Changeset 1864 for trunk/grails-app/services

Timestamp:

May 23, 2011, 4:36:00 PM (11 years ago)

Author:

s.h.sikkema@…

Message:

in exporter: module error display improvements (ie. display on screen but still able to export); removed changes to simplewizard; removed unnecessary imports; should handle 'null' parent subject from samples correctly; should handle non number values from modules correctly; deselects module measurements in case of module error/no measurements; removed obsolete entry in topnav

Location:

trunk/grails-app/services/dbnp

Files:

• modules/ModuleCommunicationService.groovy (modified) (2 diffs)
• studycapturing/AssayService.groovy (modified) (8 diffs)

trunk/grails-app/services/dbnp/modules/ModuleCommunicationService.groovy

@@ -15 +15 @@
 package dbnp.modules
 
-import dbnp.studycapturing.*
-import dbnp.authentication.*
 import grails.converters.*
 import javax.servlet.http.HttpServletResponse
@@ -75 +73 @@
         }
 
-        /**
+    /**
          * Calls a rest method on a module
          * 

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

@@ -50 +50 @@
                 }
 
+        def moduleError = '', moduleMeasurements = []
+
+        try {
+            moduleMeasurements = requestModuleMeasurementNames(assay)
+        } catch (e) {
+            moduleError = e.message
+        }
+
                 def samples = assay.samples
                 [               'Subject Data' :            getUsedTemplateFields( samples*."parentSubject".unique() ),
@@ -55 +63 @@
                                         'Sample Data' :             getUsedTemplateFields( samples ),
                                         'Event Group' :             [[name: 'name', comment: 'Name of Event Group', displayName: 'name']],
-
-                                        // If module is not reachable, only the field 'module error' is returned, and is filled later on.
-                                        'Module Measurement Data':  moduleCommunicationService.isModuleReachable(assay.module.url) ? requestModuleMeasurementNames(assay) : [ [ name: "Module error" ] ]
+                                        'Module Measurement Data':  moduleMeasurements,
+                    'ModuleError':              moduleError
                 ]
 
@@ -83 +90 @@
                         headerFields.inject([:]) { map, headerField ->
 
-                                map + [(headerField.displayName): templateEntities.collect {
+                                map + [(headerField.displayName): templateEntities.collect { entity ->
 
                     // default to an empty string
                     def val = ''
 
-                    def field
-                    try {
-
-                        val = it.getFieldValue(headerField.name)
-
-                        // Convert RelTime fields to human readable strings
-                        field = it.getField(headerField.name)
-                        if (field.type == TemplateFieldType.RELTIME)
-                            val = new RelTime( val as long )
-
-                    } catch (NoSuchFieldException e) { /* pass */ }
+                    if (entity) {
+                        def field
+                        try {
+
+                            val = entity.getFieldValue(headerField.name)
+
+                            // Convert RelTime fields to human readable strings
+                            field = entity.getField(headerField.name)
+                            if (field.type == TemplateFieldType.RELTIME)
+                                val = new RelTime( val as long )
+
+                        } catch (NoSuchFieldException e) { /* pass */ }
+                    }
 
                     (val instanceof Number) ? val : val.toString()}]
@@ -177 +186 @@
                 }
 
+                def moduleError = '', moduleMeasurementData = [:]
+
+                if (measurementTokens) {
+
+            try {
+                moduleMeasurementData = requestModuleMeasurements(assay, measurementTokens, samples)
+            } catch (e) {
+                moduleMeasurementData = ['error' : ['Module error, module not available or unknown assay'] * samples.size() ]
+                moduleError =  e.message
+            }
+
+                }
+
                 [       'Subject Data' :            getFieldValues(samples, fieldMap['Subject Data'], 'parentSubject'),
                                 'Sampling Event Data' :     getFieldValues(samples, fieldMap['Sampling Event Data'], 'parentEvent'),
                 'Sample Data' :             getFieldValues(samples, fieldMap['Sample Data']),
                 'Event Group' :             eventFieldMap,
-
-                // If module is not reachable, only the message 'module not reachable' is given for each sample
-                'Module Measurement Data':  moduleCommunicationService.isModuleReachable(assay.module.url) ?
-                                                ( measurementTokens ? requestModuleMeasurements(assay, measurementTokens, samples) : [:] ) :
-                                                [ "Module error": [ "Module not reachable" ] * samples.size() ]
+                'Module Measurement Data' : moduleMeasurementData,
+                'ModuleError' :             moduleError
                                 ]
         }
@@ -249 +268 @@
 
                 def path = moduleUrl + "/rest/getMeasurements/query"
-        def query = "assayToken=$assay.assayUUID"
+        def query = "assayToken=${assay.giveUUID()}"
         def jsonArray
 
@@ -274 +293 @@
          * @param assay                         Assay for which the module measurements should be retrieved
          * @param measurementTokens     List with the names of the fields to be retrieved. Format: [ 'measurementName1', 'measurementName2' ]
-         * @param samples                       Samples for which the module
+         * @param samples                       Samples to collect measurements for
          * @return
          */
@@ -329 +348 @@
                                                 measurements << null
                                         }  else {
-                                                measurements << ( moduleData[ valueIndex ] == JSONObject.NULL ? "" : moduleData[ valueIndex ].toDouble() );
+
+                        def val
+                        def measurement = moduleData[ valueIndex ]
+
+                        if          (measurement == JSONObject.NULL)    val = ""
+                        else if     (measurement instanceof Number)     val = measurement
+                        else if     (measurement.isDouble())            val = measurement.toDouble()
+                        else val =   measurement.toString()
+                                                measurements << val
                                         }
                                 } else {
@@ -487 +514 @@
                         // transpose d into row wise data and combine with header rows
                         headers + d.transpose()
-                }
+                } else []
 
         }