Changeset 515 for trunk/grails-app/controllers/RestController.groovy

Timestamp:

Jun 3, 2010, 9:48:33 AM (8 years ago)

Author:

jahn

Message:

REST resources for communicating with the Simple Assay Module.

File:

• trunk/grails-app/controllers/RestController.groovy (modified) (2 diffs)

trunk/grails-app/controllers/RestController.groovy

@@ -1 +1 @@
 /**
- * RestController Controler
+ * ModuleCommunicationController Controler
  *
- * Description this is for testing the dbNP.rest.CCMCommunicationManager only and should be removed,
- * once the CCMCommunicationManager works with an exteneral server (nbx5)!!!!
+ * 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.
  * 
- * This class renders two REST related requests (features and get_json). 
- *
- * @author  Jahn 
- * @since   20100526
+ * @author      Jahn 
+ * @since       20100601
  *
  */
 
-import grails.converters.JSON
+import data.*
+import dbnp.studycapturing.Study
+import dbnp.studycapturing.Assay
+import grails.converters.*
 import org.codehaus.groovy.grails.web.json.*
-import dbnp.studycapturing.TemplateFieldListItem
-import dbnp.studycapturing.Template
-import dbnp.rest.CCMCommunicationManager
+
 
 
@@ -22 +27 @@
 
 
-    /**
-     * result of querying the Clinical Chemistry Module
-     * if assay in the database : return the Clinical Assay
-     * else : return the list of all Assays in the database
-     * @return Clinical Assay
-     */
-    def features = {
-            //def items = TemplateFieldListItem.list()
-            def items = Template.list()
-            items.each{ render (it as JSON) } 
-            render params
-    }
+        /* REST resources for Simple Assay Module (SAM) */ 
 
 
-    /* Use a REST resource to get data using the CCMCommunicationManager */
-    def get_json = {
-        def json_result = new CCMCommunicationManager().getFeatures()
-        json_result.each { render "Value : ${it}\n"}
-    }
+        /**
+        * REST resource for the Simple Assay Module.
+        * Provide a list of all studies. 
+        *
+        *
+        * Examlpe call of the getAssays REST resource: http://localhost:8080/gscf/rest/getAssays/json?externalStudyID=1
+        *
+        * @return as JSON object list of members externalStudyID, and title for all studies
+        */
+        def getStudies = {
+                List studies = [] 
+                Study.list().each { study ->
+                    studies.push( [ 'externalStudyID': study.externalStudyID, 'name':study.title ] )
+                }
+                render studies as JSON 
+        }
+
+
+        /**
+        * REST resource for the Simple Assay Module.
+        * Provide a list of all assays for a given study
+        *
+        * Example for calling this resource: http://localhost:8080/gscf/rest/getAssays/json?externalStudyID=2
+        *
+        * @param  externalStudyID 
+        * @return list of assays as JSON object 
+        */
+        def getAssays = {
+                List assays = [] 
+                if( params.externalStudyID ) {
+                        def id = Long.parseLong(params.externalStudyID)
+                        def study = Study.find( "from Study as s where s.externalStudyID=?", [id])
+                        study.assays.each{ assay -> assays.push assay.externalAssayID }
+                }
+                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. 
+        *
+        * Example for calling this resource: http://localhost:8080/gscf/rest/getAssays/json?externalStudyID=2
+        *
+        * @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 id = Long.parseLong(params.externalAssayID)
+                        Assay.find( "from Assay as a where externalAssayID=?",[id]).getSamples().each { sample ->
+                                def item = [ 
+                                        'name'            : sample.name,
+                                        'material'        : sample.material.name,
+                                        'subject'         : sample.parentSubject.name,
+                                        //'event'         : sample.parentEvent.name,  // get the freaking name 
+                                        'startTime'       : sample.parentEvent.startTime
+                                ] 
+                                items.push item 
+                        }
+                }
+                render items as JSON
+        }
 
 }