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source: trunk/grails-app/conf/BootStrap.groovy @ 386

Last change on this file since 386 was 386, checked in by roberth, 13 years ago
Updated the template entities to be able to return domain fields, template fields and both. Rolled back the change of Kees in the Event object, so the startTime and endTime fields returned. Also updated the studies list with a new layout.
Property svn:keywords set to `Author Rev Date`
File size: 36.8 KB

Line
1	import dbnp.studycapturing.*
2
3	import dbnp.data.Ontology
4	import dbnp.data.Term
5
6	/**
7	* Application Bootstrapper
8	* @Author Jeroen Wesbeek
9	* @Since 20091021
10	*
11	* Revision information:
12	* $Rev: 386 $
13	* $Author: roberth $
14	* $Date: 2010-04-27 13:53:06 +0000 (di, 27 apr 2010) $
15	*/
16	class BootStrap {
17	def init = {servletContext ->
18	// define timezone
19	System.setProperty('user.timezone', 'CET')
20
21	// we could also check if we are in development by GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT
22	if (Study.count() == 0) {
23	println ".development bootstrapping...";
24
25	// add NCBI species ontology
26	println ".adding NCBI species ontology"
27	def speciesOntology = new Ontology(
28	name: 'NCBI organismal classification',
29	description: 'A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases.',
30	url: 'http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/',
31	versionNumber: '1.2',
32	ncboId: '1132',
33	ncboVersionedId: '38802'
34	).with { if (!validate()) { errors.each { println it} } else save()}
35
36	// add TERMS
37	println ".adding mouse term"
38	def mouseTerm = new Term(
39	name: 'Mus musculus',
40	ontology: speciesOntology,
41	accession: '10090'
42	).with { if (!validate()) { errors.each { println it} } else save()}
43	println ".adding human term"
44	def humanTerm = new Term(
45	name: 'Homo sapiens',
46	ontology: speciesOntology,
47	accession: '9606'
48	).with { if (!validate()) { errors.each { println it} } else save()}
49
50	def bloodTerm = new Term(
51	name: 'Portion of blood',
52	ontology: speciesOntology,
53	accession: '9670'
54	).with { if (!validate()) { errors.each { println it} } else save()}
55
56
57	// Create a few persons, roles and Affiliations
58	println ".adding persons, roles and affiliations"
59	def affiliation1 = new PersonAffiliation(
60	name: "Science Institute NYC"
61	).save();
62	def affiliation2 = new PersonAffiliation(
63	name: "InfoStats GmbH, Hamburg"
64	).save();
65	def role1 = new PersonRole(
66	name: "Principal Investigator"
67	).save();
68	def role2 = new PersonRole(
69	name: "Statician"
70	).save();
71
72	// Create 30 roles to test pagination
73	def roleCounter = 1;
74	30.times { new PersonRole( name: "Rol #${roleCounter++}" ).save() }
75
76	// Create persons
77	def person1 = new Person(
78	lastName: "Scientist",
79	firstName: "John",
80	gender: "Male",
81	initials: "J.R.",
82	email: "john@scienceinstitute.com",
83	phone: "1-555-3049",
84	address: "First street 2,NYC"
85	)
86	.addToAffiliations( affiliation1 )
87	.addToAffiliations( affiliation2 )
88	.save();
89
90	def person2 = new Person(
91	lastName: "Statician",
92	firstName: "Jane",
93	gender: "Female",
94	initials: "W.J.",
95	email: "jane@statisticalcompany.de",
96	phone: "49-555-8291",
97	address: "Dritten strasse 38, Hamburg, Germany"
98	)
99	.addToAffiliations( affiliation2 )
100	.save();
101
102	// Create 30 persons to test pagination
103	def personCounter = 1;
104	30.times { new Person( firstName: "Person #${personCounter}", lastName: "Testperson", email: "email${personCounter++}@testdomain.com" ).save() }
105
106	/* COMMENTED OUT BECAUSE IT BREAKS EVERYTHING AFTER REFACTORING THE DATAMODEL
107
108	// ontologies
109	def speciesOntology = new Ontology(
110	name: 'NCBI Taxonomy',
111	shortName: 'Taxon',
112	url: 'http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy'
113	).with { if (!validate()) { errors.each { println it} } else save()}
114
115	def humanBodyOntology = new Ontology(
116	name: 'Foundational Model of Anatomy',
117	shortName: 'HumanBody',
118	url: 'http://bioportal.bioontology.org/ontologies/39966'
119	).with { if (!validate()) { errors.each { println it} } else save()}
120
121	def nciOntology = new Ontology(
122	name: 'NCI Thesaurus',
123	shortName: 'NCI',
124	url: 'http://bioportal.bioontology.org/ontologies/42331'
125	).with { if (!validate()) { errors.each { println it} } else save()}
126
127	// terms
128	def mouseTerm = new Term(
129	name: 'Mus musculus',
130	ontology: speciesOntology,
131	accession: '10090'
132	).with { if (!validate()) { errors.each { println it} } else save()}
133	def humanTerm = new Term(
134	name: 'Homo sapiens',
135	ontology: speciesOntology,
136	accession: '9606'
137	).with { if (!validate()) { errors.each { println it} } else save()}
138	def arabTerm = new Term(
139	name: 'Arabidopsis thaliana',
140	ontology: speciesOntology,
141	accession: '3702'
142	).with { if (!validate()) { errors.each { println it} } else save()}
143
144
145	def c57bl6Term = new Term(
146	name: 'C57BL/6 Mouse',
147	ontology: nciOntology,
148	accession: 'C14424'
149	).with { if (!validate()) { errors.each { println it} } else save()}
150
151	def madmaxOntology = new Ontology(
152	name: 'Madmax ontology',
153	shortName: 'MDMX',
154	url: 'madmax.bioinformatics.nl'
155	).with { if (!validate()) { errors.each { println it} } else save()}
156
157	def treatmentTerm = new Term(
158	name: 'ExperimentalProtocol',
159	ontology: madmaxOntology,
160	accession: 'P-MDMXGE-264'
161	).with { if (!validate()) { errors.each { println it} } else save()}
162
163	def dietProtocol = new Protocol(
164	name: 'Diet treatment Protocol NuGO PPS3 leptin module',
165	reference: treatmentTerm
166	).with { if (!validate()) { errors.each { println it} } else save()}
167
168	def boostProtocol = new Protocol(
169	name: 'Boost treatment Protocol NuGO PPS3 leptin module',
170	reference: treatmentTerm
171	).with { if (!validate()) { errors.each { println it} } else save()}
172
173	def fastingProtocol = new Protocol(
174	name: 'Fasting',
175	reference: treatmentTerm
176	).with { if (!validate()) { errors.each { println it} } else save()}
177
178
179	// ParameterStringListItems
180	def oil10= new ParameterStringListItem(
181	name: '10% fat (palm oil)'
182	).with { if (!validate()) { errors.each { println it} } else save()}
183	def oil45= new ParameterStringListItem(
184	name: '45% fat (palm oil)'
185	).with { if (!validate()) { errors.each { println it} } else save()}
186	def vehicle= new ParameterStringListItem(
187	name: 'Vehicle'
188	).with { if (!validate()) { errors.each { println it} } else save()}
189	def leptin= new ParameterStringListItem(
190	name: 'Leptin'
191	).with { if (!validate()) { errors.each { println it} } else save()}
192
193
194	dietProtocol
195	.addToParameters(new ProtocolParameter(
196	name: 'Diet',
197	type: ProtocolParameterType.STRINGLIST,
198	listEntries: [oil10,oil45]))
199	.save()
200
201	boostProtocol
202	.addToParameters(new ProtocolParameter(
203	name: 'Compound',
204	type: ProtocolParameterType.STRINGLIST,
205	listEntries: [vehicle,leptin]))
206	.save()
207
208	fastingProtocol
209	.addToParameters(new ProtocolParameter(
210	name: 'Fasting period',
211	type: ProtocolParameterType.STRING))
212	.save()
213
214
215	// sampling event protocols
216
217	def liverSamplingProtocol = new Protocol(
218	name: 'Liver sampling'
219	).with { if (!validate()) { errors.each { println it} } else save()}
220
221	liverSamplingProtocol
222	.addToParameters(new ProtocolParameter(
223	name: 'Sample weight',
224	unit: 'mg',
225	type: ProtocolParameterType.FLOAT))
226	.save()
227
228	def bloodSamplingProtocol = new Protocol(
229	name: 'Blood sampling'
230	).with { if (!validate()) { errors.each { println it} } else save()}
231
232	bloodSamplingProtocol
233	.addToParameters(new ProtocolParameter(
234	name: 'Sample volume',
235	unit: 'ml',
236	type: ProtocolParameterType.FLOAT))
237	.save()
238	*/
239	// create system user
240
241	/*def systemUser = userService.createUser(InstanceGenerator.user(
242	username: 'system',
243	pass: 'system',
244	passConfirm: 'system',
245	enabled: true
246	))*/
247
248
249	def genderField = new TemplateField(
250	name: 'Gender',type: TemplateFieldType.STRINGLIST,
251	listEntries: [new TemplateFieldListItem(name:'Male'),new TemplateFieldListItem(name: 'Female')])
252	.with { if (!validate()) { errors.each { println it} } else save()}
253
254	def ageField = new TemplateField(
255	name: 'Age (years)',type: TemplateFieldType.INTEGER,unit: 'years')
256	.with { if (!validate()) { errors.each { println it} } else save()}
257
258	def genotypeField = new TemplateField(
259	name: 'Genotype', type: TemplateFieldType.ONTOLOGYTERM)
260	.with { if (!validate()) { errors.each { println it} } else save()}
261
262	def genotypeTypeField = new TemplateField(
263	name: 'Genotype type',type: TemplateFieldType.STRINGLIST,
264	listEntries: [new TemplateFieldListItem(name:'wildtype'),
265	new TemplateFieldListItem(name:'transgenic'),
266	new TemplateFieldListItem(name:'knock-out'),
267	new TemplateFieldListItem(name:'knock-in')])
268	.with { if (!validate()) { errors.each { println it} } else save()}
269
270
271	// Nutritional study template
272
273	println ".adding academic study template..."
274	def studyTemplate = new Template(
275	name: 'Academic study', entity: dbnp.studycapturing.Study)
276	.addToFields(new TemplateField(name: 'Description',type: TemplateFieldType.TEXT))
277	.addToFields(new TemplateField(name: 'Study code',type: TemplateFieldType.STRING))
278	.addToFields(new TemplateField(name: 'Objectives',type: TemplateFieldType.TEXT))
279	.addToFields(new TemplateField(name: 'Consortium',type: TemplateFieldType.STRING))
280	.addToFields(new TemplateField(name: 'Cohort name',type: TemplateFieldType.STRING))
281	.addToFields(new TemplateField(name: 'Time zone',type: TemplateFieldType.STRING))
282	.addToFields(new TemplateField(name: 'Responsible scientist',type: TemplateFieldType.STRING))
283	.addToFields(new TemplateField(name: 'Lab id',type: TemplateFieldType.STRING))
284	.addToFields(new TemplateField(name: 'Institute',type: TemplateFieldType.STRING))
285	.with { if (!validate()) { errors.each { println it} } else save()}
286
287	// Mouse template
288	println ".adding mouse subject template..."
289	def mouseTemplate = new Template(
290	name: 'Mouse', entity: dbnp.studycapturing.Subject)
291	.addToFields(new TemplateField(
292	name: 'Strain', type: TemplateFieldType.ONTOLOGYTERM))
293	.addToFields(genotypeField)
294	.addToFields(genotypeTypeField)
295	.addToFields(genderField)
296	.addToFields(new TemplateField(
297	name: 'Age (weeks)', type: TemplateFieldType.INTEGER, unit: 'weeks'))
298	.addToFields(new TemplateField(
299	name: 'Age type',type: TemplateFieldType.STRINGLIST,
300	listEntries: [new TemplateFieldListItem(name:'postnatal'),new TemplateFieldListItem(name:'embryonal')]))
301	.addToFields(new TemplateField(
302	name: 'Cage',type: TemplateFieldType.STRING))
303	.addToFields(new TemplateField(
304	name: '#Mice in cage',type: TemplateFieldType.INTEGER))
305	.addToFields(new TemplateField(
306	name: 'Litter size',type: TemplateFieldType.INTEGER))
307	.addToFields(new TemplateField(
308	name: 'Weight (g)', type: TemplateFieldType.DOUBLE, unit: 'gram'))
309	.with { if (!validate()) { errors.each { println it} } else save()}
310
311	// Human template
312	println ".adding human subject template..."
313	def humanTemplate = new Template(
314	name: 'Human', entity: dbnp.studycapturing.Subject)
315	.addToFields(genderField)
316	.addToFields(ageField)
317	.addToFields(new TemplateField(
318	name: 'DOB',type: TemplateFieldType.DATE))
319	.addToFields(new TemplateField(
320	name: 'Height',type: TemplateFieldType.DOUBLE, unit: 'm'))
321	.addToFields(new TemplateField(
322	name: 'Weight (kg)',type: TemplateFieldType.DOUBLE, unit: 'kg'))
323	.addToFields(new TemplateField(
324	name: 'BMI',type: TemplateFieldType.DOUBLE, unit: 'kg/m2'))
325	.addToFields(new TemplateField(
326	name: 'Race',type: TemplateFieldType.STRING))
327	.addToFields(new TemplateField(
328	name: 'Waist circumference',type: TemplateFieldType.FLOAT, unit: 'cm'))
329	.addToFields(new TemplateField(
330	name: 'Hip circumference',type: TemplateFieldType.FLOAT, unit: 'cm'))
331	.addToFields(new TemplateField(
332	name: 'Systolic blood pressure',type: TemplateFieldType.FLOAT, unit: 'mmHg'))
333	.addToFields(new TemplateField(
334	name: 'Diastolic blood pressure',type: TemplateFieldType.FLOAT, unit: 'mmHg'))
335	.addToFields(new TemplateField(
336	name: 'Heart rate',type: TemplateFieldType.FLOAT, unit: 'beats/min'))
337	.addToFields(new TemplateField(
338	name: 'Run-in-food',type: TemplateFieldType.TEXT))
339	.with { if (!validate()) { errors.each { println it} } else save()}
340
341
342	def sampleDescriptionField = new TemplateField(
343	name: 'Description',type: TemplateFieldType.TEXT)
344	.with { if (!validate()) { errors.each { println it} } else save()}
345	def sampleTypeField = new TemplateField(
346	name: 'SampleType',type: TemplateFieldType.STRING)
347	.with { if (!validate()) { errors.each { println it} } else save()}
348	def sampleProtocolField = new TemplateField(
349	name: 'SampleProtocol',type: TemplateFieldType.STRING)
350	.with { if (!validate()) { errors.each { println it} } else save()}
351	def sampleVialTextField = new TemplateField(
352	name: 'Text on vial',type: TemplateFieldType.STRING)
353	.with { if (!validate()) { errors.each { println it} } else save()}
354
355	// Human sample template
356	println ".adding human sample template..."
357	def humanSampleTemplate = new Template(
358	name: 'Human tissue sample', entity: dbnp.studycapturing.Sample)
359	.addToFields(sampleDescriptionField)
360	.addToFields(sampleTypeField)
361	.addToFields(sampleProtocolField)
362	.addToFields(sampleVialTextField)
363	.with { if (!validate()) { errors.each { println it} } else save()}
364
365	//Plant template
366	println ".adding plant template..."
367	def plantTemplate = new Template(
368	name: 'Plant template', entity: dbnp.studycapturing.Subject)
369	.addToFields(new TemplateField(
370	name: 'Variety', type: TemplateFieldType.STRING))
371	.addToFields(new TemplateField(
372	name: 'Ecotype', type: TemplateFieldType.STRING))
373	.addToFields(genotypeField)
374	.addToFields(genotypeTypeField)
375	.addToFields(new TemplateField(
376	name: 'Growth location', type: TemplateFieldType.STRINGLIST,
377	listEntries: [new TemplateFieldListItem(name:'Greenhouse'),new TemplateFieldListItem(name: 'Field')]))
378	.addToFields(new TemplateField(
379	name: 'Room', type: TemplateFieldType.STRING,
380	comment: 'Chamber number in case of Greenhouse'))
381	.addToFields(new TemplateField(
382	name: 'Position X', type: TemplateFieldType.FLOAT))
383	.addToFields(new TemplateField(
384	name: 'Position Y', type: TemplateFieldType.FLOAT))
385	.addToFields(new TemplateField(
386	name: 'Block', type: TemplateFieldType.STRING))
387	.addToFields(new TemplateField(
388	name: 'Temperature at day', type: TemplateFieldType.FLOAT))
389	.addToFields(new TemplateField(
390	name: 'Temperature at night', type: TemplateFieldType.FLOAT))
391	.addToFields(new TemplateField(
392	name: 'Photo period', type: TemplateFieldType.STRING))
393	.addToFields(new TemplateField(
394	name: 'Light intensity', type: TemplateFieldType.STRING))
395	.addToFields(new TemplateField(
396	name: 'Start date', type: TemplateFieldType.DATE))
397	.addToFields(new TemplateField(
398	name: 'Harvest date', type: TemplateFieldType.DATE))
399	.addToFields(new TemplateField(
400	name: 'Growth type', type: TemplateFieldType.STRINGLIST,
401	listEntries: [new TemplateFieldListItem(name:'Standard'),new TemplateFieldListItem(name: 'Experimental')]))
402	.addToFields(new TemplateField(
403	name: 'Growth protocol', type: TemplateFieldType.TEXT))
404	.addToFields(new TemplateField(
405	name: 'Harvest delay', type: TemplateFieldType.TEXT))
406	.with { if (!validate()) { errors.each { println it} } else save()}
407
408	println ".adding plant sample template..."
409	def plantSampleTemplate = new Template(
410	name: 'Plant sample', entity: dbnp.studycapturing.Sample)
411	.addToFields(sampleDescriptionField)
412	.addToFields(sampleTypeField)
413	.addToFields(sampleProtocolField)
414	.addToFields(sampleVialTextField)
415	.with { if (!validate()) { errors.each { println it} } else save()}
416
417
418	// Event templates
419	println ".adding event templates..."
420
421	def startDateField = new TemplateField(
422	name: 'Start time', type: TemplateFieldType.DATE
423	).with { if (!validate()) { errors.each { println it} } else save()}
424
425	def endDateField = new TemplateField(
426	name: 'End time', type: TemplateFieldType.DATE
427	).with { if (!validate()) { errors.each { println it} } else save()}
428
429	Event.systemFields = [startDateField,endDateField]
430
431	def dietTreatmentTemplate = new Template(
432	name: 'Diet treatment', entity: dbnp.studycapturing.Event)
433	.addToFields(sampleDescriptionField)
434	.addToFields(new TemplateField(
435	name: 'Diet', type: TemplateFieldType.STRINGLIST,
436	listEntries: [new TemplateFieldListItem(name:'10% fat (palm oil)'),new TemplateFieldListItem(name: '45% fat (palm oil)')]))
437	.with { if (!validate()) { errors.each { println it} } else save()}
438
439	def boostTreatmentTemplate = new Template(
440	name: 'Boost treatment', entity: dbnp.studycapturing.Event)
441	.addToFields(sampleDescriptionField)
442	.addToFields(new TemplateField(
443	name: 'Compound', type: TemplateFieldType.STRING,
444	listEntries: [new TemplateFieldListItem(name:'Vehicle'),new TemplateFieldListItem(name: 'Leptin')]))
445	.with { if (!validate()) { errors.each { println it} } else save()}
446
447	def bloodSamplingEventTemplate = new Template(
448	name: 'Blood extraction', entity: dbnp.studycapturing.Event)
449	.addToFields(sampleDescriptionField)
450	.addToFields(new TemplateField(
451	name: 'Sample volume', type: TemplateFieldType.FLOAT))
452	.with { if (!validate()) { errors.each { println it} } else save()}
453
454	def fastingTreatmentTemplate = new Template(
455	name: 'Fasting treatment', entity: dbnp.studycapturing.Event)
456	.addToFields(sampleDescriptionField)
457	.addToFields(new TemplateField(
458	name: 'Fasting period', type: TemplateFieldType.STRING))
459	.with { if (!validate()) { errors.each { println it} } else save()}
460
461	/*
462	//events
463	def eventDiet = new EventDescription(
464	name: 'Diet treatment',
465	description: 'Diet treatment (fat percentage)',
466	classification: treatmentTerm,
467	protocol: dietProtocol,
468	isSamplingEvent: false
469	).with { if (!validate()) { errors.each { println it} } else save()}
470
471	def eventBoost = new EventDescription(
472	name: 'Boost treatment',
473	description: 'Boost treatment (leptin or vehicle)',
474	classification: treatmentTerm,
475	protocol: boostProtocol,
476	isSamplingEvent: false
477	).with { if (!validate()) { errors.each { println it} } else save()}
478
479	def samplingEvent = new EventDescription(
480	name: 'Liver extraction',
481	description: 'Liver sampling for transcriptomics arrays',
482	protocol: liverSamplingProtocol,
483	isSamplingEvent: true
484	).with { if (!validate()) { errors.each { println it} } else save()}
485
486	def bloodSamplingEventDescription = new EventDescription(
487	name: 'Blood extraction',
488	description: 'Blood extraction targeted at lipid assays',
489	protocol: bloodSamplingProtocol,
490	isSamplingEvent: true
491	).with { if (!validate()) { errors.each { println it} } else save()}
492
493
494	def fastingTreatment = new EventDescription(
495	name: 'Fasting treatment',
496	description: 'Fasting Protocol NuGO PPSH',
497	protocol: fastingProtocol,
498	isSamplingEvent: false
499	).with { if (!validate()) { errors.each { println it} } else save()}
500
501	println('Adding PPS3 study...')
502	*/
503	// studies
504	println ".adding NuGO PPS3 leptin example study..."
505	def exampleStudy = new Study(
506	template: studyTemplate,
507	title:"NuGO PPS3 mouse study leptin module",
508	code:"PPS3_leptin_module",
509	researchQuestion:"Leptin etc.",
510	ecCode:"2007117.c",
511	startDate: Date.parse('yyyy-MM-dd','2007-12-11')
512	)
513	.with { if (!validate()) { errors.each { println it} } else save()}
514
515	exampleStudy.setFieldValue( 'Description', "C57Bl/6 mice were fed a high fat (45 en%) or low fat (10 en%) diet after a four week run-in on low fat diet. After 1 week 10 mice that received a low fat diet were given an IP leptin challenge and 10 mice of the low-fat group received placebo injections. The same procedure was performed with mice that were fed the high-fat diet. After 4 weeks the procedure was repeated. In total 80 mice were culled." )
516	exampleStudy.save()
517
518
519	/* Test output of fields things */
520	println "-----------------------------"
521	print "Diet domain fields: "
522	println exampleStudy.giveDomainFields().join( ", " )
523
524	print "Diet template fields: "
525	println exampleStudy.giveTemplateFields().join( ", " )
526
527	print "Diet all fields: "
528	println exampleStudy.giveFields().join( ", " )
529
530	println "-----------------------------"
531
532	println ".adding NuGO PPSH example study..."
533	def exampleHumanStudy = new Study(
534	template: studyTemplate,
535	title:"Human example template",
536	code:"Human example code",
537	researchQuestion:"Leptin etc.",
538	ecCode:"2007117.c",
539	startDate: Date.parse('yyyy-MM-dd','2007-12-11')
540	)
541	.with { if (!validate()) { errors.each { println it} } else save()}
542
543	exampleHumanStudy.setFieldValue( 'Description', "C57Bl/6 mice were fed a high fat (45 en%) or low fat (10 en%) diet after a four week run-in on low fat diet. After 1 week 10 mice that received a low fat diet were given an IP leptin challenge and 10 mice of the low-fat group received placebo injections. The same procedure was performed with mice that were fed the high-fat diet. After 4 weeks the procedure was repeated. In total 80 mice were culled." )
544	exampleHumanStudy.save()
545
546	def evLF = new Event(
547	template: dietTreatmentTemplate,
548	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
549	endTime: Date.parse('yyyy-MM-dd','2008-01-14')
550	)
551	.with { if (!validate()) { errors.each { println it} } else save()}
552
553	evLF.setFieldValue( 'Diet','10% fat (palm oil)' )
554	evLF.save(flush:true)
555
556	println "Saved diet treatment"
557	// TODO: find out why Diet is not set and Compound is
558
559	def evHF = new Event(
560	template: dietTreatmentTemplate,
561	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
562	endTime: Date.parse('yyyy-MM-dd','2008-01-14')
563	)
564	.setFieldValue( 'Diet','45% fat (palm oil)' )
565	.with { if (!validate()) { errors.each { println it} } else save()}
566
567	def evBV = new Event(
568	template: boostTreatmentTemplate,
569	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
570	endTime: Date.parse('yyyy-MM-dd','2008-01-14')
571	)
572	.setFieldValue( 'Compound','Vehicle' )
573	.with { if (!validate()) { errors.each { println it} } else save()}
574
575	def evBL = new Event(
576	template: boostTreatmentTemplate,
577	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
578	endTime: Date.parse('yyyy-MM-dd','2008-01-14')
579	)
580	.setFieldValue( 'Compound','Leptin' )
581	.with { if (!validate()) { errors.each { println it} } else save()}
582
583	/*
584	def evLF4 = new Event(
585	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
586	endTime: Date.parse('yyyy-MM-dd','2008-02-04'),
587	eventDescription: eventDiet,
588	parameterStringValues: ['Diet':'10% fat (palm oil)']
589	).with { if (!validate()) { errors.each { println it} } else save()}
590
591	def evHF4 = new Event(
592	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
593	endTime: Date.parse('yyyy-MM-dd','2008-02-04'),
594	eventDescription: eventDiet,
595	parameterStringValues: ['Diet':'45% fat (palm oil)']
596	).with { if (!validate()) { errors.each { println it} } else save()}
597
598	def evBV4 = new Event(
599	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
600	endTime: Date.parse('yyyy-MM-dd','2008-02-04'),
601	eventDescription: eventBoost,
602	parameterStringValues: ['Compound':'Vehicle']
603	).with { if (!validate()) { errors.each { println it} } else save()}
604
605	def evBL4 = new Event(
606	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
607	endTime: Date.parse('yyyy-MM-dd','2008-02-04'),
608	eventDescription: eventBoost,
609	parameterStringValues: ['Compound':'Leptin']
610	).with { if (!validate()) { errors.each { println it} } else save()}
611
612	def evS = new SamplingEvent(
613	startTime: Date.parse('yyyy-MM-dd','2008-01-14'),
614	endTime: Date.parse('yyyy-MM-dd','2008-01-14'),
615	eventDescription: samplingEvent,
616	parameterFloatValues: ['Sample weight':5F]
617	).with { if (!validate()) { errors.each { println it} } else save()}
618
619	def evS4 = new SamplingEvent(
620	startTime: Date.parse('yyyy-MM-dd','2008-02-04'),
621	endTime: Date.parse('yyyy-MM-dd','2008-02-04'),
622	eventDescription: samplingEvent,
623	parameterFloatValues: ['Sample weight':5F]
624	).with { if (!validate()) { errors.each { println it} } else save()}
625	*/
626
627	// Add events to study
628	exampleStudy
629	.addToEvents(evLF)
630	.addToEvents(evHF)
631	.addToEvents(evBV)
632	.addToEvents(evBL)
633	/*
634	.addToEvents(evLF4)
635	.addToEvents(evHF4)
636	.addToEvents(evBV4)
637	.addToEvents(evBL4)
638	.addToSamplingEvents(evS)
639	.addToSamplingEvents(evS4)
640	*/
641	.save()
642
643	def LFBV1 = new EventGroup(name:"10% fat + vehicle for 1 week")
644	.addToEvents(evLF)
645	.addToEvents(evBV)
646	.with { if (!validate()) { errors.each { println it} } else save()}
647
648	def LFBL1 = new EventGroup(name:"10% fat + leptin for 1 week")
649	.addToEvents(evLF)
650	.addToEvents(evBL)
651	.with { if (!validate()) { errors.each { println it} } else save()}
652
653	def HFBV1 = new EventGroup(name:"45% fat + vehicle for 1 week")
654	.addToEvents(evHF)
655	.addToEvents(evBV)
656	.with { if (!validate()) { errors.each { println it} } else save()}
657
658	def HFBL1 = new EventGroup(name:"45% fat + leptin for 1 week")
659	.addToEvents(evHF)
660	.addToEvents(evBL)
661	.with { if (!validate()) { errors.each { println it} } else save()}
662
663	/*
664	def LFBV4 = new EventGroup(name:"10% fat + vehicle for 4 weeks")
665	.addToEvents(evLF4)
666	.addToEvents(evBV4)
667	.with { if (!validate()) { errors.each { println it} } else save()}
668
669	def LFBL4 = new EventGroup(name:"10% fat + leptin for 4 weeks")
670	.addToEvents(evLF4)
671	.addToEvents(evBL4)
672	.with { if (!validate()) { errors.each { println it} } else save()}
673
674	def HFBV4 = new EventGroup(name:"45% fat + vehicle for 4 weeks")
675	.addToEvents(evHF4)
676	.addToEvents(evBV4)
677	.with { if (!validate()) { errors.each { println it} } else save()}
678
679	def HFBL4 = new EventGroup(name:"45% fat + leptin for 4 weeks")
680	.addToEvents(evHF4)
681	.addToEvents(evBL4)
682	.with { if (!validate()) { errors.each { println it} } else save()}
683	*/
684
685	// Add subjects and samples and compose EventGroups
686
687	def x=1
688	12.times {
689	def currentSubject = new Subject(
690	name: "A" + x++,
691	species: mouseTerm,
692	template: mouseTemplate,
693	)
694	.setFieldValue("Gender", "Male")
695	//.setFieldValue("Genotype", c57bl6Term)
696	.setFieldValue("Age (weeks)", 17)
697	.setFieldValue("Cage", "" + (int)(x/2))
698	.with { if (!validate()) { errors.each { println it} } else save(flush:true)}
699
700	exampleStudy.addToSubjects(currentSubject)
701	.with { if (!validate()) { errors.each { println it} } else save()}
702
703	// Add subject to appropriate EventGroup
704	/*
705	if (x > 70) { HFBL4.addToSubjects(currentSubject).save() }
706	else if (x > 60) { HFBV4.addToSubjects(currentSubject).save() }
707	else if (x > 50) { LFBL4.addToSubjects(currentSubject).save() }
708	else if (x > 40) { LFBV4.addToSubjects(currentSubject).save() }
709	else if (x > 30) { HFBL1.addToSubjects(currentSubject).save() }
710	else if (x > 20) { HFBV1.addToSubjects(currentSubject).save() }
711	else if (x > 10) { LFBL1.addToSubjects(currentSubject).save() }
712	else { LFBV1.addToSubjects(currentSubject).save() }
713	*/
714
715	if (x > 9) { HFBL1.addToSubjects(currentSubject).save() }
716	else if (x > 6) { HFBV1.addToSubjects(currentSubject).save() }
717	else if (x > 3) { LFBL1.addToSubjects(currentSubject).save() }
718	else { LFBV1.addToSubjects(currentSubject).save() }
719
720	}
721
722	// Also add some human subjects
723	2.times {
724	def currentSubject = new Subject(
725	name: "H" + x++,
726	species: humanTerm,
727	template: humanTemplate,
728	)
729	.setFieldValue("Gender", "Male")
730	//.setFieldValue("Genotype", c57bl6Term)
731	.setFieldValue("Age (years)", 27)
732	.setFieldValue("Height", 1.5)
733	.with { if (!validate()) { errors.each { println it} } else save(flush:true)}
734
735	exampleStudy.addToSubjects(currentSubject)
736	.with { if (!validate()) { errors.each { println it} } else save()}
737
738	// Add subject to appropriate EventGroup
739	/*
740	if (x > 70) { HFBL4.addToSubjects(currentSubject).save() }
741	else if (x > 60) { HFBV4.addToSubjects(currentSubject).save() }
742	else if (x > 50) { LFBL4.addToSubjects(currentSubject).save() }
743	else if (x > 40) { LFBV4.addToSubjects(currentSubject).save() }
744	else if (x > 30) { HFBL1.addToSubjects(currentSubject).save() }
745	else if (x > 20) { HFBV1.addToSubjects(currentSubject).save() }
746	else if (x > 10) { LFBL1.addToSubjects(currentSubject).save() }
747	else { LFBV1.addToSubjects(currentSubject).save() }
748	*/
749
750	if (x == 0) { HFBL1.addToSubjects(currentSubject).save() }
751	else { LFBV1.addToSubjects(currentSubject).save() }
752
753	}
754
755
756	// Add EventGroups to study
757	exampleStudy
758	.addToEventGroups(LFBV1)
759	.addToEventGroups(LFBL1)
760	.addToEventGroups(HFBV1)
761	.addToEventGroups(HFBL1)
762	//.addToEventGroups(LFBV4)
763	//.addToEventGroups(LFBL4)
764	//.addToEventGroups(HFBV4)
765	//.addToEventGroups(HFBL4)
766
767	// Add persons to study
768	def studyperson1 = new StudyPerson( person: person1, role: role1 ).save();
769	def studyperson2 = new StudyPerson( person: person2, role: role2 ).save();
770
771	exampleStudy
772	.addToPersons( studyperson1 )
773	.addToPersons( studyperson2 )
774	.save()
775
776	println 'Adding PPSH study'
777
778	def humanStudy = new Study(
779	template: studyTemplate,
780	title:"NuGO PPS human study",
781	code:"PPSH",
782	researchQuestion:"How much are fasting plasma and urine metabolite levels affected by prolonged fasting ?",
783	ecCode:"unknown",
784	startDate: Date.parse('yyyy-MM-dd','2009-01-01')
785	).with { if (!validate()) { errors.each { println it} } else save()}
786
787	def fastingEvent = new Event(
788	template: fastingTreatmentTemplate,
789	startTime: Date.parse('yyyy-MM-dd','2008-01-14' ),
790	endTime: Date.parse('yyyy-MM-dd','2008-01-14' )
791	)
792	.setFieldValue( 'Fasting period','8h' )
793	.with { if (!validate()) { errors.each { println it} } else save()}
794
795	def bloodSamplingEvent = new SamplingEvent(
796	template: bloodSamplingEventTemplate,
797	startTime: Date.parse('yyyy-MM-dd','2008-01-14' ),
798	endTime: Date.parse('yyyy-MM-dd','2008-01-14' )
799	)
800	.setFieldValue( 'Sample volume',4.5F )
801	.with { if (!validate()) { errors.each { println it} } else save()}
802
803	def rootGroup = new EventGroup(name: 'Root group');
804	rootGroup.addToEvents fastingEvent
805	rootGroup.addToEvents bloodSamplingEvent
806	rootGroup.save()
807
808	def y = 1
809	11.times {
810	def currentSubject = new Subject(
811	name: "" + y++,
812	species: humanTerm,
813	template: humanTemplate).setFieldValue("Gender", (boolean) (x / 2) ? "Male" : "Female").setFieldValue("DOB", new java.text.SimpleDateFormat("dd-mm-yy").parse("01-02-19" + (10 + (int) (Math.random() * 80)))).setFieldValue("Age (years)", 30).setFieldValue("Height", Math.random() * 2F).setFieldValue("Weight (kg)", Math.random() * 150F).setFieldValue("BMI", 20 + Math.random() * 10F).with { if (!validate()) { errors.each { println it} } else save()}
814
815	rootGroup.addToSubjects currentSubject
816	rootGroup.save()
817
818	def currentSample = new Sample(
819	name: currentSubject.name + '_B',
820	material: bloodTerm,
821	parentSubject: currentSubject,
822	parentEvent: bloodSamplingEvent);
823
824	humanStudy.addToSubjects(currentSubject).addToSamples(currentSample).with { if (!validate()) { errors.each { println it} } else save()}
825	}
826
827	humanStudy.addToEvents(fastingEvent)
828	humanStudy.addToSamplingEvents(bloodSamplingEvent)
829	humanStudy.addToEventGroups rootGroup
830	humanStudy.save()
831	// Add clinical data
832
833	def lipidAssay = new dbnp.clinicaldata.ClinicalAssay(
834	name: 'Lipid profile',
835	approved: true
836	).with { if (!validate()) { errors.each { println it} } else save()}
837
838	def ldlMeasurement = new dbnp.clinicaldata.ClinicalMeasurement(
839	name: 'LDL',
840	unit: 'mg/dL',
841	type: dbnp.data.FeatureType.QUANTITATIVE,
842	referenceValues: '100 mg/dL',
843	detectableLimit: 250,
844	isDrug: false, isIntake: true, inSerum: true
845	).with { if (!validate()) { errors.each { println it} } else save()}
846
847	def hdlMeasurement = new dbnp.clinicaldata.ClinicalMeasurement(
848	name: 'HDL',
849	unit: 'mg/dL',
850	type: dbnp.data.FeatureType.QUANTITATIVE,
851	referenceValues: '50 mg/dL',
852	detectableLimit: 100,
853	isDrug: false, isIntake: true, inSerum: true
854	).with { if (!validate()) { errors.each { println it} } else save()}
855
856	lipidAssay.addToMeasurements ldlMeasurement
857	lipidAssay.addToMeasurements hdlMeasurement
858
859	def lipidAssayInstance = new dbnp.clinicaldata.ClinicalAssayInstance(
860	assay: lipidAssay
861	).with { if (!validate()) { errors.each { println it} } else save()}
862
863	humanStudy.samples*.each {
864	new dbnp.clinicaldata.ClinicalFloatData(
865	assay: lipidAssayInstance,
866	measurement: ldlMeasurement,
867	sample: it.name,
868	value: Math.round(Math.random()*ldlMeasurement.detectableLimit)
869	).with { if (!validate()) { errors.each { println it} } else save()}
870
871	new dbnp.clinicaldata.ClinicalFloatData(
872	assay: lipidAssayInstance,
873	measurement: hdlMeasurement,
874	sample: it.name,
875	value: Math.round(Math.random()*hdlMeasurement.detectableLimit)
876	).with { if (!validate()) { errors.each { println it} } else save()}
877	}
878
879	// Add assay to study capture module
880	def clinicalModule = new AssayModule(
881	name: 'Clinical data',
882	type: AssayType.CLINICAL_DATA,
883	platform: 'clinical measurements',
884	url: 'http://localhost:8080/gscf'
885	).with { if (!validate()) { errors.each { println it} } else save()}
886
887	def lipidAssayRef = new Assay(
888	name: 'Lipid profiling',
889	module: clinicalModule,
890	externalAssayId: lipidAssayInstance.id
891	).with { if (!validate()) { errors.each { println it} } else save()}
892
893	humanStudy.samples*.each {
894	lipidAssayRef.addToSamples(it)
895	}
896	lipidAssayRef.save()
897
898	humanStudy.addToAssays(lipidAssayRef);
899
900	// Add some sample assay
901	// Add assay to study capture module
902	def dummyModule = new AssayModule(
903	name: 'Dummy data',
904	type: AssayType.CLINICAL_DATA,
905	platform: 'other type of measurement platform',
906	url: 'http://localhost:8080/gscf'
907	).with { if (!validate()) { errors.each { println it} } else save()}
908
909	def dummyAssayRef = new Assay(
910	name: 'Test assay',
911	module: dummyModule,
912	externalAssayId: lipidAssayInstance.id
913	).with { if (!validate()) { errors.each { println it} } else save()}
914
915	humanStudy.addToAssays(dummyAssayRef);
916
917	humanStudy.save()
918	}
919	}
920
921	def destroy = {
922	}
923	}

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