Add serializer for DataType retrieval

grails-app/controllers/org/transmartproject/rest/ExportController.groovy

@@ -3,9 +3,9 @@ package org.transmartproject.rest
 import grails.validation.Validateable
 import groovy.json.JsonException
 import groovy.json.JsonSlurper
-import org.apache.commons.lang.NullArgumentException
 import org.springframework.beans.factory.annotation.Autowired
 import org.transmartproject.core.exceptions.InvalidArgumentsException
+import org.transmartproject.core.exceptions.NoSuchResourceException
 import org.transmartproject.db.RestExportService
 
 class ExportController {
@@ -29,31 +29,8 @@ class ExportController {
      *  Returns datatypes and patient number of given concepts.
      *
      */
-    def datatypes(){
-        def jsonSlurper = new JsonSlurper()
-        if (!(params.containsKey('concepts'))){
-            throw new NoSuchElementException(
-                    "No parameter named concepts."
-            )
-        }
-        def test = params.get('concepts').decodeURL()
-        try {
-            def concept_arguments = jsonSlurper.parseText(test)
-            if (concept_arguments==null){
-                throw new NullArgumentException(
-                        "Parameter concepts has no value."
-                )
-            }
-            List datatypes = []
-            concept_arguments.each { it ->
-                List conceptKeysList = it.conceptKeys
-                datatypes += restExportService.getDataTypes(conceptKeysList)
-            }
-            respond(restExportService.formatDataTypes(datatypes))
-        } catch(JsonException e){
-            "Given value was non valid JSON."
-        }
-
+    def datatypes() throws NoSuchResourceException {
+        respond restExportService.retrieveDataTypes(params)
     }
 
     private void throwIfInvalid(command) {

grails-app/controllers/org/transmartproject/rest/PatientSetController.groovy

@@ -34,7 +34,10 @@ class PatientSetController {
      * GET /patient_sets
      */
     def index() {
-        respond queriesResource.getQueryResultsSummaryByUsername(currentUser.getUsername() )
+        String noPatients = "There are no saved patient sets by $currentUser.username"
+        def patientSets = queriesResource.getQueryResultsSummaryByUsername(currentUser.getUsername() )
+        patientSets = patientSets == null ? noPatients : patientSets
+        respond patientSets
     }
 
     /**

src/groovy/org/transmartproject/rest/marshallers/DataTypeSerializationHelper.groovy

@@ -0,0 +1,31 @@
+package org.transmartproject.rest.marshallers
+
+import org.transmartproject.export.DataTypeRetrieved
+
+class DataTypeSerializationHelper  extends AbstractHalOrJsonSerializationHelper<DataTypeRetrieved>{
+
+    final Class targetType = DataTypeRetrieved
+    final String collectionName = 'dataTypeRetrieved'
+
+    @Override
+    Map<String, Object> convertToMap(DataTypeRetrieved dataTypeRetrieved) {
+        def cohortInfoList = []
+        def cohortsMap = [:]
+        dataTypeRetrieved.OntologyTermsMap.each { ID, terms ->
+            terms.collect { term ->
+                if (ID in cohortsMap.keySet()) {
+                    cohortsMap[ID].add([subjects: term.patients.collect({ it.id }), conceptPath: term.fullName])
+                } else {
+                    cohortsMap[ID] = [[subjects: term.patients.collect({ it.id }), conceptPath: term.fullName]]
+                }
+            }
+        }
+        cohortsMap.each{ key, value ->
+            cohortInfoList.add([concepts:value])
+        }
+        def datatypeMap = [dataType:dataTypeRetrieved.dataType,
+                           dataTypeCode: dataTypeRetrieved.dataTypeCode,
+                           cohorts:cohortInfoList]
+    }
+
+}

test/functional/org/transmartproject/rest/ExportTests.groovy

@@ -1,7 +1,6 @@
 package org.transmartproject.rest
 
-import org.codehaus.groovy.grails.web.mime.MimeType
-
+import org.codehaus.groovy.grails.web.json.JSONArray
 import static org.hamcrest.MatcherAssert.assertThat
 import static org.hamcrest.Matchers.*
 
@@ -22,7 +21,7 @@ class ExportTests extends ResourceTestCase{
                         hasEntry('dataTypeCode', 'mrna'),
                         hasEntry(is('cohorts'), contains(allOf(
                                 hasEntry(is('concepts'), contains(allOf(
-                                        hasEntry('numOfPatients', 0),
+                                        hasEntry(is('subjects'), contains(-101)),
                                         hasEntry('conceptPath', "\\foo\\study1\\bar\\")
                                 )))
                         ))),
@@ -31,17 +30,16 @@ class ExportTests extends ResourceTestCase{
                         hasEntry('dataType', 'Clinical data'),
                         hasEntry('dataTypeCode', 'clinical'),
                         hasEntry(is('cohorts'), contains(allOf(
-                                hasEntry(is('concepts'), allOf(
-                                        contains(
+                                hasEntry(is('concepts'), contains(
                                                 allOf(
-                                                        hasEntry('numOfPatients', 0),
+                                                        hasEntry(is('subjects'), is(JSONArray.class)),
                                                         hasEntry('conceptPath', "\\foo\\study2\\long path\\")
                                                 ),
                                                 allOf(
-                                                        hasEntry('numOfPatients', 0),
+                                                        hasEntry(is('subjects'), containsInAnyOrder(-201, -202)),
                                                         hasEntry('conceptPath', "\\foo\\study2\\sex\\")
                                                 ))
-                                ))
+                                )
                         ))),
                 )
         )))