root/trunk/grails-app/domain/dbnp/studycapturing/Sample.groovy @ 754

package dbnp.studycapturing

import dbnp.data.Term

/**
 * The Sample class describes an actual sample which results from a SamplingEvent.
 */
class Sample extends TemplateEntity {
        // uncommented due to searchable issue
        // @see http://jira.codehaus.org/browse/GRAILSPLUGINS-1577
        //static searchable = { [only: ['name']] }

        // A Sample always belongs to one study.
        static belongsTo = [parent : Study]

        // A Sample optionally has a parent Subject from which it was taken, this Subject should be in the same parent study.
        Subject parentSubject

        // Also, it has a parent SamplingEvent describing the actual sampling, also within the same parent study.
        SamplingEvent parentEvent

        String name             // should be unique with respect to the parent study (which can be inferred)
        Term material           // material of the sample (should normally be bound to the BRENDA ontology)

        def getExternalSampleId() { name }

        /**
         * return the domain fields for this domain class
         * @return List
         */
        static List<TemplateField> giveDomainFields() { return Sample.domainFields }

        // We have to specify an ontology list for the material property. However, at compile time, this ontology does of course not exist.
        // Therefore, the ontology is added at runtime in the bootstrap, possibly downloading the ontology properties if it is not present in the database yet.
        static List<TemplateField> domainFields = [
                new TemplateField(
                        name: 'name',
                        type: TemplateFieldType.STRING,
                        preferredIdentifier: true,
                        required: true
                ),
                new TemplateField(
                        name: 'material',
                        type: TemplateFieldType.ONTOLOGYTERM
                )
        ]

        static constraints = {
                // The parent subject is optional, e.g. in a biobank of samples the subject could be unknown or non-existing.
                parentSubject(nullable:true)

                // The material domain field is optional
                material(nullable: true)

                // Check if the externalSampleId (currently defined as name) is really unique within each parent study of this sample.
                // This feature is tested by integration test SampleTests.testSampleUniqueNameConstraint
                name(unique:['parent'])
        }

        static getSamplesFor( event ) {
                return  Sample.findAll( 'from Sample s where s.parentEvent =:event', [event:event] )
        }

        def String toString() {
                return name
        }
}