source: trunk/grails-app/controllers/RestController.groovy @ 834

/**
 * RestControler
 *
 * This controler provides a REST service.
 * The names of the RESET resources are the same as the names of this
 * controller's actions. E.g., the resources called getStudies simply
 * corresponds to the action getStudies. Some of the resources are parameterized. 
 * The parameters are passed as parameters in the url and are available in the
 * params respecting Grails' conventions. In this file, we adher to the javadoc  
 * convention for describing parameters ("@param"), but actually we mean
 * key-value pairs in the params object of each Grails action we comment on.
 * 
 * @author      Jahn-Takeshi Saito
 * @since       20100601
 *
 */

import dbnp.studycapturing.Study
import dbnp.studycapturing.Assay
import grails.converters.*
import nl.metabolomicscentre.dsp.http.BasicAuthentication


class RestController {



       /**************************************************/
      /** Rest resources for Simple Assay Module (SAM) **/
     /**************************************************/

        def authService
        def beforeInterceptor = [action:this.&auth]
        def credentials
        def requestUser
// defined as a regular method so its private

        /**
         * Authorization closure, which is run before executing any of the REST resource actions
         * It fetches a username/password combination from basic HTTP authentication and checks whether
         * that is an active (nimble) account
         * @return
         */
        def auth() {
            credentials = BasicAuthentication.credentialsFromRequest(request)
                requestUser = authService.authUser(credentials.u,credentials.p)
                if(!requestUser) {
                    response.sendError(403)
                return false
            }
                else {
                        return true
                }
        }



        /**
        * REST resource for the Simple Assay Module.
        * Provide a list of all studies. 
        *
        *
        * @return as JSON object list of members externalStudyID, and title for all studies
        */
        def getStudies = {
                List studies = [] 
                Study.findAllByOwner(requestUser).each { study ->
                        studies.push( [ 'externalStudyID': study.code, 'name':study.title ] )
                }
                render studies as JSON 
        }


        /**
        * REST resource for the Simple Assay Module.
        * Provide a list of all subjects belonging to a study. 
        *
        * @param  externalStudyID
        * @return as JSON object list of subject names 
        */
        def getSubjects = {
                List subjects = [] 
                if( params.externalStudyID ) {
                        def id = params.externalStudyID
                        def study = Study.find( "from Study as s where s.code=?", [id])
                        if(study) study.subjects.each { subjects.push it.name }
                }
                render subjects as JSON 
        }


        /**
        * REST resource for the Simple Assay Module.
        * 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
        *
        * @param externalStudyID The external study id (code) of the target GSCF Study object
        * @param moduleURL The base URL of the calling dbNP module
        * @return list of assays in the study as JSON object, filtered to only contain assays for the specified module
        */
        def getAssays = {
                List assays = [] 
                if( params.externalStudyID ) {
                        def study = Study.find( "from Study as s where s.code=?", [params.externalStudyID])
                        if(study && study.owner == requestUser) study.assays.each{ assay ->
                                if (assay.module.url.equals(params.moduleURL)) {
                                def map = ['name':assay.name, 'externalAssayID':assay.externalAssayID]
                                        assays.push( map )
                                }
                        }
                }
                render assays as JSON 
        }


        /**
        * REST resource for the Simple Assay Module.
        * Provide all samples of a given Assay. The result is an enriched list with additional informatin on a sample. 
        *
        * @param  assayID (externalAssayID of some Assay in GSCF)
        * @return list of element of  Sample.name x Sample.material x Sample.subject.name x Sample.Event.name x Sample.Event.time
        */
        def getSamples = {
                def items = []
                if( params.externalAssayID ) {
                        def assay = Assay.find( "from Assay as a where externalAssayID=?",[params.externalAssayID])
                        assay.getSamples().each { sample ->
                                def item = [ 
                                        'name'                : sample.name,
                                        'material'            : sample.material.name,
                                        'subject'             : sample.parentSubject.name,
                                        'event'               : sample.parentEvent.template.name,
                                        'startTime'           : sample.parentEvent.getStartTimeString(),
                                        'externalSampleId': sample.externalSampleId
                                ] 
                                items.push item 
                        }
                }
                render items as JSON
        }





       /****************************/
      /** 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 = {
                render( dbnp.rest.common.CommunicationManager.getQueryResultWithOperator("Insulin",">",200) )
    }
}