/** @see {@link CohortService#voidCohort(Cohort,String)} */
@Test
@Verifies(value = "should fail if reason is null", method = "voidCohort(Cohort,String)")
public void voidCohort_shouldFailIfReasonIsNull() throws Exception {
executeDataSet(COHORT_XML);
// Get a non-voided, valid Cohort and try to void it with a null reason
Cohort exampleCohort = service.getCohort("Example Cohort");
assertNotNull(exampleCohort);
assertFalse(exampleCohort.isVoided());
try {
service.voidCohort(exampleCohort, null);
Assert.fail("voidCohort should fail with exception if reason is null.");
} catch (Exception e) {
}
// Now get the Cohort and try to void it with an empty reason
exampleCohort = service.getCohort("Example Cohort");
assertNotNull(exampleCohort);
assertFalse(exampleCohort.isVoided());
try {
service.voidCohort(exampleCohort, "");
Assert.fail("voidCohort should fail with exception if reason is empty");
} catch (Exception e) {
}
}
/** @see {@link CohortService#purgeCohort(Cohort)} */
@Test
@Verifies(value = "should delete cohort from database", method = "purgeCohort(Cohort)")
public void purgeCohort_shouldDeleteCohortFromDatabase() throws Exception {
executeDataSet(COHORT_XML);
List<Cohort> allCohorts = service.getAllCohorts(true);
assertEquals(2, allCohorts.size());
service.purgeCohort(allCohorts.get(0));
allCohorts = service.getAllCohorts(true);
assertEquals(1, allCohorts.size());
}
/** @see {@link CohortService#addPatientToCohort(Cohort,Patient)} */
@Test
@Verifies(
value = "should add a patient and save the cohort",
method = "addPatientToCohort(Cohort,Patient)")
public void addPatientToCohort_shouldAddAPatientAndSaveTheCohort() throws Exception {
executeDataSet(COHORT_XML);
// make a patient, add it using the method
Patient patientToAdd = new Patient(4);
service.addPatientToCohort(service.getCohort(2), patientToAdd);
// proof of "save the cohort": see if the patient is in the cohort
assertTrue(service.getCohort(2).contains(4));
}
/** @see {@link CohortService#getCohorts(String)} */
@Test
@Verifies(value = "should match cohorts by partial name", method = "getCohorts(String)")
public void getCohorts_shouldMatchCohortsByPartialName() throws Exception {
executeDataSet(COHORT_XML);
List<Cohort> matchedCohorts = service.getCohorts("Example");
assertEquals(2, matchedCohorts.size());
matchedCohorts = service.getCohorts("e Coh");
assertEquals(2, matchedCohorts.size());
matchedCohorts = service.getCohorts("hort");
assertEquals(2, matchedCohorts.size());
matchedCohorts = service.getCohorts("Examples");
assertEquals(0, matchedCohorts.size());
}
/** @see {@link CohortService#saveCohort(Cohort)} */
@Test
@Verifies(value = "should update an existing cohort", method = "saveCohort(Cohort)")
public void saveCohort_shouldUpdateAnExistingCohort() throws Exception {
executeDataSet(COHORT_XML);
// get and modify a cohort in the data set
String modifiedCohortDescription = "This description has been modified in a test";
Cohort cohortToModify = service.getCohort(2);
cohortToModify.setDescription(modifiedCohortDescription);
// save the modified cohort back to the data set, see if the modification is there
service.saveCohort(cohortToModify);
assertTrue(service.getCohort(2).getDescription().equals(modifiedCohortDescription));
}
/** @see {@link CohortService#voidCohort(Cohort,String)} */
@Test
@Verifies(value = "should void cohort", method = "voidCohort(Cohort,String)")
public void voidCohort_shouldVoidCohort() throws Exception {
executeDataSet(COHORT_XML);
// make sure we have a cohort that is not voided
List<Cohort> allCohorts = service.getAllCohorts(true);
assertNotNull(allCohorts);
assertEquals(2, allCohorts.size());
assertFalse(allCohorts.get(1).isVoided());
// now void the cohort and see if it's voided
Cohort voidedCohort = service.voidCohort(allCohorts.get(1), "voided for Test");
assertTrue(allCohorts.get(1).isVoided());
}
/** @see {@link CohortService#getCohortsContainingPatient(Patient)} */
@Test
@Verifies(
value = "should return cohorts that have given patient",
method = "getCohortsContainingPatient(Patient)")
public void getCohortsContainingPatient_shouldReturnCohortsThatHaveGivenPatient()
throws Exception {
executeDataSet(COHORT_XML);
Patient patientToAdd = new Patient(4);
service.addPatientToCohort(service.getCohort(2), patientToAdd);
assertTrue(service.getCohort(2).contains(patientToAdd));
List<Cohort> cohortsWithGivenPatient = service.getCohortsContainingPatient(patientToAdd);
assertTrue(cohortsWithGivenPatient.contains(service.getCohort(2)));
}
/** @see {@link CohortService#getCohort(String)} */
@Test
@Verifies(value = "should get cohort given a name", method = "getCohort(String)")
public void getCohort_shouldGetCohortGivenAName() throws Exception {
executeDataSet(COHORT_XML);
Cohort cohortToGet = service.getCohort("Example Cohort");
assertTrue(cohortToGet.getCohortId() == 2);
}
/** @see {@link CohortService#getCohort(Integer)} */
@Test
@Verifies(value = "should get cohort by id", method = "getCohort(Integer)")
public void getCohort_shouldGetCohortById() throws Exception {
executeDataSet(COHORT_XML);
Cohort cohortToGet = service.getCohort(2);
assertNotNull(cohortToGet);
assertTrue(cohortToGet.getCohortId() == 2);
}
/** @see {@link CohortService#getCohort(String)} */
@Test
@Verifies(value = "should only get non voided cohorts by name", method = "getCohort(String)")
public void getCohort_shouldOnlyGetNonVoidedCohortsByName() throws Exception {
executeDataSet(COHORT_XML);
// make sure we have two cohorts with the same name and the first is voided
List<Cohort> allCohorts = service.getAllCohorts(true);
assertNotNull(allCohorts);
assertEquals(2, allCohorts.size());
assertTrue(allCohorts.get(0).isVoided());
assertFalse(allCohorts.get(1).isVoided());
// now do the actual test: getCohort by name and expect a non voided cohort
Cohort exampleCohort = service.getCohort("Example Cohort");
assertNotNull(exampleCohort);
assertEquals(2, exampleCohort.size());
assertFalse(exampleCohort.isVoided());
}
/** @see {@link CohortService#getAllCohorts()} */
@Test
@Verifies(value = "should not return any voided cohorts", method = "getAllCohorts()")
public void getAllCohorts_shouldNotReturnAnyVoidedCohorts() throws Exception {
executeDataSet(COHORT_XML);
// make sure we have two cohorts, the first of which is voided
List<Cohort> allCohorts = service.getAllCohorts(true);
assertNotNull(allCohorts);
assertEquals(2, allCohorts.size());
assertTrue(allCohorts.get(0).isVoided());
assertFalse(allCohorts.get(1).isVoided());
// now call the target method and see if the voided cohort shows up
allCohorts = service.getAllCohorts();
assertNotNull(allCohorts);
// only the non-voided cohort should be returned
assertEquals(1, allCohorts.size());
assertFalse(allCohorts.get(0).isVoided());
}
/** @see {@link CohortService#addPatientToCohort(Cohort,Patient)} */
@Test
@Verifies(
value = "should not fail if cohort already contains patient",
method = "addPatientToCohort(Cohort,Patient)")
public void addPatientToCohort_shouldNotFailIfCohortAlreadyContainsPatient() throws Exception {
executeDataSet(COHORT_XML);
// make a patient, add it using the method
Patient patientToAdd = new Patient(4);
service.addPatientToCohort(service.getCohort(2), patientToAdd);
assertTrue(service.getCohort(2).contains(4));
// do it again to see if it fails
try {
service.addPatientToCohort(service.getCohort(2), patientToAdd);
} catch (Exception e) {
Assert.fail("addPatientToCohort(Cohort,Patient) fails when cohort already contains patient.");
}
}
/** @see {@link CohortService#getCohorts(String)} */
@Test
@Verifies(value = "should never return null", method = "getCohorts(String)")
public void getCohorts_shouldNeverReturnNull() throws Exception {
executeDataSet(COHORT_XML);
String invalidFragment = "Not Present";
// data set should have two cohorts, one of which is voided
List<Cohort> allCohorts = service.getCohorts(invalidFragment);
assertNotNull(allCohorts);
}
/** @see {@link CohortService#getAllCohorts(null)} */
@Test
@Verifies(value = "should return all cohorts and voided", method = "getAllCohorts(null)")
public void getAllCohorts_shouldReturnAllCohortsAndVoided() throws Exception {
executeDataSet(COHORT_XML);
// data set should have two cohorts, one of which is voided
List<Cohort> allCohorts = service.getAllCohorts(true);
assertNotNull(allCohorts);
assertEquals(2, allCohorts.size());
assertTrue(allCohorts.get(0).isVoided());
assertFalse(allCohorts.get(1).isVoided());
// if called with false parameter, should not return the voided one
allCohorts = service.getAllCohorts(false);
assertNotNull(allCohorts);
// only the non-voided cohort should be returned
assertEquals(1, allCohorts.size());
assertFalse(allCohorts.get(0).isVoided());
}
/**
* @verifies {@link CohortService#removePatientFromCohort(Cohort,Patient)} test = should not fail
* if cohort does not contain patient
*/
@Test
@Verifies(
value = "should not fail if cohort doesn't contain patient",
method = "removePatientFromCohort(Cohort,Patient)")
public void removePatientFromCohort_shouldNotFailIfCohortDoesNotContainPatient()
throws Exception {
executeDataSet(COHORT_XML);
// make a patient
Patient patientToAddThenRemove = new Patient(4);
// verify that the patient is not already in the Cohort
assertFalse(service.getCohort(2).contains(patientToAddThenRemove));
// try to remove it from the cohort without failing
try {
service.removePatientFromCohort(service.getCohort(2), patientToAddThenRemove);
} catch (Exception e) {
Assert.fail(
"removePatientFromCohort(Cohort,Patient) should not fail if cohort doesn't contain patient");
}
}
/** @see {@link CohortService#saveCohort(Cohort)} */
@Test
@Verifies(value = "should create new cohorts", method = "saveCohort(Cohort)")
public void saveCohort_shouldCreateNewCohorts() throws Exception {
executeDataSet(COHORT_XML);
// make sure we have two cohorts
List<Cohort> allCohorts = service.getAllCohorts(true);
assertNotNull(allCohorts);
assertEquals(2, allCohorts.size());
// make and save a new one
Integer[] ids = {2, 3};
Cohort newCohort = new Cohort("a third cohort", "a cohort to add for testing", ids);
service.saveCohort(newCohort);
// see if the new cohort shows up in the list of cohorts
allCohorts = service.getAllCohorts(true);
assertNotNull(allCohorts);
assertEquals(3, allCohorts.size());
}
/** @see {@link CohortService#getCohort(String)} */
@Test
@Verifies(
value = "should get the nonvoided cohort if two exist with same name",
method = "getCohort(String)")
public void getCohort_shouldGetTheNonvoidedCohortIfTwoExistWithSameName() throws Exception {
executeDataSet(COHORT_XML);
// check to see if both cohorts have the same name and if one is voided
List<Cohort> allCohorts = service.getAllCohorts(true);
assertNotNull(allCohorts);
assertEquals(allCohorts.get(0).getName(), allCohorts.get(1).getName());
assertTrue(allCohorts.get(0).isVoided());
assertFalse(allCohorts.get(1).isVoided());
// the non-voided cohort should have an id of 2
assertTrue(allCohorts.get(1).getCohortId() == 2);
// ask for the cohort by name
Cohort cohortToGet = service.getCohort("Example Cohort");
// see if the non-voided one got returned
assertTrue(cohortToGet.getCohortId() == 2);
}
/**
* @verifies {@link CohortService#getAllCohorts()} test = should get all nonvoided cohorts in
* database
*/
@Test
@Verifies(value = "should get all nonvoided cohorts in database", method = "getAllCohorts()")
public void getAllCohorts_shouldGetAllNonvoidedCohortsInDatabase() throws Exception {
executeDataSet(COHORT_XML);
// call the method
List<Cohort> allCohorts = service.getAllCohorts();
assertNotNull(allCohorts);
// there is only one non-voided cohort in the data set
assertEquals(1, allCohorts.size());
assertFalse(allCohorts.get(0).isVoided());
}
/** @see {@link CohortService#voidCohort(Cohort,String)} */
@Test
@Verifies(
value = "should not change an already voided cohort",
method = "voidCohort(Cohort,String)")
public void voidCohort_shouldNotChangeAnAlreadyVoidedCohort() throws Exception {
executeDataSet(COHORT_XML);
// make sure we have an already voided cohort
List<Cohort> allCohorts = service.getAllCohorts(true);
assertNotNull(allCohorts);
assertEquals(2, allCohorts.size());
assertTrue(allCohorts.get(0).isVoided());
// Make sure the void reason is different from the reason to be given in the test
assertNotNull(allCohorts.get(0).getVoidReason());
String reasonAlreadyVoided = allCohorts.get(0).getVoidReason();
String voidedForTest = "Voided for test";
assertFalse(voidedForTest.equals(reasonAlreadyVoided));
// Try to void and see if the void reason changes as a result
Cohort voidedCohort = service.voidCohort(allCohorts.get(0), voidedForTest);
assertFalse(voidedCohort.getVoidReason().equals(voidedForTest));
assertTrue(voidedCohort.getVoidReason().equals(reasonAlreadyVoided));
}
/** @see {@link CohortService#evaluate(CohortDefinition,EvaluationContext)} */
@Test
@SkipBaseSetup
@Verifies(
value = "should return all patients with blank patient search cohort definition provider",
method = "evaluate(CohortDefinition,EvaluationContext)")
public void evaluate_shouldReturnAllPatientsWithBlankPatientSearchCohortDefinitionProvider()
throws Exception {
initializeInMemoryDatabase();
executeDataSet(CREATE_PATIENT_XML);
authenticate();
CohortDefinition def = PatientSearch.createFilterSearch(PatientCharacteristicFilter.class);
Cohort result = service.evaluate(def, null);
assertNotNull("Should not return null", result);
assertEquals("Should return one member", 1, result.size());
}
/**
* @verifies {@link CohortService#removePatientFromCohort(Cohort,Patient)} test = should save
* cohort after removing patient
*/
@Test
@Verifies(
value = "should save cohort after removing patient",
method = "removePatientFromCohort(Cohort,Patient)")
public void removePatientFromCohort_shouldSaveCohortAfterRemovingPatient() throws Exception {
executeDataSet(COHORT_XML);
// make a patient, add it using the method
Patient patientToAddThenRemove = new Patient(4);
service.addPatientToCohort(service.getCohort(2), patientToAddThenRemove);
assertTrue(service.getCohort(2).contains(patientToAddThenRemove));
service.removePatientFromCohort(service.getCohort(2), patientToAddThenRemove);
assertFalse(service.getCohort(2).contains(patientToAddThenRemove));
}
/** @see {@link CohortService#getCohortsContainingPatient(Patient)} */
@Test
@Verifies(
value = "should not return voided cohorts",
method = "getCohortsContainingPatient(Patient)")
public void getCohortsContainingPatient_shouldNotReturnVoidedCohorts() throws Exception {
executeDataSet(COHORT_XML);
// make sure we have two cohorts, the first of which is voided
assertTrue(service.getCohort(1).isVoided());
assertFalse(service.getCohort(2).isVoided());
// add a patient to both cohorts
Patient patientToAdd = new Patient(4);
service.addPatientToCohort(service.getCohort(1), patientToAdd);
service.addPatientToCohort(service.getCohort(2), patientToAdd);
assertTrue(service.getCohort(1).contains(patientToAdd));
assertTrue(service.getCohort(2).contains(patientToAdd));
// call the method and it should not return the voided cohort
List<Cohort> cohortsWithPatientAdded = service.getCohortsContainingPatient(patientToAdd);
assertNotNull(cohortsWithPatientAdded);
assertFalse(cohortsWithPatientAdded.contains(service.getCohort(1)));
}