source: trunk/grails-app/controllers/dbnp/studycapturing/AssayController.groovy @ 1261

package dbnp.studycapturing

class AssayController {

    def assayService
    def authenticationService
    
    static allowedMethods = [save: "POST", update: "POST", delete: "POST"]

    def index = {
        redirect(action: "list", params: params)
    }

    def list = {
        params.max = Math.min(params.max ? params.int('max') : 10, 100)
        [assayInstanceList: Assay.list(params), assayInstanceTotal: Assay.count()]
    }

    def create = {
        def assayInstance = new Assay()
        assayInstance.properties = params
        return [assayInstance: assayInstance]
    }

    def save = {
        def assayInstance = new Assay(params)

        // The following lines deviate from the generate-all generated code.
        // See http://jira.codehaus.org/browse/GRAILS-3783 for why we have this shameful workaround...
        def study = assayInstance.parent
        study.addToAssays(assayInstance)

        if (assayInstance.save(flush: true)) {
            flash.message = "${message(code: 'default.created.message', args: [message(code: 'assay.label', default: 'Assay'), assayInstance.id])}"
            redirect(action: "show", id: assayInstance.id)
        }
        else {
            render(view: "create", model: [assayInstance: assayInstance])
        }
    }

    def show = {
        def assayInstance = Assay.get(params.id)
        if (!assayInstance) {
            flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
            redirect(action: "list")
        }
        else {
            [assayInstance: assayInstance]
        }
    }

        def showByToken = {
            def assayInstance = Assay.findByExternalAssayID(params.id)
            if (!assayInstance) {
                flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
                redirect(action: "list")
            }
            else {
                    redirect(action: "show", id: assayInstance.id)
            }
        }

    def edit = {
        def assayInstance = Assay.get(params.id)
        if (!assayInstance) {
            flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
            redirect(action: "list")
        }
        else {
            return [assayInstance: assayInstance]
        }
    }

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

    def delete = {
        def assayInstance = Assay.get(params.id)
        if (assayInstance) {
            try {
                assayInstance.delete(flush: true)
                flash.message = "${message(code: 'default.deleted.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
                redirect(action: "list")
            }
            catch (org.springframework.dao.DataIntegrityViolationException e) {
                flash.message = "${message(code: 'default.not.deleted.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
                redirect(action: "show", id: params.id)
            }
        }
        else {
            flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
            redirect(action: "list")
        }
    }

    /**
     * Shows a page where an assay from a study can be selected
     *
     * @param none
     */
    def selectAssay = {
        def user = authenticationService.getLoggedInUser()
        def studies = Study.findAllByOwner(user)
        def assays = Assay.findAllByParent(studies[0])

        [userStudies: studies, assays: assays]
    }

    /**
     * Exports all assay information as an Excel file.
     *
     * @param params.id Assay id
     */
    def exportAssayAsExcel = {
        Assay assay = Assay.get(params.id)

        if (!assay) {
            flash.errorMessage = "No assay found with id: $params.id."
            redirect action: 'selectAssay'
            return
        }

        // TODO: refactor into service

        // Gather sample meta data from GSCF
        def samples = assay.samples

        def collectUsedTemplateFields = { templateEntityList ->

            def templateFields = templateEntityList*.giveFields().flatten().unique().findAll{it}
            def usedTemplateFields = templateFields.findAll{ tf ->

                templateEntityList.any { it.fieldExists(tf.name) && it.getFieldValue(tf.name) }
            }

            def m = [:]
            usedTemplateFields.each { tf ->
                m["${tf.name}"] = templateEntityList.collect{ it.fieldExists(tf.name) ? it.getFieldValue(tf.name) : '' }
            }
            m
        }

        // get all sample related subjects
        def assayData = [
                'Subject Data':         collectUsedTemplateFields(samples*.parentSubject.unique()),
                'Sampling Event Data':  collectUsedTemplateFields(samples*.parentEvent.unique()),
                'Event Data':           collectUsedTemplateFields(samples*.parentEventGroup.events.flatten().unique()),
                'Sample Data':          collectUsedTemplateFields(samples)]

        // Gather sample meta data from the module

        // - sample metadata

        // Gather measurement data from the module

        // - measurements

        // Write to excel

        println assayData

        try {
            assayService.exportAssayDataAsExcelFile(assayData)
        } catch (Exception e) {
            flash.errorMessage = e.message
            redirect action: 'selectAssay'
        }
    }
}