Changeset 1027

Timestamp:

Nov 1, 2010, 12:42:49 PM (13 years ago)

Author:

robert@…

Message:

Implemented compare templates feature and fixed show studies overview (tickets #7 and #137)

Location:

trunk

Files:

• application.properties (modified) (1 diff)
• grails-app/conf/BootStrapStudies.groovy (modified) (2 diffs)
• grails-app/controllers/RestController.groovy (modified) (2 diffs)
• grails-app/controllers/dbnp/studycapturing/TemplateEditorController.groovy (modified) (5 diffs)
• grails-app/domain/dbnp/studycapturing/AssayModule.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/Template.groovy (modified) (1 diff)
• grails-app/views/study/show.gsp (modified) (1 diff)
• grails-app/views/templateEditor/compare.gsp (added)
• grails-app/views/templateEditor/elements/_liTemplate.gsp (modified) (1 diff)
• grails-app/views/templateEditor/elements/_liTemplateEditable.gsp (modified) (1 diff)
• grails-app/views/templateEditor/elements/_liTemplateNonEditable.gsp (modified) (1 diff)
• grails-app/views/templateEditor/index.gsp (modified) (4 diffs)
• grails-app/views/templateEditor/template.gsp (modified) (4 diffs)
• web-app/css/templateEditor.css (modified) (1 diff)
• web-app/js/jquery.dataTables.min.js (added)

trunk/application.properties

@@ -1 +1 @@
 #Grails Metadata file
-#Tue Oct 26 15:12:32 CEST 2010
+#Tue Oct 26 16:55:24 CEST 2010
 app.grails.version=1.3.5
 app.name=gscf

trunk/grails-app/conf/BootStrapStudies.groovy

@@ -480 +480 @@
                         name: 'SAM module for clinical data',
                         platform: 'clinical measurements',
-                        consumer: samURL 
+                        url: samURL
                 ).with { if (!validate()) { errors.each { println it} } else save()}
 
@@ -487 +487 @@
                         name: 'Metabolomics module',
                         platform: 'GCMS/LCMS',
-                        consumer: nmcdspURL
+                        url: nmcdspURL
                 ).with { if (!validate()) { errors.each { println it} } else save()}
 

trunk/grails-app/controllers/RestController.groovy

@@ -145 +145 @@
                         if(study) {
                                 // Check whether the person is allowed to read the data of this study
-/*
                                 if( !study.canRead(AuthenticationService.getRemotelyLoggedInUser( params.consumer, params.token ))) {
                                         response.sendError(401)
                                         return false
                                 }
-*/
+                                
                                 def items = [:]
                                 study.giveFields().each { field ->
@@ -283 +282 @@
 
                                 assays.each{ assay ->
-                                        if (assay.module.consumer.equals(params.consumer )) {
+                                        if (assay.module.url.equals(params.consumer )) {
                                                 if(assay) {
                                                         def map = [:]

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

@@ -16 +16 @@
 import dbnp.data.*
 import dbnp.studycapturing.*
+
 import dbnp.authentication.AuthenticationService
+import grails.plugins.springsecurity.Secured
+
 import cr.co.arquetipos.crypto.Blowfish
 import grails.converters.*
 import java.lang.reflect.*;
 
+@Secured(['IS_AUTHENTICATED_REMEMBERED'])
 class TemplateEditorController {
     def entityName;
     def entity;
-
         def AuthenticationService
+
+        /**
+     * Fires after every action and determines the layout of the page
+     */
+    def afterInterceptor = { model, modelAndView ->
+      if ( params['standalone'] ) {
+        model.layout = 'main';
+        model.extraparams = [ 'standalone': 'true' ] ;
+      } else {
+        model.layout = 'dialog';
+        model.extraparams = [] ;
+      }
+    }
         
         /**
@@ -81 +97 @@
 
                 // redirect to template editor page of the specified entity
-                redirect(action: "index",params:[entity: resultEntity])
+                params.entity = resultEntity
+                redirect(action: "index", params:params)
         }
-
 
     /**
@@ -110 +126 @@
     }
 
+    /**
+     * compare two or more templates
+     */
+    def compare = {
+        // Check whether a right entity is given
+        if( !_checkEntity() ) {
+                        return
+                }
+
+        // fetch all templates for this entity
+        def templates = Template.findAllByEntity(entity)
+
+                // Find all available fields
+                def allFields = TemplateField.findAllByEntity( entity ).sort { a, b -> a.name <=> b.name }
+
+                // Generate a human readable entity name
+                def parts = entityName.tokenize( '.' );
+                def humanReadableEntity = parts[ parts.size() - 1 ];
+
+        return [
+            entity: entity,
+            templates: templates,
+                        allFields: allFields,
+            encryptedEntity: params.entity,
+            humanReadableEntity: humanReadableEntity,
+                        ontologies: params.ontologies,
+                        templateEntities: this.templateEntityList()
+        ];
+    }
+
         /**
          * Shows the editing of a template
@@ -138 +184 @@
                 def parts = entityName.tokenize( '.' );
                 def humanReadableEntity = parts[ parts.size() - 1 ];
-
-
 
                 // Find all available fields
@@ -836 +880 @@
 
     }
+
+        def templateEntityList = {
+                def entities = [
+                        [ name: 'Study', entity: 'dbnp.studycapturing.Study' ],
+                        [ name: 'Subject', entity: 'dbnp.studycapturing.Subject' ],
+                        [ name: 'Event', entity: 'dbnp.studycapturing.Event' ],
+                        [ name: 'Sampling Event', entity: 'dbnp.studycapturing.SamplingEvent' ],
+                        [ name: 'Sample', entity: 'dbnp.studycapturing.Sample' ],
+                        [ name: 'Assay', entity: 'dbnp.studycapturing.Assay' ]
+                ]
+
+                entities.each { 
+                        // add the entity class name to the element
+                        // do we have crypto information available?
+                        if (grailsApplication.config.crypto) {
+                                // generate a Blowfish encrypted and Base64 encoded string.
+                                it.encoded = URLEncoder.encode(
+                                        Blowfish.encryptBase64(
+                                                it.entity.toString().replaceAll(/^class /, ''),
+                                                grailsApplication.config.crypto.shared.secret
+                                        )
+                                )
+                        } else {
+                                // base64 only; this is INSECURE! As this class
+                                // is instantiated elsewehere. Possibly exploitable!
+                                it.encoded = URLEncoder.encode(it.entity.toString().replaceAll(/^class /, '').bytes.encodeBase64())
+                        }
+                }
+
+                return entities
+        }
 }

trunk/grails-app/domain/dbnp/studycapturing/AssayModule.groovy

@@ -12 +12 @@
         String platform
 
-        /** Consumer id (e.g., OAuth consuemr key) of module where instance is located */
-        String consumer 
+        /** The base URL at which the module instance is located. This is also used
+         * as a consumer parameter to identify the module in the authentication process.
+         */
+        String url
 
         static constraints = {

trunk/grails-app/domain/dbnp/studycapturing/Template.groovy

@@ -89 +89 @@
          */
         public Template( Template otherTemplate) {
-                this()
-
-                //authenticationService = new AuthenticationService()
-
-                this.name = otherTemplate.name + " (Copy)"
-                this.description = otherTemplate.description
-                this.entity = otherTemplate.entity
-                this.owner = otherTemplate.owner
-
-                // The fields are copied by reference
-                this.fields = otherTemplate.fields
+                this( otherTemplate, otherTemplate.owner )
         }
 

trunk/grails-app/views/study/show.gsp

@@ -240 +240 @@
                   <td>${field}</td>
                   <g:each in="${studyList}" var="studyInstance">
-                    <td>${studyInstance.getFieldValue(field.name)}</td>
+                    <td>
+                                          <g:if test="${studyInstance.fieldExists(field.name)}">
+                                                ${studyInstance.getFieldValue(field.name)}
+                                          </g:if>
+                                          <g:else>
+                                                -
+                                          </g:else>
+                                        </td>
                   </g:each>
                 </tr>

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

@@ -1 +1 @@
 <li id="template_${template.id}"class="ui-state-default">
   <g:if test="${template.inUse()}">
-        <g:render template="elements/liTemplateNonEditable" model="['template': template]"/>
+        <g:render template="elements/liTemplateNonEditable" model="['template': template, , 'standalone': standalone]"/>
   </g:if>
   <g:else>
-        <g:render template="elements/liTemplateEditable" model="['template': template]"/>
+        <g:render template="elements/liTemplateEditable" model="['template': template, 'standalone': standalone]"/>
   </g:else>
 </li>

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

@@ -7 +7 @@
 ${template.name}
 
-
 <form class="templateField_form" id="template_${template.id}_form" action="updateTemplate">
         <g:hiddenField name="id" value="${template.id}" />
         <g:hiddenField name="version" value="${template.version}" />
+        <g:hiddenField name="standalone" value="${standalone}" />
         <g:render template="elements/templateForm" model="['template': template]"/>
         <div class="templateFieldButtons">

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

@@ -12 +12 @@
         <g:hiddenField name="id" value="${template.id}" />
         <g:hiddenField name="version" value="${template.version}" />
+        <g:hiddenField name="standalone" value="${standalone}" />
         <g:render template="elements/templateForm" model="['template': template]"/>
         <div class="templateFieldButtons">

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

@@ -17 +17 @@
 <html>
         <head>
-                <meta name="layout" content="dialog"/>
+                <meta name="layout" content="${layout}"/>
                 <title>template editor</title>
                 <script src="${createLinkTo(dir: 'js', file: 'templateEditor.js')}" type="text/javascript"></script>
                 <link rel="stylesheet" href="${createLinkTo(dir: 'css', file: 'templateEditor.css')}" />
+                <style type="text/css">
+                  #content .templateEditorStep { font-size: 0.8em; }
+                </style>
+                <script type="text/javascript" language="javascript">
+                  var standalone = ${extraparams?.standalone ? 'true' : 'false'};
+                </script>
         </head>
         <body>
@@ -32 +38 @@
                                 <li class="empty ui-state-default" <g:if test="${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">
-                                  <g:render template="elements/liTemplate" model="['template': currentTemplate]"/>
+                                  <g:render template="elements/liTemplate" model="['template': currentTemplate, 'extraparams': extraparams]"/>
                                 </g:each>
                         </ul>
@@ -44 +50 @@
                                         <g:hiddenField name="entity" value="${encryptedEntity}" />
                                         <g:hiddenField name="ontologies" value="${ontologies}" />
+                                        <g:hiddenField name="standalone" value="${extraparams?.standalone}" />
                                         <g:render template="elements/templateForm" model="['template': null]"/>
                                         <div class="templateFieldButtons">
@@ -55 +62 @@
                                 <g:hiddenField name="entity" value="${encryptedEntity}" />
                                 <g:hiddenField name="ontologies" value="${ontologies}" />
+                                <g:hiddenField name="standalone" value="${extraparams?.standalone}" />
                                 <input type="hidden" name="template" id="templateSelect" value="${template?.id}">
                         </g:form>
                 </div>
-
+                <br clear="all" />
                 <div id="wait" class="wait">
                   &nbsp;

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

@@ -17 +17 @@
 <html>
         <head>
-                <meta name="layout" content="dialog"/>
+                <meta name="layout" content="${layout}"/>
                 <title>template editor</title>
                 <script src="${createLinkTo(dir: 'js', file: 'templateEditor.js')}" type="text/javascript"></script>
@@ -26 +26 @@
                   <script type="text/javascript" src="${resource(dir: 'js', file: 'ontology-chooser.js')}"></script>
                 </g:else>
+
+                <style type="text/css">
+                  #content .templateEditorStep { font-size: 0.8em; }
+                </style>
         </head>
         <body>
@@ -80 +84 @@
                 <g:if test="${template}">
                         <div class="templateEditorStep" id="step2_selectedFields">
-                                <h3 class="templateName">${template.name} (<a class="switch" href="${createLink(action:'index')}?entity=${encryptedEntity.encodeAsURL()}">switch</a>)</h3>
+                                <h3 class="templateName">${template.name} (<a class="switch" href="${createLink(action:'index',params: extraparams + [ 'entity': encryptedEntity ])}">switch</a>)</h3>
 
                                 <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>
@@ -117 +121 @@
                         </div>
                 </g:if>
-
+                <br clear="all" />
                 <div id="ontologyDialog">
                   <g:render template="ontologyDialog" />

trunk/web-app/css/templateEditor.css

@@ -97 +97 @@
 .wait { display: none; }
 
+/* Compare templates view */
+.dataTables_length { float: left; width: 40%; }
+.dataTables_filter { float: right; width: 50%; text-align: right; }
+table#compare_templates { clear: both; }
+.dataTables_info { float: left; width: 40%; line-height: 25px; }
+.dataTables_paginate { float: right; text-align: right; width: 50%; padding-top: 5px; }
+
+.paging_full_numbers span.paginate_active { background:none repeat scroll 0 0 #2E6AB1; color:#FFFFFF; }
+.paging_full_numbers span.paginate_button, .paging_full_numbers span.paginate_active {
+        border:1px solid #CCCCCC; margin-right:2px; padding:1px 6px; text-decoration:none;
+        cursor: pointer;
+}
+
+
+
+
 /* Add Ontology dialog */
 #addOntology { list-style-type: none; padding-left: 0; }