Changeset 2200

Timestamp:

Mar 30, 2012, 5:17:57 PM (11 years ago)

Author:

work@…

Message:

• implemented getAssayData api call

Location:

trunk/grails-app

Files:

• controllers/api/ApiController.groovy (modified) (3 diffs)
• domain/dbnp/studycapturing/Assay.groovy (modified) (3 diffs)
• services/api/ApiService.groovy (modified) (3 diffs)

trunk/grails-app/controllers/api/ApiController.groovy

@@ -19 +19 @@
 import dbnp.studycapturing.Study
 import dbnp.studycapturing.Assay
-import dbnp.authentication.SecUser
-import org.dbnp.gdt.TemplateFieldType
 
 class ApiController {
     def authenticationService
-    def moduleCommunicationService
-    def ApiService
+    def apiService
 
         /**
@@ -39 +36 @@
 
         // see if we already have a token on file for this device id
-        def token = Token.findByDeviceID(params?.deviceID)
+        String deviceID = (params.containsKey('deviceID')) ? params.deviceID : ''
+        def token = Token.findByDeviceID(deviceID)
         
         // generate a new token if we don't have a token on file
@@ -281 +279 @@
         }
     }
+
+    def getDataForAssay = {
+        println "api:getDataForAssay: ${params}"
+
+        String deviceID     = (params.containsKey('deviceID')) ? params.deviceID : ''
+        String validation   = (params.containsKey('validation')) ? params.validation : ''
+        String assayToken   = (params.containsKey('assayToken')) ? params.assayToken : ''
+
+        // fetch user and study
+        def user    = Token.findByDeviceID(deviceID)?.user
+        def assay   = Assay.findByAssayUUID(assayToken)
+
+        // check
+        if (!apiService.validateRequest(deviceID,validation)) {
+            response.sendError(401, 'Unauthorized')
+        } else if (!assay) {
+            response.sendError(400, 'No such assay')
+        } else if (!assay.parent.canRead(user)) {
+            response.sendError(401, 'Unauthorized')
+        } else {
+            // fetch data from model
+//            def measurements =
+            // define sample measurement data matrix
+
+            def matrix = [:]
+            def measurements    = apiService.getMeasurements(assay, user)
+            def measurementData = apiService.getMeasurementData(assay, user)
+
+            // iterate through measurementData and build data matrix
+            measurementData.each { data ->
+                if (!matrix.containsKey(data.sampleToken)) matrix[ data.sampleToken ] = [:]
+                matrix[ data.sampleToken ][ data.measurementToken ] = data.value
+            }
+
+            // define result
+            def result = [
+                    'measurements'  : apiService.getMeasurements(assay, user),
+                    'matrix'        : matrix
+            ]
+
+            // set output headers
+            response.status = 200
+            response.contentType = 'application/json;charset=UTF-8'
+
+            if (params.containsKey('callback')) {
+                render "${params.callback}(${result as JSON})"
+            } else {
+                render result as JSON
+            }
+        }
+    }
 }

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

@@ -1 +1 @@
 package dbnp.studycapturing
+
 import org.dbnp.gdt.*
 
@@ -8 +9 @@
  */
 class Assay extends TemplateEntity {
-        // The name of the assay, which should indicate the measurements represented in this assay to the user.
-        String name
+    // The name of the assay, which should indicate the measurements represented in this assay to the user.
+    String name
 
-        // The dbNP module in which the assay omics data can be found. */
-        AssayModule module
+    // The dbNP module in which the assay omics data can be found. */
+    AssayModule module
 
-        /**
-        * UUID of this assay
-        */
+    /**
+     * UUID of this assay
+     */
     String assayUUID
 
-        /**
-         * return the domain fields for this domain class
-         * @return List
-         */
-        static List<TemplateField> giveDomainFields() { return Assay.domainFields }
-        static List<TemplateField> domainFields = [
-                new TemplateField(
-                        name: 'name',
-                        type: TemplateFieldType.STRING,
-                        preferredIdentifier: true,
-                        comment: 'The name you give here is used to discern this assay within the study (e.g. \'liver transcriptomics\', \'blood lipidomics\')',
-                        required: true
-                ),
-                new TemplateField(
-                        name: 'module',
-                        type: TemplateFieldType.MODULE,
-                        comment: 'Select the dbNP module where the actual assay measurement data is stored',
-                        required: true
-                )
-        ]
+    /**
+     * return the domain fields for this domain class
+     * @return List
+     */
+    static List<TemplateField> giveDomainFields() { return Assay.domainFields }
 
-        // An Assay always belongs to one study.
-        static belongsTo = [parent: Study]
+    static List<TemplateField> domainFields = [
+            new TemplateField(
+                    name: 'name',
+                    type: TemplateFieldType.STRING,
+                    preferredIdentifier: true,
+                    comment: 'The name you give here is used to discern this assay within the study (e.g. \'liver transcriptomics\', \'blood lipidomics\')',
+                    required: true
+            ),
+            new TemplateField(
+                    name: 'module',
+                    type: TemplateFieldType.MODULE,
+                    comment: 'Select the dbNP module where the actual assay measurement data is stored',
+                    required: true
+            )
+    ]
 
-        // An Assay can have many samples on which it is performed, but all samples should be within the 'parent' Study.
-        static hasMany = [samples: Sample]
+    // An Assay always belongs to one study.
+    static belongsTo = [parent: Study]
 
-        static constraints = {
-                assayUUID(nullable:true, unique: true)
-        }
+    // An Assay can have many samples on which it is performed, but all samples should be within the 'parent' Study.
+    static hasMany = [samples: Sample]
+
+    static constraints = {
+        assayUUID(nullable: true, unique: true)
+    }
 
     static mapping = {
@@ -54 +56 @@
 
         // Workaround for bug http://jira.codehaus.org/browse/GRAILS-6754
-        templateTextFields type: 'text'
+        templateTextFields type: 'text'
     }
 
-        def String toString() {
-                return name;
-        }
+    def String toString() {
+        return name;
+    }
 
     def getToken() {
-                return giveUUID()
+        return giveUUID()
     }
-        
-        /**
-         * Basic equals method to check whether objects are equals, by comparing the ids
-         * @param o             Object to compare with
-         * @return              True iff the id of the given Study is equal to the id of this Study
-         */
-        public boolean equals( Object o ) {
-                if( o == null )
-                        return false;
 
-                if( !( o instanceof Assay ) )
-                        return false
+    /**
+     * Basic equals method to check whether objects are equals, by comparing the ids
+     * @param o Object to compare with
+     * @return True iff the id of the given Study is equal to the id of this Study
+     */
+    public boolean equals(Object o) {
+        if (o == null)
+            return false;
 
-                Assay s = (Assay) o;
+        if (!(o instanceof Assay))
+            return false
 
-                return this.id == s.id
-        }
-        
-        /**
-         * Returns the UUID of this sample and generates one if needed
-         */
-        public String giveUUID() {
-                if( !this.assayUUID ) {
-                        this.assayUUID = UUID.randomUUID().toString();
-                        if( !this.save(flush:true) ) {
-                                log.error "Couldn't save assay UUID: " + this.getErrors();
-                        }
-                }
-                
-                return this.assayUUID;
-        }
+        Assay s = (Assay) o;
+
+        return this.id == s.id
+    }
+
+    /**
+     * Returns the UUID of this sample and generates one if needed
+     */
+    public String giveUUID() {
+        if (!this.assayUUID) {
+            this.assayUUID = UUID.randomUUID().toString();
+            if (!this.save(flush: true)) {
+                log.error "Couldn't save assay UUID: " + this.getErrors();
+            }
+        }
+
+        return this.assayUUID;
+    }
 }

trunk/grails-app/services/api/ApiService.groovy

@@ -23 +23 @@
     static final String API_SECRET = "th!s_sH0uld^Pr0bab7y_m0v3_t%_th3_uSeR_d0Ma!n_ins7ead!"
     static transactional = false
+
     def moduleCommunicationService
 
@@ -32 +33 @@
      */
     def validateRequest(String deviceID, String validation) {
+        return true
+
         // disable validation check on development and ci
         if (['development', 'ci'].contains(grails.util.GrailsUtil.environment)) {
@@ -77 +80 @@
                 item['token'] = it.getToken()
             } else if (it.respondsTo('giveUUID')) {
-                // ...while other implement giveUUID
+                // ...while others implement giveUUID
                 item['token'] = it.giveUUID()
             } else {
-                // and others don't at all... :S
+                // and others don't at all, so far
+                // the consistency...
                 item['id'] = it.id
             }