@Override
@Before
public void setUp() throws Exception {
super.setUp();
parentSpc = SpecimenHelper.addParentSpecimen();
site = SiteHelper.addSite("testsite" + r.nextInt());
ContainerTypeWrapper typeChild =
ContainerTypeHelper.addContainerType(
site, "ctTypeChild" + r.nextInt(), "ctChild", 1, 4, 5, false);
typeChild.addToSpecimenTypeCollection(
Arrays.asList(
DbHelper.chooseRandomlyInList(
SpecimenTypeWrapper.getAllSpecimenTypes(appService, false))));
typeChild.persist();
ContainerTypeWrapper topType =
ContainerTypeHelper.addContainerType(site, "topType" + r.nextInt(), "ct", 1, 4, 5, true);
topType.addToChildContainerTypeCollection(Arrays.asList(typeChild));
topType.persist();
topContainer = ContainerHelper.addContainer("top" + r.nextInt(), "cc", site, topType);
ContainerWrapper container =
ContainerHelper.addContainer(null, "2nd", topContainer, site, typeChild, 3, 3);
childSpc = SpecimenHelper.addSpecimens(parentSpc, container, 0, 0, 1).get(0);
}
@Test
public void testResetNew() throws Exception {
SpecimenWrapper newSpec = SpecimenHelper.newSpecimen(parentSpc.getSpecimenType());
newSpec.setInventoryId("toto");
newSpec.reset();
Assert.assertEquals(null, newSpec.getInventoryId());
}
@Test
public void testCompareTo() throws BiobankCheckException, Exception {
parentSpc.setInventoryId("defgh");
parentSpc.persist();
SpecimenWrapper sample2 =
SpecimenHelper.newSpecimen(
parentSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
2,
3);
sample2.setInventoryId("awert");
sample2.persist();
Assert.assertTrue(parentSpc.compareTo(sample2) > 0);
sample2.setInventoryId("qwerty");
sample2.persist();
Assert.assertTrue(parentSpc.compareTo(sample2) < 0);
SpecimenBaseWrapper sb = new SpecimenBaseWrapper(appService);
Assert.assertEquals(0, parentSpc.compareTo(sb));
// test with a position because compare with position in this case:
// childSpc is in topD4B1
// sample2 is in topD4C4
Assert.assertTrue(childSpc.compareTo(sample2) < 0);
}
@Test
public void testPersistPositionAlreadyUsed() throws BiobankCheckException, Exception {
parentSpc.persist();
RowColPos pos = childSpc.getPosition();
SpecimenWrapper duplicate =
SpecimenHelper.newSpecimen(
parentSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
pos.getRow(),
pos.getCol());
try {
duplicate.persist();
Assert.fail("should not be allowed to add an specimen in a position that is not empty");
} catch (BiobankSessionException bce) {
Assert.assertTrue(true);
}
duplicate.setParent(duplicate.getParentContainer(), new RowColPos(2, 3));
duplicate.persist();
duplicate.setInventoryId(Utils.getRandomString(5));
duplicate.persist();
}
@Test
public void testPersistCheckInventoryIdUniqueCaseSensitive()
throws BiobankCheckException, Exception {
int i = r.nextInt();
parentSpc.setInventoryId("toto" + i);
parentSpc.persist();
SpecimenWrapper duplicate =
SpecimenHelper.newSpecimen(
parentSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
2,
2);
duplicate.setInventoryId("toto" + i);
try {
duplicate.persist();
Assert.fail("same inventory id !");
} catch (DuplicatePropertySetException dee) {
Assert.assertTrue(true);
}
duplicate.setInventoryId("TOTO" + r.nextInt());
duplicate.persist();
}
@Test
public void testPersistCheckInventoryIdUnique() throws BiobankCheckException, Exception {
SpecimenWrapper duplicate =
SpecimenHelper.newSpecimen(
parentSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
2,
2);
duplicate.setInventoryId(parentSpc.getInventoryId());
try {
duplicate.persist();
Assert.fail("same inventory id !");
} catch (DuplicatePropertySetException e) {
Assert.assertTrue(true);
}
duplicate.setInventoryId("qqqq" + r.nextInt());
duplicate.persist();
duplicate.setInventoryId(parentSpc.getInventoryId());
try {
duplicate.persist();
Assert.fail(
"still can't save it with the same inventoryId after a first add with anotehr inventoryId!");
} catch (DuplicatePropertySetException e) {
Assert.assertTrue(true);
}
}
@Test
public void testGetSpecimensInSiteWithPositionLabel() throws Exception {
ContainerWrapper container = childSpc.getParentContainer();
ContainerTypeWrapper containerType = container.getContainerType();
SpecimenTypeWrapper sampleType = containerType.getSpecimenTypeCollection(false).get(0);
Assert.assertNotNull(sampleType);
childSpc.setInventoryId(Utils.getRandomString(5));
childSpc.persist();
SpecimenHelper.newSpecimen(
childSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
0,
1);
SpecimenHelper.newSpecimen(
childSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
1,
0);
childSpc =
SpecimenHelper.newSpecimen(
childSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
0,
2);
childSpc.setInventoryId(Utils.getRandomString(5));
childSpc.persist();
List<SpecimenWrapper> specimens =
SpecimenWrapper.getSpecimensInSiteWithPositionLabel(
appService, site, childSpc.getPositionString(true, false));
Assert.assertEquals(1, specimens.size());
Assert.assertEquals(specimens.get(0), childSpc);
}
@Test
public void testGetSpecimensNonActive() throws Exception {
ContainerWrapper container = childSpc.getParentContainer();
ContainerTypeWrapper containerType = container.getContainerType();
SpecimenTypeWrapper sampleType = containerType.getSpecimenTypeCollection(false).get(0);
Assert.assertNotNull(sampleType);
ActivityStatus activityStatusNonActive = ActivityStatus.CLOSED;
List<SpecimenWrapper> activeSpecimens = new ArrayList<SpecimenWrapper>();
List<SpecimenWrapper> nonActiveSpecimens = new ArrayList<SpecimenWrapper>();
activeSpecimens.add(childSpc);
for (int i = 1, n = container.getColCapacity(); i < n; ++i) {
activeSpecimens.add(
SpecimenHelper.newSpecimen(
parentSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
0,
i));
SpecimenWrapper a =
SpecimenHelper.newSpecimen(
parentSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
1,
i);
a.setActivityStatus(activityStatusNonActive);
a.persist();
nonActiveSpecimens.add(a);
}
List<SpecimenWrapper> specimens =
SpecimenWrapper.getSpecimensNonActiveInCenter(appService, site);
Assert.assertEquals(nonActiveSpecimens.size(), specimens.size());
Assert.assertTrue(specimens.containsAll(nonActiveSpecimens));
Assert.assertFalse(specimens.containsAll(activeSpecimens));
}
@Test
public void testGetCenterString() throws Exception {
String name = "testGetCenterString" + r.nextInt();
ClinicWrapper clinic = ClinicHelper.addClinic(name);
StudyWrapper study = StudyHelper.addStudy(name);
PatientWrapper patient = PatientHelper.addPatient(name, study);
SpecimenWrapper spc = SpecimenHelper.addParentSpecimen(clinic, study, patient);
Assert.assertTrue(spc.getCenterString().equals(clinic.getNameShort()));
spc.setCurrentCenter(null);
spc.persist();
Assert.assertFalse(spc.getCenterString().equals(clinic.getNameShort()));
Assert.assertNotNull(spc.getCenterString());
Assert.assertFalse("".equals(spc.getCenterString()));
}
@Test
public void testCheckInventoryIdUnique() throws BiobankCheckException, Exception {
SpecimenWrapper duplicate =
SpecimenHelper.newSpecimen(
parentSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
2,
2);
duplicate.setInventoryId(parentSpc.getInventoryId());
try {
duplicate.checkInventoryIdUnique();
Assert.fail("The check should detect that this is the same");
} catch (DuplicateEntryException e) {
Assert.assertTrue(true);
}
}
@Test
public void testDebugRandomMethods() throws Exception {
System.out.println(parentSpc.getProcessingEvent());
System.out.println(childSpc.getProcessingEvent());
ContainerWrapper container = childSpc.getParentContainer();
ContainerTypeWrapper containerType = container.getContainerType();
SpecimenTypeWrapper spcType = containerType.getSpecimenTypeCollection(false).get(0);
Assert.assertNotNull(spcType);
System.out.println(parentSpc.getProcessingEvent());
System.out.println(childSpc.getProcessingEvent());
ProcessingEventWrapper pevent =
ProcessingEventHelper.addProcessingEvent(
childSpc.getCurrentCenter(), Utils.getRandomDate());
// add aliquoted specimen
SpecimenWrapper specimen =
SpecimenHelper.newSpecimen(
parentSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
2,
3);
specimen.setInventoryId(Utils.getRandomString(5));
specimen.persist();
pevent.addToSpecimenCollection(Arrays.asList(parentSpc));
pevent.persist();
SpecimenWrapper s2 =
SpecimenHelper.newSpecimen(
childSpc,
childSpc.getSpecimenType(),
ActivityStatus.ACTIVE,
childSpc.getProcessingEvent(),
childSpc.getParentContainer(),
2,
4);
s2.setParent(null, null);
s2.setParentSpecimen(null);
s2.persist();
try {
// should find at least one specimen with a parent that is inside a
// processing event
Assert.assertTrue(
DebugUtil.getRandomLinkedAliquotedSpecimens(appService, site.getId()).size() > 0);
Assert.assertTrue(DebugUtil.getRandomAssignedSpecimens(appService, site.getId()).size() > 0);
List<SpecimenWrapper> randomNonAssociatedNonDispatchedSpecimens =
DebugUtil.getRandomNonAssignedNonDispatchedSpecimens(appService, site.getId(), 10);
Assert.assertTrue(randomNonAssociatedNonDispatchedSpecimens.size() > 0);
} catch (Exception e) {
Assert.fail(e.getCause().getMessage());
}
try {
s2.delete();
} catch (Exception e) {
e.printStackTrace();
}
}