Changeset 2060

Timestamp:

Oct 17, 2011, 10:09:28 AM (12 years ago)

Author:

s.h.sikkema@…

Message:

• removed default value for samples argument in AssayService?.collectAssayData to comply with default value for remoteUser. Made adjustments where necessary
• updated user guide to new one by Janneke

Location:

trunk

Files:

• grails-app/controllers/dbnp/studycapturing/AssayController.groovy (modified) (4 diffs)
• grails-app/services/dbnp/studycapturing/AssayService.groovy (modified) (1 diff)
• grails-app/views/home/index.gsp (modified) (1 diff)
• test/unit/dbnp/studycapturing/AssayServiceTests.groovy (modified) (2 diffs)
• web-app/downloads/gscf_user_guide.pdf (added)

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

@@ -177 +177 @@
 
                                 // collect the assay data according to user selecting
-                                def assayData           = assayService.collectAssayData(flow.assay, fieldMapSelection, measurementTokens)
+                                def assayData           = assayService.collectAssayData(flow.assay, fieldMapSelection, measurementTokens, [])
 
                                 flash.errorMessage      = assayData.remove('Module Error')
@@ -295 +295 @@
 
                 def measurementTokens = fieldMap.remove('Module Measurement Data');
-                def assayData = assayService.collectAssayData(assay, fieldMap, measurementTokens, null, remoteUser)
+                def assayData = assayService.collectAssayData(assay, fieldMap, measurementTokens, [], remoteUser)
 
                 def rowData   = assayService.convertColumnToRowStructure(assayData)
@@ -406 +406 @@
 
                                 // Retrieve row based data for this assay
-                                def assayData = assayService.collectAssayData( assay, fieldMap, measurementTokens );
+                                def assayData = assayService.collectAssayData( assay, fieldMap, measurementTokens, [] );
                                 def rowData   = assayService.convertColumnToRowStructure(assayData)
 
@@ -448 +448 @@
 
                                 // Retrieve row based data for this assay
-                                def assayData = assayService.collectAssayData( assay, fieldMap, measurementTokens );
+                                def assayData = assayService.collectAssayData( assay, fieldMap, measurementTokens, [] );
 
                                 // Prepend study and assay data to the list

trunk/grails-app/services/dbnp/studycapturing/AssayService.groovy

@@ -82 +82 @@
          * @param measurementTokens     selection of measurementTokens
          * @param samples                               list of samples for which the data should be retrieved. 
-         *                                                              Defaults to all samples from this assay.
+         *                                                              Defaults to all samples from this assay. Supply [] or
+         *                                                              null to include all samples.
          * @return                              The assay data structure as described above.
          */
-        def collectAssayData(assay, fieldMap, measurementTokens, samples = null, SecUser remoteUser = null) throws Exception {
+        def collectAssayData(assay, fieldMap, measurementTokens, samples, SecUser remoteUser = null) throws Exception {
 
                 def collectFieldValuesForTemplateEntities = { headerFields, templateEntities ->

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

@@ -355 +355 @@
                         </p>
                         <p>
-                                <i>A more in depth quickstart guide is available for download <a href="${resource(dir:'downloads', file: 'quickstart_'+session.style+'.pdf')}">here</a>.</i>
+                                <i>A more in depth user guide is available for download <a href="${resource(dir:'downloads', file: 'gscf_user_guide.pdf')}">here</a>.</i>
                         </p>
                 </div>

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

@@ -5 +5 @@
 import org.apache.poi.ss.usermodel.WorkbookFactory
 import org.apache.poi.ss.usermodel.Cell
-import grails.converters.JSON
 import org.dbnp.gdt.*
 import org.dbnp.gdt.AssayModule
-import org.dbnp.gdt.TemplateEntity
-import groovy.mock.interceptor.MockFor
-import org.dbnp.gdt.GdtService
 import org.dbnp.gdt.TemplateStringField
 
@@ -210 +206 @@
         String.metaClass.'encodeAsURL' = {delegate}
 
-        def assayData = service.collectAssayData(assay, fieldMap, measurementTokens)
+        def assayData = service.collectAssayData(assay, fieldMap, measurementTokens, [])
 
         def sample1index = assayData.'Sample Data'.'name'.findIndexOf{it == 'sample1'}