Changeset 2049 for trunk/grails-app/services/dbnp

Timestamp:

Oct 6, 2011, 1:19:21 PM (11 years ago)

Author:

s.h.sikkema@…

Message:

enabled collecting module measurements for galaxy integration

Location:

trunk/grails-app/services/dbnp

Files:

• modules/ModuleCommunicationService.groovy (modified) (3 diffs)
• studycapturing/AssayService.groovy (modified) (11 diffs)

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

@@ -18 +18 @@
 import javax.servlet.http.HttpServletResponse
 import org.codehaus.groovy.grails.commons.ConfigurationHolder
-import org.hibernate.*;
+import org.hibernate.*
+import dbnp.authentication.SecUser;
 
 class ModuleCommunicationService implements Serializable {
@@ -105 +106 @@
         * @return                       JSON    JSON object of the parsed text
         */
-        def callModuleMethod( String consumer, String restUrl, String args = null, String requestMethod = "GET" ) {
-                if (!authenticationService.isLoggedIn()) {
+        def callModuleMethod( String consumer, String restUrl, String args = null, String requestMethod = "GET", SecUser remoteUser = null) {
+                if (!remoteUser && !authenticationService.isLoggedIn()) {
                         // should not happen because we can only get here when a user is
                         // logged in...
@@ -124 +125 @@
 
                 // put the session token to work
-                authenticationService.logInRemotely( consumer, sessionToken, authenticationService.getLoggedInUser() )
-                
+                authenticationService.logInRemotely( consumer, sessionToken, remoteUser ?: authenticationService.getLoggedInUser())
+
                 // Append the sessionToken to the parameters
                 if( !args ) {

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

@@ -19 +19 @@
 import org.dbnp.gdt.RelTime
 import org.dbnp.gdt.TemplateFieldType
-import java.text.DecimalFormat
 import java.text.NumberFormat
-import org.dbnp.gdt.Template
-import org.dbnp.gdt.TemplateField
+import dbnp.authentication.SecUser
 
 class AssayService {
@@ -39 +37 @@
          *  values
          */
-        def collectAssayTemplateFields(assay, samples = null) throws Exception {
+        def collectAssayTemplateFields(assay, samples, SecUser remoteUser = null) throws Exception {
 
                 def getUsedTemplateFields = { templateEntities ->
@@ -54 +52 @@
 
                 try {
-                        moduleMeasurements = requestModuleMeasurementNames(assay)
+                        moduleMeasurements = requestModuleMeasurementNames(assay, remoteUser)
                 } catch (e) {
                         moduleError = e.message
@@ -67 +65 @@
                                         'Event Group' :             [[name: 'name', comment: 'Name of Event Group', displayName: 'name']],
                                         'Module Measurement Data':  moduleMeasurements,
-                                        'ModuleError':              moduleError
+                                        'Module Error':             moduleError
                                 ]
 
@@ -87 +85 @@
          * @return                              The assay data structure as described above.
          */
-        def collectAssayData(assay, fieldMap, measurementTokens, samples = null) throws Exception {
+        def collectAssayData(assay, fieldMap, measurementTokens, samples = null, SecUser remoteUser = null) throws Exception {
 
                 def collectFieldValuesForTemplateEntities = { headerFields, templateEntities ->
@@ -197 +195 @@
 
                         try {
-                                moduleMeasurementData = requestModuleMeasurements(assay, measurementTokens, samples)
+                                moduleMeasurementData = requestModuleMeasurements(assay, measurementTokens, samples, remoteUser)
                         } catch (e) {
                                 moduleMeasurementData = ['error' : ['Module error, module not available or unknown assay'] * samples.size() ]
@@ -205 +203 @@
                 }
 
-                [       '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,
-                                        'Module Measurement Data' : moduleMeasurementData,
-                                        'ModuleError' :             moduleError
-                                ]
+                [   '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,
+                        'Module Measurement Data' : moduleMeasurementData,
+                        'Module Error' :            moduleError
+                ]
         }
 
@@ -269 +267 @@
          * @return
          */
-        def requestModuleMeasurementNames(assay) {
+        def requestModuleMeasurementNames(assay, SecUser remoteUser = null) {
 
                 def moduleUrl = assay.module.url
@@ -278 +276 @@
 
                 try {
-                        jsonArray = moduleCommunicationService.callModuleMethod(moduleUrl, path, query, "POST")
+                        jsonArray = moduleCommunicationService.callModuleMethod(moduleUrl, path, query, "POST", remoteUser)
                 } catch (e) {
                         throw new Exception("An error occured while trying to get the measurement tokens from the $assay.module.name. \
@@ -303 +301 @@
          * @return
          */
-        def requestModuleMeasurements(assay, inputMeasurementTokens, samples) {
+        def requestModuleMeasurements(assay, inputMeasurementTokens, samples, SecUser remoteUser = null) {
 
                 def moduleUrl = assay.module.url
@@ -320 +318 @@
 
                 try {
-                        (sampleTokens, measurementTokens, moduleData) = moduleCommunicationService.callModuleMethod(moduleUrl, path, query, "POST")
+                        (sampleTokens, measurementTokens, moduleData) = moduleCommunicationService.callModuleMethod(moduleUrl, path, query, "POST", remoteUser)
                 } catch (e) {
                         throw new Exception("An error occured while trying to get the measurement data from the $assay.module.name. \