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ExampleStudies.groovy @ 1588

Revision 1588, 36.7 KB checked in by s.h.sikkema@…, 6 years ago (diff)
Fixed tests (except webtests); cleaned up Example{Studies,Templates}.groovy; decapitalized injected services; made 'transactional' properties static
Property svn:keywords set to `Rev Author Date`

Line
1	package dbnp.configuration
2
3	/**
4	* @Author kees
5	* @Since Jun 25, 2010
6	*
7	* Revision information:
8	* $Rev$
9	* $Author$
10	* $Date$
11	*/
12
13	import dbnp.studycapturing.*
14	import org.dbnp.gdt.*
15	import org.codehaus.groovy.grails.commons.GrailsApplication
16	import grails.util.GrailsUtil
17	import dbnp.rest.common.CommunicationManager
18	import org.codehaus.groovy.grails.commons.*
19
20
21	class ExampleStudies {
22
23	/**
24	* Add example studies. This function is meant to be called only in development mode
25	*/
26	public static void addExampleStudies(dbnp.authentication.SecUser owner, dbnp.authentication.SecUser otherUser) {
27	"inserting initial studies".grom()
28
29	// get configuration
30	def config = ConfigurationHolder.config
31
32	// Look up the used ontologies which should be in the database by now
33	def speciesOntology = Ontology.getOrCreateOntologyByNcboId(1132)
34	def brendaOntology = Ontology.getOrCreateOntologyByNcboId(1005)
35	def nciOntology = Ontology.getOrCreateOntologyByNcboId(1032)
36	def chebiOntology = Ontology.getOrCreateOntologyByNcboId(1007)
37
38	// Look up the used templates which should also be in the database by now
39	def studyTemplate = Template.findByName("Academic study")
40	def mouseTemplate = Template.findByName("Mouse")
41	def humanTemplate = Template.findByName("Human")
42	def dietTreatmentTemplate = Template.findByName("Diet treatment")
43	def boostTreatmentTemplate = Template.findByName("Compound challenge")
44	def liverSamplingEventTemplate = Template.findByName("Liver extraction")
45	def fastingTreatmentTemplate = Template.findByName("Fasting treatment")
46	def bloodSamplingEventTemplate = Template.findByName("Blood extraction")
47	def humanTissueSampleTemplate = Template.findByName("Human tissue sample")
48	def humanBloodSampleTemplate = Template.findByName("Human blood sample")
49	def ccAssayTemplate = Template.findByName("Clinical chemistry assay")
50	def metAssayTemplate = Template.findByName("Metabolomics assay")
51
52	// Add terms manually, to avoid having to do many HTTP requests to the BioPortal website
53	def mouseTerm = new Term(
54	name : 'Mus musculus',
55	ontology : speciesOntology,
56	accession : '10090'
57	).save(failOnError:true)
58
59	def humanTerm = new Term(
60	name : 'Homo sapiens',
61	ontology : speciesOntology,
62	accession : '9606'
63	).save(failOnError:true)
64
65	def arabTerm = new Term(
66	name : 'Arabidopsis thaliana',
67	ontology : speciesOntology,
68	accession : '3702'
69	).save(failOnError:true)
70
71	def tomatoTerm = new Term(
72	name : 'Solanum lycopersicum',
73	ontology : speciesOntology,
74	accession : '4081'
75	).save(failOnError:true)
76
77	def potatoTerm = new Term(
78	name : 'Solanum tuberosum',
79	ontology : speciesOntology,
80	accession : '0000'
81	).save(failOnError:true)
82
83	def bloodTerm = new Term(
84	name : 'blood plasma',
85	ontology : brendaOntology,
86	accession : 'BTO:0000131'
87	).save(failOnError:true)
88
89	def c57bl6Term = new Term(
90	name : 'C57BL/6 Mouse',
91	ontology : nciOntology,
92	accession : 'C14424'
93	).save(failOnError:true)
94
95	def glucoseTerm = new Term(
96	name : 'glucose',
97	ontology : chebiOntology,
98	accession : 'CHEBI:17234'
99	).save(failOnError:true)
100
101	// Create a few persons, roles and Affiliations
102	def affiliation1 = new PersonAffiliation(
103	institute : "Science Institute NYC",
104	department : "Department of Mathematics"
105	).save(failOnError:true)
106
107	def affiliation2 = new PersonAffiliation(
108	institute : "InfoStats GmbH, Hamburg",
109	department : "Life Sciences"
110	).save(failOnError:true)
111
112	def role1 = new PersonRole(
113	name : "Principal Investigator"
114	).save(failOnError:true)
115
116	def role2 = new PersonRole(
117	name : "Statician"
118	).save(failOnError:true)
119
120	// Create persons
121	def person1 = new Person(
122	lastName : "Scientist",
123	firstName : "John",
124	gender : "Male",
125	initials : "J.R.",
126	email : "john@scienceinstitute.com",
127	phone : "1-555-3049",
128	address : "First street 2,NYC"
129	).addToAffiliations(affiliation1).addToAffiliations(affiliation2).save(failOnError:true)
130
131	def person2 = new Person(
132	lastName : "Statician",
133	firstName : "Jane",
134	gender : "Female",
135	initials : "W.J.",
136	email : "jane@statisticalcompany.de",
137	phone : "49-555-8291",
138	address : "Dritten strasse 38, Hamburg, Germany"
139	).addToAffiliations(affiliation2).save(failOnError:true)
140
141	// Create 30 persons to test pagination
142	def personCounter = 1
143	30.times {
144	new Person(
145	firstName : "Person #${personCounter}",
146	lastName : "Testperson",
147	email : "email${personCounter++}@testdomain.com"
148	).save(failOnError:true)
149	}
150
151	// Create a few publications
152	def publication1 = new Publication(
153	title : "Postnatal development of hypothalamic leptin receptors",
154	authorsList : "Cottrell EC, Mercer JG, Ozanne SE.",
155	pubMedID : "20472140",
156	comments : "Not published yet",
157	DOI : "unknown"
158	).save(failOnError:true)
159
160	def publication2 = new Publication(
161	title : "Induction of regulatory T cells decreases adipose inflammation and alleviates insulin resistance in ob/ob mice",
162	authorsList : "Ilan Y, Maron R, Tukpah AM, Maioli TU, Murugaiyan G, Yang K, Wu HY, Weiner HL.",
163	pubMedID : "20445103",
164	comments : "",
165	DOI : ""
166	).save(failOnError:true)
167
168	// Add example mouse study
169	def mouseStudy = new Study(
170	template : studyTemplate,
171	title : "NuGO PPS3 mouse study leptin module",
172	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.",
173	code : "PPS3_leptin_module",
174	researchQuestion: "Leptin etc.",
175	ecCode : "2007117.c",
176	startDate : Date.parse('yyyy-MM-dd', '2008-01-02'),
177	owner : owner,
178	readers : [otherUser]
179	).save(failOnError:true)
180
181	def evLF = new Event(
182	startTime : 3600,
183	endTime : 3600 + 7 * 24 * 3600,
184	template : dietTreatmentTemplate
185	).setFieldValue('Diet', 'low fat')
186
187	def evHF = new Event(
188	startTime : 3600,
189	endTime : 3600 + 7 * 24 * 3600,
190	template : dietTreatmentTemplate
191	).setFieldValue('Diet', 'high fat')
192
193	def evBV = new Event(
194	startTime : 3600,
195	endTime : 3600 + 7 * 24 * 3600,
196	template : boostTreatmentTemplate
197	).setFieldValue('Control', 'true')
198
199	def evBL = new Event(
200	startTime : 3600,
201	endTime : 3600 + 7 * 24 * 3600,
202	template : boostTreatmentTemplate
203	).setFieldValue('Control', 'false')
204
205	def evLF4 = new Event(
206	startTime : 3600,
207	endTime : 3600 + 4 * 7 * 24 * 3600,
208	template : dietTreatmentTemplate
209	).setFieldValue('Diet', 'low fat')
210
211	def evHF4 = new Event(
212	startTime : 3600,
213	endTime : 3600 + 4 * 7 * 24 * 3600,
214	template : dietTreatmentTemplate
215	).setFieldValue('Diet', 'high fat')
216
217	def evBV4 = new Event(
218	startTime : 3600,
219	endTime : 3600 + 4 * 7 * 24 * 3600,
220	template : boostTreatmentTemplate
221	).setFieldValue('Control', 'true')
222
223	def evBL4 = new Event(
224	startTime : 3600,
225	endTime : 3600 + 4 * 7 * 24 * 3600,
226	template : boostTreatmentTemplate
227	).setFieldValue('Control', 'false')
228
229	def evS = new SamplingEvent(
230	startTime : 3600 + 7 * 24 * 3600,
231	template : liverSamplingEventTemplate,
232	sampleTemplate: humanTissueSampleTemplate).setFieldValue('Sample weight', 5F)
233
234	def evS4 = new SamplingEvent(
235	startTime : 3600 + 7 * 24 * 3600,
236	template : liverSamplingEventTemplate,
237	sampleTemplate: humanTissueSampleTemplate).setFieldValue('Sample weight', 5F)
238
239	// Add events to study
240	mouseStudy.addToEvents(evLF).addToEvents(evHF).addToEvents(evBV).addToEvents(evBL).addToEvents(evLF4).addToEvents(evHF4).addToEvents(evBV4).addToEvents(evBL4).addToSamplingEvents(evS).addToSamplingEvents(evS4).save(failOnError:true)
241
242	// Extra check if the SamplingEvents are saved correctly
243	evS.save(failOnError:true)
244	evS4.save(failOnError:true)
245
246	def LFBV1 = new EventGroup(name: "10% fat + vehicle for 1 week").addToEvents(evLF).addToEvents(evBV).addToSamplingEvents(evS)
247
248	def LFBL1 = new EventGroup(name: "10% fat + leptin for 1 week").addToEvents(evLF).addToEvents(evBL).addToSamplingEvents(evS)
249
250	def HFBV1 = new EventGroup(name: "45% fat + vehicle for 1 week").addToEvents(evHF).addToEvents(evBV).addToSamplingEvents(evS)
251
252	def HFBL1 = new EventGroup(name: "45% fat + leptin for 1 week").addToEvents(evHF).addToEvents(evBL).addToSamplingEvents(evS)
253
254	def LFBV4 = new EventGroup(name: "10% fat + vehicle for 4 weeks").addToEvents(evLF4).addToEvents(evBV4).addToSamplingEvents(evS4)
255
256	def LFBL4 = new EventGroup(name: "10% fat + leptin for 4 weeks").addToEvents(evLF4).addToEvents(evBL4).addToSamplingEvents(evS4)
257
258	def HFBV4 = new EventGroup(name: "45% fat + vehicle for 4 weeks").addToEvents(evHF4).addToEvents(evBV4).addToSamplingEvents(evS4)
259
260	def HFBL4 = new EventGroup(name: "45% fat + leptin for 4 weeks").addToEvents(evHF4).addToEvents(evBL4).addToSamplingEvents(evS4)
261
262	// Add subjects and samples and compose EventGroups
263	def x = 1
264	80.times {
265	def currentSubject = new Subject(
266	name: "A" + x++,
267	species: mouseTerm,
268	template: mouseTemplate,
269	).setFieldValue("Gender", "Male").setFieldValue("Genotype", c57bl6Term).setFieldValue("Age", 17).setFieldValue("Cage", "" + (int) (x / 2))
270
271	// We have to save the subject first, otherwise the parentEvent property of the sample cannot be set
272	// (this is possibly a Grails or Hibernate bug)
273	mouseStudy.addToSubjects(currentSubject)
274
275	currentSubject.save(failOnError:true)
276
277	// Add subject to appropriate EventGroup
278	def tmpEventGroup
279	if (x > 70) { tmpEventGroup = HFBL4 }
280	else if (x > 60) { tmpEventGroup = HFBV4 }
281	else if (x > 50) { tmpEventGroup = LFBL4 }
282	else if (x > 40) { tmpEventGroup = LFBV4 }
283	else if (x > 30) { tmpEventGroup = HFBL1 }
284	else if (x > 20) { tmpEventGroup = HFBV1 }
285	else if (x > 10) { tmpEventGroup = LFBL1 }
286	else { tmpEventGroup = LFBV1 }
287
288	tmpEventGroup.addToSubjects(currentSubject)
289
290	// Create sample
291	def currentSample = new Sample(
292	name: currentSubject.name + '_B',
293	material: bloodTerm,
294	template: humanBloodSampleTemplate,
295	parentSubject: currentSubject,
296	parentEvent: evS //x > 40 ? evS4 : evS
297	)
298
299	mouseStudy.addToSamples(currentSample)
300	currentSample.setFieldValue("Text on vial", "T" + (Math.random() * 100L))
301	currentSample.save(failOnError:true)
302	}
303
304	// Add EventGroups to study
305	mouseStudy.addToEventGroups(LFBV1).addToEventGroups(LFBL1).addToEventGroups(HFBV1).addToEventGroups(HFBL1).addToEventGroups(LFBV4).addToEventGroups(LFBL4).addToEventGroups(HFBV4).addToEventGroups(HFBL4).save(failOnError:true)
306
307	// Add persons and publications to study
308	def studyperson1 = new StudyPerson(person: person1, role: role1)
309	def studyperson2 = new StudyPerson(person: person2, role: role2)
310
311	mouseStudy.addToPersons(studyperson1).addToPersons(studyperson2).addToPublications(publication1).addToPublications(publication2).save(failOnError:true)
312
313	def humanStudy = new Study(
314	template : studyTemplate,
315	title : "NuGO PPS human study",
316	code : "PPSH",
317	researchQuestion: "How much are fasting plasma and urine metabolite levels affected by prolonged fasting ?",
318	description : "Human study performed at RRI; centres involved: RRI, IFR, TUM, Maastricht U.",
319	ecCode : "unknown",
320	startDate : Date.parse('yyyy-MM-dd', '2008-01-14'),
321	owner : owner
322	).addToWriters(otherUser).save(failOnError:true)
323
324	def rootGroup = new EventGroup(name: 'Root group')
325
326	def fastingEvent = new Event(
327	startTime : 3 * 24 * 3600 + 22 * 3600,
328	endTime : 3 * 24 * 3600 + 30 * 3600,
329	template : fastingTreatmentTemplate).setFieldValue('Fasting period', '8h')
330
331	def bloodSamplingEventBefore = new SamplingEvent(
332	startTime : 0,
333	template : bloodSamplingEventTemplate,
334	sampleTemplate : humanBloodSampleTemplate).setFieldValue('Sample volume', 4.5F)
335
336	def bloodSamplingEventAfter = new SamplingEvent(
337	startTime : 3 * 24 * 3600 + 30 * 3600,
338	template : bloodSamplingEventTemplate,
339	sampleTemplate : humanBloodSampleTemplate).setFieldValue('Sample volume', 4.5F)
340
341	rootGroup.addToEvents fastingEvent
342	rootGroup.addToSamplingEvents bloodSamplingEventBefore
343	rootGroup.addToSamplingEvents bloodSamplingEventAfter
344
345	humanStudy.addToEvents(fastingEvent)
346	humanStudy.addToSamplingEvents(bloodSamplingEventBefore)
347	humanStudy.addToSamplingEvents(bloodSamplingEventAfter)
348	humanStudy.addToEventGroups rootGroup
349
350	humanStudy.save(failOnError:true)
351
352	def y = 1
353	11.times {
354	def currentSubject = new Subject(
355	name : "" + y++,
356	species : humanTerm,
357	template : humanTemplate
358	).setFieldValue("Gender", (Math.random() > 0.5) ? "Male" : "Female")
359	//.setFieldValue("DOB", new java.text.SimpleDateFormat("dd-mm-yy").parse("01-02-19" + (10 + (int) (Math.random() * 80)))).setFieldValue("DOB", new Date().parse("dd/mm/yyyy", ((10 + (int) Math.random() * 18) + "/0" + (1 + (int) (Math.random() * 8)) + "/19" + (10 + (int) (Math.random() * 80))))).setFieldValue("Age", 30).setFieldValue("Height", Math.random() * 2F).setFieldValue("Weight", Math.random() * 150F).setFieldValue("BMI", 20 + Math.random() * 10F)
360
361	humanStudy.addToSubjects(currentSubject)
362	currentSubject.save(failOnError:true)
363
364	rootGroup.addToSubjects currentSubject
365	rootGroup.save(failOnError:true)
366
367	def currentSample = new Sample(
368	name : currentSubject.name + '_B',
369	material : bloodTerm,
370	template : humanBloodSampleTemplate,
371	parentSubject: currentSubject,
372	parentEvent : bloodSamplingEventBefore
373	)
374
375	humanStudy.addToSamples(currentSample)
376	currentSample.setFieldValue("Text on vial", "T" + (Math.random() * 100L))
377	currentSample.save(failOnError:true)
378
379	currentSample = new Sample(
380	name : currentSubject.name + '_A',
381	material : bloodTerm,
382	template : humanBloodSampleTemplate,
383	parentSubject: currentSubject,
384	parentEvent : bloodSamplingEventAfter
385	)
386
387	humanStudy.addToSamples(currentSample)
388	currentSample.setFieldValue("Text on vial", "T" + (Math.random() * 100L))
389	currentSample.save(failOnError:true)
390	}
391
392	// Add persons to study
393	def studyperson3 = new StudyPerson(person: person1, role: role2)
394	humanStudy.addToPersons(studyperson3).addToPublications(publication2).save(failOnError:true)
395
396	// Add SAM assay reference
397	def clinicalModule = new AssayModule(
398	name: 'SAM module for clinical data',
399	platform: 'clinical measurements',
400	url: config.modules.sam.url.toString()
401	).save(failOnError:true)
402
403	// Add metabolomics assay reference
404	def metabolomicsModule = new AssayModule(
405	name: 'Metabolomics module',
406	platform: 'GCMS/LCMS',
407	url: config.modules.metabolomics.url.toString()
408	).save(failOnError:true)
409
410	// Add metabolomics assay reference
411	def metagenomicsModule = new AssayModule(
412	name: 'Metagenomics module',
413	platform: 'High throughput sequencing',
414	url: config.modules.metagenomics.url.toString()
415	).save(failOnError:true)
416
417	def lipidAssayRef = new Assay(
418	name: 'Lipid profiling',
419	template: ccAssayTemplate,
420	module: clinicalModule,
421	externalAssayID: 'PPS3_SAM'
422	)
423
424	def metAssayRef = new Assay(
425	name: 'Lipidomics profile',
426	template: metAssayTemplate,
427	module: metabolomicsModule,
428	externalAssayID: 'PPS3_Lipidomics'
429	).setFieldValue('Spectrometry technique', 'LC/MS')
430
431	mouseStudy.samples*.each {
432	lipidAssayRef.addToSamples(it)
433	metAssayRef.addToSamples(it)
434	}
435
436	mouseStudy.addToAssays(lipidAssayRef);
437	mouseStudy.addToAssays(metAssayRef);
438	mouseStudy.save(failOnError:true)
439
440	def glucoseAssayBRef = new Assay(
441	name : 'Glucose assay before',
442	template : ccAssayTemplate,
443	module : clinicalModule,
444	externalAssayID: 'PPSH-Glu-B'
445	)
446
447	def glucoseAssayARef = new Assay(
448	name : 'Glucose assay after',
449	template : ccAssayTemplate,
450	module : clinicalModule,
451	externalAssayID: 'PPSH-Glu-A'
452	)
453
454	def metAssayRefB = new Assay(
455	name : 'Lipidomics profile before',
456	template : metAssayTemplate,
457	module : metabolomicsModule,
458	externalAssayID: 'PPSH_Lipidomics_start'
459	).setFieldValue('Spectrometry technique', 'GC/MS')
460
461	def metAssayRefA = new Assay(
462	name : 'Lipidomics profile after',
463	template : metAssayTemplate,
464	module : metabolomicsModule,
465	externalAssayID: 'PPSH_Lipidomics_end'
466	).setFieldValue('Spectrometry technique', 'GC/MS')
467
468
469	// Add sequencing (metagenomics) assays
470	def sequencingAssay16SRef = new Assay(
471	name : '16S Sequencing assay',
472	template : ccAssayTemplate,
473	module : metagenomicsModule,
474	externalAssayID: 'PPSH-SEQ-16S'
475	)
476
477	// Add sequencing (metagenomics) assays
478	def sequencingAssay18SRef = new Assay(
479	name : '18S Sequencing assay',
480	template : ccAssayTemplate,
481	module : metagenomicsModule,
482	externalAssayID: 'PPSH-SEQ-18S'
483	)
484
485	humanStudy.samples*.each {
486	if (it.parentEvent.startTime == 0) {
487	glucoseAssayBRef.addToSamples(it)
488	metAssayRefB.addToSamples(it)
489	}
490	else {
491	glucoseAssayARef.addToSamples(it)
492	metAssayRefA.addToSamples(it)
493	sequencingAssay16SRef.addToSamples(it)
494	sequencingAssay18SRef.addToSamples(it)
495	}
496	}
497
498	humanStudy.addToAssays(sequencingAssay16SRef)
499	humanStudy.addToAssays(sequencingAssay18SRef)
500	humanStudy.addToAssays(glucoseAssayARef)
501	humanStudy.addToAssays(glucoseAssayBRef)
502	humanStudy.addToAssays(metAssayRefA)
503	humanStudy.addToAssays(metAssayRefB)
504	humanStudy.save(failOnError:true)
505	}
506
507	/**
508	* Add test studies. This function is meant to be called only in test mode
509	*/
510	static addTestStudies() {
511
512	final String testStudyName = "Test study"
513	final String testStudyTemplateName = "Academic study"
514	final String testStudyCode = "AAA-Test"
515	final String testStudyDescription = "Description of Test Study"
516	final Date testStudyStartDate = Date.parse('yyyy-MM-dd','2007-12-11')
517
518	def studyTemplate = Template.findByName(testStudyTemplateName)
519	assert studyTemplate
520
521	def study = new Study(
522	title: testStudyName,
523	template: studyTemplate,
524	startDate: testStudyStartDate,
525	code: testStudyCode,
526	description: testStudyDescription
527	)
528
529	study.save(failOnError: true)
530
531	}
532	}
533
534	//package dbnp.configuration
535	//
536	///**
537	// * @Author kees
538	// * @Since Jun 25, 2010
539	// *
540	// * Revision information:
541	// * $Rev$
542	// * $Author$
543	// * $Date$
544	// */
545	//
546	//import dbnp.studycapturing.*
547	//import org.dbnp.gdt.*
548	//import org.codehaus.groovy.grails.commons.GrailsApplication
549	//import grails.util.GrailsUtil
550	//import dbnp.rest.common.CommunicationManager
551	//import org.codehaus.groovy.grails.commons.*
552	//
553	//
554	//class ExampleStudies {
555	//
556	// /**
557	// * Add example studies. This function is meant to be called only in development mode
558	// */
559	// public static void addExampleStudies(dbnp.authentication.SecUser owner, dbnp.authentication.SecUser otherUser) {
560	// "inserting initial studies".grom()
561	//
562	// // get configuration
563	// def config = ConfigurationHolder.config
564	//
565	// // Look up the used ontologies which should be in the database by now
566	// def speciesOntology = Ontology.getOrCreateOntologyByNcboId(1132)
567	// def brendaOntology = Ontology.getOrCreateOntologyByNcboId(1005)
568	// def nciOntology = Ontology.getOrCreateOntologyByNcboId(1032)
569	// def chebiOntology = Ontology.getOrCreateOntologyByNcboId(1007)
570	//
571	// // Look up the used templates which should also be in the database by now
572	// def studyTemplate = Template.findByName("Academic study")
573	// def mouseTemplate = Template.findByName("Mouse")
574	// def humanTemplate = Template.findByName("Human")
575	// def dietTreatmentTemplate = Template.findByName("Diet treatment")
576	// def boostTreatmentTemplate = Template.findByName("Compound challenge")
577	// def liverSamplingEventTemplate = Template.findByName("Liver extraction")
578	// def fastingTreatmentTemplate = Template.findByName("Fasting treatment")
579	// def bloodSamplingEventTemplate = Template.findByName("Blood extraction")
580	// def humanTissueSampleTemplate = Template.findByName("Human tissue sample")
581	// def humanBloodSampleTemplate = Template.findByName("Human blood sample")
582	// def ccAssayTemplate = Template.findByName("Clinical chemistry assay")
583	// def metAssayTemplate = Template.findByName("Metabolomics assay")
584	//
585	// // Add terms manually, to avoid having to do many HTTP requests to the BioPortal website
586	// def mouseTerm = new Term(
587	// name : 'Mus musculus',
588	// ontology : speciesOntology,
589	// accession : '10090'
590	// ).with { if (!validate()) { errors.each { println it} } else save()}
591	//
592	// def humanTerm = new Term(
593	// name : 'Homo sapiens',
594	// ontology : speciesOntology,
595	// accession : '9606'
596	// ).with { if (!validate()) { errors.each { println it} } else save()}
597	//
598	// def arabTerm = new Term(
599	// name : 'Arabidopsis thaliana',
600	// ontology : speciesOntology,
601	// accession : '3702'
602	// ).with { if (!validate()) { errors.each { println it} } else save()}
603	//
604	// def tomatoTerm = new Term(
605	// name : 'Solanum lycopersicum',
606	// ontology : speciesOntology,
607	// accession : '4081'
608	// ).with { if (!validate()) { errors.each { println it} } else save()}
609	//
610	// def potatoTerm = new Term(
611	// name : 'Solanum tuberosum',
612	// ontology : speciesOntology,
613	// accession : '0000'
614	// ).with { if (!validate()) { errors.each { println it} } else save()}
615	//
616	// def bloodTerm = new Term(
617	// name : 'blood plasma',
618	// ontology : brendaOntology,
619	// accession : 'BTO:0000131'
620	// ).with { if (!validate()) { errors.each { println it} } else save()}
621	//
622	// def c57bl6Term = new Term(
623	// name : 'C57BL/6 Mouse',
624	// ontology : nciOntology,
625	// accession : 'C14424'
626	// ).with { if (!validate()) { errors.each { println it} } else save()}
627	//
628	// def glucoseTerm = new Term(
629	// name : 'glucose',
630	// ontology : chebiOntology,
631	// accession : 'CHEBI:17234'
632	// ).with { if (!validate()) { errors.each { println it} } else save()}
633	//
634	// // Create a few persons, roles and Affiliations
635	// def affiliation1 = new PersonAffiliation(
636	// institute : "Science Institute NYC",
637	// department : "Department of Mathematics"
638	// ).save();
639	// def affiliation2 = new PersonAffiliation(
640	// institute : "InfoStats GmbH, Hamburg",
641	// department : "Life Sciences"
642	// ).save();
643	// def role1 = new PersonRole(
644	// name : "Principal Investigator"
645	// ).save();
646	// def role2 = new PersonRole(
647	// name : "Statician"
648	// ).save();
649	//
650	// // Create persons
651	// def person1 = new Person(
652	// lastName : "Scientist",
653	// firstName : "John",
654	// gender : "Male",
655	// initials : "J.R.",
656	// email : "john@scienceinstitute.com",
657	// phone : "1-555-3049",
658	// address : "First street 2,NYC"
659	// ).addToAffiliations(affiliation1).addToAffiliations(affiliation2).save();
660	//
661	// def person2 = new Person(
662	// lastName : "Statician",
663	// firstName : "Jane",
664	// gender : "Female",
665	// initials : "W.J.",
666	// email : "jane@statisticalcompany.de",
667	// phone : "49-555-8291",
668	// address : "Dritten strasse 38, Hamburg, Germany"
669	// ).addToAffiliations(affiliation2).save();
670	//
671	// // Create 30 persons to test pagination
672	// def personCounter = 1;
673	// 30.times {
674	// new Person(
675	// firstName : "Person #${personCounter}",
676	// lastName : "Testperson",
677	// email : "email${personCounter++}@testdomain.com"
678	// ).save()
679	// }
680	//
681	// // Create a few publications
682	// def publication1 = new Publication(
683	// title : "Postnatal development of hypothalamic leptin receptors",
684	// authorsList : "Cottrell EC, Mercer JG, Ozanne SE.",
685	// pubMedID : "20472140",
686	// comments : "Not published yet",
687	// DOI : "unknown"
688	// ).save();
689	//
690	// def publication2 = new Publication(
691	// title : "Induction of regulatory T cells decreases adipose inflammation and alleviates insulin resistance in ob/ob mice",
692	// authorsList : "Ilan Y, Maron R, Tukpah AM, Maioli TU, Murugaiyan G, Yang K, Wu HY, Weiner HL.",
693	// pubMedID : "20445103",
694	// comments : "",
695	// DOI : ""
696	// ).save();
697	//
698	// // Add example mouse study
699	// def mouseStudy = new Study(
700	// template : studyTemplate,
701	// title : "NuGO PPS3 mouse study leptin module",
702	// 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.",
703	// code : "PPS3_leptin_module",
704	// researchQuestion: "Leptin etc.",
705	// ecCode : "2007117.c",
706	// startDate : Date.parse('yyyy-MM-dd', '2008-01-02'),
707	// owner : owner,
708	// readers : [otherUser]
709	// ).with { if (!validate()) { errors.each { println it} } else save()}
710	//
711	// def evLF = new Event(
712	// startTime : 3600,
713	// endTime : 3600 + 7 * 24 * 3600,
714	// template : dietTreatmentTemplate
715	// ).setFieldValue('Diet', 'low fat')
716	//
717	// def evHF = new Event(
718	// startTime : 3600,
719	// endTime : 3600 + 7 * 24 * 3600,
720	// template : dietTreatmentTemplate
721	// ).setFieldValue('Diet', 'high fat')
722	//
723	// def evBV = new Event(
724	// startTime : 3600,
725	// endTime : 3600 + 7 * 24 * 3600,
726	// template : boostTreatmentTemplate
727	// ).setFieldValue('Control', 'true')
728	//
729	// def evBL = new Event(
730	// startTime : 3600,
731	// endTime : 3600 + 7 * 24 * 3600,
732	// template : boostTreatmentTemplate
733	// ).setFieldValue('Control', 'false')
734	//
735	// def evLF4 = new Event(
736	// startTime : 3600,
737	// endTime : 3600 + 4 * 7 * 24 * 3600,
738	// template : dietTreatmentTemplate
739	// ).setFieldValue('Diet', 'low fat')
740	//
741	// def evHF4 = new Event(
742	// startTime : 3600,
743	// endTime : 3600 + 4 * 7 * 24 * 3600,
744	// template : dietTreatmentTemplate
745	// ).setFieldValue('Diet', 'high fat')
746	//
747	// def evBV4 = new Event(
748	// startTime : 3600,
749	// endTime : 3600 + 4 * 7 * 24 * 3600,
750	// template : boostTreatmentTemplate
751	// ).setFieldValue('Control', 'true')
752	//
753	// def evBL4 = new Event(
754	// startTime : 3600,
755	// endTime : 3600 + 4 * 7 * 24 * 3600,
756	// template : boostTreatmentTemplate
757	// ).setFieldValue('Control', 'false')
758	//
759	// def evS = new SamplingEvent(
760	// startTime : 3600 + 7 * 24 * 3600,
761	// template : liverSamplingEventTemplate,
762	// sampleTemplate: humanTissueSampleTemplate).setFieldValue('Sample weight', 5F)
763	//
764	// def evS4 = new SamplingEvent(
765	// startTime : 3600 + 7 * 24 * 3600,
766	// template : liverSamplingEventTemplate,
767	// sampleTemplate: humanTissueSampleTemplate).setFieldValue('Sample weight', 5F)
768	//
769	// // Add events to study
770	// mouseStudy.addToEvents(evLF).addToEvents(evHF).addToEvents(evBV).addToEvents(evBL).addToEvents(evLF4).addToEvents(evHF4).addToEvents(evBV4).addToEvents(evBL4).addToSamplingEvents(evS).addToSamplingEvents(evS4).with { if (!validate()) { errors.each { println it} } else save()}
771	//
772	// // Extra check if the SamplingEvents are saved correctly
773	// evS.with { if (!validate()) { errors.each { println it} } else save()}
774	// evS4.with { if (!validate()) { errors.each { println it} } else save()}
775	//
776	// def LFBV1 = new EventGroup(name: "10% fat + vehicle for 1 week").addToEvents(evLF).addToEvents(evBV).addToSamplingEvents(evS)
777	//
778	// def LFBL1 = new EventGroup(name: "10% fat + leptin for 1 week").addToEvents(evLF).addToEvents(evBL).addToSamplingEvents(evS)
779	//
780	// def HFBV1 = new EventGroup(name: "45% fat + vehicle for 1 week").addToEvents(evHF).addToEvents(evBV).addToSamplingEvents(evS)
781	//
782	// def HFBL1 = new EventGroup(name: "45% fat + leptin for 1 week").addToEvents(evHF).addToEvents(evBL).addToSamplingEvents(evS)
783	//
784	// def LFBV4 = new EventGroup(name: "10% fat + vehicle for 4 weeks").addToEvents(evLF4).addToEvents(evBV4).addToSamplingEvents(evS4)
785	//
786	// def LFBL4 = new EventGroup(name: "10% fat + leptin for 4 weeks").addToEvents(evLF4).addToEvents(evBL4).addToSamplingEvents(evS4)
787	//
788	// def HFBV4 = new EventGroup(name: "45% fat + vehicle for 4 weeks").addToEvents(evHF4).addToEvents(evBV4).addToSamplingEvents(evS4)
789	//
790	// def HFBL4 = new EventGroup(name: "45% fat + leptin for 4 weeks").addToEvents(evHF4).addToEvents(evBL4).addToSamplingEvents(evS4)
791	//
792	// // Add subjects and samples and compose EventGroups
793	// def x = 1
794	// 80.times {
795	// def currentSubject = new Subject(
796	// name: "A" + x++,
797	// species: mouseTerm,
798	// template: mouseTemplate,
799	// ).setFieldValue("Gender", "Male").setFieldValue("Genotype", c57bl6Term).setFieldValue("Age", 17).setFieldValue("Cage", "" + (int) (x / 2))
800	//
801	// // We have to save the subject first, otherwise the parentEvent property of the sample cannot be set
802	// // (this is possibly a Grails or Hibernate bug)
803	// mouseStudy.addToSubjects(currentSubject)
804	// currentSubject.with { if (!validate()) { errors.each { println it} } else save()}
805	//
806	// // Add subject to appropriate EventGroup
807	// if (x > 70) { HFBL4.addToSubjects(currentSubject).save() }
808	// else if (x > 60) { HFBV4.addToSubjects(currentSubject).save() }
809	// else if (x > 50) { LFBL4.addToSubjects(currentSubject).save() }
810	// else if (x > 40) { LFBV4.addToSubjects(currentSubject).save() }
811	// else if (x > 30) { HFBL1.addToSubjects(currentSubject).save() }
812	// else if (x > 20) { HFBV1.addToSubjects(currentSubject).save() }
813	// else if (x > 10) { LFBL1.addToSubjects(currentSubject).save() }
814	// else { LFBV1.addToSubjects(currentSubject).save() }
815	//
816	// // Create sample
817	// def currentSample = new Sample(
818	// name: currentSubject.name + '_B',
819	// material: bloodTerm,
820	// template: humanBloodSampleTemplate,
821	// parentSubject: currentSubject,
822	// parentEvent: evS //x > 40 ? evS4 : evS
823	// );
824	// mouseStudy.addToSamples(currentSample)
825	// currentSample.with { if (!validate()) { errors.each { println it} } else save()}
826	// currentSample.setFieldValue("Text on vial", "T" + (Math.random() * 100L))
827	// }
828	//
829	// // Add EventGroups to study
830	// mouseStudy.addToEventGroups(LFBV1).addToEventGroups(LFBL1).addToEventGroups(HFBV1).addToEventGroups(HFBL1).addToEventGroups(LFBV4).addToEventGroups(LFBL4).addToEventGroups(HFBV4).addToEventGroups(HFBL4).with { if (!validate()) { errors.each { println it} } else save()}
831	//
832	// // Add persons and publications to study
833	// def studyperson1 = new StudyPerson(person: person1, role: role1)
834	// def studyperson2 = new StudyPerson(person: person2, role: role2)
835	//
836	// mouseStudy.addToPersons(studyperson1).addToPersons(studyperson2).addToPublications(publication1).addToPublications(publication2).with { if (!validate()) { errors.each { println it} } else save()}
837	//
838	// def humanStudy = new Study(
839	// template : studyTemplate,
840	// title : "NuGO PPS human study",
841	// code : "PPSH",
842	// researchQuestion: "How much are fasting plasma and urine metabolite levels affected by prolonged fasting ?",
843	// description : "Human study performed at RRI; centres involved: RRI, IFR, TUM, Maastricht U.",
844	// ecCode : "unknown",
845	// startDate : Date.parse('yyyy-MM-dd', '2008-01-14'),
846	// owner : owner,
847	// writers : [otherUser]
848	// ).with { if (!validate()) { errors.each { println it} } else save()}
849	//
850	// def rootGroup = new EventGroup(name: 'Root group');
851	//
852	// def fastingEvent = new Event(
853	// startTime : 3 * 24 * 3600 + 22 * 3600,
854	// endTime : 3 * 24 * 3600 + 30 * 3600,
855	// template : fastingTreatmentTemplate).setFieldValue('Fasting period', '8h');
856	//
857	// def bloodSamplingEventBefore = new SamplingEvent(
858	// startTime : 0,
859	// template : bloodSamplingEventTemplate,
860	// sampleTemplate : humanBloodSampleTemplate).setFieldValue('Sample volume', 4.5F);
861	//
862	// def bloodSamplingEventAfter = new SamplingEvent(
863	// startTime : 3 * 24 * 3600 + 30 * 3600,
864	// template : bloodSamplingEventTemplate,
865	// sampleTemplate : humanBloodSampleTemplate).setFieldValue('Sample volume', 4.5F);
866	//
867	// rootGroup.addToEvents fastingEvent
868	// rootGroup.addToSamplingEvents bloodSamplingEventBefore
869	// rootGroup.addToSamplingEvents bloodSamplingEventAfter
870	// rootGroup.save()
871	//
872	// humanStudy.addToEvents(fastingEvent)
873	// humanStudy.addToSamplingEvents(bloodSamplingEventBefore)
874	// humanStudy.addToSamplingEvents(bloodSamplingEventAfter)
875	// humanStudy.addToEventGroups rootGroup
876	//
877	// humanStudy.save()
878	//
879	// def y = 1
880	// 11.times {
881	// def currentSubject = new Subject(
882	// name : "" + y++,
883	// species : humanTerm,
884	// template : humanTemplate
885	// ).setFieldValue("Gender", (Math.random() > 0.5) ? "Male" : "Female")
886	// //.setFieldValue("DOB", new java.text.SimpleDateFormat("dd-mm-yy").parse("01-02-19" + (10 + (int) (Math.random() * 80)))).setFieldValue("DOB", new Date().parse("dd/mm/yyyy", ((10 + (int) Math.random() * 18) + "/0" + (1 + (int) (Math.random() * 8)) + "/19" + (10 + (int) (Math.random() * 80))))).setFieldValue("Age", 30).setFieldValue("Height", Math.random() * 2F).setFieldValue("Weight", Math.random() * 150F).setFieldValue("BMI", 20 + Math.random() * 10F)
887	//
888	// humanStudy.addToSubjects(currentSubject)
889	// currentSubject.with { if (!validate()) { errors.each { println it} } else save()}
890	//
891	// rootGroup.addToSubjects currentSubject
892	// rootGroup.save()
893	//
894	// def currentSample = new Sample(
895	// name : currentSubject.name + '_B',
896	// material : bloodTerm,
897	// template : humanBloodSampleTemplate,
898	// parentSubject: currentSubject,
899	// parentEvent : bloodSamplingEventBefore
900	// );
901	//
902	// humanStudy.addToSamples(currentSample)
903	// currentSample.with { if (!validate()) { errors.each { println it} } else save()}
904	// currentSample.setFieldValue("Text on vial", "T" + (Math.random() * 100L))
905	//
906	// currentSample = new Sample(
907	// name : currentSubject.name + '_A',
908	// material : bloodTerm,
909	// template : humanBloodSampleTemplate,
910	// parentSubject: currentSubject,
911	// parentEvent : bloodSamplingEventAfter
912	// );
913	//
914	// humanStudy.addToSamples(currentSample)
915	// currentSample.with { if (!validate()) { errors.each { println it} } else save()}
916	// currentSample.setFieldValue("Text on vial", "T" + (Math.random() * 100L))
917	// }
918	//
919	// // Add persons to study
920	// def studyperson3 = new StudyPerson(person: person1, role: role2)
921	// humanStudy.addToPersons(studyperson3).addToPublications(publication2).with { if (!validate()) { errors.each { println it} } else save()}
922	//
923	// // Add SAM assay reference
924	// def clinicalModule = new AssayModule(
925	// name: 'SAM module for clinical data',
926	// platform: 'clinical measurements',
927	// url: config.modules.sam.url.toString()
928	// ).with { if (!validate()) { errors.each { println it} } else save()}
929	//
930	// // Add metabolomics assay reference
931	// def metabolomicsModule = new AssayModule(
932	// name: 'Metabolomics module',
933	// platform: 'GCMS/LCMS',
934	// url: config.modules.metabolomics.url.toString()
935	// ).with { if (!validate()) { errors.each { println it} } else save()}
936	//
937	// // Add metabolomics assay reference
938	// def metagenomicsModule = new AssayModule(
939	// name: 'Metagenomics module',
940	// platform: 'High throughput sequencing',
941	// url: config.modules.metagenomics.url.toString()
942	// ).with { if (!validate()) { errors.each { println it} } else save()}
943	//
944	// def lipidAssayRef = new Assay(
945	// name: 'Lipid profiling',
946	// template: ccAssayTemplate,
947	// module: clinicalModule,
948	// externalAssayID: 'PPS3_SAM'
949	// )
950	//
951	// def metAssayRef = new Assay(
952	// name: 'Lipidomics profile',
953	// template: metAssayTemplate,
954	// module: metabolomicsModule,
955	// externalAssayID: 'PPS3_Lipidomics'
956	// ).setFieldValue('Spectrometry technique', 'LC/MS')
957	//
958	// mouseStudy.samples*.each {
959	// lipidAssayRef.addToSamples(it)
960	// metAssayRef.addToSamples(it)
961	// }
962	//
963	// mouseStudy.addToAssays(lipidAssayRef);
964	// mouseStudy.addToAssays(metAssayRef);
965	// mouseStudy.save()
966	//
967	// def glucoseAssayBRef = new Assay(
968	// name : 'Glucose assay before',
969	// template : ccAssayTemplate,
970	// module : clinicalModule,
971	// externalAssayID: 'PPSH-Glu-B'
972	// )
973	//
974	// def glucoseAssayARef = new Assay(
975	// name : 'Glucose assay after',
976	// template : ccAssayTemplate,
977	// module : clinicalModule,
978	// externalAssayID: 'PPSH-Glu-A'
979	// )
980	//
981	// def metAssayRefB = new Assay(
982	// name : 'Lipidomics profile before',
983	// template : metAssayTemplate,
984	// module : metabolomicsModule,
985	// externalAssayID: 'PPSH_Lipidomics_start'
986	// ).setFieldValue('Spectrometry technique', 'GC/MS')
987	//
988	// def metAssayRefA = new Assay(
989	// name : 'Lipidomics profile after',
990	// template : metAssayTemplate,
991	// module : metabolomicsModule,
992	// externalAssayID: 'PPSH_Lipidomics_end'
993	// ).setFieldValue('Spectrometry technique', 'GC/MS')
994	//
995	//
996	// // Add sequencing (metagenomics) assays
997	// def sequencingAssay16SRef = new Assay(
998	// name : '16S Sequencing assay',
999	// template : ccAssayTemplate,
1000	// module : metagenomicsModule,
1001	// externalAssayID: 'PPSH-SEQ-16S'
1002	// )
1003	//
1004	// // Add sequencing (metagenomics) assays
1005	// def sequencingAssay18SRef = new Assay(
1006	// name : '18S Sequencing assay',
1007	// template : ccAssayTemplate,
1008	// module : metagenomicsModule,
1009	// externalAssayID: 'PPSH-SEQ-18S'
1010	// )
1011	//
1012	// humanStudy.samples*.each {
1013	// if (it.parentEvent.startTime == 0) {
1014	// glucoseAssayBRef.addToSamples(it)
1015	// metAssayRefB.addToSamples(it)
1016	// }
1017	// else {
1018	// glucoseAssayARef.addToSamples(it)
1019	// metAssayRefA.addToSamples(it)
1020	// sequencingAssay16SRef.addToSamples(it)
1021	// sequencingAssay18SRef.addToSamples(it)
1022	// }
1023	// }
1024	//
1025	// humanStudy.addToAssays(sequencingAssay16SRef)
1026	// humanStudy.addToAssays(sequencingAssay18SRef)
1027	// humanStudy.addToAssays(glucoseAssayARef)
1028	// humanStudy.addToAssays(glucoseAssayBRef)
1029	// humanStudy.addToAssays(metAssayRefA)
1030	// humanStudy.addToAssays(metAssayRefB)
1031	// humanStudy.save()
1032	// }
1033	//}

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