Examples with SampleReferenceDto de.symeda.sormas.api.sample.SampleReferenceDto used on opensource projects

Example 1 with SampleReferenceDto

use of de.symeda.sormas.api.sample.SampleReferenceDto in project SORMAS-Project by hzi-braunschweig.

the class SampleController method addReferredFromButton.

/**
 * @param editForm
 *            the edit form to attach the 'Referred from' button to.
 * @param navigation
 *            instructions for what shall happen when the user chooses to open the related sample
 */
public void addReferredFromButton(CommitDiscardWrapperComponent<SampleEditForm> editForm, Consumer<SampleDto> navigation) {
    SampleReferenceDto referredFromRef = FacadeProvider.getSampleFacade().getReferredFrom(editForm.getWrappedComponent().getValue().getUuid());
    if (referredFromRef != null) {
        SampleDto referredFrom = FacadeProvider.getSampleFacade().getSampleByUuid(referredFromRef.getUuid());
        FacilityReferenceDto referredFromLab = referredFrom.getLab();
        String referredButtonCaption = referredFromLab == null ? I18nProperties.getCaption(Captions.sampleReferredFromInternal) + " (" + DateFormatHelper.formatLocalDateTime(referredFrom.getSampleDateTime()) + ")" : I18nProperties.getCaption(Captions.sampleReferredFrom) + " " + referredFromLab.toString();
        Button referredButton = ButtonHelper.createButton("referredFrom", referredButtonCaption, event -> navigation.accept(referredFrom), ValoTheme.BUTTON_LINK, VSPACE_NONE);
        editForm.getWrappedComponent().addReferredFromButton(referredButton);
    }
}

Example 2 with SampleReferenceDto

use of de.symeda.sormas.api.sample.SampleReferenceDto in project SORMAS-Project by hzi-braunschweig.

the class SampleDataView method initView.

@Override
protected void initView(String params) {
    setHeightUndefined();
    String htmlLayout = LayoutUtil.fluidRow(LayoutUtil.fluidColumnLoc(8, 0, 12, 0, EDIT_LOC), LayoutUtil.fluidColumnLoc(4, 0, 6, 0, CASE_LOC), LayoutUtil.fluidColumnLoc(4, 0, 6, 0, CONTACT_LOC), LayoutUtil.fluidColumnLoc(4, 0, 6, 0, EVENT_PARTICIPANT_LOC), LayoutUtil.fluidColumnLoc(4, 0, 6, 0, PATHOGEN_TESTS_LOC), LayoutUtil.fluidColumnLoc(4, 0, 6, 0, ADDITIONAL_TESTS_LOC), LayoutUtil.fluidColumnLoc(4, 0, 6, 0, SORMAS_TO_SORMAS_LOC));
    DetailSubComponentWrapper container = new DetailSubComponentWrapper(() -> editComponent);
    container.setWidth(100, Unit.PERCENTAGE);
    container.setMargin(true);
    setSubComponent(container);
    CustomLayout layout = new CustomLayout();
    layout.addStyleName(CssStyles.ROOT_COMPONENT);
    layout.setTemplateContents(htmlLayout);
    layout.setWidth(100, Unit.PERCENTAGE);
    layout.setHeightUndefined();
    container.addComponent(layout);
    SampleDto sampleDto = FacadeProvider.getSampleFacade().getSampleByUuid(getSampleRef().getUuid());
    Disease disease = null;
    final CaseReferenceDto associatedCase = sampleDto.getAssociatedCase();
    if (associatedCase != null) {
        final CaseDataDto caseDto = FacadeProvider.getCaseFacade().getCaseDataByUuid(associatedCase.getUuid());
        disease = caseDto.getDisease();
        final CaseInfoLayout caseInfoLayout = new CaseInfoLayout(caseDto);
        caseInfoLayout.addStyleName(CssStyles.SIDE_COMPONENT);
        layout.addComponent(caseInfoLayout, CASE_LOC);
    }
    final ContactReferenceDto associatedContact = sampleDto.getAssociatedContact();
    if (associatedContact != null) {
        final ContactDto contactDto = FacadeProvider.getContactFacade().getByUuid(associatedContact.getUuid());
        disease = contactDto.getDisease();
        final ContactInfoLayout contactInfoLayout = new ContactInfoLayout(contactDto, UiFieldAccessCheckers.getDefault(contactDto.isPseudonymized()));
        contactInfoLayout.addStyleName(CssStyles.SIDE_COMPONENT);
        layout.addComponent(contactInfoLayout, CONTACT_LOC);
    }
    final EventParticipantReferenceDto associatedEventParticipant = sampleDto.getAssociatedEventParticipant();
    if (associatedEventParticipant != null) {
        final EventParticipantDto eventParticipantDto = FacadeProvider.getEventParticipantFacade().getEventParticipantByUuid(associatedEventParticipant.getUuid());
        final EventDto eventDto = FacadeProvider.getEventFacade().getEventByUuid(eventParticipantDto.getEvent().getUuid(), false);
        disease = eventDto.getDisease();
        final EventParticipantInfoLayout eventParticipantInfoLayout = new EventParticipantInfoLayout(eventParticipantDto, eventDto, UiFieldAccessCheckers.getDefault(eventParticipantDto.isPseudonymized()));
        eventParticipantInfoLayout.addStyleName(CssStyles.SIDE_COMPONENT);
        layout.addComponent(eventParticipantInfoLayout, EVENT_PARTICIPANT_LOC);
    }
    SampleController sampleController = ControllerProvider.getSampleController();
    editComponent = sampleController.getSampleEditComponent(getSampleRef().getUuid(), sampleDto.isPseudonymized(), disease, true);
    Consumer<Disease> createReferral = (relatedDisease) -> {
        // save changes before referral creation
        editComponent.commit();
        SampleDto committedSample = editComponent.getWrappedComponent().getValue();
        sampleController.createReferral(committedSample, relatedDisease);
    };
    Consumer<SampleDto> openReferredSample = referredSample -> sampleController.navigateToData(referredSample.getUuid());
    sampleController.addReferOrLinkToOtherLabButton(editComponent, disease, createReferral, openReferredSample);
    Consumer<SampleDto> navigate = targetSampleDto -> sampleController.navigateToData(targetSampleDto.getUuid());
    sampleController.addReferredFromButton(editComponent, navigate);
    editComponent.setMargin(new MarginInfo(false, false, true, false));
    editComponent.setWidth(100, Unit.PERCENTAGE);
    editComponent.getWrappedComponent().setWidth(100, Unit.PERCENTAGE);
    editComponent.addStyleName(CssStyles.MAIN_COMPONENT);
    layout.addComponent(editComponent, EDIT_LOC);
    BiConsumer<PathogenTestDto, Runnable> onSavedPathogenTest = (pathogenTestDto, callback) -> callback.run();
    // why? if(sampleDto.getSamplePurpose() !=null && sampleDto.getSamplePurpose().equals(SamplePurpose.EXTERNAL)) {
    Supplier<Boolean> createOrEditAllowedCallback = () -> editComponent.getWrappedComponent().getFieldGroup().isValid();
    SampleReferenceDto sampleReferenceDto = getSampleRef();
    PathogenTestListComponent pathogenTestListComponent = new PathogenTestListComponent(sampleReferenceDto);
    pathogenTestListComponent.addSideComponentCreateEventListener(e -> showNavigationConfirmPopupIfDirty(() -> {
        if (createOrEditAllowedCallback.get()) {
            ControllerProvider.getPathogenTestController().create(sampleReferenceDto, 0, pathogenTestListComponent::reload, onSavedPathogenTest);
        } else {
            Notification.show(null, I18nProperties.getString(Strings.messageFormHasErrorsPathogenTest), Notification.Type.ERROR_MESSAGE);
        }
    }));
    pathogenTestListComponent.addSideComponentEditEventListener(e -> showNavigationConfirmPopupIfDirty(() -> {
        String uuid = e.getUuid();
        if (createOrEditAllowedCallback.get()) {
            ControllerProvider.getPathogenTestController().edit(uuid, pathogenTestListComponent::reload, onSavedPathogenTest);
        } else {
            Notification.show(null, I18nProperties.getString(Strings.messageFormHasErrorsPathogenTest), Notification.Type.ERROR_MESSAGE);
        }
    }));
    layout.addComponent(new SideComponentLayout(pathogenTestListComponent), PATHOGEN_TESTS_LOC);
    if (UserProvider.getCurrent() != null && UserProvider.getCurrent().hasUserRight(UserRight.ADDITIONAL_TEST_VIEW) && FacadeProvider.getFeatureConfigurationFacade().isFeatureEnabled(FeatureType.ADDITIONAL_TESTS)) {
        AdditionalTestListComponent additionalTestList = new AdditionalTestListComponent(sampleReferenceDto.getUuid());
        additionalTestList.addStyleName(CssStyles.SIDE_COMPONENT);
        layout.addComponent(additionalTestList, ADDITIONAL_TESTS_LOC);
    }
    boolean sormasToSormasEnabled = FacadeProvider.getSormasToSormasFacade().isSharingCasesContactsAndSamplesEnabledForUser();
    if (sormasToSormasEnabled || sampleDto.getSormasToSormasOriginInfo() != null) {
        VerticalLayout sormasToSormasLocLayout = new VerticalLayout();
        sormasToSormasLocLayout.setMargin(false);
        sormasToSormasLocLayout.setSpacing(false);
        SormasToSormasListComponent sormasToSormasListComponent = new SormasToSormasListComponent(sampleDto);
        sormasToSormasListComponent.addStyleNames(CssStyles.SIDE_COMPONENT);
        sormasToSormasLocLayout.addComponent(sormasToSormasListComponent);
        layout.addComponent(sormasToSormasLocLayout, SORMAS_TO_SORMAS_LOC);
    }
    // }
    setSampleEditPermission(container);
}

Example 3 with SampleReferenceDto

use of de.symeda.sormas.api.sample.SampleReferenceDto in project SORMAS-Project by hzi-braunschweig.

the class SampleReadActivity method processActionbarMenu.

@Override
protected void processActionbarMenu() {
    super.processActionbarMenu();
    final MenuItem editMenu = getEditMenu();
    final ReferenceDto referenceDto = new SampleReferenceDto(getRootUuid());
    final Sample selectedSample = DatabaseHelper.getSampleDao().getByReferenceDto(referenceDto);
    if (editMenu != null) {
        if (SampleEditAuthorization.isSampleEditAllowed(selectedSample)) {
            editMenu.setVisible(true);
        } else {
            editMenu.setVisible(false);
        }
    }
}

Example 4 with SampleReferenceDto

use of de.symeda.sormas.api.sample.SampleReferenceDto in project SORMAS-Project by hzi-braunschweig.

the class LabMessageFacadeEjbMappingTest method testFromDto.

@Test
public void testFromDto() {
    LabMessageDto source = new LabMessageDto();
    TestReport testReport = new TestReport();
    TestReportDto testReportDto = TestReportFacadeEjb.toDto(testReport);
    Sample sample = new Sample();
    sample.setUuid("Uuid");
    SampleReferenceDto sampleRef = sample.toReference();
    User assignee = new User();
    assignee.setUuid("12345");
    when(sampleService.getByReferenceDto(sampleRef)).thenReturn(sample);
    when(testReportFacade.fromDto(eq(testReportDto), any(LabMessage.class), eq(false))).thenReturn(testReport);
    when(userservice.getByReferenceDto(assignee.toReference())).thenReturn(assignee);
    source.addTestReport(testReportDto);
    source.setCreationDate(new Date());
    source.setChangeDate(new Date());
    source.setUuid("UUID");
    source.setMessageDateTime(new Date());
    source.setSampleDateTime(new Date());
    source.setSampleReceivedDate(new Date());
    source.setLabSampleId("Lab Sample Id");
    source.setSampleMaterial(SampleMaterial.NASAL_SWAB);
    source.setSampleMaterialText("Sample material text");
    source.setLabName("Test Lab Name");
    source.setLabExternalId("Test Lab External Id");
    source.setLabPostalCode("Test Lab Postal Code");
    source.setLabCity("Test Lab City");
    source.setSpecimenCondition(SpecimenCondition.ADEQUATE);
    source.setTestedDisease(Disease.CORONAVIRUS);
    source.setPersonFirstName("Person First Name");
    source.setPersonLastName("Person Last Name");
    source.setPersonSex(Sex.OTHER);
    source.setPersonBirthDateDD(1);
    source.setPersonBirthDateDD(1);
    source.setPersonBirthDateYYYY(1970);
    source.setPersonPostalCode("Person Postal Code");
    source.setPersonCity("Person City");
    source.setPersonStreet("Person Street");
    source.setPersonHouseNumber("Person House Number");
    source.setPersonPhone("0123456789");
    source.setPersonEmail("mail@domain.com");
    source.setLabMessageDetails("Lab Message Details");
    source.setSampleOverallTestResult(PathogenTestResultType.POSITIVE);
    source.setSample(sampleRef);
    source.setAssignee(assignee.toReference());
    LabMessage result = sut.fromDto(source, null, true);
    assertEquals(source.getTestReports(), result.getTestReports());
    assertNotSame(source.getCreationDate().getTime(), result.getCreationDate().getTime());
    assertNotSame(source.getChangeDate(), result.getChangeDate());
    assertEquals(source.getUuid(), result.getUuid());
    assertEquals(source.getMessageDateTime(), result.getMessageDateTime());
    assertEquals(source.getSampleDateTime(), result.getSampleDateTime());
    assertEquals(source.getSampleReceivedDate(), result.getSampleReceivedDate());
    assertEquals(source.getLabSampleId(), result.getLabSampleId());
    assertEquals(source.getSampleMaterial(), result.getSampleMaterial());
    assertEquals(source.getSampleMaterialText(), result.getSampleMaterialText());
    assertEquals(source.getLabName(), result.getLabName());
    assertEquals(source.getLabExternalId(), result.getLabExternalId());
    assertEquals(source.getLabPostalCode(), result.getLabPostalCode());
    assertEquals(source.getLabCity(), result.getLabCity());
    assertEquals(source.getSpecimenCondition(), result.getSpecimenCondition());
    assertEquals(source.getTestedDisease(), result.getTestedDisease());
    assertEquals(source.getPersonFirstName(), result.getPersonFirstName());
    assertEquals(source.getPersonLastName(), result.getPersonLastName());
    assertEquals(source.getPersonSex(), result.getPersonSex());
    assertEquals(source.getPersonBirthDateDD(), result.getPersonBirthDateDD());
    assertEquals(source.getPersonBirthDateMM(), result.getPersonBirthDateMM());
    assertEquals(source.getPersonBirthDateYYYY(), result.getPersonBirthDateYYYY());
    assertEquals(source.getPersonPostalCode(), result.getPersonPostalCode());
    assertEquals(source.getPersonCity(), result.getPersonCity());
    assertEquals(source.getPersonStreet(), result.getPersonStreet());
    assertEquals(source.getPersonHouseNumber(), result.getPersonHouseNumber());
    assertEquals(source.getLabMessageDetails(), result.getLabMessageDetails());
    assertEquals(source.getSampleOverallTestResult(), result.getSampleOverallTestResult());
    assertEquals(sample, result.getSample());
    assertEquals(assignee.getUuid(), result.getAssignee().getUuid());
}

Example 5 with SampleReferenceDto

use of de.symeda.sormas.api.sample.SampleReferenceDto in project SORMAS-Project by hzi-braunschweig.

the class SampleDtoHelper method fillInnerFromAdo.

@Override
public void fillInnerFromAdo(SampleDto target, Sample source) {
    if (source.getAssociatedCase() != null) {
        Case associatedCase = DatabaseHelper.getCaseDao().queryForId(source.getAssociatedCase().getId());
        target.setAssociatedCase(CaseDtoHelper.toReferenceDto(associatedCase));
    } else {
        target.setAssociatedCase(null);
    }
    if (source.getReportingUser() != null) {
        User user = DatabaseHelper.getUserDao().queryForId(source.getReportingUser().getId());
        target.setReportingUser(UserDtoHelper.toReferenceDto(user));
    } else {
        target.setReportingUser(null);
    }
    if (source.getLab() != null) {
        Facility lab = DatabaseHelper.getFacilityDao().queryForId(source.getLab().getId());
        target.setLab(FacilityDtoHelper.toReferenceDto(lab));
    } else {
        target.setLab(null);
    }
    if (source.getReferredToUuid() != null) {
        target.setReferredTo(new SampleReferenceDto(source.getReferredToUuid()));
    } else {
        target.setReferredTo(null);
    }
    target.setLabDetails(source.getLabDetails());
    target.setLabSampleID(source.getLabSampleID());
    target.setFieldSampleID(source.getFieldSampleID());
    target.setSampleDateTime(source.getSampleDateTime());
    target.setReportDateTime(source.getReportDateTime());
    target.setSampleMaterial(source.getSampleMaterial());
    target.setSampleMaterialText(source.getSampleMaterialText());
    target.setSamplePurpose(source.getSamplePurpose());
    target.setShipmentDate(source.getShipmentDate());
    target.setShipmentDetails(source.getShipmentDetails());
    target.setReceivedDate(source.getReceivedDate());
    target.setSpecimenCondition(source.getSpecimenCondition());
    target.setNoTestPossibleReason(source.getNoTestPossibleReason());
    target.setComment(source.getComment());
    target.setSampleSource(source.getSampleSource());
    target.setShipped(source.isShipped());
    target.setReceived(source.isReceived());
    target.setPathogenTestResult(source.getPathogenTestResult());
    target.setPathogenTestingRequested(source.getPathogenTestingRequested());
    target.setAdditionalTestingRequested(source.getAdditionalTestingRequested());
    target.setRequestedPathogenTests(source.getRequestedPathogenTests());
    target.setRequestedAdditionalTests(source.getRequestedAdditionalTests());
    target.setRequestedOtherPathogenTests(source.getRequestedOtherPathogenTests());
    target.setRequestedOtherAdditionalTests(source.getRequestedOtherAdditionalTests());
    target.setReportLat(source.getReportLat());
    target.setReportLon(source.getReportLon());
    target.setReportLatLonAccuracy(source.getReportLatLonAccuracy());
    target.setSamplingReason(source.getSamplingReason());
    target.setSamplingReasonDetails(source.getSamplingReasonDetails());
    if (source.getSormasToSormasOriginInfo() != null) {
        target.setSormasToSormasOriginInfo(sormasToSormasOriginInfoDtoHelper.adoToDto(source.getSormasToSormasOriginInfo()));
    }
    target.setPseudonymized(source.isPseudonymized());
}