source: trunk/test/integration/gscf/SampleTests.groovy @ 662

package gscf

import dbnp.studycapturing.Study
import dbnp.studycapturing.Template
import grails.test.GrailsUnitTestCase
import dbnp.studycapturing.SamplingEvent
import dbnp.studycapturing.Sample
import dbnp.studycapturing.TemplateFieldType

/**
 * Test the creation of a Sample and its TemplateEntity functionality on data model level
 *
 * @author keesvb
 * @since 20100511
 * @package dbnp.studycapturing
 *
 * Revision information:
 * $Rev$
 * $Author$
 * $Date$
 */

class SampleTests extends StudyTests {

        // This test extends StudyTests, so that we have a test study to assign as a parent study

        final String testSampleName = "Test sample"
        final String testSampleTemplateName = "Human blood sample"

        final String testSamplingEventName = "Test sampling event"
        final String testSamplingEventTemplateName = "Blood extraction"
        final long testSamplingEventTime = 34534534L


        protected void setUp() {
                super.setUp()

                // Retrieve the study that should have been created in StudyTests
                def study = Study.findByTitle(testStudyName)
                assert study

                // Look up sampling event template
                def samplingEventTemplate = Template.findByName(testSamplingEventTemplateName)
                assert samplingEventTemplate

                // Create parent sampling event
                def samplingEvent = new SamplingEvent(
                        startTime: testSamplingEventTime,
                        endTime: testSamplingEventTime,
                        template: samplingEventTemplate
                )

                if (!samplingEvent.validate()) {
                        samplingEvent.errors.each { println it}
                }
                assert samplingEvent.validate()

                assert samplingEvent.save(flush:true)

                // Look up sample template
                def sampleTemplate = Template.findByName(testSampleTemplateName)
                assert sampleTemplate

                // Create sample with the retrieved study as parent
                def sample = new Sample(
                    name: testSampleName,
                    template: sampleTemplate,
                    parentEvent: samplingEvent
                )

                // At this point, the sample should not validate, because it doesn't have a parent study assigned
                assert !sample.validate()

                // Add the sample to the retrieved parent study
                study.addToSamples(sample)
                assert study.samples.find { it.name == sample.name}

                // Now, the sample should validate
                if (!sample.validate()) {
                        sample.errors.each { println it}
                }
                assert sample.validate()

                // Make sure the sample is saved to the database
                assert sample.save(flush: true)

        }

        void testSave() {
                // Try to retrieve the sample and make sure it's the same
                def sampleDB = Sample.findByName(testSampleName)
                assert sampleDB
                assert sampleDB.name.equals(testSampleName)
                assert sampleDB.template.name.equals(testSampleTemplateName)
                assert sampleDB.parentEvent
                assert sampleDB.parentEvent.startTime.equals(testSamplingEventTime)

                // A sample without a name should not be saveable
                sampleDB.name = null
                assert !sampleDB.validate()

                // A sample without a parent SamplingEvent should not be saveable
                sampleDB.name = testSampleName
                sampleDB.parentEvent = null
                assert !sampleDB.validate()
        }

        void testStudyRelation() {
                // Retrieve the parent study
                def study = Study.findByTitle(testStudyName)
                assert study

                // Test giveSampleTemplates
                def templates = study.giveSampleTemplates()
                assert templates
                assert templates.size() == 1
                assert templates.asList().first().name == testSampleTemplateName

                // Test if the sample is in the samples collection
                assert study.samples
                assert study.samples.size() == 1
                assert study.samples.first().name == testSampleName
        }


        void testParentStudy() {
                def sample = Sample.findByName(testSampleName)
                assert sample

                assert sample.parent
                assert sample.parent.code == testStudyCode
        }

        void testSampleUniqueNameConstraint() {
                def sample = Sample.findByName(testSampleName)
                assert sample

                def study = sample.parent
                assert study

                def sample2 = new Sample(
                    name: testSampleName,
                    template: sampleTemplate,
                    parentEvent: samplingEvent
                )

                // Add the sample to the retrieved parent study
                study.addToSamples(sample2)

                // At this point, the sample should not validate or save, because there is already a sample with that name in the study
                assert !sample2.validate()
                assert !sample2.save(flush:true)

        }

        void testFindViaSamplingEvent() {
                // Try to retrieve the sampling event by using the time...
                // (should be also the parent study but that's not yet implemented)
                def samplingEventDB = SamplingEvent.findByStartTime(testSamplingEventTime)
                assert samplingEventDB

                def samples = samplingEventDB.getSamples()
                assert samples
                assert samples.size() == 1
                assert samples.first().name == testSampleName
        }

        void testDomainFields() {
                def sample = Sample.findByName(testSampleName)
                assert sample

                // Make sure the domain fields exist
                assert sample.fieldExists('name')
                assert sample.fieldExists('material')

                // Make sure they are domain fields
                assert sample.isDomainField('name')
                assert sample.isDomainField('material')

                // Make sure that they have the right type
                assert sample.giveFieldType('name') == TemplateFieldType.STRING
                assert sample.giveFieldType('material') == TemplateFieldType.ONTOLOGYTERM

        }

        protected void tearDown() {
                super.tearDown()
        }

}