Changeset 774 for trunk/test

Timestamp:

Aug 4, 2010, 4:12:38 PM (13 years ago)

Author:

keesvb

Message:

added deleteSubject method to Study, updated Study and Sample integration tests, disabled unused ontology tests

Location:

trunk/test/integration/gscf

Files:

• OntologyTests.groovy (modified) (2 diffs)
• SampleTests.groovy (modified) (3 diffs)
• SubjectTests.groovy (modified) (6 diffs)

trunk/test/integration/gscf/OntologyTests.groovy

@@ -152 +152 @@
          * Add all OLS ontologies to the database via the Ontocat framework
          */
-        void testOntocatOLSOntologies() {
+        private void testOntocatOLSOntologies() {
                 // Instantiate EBI OLS service
                 uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.ols.OlsOntologyService()
@@ -161 +161 @@
          * Add all BioPortal ontologies to the database via the Ontocat framework
          */
-        void testOntocatBioPortalOntologies() {
+        private void testOntocatBioPortalOntologies() {
                 // Instantiate BioPortal service
                 uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()

trunk/test/integration/gscf/SampleTests.groovy

@@ -7 +7 @@
 import dbnp.studycapturing.Sample
 import dbnp.studycapturing.TemplateFieldType
+import dbnp.studycapturing.Subject
 
 /**
@@ -54 +55 @@
                         samplingEvent.errors.each { println it}
                 }
+                // The SamplingEvent should not validate at this point because it doesn't have a parent study
+                assert !samplingEvent.validate()
+
+                study.addToSamplingEvents(samplingEvent)
+                // It should do fine now
                 assert samplingEvent.validate()
-
                 assert samplingEvent.save(flush:true)
 
@@ -125 +130 @@
                 // Make sure the sample doesn't exist anymore at this point
                 assert !Sample.findByName(testSampleName)
+                assert Sample.count() == 0
                 assert study.samples.size() == 0
+        }
+
+        void testDeleteViaParentSubject() {
+
+                def sampleDB = Sample.findByName(testSampleName)
+                assert sampleDB
+
+                // Retrieve the parent study
+                def study = Study.findByTitle(testStudyName)
+                assert study
+
+                def subject = SubjectTests.createSubject(study)
+                assert subject
+
+                sampleDB.parentSubject = subject
+                assert sampleDB.validate()
+                assert sampleDB.save()
+
+                // Use the deleteSubject method
+                def msg = study.deleteSubject(subject)
+                println msg
+                assert study.save()
+
+                assert !study.subjects.contains(subject)
+
+                assert !Subject.findByName(testSampleName)
+                assert !Sample.findByName(testSampleName)
+
+                assert Subject.count() == 0
+                assert Sample.count() == 0
+
         }
 

trunk/test/integration/gscf/SubjectTests.groovy

@@ -19 +19 @@
  * $Date$
  */
-class SubjectTests extends GrailsUnitTestCase {
-
-        final String testSubjectName = "Test subject"
-        final String testSubjectTemplateName = "Human"
-        final String testSubjectSpeciesTerm = "Homo sapiens"
-        final String testSubjectBMITemplateFieldName = "BMI"
-        final double testSubjectBMI = 25.32
-        final String testSubjectGenderTemplateFieldName = "Gender"
-        final String testSubjectGender = "female"
-        final String testSubjectGenderDBName = "Female"
+class SubjectTests extends StudyTests {
+
+        static final String testSubjectName = "Test subject"
+        static final String testSubjectTemplateName = "Human"
+        static final String testSubjectSpeciesTerm = "Homo sapiens"
+        static final String testSubjectBMITemplateFieldName = "BMI"
+        static final double testSubjectBMI = 25.32
+        static final String testSubjectGenderTemplateFieldName = "Gender"
+        static final String testSubjectGender = "female"
+        static final String testSubjectGenderDBName = "Female"
 
         /**
@@ -35 +35 @@
         protected void setUp() {
                 super.setUp()
+
+                // Retrieve the study that should have been created in StudyTests
+                def study = Study.findByTitle(testStudyName)
+                assert study
+
+                createSubject(study)
+        }
+
+        public static Subject createSubject(Study parentStudy) {
 
                 // Look up human template
@@ -40 +49 @@
                 assert humanTemplate
 
-                def humanTerm = Term.findByName(testSubjectSpeciesTerm)
+                def speciesOntology = Ontology.getOrCreateOntologyByNcboId(1132)
+                def humanTerm = new Term(
+                        name: 'Homo sapiens',
+                        ontology: speciesOntology,
+                        accession: '9606')
+
+                assert humanTerm.validate()
+                assert humanTerm.save(flush:true)
                 assert humanTerm
 
@@ -49 +65 @@
                 )
 
-                assert subject.save(flush:true)
+                // At this point, the sample should not validate, because it doesn't have a parent study assigned
+                assert !subject.validate()
+
+                // Add the subject to the retrieved parent study
+                parentStudy.addToSubjects(subject)
+                assert parentStudy.subjects.find { it.name == subject.name}
+
+                // Now, the subject should validate
+                if (!subject.validate()) {
+                        subject.errors.each { println it}
+                }
+                assert subject.validate()
+
+                // Make sure the subject is saved to the database
+                assert subject.save(flush: true)
+
+                return subject
+
         }
 
@@ -60 +93 @@
                 assert subjectDB.species.name.equals(testSubjectSpeciesTerm)
         }
+
+        void testDelete() {
+                def subjectDB = Subject.findByName(testSubjectName)
+                subjectDB.delete()
+                try {
+                        subjectDB.save()
+                        assert false // The save should not succeed since the subject is referenced by a study
+                }
+                catch(org.springframework.dao.InvalidDataAccessApiUsageException e) {
+                        subjectDB.discard()
+                        assert true // OK, correct exception (at least for the in-mem db, for PostgreSQL it's probably a different one...)
+                }
+
+                // Now, delete the subject from the study subjects collection, and then the delete action should be cascaded to the subject itself
+                def study = Study.findByTitle(testStudyName)
+                assert study
+                study.removeFromSubjects subjectDB
+
+                // Make sure the subject doesn't exist anymore at this point
+                assert !Subject.findByName(testSubjectName)
+                assert Subject.count() == 0
+                assert study.subjects.size() == 0
+        }
+
 
         void testValidators() {
@@ -74 +131 @@
 
                 subject.species = Term.findByName(testSubjectSpeciesTerm)
-                assert subject.validate()
-
-                // TODO: Set study and change name to already existing name, should fail within one study
-                // subject.name = testSubjectName
-                // assert !subject.validate()
+                // Still, no parent study assigned
+                assert !subject.validate()
+
+                def study = Study.findByTitle(testStudyName)
+                assert study
+                study.addToSubjects subject
+
+                // Now, the new subject should validate
+                assert subject.validate()
+                assert subject.save()
+
+                // If the subject has the same name as another subject within the same study, it should not validate or save
+                subject.name = testSubjectName
+                assert !subject.validate()
+                assert !subject.save()
         }