source: trunk/grails-app/conf/BootStrap.groovy @ 2154

import dbnp.authentication.SecRole
import dbnp.authentication.SecUser
import org.codehaus.groovy.grails.commons.GrailsApplication
import org.dbnp.gdt.*
import dbnp.studycapturing.Study
import dbnp.studycapturing.Subject
import dbnp.studycapturing.Sample
import dbnp.rest.common.CommunicationManager
import dbnp.configuration.*

/**
 * Application Bootstrapper
 * @Author Jeroen Wesbeek
 * @Since 20091021
 *
 * Revision information:
 * $Rev: 1815 $
 * $Author: m.s.vanvliet@lacdr.leidenuniv.nl $
 * $Date: 2011-05-05 14:50:15 +0000 (do, 05 mei 2011) $
 */
class BootStrap {
        // user spring security
        def springSecurityService

        // inject the datasource
        def dataSource

        // inject the grails application
        def grailsApplication

        def init = { servletContext ->
                // Grom a development message
                if (String.metaClass.getMetaMethod("grom")) "bootstrapping application".grom()

                // get configuration
                def config = grailsApplication.config

                // define timezone
                System.setProperty('user.timezone', 'CET')

                // set up authentication (if required)
                if (!SecRole.count() || !SecUser.count()) BootStrapAuthentication.initDefaultAuthentication(springSecurityService)

                // set up the SAM communication manager
                // this should probably more dynamic and put into the modules
                // section instead of the bootstrap as not all instances will
                // probably run WITH sam. GSCF should be able to run independently
                // from other modules. Part of gscf ticket #185
                if (config.modules) {
                        // Grom a development message
                        if (String.metaClass.getMetaMethod("grom")) "Registering SAM REST methods".grom()
                        CommunicationManager.registerModule('gscf', config.grails.serverURL, config.modules)
                        CommunicationManager.registerRestWrapperMethodsFromSAM()
                }

                // automatically handle database upgrades
                DatabaseUpgrade.handleUpgrades(dataSource)

                // developmental/test/demo bootstrapping:
                //      - templates
                //      - ontologies
                //      - and/or studies
                if (    grails.util.GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT ||
                grails.util.GrailsUtil.environment == GrailsApplication.ENV_TEST ||
                grails.util.GrailsUtil.environment == "dbnpdemo") {
                        // add ontologies?
                        if (!Ontology.count()) ExampleTemplates.initTemplateOntologies()

                        // add templates?
                        if (!Template.count()) ExampleTemplates.initTemplates()

                        // add data required for the webtests?
                        if (grails.util.GrailsUtil.environment == GrailsApplication.ENV_TEST) ExampleStudies.addTestData()

                        // add example studies?
                        if (!Study.count() && grails.util.GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT)
                                ExampleStudies.addExampleStudies(SecUser.findByUsername('user'), SecUser.findByUsername('admin'))
                }

                /**
                 * attach ontologies in runtime. Possible problem is that you need
                 * an internet connection when bootstrapping though.
                 * @see dbnp.studycapturing.Subject
                 * @see dbnp.studycapturing.Sample
                 */
                TemplateEntity.getField(Subject.domainFields, 'species').ontologies = [
                        Ontology.getOrCreateOntologyByNcboId(1132),             // NCBI Organismal Classification
                        Ontology.getOrCreateOntologyByNcboId(1069)              // Environmental Ontology
                ]
                TemplateEntity.getField(Sample.domainFields, 'material').ontologies = [
                        Ontology.getOrCreateOntologyByNcboId(1005)              // BRENDA Tissue / enzyme source
                ]
        }

        def destroy = {
                // Grom a development message
                if (String.metaClass.getMetaMethod("grom")) "stopping application...".grom()
        }
}