseName" title="Please enter a 7-digit case id" 
250                style="width: 15em;"></td>
251              <td><base:button id="btnCaseSummary" title="Go" image="<%=home+"/images/gonext.png"%>" /></td>
252            </tr>
253            </table>
254          </dd>
255       
256          <dt>
257            <base:icon image="<%=home+"/images/report.png" %>" />
258            <span class="require-permission" data-role="" data-link="reports/samplereportgenerator.jsp?ID=<%=ID%>"
259              >Sample source report</span>
260          </dt>       
261          <dd>       
262            <ul>
263            <li>Sample count report</li> 
264            <li>Consent count report</li> 
265            <li>Patient count report</li> 
266            <li>Overview report</li> 
267            <li>Missing sample data report</li> 
268            </ul>
269          </dd>
270          <dt>
271            <base:icon image="<%=home+"/images/chart_bar.png" %>" />
272            <span class="require-permission" data-role="" data-link="reports/scanbquartermonthreportgenerator.jsp?ID=<%=ID%>"
273              >Sample processing statistics</span>
274          </dt>       
275          <dd>       
276            <ul>
277            <li>SCAN-B quarter/month report</li> 
278            </ul>
279          </dd>
280          <dt>
281            <base:icon image="<%=home+"/images/yellow-label.png" %>" />
282            <span class="require-permission" data-role="" data-link="yellowlabel/list.jsp?ID=<%=ID%>"
283              >YellowLabel tracking and reporting</span>
284              <span class="counter" data-counter="specimen-active-yellow-label" 
285                title="Number of active YellowLabel specimen"></span>
286          </dt> 
287        </dl>
288     
289        <%
290        if (isPatientCurator || isAdmin)
291        {
292          %>
293          <h3>Personal information wizards</h3>
294          <dl class="leftborder rightborder bottomborder">
295          <dt>
296            <base:icon image="<%=home + "/images/personal.png" %>"/>
297            <span class="require-permission" data-role="PatientCurator" data-link="personal/persinfo.jsp?ID=<%=ID%>"
298              >Pathology referral form registration</span>
299          </dt>
300          <dd>
301            <ul>
302            <li>Register new cases and patients.
303            <li>Update existing cases and specimen tubes.
304            </ul>
305          </dd>
306         
307          <dt>
308            <base:icon image="<%=home + "/images/blood.png" %>"/>
309            Blood referral form registration
310          </dt>
311          <dd>
312            <ul>
313            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodform.jsp?ID=<%=ID%>"
314              >Register new/updated blood referral forms and patients</span>
315             
316            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodfollowupform.jsp?ID=<%=ID%>"
317              >Register new/updated follow-up blood referral forms</span>
318            </ul>
319          </dd>
320         
321          <dt>
322            <base:icon image="<%=home+"/images/consent.png" %>"/>
323            <span class="require-permission" data-role="PatientCurator" data-link="personal/consentform.jsp?ID=<%=ID%>"
324              >Consent form registration</span>
325              <span class="counter" data-counter="case-or-blood-without-consent" 
326                title="Number of cases and blood samples without consent"></span>
327          </dt>
328          <dd>
329            <ul>
330            <li>Register consent forms.
331            </ul>
332          </dd>
333         
334          <dt>
335            <base:icon image="<%=home+"/images/export_import.png" %>" />
336            Export/import information to/from external registers.
337          </dt>
338          <dd>
339            <ul>
340            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export-monthly-oplist.jsp?ID=<%=ID%>"
341              >Export monthly operation list</span>
342             
343            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export-inca.jsp?ID=<%=ID%>"
344              >INCA export</span>
345
346            <li><span id="inca-import" 
347              class="require-permission experimental not-implemented" 
348              data-role="PatientCurator"
349              data-link="personal/import-inca.jsp?ID=<%=ID%>"
350              >INCA import</span>
351
352            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_data_sample_list.jsp?ID=<%=ID%>"
353              >Export missing data sample list</span>
354
355            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_consent_data_sample_list.jsp?ID=<%=ID%>"
356              >Export missing consent data sample list</span>
357             
358            <li><span class="require-permission" data-role="PatientCurator" data-link="batch/frozen-tissue-date.jsp?ID=<%=ID%>"
359              >Import frozen tissue date</span> 
360            </ul>
361          </dd>
362
363          <dt>
364            <base:icon image="<%=home+"/images/delete.png" %>" />
365            Retraction wizard
366          </dt>
367          <dd>
368            <ul>
369            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/retractionform.jsp?ID=<%=ID%>"
370              >Mark extracts for retraction</span>
371
372            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/retraction_followup_form.jsp?ID=<%=ID%>"
373              >Retraction follow-up and destruction</span>
374              <span class="counter more" data-counter="patientitems-ready-for-retraction-followup" 
375                title="Number of patient items ready for retraction follow-up"></span><span 
376                class="counter" data-counter="patientitems-ready-for-destruction" 
377                title="Number of patient items ready for destruction"></span>
378
379            </ul>
380          </dd>
381          </dl>
382          <%
383        }
384        %>
385     
386      </div>
387    </div>
388   
389    <div class="absolutefull" style="width: 34%; left: 33%; right: auto;">
390      <div class="absolutefull" style="left: 0.5em; right: 0.5em;">
391     
392        <h3>Sample processing wizards</h3>
393        <dl class="leftborder rightborder bottomborder has-lib-prep">
394
395        <dt>
396          <base:icon image="<%=home+"/images/specimen.png" %>" />
397          <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/specimentube.jsp?ID=<%=ID%>"
398            >Specimen tube registration</span>
399        </dt>
400        <dd>
401          <ul>
402          <li>Register new specimen tubes.
403          </ul>
404        </dd>
405
406        <dt>
407          <base:icon image="<%=home+"/images/partition.png" %>" />
408          <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/partitionform.jsp?ID=<%=ID%>"
409            >Partition wizard</span>
410        </dt>
411        <dd>
412          <ul>
413          <li>Register new partitions of existing specimens
414            <span class="counter more" data-counter="specimen-for-partition"
415              title="Number of unpartitioned specimen"></span><span 
416            class="counter" data-counter="specimen-for-reextraction" 
417              title="Number of specimen for re-extration"></span>
418          </ul>
419        </dd>
420         
421        <dt>
422          <base:icon image="<%=home+"/images/extraction.png" %>" />
423          DNA/RNA extraction wizards
424        </dt>
425        <dd>
426          <ul>
427          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/allprep_protocol.jsp?ID=<%=ID%>"
428            >Lab tracking protocol for Allprep isolation</span> 
429            <span class="counter" data-counter="lysates-for-allprep" 
430              title="Number of unprocessed lysates"></span>
431
432          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/extraction_registration.jsp?ID=<%=ID%>"
433            >DNA/RNA/FlowThrough registration</span> 
434            <span class="counter" data-counter="lysates-for-allprep" 
435              title="Number of unprocessed lysates"></span>
436             
437          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rna_normalization.jsp?ID=<%=ID%>"
438            >RNA concentration normalization</span> 
439            <span class="counter" data-counter="rna-to-normalize" 
440              title="Number of RNA not yet normalized"></span>
441          </ul>
442        </dd>
443        <dt>
444          <base:icon image="<%=home+"/images/rnaqc.png" %>" />
445          RNA quality control wizards
446        </dt>
447        <dd>
448          <ul>
449          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_aliquot.jsp?ID=<%=ID%>"
450            >Create aliquots on Bioanalyzer/Caliper plates</span> 
451            <span class="counter" data-counter="rna-without-rnaqc" 
452              title="Number of RNA waiting for QC"></span>
453         
454          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_plate_export.jsp?ID=<%=ID%>"
455            >Export Caliper sample names and run parameters</span> 
456            <span class="counter" data-counter="caliper-rnaqc-waiting" 
457              title="Number of active Caliper plates"></span>
458         
459          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_plate_import.jsp?ID=<%=ID%>"
460            >Import RQS scores from Caliper well table file</span> 
461            <span class="counter" data-counter="caliper-rnaqc-waiting"
462              title="Number of active Caliper plates"></span>
463             
464          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_baprotocol.jsp?ID=<%=ID%>"
465            >Lab protocol for BioAnalyzer plates</span> 
466            <span class="counter" data-counter="bioanalyzer-rnaqc-waiting" 
467              title="Number of active BioAnalyzer plates"></span>
468             
469          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_bioanalyzer.jsp?ID=<%=ID%>"
470            >Register RIN scores for BioAnalyzer plates</span> 
471            <span class="counter" data-counter="bioanalyzer-rnaqc-waiting" 
472              title="Number of active BioAnalyzer plates"></span>
473          </ul>
474        </dd>     
475        </dl>
476     
477        <h3>Histology wizards</h3>
478        <dl class="leftborder rightborder bottomborder">     
479        <dt>
480          <base:icon image="<%=home+"/images/histology.png" %>" />
481          Embedding and staining wizards
482        </dt>
483        <dd>
484          <ul>
485          <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_protocol.jsp?ID=<%=ID%>"
486            >Lab tracking protocol for FFPE/HE</span> 
487            <span class="counter" data-counter="histology-active-lists" 
488              title="Number of active histology work lists"></span>
489         
490          <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_block.jsp?ID=<%=ID%>"
491            >Register paraffin blocks</span> 
492            <span class="counter" data-counter="paraffin-blocks-not-embedded"
493              title="Number of paraffin blocks waiting for registration"></span>
494
495          <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_labels.jsp?ID=<%=ID%>"
496            >Download HE glass labels</span>
497         
498          <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_glass.jsp?ID=<%=ID%>"
499            >Register HE glass</span> 
500            <span class="counter" data-counter="paraffin-blocks-without-heglass" 
501              title="Number of paraffin blocks without HE glass"></span>
502          </ul>
503        </dd>
504       
505        <dt>
506          <base:icon image="<%=home+"/images/microscope.png" %>" />
507          Scoring wizard
508        </dt>
509        <dd>
510          <ul>
511          <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_score.jsp?ID=<%=ID%>"
512            >Score HE glass</span> 
513            <span class="counter" data-counter="heglass-not-scored" 
514              title="Number of unscored HE glass"></span>
515          </ul>
516        </dd>
517        </dl>
518     
519        <h3>Sample curation wizards</h3>
520        <dl class="leftborder rightborder bottomborder">
521          <dt>
522            <base:icon image="<%=home+"/images/flag.png" %>" />
523            Re-processing wizards
524          </dt>
525          <dd>
526            <ul>
527            <li><span class="require-permission" data-role="PrepCurator" data-link="flaggedrna/search.jsp?ID=<%=ID%>"
528              >Flagged RNA</span> 
529              <span class="counter" data-counter="flagged-rna" 
530                title="Number of flagged RNA items"></span>
531            </ul>
532          </dd>
533
534          <dt>
535            <base:icon image="<%=home+"/images/smile.png" %>" />
536            Batch update wizards
537          </dt>
538          <dd>
539            <ul>
540            <li><span class="require-permission" data-role="PrepCurator" data-link="batch/linked-specimen.jsp?ID=<%=ID%>"
541              >Linked specimen</span> 
542            </ul>
543          </dd>
544
545        </dl>
546       
547        <%
548        if (isAdmin)
549        {
550          %>
551          <h3>Server administrator wizards</h3>
552          <dl class="leftborder rightborder bottomborder">
553          <dt>
554            <base:icon image="<%=home + "/images/install.png" %>" />
555            <span class="require-permission" data-role="Administrator" data-link="admin/install.jsp?ID=<%=ID%>">Installation wizard</span>
556          </dt>
557          <dd>
558            <ul>
559            <li>Check that items needed by Reggie exists in BASE.
560            <li>Create and fix items.
561            </ul>
562          </dd>
563          <dt>
564            <base:icon image="<%=home + "/images/ogs-cluster.png"%>" />
565            Other tasks
566          </dt>
567          <dd>
568            <ul>
569            <li><span class="require-permission" data-role="Administrator" data-link="admin/remote/list-hosts.jsp?ID=<%=ID%>"
570              >Access remote hosts including Open Grid Scheduler hosts</span>
571             
572            <li><span class="require-permission" data-role="Administrator" data-link="admin/stray-files.jsp?ID=<%=ID%>"
573              >Stray files wizard</span>
574              <span class="counter" data-counter="stray-folders" 
575                title="Number of stray folders"></span>
576            </ul>
577          </dd>
578          </dl>
579          <%
580        }
581        %>
582       
583      </div>
584    </div>
585   
586    <div class="absolutefull" style="width: 33%; left: auto;">
587      <div class="absolutefull" style="left: 0.5em; right: 1em; bottom: 2em;">
588       
589       
590        <h3>Library preparation wizards</h3>
591        <dl class="leftborder rightborder bottomborder">
592     
593        <dt>
594          <base:icon image="<%=home+"/images/libprep.png" %>" />
595          Library preparation design wizards <span class="counter more" data-counter="rna-without-mrna-or-lib"
596              title="Number of RNA with no child mRNA or Library"></span><span 
597            class="counter" data-counter="normalized-rna-without-mrna-or-lib" 
598              title="Number of pre-normalized RNA with no child mRNA or Library"></span>
599        </dt>
600        <dd>
601          <ul>
602          <li><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/select_rna.jsp?ID=<%=ID%>"
603            >New manual library preparation</span> 
604            (<span class="require-permission" data-role="LibraryPrep" data-link="libprep/select_rna.jsp?ID=<%=ID%>&autoDesign=1"
605            >auto-design</span>)
606          <li><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/select_rna.jsp?ID=<%=ID%>&neoprep=1"
607            >New NeoPrep library preparation</span> 
608            (<span class="require-permission" data-role="LibraryPrep" data-link="libprep/select_rna.jsp?ID=<%=ID%>&neoprep=1&autoDesign=1"
609            >auto-design</span>)
610          </ul>
611        </dd>
612       
613        <dt>
614          <base:icon image="<%=home+"/images/pipette.png" %>" />
615          Manual library preparation wizards
616        </dt>
617        <dd>
618          <ul>
619          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_protocol.jsp?ID=<%=ID%>"
620            >Lab protocols for mRNA and cDNA preparation</span> 
621            <span class="counter" data-counter="mrna-plates-not-registered" 
622              title="Number of mRNA plates waiting for registration"></span>
623         
624          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/rna_dilution_registration.jsp?ID=<%=ID%>"
625            >RNA dilution registration</span>
626            <span class="counter" data-counter="mrna-plates-not-diluted" 
627              title="Number of mRNA plates waiting for dilution"></span>
628         
629          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_registration.jsp?ID=<%=ID%>"
630            >mRNA registration and quality control results</span> 
631            <span class="counter" data-counter="mrna-plates-diluted-not-registered" 
632              title="Number of mRNA plates waiting for registration"></span>
633         
634          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/cdna_registration.jsp?ID=<%=ID%>"
635            >cDNA registration</span> 
636            <span class="counter" data-counter="cdna-plates-not-registered" 
637              title="Number of cDNA plates waiting for registration"></span>
638         
639          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/assign_barcode.jsp?ID=<%=ID%>"
640            >Assign barcodes to cDNA plate</span> 
641            <span class="counter" data-counter="cdna-plates-for-barcoding" 
642              title="Number of cDNA plates waiting for barcode layout"></span>
643         
644          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/libprep_protocol.jsp?ID=<%=ID%>"
645            >Lab protocols and files for library preparation</span> 
646            <span class="counter" data-counter="lib-plates-for-libprep" 
647              title="Number of Lib plates waiting for registration"></span>
648         
649          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/libqc_registration.jsp?ID=<%=ID%>"
650            >Register quality control results</span> 
651            <span class="counter" data-counter="lib-plates-for-libprep" 
652              title="Number of Lib plates waiting for registration"></span>
653         
654          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/lib_registration.jsp?ID=<%=ID%>"
655            >Library registration</span> 
656            <span class="counter" data-counter="lib-plates-for-libprep"
657              title="Number of Lib plates waiting for registration"></span>
658          </ul>
659        </dd>
660       
661        <dt>
662          <base:icon image="<%=home+"/images/neoprep.png" %>" />
663          NeoPrep library preparation wizards
664        </dt>
665        <dd>
666          <ul>
667          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/neoprep_protocol.jsp?ID=<%=ID%>"
668            >Lab protocols for NeoPrep library preparation</span> 
669            <span class="counter" data-counter="neoprep-plates-for-libprep" 
670              title="Number of NeoPrep plates waiting for registration"></span>
671         
672          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/lib_registration.jsp?ID=<%=ID%>&neoprep=1"
673            >NeoPrep library registration</span> 
674            <span class="counter" data-counter="neoprep-plates-for-libprep"
675              title="Number of NeoPrep plates waiting for registration"></span>
676          </ul>
677        </dd>
678       
679        <dt>
680          <base:icon image="<%=home+"/images/pool.png" %>" />
681          Pooling wizards
682        </dt>
683        <dd>
684          <ul>
685          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/create_pools.jsp?ID=<%=ID%>"
686            >Create pooled libraries</span> 
687            <span class="counter more" data-counter="lib-plates-for-pooling"
688              title="Number of Lib plates waiting for pooling"></span><span 
689            class="counter" data-counter="neoprep-plates-for-pooling"
690              title="Number of NeoPrep plates waiting for registration"></span>
691         
692          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/pool_protocol.jsp?ID=<%=ID%>"
693            >Lab protocols for pooling</span> 
694            <span class="counter" data-counter="pools-not-registered" 
695              title="Number of pools waiting for registration"></span>
696         
697          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/pool_registration.jsp?ID=<%=ID%>"
698            >Register pooled libraries</span> 
699            <span class="counter" data-counter="pools-not-registered" 
700              title="Number of pools waiting for registration"></span>
701          </ul>
702        </dd>
703        </dl>
704       
705        <h3>Sequencing wizards</h3>
706        <dl class="leftborder rightborder bottomborder">
707       
708        <dt>
709          <base:icon image="<%=home+"/images/flowcell.png" %>" />
710          Clustering and sequencing wizards
711        </dt>
712        <dd>
713          <ul>
714          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/create_flowcells.jsp?ID=<%=ID%>"
715            >Create flow cells</span> 
716            <span class="counter" data-counter="pools-not-used" 
717              title="Number of pools waiting for sequencing"></span>
718         
719          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/flowcell_protocol.jsp?ID=<%=ID%>"
720            >Lab protocol for sequencing</span> 
721            <span class="counter" data-counter="flow-cells-not-sequenced" 
722              title="Number of flow cells waiting to be sequenced"></span>
723         
724          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/sequencing_started.jsp?ID=<%=ID%>"
725            >Register sequencing started</span> 
726            <span class="counter" data-counter="flow-cells-not-sequenced" 
727              title="Number of flow cells waiting to be sequenced"></span>
728
729          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/sequencing_ended.jsp?ID=<%=ID%>"
730            >Register sequencing ended</span> 
731            <span class="counter" data-counter="sequencing-runs-active" 
732              title="Number of active sequencing runs"></span>
733          </ul>
734        </dd>
735       
736        </dl>
737     
738        <h3>Secondary analysis wizards</h3>
739        <dl class="leftborder rightborder bottomborder">
740          <dt>
741            <base:icon image="<%=home+"/images/server.png" %>" />
742            Demux and merge wizards
743          </dt>
744          <dd>
745            <ul>
746            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/sequencing_confirm.jsp?ID=<%=ID%>"
747              >Confirm sequencing completed</span> 
748              <span class="counter" data-counter="sequencing-runs-unconfirmed" 
749                title="Number of ended but not confirmed sequencing runs"></span>
750           
751            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>"
752              >Start demux and merge</span> 
753              <span class="counter" data-counter="sequencing-runs-for-demux" 
754                title="Number of confirmed sequencing runs waiting to be demuxed"></span>
755           
756            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/demux_confirm.jsp?ID=<%=ID%>"
757              >Confirm demux and merge completed</span> 
758              <span class="counter" data-counter="demux-jobs-not-confirmed"
759                title="Number of demux jobs waiting for confirmation"></span>
760            </ul>
761          </dd>
762         
763          <dt>
764            <base:icon image="<%=home+"/images/align.png" %>" />
765            Masking and alignment wizards
766          </dt>
767          <dd>
768            <ul>
769            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/align_start.jsp?ID=<%=ID%>"
770              >Start masking and alignment</span> 
771              <span class="counter" data-counter="merged-sequences-for-alignment"
772                title="Number of merged sequences waiting for alignment"></span>
773               
774            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/align_confirm.jsp?ID=<%=ID%>"
775              >Confirm masking and alignment completed</span> 
776              <span class="counter" data-counter="aligned-sequences-not-confirmed" 
777                title="Number of aligned sequences waiting for confirmation"></span>
778            </ul>
779          </dd>
780          <dt>
781            <base:icon image="<%=home+"/images/wizard.png" %>" />
782            Feature extraction wizards
783          </dt>
784          <dd>
785            <ul>
786            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/cufflinks_start.jsp?ID=<%=ID%>"
787              >Start feature extraction</span> 
788            <span class="counter" data-counter="aligned-sequences-for-cufflinks" 
789                title="Number of aligned sequences confirmed for Cufflinks"></span>
790            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/cufflinks_confirm.jsp?ID=<%=ID%>"
791              >Confirm feature extraction completed</span>
792            <span class="counter" data-counter="cufflinks-not-confirmed" 
793              title="Number of Cufflinks jobs waiting for confirmation"></span>
794            </ul>
795          </dd>
796
797          <dt>
798            <base:icon image="<%=home+"/images/pdffile.png" %>" />
799            Report wizards
800          </dt>
801         
802          <dd>
803            <ul>
804            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=GENE_REPORT"
805              >Gene report</span> 
806            <span class="counter" data-counter="rawbioassys-without-genereport" 
807                title="Number of rawbioassays without a Gene report PDF"></span>
808            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=PILOT_REPORT"
809              >Pilot report</span> 
810            <span class="counter" data-counter="rawbioassys-without-pilotreport" 
811                title="Number of rawbioassays without a Pilot report PDF"></span>
812            </ul>
813          </dd>
814        </dl>
815       
816     
817      </div>
818      <div id="counter-age"><b>Counters last updated</b> ?</div>
819    </div>
820    </form>
821   
822  </div>
823 
824</base:body>
825</base:page>
826<%
827}
828finally
829{
830  if (dc != null) dc.close();
831}
832%>
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