source: trunk/grails-app/controllers/nmc/PilotController.groovy @ 1348

/**
 * PilotController Controler
 *
 * Description of my controller
 *
 * @author  m.s.vanvliet@lacdr.leidenuniv.nl (Michael van Vliet)
 * @since       20101019
 * @package     nmc
 *
 * Revision information:
 * $Rev: 1222 $
 * $Author: work@osx.eu $
 * $Date: 2010-11-30 13:10:42 +0000 (di, 30 nov 2010) $
 */
package nmc

import dbnp.studycapturing.*;
import grails.plugins.springsecurity.Secured


class PilotController {
        
        def authenticationService
        
        static allowedMethods = [save: "POST", update: "POST", delete: "POST"]
        
        /**
        * Fires after every action and determines the layout of the page
        */
   def afterInterceptor = { model, modelAndView ->
         
         if ( params['dialog'] ) {
           model.layout = 'dialog';
           model.extraparams = [ 'dialog': 'true' ] ;
         } else {
           model.layout = 'main';
           model.extraparams = [] ;
         }
   }
        
    @Secured(['IS_AUTHENTICATED_REMEMBERED'])
        def index = {
                
                session.pilot = true

                def user = authenticationService.getLoggedInUser()
                def max = Math.min(params.max ? params.int('max') : 10, 100)
                def studies = Study.giveReadableStudies(user, max);
                
                def studyInstance = new Study()
                studyInstance.properties = params
                
                [studyInstanceList: studies, studyInstance: studyInstance]
    }

    def list = {
        params.max = Math.min(params.max ? params.int('max') : 10, 100)
        [studyInstanceList: Study.list(params), studyInstanceTotal: Study.count()]
    }
          
   def save = {
           def studyInstance = new Study(params)
           
           //For Pilot we do not ask for code, we generate it for the user
           studyInstance.code = params?.title?.encodeAsMD5()
           studyInstance.owner = authenticationService.getLoggedInUser()
           
           def extraparams = new LinkedHashMap();

           if( params[ 'dialog' ] ) {
                 extraparams[ 'dialog' ] = params[ 'dialog' ]
           }

           if (studyInstance.save(flush: true)) {
                   
                   //Study was created, now setup a NMC - Metabolomics Assay for testing
                   def assayInstance = new Assay()
                   assayInstance.name = "${studyInstance.title} - Metabolomics Assay"
                   assayInstance.module = AssayModule.findByName("Metabolomics module")
                   assayInstance.externalAssayID = assayInstance?.name?.encodeAsMD5()
                   studyInstance.addToAssays(assayInstance)
                   assayInstance.save(flush: true)
                                   
                   //flash.message = "${message(code: 'default.created.message', args: [message(code: 'study.label', default: 'Study'), ( studyInstance.title ? studyInstance.title : "" ) + " " + ( studyInstance.code ? studyInstance.code : "" )])}"
                   
                   redirect(action: "show", id: studyInstance.id, params: extraparams )
           }
           else {
                   render(view: "index", model: [studyInstance: studyInstance])
           }
   }
   
   def show = {
                           
           def studyInstance = Study.get(params.id)
           if (!studyInstance) {
                   flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'study.label', default: 'Study'), params.id])}"
                   redirect(action: "list")
           }
           else {
                   
                   //add all samples to the assay when not there yet!
                   studyInstance.assays.each { assay ->
                           //if (assay.samples.size() <= 0){ // needs improving!!! too much overhead, okay for pilot
                                   studyInstance.samples.each { sample ->
                                           log.info("ADD THE DIRTY WAY!!!")
                                           assay.addToSamples(sample)
                                   }
                                   assay.save()
                           //}                     
                   }
                   
                   [studyInstance: studyInstance]
           }
   }
   
   def edit = {
           def studyInstance = Study.get(params.id)
           if (!studyInstance) {
                   flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'study.label', default: 'Study'), params.id])}"
                   redirect(action: "list")
           }
           else {
                   return [studyInstance: studyInstance]
           }
   }

   def update = {
           def studyInstance = Study.get(params.id)
           
           //For Pilot we do not ask for code, we generate it for the user
           studyInstance.code = studyInstance?.title?.encodeAsMD5()

           def extraparams = new LinkedHashMap();

           if( params[ 'dialog' ] ) {
                 extraparams[ 'dialog' ] = params[ 'dialog' ]
           }

           if (studyInstance) {
                   if (params.version) {
                           def version = params.version.toLong()
                           if (studyInstance.version > version) {
                                   
                                   studyInstance.errors.rejectValue("version", "default.optimistic.locking.failure", [message(code: 'study.label', default: 'Study')] as Object[], "Another user has updated this Study while you were editing")
                                   render(view: "edit", model: [studyInstance: studyInstance])
                                   return
                           }
                   }
                   studyInstance.properties = params
                   if (!studyInstance.hasErrors() && studyInstance.save(flush: true)) {
                           flash.message = "${message(code: 'default.created.message', args: [message(code: 'study.label', default: 'Study'), ( studyInstance.title ? studyInstance.title : "" ) + " " + ( studyInstance.code ? studyInstance.code : "" )])}"
                           redirect(action: "show", id: studyInstance.id, params: extraparams)
                   }
                   else {
                           render(view: "edit", model: [studyInstance: studyInstance])
                   }
           }
           else {
                   flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'study.label', default: 'Study'), params.id])}"
                   redirect(action: "list", params: extraparams)
           }
   }

   def delete = {
           def studyInstance = Study.get(params.id)

           def extraparams = new LinkedHashMap();

           if( params[ 'dialog' ] ) {
                 extraparams[ 'dialog' ] = params[ 'dialog' ]
           }

           if (studyInstance) {
                   def studyName = ( studyInstance.title ? studyInstance.title : "" ) + " " + ( studyInstance.code ? studyInstance.code : "" );
                   try {
                           studyInstance.delete(flush: true)
                           flash.message = "${message(code: 'default.deleted.message', args: [message(code: 'study.label', default: 'Study'), studyName])}"
                           redirect(action: "list", params: extraparams)
                   }
                   catch (org.springframework.dao.DataIntegrityViolationException e) {
                           flash.message = "${message(code: 'default.not.deleted.message', args: [message(code: 'study.label', default: 'Study'), studyName])}"
                           redirect(action: "show", id: params.id, params: extraparams)
                   }
           }
           else {
                   flash.message = "${message(code: 'default.not.deleted.message', args: [message(code: 'study.label', default: 'Study'), studyName])}"
                   redirect(action: "list", params: extraparams)
           }
   }
}