source: trunk/grails-app/domain/dbnp/data/Term.groovy @ 756

package dbnp.data

import dbnp.data.Ontology

/**
 * The Term object describes a term in the ontology that is referred to in other entities such as events.
 * The Term object should point to an existing term in an online ontology, therefore instances of this class can also
 * be seen as a cache of elements of the external ontology.
 * BioPortal example: Mus musculus: http://rest.bioontology.org/bioportal/concepts/38802/NCBITaxon:10090
 *
 * Revision information:
 * $Rev: 756 $
 * $Author: keesvb $
 * $Date: 2010-08-02 10:29:50 +0000 (ma, 02 aug 2010) $
 */
class Term implements Serializable {
    //static searchable = { [only: ['ontology']] }

        String name             // BioPortal: label (preferred name)
        Ontology ontology       // Parent ontology. To enable the unique constraints, we describe the Ontology-Term relation here
        String accession        // BioPortal: conceptId

        static constraints = {
                accession(unique: true)     // Accession should be unique db-wide
                name(unique: 'ontology')    // Preferred name should be unique within an ontology
        name(size: 1..255)          // Name should be a non-empty string
        }

        def String toString() {
                return name
        }

        /**
         * Return all terms for a string of comma separated ontology ncboId's.
         * @see Ontology.groovy
         * @param ontologies
         * @return
         */
        def giveAllByOntologies( ontologies ) {
                // this method does not seem to work (see taglibrary:termSelect)
                // i'll try to get it working later, or delete this altogether
                // - Jeroen
                def data = []
                def terms = []

                // got a string?
                if (ontologies instanceof String) {
                        // split the ontologies string
                        ontologies.split(/\,/).each() { ncboId ->
                                // trim the id
                                ncboId.trim()

                                // fetch all terms for this ontology
                                def ontology = Ontology.findAllByNcboId(ncboId)

                                // does this ontology exist?
                                if (ontology) {
                                        ontology.each() {
                                                data[ data.size() ] = it
                                        }
                                }
                        }

                        ontologies = data
                }

                // iterate through ontologies
                ontologies.each() { ontology ->
                        Term.findAllByOntology( ontology ).each() { term ->
                                terms[ terms.size() ] = term
                        }
                }

                // sort alphabetically
                terms.sort()
        }
}