Feature 4058 sample selection (SORMAS-Foundation#4144)

* SORMAS-Foundation#4058: Add sample selection

Author: ChristopherRiedel

sormas-api/src/main/java/de/symeda/sormas/api/i18n/Captions.java

@@ -1397,6 +1397,7 @@ public interface Captions {
 	String sampleAllSamples = "sampleAllSamples";
 	String sampleArchivedSamples = "sampleArchivedSamples";
 	String sampleAssociationType = "sampleAssociationType";
+	String sampleCreateNew = "sampleCreateNew";
 	String SampleExport_additionalTestingRequested = "SampleExport.additionalTestingRequested";
 	String SampleExport_altSgpt = "SampleExport.altSgpt";
 	String SampleExport_arterialVenousBloodGas = "SampleExport.arterialVenousBloodGas";
@@ -1481,6 +1482,7 @@ public interface Captions {
 	String sampleReferredTo = "sampleReferredTo";
 	String sampleReferredToInternal = "sampleReferredToInternal";
 	String sampleSamplesList = "sampleSamplesList";
+	String sampleSelect = "sampleSelect";
 	String sampleShipped = "sampleShipped";
 	String sampleSpecimenNotAdequate = "sampleSpecimenNotAdequate";
 	String sex = "sex";

sormas-api/src/main/java/de/symeda/sormas/api/i18n/Strings.java

@@ -409,6 +409,7 @@ public interface Strings {
 	String headingPickOrCreateEntry = "headingPickOrCreateEntry";
 	String headingPickOrCreateEvent = "headingPickOrCreateEvent";
 	String headingPickOrCreatePerson = "headingPickOrCreatePerson";
+	String headingPickOrCreateSample = "headingPickOrCreateSample";
 	String headingPointOfEntryImport = "headingPointOfEntryImport";
 	String headingPointOfEntryInformation = "headingPointOfEntryInformation";
 	String headingPrescriptionsDeleted = "headingPrescriptionsDeleted";
@@ -524,6 +525,7 @@ public interface Strings {
 	String infoPickOrCreateCaseNewCase = "infoPickOrCreateCaseNewCase";
 	String infoPickOrCreateEventForCase = "infoPickOrCreateEventForCase";
 	String infoPickOrCreateEventForContact = "infoPickOrCreateEventForContact";
+	String infoPickOrCreateSample = "infoPickOrCreateSample";
 	String infoPickOrCreateSuperordinateEventForEvent = "infoPickOrCreateSuperordinateEventForEvent";
 	String infoPopulationCollectionDate = "infoPopulationCollectionDate";
 	String infoPopulationDataView = "infoPopulationDataView";

sormas-api/src/main/java/de/symeda/sormas/api/sample/SampleFacade.java

@@ -66,5 +66,7 @@ public interface SampleFacade {
 
 	Boolean isSampleEditAllowed(String sampleUuid);
 
+	List<SampleDto> getByContactUuids(List<String> contactUuids);
+
 	boolean exists(String uuid);
 }

sormas-api/src/main/resources/captions.properties

@@ -1482,6 +1482,7 @@ Region.population=Population
 Region.externalID=External ID
 
 # Sample
+sampleCreateNew=Create new sample
 sampleIncludeTestOnCreation=Create test result for this sample now
 sampleNewSample=New sample
 sampleNoSamplesForCase=There are no samples for this case
@@ -1499,6 +1500,7 @@ sampleReferredShort=Referred
 sampleReferredTo=Referred to
 sampleReferredToInternal=Referred to internal sample
 sampleSamplesList=Samples list
+sampleSelect=Select sample
 sampleShipped=Shipped
 sampleSpecimenNotAdequate=Specimen not adequate
 sampleActiveSamples=Active samples

sormas-api/src/main/resources/strings.properties

@@ -416,6 +416,7 @@ headingPickOrCreateCase = Pick or Create a Case
 headingPickOrCreatePerson = Pick or create person
 headingPickOrCreateEvent = Pick or create event
 headingPickOrCreateEntry = Pick or create entry
+headingPickOrCreateSample = Pick or create sample
 headingPointOfEntryInformation = Point of entry information
 headingPrescriptionsDeleted = Prescriptions deleted
 headingReferSample = Refer sample to another laboratory
@@ -540,6 +541,7 @@ infoCaseIncidenceIncompatible = No population data is available for communities
 infoNoPathogenTests = No pathogen tests have been created for this sample
 infoPickOrCreateCase = There are existing cases in the database that seem very similar to the one you are about to create. Please have a look at the list of existing cases and verify that the case you want to create is not a duplicate of one of them. If you find a case that is most likely the same as yours, please <b>click on it in the list</b> and confirm.
 infoPickOrCreateCaseNewCase = Newly added case information
+infoPickOrCreateSample = The database already contains at least one sample that seems to be very similar to the details of the lab message.<br/><br/>Please look through the lists of samples. If you feel certain that one matches the lab message details, select it and click on the <i>Save</i> button. Otherwise, click on <i>Create new sample</i> to create a new sample for the entry.<br/><br/>If you are unsure, you can discard this window and cancel the process.
 infoSampleAdditionalTesting = Please tick every type of additional test you would like to be performed on this sample.
 infoSampleExport = Export the samples of all cases displayed in the table rows with an extended set of columns. This may take a while.
 infoSamplePathogenTesting = Please tick every type of pathogen test you would like to be performed on this sample.

sormas-backend/src/main/java/de/symeda/sormas/backend/sample/SampleFacadeEjb.java

@@ -210,6 +210,12 @@ public List<SampleDto> getByCaseUuids(List<String> caseUuids) {
 		return sampleService.getByCaseUuids(caseUuids).stream().map(c -> convertToDto(c, pseudonymizer)).collect(Collectors.toList());
 	}
 
+	@Override
+	public List<SampleDto> getByContactUuids(List<String> contactUuids) {
+		Pseudonymizer pseudonymizer = Pseudonymizer.getDefault(userService::hasRight);
+		return sampleService.getByContactUuids(contactUuids).stream().map(c -> convertToDto(c, pseudonymizer)).collect(Collectors.toList());
+	}
+
 	@Override
 	public boolean exists(String uuid) {
 		return sampleService.exists(uuid);

sormas-backend/src/main/java/de/symeda/sormas/backend/sample/SampleService.java

@@ -235,6 +235,19 @@ public List<Sample> getByCaseUuids(List<String> caseUuids) {
 		return em.createQuery(cq).getResultList();
 	}
 
+	public List<Sample> getByContactUuids(List<String> contactUuids) {
+
+		CriteriaBuilder cb = em.getCriteriaBuilder();
+		CriteriaQuery<Sample> cq = cb.createQuery(Sample.class);
+		Root<Sample> sampleRoot = cq.from(Sample.class);
+		Join<Sample, Contact> contactJoin = sampleRoot.join(Sample.ASSOCIATED_CONTACT, JoinType.LEFT);
+
+		Predicate filter = cb.and(createDefaultFilter(cb, sampleRoot), contactJoin.get(AbstractDomainObject.UUID).in(contactUuids));
+
+		cq.where(filter);
+		return em.createQuery(cq).getResultList();
+	}
+
 	public Map<PathogenTestResultType, Long> getNewTestResultCountByResultType(List<Long> caseIds) {
 
 		if (CollectionUtils.isEmpty(caseIds)) {

sormas-ui/src/main/java/de/symeda/sormas/ui/labmessage/LabMessageController.java

@@ -1,5 +1,6 @@
 package de.symeda.sormas.ui.labmessage;
 
+import java.util.Arrays;
 import java.util.List;
 
 import com.vaadin.server.Sizeable;
@@ -28,14 +29,17 @@
 import de.symeda.sormas.api.labmessage.SimilarEntriesDto;
 import de.symeda.sormas.api.person.PersonDto;
 import de.symeda.sormas.api.sample.PathogenTestDto;
+import de.symeda.sormas.api.sample.SampleCriteria;
 import de.symeda.sormas.api.sample.SampleDto;
+import de.symeda.sormas.api.utils.pseudonymization.PseudonymizableDto;
 import de.symeda.sormas.ui.ControllerProvider;
 import de.symeda.sormas.ui.SormasUI;
 import de.symeda.sormas.ui.UserProvider;
 import de.symeda.sormas.ui.caze.CaseCreateForm;
 import de.symeda.sormas.ui.contact.ContactCreateForm;
 import de.symeda.sormas.ui.samples.PathogenTestForm;
 import de.symeda.sormas.ui.samples.SampleCreateForm;
+import de.symeda.sormas.ui.samples.SampleSelectionField;
 import de.symeda.sormas.ui.utils.CommitDiscardWrapperComponent;
 import de.symeda.sormas.ui.utils.DateTimeField;
 import de.symeda.sormas.ui.utils.VaadinUiUtil;
@@ -112,6 +116,7 @@ private void pickOrCreateEntry(
 		EntrySelectionField selectField = new EntrySelectionField(labMessageDto, cases, contacts, eventParticipants);
 
 		final CommitDiscardWrapperComponent<EntrySelectionField> selectionField = new CommitDiscardWrapperComponent<>(selectField);
+		selectionField.getCommitButton().setCaption(I18nProperties.getCaption(Captions.actionConfirm));
 		selectionField.setWidth(1280, Sizeable.Unit.PIXELS);
 		selectionField.addCommitListener(() -> {
 			SimilarEntriesDto similarEntriesDto = selectField.getValue();
@@ -120,9 +125,27 @@ private void pickOrCreateEntry(
 			} else if (similarEntriesDto.isNewContact()) {
 				createContact(labMessageDto, person);
 			} else if (similarEntriesDto.getCaze() != null) {
-				createSample(FacadeProvider.getCaseFacade().getCaseDataByUuid(similarEntriesDto.getCaze().getUuid()), labMessageDto);
+				CaseDataDto caseDto = FacadeProvider.getCaseFacade().getCaseDataByUuid(similarEntriesDto.getCaze().getUuid());
+				SampleCriteria criteria = new SampleCriteria();
+				criteria.caze(caseDto.toReference());
+				criteria.setDisease(caseDto.getDisease());
+				List<SampleDto> samples = FacadeProvider.getSampleFacade().getByCaseUuids(Arrays.asList(caseDto.getUuid()));
+				if (samples.isEmpty()) {
+					createSample(caseDto, labMessageDto);
+				} else {
+					pickOrCreateSample(caseDto, labMessageDto, samples);
+				}
 			} else if (similarEntriesDto.getContact() != null) {
-				createSample(FacadeProvider.getContactFacade().getContactByUuid(similarEntriesDto.getContact().getUuid()), labMessageDto);
+				ContactDto contactDto = FacadeProvider.getContactFacade().getContactByUuid(similarEntriesDto.getContact().getUuid());
+				SampleCriteria criteria = new SampleCriteria();
+				criteria.contact(contactDto.toReference());
+				criteria.setDisease(contactDto.getDisease());
+				List<SampleDto> samples = FacadeProvider.getSampleFacade().getByContactUuids(Arrays.asList(contactDto.getUuid()));
+				if (samples.isEmpty()) {
+					createSample(contactDto, labMessageDto);
+				} else {
+					pickOrCreateSample(contactDto, labMessageDto, samples);
+				}
 			}
 		});
 
@@ -134,6 +157,34 @@ private void pickOrCreateEntry(
 		VaadinUiUtil.showModalPopupWindow(selectionField, I18nProperties.getString(Strings.headingPickOrCreateEntry));
 	}
 
+	private void pickOrCreateSample(PseudonymizableDto dto, LabMessageDto labMessageDto, List<SampleDto> samples) {
+		SampleSelectionField selectField = new SampleSelectionField(samples, I18nProperties.getString(Strings.infoPickOrCreateSample));
+
+		Window window = VaadinUiUtil.createPopupWindow();
+
+		final CommitDiscardWrapperComponent<EntrySelectionField> selectionField = new CommitDiscardWrapperComponent(selectField);
+		selectionField.getCommitButton().setCaption(I18nProperties.getCaption(Captions.actionConfirm));
+		selectionField.setWidth(1280, Sizeable.Unit.PIXELS);
+		selectionField.addCommitListener(() -> {
+			SampleDto sampleDto = selectField.getValue();
+			if (sampleDto != null) {
+				createPathogenTest(sampleDto, labMessageDto);
+			} else if (CaseDataDto.class.equals(dto.getClass())) {
+				createSample((CaseDataDto) dto, labMessageDto);
+			} else if (ContactDto.class.equals(dto.getClass())) {
+				createSample((ContactDto) dto, labMessageDto);
+			}
+			window.close();
+		});
+		selectField.setSelectionChangeCallback((commitAllowed) -> {
+			selectionField.getCommitButton().setEnabled(commitAllowed);
+		});
+		selectionField.getCommitButton().setEnabled(false);
+		selectionField.addDiscardListener(() -> window.close());
+
+		showFormWithLabMessage(labMessageDto, selectionField, window, I18nProperties.getString(Strings.headingPickOrCreateSample));
+	}
+
 	private void createCase(LabMessageDto labMessageDto, PersonDto person) {
 		CommitDiscardWrapperComponent<CaseCreateForm> caseCreateComponent =
 			ControllerProvider.getCaseController().getCaseCreateComponent(null, null, null, true);
@@ -161,7 +212,7 @@ private void createCase(LabMessageDto labMessageDto, PersonDto person) {
 		caseCreateComponent.getWrappedComponent().setValue(caseDto);
 		caseCreateComponent.getWrappedComponent().setPerson(person);
 
-		showCreateForm(labMessageDto, caseCreateComponent, window, I18nProperties.getString(Strings.headingCreateNewCase));
+		showFormWithLabMessage(labMessageDto, caseCreateComponent, window, I18nProperties.getString(Strings.headingCreateNewCase));
 	}
 
 	private void createContact(LabMessageDto labMessageDto, PersonDto person) {
@@ -191,12 +242,13 @@ private void createContact(LabMessageDto labMessageDto, PersonDto person) {
 		contactCreateComponent.getWrappedComponent().setValue(contactDto);
 		contactCreateComponent.getWrappedComponent().setPerson(person);
 
-		showCreateForm(labMessageDto, contactCreateComponent, window, I18nProperties.getString(Strings.headingCreateNewContact));
+		showFormWithLabMessage(labMessageDto, contactCreateComponent, window, I18nProperties.getString(Strings.headingCreateNewContact));
 	}
 
-	private void showCreateForm(LabMessageDto labMessageDto, CommitDiscardWrapperComponent createComponent, Window window, String heading) {
+	private void showFormWithLabMessage(LabMessageDto labMessageDto, CommitDiscardWrapperComponent createComponent, Window window, String heading) {
 		LabMessageEditForm form = new LabMessageEditForm(true);
 		form.setValue(labMessageDto);
+		form.setWidth(550, Sizeable.Unit.PIXELS);
 		HorizontalLayout layout = new HorizontalLayout(form, createComponent);
 		layout.setMargin(true);
 		window.setContent(layout);
@@ -252,7 +304,7 @@ private void createSample(SampleDto sampleDto, LabMessageDto labMessageDto) {
 		});
 		sampleCreateComponent.addDiscardListener(() -> window.close());
 
-		showCreateForm(labMessageDto, sampleCreateComponent, window, I18nProperties.getString(Strings.headingCreateNewSample));
+		showFormWithLabMessage(labMessageDto, sampleCreateComponent, window, I18nProperties.getString(Strings.headingCreateNewSample));
 	}
 
 	private void createPathogenTest(SampleDto sampleDto, LabMessageDto labMessageDto) {
@@ -274,6 +326,6 @@ private void createPathogenTest(SampleDto sampleDto, LabMessageDto labMessageDto
 		pathogenTestCreateComponent.addDiscardListener(() -> window.close());
 		pathogenTestCreateComponent.getWrappedComponent().setValue(pathogenTestDto);
 
-		showCreateForm(labMessageDto, pathogenTestCreateComponent, window, I18nProperties.getString(Strings.headingCreatePathogenTestResult));
+		showFormWithLabMessage(labMessageDto, pathogenTestCreateComponent, window, I18nProperties.getString(Strings.headingCreatePathogenTestResult));
 	}
 }

sormas-ui/src/main/java/de/symeda/sormas/ui/labmessage/LabMessageEditForm.java

@@ -21,16 +21,10 @@ public class LabMessageEditForm extends AbstractEditForm<LabMessageDto> {
 	private final boolean readOnly;
 	private Label labMessageDetails;
 
-	public LabMessageEditForm() {
-		this(false);
-	}
-
 	public LabMessageEditForm(boolean readOnly) {
 
 		super(LabMessageDto.class, LabMessageDto.I18N_PREFIX);
 
-		setWidth(800, Unit.PIXELS);
-
 		this.readOnly = readOnly;
 	}
 

sormas-ui/src/main/java/de/symeda/sormas/ui/person/PersonController.java

@@ -30,6 +30,7 @@
 import de.symeda.sormas.api.FacadeProvider;
 import de.symeda.sormas.api.caze.CaseClassification;
 import de.symeda.sormas.api.caze.CaseDataDto;
+import de.symeda.sormas.api.i18n.Captions;
 import de.symeda.sormas.api.i18n.I18nProperties;
 import de.symeda.sormas.api.i18n.Strings;
 import de.symeda.sormas.api.person.PersonContext;
@@ -62,6 +63,9 @@ public void selectOrCreatePerson(final PersonDto person, String infoText, Consum
 			// TODO add user right parameter
 			final CommitDiscardWrapperComponent<PersonSelectionField> component =
 				new CommitDiscardWrapperComponent<PersonSelectionField>(personSelect);
+			if (!saveNewPerson) {
+				component.getCommitButton().setCaption(I18nProperties.getCaption(Captions.actionConfirm));
+			}
 			component.addCommitListener(new CommitListener() {
 
 				@Override