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show.gsp @ 1206

Last change on this file since 1206 was 1206, checked in by robert@…, 10 years ago
Removed sorting of subjects in study page and added units to the template fields that need them (ticket #66 and #67)
Property svn:keywords set to `Author Date Rev`
File size: 37.8 KB

Line
1
2	<%@ page import="dbnp.studycapturing.Study" %>
3	<%@ page import="dbnp.studycapturing.EventGroup" %>
4	<%@ page import="dbnp.studycapturing.RelTime" %>
5	<html>
6	<head>
7	<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
8	<meta name="layout" content="main" />
9	<g:set var="entityName" value="${message(code: 'study.label', default: 'Study')}" />
10	<title><g:message code="default.show.label" args="[entityName]" /></title>
11	<script type="text/javascript">
12	// Flag whether the timelines have been loaded
13	var timelineloaded = false;
14
15	// Number of timelines that should be loaded
16	var numTimelines = ${studyList?.size()};
17
18	// This method is called on the event body.onLoad
19	$(function() {
20	$("#tabs").tabs({
21	show: function(event, ui) {
22	// If the events tab is shown, the timeline should be redrawn
23	if( ui.tab.hash == '#events-timeline' && !timelineloaded ) {
24	loadTimeline( 'eventstimeline', 'eventtitles', 0 );
25	timelineloaded = true;
26	}
27	}
28	});
29	});
30	</script>
31	<link rel="stylesheet" type="text/css" href="${resource(dir: 'css', file: 'studies.css')}"/>
32
33	<!-- Include scripts for the SIMILE timeline. See http://simile-widgets.org/wiki/ -->
34	<script type="text/javascript">
35	Timeline_ajax_url="${resource(dir: 'js', file: 'timeline-simile/timeline_ajax/simile-ajax-api.js')}";
36	Timeline_urlPrefix='${resource(dir: 'js', file: 'timeline-simile/')}';
37	Timeline_parameters='bundle=true';
38	</script>
39	<script src="${resource(dir: 'js', file: 'timeline-simile/timeline-api.js')}" type="text/javascript"></script>
40	<script src="${resource(dir: 'js', file: 'timeline-simile/custom-timeline.js')}" type="text/javascript"></script>
41	<script src="${resource(dir: 'js', file: 'timeline-simile/relative-time.js')}" type="text/javascript"></script>
42	<script src="${resource(dir: 'js', file: 'jquery-callback-1.2.js')}" type="text/javascript"></script>
43
44	<!-- Create the JSON objects for the timeline with events -->
45	<script type="text/javascript">
46	/*
47	* Creates timeline bands for displaying different timelines
48	*
49	* @returns array with BandInfo objects, as described on http://simile-widgets.org/wiki/Timeline_GettingStarted
50	*/
51	function createTimelineBands( timelineNr ) {
52	var bandInfos = [];
53	var eventSources = [];
54	var overviewEventSource = new Timeline.DefaultEventSource();
55
56	// The way the timeline should look. See http://www.linuxjournal.com/article/9301
57	var theme = Timeline.ClassicTheme.create();
58	var emptyEtherPainter = new Timeline.EmptyEtherPainter( { theme: theme } )
59
60	// Now create the bands for all studies, and add them to one timeline
61	// Multiple timeline on one page do not seem to work
62	<g:set var="bandNr" value="${0}" />
63	<g:each in="${studyList}" var="study" status="timelineNr">
64	// The date that the timeline should start on
65	var dateStr = "<g:formatDate format="yyyy/MM/dd HH:mm:ss" date="${study.startDate}"/>";
66	firstDate = new Date ( dateStr );
67
68	//------------- Eventgroup overview ---------------
69
70	<g:set var="datesBandNr" value="${bandNr}" />
71	// Add an empty band to show the dates
72	bandInfos[${bandNr}] =
73	Timeline.createBandInfo({
74	width: 40,
75	intervalUnit: Timeline.DateTime.DAY,
76	intervalPixels: 40,
77	showEventText: false,
78	date: firstDate,
79	timeZone: +1,
80	layout: 'original',
81	theme: theme
82	});
83
84	// Make sure the date is printed using the relative time
85	bandInfos[${bandNr}].etherPainter = new Timeline.RelativeDateEtherPainter( { theme: theme, startDate: firstDate, unit: Timeline.DateTime.DAY } );
86	bandInfos[${bandNr}].labeller = new Timeline.RelativeDateLabeller( "en", 0, firstDate );
87
88	bandTitleInfo[ timelineNr ][ ${bandNr} ] = {
89	title: "${study.title}",
90	subjects: "",
91	className: "studytitle"
92	};
93
94	<g:set var="bandNr" value="${bandNr+1}" />
95	<%
96	def sortedEventGroups = study.eventGroups.sort( { a, b ->
97	return a.name <=> b.name;
98	} as Comparator );
99
100	def orphans = study.getOrphanEvents();
101	if( orphans?.size() > 0 ) {
102	sortedEventGroups.add( new EventGroup(
103	id: -1,
104	name: 'No group',
105	events: orphans,
106	subjects: []
107	));
108	}
109
110	%>
111	<g:each in="${sortedEventGroups}" var="eventGroup" status="i">
112
113	//------------- Eventgroup ${bandNr} ---------------
114
115	// Create an eventsource for all events
116	eventSources[${bandNr}] = new Timeline.DefaultEventSource();
117
118	// Load events for this eventsource (using jquery)
119	var event_url = '${createLink(controller:'study', action:'events', id:( eventGroup.id ? eventGroup.id : -1 ), params: [ startDate: study.startDate.getTime(), study: study.id ])}';
120	$.getJSON(event_url, $.callback( _loadJSONEvents, [0, ${bandNr}, eventSources[${bandNr}], overviewEventSource, event_url] ) );
121
122	// Create a new timeline band
123	bandInfos[${bandNr}] =
124	Timeline.createBandInfo({
125	eventSource: eventSources[${bandNr}],
126	width: 30,
127	intervalUnit: Timeline.DateTime.DAY,
128	intervalPixels: 40,
129	date: firstDate,
130	timeZone: +1,
131	syncWith: 1,
132	layout: 'original',
133	theme: theme
134	});
135
136	// Make sure the date isn't printed by using the empty ether painter
137	bandInfos[${bandNr}].etherPainter = emptyEtherPainter;
138
139	// Add a title to the bandinfo
140	<%
141	sortedGroupSubjects = eventGroup.subjects.sort( { a, b -> a.name <=> b.name } as Comparator );
142	def simpleSubjects = sortedGroupSubjects.name.join( ', ' );
143
144	// We can only show appr. 30 characters per line and as many lines as there are events
145	def charsPerLine = 30;
146	def numEvents = eventGroup.events?.size();
147	def maxChars = numEvents * charsPerLine;
148
149	// If the subjects will fit, show them all
150	if( simpleSubjects?.size() < maxChars ) {
151	showSubjects = simpleSubjects;
152	} else {
153	// Always add the first name
154	def subjectNames = sortedGroupSubjects[0]?.name;
155
156	// Continue adding names until the length is to long
157	id = 0;
158	sortedGroupSubjects.each { subject ->
159	if( id > 0 ) {
160	println( "ID: " + id + " - " + subjectNames?.size() + " - " + subject.name?.size() + " - " + maxChars );
161	if( subjectNames?.size() + subject.name?.size() < maxChars - 15 ) {
162	subjectNames += ", " + subject.name;
163	} else {
164	return;
165	}
166	}
167	id++;
168	}
169
170	// Add a postfix
171	subjectNames += " and " + ( sortedGroupSubjects?.size() - id ) + " more";
172
173	showSubjects = subjectNames;
174	}
175
176
177	%>
178	bandTitleInfo[ timelineNr ][ ${bandNr} ] = {
179	title: "${eventGroup.name}",
180	className: "<g:if test="${ eventGroup.id == -1 \|\| !eventGroup.id }">no_group</g:if>",
181	subjects: "${showSubjects}"
182	};
183
184	<g:set var="bandNr" value="${bandNr+1}" />
185	</g:each>
186
187	// Synchronize all bands
188	<g:each in="${sortedEventGroups}" var="eventGroup" status="i">
189	bandInfos[${i + datesBandNr +1}].syncWith = ${datesBandNr};
190	</g:each>
191
192	</g:each>
193
194	return bandInfos;
195	}
196	</script>
197	</head>
198	<body>
199
200	<div class="body" id="studies">
201	<h1><g:message code="default.show.label" args="[entityName]" /></h1>
202	<g:if test="${flash.message}">
203	<div class="message">${flash.message}</div>
204	</g:if>
205	<div class="dialog">
206	<div id="tabs">
207	<ul>
208	<li><a href="#study">Study Information</a></li>
209	<li><a href="#subjects">Subjects</a></li>
210	<li><a href="#events-timeline">Events timeline</a></li>
211	<li><a href="#events-table">Events table</a></li>
212	<li><a href="#assays">Assays</a></li>
213	<li><a href="#samples">Samples</a></li>
214	<li><a href="#persons">Persons</a></li>
215	<li><a href="#publications">Publications</a></li>
216	</ul>
217
218	<div id="study">
219	<table>
220	<!-- only show the head section if there are multiple studies -->
221	<g:if test="${multipleStudies}">
222	<thead>
223	<tr>
224	<th></th>
225	<g:each in="${studyList}" var="studyInstance">
226	<th>${studyInstance.title}</th>
227	</g:each>
228	</tr>
229	</thead>
230	</g:if>
231	<%
232	// Determine a union of the fields from all studies, in order
233	// to show a proper list. We want every field to appear just once,
234	// so the list is filtered for unique values
235	studyFields = studyList[0].giveDomainFields() + studyList*.giveTemplateFields()?.flatten().unique()
236	%>
237	<!-- Show all template and domain fields, if filled -->
238	<g:each in="${studyFields}" var="field">
239	<%
240	// If a value is not set for any of the selected studies, the
241	// field should not appear in the list
242	showField = true in studyList.collect { it.fieldExists( field.name ) && it.getFieldValue( field.name ) != null }?.flatten()
243	%>
244	<g:if test="${showField}">
245	<tr>
246	<td>${field}</td>
247	<g:each in="${studyList}" var="studyInstance">
248	<td>
249	<g:if test="${studyInstance.fieldExists(field.name)}">
250	<wizard:showTemplateField field="${field}" entity="${studyInstance}" />
251	</g:if>
252	<g:else>
253	-
254	</g:else>
255	</td>
256	</g:each>
257	</tr>
258	</g:if>
259	</g:each>
260
261	<!-- Add some extra fields -->
262	<tr>
263	<td>Events</td>
264	<g:each in="${studyList}" var="studyInstance">
265	<td>
266	<g:if test="${studyInstance.giveEventTemplates()?.size()==0}">
267	-
268	</g:if>
269	<g:else>
270	${studyInstance.giveEventTemplates().name.join(", ")}
271	</g:else>
272	</td>
273	</g:each>
274	</tr>
275	<tr>
276	<td>Sampling events</td>
277	<g:each in="${studyList}" var="studyInstance">
278	<td>
279	<g:if test="${studyInstance.giveSamplingEventTemplates()?.size()==0}">
280	-
281	</g:if>
282	<g:else>
283	${studyInstance.giveSamplingEventTemplates().name.join(", ")}
284	</g:else>
285	</td>
286	</g:each>
287	</tr>
288	<tr>
289	<td>Public</td>
290	<g:each in="${studyList}" var="studyInstance">
291	<td>
292	${studyInstance.publicstudy}
293	</td>
294	</g:each>
295	</tr>
296	<tr>
297	<td>Owner</td>
298	<g:each in="${studyList}" var="studyInstance">
299	<td>
300	${studyInstance.owner?.username}
301	</td>
302	</g:each>
303	</tr>
304	<tr>
305	<td>Readers</td>
306	<g:each in="${studyList}" var="studyInstance">
307	<td>
308	<g:if test="${studyInstance.readers.size() == 0}">
309	-
310	</g:if>
311	<g:else>
312	${studyInstance.readers.username.join( ", " )}
313	</g:else>
314	</td>
315	</g:each>
316	</tr>
317	<tr>
318	<td>Writers</td>
319	<g:each in="${studyList}" var="studyInstance">
320	<td>
321	<g:if test="${studyInstance.writers?.size()==0}">
322	-
323	</g:if>
324	<g:else>
325	${studyInstance.writers.username.join( ", " )}
326	</g:else>
327	</td>
328	</g:each>
329	</tr>
330	</table>
331	</div>
332
333	<div id="subjects">
334
335	<g:if test="${studyList*.subjects?.flatten()?.size()==0}">
336	No subjects in the selected studies
337	</g:if>
338	<g:else>
339	<table>
340	<thead>
341	<tr>
342	<g:if test="${multipleStudies}">
343	<th></th>
344	</g:if>
345	<g:each in="${new dbnp.studycapturing.Subject().giveDomainFields()}" var="field">
346	<th>${field}</th>
347	</g:each>
348
349	<%
350	// Determine a union of the fields for all different
351	// subjects in all studies. In order to show a proper list.
352	// We want every field to appear just once,
353	// so the list is filtered for unique values
354	subjectTemplates = studyList*.giveSubjectTemplates()?.flatten().unique()
355	if( !subjectTemplates ) {
356	subjectTemplates = [];
357	subjectFields = [];
358	} else {
359	subjectFields = subjectTemplates*.fields?.flatten().unique()
360	if( !subjectFields ) {
361	subjectFields = [];
362	}
363	}
364
365	/*
366	* These lines are rewritten because
367	* performance sucked
368	*
369	* // These took about 9 seconds (for 31 subjects and
370	* allSubjects = studyList*.subjects?.flatten()
371	*
372	* subjectFields = subjectFields.findAll { subjectField ->
373	* ( true in allSubjects.collect { subject -> subject.fieldExists( subjectField.name ) && subject.getFieldValue( subjectField.name ) != null }.flatten() )
374	* }
375	*/
376
377	// Filter out all fields that are left blank for all subjects
378	allSubjects = studyList*.subjects?.flatten()
379
380	showSubjectFields = []
381	subjectFields.each { subjectField ->
382	for( subject in allSubjects )
383	{
384	// If the field is filled for this subject, we have to
385	// show the field and should not check any other
386	// subjects (hence the break)
387	if( subject.fieldExists( subjectField.name ) && subject.getFieldValue( subjectField.name ) ) {
388	showSubjectFields << subjectField;
389	break;
390	}
391	}
392	}
393	%>
394
395	<g:each in="${showSubjectFields}" var="field">
396	<th>${field}</th>
397	</g:each>
398
399	</tr>
400	</thead>
401
402	<g:set var="i" value="${1}" />
403
404	<g:each in="${studyList}" var="studyInstance">
405	<g:each in="${studyInstance.subjects}" var="subject" status="j">
406	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
407	<g:if test="${multipleStudies && j==0}">
408	<td class="studytitle" rowspan="${sortedSubjects?.size()}">
409	${studyInstance.title}
410	</td>
411	</g:if>
412	<g:each in="${subject.giveDomainFields()}" var="field">
413	<td><wizard:showTemplateField field="${field}" entity="${subject}" /></td>
414	</g:each>
415
416	<g:each in="${showSubjectFields}" var="field">
417	<td>
418	<g:if test="${subject.fieldExists(field.name)}">
419	<wizard:showTemplateField field="${field}" entity="${subject}" />
420	</g:if>
421	<g:else>
422	N/A
423	</g:else>
424	</td>
425	</g:each>
426
427	</tr>
428	<g:set var="i" value="${i + 1}" />
429	</g:each>
430	</g:each>
431	</table>
432	</g:else>
433	</div>
434
435	<div id="events-timeline">
436	<g:if test="${studyList.events?.flatten()?.size()==0 && studyInstance.samplingEvents?.flatten()?.size()==0 }">
437	No events in these studies
438	</g:if>
439	<g:else>
440	<g:each in="${studyList}" var="study" status="i">
441	<div style="margin: 10px; ">
442	<div class="eventtitles" id="eventtitles-${i}"></div>
443	<div class="eventstimeline" id="eventstimeline-${i}"></div>
444	</div>
445	</g:each>
446	<noscript>
447	<table>
448	<thead>
449	<tr>
450	<g:if test="${multipleStudies}">
451	<th></th>
452	</g:if>
453	<th>Start time</th>
454	<th>Duration</th>
455	<th>Type</th>
456	<th>Sampling event</th>
457	<th>Parameters</th>
458	</tr>
459	</thead>
460
461	<g:set var="i" value="${1}" />
462
463	<g:each in="${studyList}" var="studyInstance">
464	<%
465	// Sort events by starttime and duration
466	events = studyInstance.events + studyInstance.samplingEvents;
467	sortedEvents = events.sort( { a, b ->
468	//a.startTime == b.startTime ?
469	//a.getDuration().getValue() <=> b.getDuration().getValue() :
470	a.startTime <=> b.startTime
471	} as Comparator )
472	%>
473
474	<g:each in="${sortedEvents}" var="event" status="j">
475	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
476	<g:if test="${multipleStudies && j==0}">
477	<td class="studytitle" rowspan="${sortedEvents?.size()}">
478	${studyInstance.title}
479	</td>
480	</g:if>
481	<td>${event.getStartTimeString()}</td>
482	<td>${((event.getClass() == 'Event') ? event.getDurationString() : '')}</td>
483	<td>${event.template.name}</td>
484	<td>
485	<g:if test="${event instanceof dbnp.studycapturing.SamplingEvent}">
486	<g:checkBox name="samplingEvent" disabled="${true}" value="${true}"/>
487	</g:if>
488	<g:else>
489	<g:checkBox name="event" disabled="${true}" value="${false}" />
490	</g:else>
491	</td>
492	<td>
493	<g:set var="fieldCounter" value="${1}" />
494	<g:each in="${event.giveTemplateFields()}" var="field">
495	<g:if test="${event.getFieldValue(field.name)}">
496	<g:if test="${fieldCounter > 1}">, </g:if>
497	${field.name} = <wizard:showTemplateField field="${field}" entity="${event}" />
498	<g:set var="fieldCounter" value="${fieldCounter + 1}" />
499	</g:if>
500	</g:each>
501	</td>
502	</tr>
503
504	<g:set var="i" value="${i + 1}" />
505	</g:each>
506	</g:each>
507	</table>
508
509	</noscript>
510
511	</g:else>
512	</div>
513
514	<div id="events-table">
515	<g:if test="${studyList*.eventGroups?.flatten()?.size()==0}">
516	No event groups in this study
517	</g:if>
518	<g:else>
519	<%
520	// Determine a union of the event templates for all different
521	// eventgroups in all studies, in order to show a proper list.
522	// We want every field to appear just once,
523	// so the list is filtered for unique values
524	def groupTemplates = studyList*.giveAllEventTemplates()?.flatten().unique()
525	def showTemplates = groupTemplates;
526
527	def showProperties = [:];
528	def allEvents = studyList.events.flatten() + studyList.samplingEvents.flatten();
529	def eventColumns = 0;
530
531	showTemplates.each { template ->
532	// We want to show all properties only once. If the properties are never filled
533	// we shouldn't show them at all.
534	def showFields = []
535	template.fields.each { field ->
536	for( def event: allEvents.findAll { it.template == template } ) {
537	if( event.getFieldValue( field.name ) ) {
538	showFields << field;
539	break;
540	}
541	}
542	}
543
544	showProperties[ template.name ] = showFields;
545
546	// Compute the total number of columns under 'Events' (the +1 is
547	// because of the 'start time' column)
548	eventColumns += [ 1, showFields.size() + 1 ].max();
549	}
550
551	%>
552	<table>
553	<thead>
554	<tr>
555	<g:if test="${multipleStudies}">
556	<th></th>
557	</g:if>
558	<th>Name</th>
559	<th colspan="${eventColumns}">Events</th>
560	<th>Subjects</th>
561	</tr>
562	<tr>
563	<g:if test="${multipleStudies}">
564	<th></th>
565	</g:if>
566	<th></th>
567	<g:each in="${showTemplates}" var="eventTemplate">
568	<th colspan="${[1, showProperties[ eventTemplate.name ].size() + 1 ].max()}">${eventTemplate.name}</th>
569	</g:each>
570	<th></th>
571	</tr>
572	<tr class="templateFields">
573	<g:if test="${multipleStudies}">
574	<th></th>
575	</g:if>
576	<th></th>
577	<g:each in="${showTemplates}" var="eventTemplate">
578	<th>start time</th>
579	<g:if test="${showProperties[ eventTemplate.name ].size() > 0}">
580	<g:each in="${showProperties[ eventTemplate.name ]}" var="field">
581	<th>${field.name}</th>
582	</g:each>
583	</g:if>
584	</g:each>
585	<th></th>
586	</tr>
587	</thead>
588
589	<g:set var="i" value="${1}" />
590
591	<g:each in="${studyList}" var="studyInstance">
592	<%
593	// Sort the groups by name
594	def sortedEventGroups = studyInstance.eventGroups.sort( { a, b ->
595	return a.name <=> b.name;
596	} as Comparator );
597
598	// Determine the number of rows per group (depending on the max
599	// number of events per template in a group)
600	def maxNumberEventsPerTemplate = [:];
601	def rowsPerStudy = 0;
602	sortedEventGroups.each { group ->
603	def max = 1;
604	showTemplates.each { template ->
605	def num = ( group.events + group.samplingEvents ).findAll { it.template == template }.size();
606	if( num > max )
607	max = num;
608	}
609	maxNumberEventsPerTemplate[group.name] = max;
610	rowsPerStudy += max;
611	}
612
613	def orphans = studyInstance.getOrphanEvents();
614	if( orphans?.size() > 0 ) {
615	sortedEventGroups.add( new EventGroup(
616	id: -1,
617	name: 'No group',
618	events: orphans,
619	subjects: []
620	));
621	}
622	%>
623	<g:each in="${sortedEventGroups}" var="eventGroup" status="j">
624	<g:set var="n" value="${1}" />
625	<g:while test="${n <= maxNumberEventsPerTemplate[ eventGroup.name ]}">
626
627	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
628	<g:if test="${n == 1}">
629	<g:if test="${multipleStudies && j==0}">
630	<td class="studytitle" rowspan="${rowsPerStudy}">
631	${studyInstance.title}
632	</td>
633	</g:if>
634	<td rowspan="${maxNumberEventsPerTemplate[ eventGroup.name ]}">${eventGroup.name}</td>
635	</g:if>
636
637	<g:each in="${showTemplates}" var="currentEventTemplate">
638	<g:if test="${showProperties[ currentEventTemplate.name ].size() == 0}">
639	<td> </td>
640	</g:if>
641	<g:else>
642	<%
643	def templateEvents = (eventGroup.events + eventGroup.samplingEvents).findAll { it.template == currentEventTemplate }.sort { a, b -> a.startTime <=> b.startTime }.asType(List)
644	def event = templateEvents.size() >= n ? templateEvents[ n - 1 ] : null;
645	%>
646	<td class="templateFieldValue"><g:if test="${event}">${new RelTime( event.startTime ).toString()}</g:if></td>
647	<g:each in="${showProperties[ currentEventTemplate.name ]}" var="field">
648	<td class="templateFieldValue"><wizard:showTemplateField field="${field}" entity="${event}" /></td>
649	</g:each>
650	</g:else>
651	</g:each>
652
653	<g:if test="${n == 1}">
654	<% sortedGroupSubjects = eventGroup.subjects.sort( { a, b -> a.name <=> b.name } as Comparator ) %>
655
656	<td rowspan="${maxNumberEventsPerTemplate[ eventGroup.name ]}" title="${sortedGroupSubjects.name.join( ', ' )}">
657	<g:if test="${eventGroup.subjects.size()==0}">
658	-
659	</g:if>
660	<g:else>
661	<g:each in="${eventGroup.subjects.species.unique()}" var="currentSpecies" status="k">
662	<g:if test="${k > 0}">,</g:if>
663	<%=eventGroup.subjects.findAll { return it.species == currentSpecies; }.size() %>
664	${currentSpecies}
665	</g:each>
666	</g:else>
667	</td>
668	</g:if>
669	</tr>
670
671
672	<g:set var="n" value="${n+1}" />
673	</g:while>
674
675	<g:set var="i" value="${i + 1}" />
676	</g:each>
677
678	</g:each>
679
680	</table>
681	</g:else>
682	</div>
683
684	<div id="assays">
685	<g:if test="${studyList*.assays?.flatten()?.size()==0}">
686	No assays in these studies
687	</g:if>
688	<g:else>
689	<table>
690	<thead>
691	<tr>
692	<g:if test="${multipleStudies}">
693	<th></th>
694	</g:if>
695	<th width="100">Assay Code</th>
696	<th width="100">Assay Name</th>
697	<th width="100">Module</th>
698	<th width="150">Platform</th>
699	<th>Link</th>
700	<th>Samples</th>
701	</tr>
702	</thead>
703	<g:set var="i" value="${1}" />
704
705	<g:each in="${studyList}" var="studyInstance">
706	<g:each in="${studyInstance.assays}" var="assay" status="j">
707	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
708	<g:if test="${multipleStudies && j==0}">
709	<td class="studytitle" rowspan="${studyInstance.assays?.size()}">
710	${studyInstance.title}
711	</td>
712	</g:if>
713	<td>${assay.token}</td>
714	<td>${assay.name}</td>
715	<td>${assay.module.name}</td>
716	<td>${assay.module.platform}</td>
717	%{--<td><a href="${assay.module.url}/assay/${assay.externalAssayID}">view</a></td>--}%
718	<td><jumpbar:link
719	linkDest="${createLink(action:'show', id:studyInstance.id)}"
720	linkText='Go back to GSCF'
721	frameSource="${assay.module.url}/assay/showByToken/${assay.externalAssayID}"
722	pageTitle="Assay View in Module">
723	view
724	</jumpbar:link></td>
725	<td>
726	<% sortedAssaySamples = assay.samples.sort( { a, b -> a.name <=> b.name } as Comparator ) %>
727	${sortedAssaySamples.name.join( ', ' )}
728	</td>
729	</tr>
730	<g:set var="i" value="${i + 1}" />
731
732	</g:each>
733	</g:each>
734	</table>
735	</g:else>
736	</div>
737
738	<div id="samples">
739
740	<g:if test="${studyList*.samples.flatten()?.size()==0}">
741	No samples in the selected studies
742	</g:if>
743	<g:else>
744	<table>
745	<thead>
746	<tr>
747	<g:if test="${multipleStudies}">
748	<th></th>
749	</g:if>
750
751	<th>Parent Subject</th>
752	<th>Parent Sampling Event</th>
753
754
755	<g:each in="${new dbnp.studycapturing.Sample().giveDomainFields()}" var="field">
756	<th>${field}</th>
757	</g:each>
758
759	<%
760	// Determine a union of the fields for all different
761	// samples in all studies. In order to show a proper list.
762	// We want every field to appear just once,
763	// so the list is filtered for unique values
764	sampleTemplates = studyList*.giveSampleTemplates().flatten().unique()
765
766	if( !sampleTemplates ) {
767	sampleTemplates = [];
768	sampleFields = [];
769	showSampleFields = [];
770	} else {
771	sampleFields = sampleTemplates*.fields.flatten().unique()
772	if( !sampleFields ) {
773	sampleFields = [];
774	showSampleFields = [];
775	} else {
776	// Filter out all fields that are left blank for all samples
777	allSamples = studyList*.samples.flatten()
778
779	showSampleFields = [];
780	sampleFields.each { sampleField ->
781	for( sample in allSamples )
782	{
783	// If the field is filled for this subject, we have to
784	// show the field and should not check any other
785	// samples (hence the break)
786	if( sample.fieldExists( sampleField.name ) && sample.getFieldValue( sampleField.name ) ) {
787	showSampleFields << sampleField;
788	break;
789	}
790	}
791	}
792	}
793	}
794	%>
795
796	<g:each in="${showSampleFields}" var="field">
797	<th>${field}</th>
798	</g:each>
799
800	</tr>
801	</thead>
802
803	<g:set var="i" value="${1}" />
804
805	<g:each in="${studyList}" var="studyInstance">
806	<%
807	// Sort samples by name
808	samples = studyInstance.samples;
809	sortedSamples = samples.sort( { a, b -> a.name <=> b.name } as Comparator )
810	%>
811
812	<g:each in="${sortedSamples}" var="sample" status="j">
813	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
814	<g:if test="${multipleStudies && j==0}">
815	<td class="studytitle" rowspan="${sortedSamples?.size()}">
816	${studyInstance.title}
817	</td>
818	</g:if>
819	<td>${sample.parentSubject?.name}</td>
820	<td>${sample.parentEvent?.template?.name} at ${sample.parentEvent?.getStartTimeString()}</td>
821	<g:each in="${sample.giveDomainFields()}" var="field">
822	<td><wizard:showTemplateField field="${field}" entity="${sample}" /></td>
823	</g:each>
824
825	<g:each in="${showSampleFields}" var="field">
826	<td>
827	<g:if test="${sample.fieldExists(field.name)}">
828	<wizard:showTemplateField field="${field}" entity="${sample}" />
829	</g:if>
830	<g:else>
831	N/A
832	</g:else>
833	</td>
834	</g:each>
835
836	</tr>
837	<g:set var="i" value="${i + 1}" />
838	</g:each>
839	</g:each>
840
841	</table>
842	</g:else>
843	</div>
844
845	<div id="persons">
846	<%
847	// Determine a list of all persons
848	allPersons = studyList.persons.person.flatten().unique()
849	%>
850	<g:if test="${allPersons?.size()==0}">
851	No persons involved in these studies
852	</g:if>
853	<g:else>
854	<table>
855	<tr>
856	<thead>
857	<th>Name</th>
858	<th>Affiliations</th>
859	<th>Phone</th>
860	<th>Email</th>
861	<g:if test="${multipleStudies}">
862	<g:each in="${studyList}" var="studyInstance">
863	<th>${studyInstance.title}</th>
864	</g:each>
865	</g:if>
866	<g:else>
867	<th>Role</th>
868	</g:else>
869	</thead>
870	</tr>
871	<g:each in="${allPersons}" var="person" status="i">
872	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
873	<td>${person.firstName} ${person.prefix} ${person.lastName}</td>
874	<td>
875	${person.affiliations.join(', ')}
876	</td>
877	<td>${person.phone}</td>
878	<td>${person.email}</td>
879	<g:each in="${studyList}" var="studyInstance">
880	<%
881	studyperson = studyInstance.persons.find { it.person == person }
882	%>
883	<td>
884	<g:if test="${studyperson}">
885	${studyperson.role.name}
886	</g:if>
887	</td>
888	</g:each>
889
890	</tr>
891	</g:each>
892	</table>
893	</g:else>
894	</div>
895
896	<div id="publications">
897	<%
898	// Determine a list of all persons
899	allPublications = studyList*.publications.flatten().unique()
900	%>
901	<g:if test="${allPublications?.size()==0}">
902	No publications attached to these studies
903	</g:if>
904	<g:else>
905	<table>
906	<tr>
907	<thead>
908	<th>Title</th>
909	<th>Authors</th>
910	<th>Comments</th>
911
912	<g:if test="${multipleStudies}">
913	<g:each in="${studyList}" var="studyInstance">
914	<th>${studyInstance.title}</th>
915	</g:each>
916	</g:if>
917	</thead>
918	</tr>
919	<g:each in="${allPublications}" var="publication" status="i">
920	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
921	<td>${publication.title}</td>
922	<td>
923	${publication.authorsList}
924	</td>
925	<td>${publication.comments}</td>
926	<g:if test="${multipleStudies}">
927	<g:each in="${studyList}" var="studyInstance">
928	<td>
929	<g:if test="${publication in studyInstance.publications}">
930	x
931	</g:if>
932	</td>
933	</g:each>
934	</g:if>
935	</tr>
936	</g:each>
937	</table>
938	</g:else>
939	</div>
940
941	</div>
942	</div>
943	<br>
944	<div class="buttons">
945	<g:form action="delete">
946	<g:if test="${studyList?.size() == 1}">
947	<g:set var="studyInstance" value="${studyList[0]}" />
948	<g:hiddenField name="id" value="${studyInstance?.id}" />
949	<g:if test="${studyInstance.canWrite(loggedInUser)}">
950	<span class="button"><g:link class="edit" controller="wizard" params="[jump:'edit']" id="${studyInstance?.id}">${message(code: 'default.button.edit.label', default: 'Edit')}</g:link></span>
951	</g:if>
952	<g:if test="${studyInstance.isOwner(loggedInUser)}">
953	<span class="button"><g:actionSubmit class="delete" action="delete" value="${message(code: 'default.button.delete.label', default: 'Delete')}" onclick="return confirm('${message(code: 'default.button.delete.confirm.message', default: 'Are you sure?')}');" /></span>
954	</g:if>
955	</g:if>
956	<span class="button"><g:link class="backToList" action="list">Back to list</g:link></span>
957	</g:form>
958	</div>
959
960	</div>
961	</body>
962	</html>

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