Changeset 353

Timestamp:

Apr 20, 2010, 10:49:54 AM (13 years ago)

Author:

duh

Message:

• refactored termField tag
• refactored subjects page
• added terms and ontologies to bootstrap

Location:

trunk/grails-app

Files:

• conf/BootStrap.groovy (modified) (1 diff)
• domain/dbnp/data/Term.groovy (modified) (1 diff)
• taglib/dbnp/studycapturing/WizardTagLib.groovy (modified) (3 diffs)
• views/wizard/pages/_subjects.gsp (modified) (1 diff)

trunk/grails-app/conf/BootStrap.groovy

@@ -92 +92 @@
                         .with { if (!validate()) { errors.each { println it} } else save()}
 
+                        // add NCBI species ontology
+                        println ".adding NCBI species ontology"
+                        def speciesOntology = new Ontology(
+                                name: 'NCBI organismal classification',
+                                description: 'A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases.',
+                                url: 'http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/',
+                                versionNumber: '1.2',
+                                ncboId: '1132',
+                                ncboVersionedId: '38802'
+                        ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                        // add TERMS
+                        println ".adding mouse term"
+                        def mouseTerm = new Term(
+                                name: 'Mus musculus',
+                                ontology: speciesOntology,
+                                accession: '10090'
+                        ).with { if (!validate()) { errors.each { println it} } else save()}
+                        println ".adding human term"
+                        def humanTerm = new Term(
+                                name: 'Homo sapiens',
+                                ontology: speciesOntology,
+                                accession: '9606'
+                        ).with { if (!validate()) { errors.each { println it} } else save()}
 
 

trunk/grails-app/domain/dbnp/data/Term.groovy

@@ -19 +19 @@
         String name             // BioPortal: label (preferred name)
         Ontology ontology       // Parent ontology
-        String accession        // BioPortal: fullId
+        String accession        // BioPortal: conceptId
 
         static constraints = {

trunk/grails-app/taglib/dbnp/studycapturing/WizardTagLib.groovy

@@ -401 +401 @@
 
         /**
+         * Button form element
+         * @param Map attributes
+         * @param Closure help content
+         */
+        def buttonElement = {attrs, body ->
+                // render template element
+                baseElement.call(
+                        'ajaxButton',
+                        attrs,
+                        body
+                )
+        }
+
+
+        /**
+         * Term form element
+         * @param Map attributes
+         * @param Closure help content
+         */
+        def termElement = { attrs, body ->
+                // render term element
+                baseElement.call(
+                        'termSelect',
+                        attrs,
+                        body
+                )
+        }
+
+        /**
+         * Term select element
+         * @param Map attributes
+         */
+        def termSelect = { attrs ->
+                def from = []
+
+                // got ontologies?
+                if (attrs.ontology) {
+                        attrs.ontology.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() {
+                                                Term.findAllByOntology(it).each() {
+                                                        // key = ncboId:concept-id
+                                                        from[ from.size() ] = it.name
+                                                }
+                                        }
+                                }
+                        }
+
+                        // sort alphabetically
+                        from.sort()
+                        
+                        // define 'from'
+                        attrs.from = from
+
+                        out << select(attrs)
+                } else {
+                        out << "you should specify: <i>ontology=\"id\"</i> or <i>ontology=\"id1,id2,...,idN\"</i>"
+                }
+        }
+
+        /**
          * Template form element
          * @param Map attributes
@@ -409 +477 @@
                 baseElement.call(
                         'speciesSelect',
-                        attrs,
-                        body
-                )
-        }
-
-        /**
-         * Button form element
-         * @param Map attributes
-         * @param Closure help content
-         */
-        def buttonElement = {attrs, body ->
-                // render template element
-                baseElement.call(
-                        'ajaxButton',
                         attrs,
                         body
@@ -564 +618 @@
                         return false
                 }
-        }
-
-        /**
-         * Term form element
-         * @param Map attributes
-         * @param Closure help content
-         */
-        def termElement = {attrs, body ->
-                // render term element
-                baseElement.call(
-                        'termSelect',
-                        attrs,
-                        body
-                )
-        }
-
-        /**
-         * render a term select element
-         * @param Map attrs
-         */
-        def termSelect = {attrs ->
-                // fetch all terms
-                attrs.from = Term.findAll()     // for now, all terms as we cannot identify terms as being treatment terms...
-
-                // got a name?
-                if (!attrs.name) {
-                        attrs.name = 'term'
-                }
-
-                out << select(attrs)
         }
 

trunk/grails-app/views/wizard/pages/_subjects.gsp

@@ -29 +29 @@
                 The species of the subjects you would like to add to your study
         </wizard:ontologyElement>
+        <wizard:termElement name="species" description="of species" value="" ontology="1132">
+                The species of the subjects you would like to add to your study
+        </wizard:termElement>
         <wizard:templateElement name="template" description="with template" value="" error="template" entity="${dbnp.studycapturing.Subject}" >
                 The template to use for this study