Changeset 812 for trunk/grails-app/conf

Timestamp:

Aug 16, 2010, 6:04:00 PM (11 years ago)

Author:

keesvb

Message:

added Sample tests for deleting samples via parent sampling event and event group, corrected some small errors, updated BootStrap? to find out why Sample.parentEvent gets serialized into the db, still no luck...

Location:

trunk/grails-app/conf

Files:

• BootStrap.groovy (modified) (3 diffs)
• BootStrapStudies.groovy (modified) (12 diffs)

trunk/grails-app/conf/BootStrap.groovy

@@ -40 +40 @@
                                 BootStrapStudies.addExampleStudies()
                         }
+
+                        println "Finished adding templates and studies"
                 }
 
@@ -51 +53 @@
                 TemplateEntity.getField(Sample.domainFields, 'material').ontologies = [Ontology.getOrCreateOntologyByNcboId(1005)]
 
+                println "Registering SAM REST methods"
                 // register methods for accessing SAM's Rest services 
                 if (grails.util.GrailsUtil.environment == GrailsApplication.ENV_PRODUCTION) {
@@ -59 +62 @@
                 }
                 CommunicationManager.registerRestWrapperMethodsSAMtoGSCF()
+
+                println "Done with BootStrap"
         }
 

trunk/grails-app/conf/BootStrapStudies.groovy

@@ -231 +231 @@
                 def evS = new SamplingEvent(
                         startTime: 3600 +7 * 24 * 3600,
-                        endTime: 3600 +7 * 24 * 3600,
                         template: liverSamplingEventTemplate,
                         sampleTemplate: humanTissueSampleTemplate)
@@ -238 +237 @@
                 def evS4 = new SamplingEvent(
                         startTime: 3600 +7 * 24 * 3600,
-                        endTime: 3600 +7 * 24 * 3600,
                         template: liverSamplingEventTemplate,
                         sampleTemplate: humanTissueSampleTemplate)
@@ -314 +312 @@
                         .setFieldValue("Cage", "" + (int)(x/2))
 
+                        // We have to save the subject first, otherwise the parentEvent property of the sample cannot be set
+                        // (this is possibly a Grails or Hibernate bug)
                         mouseStudy.addToSubjects(currentSubject)
-                        .with { if (!validate()) { errors.each { println it} } else save()}
+                        currentSubject.with { if (!validate()) { errors.each { println it} } else save()}
 
                         // Add subject to appropriate EventGroup
@@ -333 +333 @@
                                 template: humanBloodSampleTemplate,
                                 parentSubject: currentSubject,
-                                parentEvent: x > 40 ? evS4 : evS
+                                parentEvent: evS //x > 40 ? evS4 : evS
                         );
+                        mouseStudy.addToSamples(currentSample)
+                        currentSample.with { if (!validate()) { errors.each { println it} } else save()}
                         currentSample.setFieldValue( "Text on vial", "T" + (Math.random() * 100L) )
-                        mouseStudy.addToSamples(currentSample).with { if (!validate()) { errors.each { println it} } else save()}
                 }
 
@@ -388 +389 @@
                 def bloodSamplingEvent = new SamplingEvent(
                         startTime: 3 * 24 * 3600 + 30 * 3600,
-                        endTime: 3 * 24 * 3600 + 30 * 3600,
                         template: bloodSamplingEventTemplate,
                         sampleTemplate: humanBloodSampleTemplate)
@@ -411 +411 @@
                         .setFieldValue("BMI", 20 + Math.random() * 10F)
 
+                        humanStudy.addToSubjects(currentSubject)
+                        currentSubject.with { if (!validate()) { errors.each { println it} } else save()}
+
                         rootGroup.addToSubjects currentSubject
                         rootGroup.save()
@@ -421 +424 @@
                                 parentEvent: bloodSamplingEvent
                         );
+
+                        humanStudy.addToSamples(currentSample)
+                        currentSample.with { if (!validate()) { errors.each { println it} } else save()}
                         currentSample.setFieldValue( "Text on vial", "T" + (Math.random() * 100L) )
-
-                        humanStudy.addToSubjects(currentSubject).addToSamples(currentSample)
-                        .with { if (!validate()) { errors.each { println it} } else save()}
                 }
 
@@ -431 +434 @@
                 humanStudy.addToEventGroups rootGroup
 
-
+                println ".adding persons and saving PPSH study..."
                 // Add persons to study
                 def studyperson3 = new StudyPerson( person: person1, role: role2 )
-
                 humanStudy
                 .addToPersons( studyperson3 )
@@ -440 +442 @@
                 .with { if (!validate()) { errors.each { println it} } else save()}
 
-                // Add clinical data       ==> to be moved to SAM
-
-                def lipidAssay = new dbnp.clinicaldata.ClinicalAssay(
-                        name: 'Lipid profile',
-                        approved: true
-                ).with { if (!validate()) { errors.each { println it} } else save()}
-
-                def ldlMeasurement = new dbnp.clinicaldata.ClinicalMeasurement(
-                        name: 'LDL',
-                        unit: 'mg/dL',
-                        type: dbnp.data.FeatureType.QUANTITATIVE,
-                        referenceValues: '100 mg/dL',
-                        detectableLimit: 250,
-                        isDrug: false, isIntake: true, inSerum: true
-                ).with { if (!validate()) { errors.each { println it} } else save()}
-
-                def hdlMeasurement = new dbnp.clinicaldata.ClinicalMeasurement(
-                        name: 'HDL',
-                        unit: 'mg/dL',
-                        type: dbnp.data.FeatureType.QUANTITATIVE,
-                        referenceValues: '50 mg/dL',
-                        detectableLimit: 100,
-                        isDrug: false, isIntake: true, inSerum: true
-                ).with { if (!validate()) { errors.each { println it} } else save()}
-
-                lipidAssay.addToMeasurements ldlMeasurement
-                lipidAssay.addToMeasurements hdlMeasurement
-
-                def lipidAssayInstance = new dbnp.clinicaldata.ClinicalAssayInstance(
-                        assay: lipidAssay
-                ).with { if (!validate()) { errors.each { println it} } else save()}
-
-                humanStudy.samples*.each {
-                        new dbnp.clinicaldata.ClinicalFloatData(
-                                assay: lipidAssayInstance,
-                                measurement: ldlMeasurement,
-                                sample: it.name,
-                                value: Math.round(Math.random()*ldlMeasurement.detectableLimit)
-                        ).with { if (!validate()) { errors.each { println it} } else save()}
-
-                        new dbnp.clinicaldata.ClinicalFloatData(
-                                assay: lipidAssayInstance,
-                                measurement: hdlMeasurement,
-                                sample: it.name,
-                                value: Math.round(Math.random()*hdlMeasurement.detectableLimit)
-                        ).with { if (!validate()) { errors.each { println it} } else save()}
-                }
-
-                // Add assay to study capture module
-
+                println ".adding assay references to mouse example study..."
+
+                // Add SAM assay references
                 def clinicalModule = new AssayModule(
                         name: 'SAM module for clinical data',
@@ -510 +465 @@
                 mouseStudy.save()
 
-                lipidAssayRef.with { if (!validate()) { errors.each { println it} } else save()}
+                //lipidAssayRef.with { if (!validate()) { errors.each { println it} } else save()}
+
+                println ".adding assay references to human example study..."
 
                 def  glucoseAssay2Ref = new Assay(
@@ -524 +481 @@
                 )
 
-                humanStudy.addToAssays(glucoseAssay2Ref)
-                humanStudy.addToAssays(glucoseAssay3Ref)
-                humanStudy.save()
-
                 humanStudy.samples*.each {
                         glucoseAssay2Ref.addToSamples(it)
@@ -533 +486 @@
                 }
 
-                glucoseAssay2Ref.with { if (!validate()) { errors.each { println it} } else save()}
-                glucoseAssay3Ref.with { if (!validate()) { errors.each { println it} } else save()}
+
+                humanStudy.addToAssays(glucoseAssay2Ref)
+                humanStudy.addToAssays(glucoseAssay3Ref)
+                humanStudy.save()
+                println "Saving"
+                //glucoseAssay2Ref.with { if (!validate()) { errors.each { println it} } else save()}
+                //glucoseAssay3Ref.with { if (!validate()) { errors.each { println it} } else save()}
 
         }