Changeset 934

Timestamp:

Oct 8, 2010, 2:47:23 PM (13 years ago)

Author:

j.saito@…

Message:

Adjusted CommunicationManager? to match closer with CommunicationManager? in SAM.
Added support for "token" notation of REST services directly in Study and Assay domain classes.
Cleaned up and tested communication further.

Location:

trunk

Files:

• grails-app/controllers/RestController.groovy (modified) (7 diffs)
• grails-app/domain/dbnp/studycapturing/Assay.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/Sample.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/Study.groovy (modified) (1 diff)
• src/groovy/dbnp/rest/common/CommunicationManager.groovy (modified) (5 diffs)

trunk/grails-app/controllers/RestController.groovy

@@ -86 +86 @@
                 def user = params.user
                 Study.findAllByOwner(requestUser).each { study ->
-                        studies.push( [ 'title':study.title, 'studyToken':study.code ] )
+                        studies.push( [ 'title':study.title, 'studyToken':study.getToken()] )
                 }
                 render studies as JSON 
@@ -131 +131 @@
                         if(study && study.owner == requestUser) study.assays.each{ assay ->
                                 //if (assay.module.url.equals(params.moduleURL)) {
-                                def map = ['name':assay.name, 'assayToken':assay.externalAssayID]
+                                def map = ['name':assay.name, 'assayToken':assay.getToken()]
                                         assays.push( map )
                                 //}
@@ -159 +159 @@
                         assay.getSamples().each { sample ->
                                 def item = [ 
-                                        'sampleToken'         : sample.name,
-                                        'material'            : sample.material.name,
-                                        'subject'             : sample.parentSubject.name,
-                                        'event'               : sample.parentEvent.template.name,
-                                        'startTime'           : sample.parentEvent.getStartTimeString()
+                                        'sampleToken' : sample.name,
+                                        'material'        : sample.material.name,
+                                        'subject'         : sample.parentSubject.name,
+                                        'event'           : sample.parentEvent.template.name,
+                                        'startTime'       : sample.parentEvent.getStartTimeString()
                                 ]
                                 items.push item 
@@ -170 +170 @@
                 render items as JSON
         }
-
-
-
 
 
@@ -198 +195 @@
                                 def name = field.name
                                 def value = study.getFieldValue( name )
-                                if(name=="code") { name = "studyToken" }
                                 items[name] = value
                         }
@@ -227 +223 @@
                                 def name = field.name
                                 def value = assay.getFieldValue( name )
-                                if(name=="externalAssayID") { name = "assayToken" }
                                 items[name] = value
                         }
@@ -272 +267 @@
                                                 def name = field.name
                                                 def value = sample.getFieldValue( name )
-                                                if(name=="name") { name = "sampleToken" }
                                                 items[name] = value
                         }

trunk/grails-app/domain/dbnp/studycapturing/Assay.groovy

@@ -53 +53 @@
                 return name;
         }
+
+    def getToken() {
+                return externalAssayID
+    }
 }

trunk/grails-app/domain/dbnp/studycapturing/Sample.groovy

@@ -29 +29 @@
         Term material           // material of the sample (should normally be bound to the BRENDA ontology)
 
-        def getExternalSampleId() { name }
 
         /**

trunk/grails-app/domain/dbnp/studycapturing/Study.groovy

@@ -55 +55 @@
         }
 
-        // The external study ID is currently defined as the code of the study.
+        // The external identifier (studyToken) is currently the code of the study.
         // It is used from within dbNP submodules to refer to particular study in this GSCF instance.
-        def getExternalStudyId() { code }
+        def getToken() { code }
 
         /**

trunk/src/groovy/dbnp/rest/common/CommunicationManager.groovy

@@ -30 +30 @@
     def public static DSPServerURL  = "http://localhost:8080/gscf"
 
-     
+
 
     /**
@@ -109 +109 @@
                         def map = [:]
                     def args = strangeGroovyArgs[0]        // groovy nests the parameters of the methods in some other array
-                        for( i in 0..(params.size-1) ) {
-                                def param = params[i]
-                            map[param] = args[i]
-                        }
+
+                        if(params.size > 0 )
+                        {
+                                for( i in 0..(params.size-1) ) {
+                                        def param = params[i]
+                                        map[param] = args[i]
+                                }
+                        }
+
                         return closure( getRestResource( serverURL, restName, map ) )
                 }
@@ -154 +159 @@
         def url = GSCFServerURL + '/rest'
                 addRestWrapper( url , 'getStudies' )
-                addRestWrapper( url , 'getSubjects', ['externalStudyID'] )
-                addRestWrapper( url , 'getAssays',   ['externalStudyID'] )
-                addRestWrapper( url , 'getSamples',  ['externalAssayID'] )
-    }
+        addRestWrapper( url , 'getSubjects', ['studyToken'] )
+                addRestWrapper( url , 'getAssays',   ['studyToken','moduleURL'] )
+                addRestWrapper( url , 'getSamples',  ['assayToken'] )
+        }
 
 
@@ -173 +178 @@
                 // register method that links to the SAM view for showing a SimpleAssay 
         // parameters: externalAssayID
-                addViewWrapper( 'getAssayShowURL', url, 'simpleAssay/showByExternalID', ['externalAssayID'] )
+                addViewWrapper( 'getAssayShowURL', url, 'simpleAssay/show', ['externalAssayID'] )
 
                 // register method that links to the SAM view for editing a SimpleAssay 
@@ -192 +197 @@
                 //                               ["studies":[NuGO PPS human study], 
                 //               "samples":[[ [...], dbnp.studycapturing.Sample: 1]]]
-                def closure1 = { map ->
-                    def studies = []
-                    def samples = []
+                def closure = { map -> 
+                    def studies = []    
+                    def assays  = []    
                         def studiesHQ = "from dbnp.studycapturing.Study as s where s.code=?"
                         map['studyIds'].each { studies.add( dbnp.studycapturing.Study.find(studiesHQ,[it]) ) }
-                        map['Samples'].each { samSample ->
-                                def sampleID = samSample['externalSampleID']
-                            def sampleHQ = "from dbnp.studycapturing.Sample as a where a.externalSampleID='${sampleID}'"
-                                def sample = dbnp.studycapturing.Sample.find(sampleHQ)
-                                samples.add( [samSample,sample] )
-                        }
-                        return [studies:studies, samples:samples]
-                }
-
-                addRestWrapper( url+'/rest', 'getQueryResult',  ['query'], closure1 )
+                        map['assays'].each { samAssay ->
+                                def assayID = samAssay['externalAssayID']
+                            def assayHQ = "from dbnp.studycapturing.Assay as a where a.externalAssayID='${assayID}'"
+                                def assay = dbnp.studycapturing.Assay.find(assayHQ)
+                                assays.add( [samAssay,assay] )
+                        } 
+                        return [studies:studies, assays:assays] 
+                }
+
+                addRestWrapper( url+'/rest', 'getQueryResult',  ['query'], closure )