source: trunk/grails-app/conf/BootStrap.groovy @ 177

import org.codehaus.groovy.grails.commons.GrailsApplication
import grails.util.GrailsUtil
import dbnp.studycapturing.*

import dbnp.data.Ontology
import dbnp.data.Term

/**
 * Application Bootstrapper
 * @Author Jeroen Wesbeek
 * @Since 20091021
 *
 * Revision information:
 * $Rev: 177 $
 * $Author: keesvb $
 * $Date: 2010-02-08 11:46:19 +0000 (ma, 08 feb 2010) $
 */
class BootStrap {
        def init = {servletContext ->
                // define timezone
                System.setProperty('user.timezone', 'CET')      

                if (GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT) {
                        printf("development bootstrapping....\n\n");

                        // ontologies
                        def speciesOntology = new Ontology(
                                name: 'NCBI Taxonomy',
                                shortName: 'Taxon',
                                url: 'http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy'
                        ).with { if (!validate()) { errors.each { println it} } else save()}


                        // terms
                        def mouseTerm = new Term(
                                name: 'Mus musculus',
                                ontology: speciesOntology,
                                accession: '10090'
                        ).with { if (!validate()) { errors.each { println it} } else save()}
                        def humanTerm = new Term(
                                name: 'Homo sapiens',
                                ontology: speciesOntology,
                                accession: '9606'
                        ).with { if (!validate()) { errors.each { println it} } else save()}

                        def madmaxOntology = new Ontology(
                                name: 'Madmax ontology',
                                shortName: 'MDMX',
                                url: 'madmax.bioinformatics.nl'
                        ).with { if (!validate()) { errors.each { println it} } else save()}

                        def treatmentTerm = new Term(
                                name: 'ExperimentalProtocol',
                                ontology: madmaxOntology,
                                accession: 'P-MDMXGE-264'
                        ).with { if (!validate()) { errors.each { println it} } else save()}


                        def treatmentProtocol = new Protocol(
                                name: 'MADMAX Experimental Protocol',
                                reference: treatmentTerm
                        ).with { if (!validate()) { errors.each { println it} } else save()}


                        // added by Jahn for testing the event views
                        def treatmentProtocol2 = new Protocol(
                                name: 'MADMAX Experimental Protocol 2',
                                reference: treatmentTerm
                        ).with { if (!validate()) { errors.each { println it} } else save()}



                        treatmentProtocol
                        .addToParameters(new ProtocolParameter(
                                name: 'Diet',
                                type: ProtocolParameterType.STRINGLIST,
                                listEntries: ['10% fat (palm oil)','45% fat (palm oil)']))
                        .addToParameters(new ProtocolParameter(
                                name: 'Compound',
                                type: ProtocolParameterType.STRINGLIST,
                                listEntries: ['Vehicle','Leptin']))
                        .addToParameters(new ProtocolParameter(
                                name: 'Administration',
                                type: ProtocolParameterType.STRING))
                        .save()


                        // added by Jahn for testing the event views
                        treatmentProtocol2
                        .addToParameters(new ProtocolParameter(
                                name: 'Diet',
                                type: ProtocolParameterType.STRINGLIST,
                                listEntries: ['99% fat (crude oil)','1% fat (palm oil)']))
                        .addToParameters(new ProtocolParameter(
                                name: 'Compound',
                                type: ProtocolParameterType.STRINGLIST,
                                listEntries: ['Vehicle','Leptin']))
                        .addToParameters(new ProtocolParameter(
                                name: 'Administration',
                                type: ProtocolParameterType.STRING))
                        .save()



                        // create system user
                        /*
                        def systemUser = userService.createUser(InstanceGenerator.user(
                                username: 'system',
                                pass: 'system',
                                passConfirm: 'system',
                                enabled: true
                        ))
                        */

                        // Mouse template
                        def mouseTemplate = new Template(
                                name: 'Mouse'
                        ).addToSubjectFields(new TemplateSubjectField(
                                name: 'Genotype',type: TemplateFieldType.STRINGLIST,
                                listEntries: ['C57/Bl6j','wild type']))
                        .addToSubjectFields(new TemplateSubjectField(
                                name: 'Gender',type: TemplateFieldType.STRINGLIST,
                                listEntries: ['Male','Female']))
                        .addToSubjectFields(new TemplateSubjectField(
                                name: 'Age',type: TemplateFieldType.INTEGER))
                        .addToSubjectFields(new TemplateSubjectField(
                                name: 'Cage',type: TemplateFieldType.INTEGER))
                        .with { if (!validate()) { errors.each { println it} } else save()}


                        //events
                        def eventTreatment = new EventDescription(
                                name: 'Treatment',
                                description: 'Experimental Treatment Protocol NuGO PPS3 leptin module',
                                classification: treatmentTerm,
                                protocol: treatmentProtocol
                        ).with { if (!validate()) { errors.each { println it} } else save()}

                        def eventTreatment2 = new EventDescription(
                                name: 'Treatment2',
                                description: 'Treatment Protocol NuGO PPS1',
                                classification: treatmentTerm,
                                protocol: treatmentProtocol2
                        ).with { if (!validate()) { errors.each { println it} } else save()}

                        // studies
                        def exampleStudy = new Study(
                                title:"NuGO PPS3 mouse study leptin module",
                                code:"PPS3_leptin_module",
                                researchQuestion:"Leptin etc.",
                                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.",
                                ecCode:"2007117.c",
                                startDate: Date.parse('yyyy-MM-dd','2007-12-11'),
                                template: mouseTemplate
                        ).with { if (!validate()) { errors.each { println it} } else save()}

                        def x=1
                        12.times {
                                def currentSubject = new Subject(
                                        name: "A" + x++,
                                        species: mouseTerm,
                                        template: mouseTemplate,
                                        templateStringFields: ["Genotype" : "C57/Bl6j", "Gender" : "Male"],
                                        templateIntegerFields: ["Age" : 17, "Cage" : (int)(x/2)]
                                ).with { if (!validate()) { errors.each { println it} } else save()}

                                exampleStudy.addToSubjects(currentSubject)
                                .addToEvents(new Event(
                                        subject: currentSubject,
                                        startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
                                        endTime: Date.parse('yyyy-MM-dd','2008-01-14'),
                                        eventDescription: eventTreatment,
                                        parameterStringValues: ['Diet':'10% fat (palm oil)','Compound':'Vehicle','Administration':'intraperitoneal injection'])
                                ).with { if (!validate()) { errors.each { println it} } else save()}
                        }


                        def secondStudy = new Study(
                                title:"NuGO PPS1 mouse study leptin module",
                                code:"PPS1",
                                researchQuestion:"etc.",
                                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.",
                                ecCode:"2007.c",
                                startDate: Date.parse('yyyy-MM-dd','2007-12-11'),
                                template: mouseTemplate
                        ).with { if (!validate()) { errors.each { println it} } else save()}

                        def y=1
                        5.times {
                                def currentSubject = new Subject(
                                        name: "A" + y++,
                                        species: mouseTerm,
                                        template: mouseTemplate,
                                        templateStringFields: ["Genotype" : "C57/Bl6j", "Gender" : "Male"],
                                        templateIntegerFields: ["Age" : 17, "Cage" : (int)(y/2)]
                                ).with { if (!validate()) { errors.each { println it} } else save()}

                                secondStudy.addToSubjects(currentSubject)
                                .addToEvents(new SamplingEvent(
                                        subject: currentSubject,
                                        startTime: Date.parse('yyyy-MM-dd','2008-01-07'),
                                        endTime: Date.parse('yyyy-MM-dd','2008-01-14'),
                                        eventDescription: eventTreatment2,
                                        parameterStringValues: ['Diet':'10% fat (palm oil)','Compound':'Vehicle','Administration':'intraperitoneal injection'])
                                ).with { if (!validate()) { errors.each { println it} } else save()}
                        }

//                        new Study(title:"example",code:"Excode",researchQuestion:"ExRquestion",description:"Exdescription",ecCode:"ExecCode",dateCreated:new Date(),lastUpdated:new Date(),startDate:new Date()).save()
//                        new Study(title:"testAgain",code:"testcode",researchQuestion:"testRquestion",description:"testdescription",ecCode:"testCode",dateCreated:new Date(),lastUpdated:new Date(),startDate:new Date()).save()
//                        new Study(title:"Exampletest",code:"Examplecode",researchQuestion:"ExampleRquestion",description:"Exampledescription",ecCode:"ExampleecCode",dateCreated:new Date(),lastUpdated:new Date(),startDate:new Date()).save()
                }
        }

        def destroy = {
        }
}