source: trunk/grails-app/conf/BootStrap.groovy @ 1107

import dbnp.studycapturing.*

import dbnp.data.Ontology
import dbnp.data.Term
import dbnp.rest.common.CommunicationManager
import org.codehaus.groovy.grails.commons.GrailsApplication
import grails.util.GrailsUtil
import dbnp.authentication.*

/**
 * Application Bootstrapper
 * @Author Jeroen Wesbeek
 * @Since 20091021
 *
 * Revision information:
 * $Rev: 1107 $
 * $Author: work@osx.eu $
 * $Date: 2010-11-09 17:12:29 +0000 (di, 09 nov 2010) $
 */
class BootStrap {
        def springSecurityService

        def init = {servletContext ->
                // define timezone
                System.setProperty('user.timezone', 'CET')

                "Bootstrapping application".grom()

                def adminRole = SecRole.findByAuthority('ROLE_ADMIN') ?: new SecRole(authority: 'ROLE_ADMIN').save()

                def user = SecUser.findByUsername('user') ?: new SecUser(
                        username: 'user',
                        password: springSecurityService.encodePassword('useR123!', 'user'),
                        email: 'user@dbnp.org',
                        userConfirmed: true, adminConfirmed: true).save(failOnError: true)

                def userAdmin = SecUser.findByUsername('admin') ?: new SecUser(
                        username: 'admin',
                        password: springSecurityService.encodePassword('admiN123!', 'admin'),
                        email: 'admin@dbnp.org',
                        userConfirmed: true, adminConfirmed: true).save(failOnError: true)

                // Make the admin user an administrator
                SecUserSecRole.create userAdmin, adminRole, true

                def userTest = SecUser.findByUsername('test') ?: new SecUser(
                        username: 'test',
                        password: springSecurityService.encodePassword('useR123!', 'test'),
                        email: 'test@dbnp.org',
                        userConfirmed: true, adminConfirmed: true).save(failOnError: true)

                println "Done with SpringSecurity bootstrap, created [user, admin, test]."

                // If there are no templates yet in the database
                if (Template.count() == 0) {
                        println "No templates in the current database.";

                        // If in development or test mode, add the ontologies manually to the database
                        // without contacting the BioPortal website, to avoid annoying hiccups when the server is busy
                        if (grails.util.GrailsUtil.environment != GrailsApplication.ENV_PRODUCTION) {
                                println "Adding ontology descriptors"
                                BootStrapTemplates.initTemplateOntologies()
                        }

                        // Add example study, subject, event etc. templates
                        BootStrapTemplates.initTemplates()

                        // If in development mode and no studies are present, add example studies
                        if (Study.count() == 0 && grails.util.GrailsUtil.environment != GrailsApplication.ENV_TEST) {
                                // check if special file is present in project directory
                                if ((new File(System.properties['user.dir'] + "/.skip-studies").exists())) {
                                        "Skipping study bootstrapping".grom()

                                        // get species ontology
                                        def speciesOntology = Ontology.getOrCreateOntologyByNcboId(1132)

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

                                        def humanTerm = new Term(
                                                name: 'Homo sapiens',
                                                ontology: speciesOntology,
                                                accession: '9606'
                                        ).with { if (!validate()) { errors.each { println it} } else save(flush: true)}
                                } else {
                                        "Bootstrapping Studies".grom()
                                        
                                        // general study boostrapping
                                        BootStrapStudies.addExampleStudies(user, userAdmin)
                                }
                        }

                        println "Finished adding templates and studies"
                }

                /**
                 * 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)]
                TemplateEntity.getField(Sample.domainFields, 'material').ontologies = [Ontology.getOrCreateOntologyByNcboId(1005)]

                println "Registering SAM REST methods"
                CommunicationManager.registerRestWrapperMethodsSAMtoGSCF()

                println "Done with BootStrap"
        }

        def destroy = {
        }
}