Changeset 649

Timestamp:

Jul 13, 2010, 5:49:15 PM (13 years ago)

Author:

jahn

Message:

Added five controller actions (RestController?) and corresponding Rest Wrapper (CommunicationManager?) methods for Rest communication with DSP.
The contents of three actions still need to be completed.
Authentication is still in a dummy method. When Michael has figured out how to do the authentication, it will be added.

Location:

trunk

Files:

• grails-app/controllers/RestController.groovy (modified) (3 diffs)
• src/groovy/dbnp/rest/common/CommunicationManager.groovy (modified) (3 diffs)

trunk/grails-app/controllers/RestController.groovy

@@ -11 +11 @@
  * key-value pairs in the params object of each Grails action we comment on.
  * 
- * @author      Jahn 
+ * @author      Jahn-Takeshi Saito
  * @since       20100601
  *
@@ -27 +27 @@
 
 
-        /* REST resources for Simple Assay Module (SAM) */ 
+
+       /**************************************************/
+      /** Rest resources for Simple Assay Module (SAM) **/
+     /**************************************************/
+    
 
 
@@ -109 +113 @@
         }
 
+
+
+
+
+       /****************************/
+      /** Rest resources for DSP **/
+     /****************************/
+    
+        
+        /* still not complete!! */
+
+        /**
+        * REST resource for DSP.
+        * call: gscf/rest/isUser/?username=username&password=password
+        *
+        * @param  String username   
+        * @param  String password
+        * @return bool
+        */
+        def isUser= {
+                def isUser = isVerifiedUser( params )
+                render isUser as JSON
+        }
+
+
+        /* still not complete!! */
+        /**
+        * REST resource for DSP.
+        * call: gscf/rest/listStudies/?username=username&password=password 
+        *
+        * @param  String username
+        * @param  String password
+        * @return list of studies 
+        */
+        def listStudies = {
+
+                if( !isVerifiedUser( params ) ) {
+                        render [:] as JSON
+                        return
+                }
+
+                List studies = [] 
+
+                // add code for filtering studies that belong to given user 
+                // (use Study.findAll( ... )  
+                // ... 
+                Study.list().each { 
+                        def map = ["study_token":it.code, "name":it.name]
+                        studies.add( map )
+                }
+                
+                render studies as JSON
+        }
+
+
+
+        /* still not complete!! */
+        /**
+        * REST resource for DSP.
+        * call: gscf/rest/getStudy/?username=username&password=password&study_token=studytoken
+        *
+        * @param  String username
+        * @param  String password
+        * @param  String study_token 
+        * @return list of studies 
+        */
+        def getStudy = {
+
+                if( !isVerifiedUser( params ) ) {
+                        render [:] as JSON
+                        return
+                }
+
+                List studyResult = [:] 
+                def code   = params.study_token
+
+                def query = "from Study as s where s.code = ?"
+                def study = Study.find( query, code )
+                studyResult = [ 'study_token' : study.code, 'name' : study.name ]
+                        /*  still not complete!! 
+                                Add features
+                                        ... study_token:”GHyJeR#g”, 
+                                        ... created: “20/06/2010 22:34:52”,
+                                        ... meta: [
+                                        ... greenhouse_id: “GH010938.AB.5”,
+                                        ... greenhouse_type: “lean-to, detached, and ridge and gutter connected” ]
+                        */
+                
+                render studyResult as JSON
+        }
+
+
+
+
+        /* still not complete!! */
+        /**
+        * REST resource for DSP.
+        * call: gscf/rest/listStudySamples/?username=username&password=password&study_token=studytoken
+        *
+        * @param  String user name
+        * @param  String password 
+        * @param  String a valid GSCF Study.code
+        * @return List of pairs; each pair is a map with keys sample_token and name and values Study.code and Sample.name.
+        */
+        def listStudySamples = {
+
+                if( !isVerifiedUser( params ) ) {
+                        render [:] as JSON
+                        return
+                }
+
+                List samples = [:] 
+                def code = params.study_token
+                def query = "from Samples as s where s.study = ?"
+                def study = Study.find( query, code )
+                if(study) study.samples.each { sample ->
+                        def map = [ sample_token:code, name:sample.name ]
+                        samples.add( map )
+                }
+                
+                render samples as JSON
+        }
+
+
+
+        /* still not complete!! */
+        /**
+        * REST resource for DSP.
+        * call: getStudySample/?username=me&password=123&study_token=GHyJeR#g&sample_name=”AHVJwR”)
+        *
+        * @param  String username
+        * @param  String password
+        * @param  String study_token 
+        * @param  String sample_name 
+        * @return list of studies 
+        */
+        def getStudySample = {
+
+                if( !isVerifiedUser( params ) ) {
+                        render [:] as JSON
+                        return
+                }
+
+                List sample = [:] 
+                def code = params.study_token
+                def name = params.sample_name
+
+                def query = "from Sample as s where s.name = ? AND s.parentStudy "
+                def study = Sample.find( query, name )
+                sample = [ 'study_token' : sample.code, 'name' : sample.name ]
+                // samples will have unique identifier strings
+                /*  still not complete!! 
+                                Add features
+                                [ 
+                                        study_token:”GHyJeR#g”, 
+                                        sample_token:”AHVJwR”, 
+                                        name: “Sample SMPL002”,
+                                        created: “25/06/2010 09:14:32”,
+                                        meta: [ subject: “SUB000294-34942.A”, subject_bmi: “29.3”, ... study_token:”GHyJeR#g”, 
+                                        ... created: “20/06/2010 22:34:52”, greenhouse_id: “GH010938.AB.5”,
+                                        greenhouse_type: “lean-to, detached, and ridge and gutter connected” 
+                                ]
+                        */
+                render sample as JSON
+        }
+
+
+
+
+        /* still not complete!! */
+        /** Convenience method for isUser and listStudies.
+        *   Verify user and password.
+        *   @param  params object with two map keys: (1) 'username', (2) 'password'
+        *   @param  String password
+        *   @return bool
+        */
+        private isVerifiedUser( params ) {
+                def isVerified = false 
+                def user = params?.username
+                def pass = params?.password
+
+                if( user && pass ) {
+                        // insert code for verification of user and 
+                        // ... 
+                        isVerified = true
+                }
+                return isVerified
+        }
+
+
+
+    /* this is just for testing! */
+    def test = {
+                def result = dbnp.rest.common.CommunicationManager.getQueryResult("Insulin")
+                render result 
+                render result["studies"]
+                render result["studies"].get(0).class
+    }
 }

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

@@ -28 +28 @@
     def public static SAMServerURL  = "http://localhost:8182/sam"
     def public static GSCFServerURL = "http://localhost:8080/gscf"
+    def public static DSPServerURL  = "http://localhost:8080/gscf"
 
      
@@ -194 +195 @@
                 //               "class":"data.SimpleAssay", "externalAssayID":"1", "id":1, "measurements":null, "unit":"Insulin", "inSerum":false, 
         //                               "name":"test Simple Assay 1", "referenceValues":"test Reference Values 1"], dbnp.studycapturing.Assay : 1]]]
-                def closure = { map -> 
-                    def studies = []    
-                    def assays  = []    
+                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]) ) }
@@ -212 +213 @@
 
 
+    /**
+     *  This method creates on run time new methods for accessing Grails views that SAM provides for GSCF.
+     *  This method should be called in grails-app/conf/BootStrap.groovy in the GSCF module.
+     */ 
+    public static registerRestWrapperMethodsGSCFtoDSP() {
+                def url = DSPServerURL
+                addRestWrapper( url, 'isUser',  ['username','password'] )
+                addRestWrapper( url, 'listStudies',  ['username','password'] )
+                addRestWrapper( url, 'listStudySamples',  ['username','password','study_token'] )
+                addRestWrapper( url, 'getStudy',  ['username','password','study_token'] )
+                addRestWrapper( url, 'getStudySample',  ['username','password','study_token','sample_token'] )
+                addRestWrapper( url, 'isUser',  ['username','password'] )
+    }
+
+
+
 }