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source: trunk/grails-app/conf/BootStrap.groovy @ 266

Last change on this file since 266 was 266, checked in by keesvb, 11 years ago
changed bootstrapping reason
Property svn:keywords set to `Author Rev Date`
File size: 19.4 KB

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1	import org.codehaus.groovy.grails.commons.GrailsApplication
2	import grails.util.GrailsUtil
3	import dbnp.studycapturing.*
4
5	import dbnp.data.Ontology
6	import dbnp.data.Term
7	import java.text.SimpleDateFormat
8
9	/**
10	* Application Bootstrapper
11	* @Author Jeroen Wesbeek
12	* @Since 20091021
13	*
14	* Revision information:
15	* $Rev: 266 $
16	* $Author: keesvb $
17	* $Date: 2010-03-15 08:28:43 +0000 (ma, 15 mrt 2010) $
18	*/
19	class BootStrap {
20	def init = {servletContext ->
21	// define timezone
22	System.setProperty('user.timezone', 'CET')
23
24	// we could also check if we are in development by GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT
25	if (Study.count() == 0) {
26	printf("development bootstrapping....\n\n");
27
28	// ontologies
29	def speciesOntology = new Ontology(
30	name: 'NCBI Taxonomy',
31	shortName: 'Taxon',
32	url: 'http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy'
33	).with { if (!validate()) { errors.each { println it} } else save()}
34
35	def humanBodyOntology = new Ontology(
36	name: 'Foundational Model of Anatomy',
37	shortName: 'HumanBody',
38	url: 'http://bioportal.bioontology.org/ontologies/39966'
39	).with { if (!validate()) { errors.each { println it} } else save()}
40
41	// terms
42	def mouseTerm = new Term(
43	name: 'Mus musculus',
44	ontology: speciesOntology,
45	accession: '10090'
46	).with { if (!validate()) { errors.each { println it} } else save()}
47	def humanTerm = new Term(
48	name: 'Homo sapiens',
49	ontology: speciesOntology,
50	accession: '9606'
51	).with { if (!validate()) { errors.each { println it} } else save()}
52
53	def bloodTerm = new Term(
54	name: 'Portion of blood',
55	ontology: humanBodyOntology,
56	accession: '9670'
57	).with { if (!validate()) { errors.each { println it} } else save()}
58
59	def madmaxOntology = new Ontology(
60	name: 'Madmax ontology',
61	shortName: 'MDMX',
62	url: 'madmax.bioinformatics.nl'
63	).with { if (!validate()) { errors.each { println it} } else save()}
64
65	def treatmentTerm = new Term(
66	name: 'ExperimentalProtocol',
67	ontology: madmaxOntology,
68	accession: 'P-MDMXGE-264'
69	).with { if (!validate()) { errors.each { println it} } else save()}
70
71	def dietProtocol = new Protocol(
72	name: 'Diet treatment Protocol NuGO PPS3 leptin module',
73	reference: treatmentTerm
74	).with { if (!validate()) { errors.each { println it} } else save()}
75
76	def boostProtocol = new Protocol(
77	name: 'Boost treatment Protocol NuGO PPS3 leptin module',
78	reference: treatmentTerm
79	).with { if (!validate()) { errors.each { println it} } else save()}
80
81	def fastingProtocol = new Protocol(
82	name: 'Fasting',
83	reference: treatmentTerm
84	).with { if (!validate()) { errors.each { println it} } else save()}
85
86
87	// ParameterStringListItems
88	def oil10= new ParameterStringListItem(
89	name: '10% fat (palm oil)'
90	).with { if (!validate()) { errors.each { println it} } else save()}
91	def oil45= new ParameterStringListItem(
92	name: '45% fat (palm oil)'
93	).with { if (!validate()) { errors.each { println it} } else save()}
94	def vehicle= new ParameterStringListItem(
95	name: 'Vehicle'
96	).with { if (!validate()) { errors.each { println it} } else save()}
97	def leptin= new ParameterStringListItem(
98	name: 'Leptin'
99	).with { if (!validate()) { errors.each { println it} } else save()}
100
101
102	dietProtocol
103	.addToParameters(new ProtocolParameter(
104	name: 'Diet',
105	type: ProtocolParameterType.STRINGLIST,
106	listEntries: [oil10,oil45]))
107	.save()
108
109	boostProtocol
110	.addToParameters(new ProtocolParameter(
111	name: 'Compound',
112	type: ProtocolParameterType.STRINGLIST,
113	listEntries: [vehicle,leptin]))
114	.save()
115
116	fastingProtocol
117	.addToParameters(new ProtocolParameter(
118	name: 'Fasting period',
119	type: ProtocolParameterType.STRING))
120	.save()
121
122
123	// sampling event protocols
124
125	def liverSamplingProtocol = new Protocol(
126	name: 'Liver sampling'
127	).with { if (!validate()) { errors.each { println it} } else save()}
128
129	liverSamplingProtocol
130	.addToParameters(new ProtocolParameter(
131	name: 'Sample weight',
132	unit: 'mg',
133	type: ProtocolParameterType.FLOAT))
134	.save()
135
136	def bloodSamplingProtocol = new Protocol(
137	name: 'Blood sampling'
138	).with { if (!validate()) { errors.each { println it} } else save()}
139
140	bloodSamplingProtocol
141	.addToParameters(new ProtocolParameter(
142	name: 'Sample volume',
143	unit: 'ml',
144	type: ProtocolParameterType.FLOAT))
145	.save()
146
147	// create system user
148
149	/*def systemUser = userService.createUser(InstanceGenerator.user(
150	username: 'system',
151	pass: 'system',
152	passConfirm: 'system',
153	enabled: true
154	))*/
155
156
157	def genderField = new TemplateField(
158	name: 'Gender',type: TemplateFieldType.STRINGLIST,
159	listEntries: [new TemplateFieldListItem(name:'Male'),new TemplateFieldListItem(name: 'Female')])
160	.with { if (!validate()) { errors.each { println it} } else save()}
161
162	def ageField = new TemplateField(
163	name: 'Age',type: TemplateFieldType.INTEGER)
164	.with { if (!validate()) { errors.each { println it} } else save()}
165
166	// Nutritional study template
167
168	def studyTemplate = new Template(
169	name: 'Nutritional study', entity: dbnp.studycapturing.Study
170	).addToFields(new TemplateField(
171	name: 'NuGO Code',type: TemplateFieldType.STRING)
172	).with { if (!validate()) { errors.each { println it} } else save()}
173
174
175	// Mouse template
176	def mouseTemplate = new Template(
177	name: 'Mouse', entity: dbnp.studycapturing.Subject
178	).addToFields(new TemplateField(
179	name: 'Genotype',type: TemplateFieldType.STRINGLIST,
180	listEntries: [new TemplateFieldListItem(name:'C57/Bl6j'),new TemplateFieldListItem(name:'wild type')]))
181	.addToFields(genderField)
182	.addToFields(ageField)
183	.addToFields(new TemplateField(
184	name: 'Cage',type: TemplateFieldType.INTEGER))
185	.addToFields(new TemplateField(
186	name: 'SomeDouble', type: TemplateFieldType.DOUBLE))
187	.addToFields(new TemplateField(
188	name: 'SomeOntology', type: TemplateFieldType.ONTOLOGYTERM))
189	.with { if (!validate()) { errors.each { println it} } else save()}
190
191	// Human template
192	def humanTemplate = new Template(
193	name: 'Human', entity: dbnp.studycapturing.Subject)
194	.addToFields(genderField)
195	.addToFields(ageField)
196	.addToFields(new TemplateField(
197	name: 'DOB',type: TemplateFieldType.DATE))
198	.addToFields(new TemplateField(
199	name: 'Height',type: TemplateFieldType.DOUBLE))
200	.addToFields(new TemplateField(
201	name: 'Weight',type: TemplateFieldType.DOUBLE))
202	.addToFields(new TemplateField(
203	name: 'BMI',type: TemplateFieldType.DOUBLE))
204	.with { if (!validate()) { errors.each { println it} } else save()}
205
206	//events
207	def eventDiet = new EventDescription(
208	name: 'Diet treatment',
209	description: 'Diet treatment (fat percentage)',
210	classification: treatmentTerm,
211	protocol: dietProtocol,
212	isSamplingEvent: false
213	).with { if (!validate()) { errors.each { println it} } else save()}
214
215	def eventBoost = new EventDescription(
216	name: 'Boost treatment',
217	description: 'Boost treatment (leptin or vehicle)',
218	classification: treatmentTerm,
219	protocol: boostProtocol,
220	isSamplingEvent: false
221	).with { if (!validate()) { errors.each { println it} } else save()}
222
223	def samplingEvent = new EventDescription(
224	name: 'Liver extraction',
225	description: 'Liver sampling for transcriptomics arrays',
226	protocol: liverSamplingProtocol,
227	isSamplingEvent: true
228	).with { if (!validate()) { errors.each { println it} } else save()}
229
230	def bloodSamplingEventDescription = new EventDescription(
231	name: 'Blood extraction',
232	description: 'Blood extraction targeted at lipid assays',
233	protocol: bloodSamplingProtocol,
234	isSamplingEvent: true
235	).with { if (!validate()) { errors.each { println it} } else save()}
236
237
238	def fastingTreatment = new EventDescription(
239	name: 'Fasting treatment',
240	description: 'Fasting Protocol NuGO PPSH',
241	protocol: fastingProtocol,
242	isSamplingEvent: false
243	).with { if (!validate()) { errors.each { println it} } else save()}
244
245	println('Adding PPS3 study...')
246
247	// studies
248	def exampleStudy = new Study(
249	template: studyTemplate,
250	title:"NuGO PPS3 mouse study leptin module",
251	code:"PPS3_leptin_module",
252	researchQuestion:"Leptin etc.",
253	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.",
254	ecCode:"2007117.c",
255	startDate: Date.parse('yyyy-MM-dd','2007-12-11')
256	).with { if (!validate()) { errors.each { println it} } else save()}
257
258	def evLF = new Event(
259	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
260	endTime: Date.parse('yyyy-MM-dd','2008-01-14'),
261	eventDescription: eventDiet,
262	parameterStringValues: ['Diet':'10% fat (palm oil)']
263	).with { if (!validate()) { errors.each { println it} } else save()}
264
265	def evHF = new Event(
266	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
267	endTime: Date.parse('yyyy-MM-dd','2008-01-14'),
268	eventDescription: eventDiet,
269	parameterStringValues: ['Diet':'45% fat (palm oil)']
270	).with { if (!validate()) { errors.each { println it} } else save()}
271
272	def evBV = new Event(
273	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
274	endTime: Date.parse('yyyy-MM-dd','2008-01-14'),
275	eventDescription: eventBoost,
276	parameterStringValues: ['Compound':'Vehicle']
277	).with { if (!validate()) { errors.each { println it} } else save()}
278
279	def evBL = new Event(
280	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
281	endTime: Date.parse('yyyy-MM-dd','2008-01-14'),
282	eventDescription: eventBoost,
283	parameterStringValues: ['Compound':'Leptin']
284	).with { if (!validate()) { errors.each { println it} } else save()}
285
286	def evLF4 = new Event(
287	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
288	endTime: Date.parse('yyyy-MM-dd','2008-02-04'),
289	eventDescription: eventDiet,
290	parameterStringValues: ['Diet':'10% fat (palm oil)']
291	).with { if (!validate()) { errors.each { println it} } else save()}
292
293	def evHF4 = new Event(
294	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
295	endTime: Date.parse('yyyy-MM-dd','2008-02-04'),
296	eventDescription: eventDiet,
297	parameterStringValues: ['Diet':'45% fat (palm oil)']
298	).with { if (!validate()) { errors.each { println it} } else save()}
299
300	def evBV4 = new Event(
301	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
302	endTime: Date.parse('yyyy-MM-dd','2008-02-04'),
303	eventDescription: eventBoost,
304	parameterStringValues: ['Compound':'Vehicle']
305	).with { if (!validate()) { errors.each { println it} } else save()}
306
307	def evBL4 = new Event(
308	startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
309	endTime: Date.parse('yyyy-MM-dd','2008-02-04'),
310	eventDescription: eventBoost,
311	parameterStringValues: ['Compound':'Leptin']
312	).with { if (!validate()) { errors.each { println it} } else save()}
313
314	def evS = new SamplingEvent(
315	startTime: Date.parse('yyyy-MM-dd','2008-01-14'),
316	endTime: Date.parse('yyyy-MM-dd','2008-01-14'),
317	eventDescription: samplingEvent,
318	parameterFloatValues: ['Sample weight':5F]
319	).with { if (!validate()) { errors.each { println it} } else save()}
320
321	def evS4 = new SamplingEvent(
322	startTime: Date.parse('yyyy-MM-dd','2008-02-04'),
323	endTime: Date.parse('yyyy-MM-dd','2008-02-04'),
324	eventDescription: samplingEvent,
325	parameterFloatValues: ['Sample weight':5F]
326	).with { if (!validate()) { errors.each { println it} } else save()}
327
328	// Add events to study
329	exampleStudy
330	.addToEvents(evLF)
331	.addToEvents(evHF)
332	.addToEvents(evBV)
333	.addToEvents(evBL)
334	.addToEvents(evLF4)
335	.addToEvents(evHF4)
336	.addToEvents(evBV4)
337	.addToEvents(evBL4)
338	.addToSamplingEvents(evS)
339	.addToSamplingEvents(evS4)
340	.save()
341
342	def LFBV1 = new EventGroup(name:"10% fat + vehicle for 1 week")
343	.addToEvents(evLF)
344	.addToEvents(evBV)
345	.with { if (!validate()) { errors.each { println it} } else save()}
346
347	def LFBL1 = new EventGroup(name:"10% fat + leptin for 1 week")
348	.addToEvents(evLF)
349	.addToEvents(evBL)
350	.with { if (!validate()) { errors.each { println it} } else save()}
351
352	def HFBV1 = new EventGroup(name:"45% fat + vehicle for 1 week")
353	.addToEvents(evHF)
354	.addToEvents(evBV)
355	.with { if (!validate()) { errors.each { println it} } else save()}
356
357	def HFBL1 = new EventGroup(name:"45% fat + leptin for 1 week")
358	.addToEvents(evHF)
359	.addToEvents(evBL)
360	.with { if (!validate()) { errors.each { println it} } else save()}
361
362	def LFBV4 = new EventGroup(name:"10% fat + vehicle for 4 weeks")
363	.addToEvents(evLF4)
364	.addToEvents(evBV4)
365	.with { if (!validate()) { errors.each { println it} } else save()}
366
367	def LFBL4 = new EventGroup(name:"10% fat + leptin for 4 weeks")
368	.addToEvents(evLF4)
369	.addToEvents(evBL4)
370	.with { if (!validate()) { errors.each { println it} } else save()}
371
372	def HFBV4 = new EventGroup(name:"45% fat + vehicle for 4 weeks")
373	.addToEvents(evHF4)
374	.addToEvents(evBV4)
375	.with { if (!validate()) { errors.each { println it} } else save()}
376
377	def HFBL4 = new EventGroup(name:"45% fat + leptin for 4 weeks")
378	.addToEvents(evHF4)
379	.addToEvents(evBL4)
380	.with { if (!validate()) { errors.each { println it} } else save()}
381
382	// Add subjects and samples and compose EventGroups
383
384	def x=1
385	80.times {
386	def currentSubject = new Subject(
387	name: "A" + x++,
388	species: mouseTerm,
389	template: mouseTemplate,
390	)
391	.setFieldValue("Gender", "Male")
392	.setFieldValue("Genotype", "C57/Bl6j")
393	.setFieldValue("Age", 17)
394	.setFieldValue("Cage", (int)(x/2))
395	.with { if (!validate()) { errors.each { println it} } else save()}
396
397	exampleStudy.addToSubjects(currentSubject)
398	.with { if (!validate()) { errors.each { println it} } else save()}
399
400	// Add subject to appropriate EventGroup
401	if (x > 70) { HFBL4.addToSubjects(currentSubject).save() }
402	else if (x > 60) { HFBV4.addToSubjects(currentSubject).save() }
403	else if (x > 50) { LFBL4.addToSubjects(currentSubject).save() }
404	else if (x > 40) { LFBV4.addToSubjects(currentSubject).save() }
405	else if (x > 30) { HFBL1.addToSubjects(currentSubject).save() }
406	else if (x > 20) { HFBV1.addToSubjects(currentSubject).save() }
407	else if (x > 10) { LFBL1.addToSubjects(currentSubject).save() }
408	else { LFBV1.addToSubjects(currentSubject).save() }
409
410	}
411
412	// Add EventGroups to study
413	exampleStudy
414	.addToEventGroups(LFBV1)
415	.addToEventGroups(LFBL1)
416	.addToEventGroups(HFBV1)
417	.addToEventGroups(HFBL1)
418	.addToEventGroups(LFBV4)
419	.addToEventGroups(LFBL4)
420	.addToEventGroups(HFBV4)
421	.addToEventGroups(HFBL4)
422	.save()
423
424	println 'Adding PPSH study'
425
426	def humanStudy = new Study(
427	template: studyTemplate,
428	title:"NuGO PPS human study",
429	code:"PPSH",
430	researchQuestion:"How much are fasting plasma and urine metabolite levels affected by prolonged fasting ?",
431	description:"Human study",
432	ecCode:"unknown",
433	startDate: Date.parse('yyyy-MM-dd','2009-01-01')
434	).with { if (!validate()) { errors.each { println it} } else save()}
435
436	def fastingEvent = new Event(
437	startTime: Date.parse('yyyy-MM-dd','2008-01-14'),
438	endTime: Date.parse('yyyy-MM-dd','2008-01-14'),
439	eventDescription: fastingTreatment,
440	parameterStringValues: ['Fasting period':'8h']);
441
442	def bloodSamplingEvent = new SamplingEvent(
443	startTime: Date.parse('yyyy-MM-dd','2008-01-14'),
444	endTime: Date.parse('yyyy-MM-dd','2008-01-14'),
445	eventDescription: bloodSamplingEventDescription,
446	parameterFloatValues: ['Sample volume':4.5F]);
447
448	def rootGroup = new EventGroup(name: 'Root group');
449	rootGroup.addToEvents fastingEvent
450	rootGroup.addToEvents bloodSamplingEvent
451	rootGroup.save()
452
453	def y = 1
454	11.times {
455	def currentSubject = new Subject(
456	name: "" + y++,
457	species: humanTerm,
458	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", 30).setFieldValue("Height", Math.random() * 2F).setFieldValue("Weight", Math.random() * 150F).setFieldValue("BMI", 20 + Math.random() * 10F).with { if (!validate()) { errors.each { println it} } else save()}
459
460	rootGroup.addToSubjects currentSubject
461	rootGroup.save()
462
463	def currentSample = new Sample(
464	name: currentSubject.name + '_B',
465	material: bloodTerm,
466	parentSubject: currentSubject,
467	parentEvent: bloodSamplingEvent);
468
469
470	humanStudy.addToSubjects(currentSubject).addToSamples(currentSample).with { if (!validate()) { errors.each { println it} } else save()}
471	}
472
473	humanStudy.addToEventGroups rootGroup
474	humanStudy.save()
475
476	// Add clinical data
477
478	def lipidAssay = new dbnp.clinicaldata.ClinicalAssay(
479	name: 'Lipid profile',
480	approved: true
481	).with { if (!validate()) { errors.each { println it} } else save()}
482
483	def ldlMeasurement = new dbnp.clinicaldata.ClinicalMeasurement(
484	name: 'LDL',
485	unit: 'mg/dL',
486	type: dbnp.data.FeatureType.QUANTITATIVE,
487	referenceValues: '100 mg/dL',
488	detectableLimit: 250,
489	isDrug: false, isIntake: true, inSerum: true
490	).with { if (!validate()) { errors.each { println it} } else save()}
491
492	def hdlMeasurement = new dbnp.clinicaldata.ClinicalMeasurement(
493	name: 'HDL',
494	unit: 'mg/dL',
495	type: dbnp.data.FeatureType.QUANTITATIVE,
496	referenceValues: '50 mg/dL',
497	detectableLimit: 100,
498	isDrug: false, isIntake: true, inSerum: true
499	).with { if (!validate()) { errors.each { println it} } else save()}
500
501	lipidAssay.addToMeasurements ldlMeasurement
502	lipidAssay.addToMeasurements hdlMeasurement
503
504	def lipidAssayInstance = new dbnp.clinicaldata.ClinicalAssayInstance(
505	assay: lipidAssay
506	).with { if (!validate()) { errors.each { println it} } else save()}
507
508	humanStudy.samples*.each {
509	new dbnp.clinicaldata.ClinicalFloatData(
510	assay: lipidAssayInstance,
511	measurement: ldlMeasurement,
512	sample: it.name,
513	value: Math.round(Math.random()*ldlMeasurement.detectableLimit)
514	).with { if (!validate()) { errors.each { println it} } else save()}
515
516	new dbnp.clinicaldata.ClinicalFloatData(
517	assay: lipidAssayInstance,
518	measurement: hdlMeasurement,
519	sample: it.name,
520	value: Math.round(Math.random()*hdlMeasurement.detectableLimit)
521	).with { if (!validate()) { errors.each { println it} } else save()}
522	}
523
524	// Add assay to study capture module
525
526	def clinicalModule = new AssayModule(
527	name: 'Clinical data',
528	type: AssayType.CLINICAL_DATA,
529	platform: 'clinical measurements',
530	url: 'http://localhost:8080/gscf'
531	).with { if (!validate()) { errors.each { println it} } else save()}
532
533	def lipidAssayRef = new Assay(
534	name: 'Lipid profiling',
535	module: clinicalModule,
536	externalAssayId: lipidAssayInstance.id
537	).with { if (!validate()) { errors.each { println it} } else save()}
538
539	humanStudy.samples*.each {
540	lipidAssayRef.addToSamples(it)
541	}
542	lipidAssayRef.save()
543
544	humanStudy.addToAssays(lipidAssayRef);
545	humanStudy.save()
546
547	}
548	}
549
550	def destroy = {
551	}
552	}

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