Changeset 1328 for trunk

Timestamp:

Jan 4, 2011, 11:13:45 AM (12 years ago)

Author:

robert@…

Message:

Added metagenomics module and improved rest controller to give 404 and 401 errors when appropriate

Location:

trunk/grails-app

Files:

• conf/BootStrapStudies.groovy (modified) (3 diffs)
• conf/Config.groovy (modified) (2 diffs)
• controllers/RestController.groovy (modified) (10 diffs)

trunk/grails-app/conf/BootStrapStudies.groovy

@@ -400 +400 @@
                         url: config.modules.metabolomics.url
                 ).with { if (!validate()) { errors.each { println it} } else save()}
-
+                
+                // Add metabolomics assay reference
+                def metagenomicsModule = new AssayModule(
+                        name: 'Metagenomics module',
+                        platform: 'High throughput sequencing',
+                        url: config.modules.metagenomics.url
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+                
                 def lipidAssayRef = new Assay(
                         name: 'Lipid profiling',
@@ -452 +459 @@
                 ).setFieldValue('Spectrometry technique', 'GC/MS')
 
+                
+                // Add sequencing (metagenomics) assays
+                def sequencingAssay16SRef = new Assay(
+                        name            : '16S Sequencing assay',
+                        template        : ccAssayTemplate,
+                        module          : metagenomicsModule,
+                        externalAssayID: 'PPSH-SEQ-16S'
+                )
+                
+                // Add sequencing (metagenomics) assays
+                def sequencingAssay18SRef = new Assay(
+                        name            : '18S Sequencing assay',
+                        template        : ccAssayTemplate,
+                        module          : metagenomicsModule,
+                        externalAssayID: 'PPSH-SEQ-18S'
+                )
+                
                 humanStudy.samples*.each {
                         if (it.parentEvent.startTime == 0) {
@@ -460 +484 @@
                                 glucoseAssayARef.addToSamples(it)
                                 metAssayRefA.addToSamples(it)
+                                sequencingAssay16SRef.addToSamples(it)
+                                sequencingAssay18SRef.addToSamples(it)
                         }
                 }
-
+                
+                humanStudy.addToAssays(sequencingAssay16SRef)
+                humanStudy.addToAssays(sequencingAssay18SRef)
                 humanStudy.addToAssays(glucoseAssayARef)
                 humanStudy.addToAssays(glucoseAssayBRef)

trunk/grails-app/conf/Config.groovy

@@ -59 +59 @@
                                 url = "http://localhost:8183/nmcdsp"
                         }
+                        metagenomics {
+                                url = "http://localhost:8184/metagenomics"
+                        }
                 }
         }
@@ -71 +74 @@
                                 url = "http://ci.metabolomics.nmcdsp.org"
                         }
+                        metagenomics {
+                                url = "http://ci.metagenomics.nmcdsp.org"
+                        }                       
                 }
         }

trunk/grails-app/controllers/RestController.groovy

@@ -95 +95 @@
          * @return  JSON object list containing 'studyToken', and 'name' (title) for each study
          *
+         * If one study is requested, a 404 error might occur if the study doesn't exist, and a 401 error if the user is not
+         * authorized to access this study. If multiple studies are requrested, non-existing studies or studies for which the 
+         * user is not authorized are not returned in the list (so the list might be empty).
          *
          * Example 1. REST call without studyToken. 
@@ -134 +137 @@
                 }
                 else if( params.studyToken instanceof String ) {
-                        studies.push Study.findByCode( params.studyToken ) 
+                        def study = Study.findByCode( params.studyToken ) 
+                        if( study ) {
+                                if( !study.canRead(AuthenticationService.getRemotelyLoggedInUser( params.consumer, params.token )) ) {
+                                        response.sendError(401)
+                                        return false
+                                }
+                                
+                                studies.push study 
+                        } else {
+                                response.sendError(404)
+                                return false
+                        }
+        
                 }
                 else { 
                         params.studyToken.each{ studyToken ->
-                                studies.push Study.findByCode( studyToken )
-                        }
-                }
+                                def study = Study.findByCode( studyToken );
+                                if( study )
+                                        studies.push study 
+                        }
+                }
+                
 
                 studies.each { study ->
@@ -171 +189 @@
          * Provide a list of all subjects belonging to a study.
          *
-         * If the user is not allowed to read the study contents, a 401 error is given
+         * If the user is not allowed to read the study contents, a 401 error is given. If the study doesn't exist, a 404 error is given
          *
          * @param       studyToken      String The external study id (code) of the target GSCF Study object
@@ -192 +210 @@
 
                                 study.subjects.each { subjects.push it.name }
+                        } else {
+                                response.sendError(404)
+                                return false
                         }
                 }
@@ -203 +224 @@
          * Provide a list of all assays for a given study.
          *
-         * If the user is not allowed to read the study contents, a 401 error is given
+         * If the user is not allowed to read the study contents, a 401 error is given. If the study doesn't exist, a 404 error is given
          *
          * @param       studyToken      String The external study id (code) of the target GSCF Study object
@@ -297 +318 @@
                                         }
                                 }
-                }
+                } else {
+                                response.sendError(404)
+                                return false
+                        }
 
                 }
@@ -313 +337 @@
          * Provide all samples of a given Assay. The result is an enriched list with additional information for each sample.
          *
+         * If the user is not allowed to read the study contents, a 401 error is given. If the assay doesn't exist, a 404 error is given
+         * 
          * @param       assayToken      String (assayToken of some Assay in GSCF)
          * @param       sampleToken Optional parameter. One or more sampleTokens to specify what sample to give exectly. 
@@ -370 +396 @@
 
                         if( assay )  {
+                                // Check whether the person is allowed to read the data of this study
+                                if( !assay.parent.canRead(AuthenticationService.getRemotelyLoggedInUser( params.consumer, params.token ))) {
+                                        response.sendError(401)
+                                        return false
+                                }
+                                
                                 def samples = assay.getSamples() // on all samples
 
@@ -427 +459 @@
                                         items.push item 
                                 }
+                        } else {
+                                // Assay not found
+                                response.sendError(404)
+                                return false
                         }
                 }
@@ -468 +504 @@
     }
 
-
-
-
-
-
 }