Changeset 558

Timestamp:

Jun 11, 2010, 4:00:10 PM (13 years ago)

Author:

roberth

Message:

Improved template editor , stringlists and ontologyfields can be edited and extra checks are built in.

Location:

trunk

Files:

• grails-app/controllers/dbnp/studycapturing/TemplateEditorController.groovy (modified) (13 diffs)
• grails-app/domain/dbnp/data/Ontology.groovy (modified) (1 diff)
• grails-app/views/templateEditor/_ontologyDialog.gsp (added)
• grails-app/views/templateEditor/elements/_available.gsp (modified) (1 diff)
• grails-app/views/templateEditor/elements/_disabledFieldForm.gsp (copied) (copied from trunk/grails-app/views/templateEditor/elements/_fieldForm.gsp) (1 diff)
• grails-app/views/templateEditor/elements/_domainField.gsp (added)
• grails-app/views/templateEditor/elements/_fieldForm.gsp (modified) (1 diff)
• grails-app/views/templateEditor/elements/_liField.gsp (modified) (1 diff)
• grails-app/views/templateEditor/elements/_liFieldDomain.gsp (added)
• grails-app/views/templateEditor/elements/_liFieldInUse.gsp (modified) (2 diffs)
• grails-app/views/templateEditor/elements/_liFieldNotInUse.gsp (modified) (2 diffs)
• grails-app/views/templateEditor/elements/_liTemplate.gsp (added)
• grails-app/views/templateEditor/elements/_selected.gsp (modified) (1 diff)
• grails-app/views/templateEditor/index.gsp (modified) (1 diff)
• grails-app/views/templateEditor/template.gsp (modified) (6 diffs)
• web-app/css/templateEditor.css (modified) (3 diffs)
• web-app/js/templateEditor.js (modified) (16 diffs)

trunk/grails-app/controllers/dbnp/studycapturing/TemplateEditorController.groovy

@@ -18 +18 @@
 import cr.co.arquetipos.crypto.Blowfish
 import grails.converters.*
+import java.lang.reflect.*;
 
 class TemplateEditorController {
@@ -59 +60 @@
         def selectedTemplate = params.template;
         def template = null;
+                def domainFields = null;
 
         if( selectedTemplate ) {
             template = Template.get( selectedTemplate );
+
+                        // Find the domain classes for this template/entity
+                        // See http://www.javaworld.com/javaworld/javaqa/1999-07/06-qa-invoke.html
+                        Method m = template.entity.getDeclaredMethod("giveDomainFields", null);
+                        domainFields = m.invoke( null, null );
         } else {
                         redirect(action:"index",params:[entity:params.entity])
@@ -84 +91 @@
             encryptedEntity: params.entity,
             fieldTypes: TemplateFieldType.list(),
+                        ontologies: Ontology.list(),
             humanReadableEntity: humanReadableEntity,
 
             template: template,
-                        allFields: allFields
+                        allFields: allFields,
+                        domainFields: domainFields
         ];
 
@@ -124 +133 @@
         if (template.save(flush: true)) {
 
-                        def html = g.render( template: 'elements/liTemplateEditable', model: [template: template] );
+                        def html = g.render( template: 'elements/liTemplate', model: [template: template] );
                         def output = [ id: template.id, html: html ];
                         render output as JSON;
@@ -166 +175 @@
         template.properties = params
         if (!template.hasErrors() && template.save(flush: true)) {
-                        def html = g.render( template: 'elements/liTemplateEditable', model: [template: template] );
+                        def html = g.render( template: 'elements/liTemplate', model: [template: template] );
                         def output = [ id: template.id, html: html ];
                         render output as JSON;
@@ -206 +215 @@
     }
 
-
-
-
     /**
      * Creates a new template field using a AJAX call
@@ -246 +252 @@
                 }
 
+                // See whether this exists as domain field. If it does, raise an error
+                Method m = template.entity.getDeclaredMethod("giveDomainFields", null);
+                def domainFields = m.invoke( null, null );
+                if( domainFields.find { it.name.toLowerCase() == params.name.toLowerCase() } ) {
+                        response.status = 500;
+                        render "All templates for entity " + template.entity + " contain a domain field with name " + params.name + ". You can not create a field with this name.";;
+                        return;
+                }
+
+                // If this field is type stringlist, we have to prepare the parameters
+                if( params.type.toString() == 'STRINGLIST' ) {
+                        def listEntries = [];
+                        params.listEntries.eachLine {
+                                // Search whether a listitem with this name already exists.
+                                // if it does, use that one to prevent pollution of the database
+                                def name = it.trim();
+                                def listitem = TemplateFieldListItem.findByName( name );7
+                                if( !listitem ) {
+                                        listitem = new TemplateFieldListItem( name: name )
+                                }
+                                listEntries.add( listitem );
+                        }
+
+                        params.listEntries = listEntries;
+                } else {
+                        params.remove( 'listEntries' );
+                }
+
+                // If this field isnot a ontologyterm, we should remove the ontologies
+                if( params.type.toString() != 'ONTOLOGYTERM' ) {
+                        params.remove( 'ontologies' );
+                }
+
                 // Create the template field and add it to the template
                 def templateField = new TemplateField( params );
         if (templateField.save(flush: true)) {
 
-                        def html = g.render( template: 'elements/liFieldNotInUse', model: [templateField: templateField, fieldTypes: TemplateFieldType.list()] );
+                        def html = g.render( template: 'elements/available', model: [templateField: templateField, ontologies: Ontology.list(), fieldTypes: TemplateFieldType.list()] );
                         def output = [ id: templateField.id, html: html ];
                         render output as JSON;
@@ -289 +328 @@
             }
         }
-        templateField.properties = params
+
+                // If this field is type stringlist or ontology, we have to prepare the parameters
+                if( params.type.toString() == 'STRINGLIST' ) {
+                        def listEntries = [];
+                        params.listEntries.eachLine {
+                                // Search whether a listitem with this name already exists.
+                                // if it does, use that one to prevent pollution of the database
+                                def name = it.trim();
+                                def listitem = TemplateFieldListItem.findByName( name );7
+                                if( !listitem ) {
+                                        listitem = new TemplateFieldListItem( name: name )
+                                }
+                                listEntries.add( listitem );
+                        }
+
+                        params.listEntries = listEntries;
+                } else {
+                        params.remove( 'listEntries' );
+                }
+
+                // If this field is a ontologyterm, we add ontology objects
+                if( params.type.toString() == 'ONTOLOGYTERM' && params.ontologies ) {
+                        params.ontologies = Ontology.getAll( params.ontologies.collect { Integer.parseInt( it ) } );
+                } else {
+                        params.remove( 'ontologies' );
+                }
+
+                // Set all parameters
+                templateField.properties = params
         if (!templateField.hasErrors() && templateField.save(flush: true)) {
-                        def html = g.render( template: 'elements/liField', model: [templateField: templateField, fieldTypes: TemplateFieldType.list()] );
+                        def html = g.render( template: 'elements/available', model: [templateField: templateField, ontologies: Ontology.list(), fieldTypes: TemplateFieldType.list()] );
                         def output = [ id: templateField.id, html: html ];
                         render output as JSON;
@@ -364 +431 @@
             return;
         }
+
+                // If the template is in use, only non-required fields can be added
+                if( template.inUse() && templateField.required ) {
+                        response.status = 500;
+                        render 'Only non-required fields can be added to templates that are in use.'
+                        return;
+                }
+
+                // All field names within a template should be unique
+                if( template.fields.find { it.name.toLowerCase() == templateField.name.toLowerCase() } ) {
+                        response.status = 500;
+                        render 'This template already contains a field with name ' + templateField.name + '. Field names should be unique within a template.'
+                        return;
+                }
+
                 if( !params.position || Integer.parseInt( params.position ) == -1) {
                         template.fields.add( templateField )
@@ -369 +451 @@
                         template.fields.add( Integer.parseInt( params.position ), templateField )
                 }
-
-                def html = g.render( template: 'elements/liFieldSelected', model: [templateField: templateField, template: template, fieldTypes: TemplateFieldType.list()] );
+                template.save(flush:true);
+
+                def html = g.render( template: 'elements/selected', model: [templateField: templateField, template: template, ontologies: Ontology.list(), fieldTypes: TemplateFieldType.list()] );
                 def output = [ id: templateField.id, html: html ];
                 render output as JSON;
     }
-
 
     /**
@@ -411 +493 @@
         }
 
+                // If the template is in use, field can not be removed
+                if( template.inUse() ) {
+                        response.status = 500;
+                        render 'No fields can be removed from templates that are in use.'
+                        return;
+                }
+
                 // Delete the field from this template
         def currentIndex = template.fields.indexOf( templateField );
         template.fields.remove( currentIndex );
-                template.save();
-
-
-                def html = g.render( template: 'elements/liField', model: [templateField: templateField, fieldTypes: TemplateFieldType.list()] );
+                template.save(flush:true);
+
+
+                def html = g.render( template: 'elements/available', model: [templateField: templateField, ontologies: Ontology.list(), fieldTypes: TemplateFieldType.list()] );
                 def output = [ id: templateField.id, html: html ];
                 render output as JSON;
@@ -462 +551 @@
         def moveField = template.fields.remove( currentIndex );
         template.fields.add( Integer.parseInt( params.position ), moveField );
-
-                def html = g.render( template: 'elements/liFieldSelected', model: [templateField: templateField, template: template, fieldTypes: TemplateFieldType.list()] );
+                template.save(flush:true);
+
+                def html = g.render( template: 'elements/selected', model: [templateField: templateField, template: template, fieldTypes: TemplateFieldType.list()] );
                 def output = [ id: templateField.id, html: html ];
                 render output as JSON;
@@ -485 +575 @@
                 render templateField.numUses();
         }
+
+        /**
+         * Adds a ontolgy based on the ID given
+         *
+         * @param       ncboID
+         * @return      JSON    Ontology object
+         */
+        def addOntologyById = {
+                def id = params.ncboID;
+
+                if( !id ) {
+                        response.status = 500;
+                        render 'No ID given'
+                        return;
+                }
+
+                if( Ontology.findByNcboId( Integer.parseInt(  id ) ) ) {
+                        response.status = 500;
+                        render 'This ontology was already added to the system';
+                        return;
+                }
+
+                def ontology = null;
+
+                try {
+                        ontology = dbnp.data.Ontology.getBioPortalOntology( id );
+                } catch( Exception e ) {
+                        response.status = 500;
+                        render e.getMessage();
+                        return;
+                }
+
+                if( !ontology ) {
+                        response.status = 404;
+                        render 'Ontology with ID ' + id + ' not found';
+                        return;
+                }
+
+                // Validate ontology
+                if (!ontology.validate()) {
+                        response.status = 500;
+                        render ontology.errors.join( '; ' );
+                        return;
+                }
+
+                // Save ontology and render the object as JSON
+                ontology.save(flush: true)
+                render ontology as JSON
+        }
+
+        /**
+         * Adds a ontolgy based on the ID given
+         *
+         * @param       ncboID
+         * @return      JSON    Ontology object
+         */
+        def addOntologyByTerm = {
+                def id = params.termID;
+
+                if( !id ) {
+                        response.status = 500;
+                        render 'No ID given'
+                        return;
+                }
+
+                def ontology = null;
+
+                try {
+                        ontology = dbnp.data.Ontology.getBioPortalOntologyByTerm( id );
+                } catch( Exception e ) {
+                        response.status = 500;
+                        render e.getMessage();
+                        return;
+                }
+
+                if( !ontology ) {
+                        response.status = 404;
+                        render 'Ontology form term ' + id + ' not found';
+                        return;
+                }
+
+                // Validate ontology
+                if (!ontology.validate()) {
+                        response.status = 500;
+                        render ontology.errors.join( '; ' );
+                        return;
+                }
+
+                // Save ontology and render the object as JSON
+                ontology.save(flush: true)
+                render ontology as JSON
+        }
+
 
     /**

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

@@ -57 +57 @@
                 );
         }
+
+        static Ontology getBioPortalOntologyByTerm(String termId) {
+                // Get ontology from BioPortal via Ontocat
+                // TODO: maybe make a static OntologyService instance to be more efficient, and decorate it with caching?
+                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()
+                uk.ac.ebi.ontocat.OntologyTerm term = os.getTerm( termId );
+                println( term );
+                uk.ac.ebi.ontocat.Ontology o = os.getOntology( term.getOntologyAccession() );
+                println( o );
+
+                // Instantiate and return Ontology object
+                new dbnp.data.Ontology(
+                        name: o.label,
+                        description: o.description,
+                        url: o.properties['homepage'] ?: "http://bioportal.bioontology.org/ontologies/${o.id}",
+                        versionNumber: o.versionNumber,
+                        ncboId: o.ontologyAccession,
+                        ncboVersionedId: o.id
+                );
+        }
 }

trunk/grails-app/views/templateEditor/elements/_available.gsp

@@ -1 @@
-<li class="ui-state-default" id="templateField_${it.id}">
-    <g:render template="elements/liField" model="['templateField': it, 'fieldTypes': fieldTypes]"/>
+<li class="ui-state-default <g:if test="${templateField.required}">required</g:if>" id="templateField_${templateField.id}">
+    <g:render template="elements/liField" model="['templateField': templateField, 'ontologies': ontologies, 'fieldTypes': fieldTypes]"/>
 </li>

trunk/grails-app/views/templateEditor/elements/_disabledFieldForm.gsp

@@ -1 @@
-        <label for="name">Name:</label> <g:textField name="name" value="${templateField?.name}" /><br />
-        <label for="type">Type:</label> <g:select from="${fieldTypes}" name="type" value="${templateField?.type}" /><br />
-        <label for="unit">Unit:</label> <g:textField name="unit" value="${templateField?.unit}" /><br />
-        <label for="comment">Comment:</label> <g:textArea name="comment" value="${templateField?.comment}" /><br />
-        <label for="required">Required:</label> <g:checkBox name="required" value="${templateField?.required}" /><br />
+        <label for="name">Name:</label> <g:textField disabled="disabled" name="name" value="${templateField?.name}" /><br />
+        <label for="type">Type:</label> <g:textField disabled="disabled" name="type" value="${templateField?.type}" /><br />
+
+        <div class="extra stringlist_options" <g:if test="${templateField?.type.toString() == 'STRINGLIST'}">style='display: block;'</g:if>>
+          <label for="type">Items:</label>
+                <g:textArea name="listEntries" disabled="disabled" value="${templateField?.listEntries?.name?.join( '\n' )}" />
+        </div>
+        <div class="extra ontologyterm_options" <g:if test="${templateField?.type.toString() == 'ONTOLOGYTERM'}">style='display: block;'</g:if>>
+          <label for="type">Ontology:</label> <g:textArea name="ontology" disabled="disabled" value="${templateField?.ontologies?.name?.join( '\n' )}" /><br />
+        </div>
+        
+        <label for="unit">Unit:</label> <g:textField disabled="disabled" name="unit" value="${templateField?.unit}" /><br />
+        <label for="comment">Comment:</label> <g:textArea disabled="disabled" name="comment" value="${templateField?.comment}" /><br />
+        <label for="required">Required:</label> <input type="checkbox" disabled <g:if test="${templateField?.required}">checked</g:if><br />

trunk/grails-app/views/templateEditor/elements/_fieldForm.gsp

@@ -1 +1 @@
         <label for="name">Name:</label> <g:textField name="name" value="${templateField?.name}" /><br />
-        <label for="type">Type:</label> <g:select from="${fieldTypes}" name="type" value="${templateField?.type}" /><br />
+        <label for="type">Type:</label> <g:select from="${fieldTypes}" name="type" value="${templateField?.type}" onChange="showExtraFields( ${templateField ? templateField.id : '\'new\''} );" /><br />
+
+        <div class="extra stringlist_options" <g:if test="${templateField?.type.toString() == 'STRINGLIST'}">style='display: block;'</g:if>>
+          <label for="type">Items (every item on a new line):</label>
+                <g:textArea name="listEntries" value="${templateField?.listEntries?.name?.join( '\n' )}" />
+        </div>
+        <div class="extra ontologyterm_options" <g:if test="${templateField?.type.toString() == 'ONTOLOGYTERM'}">style='display: block;'</g:if>>
+          <label for="type">Ontology:<br /><br /><a href="#" style="text-decoration: underline;" onClick="openOntologyDialog();">Add new</a></label>
+                <g:select multiple="yes" size="5" from="${ontologies}" class="ontologySelect" optionValue="name" optionKey="id" name="ontologies" id="ontologies_${templateField?.id}" value="${templateField?.ontologies}" /><br />
+        </div>
+
         <label for="unit">Unit:</label> <g:textField name="unit" value="${templateField?.unit}" /><br />
         <label for="comment">Comment:</label> <g:textArea name="comment" value="${templateField?.comment}" /><br />

trunk/grails-app/views/templateEditor/elements/_liField.gsp

@@ -1 +1 @@
 <g:if test="${templateField.inUse()}">
-        <g:render template="elements/liFieldInUse" model="['templateField': templateField, 'fieldTypes': fieldTypes]"/>
+        <g:render template="elements/liFieldInUse" model="['templateField': templateField, 'ontologies': ontologies, 'fieldTypes': fieldTypes]"/>
 </g:if>
 <g:else>
-        <g:render template="elements/liFieldNotInUse" model="['templateField': templateField, 'fieldTypes': fieldTypes]"/>
+        <g:render template="elements/liFieldNotInUse" model="['templateField': templateField, 'ontologies': ontologies, 'fieldTypes': fieldTypes]"/>
 </g:else>

trunk/grails-app/views/templateEditor/elements/_liFieldInUse.gsp

@@ -1 +1 @@
 <g:set var="numUses" value="${templateField.numUses()}" />
 <span class="listButtons">
-  <img class="disabled" src="${createLinkTo( dir: 'images', file: 'icons/famfamfam/application_edit.png')}" alt="Editing not possible. Field is used in ${numUses} templates." title="Editing not possible. Field is used in ${numUses} templates.">
+  <img onClick="showTemplateFieldForm( 'templateField_' + ${templateField.id}); this.blur(); return false;" src="${createLinkTo( dir: 'images', file: 'icons/famfamfam/application_edit.png')}" alt="Edit template field properties" title="Edit template field properties">
   <img class="disabled" src="${createLinkTo( dir: 'images', file: 'icons/famfamfam/delete.png')}" alt="Deleting this field is not possible. Field is used in ${numUses} templates." title="Deleting this field is not possible. Field is used in ${numUses} templates.">
-  <img onClick="addTemplateField( ${templateField.id} ); moveFieldListItem( ${templateField.id}, '#selectedTemplateFields' );" src="${createLinkTo( dir: 'images', file: 'icons/famfamfam/add.png')}" alt="Add field to template" title="Add field to template">
+  <img onClick="addTemplateField( ${templateField.id}, null, true );" src="${createLinkTo( dir: 'images', file: 'icons/famfamfam/add.png')}" alt="Add field to template" title="Add field to template">
 </span>
 
@@ -9 +9 @@
     (<g:if test="${templateField.unit}">${templateField.unit}, </g:if><g:render template="elements/${templateField.type.toString().toLowerCase().replaceAll(/ /,'_')}" model="[templateField: templateField]"/>)
     
+<form class="templateField_form" id="templateField_${templateField.id}_form" action="updateField">
+        <g:hiddenField name="id" value="${templateField.id}" />
+        <g:hiddenField name="version" value="${templateField.version}" />
+        <p class="noEditsPossible">Editing not possible. Field is used in ${numUses} template(s).</p>
+        <g:render template="elements/disabledFieldForm" model="['templateField': templateField, 'ontologies': ontologies, 'fieldTypes': fieldTypes]"/>
+        <div class="templateFieldButtons">
+                <input type="button" value="Close" onClick="hideTemplateFieldForm( ${templateField.id} );">
+        </div>
+</form>
 

trunk/grails-app/views/templateEditor/elements/_liFieldNotInUse.gsp

@@ -2 +2 @@
   <img onClick="showTemplateFieldForm( 'templateField_' + ${templateField.id}); this.blur(); return false;" src="${createLinkTo( dir: 'images', file: 'icons/famfamfam/application_edit.png')}" alt="Edit template field properties" title="Edit template field properties">
   <img onClick="if( confirm( 'Are you sure?' ) ) { deleteTemplateField( ${templateField.id} ); }" src="${createLinkTo( dir: 'images', file: 'icons/famfamfam/delete.png')}" alt="Delete this template field" title="Delete this template field">
-  <img onClick="addTemplateField( ${templateField.id} ); moveFieldListItem( ${templateField.id}, '#selectedTemplateFields' );" src="${createLinkTo( dir: 'images', file: 'icons/famfamfam/add.png')}" alt="Add field to template" title="Add field to template">
+  <img onClick="addTemplateField( ${templateField.id}, null, true );" src="${createLinkTo( dir: 'images', file: 'icons/famfamfam/add.png')}" alt="Add field to template" title="Add field to template">
 </span>
 
@@ -11 +11 @@
         <g:hiddenField name="id" value="${templateField.id}" />
         <g:hiddenField name="version" value="${templateField.version}" />
-        <g:render template="elements/fieldForm" model="['templateField': templateField, 'fieldTypes': fieldTypes]"/>
+        <g:render template="elements/fieldForm" model="['templateField': templateField, 'ontologies': ontologies, 'fieldTypes': fieldTypes]"/>
         <div class="templateFieldButtons">
                 <input type="button" value="Save" onClick="updateTemplateField( ${templateField.id} );">

trunk/grails-app/views/templateEditor/elements/_selected.gsp

@@ -1 @@
-<li class="ui-state-default <g:if test="${template.inUse()}">inUse</g:if>" id="templateField_${it.id}">
-    <g:render template="elements/liFieldSelected" model="['templateField': it, 'template': template, 'fieldTypes': fieldTypes]"/>
+<li class="ui-state-default  <g:if test="${templateField.required}">required</g:if>" id="templateField_${templateField.id}">
+    <g:render template="elements/liFieldSelected" model="['templateField': templateField, 'template': template, 'fieldTypes': fieldTypes]"/>
 </li>

trunk/grails-app/views/templateEditor/index.gsp

@@ -32 +32 @@
                                 <li class="empty ui-state-default" <g:if test="${templates.size() > 0 }">style='display: none;'</g:if>>There are no templates for ${humanReadableEntity}. Use the 'Add template' button to add fields.</li>
                                 <g:each in="${templates}" var="currentTemplate">
-                                        <li id="template_${currentTemplate.id}"class="ui-state-default">
-                                          <g:if test="${currentTemplate.inUse()}">
-                                                <g:render template="elements/liTemplateNonEditable" model="['template': currentTemplate]"/>
-                                          </g:if>
-                                          <g:else>
-                                                <g:render template="elements/liTemplateEditable" model="['template': currentTemplate]"/>
-                                          </g:else>
-                                        </li>
+                                  <g:render template="elements/liTemplate" model="['template': currentTemplate]"/>
                                 </g:each>
                         </ul>

trunk/grails-app/views/templateEditor/template.gsp

@@ -21 +21 @@
                 <script src="${createLinkTo(dir: 'js', file: 'templateEditor.js')}" type="text/javascript"></script>
                 <link rel="stylesheet" href="${createLinkTo(dir: 'css', file: 'templateEditor.css')}" />
+                <g:if env="production">
+                  <script type="text/javascript" src="${resource(dir: 'js', file: 'ontology-chooser.min.js')}"></script>
+                </g:if><g:else>
+                  <script type="text/javascript" src="${resource(dir: 'js', file: 'ontology-chooser.js')}"></script>
+                </g:else>
         </head>
         <body>
@@ -29 +34 @@
                                 $("#selectedTemplateFields").sortable({
                                         placeholder: 'ui-state-highlight',
+                                        items: 'li:not(.domain)',
                                         cancel: '.empty, input, select, button, textarea, form, label',
                                         connectWith: '.templateFields',
                                         update: updateTemplateFieldPosition,
+                                        receive: addTemplateFieldEvent,
                                         remove: removeTemplateFieldEvent,
-                                        receive: addTemplateFieldEvent
+                                        start: savePosition
                                 }).disableSelection();
 
@@ -40 +47 @@
                                         placeholder: 'ui-state-highlight',
                                         cancel: '.empty, input, select, button, textarea, form, label',
-                                        connectWith: '.templateFields'
+                                        connectWith: '.templateFields',
+                                        start: savePosition
                                 }).disableSelection();
-                                
+
+
+                                $("#ontologyDialog").dialog({
+                                  autoOpen: false,
+                                  title: 'Search for ontology',
+                                  height: 290,
+                                  width: 350,
+                                  modal: true,
+                                  buttons: {
+                                          'Add': addOntology,
+                                          Cancel: function() {
+                                                  $(this).dialog('close');
+                                          }
+                                  },
+                                  close: function() {
+                                  }
+
+                                });
+
                         });
                 </script>
@@ -56 +82 @@
 
                                 <p>Currently, this template contains the following fields. Drag fields to reorder. Drag fields to the list of available fields to remove the field from the template.</p>
-                                <ol id="selectedTemplateFields" class="templateFields">
+                                <ol id="domainFields" class="templateFields <g:if test="${template.inUse()}">inUse</g:if>">
+                                        <g:render template="elements/domainField" var="domainField" collection="${domainFields}" model="['template':template]"/>
+                                </ol>
+                                <ol id="selectedTemplateFields" class="templateFields <g:if test="${template.inUse()}">inUse</g:if>">
+                                        <g:render template="elements/selected" var="templateField" collection="${template.fields}" model="['template':template]"/>
                                         <li class="empty ui-state-default" <g:if test="${template.fields?.size() > 0 }">style='display: none;'</g:if>>This template does not yet contain any fields. Drag a field to this list or use the 'Add field button'.</li>
-                                        <g:render template="elements/selected" collection="${template.fields}" model="['template':template]"/>
                                 </ol>
                         </div>
@@ -67 +96 @@
                                 <ol id="availableTemplateFields" class="templateFields">
                                         <li class="empty ui-state-default" <g:if test="${allFields.size() > template.fields.size()}">style='display: none;'</g:if>>There are no additional fields that can be added. Use the 'Create new field' button to create new fields.</li>
-                                        <g:render template="elements/available" collection="${allFields - template.fields}" />
+                                        <g:render template="elements/available" var="templateField" collection="${allFields - template.fields}" />
                                 </ol>
 
@@ -87 +116 @@
                 </g:if>
 
+                <div id="ontologyDialog">
+                  <g:render template="ontologyDialog" />
+                </div>
 
         </body>

trunk/web-app/css/templateEditor.css

@@ -38 +38 @@
 .templateFields .empty { opacity: 0.6; padding: 5px 25px; }
 
+/* Domain fields should be yellow */
+.templateFields .domain { background: #FFFFEA; border-color: #EAEAAE; padding-left: 23px; color: #8F8408; }
+
 /* The position where an item can be dropped in the available list will be red */
 #availableTemplateFields .ui-state-highlight { background: #FFD6D6; border-color: #EAAEAE; }
@@ -45 +48 @@
 .templateField_form .templateFieldButtons { margin-top: 8px; padding-top: 8px; border-top: 1px solid #BBD; }
 .templateField_form label { width: 80px; float: left; display: block; }
-.templateField_form textarea {width: 145px; height: 100px;  }
+.templateField_form textarea {width: 205px; height: 100px;  }
 .templateField_form input[type=text],
-.templateField_form select {width: 145px; }
+.templateField_form select {width: 205px; }
+
+#step3_availableFields .templateField_form p.noEditsPossible {height: auto; margin: 4px 0; padding: 4px; background: #FFD6D6; border: 1px solid #EAAEAE; color: #660000; }
+.templateField_form .extra { display: none; }
+
 
 /* Add new form */
@@ -74 +81 @@
         margin-left: 10px; margin-right: 10px;
 }
+
+/* Add Ontology dialog */
+#addOntology { list-style-type: none; padding-left: 0; }
+#addOntology li { list-style-type: none; margin: 8px 0; padding-left: 20px; }
+#addOntology li input.text { margin-top: 5px; }
+#addOntology li .check { float: left; margin-left: -15px; margin-top: 2px; }
+

trunk/web-app/js/templateEditor.js

@@ -13 +13 @@
  */
 
+// Flag to keep track of whether a form is opened or not
 var formOpened = false;
+
+// Contains information about the original position of an item, when it is being dragged
+var currentSort = null;
 
 /*************************************
@@ -121 +125 @@
 function addTemplateListItem( id, newHTML ) {
         // Create a new listitem
-        var li = $( '<li></li>' );
-        li.attr( 'id', 'template_' + id );
-        li.addClass( "ui-state-default" );
-
-        // Insert the right HTML
-        li.html( newHTML );
+        var li = $( newHTML );
 
         // Append the listitem to the list
@@ -138 +137 @@
 function updateTemplateListItem( id, newHTML ) {
         var li = $( '#template_' + id );
-        li.html( newHTML );
+        li.replaceWith( newHTML );
 }
 
@@ -197 +196 @@
 }
 
-
-
 /**
  * Adds a new template field using AJAX
@@ -242 +239 @@
         }
     });
+}
+
+/**
+ * Deletes a template field using AJAX
+ */
+function deleteTemplateField( id ) {
+    // Delete the field
+    $.ajax({
+        url:        baseUrl + '/templateEditor/deleteField',
+        data:       'templateField=' + id,
+        type:       "POST",
+        success:    function(data, textStatus, request) {
+                        // Put the new HTML into the list item
+                        deleteFieldListItem( id );
+
+                        showHideEmpty( '#availableTemplateFields' );
+        },
+        error:      function( request ) {
+            alert( "Could not delete template field: " + request.responseText );
+        }
+    });
+
+        return true;
 }
 
@@ -288 +308 @@
         },
         error: function( request ) {
-            alert( "Could not move template field: " + request.responseText );
+                        undoMove();
+                        alert( "Could not move template field: " + request.responseText );
         }
     });
@@ -313 +334 @@
  * Adds a new template field to the template using AJAX
  */
-function addTemplateField( id, newposition ) {
+function addTemplateField( id, newposition, moveAfterwards ) {
         if( newposition == null ) {
                 newposition = -1;
         }
+
+        if( moveAfterwards == null ) {
+                moveAfterwards = false;
+        }
+
         var templateId = $('#templateSelect').val();
 
@@ -329 +355 @@
                         updateFieldListItem( id, data.html );
 
+                        if( moveAfterwards ) {
+                                moveFieldListItem( id, '#selectedTemplateFields' );
+                        }
+
                         showHideEmpty( '#selectedTemplateFields' );
                         showHideEmpty( '#availableTemplateFields' );
         },
         error:      function( request ) {
+                        // Send the item back (if it has been moved )
+                        if( !moveAfterwards ) {
+                                undoMove();
+                        }
+
             alert( "Could not add template field: " + request.responseText );
         }
     });
+
+        return true;
 }
 
@@ -346 +383 @@
     var id = item_id.substring( item_id.lastIndexOf( '_' ) + 1 );
 
-        // The field should only be removed when the study is not in use
-        // If field is used, the li has class 'inUse'
-        if( !ui.item.hasClass( 'inUse' ) ) {
-                return removeTemplateField( id );
-        } else {
-                alert( "Field can not be removed, because the template is in use." );
-                return false;
-        }
+        return removeTemplateField( id );
 }
 
@@ -359 +389 @@
  * Removes a template field from a template using AJAX
  */
-function removeTemplateField( id ) {
+function removeTemplateField( id, moveAfterwards ) {
+
+        if( moveAfterwards == null ) {
+                moveAfterwards = false;
+        }
+
         var templateId = $('#templateSelect').val();
 
@@ -371 +406 @@
                         updateFieldListItem( id, data.html );
 
+                        if( moveAfterwards ) {
+                                moveFieldListItem( id, '#availableTemplateFields' );
+                        }
+
                         showHideEmpty( '#selectedTemplateFields' );
                         showHideEmpty( '#availableTemplateFields' );
@@ -376 +415 @@
         },
         error:      function( request ) {
-            alert( "Could not delete template field: " + request.responseText );
+                        if( !moveAfterwards ) {
+                                undoMove();
+                        }
+
+                        alert( "Could not delete template field: " + request.responseText );
         }
     });
@@ -383 +426 @@
 }
 
-/**
- * Deletes a template field using AJAX
- */
-function deleteTemplateField( id ) {
-    // Delete the field
-    $.ajax({
-        url:        baseUrl + '/templateEditor/deleteField',
-        data:       'templateField=' + id,
-        type:       "POST",
-        success:    function(data, textStatus, request) {
-                        // Put the new HTML into the list item
-                        deleteFieldListItem( id );
-
-                        showHideEmpty( '#availableTemplateFields' );
-        },
-        error:      function( request ) {
-            alert( "Could not delete template field: " + request.responseText );
-        }
-    });
-
-        return true;
-}
 
 // Adds a new listitem when a field has been added
 function addFieldListItem( id, newHTML ) {
         // Create a new listitem
-        var li = $( '<li></li>' );
-        li.attr( 'id', 'templateField_' + id );
-        li.addClass( "ui-state-default" );
-        
-        // Insert the right HTML
-        li.html( newHTML );
+        var li = $( newHTML );
 
         // Append the listitem to the list
@@ -426 +442 @@
 function updateFieldListItem( id, newHTML ) {
         var li = $( '#templateField_' + id );
-        li.html( newHTML );
+        li.replaceWith( newHTML );
 }
 
@@ -445 +461 @@
         $( toSelector ).append( li );
 }
+
+/**
+ * Saves the original position of a sortable LI, in order to be able to undo the move event later on
+ * This function is called on start event of the sortable lists
+ */
+function savePosition( event, ui ) {
+        currentSort = {
+                id:   ui.item.attr( 'id' ),
+                parent: ui.item.context.parentNode,
+                previous: ui.item.context.previousElementSibling,
+                index: ui.item.index()
+        }
+}
+
+/**
+ * Undoes the move of an item, when an ajax call has failed
+ */
+function undoMove() {
+        if( currentSort ) {
+                var item = $( '#' + currentSort.id );
+                item.remove();
+                item.insertAfter( currentSort.previous );
+        }
+}
+
+/**
+ * Shows and hides the right 'extra' divs in the field form.
+ *
+ * These fields show extra input fields for stringlist and ontology fields
+ *
+ * @param       id      ID of the templateField
+ */
+function showExtraFields( id ) {
+        // Find the current selected fieldtype
+        var fieldType = $( '#templateField_' + id + '_form select[name=type]' ).val();
+
+        // Hide all extra forms, and show the right one
+        $( '#templateField_' + id + '_form .extra' ).hide();
+        $( '#templateField_' + id + '_form .' + fieldType.toLowerCase() + '_options' ).show();
+}
+
 
 /** 
@@ -457 +514 @@
         }
 }
+
+/************************************
+ *
+ * Functions for selecting ontologies
+ *
+ */
+
+function openOntologyDialog() {
+        $('#ontologyDialog').dialog('open');
+}
+
+function addOntology() {
+        // Add ontology using AJAX
+        var url; var data;
+
+    // Create a URL to call and call it
+        if( $( '#ncboID' ).val() ) {
+            url = baseUrl + '/templateEditor/addOntologyById';
+                data = 'ncboID=' + $( '#ncboID' ).val();
+                $( '#ncbo_spinner' ).show();
+        } else {
+            url = baseUrl + '/templateEditor/addOntologyByTerm';
+                data = 'termID=' + $( '#termID' ).val();
+                $( '#term_spinner' ).show();
+        }
+
+    // Move the item
+    $.ajax({
+        url: url,
+                data: data,
+                dataType: 'json',
+                type: 'POST',
+        success: function(data, textStatus, request) {
+                        updateOntologyLists( data )
+                        $( '#term_spinner' ).hide();
+                        $( '#ncbo_spinner' ).hide();
+
+                        $('#ontologyDialog').dialog('close');
+        },
+        error: function( request ) {
+                        alert( "Could not add ontology: " + request.responseText );
+                        $( '#term_spinner' ).hide();
+                        $( '#ncbo_spinner' ).hide();
+                        $('#ontologyDialog').dialog('close');
+        }
+    });
+}
+
+function updateOntologyLists( newObject ) {
+        $( '.ontologySelect' ).append( '<option value="' + newObject.id + '">' + newObject.name + '</option>');
+}