Changeset 836 for trunk

Timestamp:

Aug 25, 2010, 9:44:58 AM (13 years ago)

Author:

keesvb

Message:

added some example assay templates, started with implementation of assay and assay group steps in wizard

Location:

trunk/grails-app

Files:

• conf/BootStrapStudies.groovy (modified) (6 diffs)
• conf/BootStrapTemplates.groovy (modified) (2 diffs)
• views/wizard/pages/_assay_groups.gsp (modified) (1 diff)
• views/wizard/pages/_assays.gsp (modified) (1 diff)

trunk/grails-app/conf/BootStrapStudies.groovy

@@ -38 +38 @@
                 def humanTissueSampleTemplate = Template.findByName("Human tissue sample")
                 def humanBloodSampleTemplate = Template.findByName("Human blood sample")
-                
+                def ccAssayTemplate = Template.findByName("Clinical chemistry assay")
+                def metAssayTemplate = Template.findByName("Metabolomics assay")
 
                 // Add terms manually, to avoid having to do many HTTP requests to the BioPortal website
@@ -481 +482 @@
                 def lipidAssayRef = new Assay(
                         name: 'Lipid profiling',
+                        template: ccAssayTemplate,
                         module: clinicalModule,
                         externalAssayID: 'PPS3_SAM'
@@ -487 +489 @@
                 def metAssayRef = new Assay(
                         name: 'Lipidomics profile',
+                        template: metAssayTemplate,
                         module: metabolomicsModule,
                         externalAssayID: 'PPS3_Lipidomics'
                 )
+                .setFieldValue('Spectrometry technique','LC/MS')
 
                 mouseStudy.samples*.each {
@@ -504 +508 @@
                 def  glucoseAssayBRef = new Assay(
                         name: 'Glucose assay before',
+                        template: ccAssayTemplate,
                         module: clinicalModule,
                         externalAssayID: 'PPSH-Glu-B'
@@ -510 +515 @@
                 def  glucoseAssayARef = new Assay(
                         name: 'Glucose assay after',
+                        template: ccAssayTemplate,
                         module: clinicalModule,
                         externalAssayID: 'PPSH-Glu-A'
@@ -516 +522 @@
                 def metAssayRefB = new Assay(
                         name: 'Lipidomics profile before',
+                        template: metAssayTemplate,
                         module: metabolomicsModule,
                         externalAssayID: 'PPSH_Lipidomics_start'
                 )
+                .setFieldValue('Spectrometry technique','GC/MS')
 
                 def metAssayRefA = new Assay(
                         name: 'Lipidomics profile after',
+                        template: metAssayTemplate,
                         module: metabolomicsModule,
                         externalAssayID: 'PPSH_Lipidomics_end'
                 )
+                .setFieldValue('Spectrometry technique','GC/MS')
+
                 humanStudy.samples*.each {
                         if (it.parentEvent.startTime == 0) {

trunk/grails-app/conf/BootStrapTemplates.groovy

@@ -591 +591 @@
                 println ".adding plant sampling event template"
                 def plantSamplingEventTemplate = new Template(
-                        name: 'Plant-sample ',
+                        name: 'Plant-sample',
                         description: 'plant sample ',
                         entity: dbnp.studycapturing.SamplingEvent,
@@ -629 +629 @@
                 .with { if (!validate()) { errors.each { println it} } else save()}
 
+
+                // assay templates
+
+                def assayDescriptionField = new TemplateField(
+                                name: 'Description',
+                            comment: 'add general assay information here',
+                                entity: Assay,
+                                type: TemplateFieldType.STRING
+                );
+                assayDescriptionField.with { if (!validate()) { errors.each { println it} } else save()}
+
+                println ".adding clinical chemistry assay template"
+                def ccAssayTemplate = new Template(
+                        name: 'Clinical chemistry assay',
+                        description: 'Clinical chemistry assay stored in a SAM module',
+                        entity: dbnp.studycapturing.Assay
+                )
+                .addToFields(assayDescriptionField)
+                .with { if (!validate()) { errors.each { println it} } else save()}
+
+                println ".adding metabolomics assay template"
+                def metAssayTemplate = new Template(
+                        name: 'Metabolomics assay',
+                        description: 'Metabolomics assay stored in a metabolomics module',
+                        entity: dbnp.studycapturing.Assay
+                )
+                .addToFields(assayDescriptionField)
+                .addToFields(
+                        new TemplateField(
+                                name: 'Spectrometry technique',
+                            comment: 'Select the used metabolomics technique',
+                                entity: Assay,
+                                type: TemplateFieldType.STRINGLIST,
+                            listEntries: [
+                                        new TemplateFieldListItem(name: 'GC/MS'),
+                                new TemplateFieldListItem(name: 'LC/MS'),
+                                new TemplateFieldListItem(name: 'NMR'),
+                                new TemplateFieldListItem(name: 'HPLC')
+                            ])
+                )
+                .with { if (!validate()) { errors.each { println it} } else save()}
         }
 

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

@@ -16 +16 @@
 %>
 <wizard:pageContent>
-assay groups
+        <span class="info">
+                <span class="title">Assign samples to assays</span>
+                In the previous page you defined assays. In this page, you can define which assays are performed on which samples.
+                The samples are grouped according to the EventGroups of their defining SamplingEvents.
+        </span>
+
+        <%
+            // TODO: render a table of assays (in the columns) versus samples (in the rows)
+                // with the samples grouped according to the EventGroups of the parent SamplingEvents
+                // and with all boxes checked by default
+        %>
+
 </wizard:pageContent>

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

@@ -18 +18 @@
         <span class="info">
                 <span class="title">Add assays to your study</span>
-                WE NEED SOME CONTENT OVER HERE, who's the brilliant copy writer? :)
+                In this step you can define the various assays that were performed within this study.
+                The actual (omics) data for these assays should reside in one of the assay modules that is coupled to this database (see Assay Modules).
         </span>
 
+        <wizard:textFieldElement name="addNumber" description="Number of assays to add" error="addNumber" value="${values?.addNumber}" size="4" maxlength="4">
+                The number of subjects to add to your study
+        </wizard:textFieldElement>
         <wizard:templateElement name="template" description="Template" value="${assay?.template}" entity="${dbnp.studycapturing.Assay}" addDummy="true" ajaxOnChange="switchTemplate" url="[controller:'wizard',action:'pages']" update="[success:'wizardPage',failure:'wizardError']" afterSuccess="onWizardPage()" >
                 Choose the type of assay you would like to add
         </wizard:templateElement>
+        <%
+            // TODO: switch single flow.assay to multiple flow.assays and finish this page
+        %>
         <g:if test="${assay}">
         <wizard:templateElements entity="${assay}" />
         </g:if>
+        <wizard:ajaxButtonElement name="add" value="Add" url="[controller:'wizard',action:'pages']" update="[success:'wizardPage',failure:'wizardError']" afterSuccess="onWizardPage()">
+        </wizard:ajaxButtonElement>
 
+        
 </wizard:pageContent>