@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 testCheckPosition() throws Exception {
ContainerWrapper container = childSpc.getParentContainer();
Assert.assertFalse(container.isPositionFree(childSpc.getPosition()));
Assert.assertTrue(container.isPositionFree(new RowColPos(2, 3)));
}
@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 testResetAlreadyInDatabase() throws Exception {
parentSpc.persist();
String old = parentSpc.getInventoryId();
parentSpc.setInventoryId("toto");
parentSpc.reset();
Assert.assertEquals(old, parentSpc.getInventoryId());
}
@Test
public void testGetFormattedLinkDate() throws Exception {
Date date = Utils.getRandomDate();
parentSpc.setCreatedAt(date);
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd HH:mm");
Assert.assertTrue(sdf.format(date).equals(parentSpc.getFormattedCreatedAt()));
}
@Test
public void testCheckProcessingEventNotNull() throws BiobankCheckException, Exception {
parentSpc.setCollectionEvent(null);
try {
parentSpc.persist();
Assert.fail("Patient visit should be set!");
} catch (ValueNotSetException vnse) {
Assert.assertTrue(true);
}
}
@Test
public void testGetSpecimen() throws Exception {
SpecimenWrapper foundSpecimen =
SpecimenWrapper.getSpecimen(appService, childSpc.getInventoryId());
Assert.assertNotNull(foundSpecimen);
Assert.assertEquals(foundSpecimen, childSpc);
foundSpecimen = SpecimenWrapper.getSpecimen(appService, Utils.getRandomString(5));
Assert.assertNull(foundSpecimen);
Assert.fail("how to test the exception throwing?");
}
@Test
public void testPersistFailActivityStatusNull() throws Exception {
parentSpc.setActivityStatus(null);
try {
parentSpc.persist();
Assert.fail("Should not insert the specimen : no activity status");
} catch (ValueNotSetException vnse) {
Assert.assertTrue(true);
}
parentSpc.setActivityStatus(ActivityStatus.ACTIVE);
parentSpc.persist();
}
@Test
public void testHasUnknownImportType() throws ApplicationException {
Assert.assertFalse(childSpc.hasUnknownImportType());
SpecimenTypeWrapper unknownType = null;
for (SpecimenTypeWrapper type :
SpecimenTypeWrapper.getAllSourceOnlySpecimenTypes(appService, false)) {
if (type.isUnknownImport()) {
unknownType = type;
break;
}
}
childSpc.setSpecimenType(unknownType);
Assert.assertTrue(childSpc.hasUnknownImportType());
}
@Test
public void testPersistCheckParentAcceptSpecimenType() throws BiobankCheckException, Exception {
SpecimenTypeWrapper oldSpecimenType = childSpc.getSpecimenType();
SpecimenTypeWrapper type2 = SpecimenTypeHelper.addSpecimenType("sampletype_2");
childSpc.setSpecimenType(type2);
try {
childSpc.persist();
Assert.fail("Container can't hold this type !");
} catch (InvalidOptionException e) {
Assert.assertTrue(true);
}
childSpc.setSpecimenType(oldSpecimenType);
childSpc.persist();
}
@Test
public void testGetPositionString() throws Exception {
childSpc.setParentFromPositionString("A1", childSpc.getParentContainer());
Assert.assertTrue(childSpc.getPositionString(false, false).equals("A1"));
String parentLabel = childSpc.getParentContainer().getLabel();
Assert.assertTrue(childSpc.getPositionString(true, false).equals(parentLabel + "A1"));
// getPositionString with no parameters is equivalent to
// getPositionString(true, true)
Assert.assertTrue(
childSpc
.getPositionString()
.equals(parentLabel + "A1 (" + topContainer.getContainerType().getNameShort() + ")"));
childSpc.setParent(null, null);
Assert.assertNull(childSpc.getPositionString(false, false));
}
@Test
public void testGetSetSpecimenType() throws BiobankCheckException, Exception {
SpecimenTypeWrapper stw = parentSpc.getSpecimenType();
SpecimenTypeWrapper newType = SpecimenTypeHelper.addSpecimenType("newStw");
stw.persist();
Assert.assertTrue(stw.getId() != newType.getId());
parentSpc.setSpecimenType(newType);
Assert.assertTrue(newType.getId() == parentSpc.getSpecimenType().getId());
SpecimenWrapper sample1 = new SpecimenWrapper(appService);
sample1.setSpecimenType(null);
Assert.assertNull(sample1.getSpecimenType());
}
@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 testGetSetQuantityFromType() throws Exception {
BigDecimal quantity = parentSpc.getQuantity();
parentSpc.setQuantityFromType();
// no sample storages defined yet, should be null
Assert.assertTrue(quantity == null);
ActivityStatus activeStatus = ActivityStatus.ACTIVE;
AliquotedSpecimenWrapper ss1 = new AliquotedSpecimenWrapper(appService);
ss1.setSpecimenType(SpecimenTypeHelper.addSpecimenType("ss1"));
ss1.setVolume(new BigDecimal(1.0));
ss1.setStudy(parentSpc.getCollectionEvent().getPatient().getStudy());
ss1.setActivityStatus(activeStatus);
ss1.persist();
AliquotedSpecimenWrapper ss2 = new AliquotedSpecimenWrapper(appService);
ss2.setSpecimenType(SpecimenTypeHelper.addSpecimenType("ss2"));
ss2.setVolume(new BigDecimal(2.0));
ss2.setStudy(parentSpc.getCollectionEvent().getPatient().getStudy());
ss2.setActivityStatus(activeStatus);
ss2.persist();
AliquotedSpecimenWrapper ss3 = new AliquotedSpecimenWrapper(appService);
ss3.setSpecimenType(parentSpc.getSpecimenType());
ss3.setVolume(new BigDecimal(3.0));
ss3.setStudy(parentSpc.getCollectionEvent().getPatient().getStudy());
ss3.setActivityStatus(activeStatus);
ss3.persist();
parentSpc
.getCollectionEvent()
.getPatient()
.getStudy()
.addToAliquotedSpecimenCollection(Arrays.asList(ss1, ss2, ss3));
// should be 3
parentSpc.setQuantityFromType();
Assert.assertTrue(parentSpc.getQuantity().equals(3.0));
}
@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 testDelete() throws Exception {
String name = "testDelete" + r.nextInt();
SpecimenTypeWrapper type1 = childSpc.getSpecimenType();
try {
type1.delete();
Assert.fail("cannot delete a type in use by a specimen");
} catch (ModelIsUsedException e) {
Assert.assertTrue(true);
}
SpecimenTypeWrapper type2 = SpecimenTypeHelper.addSpecimenType(name + "_st2");
SpecimenTypeHelper.removeFromCreated(type2);
ContainerTypeWrapper typeChild = childSpc.getParentContainer().getContainerType();
typeChild.addToSpecimenTypeCollection(Arrays.asList(type2));
typeChild.persist();
childSpc.reload();
childSpc.setSpecimenType(type2);
childSpc.persist();
try {
type2.delete();
Assert.fail("cannot delete a type in use by a specimen");
} catch (ModelIsUsedException e) {
Assert.assertTrue(true);
}
childSpc.setSpecimenType(type1);
childSpc.persist();
typeChild.removeFromSpecimenTypeCollectionWithCheck(Arrays.asList(type2));
typeChild.persist();
type2.delete();
}
@Test
public void testGetTop() throws Exception {
Assert.assertFalse(childSpc.getParentContainer().equals(childSpc.getTop()));
Assert.assertEquals(topContainer, childSpc.getTop());
}
@Test
public void testIsActive() {
Assert.assertTrue(parentSpc.isActive());
}
@Test
public void testFlagged() {
Assert.assertFalse(parentSpc.isFlagged());
parentSpc.setActivityStatus(ActivityStatus.FLAGGED);
Assert.assertTrue(parentSpc.isFlagged());
}
@Test
public void testSetQuantityFromType() throws Exception {
SpecimenTypeWrapper type = parentSpc.getSpecimenType();
Assert.assertNull(parentSpc.getQuantity());
parentSpc.setSpecimenType(null);
parentSpc.setQuantityFromType();
// no specimen type, no change
Assert.assertNull(parentSpc.getQuantity());
parentSpc.setSpecimenType(type);
parentSpc.setQuantityFromType();
// no aliquotedspecimen with this type in study, no change
Assert.assertNull(parentSpc.getQuantity());
StudyWrapper study = parentSpc.getCollectionEvent().getPatient().getStudy();
AliquotedSpecimenWrapper as =
AliquotedSpecimenHelper.addAliquotedSpecimen(study, parentSpc.getSpecimenType());
study.reload();
Assert.assertNotNull(as.getVolume());
Assert.assertTrue(!as.getVolume().equals(BigDecimal.ZERO));
parentSpc.setQuantityFromType();
Assert.assertTrue(as.getVolume().equals(parentSpc.getQuantity()));
}
@Test
public void testToString() {
String res = parentSpc.toString();
Assert.assertNotNull(res);
Assert.assertFalse(res.isEmpty());
}
/*
* childSpc created in setUp()
*/
@Test
public void testGetDispatches() throws Exception {
String name = "testGetDispatches" + r.nextInt();
SiteWrapper destSite = SiteHelper.addSite(name);
ShippingMethodWrapper method = ShippingMethodWrapper.getShippingMethods(appService).get(0);
DispatchWrapper d = DispatchHelper.addDispatch(site, destSite, method);
d.addSpecimens(Arrays.asList(childSpc), DispatchSpecimenState.NONE);
d.persist();
childSpc.reload();
List<DispatchWrapper> specimenDispatches = childSpc.getDispatches();
Assert.assertEquals(1, specimenDispatches.size());
Assert.assertTrue(specimenDispatches.contains(d));
Assert.assertTrue(d.isInCreationState());
// site send specimens
d.setState(DispatchState.IN_TRANSIT);
d.persist();
Assert.assertTrue(d.isInTransitState());
// dest site receive specimen
d.setState(DispatchState.RECEIVED);
d.receiveSpecimens(Arrays.asList(childSpc));
d.persist();
Assert.assertTrue(d.isInReceivedState());
// make sure spc now belongs to destSite
destSite.reload();
childSpc.reload();
Assert.assertEquals(destSite, childSpc.getCurrentCenter());
// dispatch specimen to second site
SiteWrapper destSite2 = SiteHelper.addSite(name + "_2");
DispatchWrapper d2 = DispatchHelper.addDispatch(destSite, destSite2, method);
d2.addSpecimens(Arrays.asList(childSpc), DispatchSpecimenState.NONE);
parentSpc.reload();
// assign a position to this specimen
ContainerTypeWrapper topType =
ContainerTypeHelper.addContainerType(destSite, "ct11", "ct11", 1, 5, 6, true);
ContainerWrapper topCont = ContainerHelper.addContainer("11", "11", destSite, topType);
ContainerTypeWrapper childType =
ContainerTypeHelper.addContainerType(destSite, "ct22", "ct22", 2, 4, 7, false);
topType.addToChildContainerTypeCollection(Arrays.asList(childType));
topType.persist();
ContainerWrapper cont =
ContainerHelper.addContainer("22", "22", topCont, destSite, childType, 4, 5);
childType.addToSpecimenTypeCollection(Arrays.asList(childSpc.getSpecimenType()));
childType.persist();
cont.reload();
cont.addSpecimen(2, 3, childSpc);
parentSpc.persist();
// add to new dispatch
d2.addSpecimens(Arrays.asList(childSpc), DispatchSpecimenState.NONE);
d2.persist();
// make sure spc still belongs to destSite
destSite2.reload();
childSpc.reload();
Assert.assertEquals(destSite2, childSpc.getCurrentCenter());
childSpc.reload();
specimenDispatches = childSpc.getDispatches();
Assert.assertEquals(2, specimenDispatches.size());
Assert.assertTrue(specimenDispatches.contains(d));
Assert.assertTrue(specimenDispatches.contains(d2));
}
@Test
public void testGetSetPosition() throws Exception {
RowColPos position = new RowColPos(1, 3);
childSpc.setParent(childSpc.getParentContainer(), position);
RowColPos newPosition = childSpc.getPosition();
Assert.assertEquals(position.getRow(), newPosition.getRow());
Assert.assertEquals(position.getCol(), newPosition.getCol());
// ensure position remains after persist
childSpc.persist();
childSpc.reload();
newPosition = childSpc.getPosition();
Assert.assertEquals(position.getRow(), newPosition.getRow());
Assert.assertEquals(position.getCol(), newPosition.getCol());
// test setting position to null
childSpc.setParent(null, null);
childSpc.persist();
childSpc.reload();
Assert.assertEquals(null, childSpc.getPosition());
Assert.assertEquals(null, childSpc.getParentContainer());
}
@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();
}
}
@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(expected = UnsupportedOperationException.class)
public void testToSpecimen() {
childSpc.setTopSpecimen(null);
}
@Test
public void testSetSpecimenPositionFromString() throws Exception {
childSpc.setParentFromPositionString("A1", childSpc.getParentContainer());
childSpc.persist();
Assert.assertTrue(childSpc.getPositionString(false, false).equals("A1"));
RowColPos pos = childSpc.getPosition();
Assert.assertTrue((pos.getCol() == 0) && (pos.getRow() == 0));
childSpc.setParentFromPositionString("C2", childSpc.getParentContainer());
childSpc.persist();
Assert.assertTrue(childSpc.getPositionString(false, false).equals("C2"));
pos = childSpc.getPosition();
Assert.assertTrue((pos.getCol() == 1) && (pos.getRow() == 2));
try {
childSpc.setParentFromPositionString("79", childSpc.getParentContainer());
Assert.fail("invalid position");
} catch (Exception bce) {
Assert.assertTrue(true);
}
SpecimenWrapper specimen = new SpecimenWrapper(appService);
Assert.assertNull(specimen.getPositionString());
}
@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 testGetSetParent() throws Exception {
Assert.assertTrue(childSpc.hasParent());
ContainerWrapper oldParent = childSpc.getParentContainer();
ContainerTypeWrapper type =
ContainerTypeHelper.addContainerType(site, "newCtType", "ctNew", 1, 4, 5, true);
type.addToSpecimenTypeCollection(Arrays.asList(childSpc.getSpecimenType()));
type.persist();
ContainerWrapper parent =
ContainerHelper.addContainer("newcontainerParent", "ccNew", site, type);
childSpc.setParent(parent, childSpc.getPosition());
childSpc.persist();
// check to make sure gone from old parent
oldParent.reload();
Assert.assertTrue(oldParent.getSpecimens().size() == 0);
// check to make sure added to new parent
parent.reload();
Assert.assertTrue(childSpc.getParentContainer() != null);
Collection<SpecimenWrapper> sampleWrappers = parent.getSpecimens().values();
boolean found = false;
for (SpecimenWrapper sampleWrapper : sampleWrappers) {
if (sampleWrapper.getId().equals(childSpc.getId())) found = true;
}
Assert.assertTrue(found);
// test for no parent
SpecimenWrapper specimen2 = new SpecimenWrapper(appService);
Assert.assertFalse(specimen2.hasParent());
}
