Changeset 901

Timestamp:

Sep 27, 2010, 5:04:47 PM (13 years ago)

Author:

jahn

Message:

Added and tested new Rest methods in accordance with specs.
Tested most of them. User related information is not integrated
yet. Furthermore, added new convention for refering to TemplateEntities?
by REST. For the time being, the old conventions and the new
conventions are supported in parallel. However, this should change
soon. Thus, currently externalAssayID, code, and externdaSampleID
are supported, as are assayToken, studyToken, sampleToken.

Location:

trunk/grails-app

Files:

• controllers/RestController.groovy (modified) (4 diffs)
• domain/dbnp/studycapturing/TemplateEntity.groovy (modified) (1 diff)

trunk/grails-app/controllers/RestController.groovy

@@ -42 +42 @@
          */
         private def auth() {
+
             credentials = BasicAuthentication.credentialsFromRequest(request)
                 requestUser = authService.authUser(credentials.u,credentials.p)
@@ -83 +84 @@
         def getStudies = {
                 List studies = [] 
+                def user = params.user
                 Study.findAllByOwner(requestUser).each { study ->
-                        studies.push( [ 'externalStudyID': study.code, 'name':study.title ] )
+                        studies.push( [ 'externalStudyID': study.code, 'name':study.title, 'studyToken':study.code ] )
                 }
                 render studies as JSON 
@@ -114 +116 @@
         * Provide a list of all assays for a given study
         *
-        * Example call of the getAssays REST resource: http://localhost:8080/gscf/rest/getAssays?externalStudyID=PPSH&moduleURL=http://localhost:8182/sam
+        * Example call of the getAssays REST resource: 
+        * http://localhost:8080/gscf/rest/getAssays?externalStudyID=PPSH&moduleURL=http://localhost:8182/sam
         *
         * @param externalStudyID String The external study id (code) of the target GSCF Study object
         * @param moduleURL String The base URL of the calling dbNP module
-        * @return list of assays in the study as JSON object list, filtered to only contain assays for the specified module, with 'externalAssayID' and 'name' for each assay
+        * @return list of assays in the study as JSON object list, filtered to only contain assays 
+        *         for the specified module, with 'externalAssayID' and 'name' for each assay
         */
         def getAssays = {
                 List assays = [] 
-                if( params.externalStudyID ) {
-                        def study = Study.find( "from Study as s where s.code=?", [params.externalStudyID])
+                if( params.externalStudyID || params.studyToken ) {
+                        def id = params.studyToken ?: params.externalStudyID
+                        def study = Study.find( "from Study as s where s.code=?", [id] )
                         if(study && study.owner == requestUser) study.assays.each{ assay ->
                                 if (assay.module.url.equals(params.moduleURL)) {
-                                def map = ['name':assay.name, 'externalAssayID':assay.externalAssayID]
+                                def map = ['name':assay.name, 'externalAssayID':assay.externalAssayID, 'assayToken':assay.externalAssayID]
                                         assays.push( map )
                                 }
@@ -167 +172 @@
 
 
-    /* this is just for testing! */
-    /*def test = {
-                render( dbnp.rest.common.CommunicationManager.getQueryResultWithOperator("Insulin",">",200) )
-    }*/
+
+
+
+        /**
+        * REST resource for dbNP modules.
+        *
+        * @param studyToken String, the external identifier of the study
+        * @return List of all fields of this study
+        * @return 
+        *
+        * Example REST call (without authentication): 
+    * http://localhost:8080/gscf/rest/getStudy/study?studyToken=PPSH
+    *
+        * Returns the JSON object: 
+        * {"title":"NuGO PPS human study","studyToken":"PPSH","startDate":"2008-01-13T23:00:00Z",
+        * "Description":"Human study performed at RRI; centres involved: RRI, IFR, TUM, Maastricht U.",
+        * "Objectives":null,"Consortium":null,"Cohort name":null,"Lab id":null,"Institute":null,
+        * "Study protocol":null}
+        */
+        def getStudy = {
+                def items = [:]
+                if( params.studyToken ) {
+                        def study = Study.find( "from Study as s where code=?",[params.studyToken])
+                        study.giveFields().each { field ->
+                                def name = field.name
+                                def value = study.getFieldValue( name )
+                                if(name=="code") { name = "studyToken" }
+                                items[name] = value
+                        }
+        }
+                render items as JSON
+        }
+
+
+
+        /**
+        * REST resource for dbNP modules.
+        *
+        * @param assayToken String, the external identifier of the study
+        * @return List of all fields of this assay 
+        *
+        * Example REST call (without authentication): 
+    * http://localhost:8080/gscf/rest/getAssay/assay?assayToken=PPS3_SAM
+    *
+        * Returns the JSON object: {"name":"Lipid profiling","module":{"class":"dbnp.studycapturing.AssayModule","id":1,
+        * "name":"SAM module for clinical data","platform":"clinical measurements","url":"http://sam.nmcdsp.org"},
+        * "assayToken":"PPS3_SAM","Description":null}
+        */
+        def getAssay = {
+                def items = [:]
+                if( params.assayToken ) {
+                        def assay = Assay.find( "from Assay as a where externalAssayID=?",[params.assayToken])
+                        assay.giveFields().each { field ->
+                                def name = field.name
+                                def value = assay.getFieldValue( name )
+                                if(name=="externalAssayID") { name = "assayToken" }
+                                items[name] = value
+                        }
+        }
+                render items as JSON
+        }
+
+
+
+        /**
+        * REST resource for data modules.
+        * Username and password should be supplied via HTTP Basic Authentication.
+        * One specific sample of a given Assay.
+        *
+        * @param externalAssayID String (externalAssayID of some Assay in GSCF)
+        * @return As a JSON object list, for each sample in that assay:
+        * @return 'name' (Sample name, which is unique)
+        * @return 'material' (Sample material)
+        * @return 'subject' (The name of the subject from which the sample was taken)
+        * @return 'event' (the name of the template of the SamplingEvent describing the sampling)
+        * @return 'startTime' (the time the sample was taken relative to the start of the study, as a string)
+        *
+        * Example REST call (without authentication): 
+    * http://localhost:8080/gscf/rest/getSample/sam?assayToken=PPS3_SAM&sampleToken=A30_B 
+    *
+        * Returns the JSON object: 
+        * {"subject":"A30","event":"Liver extraction","startTime":"1 week, 1 hour",
+        * "sampleToken":"A30_B","material":{"class":"dbnp.data.Term","id":6,"accession":"BTO:0000131",
+        * "name":"blood plasma","ontology":{"class":"Ontology","id":2}},"Remarks":null,
+        * "Text on vial":"T70.91709057820039","Sample measured volume":null}
+        */
+        def getSample = {
+                def items = [:]
+                if( params.assayToken && params.sampleToken ) {
+                        def assay = Assay.find( "from Assay as a where externalAssayID=?",[params.assayToken])
+                        assay.getSamples().each { sample ->
+                                if( sample.name == params.sampleToken ) {
+                                        items = [ 
+                                                'subject'             : sample.parentSubject.name,
+                                                'event'               : sample.parentEvent.template.name,
+                                                'startTime'           : sample.parentEvent.getStartTimeString()
+                                        ]
+                                        sample.giveFields().each { field ->
+                                                def name = field.name
+                                                def value = sample.getFieldValue( name )
+                                                if(name=="name") { name = "sampleToken" }
+                                                items[name] = value
+                        }
+                                }
+                        }
+                }
+                render items as JSON
+        }
 }

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

@@ -717 +717 @@
          * domain fields of this entity
          */
-        def List<TemplateField> giveFields() {
+        def public List<TemplateField> giveFields() {
                 return this.giveDomainFields() + this.giveTemplateFields();
         }