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source: trunk/grails-app/conf/BootStrap.groovy @ 383

Last change on this file since 383 was 383, checked in by duh, 11 years ago
initial event template
Property svn:keywords set to `Author Rev Date`
File size: 32.5 KB

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

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