Changeset 1261

Timestamp:

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

Author:

s.h.sikkema@…

Message:

Changed jumbar layout to simple iframe for modules

Location:

trunk

Files:

• application.properties (modified) (1 diff)
• grails-app/conf/BuildConfig.groovy (modified) (1 diff)
• grails-app/conf/Config.groovy (modified) (1 diff)
• grails-app/controllers/dbnp/studycapturing/AssayController.groovy (modified) (2 diffs, 1 prop)
• grails-app/controllers/dbnp/studycapturing/StudyController.groovy (modified) (1 diff, 1 prop)
• grails-app/views/exporter/selectAssay.gsp (added)
• grails-app/views/study/show_assays.gsp (modified) (1 diff, 1 prop)
• test/unit/dbnp/studycapturing/AssayControllerTests.groovy (modified) (3 diffs)
• test/unit/dbnp/studycapturing/StudyControllerTests.groovy (modified) (2 diffs)

trunk/application.properties

@@ -17 +17 @@
 plugins.hibernate=1.3.5
 plugins.jquery=1.4.3.2
-plugins.jumpbar=0.1.2
+plugins.jumpbar=0.1.4
 plugins.mail=0.9
 plugins.oauth=0.10

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>

trunk/test/unit/dbnp/studycapturing/AssayControllerTests.groovy

@@ -2 +2 @@
 
 import grails.test.*
+
+import dbnp.data.Term
 
 /**
@@ -20 +22 @@
     protected void setUp() {
         super.setUp()
+
+        mockDomain(Term,          [ new Term(id: 1, name: 'Human')])
+
+        mockDomain(TemplateField, [ new TemplateField(id: 1, name: 'tf1', type: TemplateFieldType.STRING),
+                                    new TemplateField(id: 2, name: 'tf2', type: TemplateFieldType.STRING),
+                                    new TemplateField(id: 3, name: 'tf3', type: TemplateFieldType.STRING)])
+
+        mockDomain(Template,      [ new Template(id: 1, fields: [TemplateField.get(1), TemplateField.get(2)]),
+                                    new Template(id: 2, fields: [TemplateField.get(3)])])
+
+        mockDomain(Subject,       [ new Subject(id: 1, name:'subject1', template: Template.get(1), species: Term.get(1)),
+                                    new Subject(id: 2, name:'subject2', template: Template.get(2), species: Term.get(1))])
+
+        mockDomain(SamplingEvent, [ new SamplingEvent(id:1, startTime: 2, duration: 5, sampleTemplate: new Template())])
+
+        mockDomain(Event,         [ new Event(id: 1, startTime: 6, endTime: 7)])//, new Event(id: 2, startTime: 8, endTime: 9)])
+
+        mockDomain(EventGroup,    [ new EventGroup(id:1, events: [Event.get(1)]) ])
+
+        mockDomain(Sample,        [ new Sample(id: 1, name:'sample1', parentSubject: Subject.get(1), parentEvent: SamplingEvent.get(1), parentEventGroup: EventGroup.get(1)),
+                                    new Sample(id: 2, name:'sample2', parentSubject: Subject.get(2), parentEvent: SamplingEvent.get(1))])
+
+        mockDomain(Assay,         [ new Assay(id: 1, samples:[Sample.get(1),Sample.get(2)]),
+                                    new Assay(id: 2, samples:[])])
+
+        Subject.get(1).setFieldValue('tf1', 'tfv1')
+        Subject.get(1).setFieldValue('tf2', 'tfv2')
+        Subject.get(2).setFieldValue('tf3', 'tfv3')
     }
 
@@ -26 +56 @@
     }
 
-    void testSomething() {
+    void testWrongAssayID() {
+        mockParams.id = 3
 
+        controller.exportAssayAsExcel()
+
+        assertEquals 'Redirected action should match', [action: 'selectAssay'], redirectArgs
+        assertEquals 'Error message', 'No assay found with id: 3.', mockFlash.errorMessage
+    }
+
+    void testExceptionHandling() {
+        mockParams.id = 1
+
+        controller.assayService = [exportAssayDataAsExcelFile:{throw new Exception('msg')}]
+        controller.exportAssayAsExcel()
+
+        assertEquals 'Redirected action should match', [action: 'selectAssay'], redirectArgs
+        assertEquals 'Error message', 'msg', mockFlash.errorMessage
+    }
+
+    void testEmptySampleList() {
+        mockParams.id = 2
+
+        def passedAssayData = []
+
+        controller.assayService = [exportAssayDataAsExcelFile:{a -> passedAssayData = a}]
+        controller.exportAssayAsExcel()
+
+        assertEquals 'Assay data', [], passedAssayData*.value.flatten()
+    }
+
+    void testTemplateFieldsAreCollected() {
+
+        mockParams.id = 1
+
+        Map passedAssayData
+
+        controller.assayService = [exportAssayDataAsExcelFile:{a -> passedAssayData = a}]
+        controller.exportAssayAsExcel()
+
+        def sample1index = passedAssayData.'Sample Data'.'name'.findIndexOf{it == 'sample1'}
+        def sample2index = passedAssayData.'Sample Data'.'name'.findIndexOf{it == 'sample2'}
+
+        assertEquals 'Subject template field', ['tfv1',''], passedAssayData.'Subject Data'.tf1[sample1index, sample2index]
+        assertEquals 'Subject template field', ['tfv2',''], passedAssayData.'Subject Data'.tf2[sample1index, sample2index]
+        assertEquals 'Subject template field', ['','tfv3'], passedAssayData.'Subject Data'.tf3[sample1index, sample2index]
+        assertEquals 'Subject species template field', ['Human', 'Human'], passedAssayData.'Subject Data'.species*.toString()
+        assertEquals 'Subject name template field', ['subject1','subject2'], passedAssayData.'Subject Data'.name[sample1index, sample2index]
+
+        assertEquals 'Sampling event template fields', [2], passedAssayData.'Sampling Event Data'.startTime
+        assertEquals 'Sampling event template fields', [5], passedAssayData.'Sampling Event Data'.duration
+        assertEquals 'Sampling event template fields', '[null]', passedAssayData.'Sampling Event Data'.sampleTemplate.toString()
+        assertEquals 'Event template fields', [6], passedAssayData.'Event Data'.startTime
+        assertEquals 'Event template fields', [7], passedAssayData.'Event Data'.endTime
+        assertEquals 'Sample template fields', ['sample1', 'sample2'], passedAssayData.'Sample Data'.name[sample1index, sample2index]
     }
 }

trunk/test/unit/dbnp/studycapturing/StudyControllerTests.groovy

@@ -4 +4 @@
 class StudyControllerTests extends ControllerUnitTestCase {
     protected void setUp() {
+
         super.setUp()
+        mockDomain(Study, [ new Study(id: 1, assays: [[id:1, name:'assay1'], [id:2, name:'assay2']]),
+                            new Study(id: 2, assays: [])])
+
     }
 
@@ -11 +15 @@
     }
 
-    void testSomething() {
+    void testAjaxGetAssays() {
 
+        mockParams.id = 1
+        controller.ajaxGetAssays()
+        assertEquals '[{"name":"assay1","id":1},{"name":"assay2","id":2}]', mockResponse.contentAsString
+    }
+
+
+    void testAjaxGetAssaysEmptyList() {
+
+        mockParams.id = 2
+        controller.ajaxGetAssays()
+        assertEquals '[]', mockResponse.contentAsString
     }
 }