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show.gsp @ 467

Last change on this file since 467 was 467, checked in by roberth, 9 years ago
Updated study view to show the events on a timeline.
Property svn:keywords set to `Date Author Rev`
File size: 26.9 KB

Line
1
2	<%@ page import="dbnp.studycapturing.Study" %>
3	<html>
4	<head>
5	<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
6	<meta name="layout" content="main" />
7	<g:set var="entityName" value="${message(code: 'study.label', default: 'Study')}" />
8	<title><g:message code="default.show.label" args="[entityName]" /></title>
9	<script type="text/javascript">
10	// Flag whether the timelines have been loaded
11	var timelineloaded = false;
12
13	// Number of timelines that should be loaded
14	var numTimelines = ${studyList.size()};
15
16	// This method is called on the event body.onLoad
17	$(function() {
18	$("#tabs").tabs({
19	show: function(event, ui) {
20	// If the events tab is shown, the timeline should be redrawn
21	if( ui.tab.hash == '#events' && !timelineloaded ) {
22	loadTimeline( 'eventstimeline', 'eventtitles', 0 );
23	timelineloaded = true;
24	}
25	}
26	});
27	});
28	</script>
29	<link rel="stylesheet" type="text/css" href="${resource(dir: 'css', file: 'studies.css')}"/>
30
31	<!-- Include scripts for the SIMILE timeline. See http://simile-widgets.org/wiki/ -->
32	<script type="text/javascript">
33	Timeline_ajax_url="${resource(dir: 'js', file: 'timeline-simile/timeline_ajax/simile-ajax-api.js')}";
34	Timeline_urlPrefix='${resource(dir: 'js', file: 'timeline-simile/')}';
35	Timeline_parameters='bundle=true';
36	</script>
37	<script src="${resource(dir: 'js', file: 'timeline-simile/timeline-api.js')}" type="text/javascript"></script>
38	<script src="${resource(dir: 'js', file: 'timeline-simile/custom-timeline.js')}" type="text/javascript"></script>
39	<script src="${resource(dir: 'js', file: 'jquery-callback-1.2.js')}" type="text/javascript"></script>
40
41	<!-- Create the JSON objects for the timeline with events -->
42	<script type="text/javascript">
43	/*
44	* Creates timeline bands for displaying different timelines
45	*
46	* @returns array with BandInfo objects, as described on http://simile-widgets.org/wiki/Timeline_GettingStarted
47	*/
48	function createTimelineBands( timelineNr ) {
49	var bandInfos = [];
50	var eventSources = [];
51	var overviewEventSource = new Timeline.DefaultEventSource();
52
53	// The way the timeline should look. See http://www.linuxjournal.com/article/9301
54	var theme = Timeline.ClassicTheme.create();
55	var emptyEtherPainter = new Timeline.EmptyEtherPainter( { theme: theme } )
56
57	// Now create the bands for all studies, and add them to one timeline
58	// Multiple timeline on one page do not seem to work
59	<g:set var="bandNr" value="${0}" />
60	<g:each in="${studyList}" var="study" status="timelineNr">
61	// The date that the timeline should start on
62	var dateStr = "<g:formatDate format="yyyy/MM/dd HH:mm:ss" date="${study.startDate}"/>";
63	firstDate = new Date ( dateStr );
64
65	//------------- Eventgroup overview ---------------
66
67	<g:set var="datesBandNr" value="${bandNr}" />
68	// Add an empty band to show the dates
69	bandInfos[${bandNr}] =
70	Timeline.createBandInfo({
71	width: 40,
72	intervalUnit: Timeline.DateTime.DAY,
73	intervalPixels: 40,
74	showEventText: false,
75	date: firstDate,
76	timeZone: +1,
77	layout: 'original',
78	theme: theme
79	});
80	bandTitleInfo[ timelineNr ][ ${bandNr} ] = {
81	title: "${study.title}",
82	subjects: "",
83	className: "studytitle"
84	};
85
86	<g:set var="bandNr" value="${bandNr+1}" />
87
88	<g:each in="${study.eventGroups}" var="eventGroup" status="i">
89
90	//------------- Eventgroup ${bandNr} ---------------
91
92	// Create an eventsource for all events
93	eventSources[${bandNr}] = new Timeline.DefaultEventSource();
94
95	// Load events for this eventsource (using jquery)
96	var event_url = '${createLink(controller:'study', action:'events', id:eventGroup.id, params: [startDate: study.startDate])}';
97	$.getJSON(event_url, $.callback( _loadJSONEvents, [0, ${bandNr}, eventSources[${bandNr}], overviewEventSource, event_url] ) );
98
99	// Create a new timeline band
100	bandInfos[${bandNr}] =
101	Timeline.createBandInfo({
102	eventSource: eventSources[${bandNr}],
103	width: 30,
104	intervalUnit: Timeline.DateTime.DAY,
105	intervalPixels: 40,
106	date: firstDate,
107	timeZone: +1,
108	syncWith: 1,
109	layout: 'original',
110	theme: theme
111	});
112
113	// Make sure the date isn't printed by using the empty ether painter
114	bandInfos[${bandNr}].etherPainter = emptyEtherPainter;
115
116	// Add a title to the bandinfo
117	<% sortedGroupSubjects = eventGroup.subjects.sort( { a, b -> a.name <=> b.name } as Comparator ) %>
118	bandTitleInfo[ timelineNr ][ ${bandNr} ] = {
119	title: "${eventGroup.name}",
120	subjects: "${sortedGroupSubjects.name.join( ', ' )}"
121	};
122
123	<g:set var="bandNr" value="${bandNr+1}" />
124	</g:each>
125
126	// Synchronize all bands
127	<g:each in="${study.eventGroups}" var="eventGroup" status="i">
128	bandInfos[${i + datesBandNr +1}].syncWith = ${datesBandNr};
129	</g:each>
130
131	</g:each>
132
133	return bandInfos;
134	}
135	</script>
136	</head>
137	<body>
138
139	<div class="body" id="studies">
140	<h1><g:message code="default.show.label" args="[entityName]" /></h1>
141	<g:if test="${flash.message}">
142	<div class="message">${flash.message}</div>
143	</g:if>
144	<div class="dialog">
145	<div id="tabs">
146	<ul>
147	<li><a href="#study">Study Information</a></li>
148	<li><a href="#subjects">Subjects</a></li>
149	<li><a href="#events">Events</a></li>
150	<li><a href="#event-group">Event Groups</a></li>
151	<li><a href="#assays">Assays</a></li>
152	<li><a href="#persons">Persons</a></li>
153	<li><a href="#publications">Publications</a></li>
154	</ul>
155
156	<div id="study">
157	<table>
158	<!-- only show the head section if there are multiple studies -->
159	<g:if test="${multipleStudies}">
160	<thead>
161	<tr>
162	<th></th>
163	<g:each in="${studyList}" var="studyInstance">
164	<th>${studyInstance.title}</th>
165	</g:each>
166	</tr>
167	</thead>
168	</g:if>
169	<%
170	// Determine a union of the fields from all studies, in order
171	// to show a proper list. We want every field to appear just once,
172	// so the list is filtered for unique values
173	studyFields = studyList[0].giveDomainFields() + studyList*.giveTemplateFields().flatten().unique()
174	%>
175	<!-- Show all template and domain fields, if filled -->
176	<g:each in="${studyFields}" var="field">
177	<%
178	// If a value is not set for any of the selected studies, the
179	// field should not appear in the list
180	showField = true in studyList.collect { it.fieldExists( field.name ) && it.getFieldValue( field.name ) != null }.flatten()
181	%>
182	<g:if test="${showField}">
183	<tr>
184	<td>${field}</td>
185	<g:each in="${studyList}" var="studyInstance">
186	<td>${studyInstance.getFieldValue(field.name)}</td>
187	</g:each>
188	</tr>
189	</g:if>
190	</g:each>
191
192	<!-- Add some extra fields -->
193	<tr>
194	<td>Events</td>
195	<g:each in="${studyList}" var="studyInstance">
196	<td>
197	<g:if test="${studyInstance.giveEventTemplates().size()==0}">
198	-
199	</g:if>
200	<g:else>
201	${studyInstance.giveEventTemplates().name.join(", ")}
202	</g:else>
203	</td>
204	</g:each>
205	</tr>
206	<tr>
207	<td>Sampling events</td>
208	<g:each in="${studyList}" var="studyInstance">
209	<td>
210	<g:if test="${studyInstance.giveSamplingEventTemplates().size()==0}">
211	-
212	</g:if>
213	<g:else>
214	${studyInstance.giveSamplingEventTemplates().name.join(", ")}
215	</g:else>
216	</td>
217	</g:each>
218	</tr>
219	<tr>
220	<td>Readers</td>
221	<g:each in="${studyList}" var="studyInstance">
222	<td>
223	<g:if test="${studyInstance.readers.size()==0}">
224	-
225	</g:if>
226	<g:else>
227	<g:each in="${studyInstance.readers}" var="r" status="i">
228	<g:if test="${i > 0}">, </g:if>
229	<g:link controller="user" action="show" id="${r.id}">${r?.encodeAsHTML()}</g:link>
230	</g:each>
231	</g:else>
232	</td>
233	</g:each>
234	</tr>
235	<tr>
236	<td>Editors</td>
237	<g:each in="${studyList}" var="studyInstance">
238	<td>
239	<g:if test="${studyInstance.editors.size()==0}">
240	-
241	</g:if>
242	<g:else>
243	<g:each in="${studyInstance.editors}" var="r" status="i">
244	<g:if test="${i > 0}">, </g:if>
245	<g:link controller="user" action="show" id="${r.id}">${r?.encodeAsHTML()}</g:link>
246	</g:each>
247	</g:else>
248	</td>
249	</g:each>
250	</tr>
251
252	</table>
253	</div>
254
255	<div id="subjects">
256
257	<g:if test="${studyList*.subjects.flatten().size()==0}">
258	No subjects in the selected studies
259	</g:if>
260	<g:else>
261	<table>
262	<thead>
263	<tr>
264	<g:if test="${multipleStudies}">
265	<th></th>
266	</g:if>
267	<g:each in="${new dbnp.studycapturing.Subject().giveDomainFields()}" var="field">
268	<th>${field}</th>
269	</g:each>
270
271	<%
272	// Determine a union of the fields for all different
273	// subjects in all studies. In order to show a proper list.
274	// We want every field to appear just once,
275	// so the list is filtered for unique values
276	subjectTemplates = studyList*.giveSubjectTemplates().flatten().unique()
277	subjectFields = subjectTemplates*.fields.flatten().unique()
278
279	showSubjectFields = subjectFields
280
281	/*
282	* These lines are rewritten because
283	* performance sucked
284	*
285	* // These took about 9 seconds (for 31 subjects and
286	* allSubjects = studyList*.subjects.flatten()
287	*
288	* subjectFields = subjectFields.findAll { subjectField ->
289	* ( true in allSubjects.collect { subject -> subject.fieldExists( subjectField.name ) && subject.getFieldValue( subjectField.name ) != null }.flatten() )
290	* }
291	*/
292
293	// Filter out all fields that are left blank for all subjects
294	allSubjects = studyList*.subjects.flatten()
295
296	showSubjectFields = []
297	subjectFields.each { subjectField ->
298	for( subject in allSubjects )
299	{
300	// If the field is filled for this subject, we have to
301	// show the field and should not check any other
302	// subjects (hence the break)
303	if( subject.fieldExists( subjectField.name ) && subject.getFieldValue( subjectField.name ) ) {
304	showSubjectFields << subjectField;
305	break;
306	}
307	}
308	}
309	%>
310
311	<g:each in="${showSubjectFields}" var="field">
312	<th>${field}</th>
313	</g:each>
314
315	</tr>
316	</thead>
317
318	<g:set var="i" value="${1}" />
319
320	<g:each in="${studyList}" var="studyInstance">
321	<%
322	// Sort subjects by name
323	subjects = studyInstance.subjects;
324	sortedSubjects = subjects.sort( { a, b -> a.name <=> b.name } as Comparator )
325	%>
326
327	<g:each in="${sortedSubjects}" var="subject" status="j">
328	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
329	<g:if test="${multipleStudies && j==0}">
330	<td class="studytitle" rowspan="${sortedSubjects.size()}">
331	${studyInstance.title}
332	</td>
333	</g:if>
334	<g:each in="${subject.giveDomainFields()}" var="field">
335	<td>${subject.getFieldValue(field.name)}</td>
336	</g:each>
337
338	<g:each in="${showSubjectFields}" var="field">
339	<td>
340	<g:if test="${subject.fieldExists(field.name)}">
341	${subject.getFieldValue(field.name)}
342	</g:if>
343	<g:else>
344	N/A
345	</g:else>
346	</td>
347	</g:each>
348
349	</tr>
350	<g:set var="i" value="${i + 1}" />
351	</g:each>
352	</g:each>
353	</table>
354	</g:else>
355	</div>
356
357	<div id="events">
358	<g:if test="${studyList.events.flatten().size()==0 && studyInstance.samplingEvents.flatten().size()==0 }">
359	No events in these studies
360	</g:if>
361	<g:else>
362	<g:each in="${studyList}" var="study" status="i">
363	<div style="margin: 10px; ">
364	<div class="eventtitles" id="eventtitles-${i}"></div>
365	<div class="eventstimeline" id="eventstimeline-${i}"></div>
366	</div>
367	</g:each>
368	<noscript>
369	<table>
370	<thead>
371	<tr>
372	<g:if test="${multipleStudies}">
373	<th></th>
374	</g:if>
375	<th>Start time</th>
376	<th>Duration</th>
377	<th>Type</th>
378	<th>Sampling event</th>
379	<th>Parameters</th>
380	</tr>
381	</thead>
382
383	<g:set var="i" value="${1}" />
384
385	<g:each in="${studyList}" var="studyInstance">
386	<%
387	// Sort events by starttime and duration
388	events = studyInstance.events + studyInstance.samplingEvents;
389	sortedEvents = events.sort( { a, b ->
390	a.startTime == b.startTime ?
391	a.getDuration().toMilliseconds() <=> b.getDuration().toMilliseconds() :
392	a.startTime <=> b.startTime
393	} as Comparator )
394	%>
395
396	<g:each in="${sortedEvents}" var="event" status="j">
397	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
398	<g:if test="${multipleStudies && j==0}">
399	<td class="studytitle" rowspan="${sortedEvents.size()}">
400	${studyInstance.title}
401	</td>
402	</g:if>
403	<td>${event.getPrettyDuration(studyInstance.startDate,event.startTime)}</td>
404	<td>${event.getPrettyDuration()}</td>
405	<td>${event.template.name}</td>
406	<td>
407	<g:if test="${event instanceof dbnp.studycapturing.SamplingEvent}">
408	<g:checkBox name="samplingEvent" disabled="${true}" value="${true}"/>
409	</g:if>
410	<g:else>
411	<g:checkBox name="event" disabled="${true}" value="${false}" />
412	</g:else>
413	</td>
414	<td>
415	<g:set var="fieldCounter" value="${1}" />
416	<g:each in="${event.giveTemplateFields()}" var="field">
417	<g:if test="${event.getFieldValue(field.name)}">
418	<g:if test="${fieldCounter > 1}">, </g:if>
419	${field.name} = ${event.getFieldValue( field.name )}
420	<g:set var="fieldCounter" value="${fieldCounter + 1}" />
421	</g:if>
422	</g:each>
423	</td>
424	</tr>
425
426	<g:set var="i" value="${i + 1}" />
427	</g:each>
428	</g:each>
429	</table>
430
431	</noscript>
432
433	</g:else>
434	</div>
435
436	<div id="event-group">
437	<g:if test="${studyList*.eventGroups.flatten().size()==0}">
438	No event groups in this study
439	</g:if>
440	<g:else>
441	<%
442	// Determine a union of the event templates for all different
443	// eventgroups in all studies, in order to show a proper list.
444	// We want every field to appear just once,
445	// so the list is filtered for unique values
446	groupTemplates = studyList*.giveAllEventTemplates().flatten().unique()
447	subjectFields = subjectTemplates*.fields.flatten().unique()
448	%>
449	<table>
450	<thead>
451	<tr>
452	<g:if test="${multipleStudies}">
453	<th></th>
454	</g:if>
455	<th>Name</th>
456	<th colspan="${groupTemplates.size()}">Events</th>
457	<th>Subjects</th>
458	</tr>
459	<tr>
460	<g:if test="${multipleStudies}">
461	<th></th>
462	</g:if>
463	<th></th>
464	<g:each in="${groupTemplates}" var="eventTemplate">
465	<th>${eventTemplate.name}</th>
466	</g:each>
467	<th></th>
468	</tr>
469	</thead>
470
471	<g:set var="i" value="${1}" />
472
473	<g:each in="${studyList}" var="studyInstance">
474
475	<g:each in="${studyInstance.eventGroups}" var="eventGroup" status="j">
476	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
477	<g:if test="${multipleStudies && j==0}">
478	<td class="studytitle" rowspan="${studyInstance.eventGroups.size()}">
479	${studyInstance.title}
480	</td>
481	</g:if>
482	<td>${eventGroup.name}</td>
483
484	<g:each in="${groupTemplates}" var="currentEventTemplate">
485	<td>
486	<g:each in="${eventGroup.events}" var="event">
487	<g:if test="${event.template.name==currentEventTemplate.name}">
488
489	<g:set var="fieldCounter" value="${1}" />
490	<g:each in="${event.giveTemplateFields()}" var="field">
491	<g:if test="${event.getFieldValue(field.name)}">
492	<g:if test="${fieldCounter > 1}">, </g:if>
493	${field.name} = ${event.getFieldValue( field.name )}
494	<g:set var="fieldCounter" value="${fieldCounter + 1}" />
495	</g:if>
496	</g:each>
497	</g:if>
498	</g:each>
499	</td>
500	</g:each>
501	<td>
502	<% sortedGroupSubjects = eventGroup.subjects.sort( { a, b -> a.name <=> b.name } as Comparator ) %>
503	${sortedGroupSubjects.name.join( ', ' )}
504	</td>
505	</tr>
506
507	<g:set var="i" value="${i + 1}" />
508	</g:each>
509
510	</g:each>
511
512	</table>
513	</g:else>
514	</div>
515
516	<div id="assays">
517	<g:if test="${studyList*.assays.flatten().size()==0}">
518	No assays in these studies
519	</g:if>
520	<g:else>
521	<table>
522	<thead>
523	<tr>
524	<g:if test="${multipleStudies}">
525	<th></th>
526	</g:if>
527	<th width="100">Assay Name</th>
528	<th width="100">Module</th>
529	<th>Type</th>
530	<th width="150">Platform</th>
531	<th>Url</th>
532	<th>Samples</th>
533	</tr>
534	</thead>
535	<g:set var="i" value="${1}" />
536
537	<g:each in="${studyList}" var="studyInstance">
538	<g:each in="${studyInstance.assays}" var="assay" status="j">
539	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
540	<g:if test="${multipleStudies && j==0}">
541	<td class="studytitle" rowspan="${studyInstance.assays.size()}">
542	${studyInstance.title}
543	</td>
544	</g:if>
545	<td>${assay.name}</td>
546	<td>${assay.module.name}</td>
547	<td>${assay.module.type}</td>
548	<td>${assay.module.platform}</td>
549	<td>${assay.module.url}</td>
550	<td>
551	<% sortedAssaySamples = assay.samples.sort( { a, b -> a.name <=> b.name } as Comparator ) %>
552	${sortedAssaySamples.name.join( ', ' )}
553	</td>
554	</tr>
555	<g:set var="i" value="${i + 1}" />
556
557	</g:each>
558	</g:each>
559	</table>
560	</g:else>
561	</div>
562
563	<div id="persons">
564	<%
565	// Determine a list of all persons
566	allPersons = studyList.persons.person.flatten().unique()
567	%>
568	<g:if test="${allPersons.size()==0}">
569	No persons involved in these studies
570	</g:if>
571	<g:else>
572	<table>
573	<tr>
574	<thead>
575	<th>Name</th>
576	<th>Affiliations</th>
577	<th>Phone</th>
578	<th>Email</th>
579	<g:if test="${multipleStudies}">
580	<g:each in="${studyList}" var="studyInstance">
581	<th>${studyInstance.title}</th>
582	</g:each>
583	</g:if>
584	<g:else>
585	<th>Role</th>
586	</g:else>
587	</thead>
588	</tr>
589	<g:each in="${allPersons}" var="person" status="i">
590	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
591	<td>${person.firstName} ${person.prefix} ${person.lastName}</td>
592	<td>
593	${person.affiliations.join(', ')}
594	</td>
595	<td>${person.phone}</td>
596	<td>${person.email}</td>
597	<g:each in="${studyList}" var="studyInstance">
598	<%
599	studyperson = studyInstance.persons.find { it.person == person }
600	%>
601	<td>
602	<g:if test="${studyperson}">
603	${studyperson.role.name}
604	</g:if>
605	</td>
606	</g:each>
607
608	</tr>
609	</g:each>
610	</table>
611	</g:else>
612	</div>
613
614	<div id="publications">
615	<%
616	// Determine a list of all persons
617	allPublications = studyList*.publications.flatten().unique()
618	%>
619	<g:if test="${allPublications.size()==0}">
620	No publications attached to these studies
621	</g:if>
622	<g:else>
623	<table>
624	<tr>
625	<thead>
626	<th>Title</th>
627	<th>Authors</th>
628	<th>Comments</th>
629
630	<g:if test="${multipleStudies}">
631	<g:each in="${studyList}" var="studyInstance">
632	<th>${studyInstance.title}</th>
633	</g:each>
634	</g:if>
635	</thead>
636	</tr>
637	<g:each in="${allPublications}" var="publication" status="i">
638	<tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
639	<td>${publication.title}</td>
640	<td>
641	${publication.authorsList}
642	</td>
643	<td>${publication.comments}</td>
644	<g:if test="${multipleStudies}">
645	<g:each in="${studyList}" var="studyInstance">
646	<td>
647	<g:if test="${publication in studyInstance.publications}">
648	x
649	</g:if>
650	</td>
651	</g:each>
652	</g:if>
653	</tr>
654	</g:each>
655	</table>
656	</g:else>
657	</div>
658
659	</div>
660	</div>
661	<br>
662	<div class="buttons">
663	<g:form>
664	<g:if test="${studyList.size() == 1}">
665	<g:set var="studyInstance" value="${studyList[0]}" />
666	<g:hiddenField name="id" value="${studyInstance?.id}" />
667	<span class="button"><g:actionSubmit class="edit" action="edit" value="${message(code: 'default.button.edit.label', default: 'Edit')}" /></span>
668	<span class="button"><g:actionSubmit class="delete" action="delete" value="${message(code: 'default.button.delete.label', default: 'Delete')}" onclick="return confirm('${message(code: 'default.button.delete.confirm.message', default: 'Are you sure?')}');" /></span>
669	</g:if>
670	<span class="button"><g:link class="backToList" action="list">Back to list</g:link></span>
671	</g:form>
672	</div>
673
674	</div>
675	</body>
676	</html>

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