Changeset 966

Timestamp:

Oct 21, 2010, 3:54:12 PM (13 years ago)

Author:

business@…

Message:

also added assays check in Study.deleteEventGroup, added test to check whether a study with orphan events cannot be published (functionality is still to be implemented)

Location:

trunk

Files:

• grails-app/domain/dbnp/studycapturing/Study.groovy (modified) (2 diffs)
• test/integration/gscf/SampleTests.groovy (modified) (6 diffs)

trunk/grails-app/domain/dbnp/studycapturing/Study.groovy

@@ -44 +44 @@
                 owner(nullable: true, blank: true)
                 code(nullable:false, blank:true,unique:true)
+
+                // TODO: add custom validator for 'published' to assess whether the study meets all quality criteria for publication
+                // tested by SampleTests.testStudyPublish
         }
 
@@ -360 +363 @@
                                         }
 
-                                        // TODO: remove the sample from any assays it belongs to
+                                        // remove the sample from any assays it belongs to
+                                        this.assays.findAll { it.samples.any { it == sample }} .each {
+                                                println ".removed sample ${sample.name} from assay ${it.name}"
+                                                it.removeFromSamples(sample)
+                                        }
 
                                         // Also here, contrary to documentation, an extra delete() is needed

trunk/test/integration/gscf/SampleTests.groovy

@@ -112 +112 @@
         }
 
+        private void addParentSubject() {
+
+                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()
+
+        }
+
+        /**
+         * Test whether a study which has orphan (without parent subject/event) samples cannot be published
+         */
         void testStudyPublish() {
                 def sampleDB = Sample.findByName(testSampleName)
@@ -124 +145 @@
 
                 // Try to publish the study, should fail as it has a sample without a parent sampling event
-                //study.published = true
+                study.published = true
                 assert !study.validate()
 
@@ -131 +152 @@
 
                 // Add parent subject
+                addParentSubject()
 
                 // Now the study should validate
@@ -184 +206 @@
                 assert study
 
-                def subject = SubjectTests.createSubject(study)
-                assert subject
-
-                sampleDB.parentSubject = subject
-                assert sampleDB.validate()
-                assert sampleDB.save()
+                // Add parent subject
+                addParentSubject()
+                Subject subject = sampleDB.parentSubject
 
                 // Use the deleteSubject method
@@ -250 +269 @@
                 assert event
 
-                // Create a subject and add it at the sample's parent
-                def subject = SubjectTests.createSubject(study)
-                assert subject
-                sampleDB.parentSubject = subject
-                assert sampleDB.validate()
-                assert sampleDB.save()
-
-                // Create an event group in this study with the sample's sampling event
+                // Add parent subject
+                addParentSubject()
+                Subject subject = sampleDB.parentSubject
+
+                // Create an event group in this study with the sample's sampling event and subject
                 def group = new EventGroup(
                     name: testEventGroupName
@@ -264 +280 @@
                 assert group.validate()
 
-
                 group.addToSubjects(subject)
                 group.addToSamplingEvents(event)
+
                 assert study.eventGroups.find { it.name == group.name}
                 assert group.validate()