Changeset 515

Timestamp:

Jun 3, 2010, 9:48:33 AM (14 years ago)

Author:

jahn

Message:

REST resources for communicating with the Simple Assay Module.

Location:

trunk

Files:

• grails-app/controllers/RestController.groovy (modified) (2 diffs)
• src/groovy/dbnp/rest/CCMCommunicationManager.groovy (modified) (4 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
+        }
 
 }

trunk/src/groovy/dbnp/rest/CCMCommunicationManager.groovy

@@ -11 +11 @@
 
 
+
+/**  CCMCommunicationManager 
+ *
+ *   This class implements a REST client to fetch data from the Clinical Chemistry Module (CCM).
+ *   The communicatino manager provides methods for accessing each resources.
+ *   Every REST resource corresponds to exactly one method in this class that makes
+ *   the communication with the resource available. 
+ *
+ *   For instance, the getSearchable() method calls the getMeasurements resource of the CCM
+ *   by passing arguments to it and returning the result of the calling that resource. 
+ */
+
+
 class CCMCommunicationManager implements CleanDataLayer {
 
+    
+    /** ServerULR contains a string that represents the URL of the 
+     *  rest resources that this communication manager connects to.
+     */ 
+    def static ServerURL = "http://nbx5.nugo.org:8182/ClinicalChemistry/rest";
     //def static ServerURL = "http://localhost:8080/gscf/rest";
-    def static ServerURL = "http://nbx5.nugo.org:8182/ClinicalChemistry/rest";
 
 
@@ -43 +60 @@
 
 
-
-
-
     /**
      * Testing REST. Remove when connection to nbx5 is established.
@@ -52 +66 @@
      */
     public Object getFeatures() {
-        def url = new URL( ServerURL + "/features" )
-        return  JSON.parse(url.newReader())
+    //    return  request( "features" ) 
+        return  getStudiesForKeyword("ldl")
     }
 
 
     /**
-     * Testing REST. Remove when connection to nbx5 is established.
+     * For a string for the searchable plugin.
+     * This works for one keyeword, but protection should be built in using 
+     * the methods that searchable uses for building query strings. 
      *
      * @return list of ClinicalFloatData
      */
     private String getSearchable( keyword ) {
-        return "submit=Query&q=" + keyword 
+        return  "?submit=Query&q=" + keyword 
     }
 
 
     /**
-     * Testing REST. Remove when connection to nbx5 is established.
+     * Get all meassurements that contain a given keyword as feature.
      *
+     * @param  keyword, the keyword used
      * @return list of ClinicalFloatData
      */
     public String getStudiesForKeyword( String keyword ) {
+        def resource = "getMeasurementsForValue"
+        request( resource + getSearchable(keyword) )
     }
 
 
+    /**
+     * Get all meassurements that contain a given keyword as feature.
+     *
+     * @param  keyword, the keyword used
+     * @return list of ClinicalFloatData
+     */
     public Object getMeasurementsResource( String keyword ) {
         def url = new URL( ServerURL + "/" + getSearchable(keyword) )
@@ -94 +119 @@
 
 
+
+
+
+
     /** Send a request for the REST resource to the server and deliver the 
-     *  resulting JSON object.
+     *  resulting JSON object. (This is just a convenience method.)
      *
      *  @param resource: the name of the resource including parameters
      *  @return JSON object
      */
-    private Object requesService( String resource ) { 
+    private Object request( String resource ) { 
         def url = new URL( ServerURL + "/" + resource );
         return  JSON.parse( url.newReader() );
     }
 
+
+
+
+
 }