Changeset 1261 for trunk/grails-app

Timestamp:

Dec 13, 2010, 11:50:28 AM (10 years ago)

Author:

s.h.sikkema@…

Message:

Changed jumbar layout to simple iframe for modules

Location:

trunk/grails-app

Files:

• conf/BuildConfig.groovy (modified) (1 diff)
• conf/Config.groovy (modified) (1 diff)
• controllers/dbnp/studycapturing/AssayController.groovy (modified) (2 diffs, 1 prop)
• controllers/dbnp/studycapturing/StudyController.groovy (modified) (1 diff, 1 prop)
• views/exporter/selectAssay.gsp (added)
• views/study/show_assays.gsp (modified) (1 diff, 1 prop)

trunk/grails-app/conf/BuildConfig.groovy

@@ -47 +47 @@
 //grails.plugin.location.'grom' = '../grom'
 //grails.plugin.location.'ajax-flow' = '../AjaxFlow'
+//grails.plugin.location.'jumpbar' = '../jumpbar'

trunk/grails-app/conf/Config.groovy

@@ -93 +93 @@
                         metabolomics {
                                 url = "http://test.metabolomics.dbnp.org"
+                
                         }
                 }

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

@@ -3 +3 @@
 class AssayController {
 
+    def assayService
+    def authenticationService
+    
     static allowedMethods = [save: "POST", update: "POST", delete: "POST"]
 
@@ -115 +118 @@
         }
     }
+
+    /**
+     * Shows a page where an assay from a study can be selected
+     *
+     * @param none
+     */
+    def selectAssay = {
+        def user = authenticationService.getLoggedInUser()
+        def studies = Study.findAllByOwner(user)
+        def assays = Assay.findAllByParent(studies[0])
+
+        [userStudies: studies, assays: assays]
+    }
+
+    /**
+     * Exports all assay information as an Excel file.
+     *
+     * @param params.id Assay id
+     */
+    def exportAssayAsExcel = {
+        Assay assay = Assay.get(params.id)
+
+        if (!assay) {
+            flash.errorMessage = "No assay found with id: $params.id."
+            redirect action: 'selectAssay'
+            return
+        }
+
+        // TODO: refactor into service
+
+        // Gather sample meta data from GSCF
+        def samples = assay.samples
+
+        def collectUsedTemplateFields = { templateEntityList ->
+
+            def templateFields = templateEntityList*.giveFields().flatten().unique().findAll{it}
+            def usedTemplateFields = templateFields.findAll{ tf ->
+
+                templateEntityList.any { it.fieldExists(tf.name) && it.getFieldValue(tf.name) }
+            }
+
+            def m = [:]
+            usedTemplateFields.each { tf ->
+                m["${tf.name}"] = templateEntityList.collect{ it.fieldExists(tf.name) ? it.getFieldValue(tf.name) : '' }
+            }
+            m
+        }
+
+        // get all sample related subjects
+        def assayData = [
+                'Subject Data':         collectUsedTemplateFields(samples*.parentSubject.unique()),
+                'Sampling Event Data':  collectUsedTemplateFields(samples*.parentEvent.unique()),
+                'Event Data':           collectUsedTemplateFields(samples*.parentEventGroup.events.flatten().unique()),
+                'Sample Data':          collectUsedTemplateFields(samples)]
+
+        // Gather sample meta data from the module
+
+        // - sample metadata
+
+        // Gather measurement data from the module
+
+        // - measurements
+
+        // Write to excel
+
+        println assayData
+
+        try {
+            assayService.exportAssayDataAsExcelFile(assayData)
+        } catch (Exception e) {
+            flash.errorMessage = e.message
+            redirect action: 'selectAssay'
+        }
+    }
 }

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

@@ -367 +367 @@
     }
 
-    /*def edit = {
-        def studyInstance = Study.get(params.id)
-        if (!studyInstance) {
-            flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'study.label', default: 'Study'), params.id])}"
-            redirect(action: "list")
-        }
-        else {
-            return [studyInstance: studyInstance]
-        }
-    }
-
-    def update = {
-        def studyInstance = Study.get(params.id)
-        if (studyInstance) {
-            if (params.version) {
-                def version = params.version.toLong()
-                if (studyInstance.version > version) {
-                    
-                    studyInstance.errors.rejectValue("version", "default.optimistic.locking.failure", [message(code: 'study.label', default: 'Study')] as Object[], "Another user has updated this Study while you were editing")
-                    render(view: "edit", model: [studyInstance: studyInstance])
-                    return
-                }
-            }
-            studyInstance.properties = params
-            if (!studyInstance.hasErrors() && studyInstance.save(flush: true)) {
-                flash.message = "${message(code: 'default.updated.message', args: [message(code: 'study.label', default: 'Study'), studyInstance.id])}"
-                redirect(action: "show", id: studyInstance.id)
-            }
-            else {
-                render(view: "edit", model: [studyInstance: studyInstance])
-            }
-        }
-        else {
-            flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'study.label', default: 'Study'), params.id])}"
-            redirect(action: "list")
-        }
-    }
-*/
+    /**
+     * Renders assay names and id's as JSON
+     */
+    def ajaxGetAssays = {
+
+        def study = Study.read(params.id)
+        render study?.assays?.collect{[name: it.name, id: it.id]} as JSON
+    }
+
+
 }

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

@@ -31 +31 @@
                   <td>${assay.module.name}</td>
                   <td>${assay.module.platform}</td>
-                  %{--<td><a href="${assay.module.url}/assay/${assay.externalAssayID}">view</a></td>--}%
-                  <td><jumpbar:link
-                        linkDest="${createLink(action:'show', id:studyInstance.id)}/#Assays"
-                        linkText='Go back to GSCF'
-                        frameSource="${assay.module.url}/assay/showByToken/${assay.externalAssayID}"
-                        pageTitle="Assay View in Module">
+                  <td>
+          <jumpbar:link frameSource="${assay.module.url}/assay/showByToken/${assay.externalAssayID}" pageTitle="Metabolomics Module">
                         view
                   </jumpbar:link></td>