Examples with TestDataCreator de.symeda.sormas.ui.TestDataCreator used on opensource projects

Example 1 with TestDataCreator

use of de.symeda.sormas.ui.TestDataCreator in project SORMAS-Project by hzi-braunschweig.

the class GermanCaseClassificationValidatorTest method testCaseClassificationValidator.

@Test
@Ignore("see #2599")
public void testCaseClassificationValidator() {
    final TestDataCreator creator = new TestDataCreator();
    final TestDataCreator.RDCF rdcf = creator.createRDCF("region", "district", "community", "facility");
    final UserDto user = creator.createUser(rdcf.region.getUuid(), rdcf.district.getUuid(), rdcf.facility.getUuid(), "Surv", "Sup", UserRole.SURVEILLANCE_SUPERVISOR);
    final PersonDto cazePerson = creator.createPerson("Case", "Person");
    final CaseDataDto caze = creator.createCase(user.toReference(), cazePerson.toReference(), Disease.CORONAVIRUS, CaseClassification.PROBABLE, InvestigationStatus.PENDING, new Date(), rdcf);
    final SymptomsDto symptoms = SymptomsDto.build();
    caze.setSymptoms(symptoms);
    final GermanCaseClassificationValidator validator = new GermanCaseClassificationValidator(caze.getUuid(), INVALID_CASE_CLASSIFICATION);
    // assert classifications when no symptoms & no lab result
    valid(CaseClassification.NOT_CLASSIFIED, validator);
    invalid(CaseClassification.SUSPECT, validator);
    valid(CaseClassification.PROBABLE, validator);
    invalid(CaseClassification.CONFIRMED, validator);
    invalid(CaseClassification.CONFIRMED_NO_SYMPTOMS, validator);
    invalid(CaseClassification.CONFIRMED_UNKNOWN_SYMPTOMS, validator);
    valid(CaseClassification.NO_CASE, validator);
    // assert classifications when no symptoms & non-positive lab result
    final SampleDto sample = creator.createSample(caze.toReference(), new Date(), new Date(), user.toReference(), SampleMaterial.BLOOD, rdcf.facility.toReference());
    valid(CaseClassification.NOT_CLASSIFIED, validator);
    invalid(CaseClassification.SUSPECT, validator);
    valid(CaseClassification.PROBABLE, validator);
    invalid(CaseClassification.CONFIRMED, validator);
    invalid(CaseClassification.CONFIRMED_NO_SYMPTOMS, validator);
    invalid(CaseClassification.CONFIRMED_UNKNOWN_SYMPTOMS, validator);
    valid(CaseClassification.NO_CASE, validator);
    // assert classifications when no symptoms & positive lab result
    sample.setPathogenTestResult(PathogenTestResultType.POSITIVE);
    getSampleFacade().saveSample(sample);
    valid(CaseClassification.NOT_CLASSIFIED, validator);
    invalid(CaseClassification.SUSPECT, validator);
    valid(CaseClassification.PROBABLE, validator);
    invalid(CaseClassification.CONFIRMED, validator);
    invalid(CaseClassification.CONFIRMED_NO_SYMPTOMS, validator);
    valid(CaseClassification.CONFIRMED_UNKNOWN_SYMPTOMS, validator);
    valid(CaseClassification.NO_CASE, validator);
    // assert classifications when no symptoms & positive lab result
    sample.setPathogenTestResult(PathogenTestResultType.POSITIVE);
    getSampleFacade().saveSample(sample);
    valid(CaseClassification.NOT_CLASSIFIED, validator);
    invalid(CaseClassification.SUSPECT, validator);
    valid(CaseClassification.PROBABLE, validator);
    invalid(CaseClassification.CONFIRMED, validator);
    invalid(CaseClassification.CONFIRMED_NO_SYMPTOMS, validator);
    valid(CaseClassification.CONFIRMED_UNKNOWN_SYMPTOMS, validator);
    valid(CaseClassification.NO_CASE, validator);
    // assert classifications when other symptoms & positive lab result
    caze.getSymptoms().setFever(SymptomState.YES);
    CaseDataDto savedCase1 = getCaseFacade().save(caze);
    valid(CaseClassification.NOT_CLASSIFIED, validator);
    invalid(CaseClassification.SUSPECT, validator);
    valid(CaseClassification.PROBABLE, validator);
    invalid(CaseClassification.CONFIRMED, validator);
    valid(CaseClassification.CONFIRMED_NO_SYMPTOMS, validator);
    invalid(CaseClassification.CONFIRMED_UNKNOWN_SYMPTOMS, validator);
    valid(CaseClassification.NO_CASE, validator);
    // assert classifications when other & covid symptoms & positive lab result
    savedCase1.getSymptoms().setPneumoniaClinicalOrRadiologic(SymptomState.YES);
    CaseDataDto savedCase2 = getCaseFacade().save(savedCase1);
    valid(CaseClassification.NOT_CLASSIFIED, validator);
    valid(CaseClassification.SUSPECT, validator);
    valid(CaseClassification.PROBABLE, validator);
    valid(CaseClassification.CONFIRMED, validator);
    valid(CaseClassification.CONFIRMED_NO_SYMPTOMS, validator);
    invalid(CaseClassification.CONFIRMED_UNKNOWN_SYMPTOMS, validator);
    valid(CaseClassification.NO_CASE, validator);
    // assert classifications when other & covid symptoms & negative lab result
    sample.setPathogenTestResult(PathogenTestResultType.NEGATIVE);
    getSampleFacade().saveSample(sample);
    valid(CaseClassification.NOT_CLASSIFIED, validator);
    valid(CaseClassification.SUSPECT, validator);
    valid(CaseClassification.PROBABLE, validator);
    invalid(CaseClassification.CONFIRMED, validator);
    invalid(CaseClassification.CONFIRMED_NO_SYMPTOMS, validator);
    invalid(CaseClassification.CONFIRMED_UNKNOWN_SYMPTOMS, validator);
    valid(CaseClassification.NO_CASE, validator);
}

Example 2 with TestDataCreator

use of de.symeda.sormas.ui.TestDataCreator in project SORMAS-Project by hzi-braunschweig.

the class CaseImporterTest method testImportWithVaccinations.

@Test
@Ignore("Remove ignore once we have replaced H2, and feature properties can be changed by code")
public void testImportWithVaccinations() throws IOException, InterruptedException, CsvValidationException, InvalidColumnException, URISyntaxException {
    TestDataCreator creator = new TestDataCreator();
    TestDataCreator.RDCF rdcf = creator.createRDCF();
    creator.createFacility("Lab", FacilityType.LABORATORY, rdcf.region.toReference(), rdcf.district.toReference(), rdcf.community.toReference());
    UserDto user = creator.createUser(rdcf.region.getUuid(), rdcf.district.getUuid(), rdcf.facility.getUuid(), "Surv", "Sup", UserRole.SURVEILLANCE_SUPERVISOR);
    // import of 3 cases with different number of vaccinations
    File csvFile = new File(getClass().getClassLoader().getResource("sormas_case_import_test_vaccinations.csv").toURI());
    CaseImporterExtension caseImporter = new CaseImporterExtension(csvFile, true, user);
    ImportResultStatus importResult = caseImporter.runImport();
    assertEquals(caseImporter.stringBuilder.toString(), ImportResultStatus.COMPLETED, importResult);
    CaseDataDto case1 = getCaseFacade().getByExternalId("case1").get(0);
    CaseDataDto case2 = getCaseFacade().getByExternalId("case2").get(0);
    CaseDataDto case3 = getCaseFacade().getByExternalId("case3").get(0);
    List<VaccinationDto> case1Vaccinations = FacadeProvider.getVaccinationFacade().getAllVaccinations(case1.getPerson().getUuid(), Disease.CORONAVIRUS);
    assertEquals(0, case1Vaccinations.size());
    List<VaccinationDto> case2Vaccinations = FacadeProvider.getVaccinationFacade().getAllVaccinations(case2.getPerson().getUuid(), Disease.CORONAVIRUS);
    assertEquals(1, case2Vaccinations.size());
    assertEquals(Vaccine.COMIRNATY, case2Vaccinations.get(0).getVaccineName());
    assertNull(case2Vaccinations.get(0).getHealthConditions().getChronicPulmonaryDisease());
    List<VaccinationDto> case3Vaccinations = FacadeProvider.getVaccinationFacade().getAllVaccinations(case3.getPerson().getUuid(), Disease.CORONAVIRUS);
    assertEquals(2, case3Vaccinations.size());
    assertEquals(Vaccine.MRNA_1273, case3Vaccinations.get(0).getVaccineName());
    assertEquals(YesNoUnknown.YES, case3Vaccinations.get(0).getHealthConditions().getChronicPulmonaryDisease());
    assertEquals(Vaccine.MRNA_1273, case3Vaccinations.get(1).getVaccineName());
    assertNull(case3Vaccinations.get(1).getHealthConditions().getChronicPulmonaryDisease());
}

Example 3 with TestDataCreator

use of de.symeda.sormas.ui.TestDataCreator in project SORMAS-Project by hzi-braunschweig.

the class CaseImporterTest method testImportAllCases.

@Test
public void testImportAllCases() throws IOException, InvalidColumnException, InterruptedException, CsvValidationException, URISyntaxException {
    TestDataCreator creator = new TestDataCreator();
    TestDataCreator.RDCF rdcf = creator.createRDCF("Abia", "Umuahia North", "Urban Ward 2", "Anelechi Hospital");
    UserDto user = creator.createUser(rdcf.region.getUuid(), rdcf.district.getUuid(), rdcf.facility.getUuid(), "Surv", "Sup", UserRole.SURVEILLANCE_SUPERVISOR);
    // Successful import of 5 cases
    File csvFile = new File(getClass().getClassLoader().getResource("sormas_import_test_success.csv").toURI());
    CaseImporterExtension caseImporter = new CaseImporterExtension(csvFile, true, user);
    ImportResultStatus importResult = caseImporter.runImport();
    assertEquals(caseImporter.stringBuilder.toString(), ImportResultStatus.COMPLETED, importResult);
    assertEquals(5, getCaseFacade().count(null));
    // Failed import of 5 cases because of errors
    csvFile = new File(getClass().getClassLoader().getResource("sormas_import_test_errors.csv").toURI());
    caseImporter = new CaseImporterExtension(csvFile, true, user);
    importResult = caseImporter.runImport();
    assertEquals(ImportResultStatus.COMPLETED_WITH_ERRORS, importResult);
    assertEquals(5, getCaseFacade().count(null));
    // Similarity: skip
    csvFile = new File(getClass().getClassLoader().getResource("sormas_import_test_similarities.csv").toURI());
    caseImporter = new CaseImporterExtension(csvFile, true, user) {

        @Override
        protected <T extends PersonImportSimilarityResult> void handlePersonSimilarity(PersonDto newPerson, Consumer<T> resultConsumer, BiFunction<SimilarPersonDto, ImportSimilarityResultOption, T> createSimilarityResult, String infoText, UI currentUI) {
            resultConsumer.accept((T) new CaseImportSimilarityResult(null, null, ImportSimilarityResultOption.SKIP));
        }
    };
    importResult = caseImporter.runImport();
    assertEquals(ImportResultStatus.COMPLETED, importResult);
    assertEquals(5, getCaseFacade().count(null));
    assertEquals("ABC-DEF-GHI-19-5", getCaseFacade().getAllActiveCasesAfter(null).get(4).getEpidNumber());
    // Similarity: pick
    List<SimilarPersonDto> persons = FacadeProvider.getPersonFacade().getSimilarPersonDtos(new PersonSimilarityCriteria());
    csvFile = new File(getClass().getClassLoader().getResource("sormas_import_test_similarities.csv").toURI());
    caseImporter = new CaseImporterExtension(csvFile, true, user) {

        @Override
        protected <T extends PersonImportSimilarityResult> void handlePersonSimilarity(PersonDto newPerson, Consumer<T> resultConsumer, BiFunction<SimilarPersonDto, ImportSimilarityResultOption, T> createSimilarityResult, String infoText, UI currentUI) {
            List<SimilarPersonDto> entries = new ArrayList<>();
            for (SimilarPersonDto person : persons) {
                if (PersonHelper.areNamesSimilar(newPerson.getFirstName(), newPerson.getLastName(), person.getFirstName(), person.getLastName(), null)) {
                    entries.add(person);
                }
            }
            resultConsumer.accept((T) new CaseImportSimilarityResult(entries.get(0), null, ImportSimilarityResultOption.PICK));
        }

        @Override
        protected void handleCaseSimilarity(CaseImportSimilarityInput input, Consumer<CaseImportSimilarityResult> resultConsumer) {
            resultConsumer.accept(new CaseImportSimilarityResult(null, input.getSimilarCases().get(0), ImportSimilarityResultOption.PICK));
        }
    };
    importResult = caseImporter.runImport();
    assertEquals(ImportResultStatus.COMPLETED, importResult);
    assertEquals(5, getCaseFacade().count(null));
    assertEquals("ABC-DEF-GHI-19-5", getCaseFacade().getAllActiveCasesAfter(null).get(4).getEpidNumber());
    // Similarity: cancel
    csvFile = new File(getClass().getClassLoader().getResource("sormas_import_test_similarities.csv").toURI());
    caseImporter = new CaseImporterExtension(csvFile, true, user) {

        @Override
        protected <T extends PersonImportSimilarityResult> void handlePersonSimilarity(PersonDto newPerson, Consumer<T> resultConsumer, BiFunction<SimilarPersonDto, ImportSimilarityResultOption, T> createSimilarityResult, String infoText, UI currentUI) {
            resultConsumer.accept((T) new CaseImportSimilarityResult(null, null, ImportSimilarityResultOption.CANCEL));
        }
    };
    importResult = caseImporter.runImport();
    assertEquals(ImportResultStatus.CANCELED, importResult);
    assertEquals(5, getCaseFacade().count(null));
    assertEquals("ABC-DEF-GHI-19-5", getCaseFacade().getAllActiveCasesAfter(null).get(4).getEpidNumber());
    // Similarity: override
    csvFile = new File(getClass().getClassLoader().getResource("sormas_import_test_similarities.csv").toURI());
    caseImporter = new CaseImporterExtension(csvFile, true, user) {

        @Override
        protected <T extends PersonImportSimilarityResult> void handlePersonSimilarity(PersonDto newPerson, Consumer<T> resultConsumer, BiFunction<SimilarPersonDto, ImportSimilarityResultOption, T> createSimilarityResult, String infoText, UI currentUI) {
            List<SimilarPersonDto> entries = new ArrayList<>();
            for (SimilarPersonDto person : persons) {
                if (PersonHelper.areNamesSimilar(newPerson.getFirstName(), newPerson.getLastName(), person.getFirstName(), person.getLastName(), null)) {
                    entries.add(person);
                }
            }
            resultConsumer.accept((T) new CaseImportSimilarityResult(entries.get(0), null, ImportSimilarityResultOption.PICK));
        }

        @Override
        protected void handleCaseSimilarity(CaseImportSimilarityInput input, Consumer<CaseImportSimilarityResult> resultConsumer) {
            resultConsumer.accept(new CaseImportSimilarityResult(null, input.getSimilarCases().get(0), ImportSimilarityResultOption.OVERRIDE));
        }
    };
    importResult = caseImporter.runImport();
    assertEquals(ImportResultStatus.COMPLETED, importResult);
    assertEquals(5, getCaseFacade().count(null));
    assertEquals("ABC-DEF-GHI-19-10", getCaseFacade().getAllActiveCasesAfter(null).get(4).getEpidNumber());
    // Similarity: create -> fail because of duplicate epid number
    csvFile = new File(getClass().getClassLoader().getResource("sormas_import_test_similarities.csv").toURI());
    caseImporter = new CaseImporterExtension(csvFile, true, user) {

        @Override
        protected <T extends PersonImportSimilarityResult> void handlePersonSimilarity(PersonDto newPerson, Consumer<T> resultConsumer, BiFunction<SimilarPersonDto, ImportSimilarityResultOption, T> createSimilarityResult, String infoText, UI currentUI) {
            List<SimilarPersonDto> entries = new ArrayList<>();
            for (SimilarPersonDto person : persons) {
                if (PersonHelper.areNamesSimilar(newPerson.getFirstName(), newPerson.getLastName(), person.getFirstName(), person.getLastName(), null)) {
                    entries.add(person);
                }
            }
            resultConsumer.accept((T) new CaseImportSimilarityResult(entries.get(0), null, ImportSimilarityResultOption.PICK));
        }

        @Override
        protected void handleCaseSimilarity(CaseImportSimilarityInput input, Consumer<CaseImportSimilarityResult> resultConsumer) {
            resultConsumer.accept(new CaseImportSimilarityResult(null, null, ImportSimilarityResultOption.CREATE));
        }
    };
    importResult = caseImporter.runImport();
    assertEquals(ImportResultStatus.COMPLETED_WITH_ERRORS, importResult);
    assertEquals(5, getCaseFacade().count(null));
    assertEquals("ABC-DEF-GHI-19-10", getCaseFacade().getAllActiveCasesAfter(null).get(4).getEpidNumber());
    // Change epid number of the case in database to pass creation test
    CaseDataDto caze = getCaseFacade().getAllActiveCasesAfter(null).get(4);
    caze.setEpidNumber("ABC-DEF-GHI-19-99");
    getCaseFacade().save(caze);
    assertEquals("ABC-DEF-GHI-19-99", getCaseFacade().getAllActiveCasesAfter(null).get(4).getEpidNumber());
    // Similarity: create -> pass
    csvFile = new File(getClass().getClassLoader().getResource("sormas_import_test_similarities.csv").toURI());
    caseImporter = new CaseImporterExtension(csvFile, true, user);
    importResult = caseImporter.runImport();
    assertEquals(ImportResultStatus.COMPLETED, importResult);
    assertEquals(6, getCaseFacade().count(null));
    assertEquals("ABC-DEF-GHI-19-10", getCaseFacade().getAllActiveCasesAfter(null).get(5).getEpidNumber());
    // Successful import of a case with different infrastructure combinations
    creator.createRDCF("R1", "D1", "C1", "F1");
    creator.createRDCF("R2", "D2", "C2", "F2");
    creator.createRDCF("R3", "D3", "C3", "F3");
    csvFile = new File(getClass().getClassLoader().getResource("sormas_case_import_test_different_infrastructure.csv").toURI());
    caseImporter = new CaseImporterExtension(csvFile, true, user);
    importResult = caseImporter.runImport();
    assertEquals(ImportResultStatus.COMPLETED, importResult);
    assertEquals(7, getCaseFacade().count(null));
    // Successful import of 5 cases from a commented CSV file
    csvFile = new File(getClass().getClassLoader().getResource("sormas_import_test_comment_success.csv").toURI());
    caseImporter = new CaseImporterExtension(csvFile, true, user);
    importResult = caseImporter.runImport();
    assertEquals(caseImporter.stringBuilder.toString(), ImportResultStatus.COMPLETED, importResult);
    assertEquals(12, getCaseFacade().count(null));
}

Example 4 with TestDataCreator

use of de.symeda.sormas.ui.TestDataCreator in project SORMAS-Project by hzi-braunschweig.

the class CaseImporterTest method testLineListingImport.

@Test
public void testLineListingImport() throws IOException, InvalidColumnException, InterruptedException, CsvValidationException, URISyntaxException {
    TestDataCreator.RDCF rdcf = new TestDataCreator().createRDCF("Abia", "Bende", "Bende Ward", "Bende Maternity Home");
    UserDto user = creator.createUser(rdcf.region.getUuid(), rdcf.district.getUuid(), rdcf.facility.getUuid(), "Surv", "Sup", UserRole.SURVEILLANCE_SUPERVISOR);
    // Successful import of 5 cases
    File csvFile = new File(getClass().getClassLoader().getResource("sormas_import_test_line_listing.csv").toURI());
    CaseImporterExtension caseImporter = new CaseImporterExtension(csvFile, false, user);
    ImportResultStatus importResult = caseImporter.runImport();
    assertEquals(caseImporter.stringBuilder.toString(), ImportResultStatus.COMPLETED, importResult);
    assertEquals(5, getCaseFacade().count(null));
    // Successful import of 5 cases from commented CSV file
    csvFile = new File(getClass().getClassLoader().getResource("sormas_import_test_comment_line_listing.csv").toURI());
    caseImporter = new CaseImporterExtension(csvFile, false, user);
    importResult = caseImporter.runImport();
    assertEquals(caseImporter.stringBuilder.toString(), ImportResultStatus.COMPLETED, importResult);
    assertEquals(10, getCaseFacade().count(null));
}

Example 5 with TestDataCreator

use of de.symeda.sormas.ui.TestDataCreator in project SORMAS-Project by hzi-braunschweig.

the class CaseImporterTest method testImportAddressTypes.

@Test
public void testImportAddressTypes() throws IOException, InvalidColumnException, InterruptedException, CsvValidationException, URISyntaxException {
    TestDataCreator creator = new TestDataCreator();
    TestDataCreator.RDCF rdcf = creator.createRDCF("Saarland", "RV Saarbrücken", "Kleinblittersdorf", "Winterberg");
    UserDto user = creator.createUser(rdcf.region.getUuid(), rdcf.district.getUuid(), rdcf.facility.getUuid(), "Surv", "Sup", UserRole.SURVEILLANCE_SUPERVISOR);
    // import of 3 cases with different address types
    File csvFile = new File(getClass().getClassLoader().getResource("sormas_case_import_address_type.csv").toURI());
    CaseImporterExtension caseImporter = new CaseImporterExtension(csvFile, true, user);
    ImportResultStatus importResult = caseImporter.runImport();
    PersonDto casePerson1 = getPersonFacade().getPersonByUuid(getCaseFacade().getByExternalId("SL-DEF-GHI-19-1").get(0).getPerson().getUuid());
    PersonDto casePerson2 = getPersonFacade().getPersonByUuid(getCaseFacade().getByExternalId("SL-DEF-GHI-19-2").get(0).getPerson().getUuid());
    PersonDto casePerson3 = getPersonFacade().getPersonByUuid(getCaseFacade().getByExternalId("SL-DEF-GHI-19-3").get(0).getPerson().getUuid());
    assertTrue(CollectionUtils.isEmpty(casePerson1.getAddresses()));
    assertEquals("131", casePerson1.getAddress().getHouseNumber());
    assertTrue(CollectionUtils.isEmpty(casePerson2.getAddresses()));
    assertEquals("132", casePerson2.getAddress().getHouseNumber());
    assertTrue(casePerson3.getAddress().checkIsEmptyLocation());
    assertEquals(1, casePerson3.getAddresses().size());
    assertEquals("133", casePerson3.getAddresses().get(0).getHouseNumber());
}