Changeset 1813

Timestamp:

05-05-11 13:01:04 (3 years ago)

Author:

robert@…

Message:

Added possibility to ask for all assays for the given module (without specifying the studyToken). See #428.

Files:

• trunk/grails-app/controllers/RestController.groovy (modified) (22 diffs)

trunk/grails-app/controllers/RestController.groovy

@@ -26 +26 @@
 class RestController {
 
-       /**************************************************/
-      /** Rest resources for Simple Assay Module (SAM) **/
-     /**************************************************/
+        /**************************************************/
+        /** Rest resources for Simple Assay Module (SAM) **/
+        /**************************************************/
 
         def authenticationService
@@ -92 +92 @@
 
         /**
-         * REST resource for data modules.
-         * Consumer and token should be supplied via URL parameters.
-         * Provide a list of all studies owned by the supplied user.
+         * REST resource for data modules.
+         * Consumer and token should be supplied via URL parameters.
+         * Provide a list of all studies owned by the supplied user.
          *
          * @param       studyToken  optional parameter. If no studyToken is given, all studies available to user are returned.
@@ -137 +137 @@
         def getStudies = {
 
-                List returnStudies = [] 
-                List studies = [] 
+                List returnStudies = []
+                List studies = []
 
                 if( !params.studyToken ) {
@@ -144 +144 @@
                 }
                 else if( params.studyToken instanceof String ) {
-                        def study = Study.findByStudyUUID( params.studyToken ) 
+                        def study = Study.findByStudyUUID( params.studyToken )
                         if( study ) {
                                 if( !study.canRead(authenticationService.getRemotelyLoggedInUser( params.consumer, params.token )) ) {
@@ -150 +150 @@
                                         return false
                                 }
-                                
-                                studies.push study 
+
+                                studies.push study
                         } else {
                                 response.sendError(404)
                                 return false
                         }
-        
-                }
-                else { 
+
+                }
+                else {
                         params.studyToken.each{ studyToken ->
                                 def study = Study.findByStudyUUID( studyToken );
                                 if( study )
-                                        studies.push study 
-                        }
-                }
-                
+                                        studies.push study
+                        }
+                }
+
 
                 studies.each { study ->
@@ -173 +173 @@
                                 if( study.canRead(authenticationService.getRemotelyLoggedInUser( params.consumer, params.token ))) {
 
-                    def items = [studyToken:study.giveUUID()]
-                    study.giveFields().each { field ->
-                        def name = field.name
-                        def value = study.getFieldValue( name )
-                        items[name] = value
-                    }
-                                        
-                                        // Add study version number 
+                                        def items = [studyToken:study.giveUUID()]
+                                        study.giveFields().each { field ->
+                                                def name = field.name
+                                                def value = study.getFieldValue( name )
+                                                items[name] = value
+                                        }
+
+                                        // Add study version number
                                         items['version'] = study.version;
-                                        
-                    returnStudies.push items
-                }
+
+                                        returnStudies.push items
+                                }
                         }
                 }
@@ -217 +217 @@
                 def versionInfo = [:];
                 def study
-                
+
                 if( !params.studyToken || !(params.studyToken instanceof String)) {
                         response.sendError(400)
@@ -256 +256 @@
          */
         def getSubjects = {
-                List subjects = [] 
+                List subjects = []
                 if( params.studyToken ) {
-                        def study = Study.findByStudyUUID( params.studyToken)
+                        def study = Study.findByStudyUUID( params.studyToken)
 
                         if(study) {
@@ -292 +292 @@
          * @return list of assays in the study as JSON object list, filtered to only contain assays
          *         for the specified module, with 'assayToken' and 'name' for each assay
-         *
-         *
-         * Example 1. REST call without assayToken 
-         *            http://localhost:8080/gscf/rest/getAssays/aas?studyToken=PPSH
+         *
+         *
+         * Example 1. REST call without assayToken 
+         *            http://localhost:8080/gscf/rest/getAssays/aas?studyToken=PPSH
          *                              &consumer=http://localhost:8182/sam
-         *
-         * Result: [{"name":"Glucose assay after",
+         *
+         * Result: [{"name":"Glucose assay after",
          *                      "module":{"class":"dbnp.studycapturing.AssayModule","id":1,"name":"SAM module for clinical data",
          *                              "platform":"clinical measurements","url":"http://localhost:8182/sam"},
@@ -306 +306 @@
          *                              "platform":"clinical measurements","url":"http://localhost:8182/sam"},
          *                              "externalAssayID":"PPSH-Glu-B","Description":null,"parentStudyToken":"PPSH"}]
-         *
-         *
-         * Example 2. REST call with one assayToken 
-         *                        http://localhost:8080/gscf/rest/getAssays/queryOneTokenz?studyToken=PPSH
+         *
+         *
+         * Example 2. REST call with one assayToken 
+         *                        http://localhost:8080/gscf/rest/getAssays/queryOneTokenz?studyToken=PPSH
          *                              &consumer=http://localhost:8182/sam&assayToken=PPSH-Glu-A
-         *
+         *
          * Result: [{"name":"Glucose assay after","module":{"class":"dbnp.studycapturing.AssayModule","id":1,
          *                      "name":"SAM module for clinical data","platform":"clinical measurements","url":"http://localhost:8182/sam"},
          *                      "externalAssayID":"PPSH-Glu-A","Description":null,"parentStudyToken":"PPSH"}]
          *
-         *
-         * Example 3. REST call with two assayTokens.
-         *
-         * Result: Same as result in Example 1.
+         *
+         * Example 3. REST call with two assayTokens.
+         *
+         * Result: Same as result in Example 1.
          */
         def getAssays = {
@@ -325 +325 @@
                 response.contentType = 'application/json'
 
-                List returnList = []    // return list of hashes each containing fields and values belonging to an assay 
-
-                // Check if required parameters are present 
-                def validCall = CommunicationManager.hasValidParams( params, "consumer", "studyToken" )
-                if( !validCall ) { 
+                List returnList = []    // return list of hashes each containing fields and values belonging to an assay
+
+                // Check if required parameters are present
+                def validCall = CommunicationManager.hasValidParams( params, "consumer" )
+                if( !validCall ) {
                         render "Error. Wrong or insufficient parameters." as JSON
                         return
                 }
-
+                
+                def assays = []
+                
                 if( params.studyToken ) {
 
-                        def study = Study.findByStudyUUID(params.studyToken)
+                        def study = Study.findByStudyUUID(params.studyToken)
 
                         if(study) {
@@ -345 +347 @@
                                 }
 
-                                def assays = []
                                 if(params.assayToken==null) {
                                         assays = study.assays
                                 }
-                                else if( params.assayToken instanceof String ) { 
+                                else if( params.assayToken instanceof String ) {
                                         def assay = study.assays.find{ it.giveUUID() == params.assayToken }
                                         if( assay ) {
-                                                 assays.push assay
+                                                assays.push assay
                                         }
                                 }
@@ -364 +365 @@
                                 }
 
-                                assays.each{ assay ->
-                                        if (assay.module?.url && assay.module.url.equals(params.moduleURL)) {
-                                                if(assay) {
-                                                        def map = [assayToken : assay.giveUUID()]
-                                                        assay.giveFields().each { field ->
-                                                                def name = field.name
-                                                                def value = assay.getFieldValue( name )
-                                                                map[name] = value
-                                                        }
-                                                        map["parentStudyToken"] = assay.parent.giveUUID()
-                                                        returnList.push( map )
-                                                }
-                                        }
-                                }
-                } else {
+                        } else {
                                 response.sendError(404)
                                 return false
                         }
 
-                }
+                } else {
+                        // Return all assays for the given module
+                        assays = Assay.list().findAll{ it.parent.canRead(authenticationService.getRemotelyLoggedInUser( params.consumer, params.token ) ) }
+                }
+
+                // Create data for all assays
+                assays.each{ assay ->
+                        if (assay.module?.url && assay.module.url.equals(params.moduleURL)) {
+                                if(assay) {
+                                        def map = [assayToken : assay.giveUUID()]
+                                        assay.giveFields().each { field ->
+                                                def name = field.name
+                                                def value = assay.getFieldValue( name )
+                                                map[name] = value
+                                        }
+                                        map["parentStudyToken"] = assay.parent.giveUUID()
+                                        returnList.push( map )
+                                }
+                        }
+                }
+
                 render returnList as JSON
         }
@@ -405 +412 @@
          * @return 'startTime' (the time the sample was taken relative to the start of the study, as a string)
          * @return additional template fields are returned
-         * 
-         * 
-         * 
-         * Example 1: no sampleTokens given.
+         * 
+         * 
+         * 
+         * Example 1: no sampleTokens given.
          * Query: 
-         * http://localhost:8080/gscf/rest/getSamples/query?assayToken=PPSH-Glu-A
-         * 
+         * http://localhost:8080/gscf/rest/getSamples/query?assayToken=PPSH-Glu-A
+         * 
          * Result: 
-         * [{"sampleToken":"5_A","material":"blood plasma","subject":"5","event":"Blood extraction","startTime":"4 days, 6 hours"},
+         * [{"sampleToken":"5_A","material":"blood plasma","subject":"5","event":"Blood extraction","startTime":"4 days, 6 hours"},
          * {"sampleToken":"6_A","material":"blood plasma","subject":"6","event":"Blood extraction","startTime":"4 days, 6 hours"},
          * {"sampleToken":"10_A","material":"blood plasma","subject":"10","event":"Blood extraction","startTime":"4 days, 6 hours"},
@@ -424 +431 @@
          * {"sampleToken":"7_A","material":"blood plasma","subject":"7","event":"Blood extraction","startTime":"4 days, 6 hours"},
          * {"sampleToken":"3_A","material":"blood plasma","subject":"3","event":"Blood extraction","startTime":"4 days, 6 hours"}]
-         * 
-         * 
-         * 
-         * Example 2: one sampleToken given.
+         * 
+         * 
+         * 
+         * Example 2: one sampleToken given.
          * Query: 
          * http://localhost:8080/gscf/rest/getSamples/query?assayToken=PPSH-Glu-A&sampleToken=5_A
-         * 
-         * Result: 
+         * 
+         * Result: 
          * [{"sampleToken":"5_A","material":"blood plasma","subject":"5","event":"Blood extraction","startTime":"4 days, 6 hours"}]
-         * 
-         * 
-         * 
-         * Example 3: two sampleTokens given.
+         * 
+         * 
+         * 
+         * Example 3: two sampleTokens given.
          * Query: 
          * http://localhost:8080/gscf/rest/getSamples/query?assayToken=PPSH-Glu-A&sampleToken=5_A&sampleToken=6_A
-         * 
-         * Result: 
+         * 
+         * Result: 
          * [{"sampleToken":"5_A","material":"blood plasma","subject":"5","event":"Blood extraction","startTime":"4 days, 6 hours"},
          *  {"sampleToken":"6_A","material":"blood plasma","subject":"6","event":"Blood extraction","startTime":"4 days, 6 hours"}]
          *
          *
-         * Example 4: no assaytoken given
+         * Example 4: no assaytoken given
          * Query: 
          * http://localhost:8080/gscf/rest/getSamples/query?sampleToken=5_A&sampleToken=6_A
-         * 
-         * Result: 
+         * 
+         * Result: 
          * [{"sampleToken":"5_A","material":"blood plasma","subject":"5","event":"Blood extraction","startTime":"4 days, 6 hours"},
          *  {"sampleToken":"6_A","material":"blood plasma","subject":"6","event":"Blood extraction","startTime":"4 days, 6 hours"}]
@@ -458 +465 @@
                 def samples
                 if( params.assayToken ) {
-                        def assay = Assay.findByAssayUUID( params.assayToken );
+                        def assay = Assay.findByAssayUUID( params.assayToken );
 
                         if( assay )  {
@@ -466 +473 @@
                                         return false
                                 }
-                                
+
                                 samples = assay.getSamples() // on all samples
                         } else {
@@ -478 +485 @@
                         samples = studies*.getSamples().flatten();
                 }
-                
+
                 // Check whether only a subset of samples should be returned
                 if( params.sampleToken ) {
                         def sampleTokens = params.list( "sampleToken" );
-                        samples = samples.findAll { sampleTokens.contains( it.giveUUID() ) } 
+                        samples = samples.findAll { sampleTokens.contains( it.giveUUID() ) }
                 }
 
                 samples.each { sample ->
 
-                        def item = [ 
-                                'sampleToken' : sample.giveUUID(),
-                                'material'        : sample.material?.name,
-                                'subject'         : sample.parentSubject?.name,
-                                'event'           : sample.parentEvent?.template?.name,
-                                'startTime'       : sample.parentEvent?.getStartTimeString()
-                        ]
+                        def item = [
+                                                'sampleToken' : sample.giveUUID(),
+                                                'material'        : sample.material?.name,
+                                                'subject'         : sample.parentSubject?.name,
+                                                'event'           : sample.parentEvent?.template?.name,
+                                                'startTime'       : sample.parentEvent?.getStartTimeString()
+                                        ]
 
                         sample.giveFields().each { field ->
@@ -514 +521 @@
                                         }
                                 }
-                                item['eventObject'] = eventHash 
+                                item['eventObject'] = eventHash
                         }
 
@@ -527 +534 @@
                                         }
                                 }
-                                item['subjectObject'] = subject 
-                        }
-
-                        items.push item 
+                                item['subjectObject'] = subject
+                        }
+
+                        items.push item
                 }
 
@@ -552 +559 @@
         def getAuthorizationLevel = {
                 if( params.studyToken ) {
-                        def study = Study.findByStudyUUID(params.studyToken)
+                        def study = Study.findByStudyUUID(params.studyToken)
 
                         if( !study ) {
@@ -571 +578 @@
                         return false
                 }
-    }
+        }
 }