Examples with CaseIndexDto de.symeda.sormas.api.caze.CaseIndexDto used on opensource projects

Example 1 with CaseIndexDto

use of de.symeda.sormas.api.caze.CaseIndexDto in project SORMAS-Project by hzi-braunschweig.

the class CaseFacadeEjb method getIndexList.

@Override
public List<CaseIndexDto> getIndexList(CaseCriteria caseCriteria, Integer first, Integer max, List<SortProperty> sortProperties) {
    CriteriaQuery<CaseIndexDto> cq = listQueryBuilder.buildIndexCriteria(caseCriteria, sortProperties);
    List<CaseIndexDto> cases = QueryHelper.getResultList(em, cq, first, max);
    List<Long> caseIds = cases.stream().map(CaseIndexDto::getId).collect(Collectors.toList());
    Map<String, ExternalShareInfoCountAndLatestDate> survToolShareCountAndDates = null;
    if (externalSurveillanceToolGatewayFacade.isFeatureEnabled()) {
        survToolShareCountAndDates = externalShareInfoService.getCaseShareCountAndLatestDate(caseIds).stream().collect(Collectors.toMap(ExternalShareInfoCountAndLatestDate::getAssociatedObjectUuid, Function.identity()));
    }
    Pseudonymizer pseudonymizer = Pseudonymizer.getDefault(userService::hasRight, I18nProperties.getCaption(Captions.inaccessibleValue));
    for (CaseIndexDto caze : cases) {
        if (survToolShareCountAndDates != null) {
            ExternalShareInfoCountAndLatestDate survToolShareCountAndDate = survToolShareCountAndDates.get(caze.getUuid());
            if (survToolShareCountAndDate != null) {
                caze.setSurveillanceToolShareCount(survToolShareCountAndDate.getCount());
                caze.setSurveillanceToolLastShareDate(survToolShareCountAndDate.getLatestDate());
                caze.setSurveillanceToolStatus(survToolShareCountAndDate.getLatestStatus());
            }
        }
        Boolean isInJurisdiction = caze.getInJurisdiction();
        pseudonymizer.pseudonymizeDto(CaseIndexDto.class, caze, isInJurisdiction, c -> pseudonymizer.pseudonymizeDto(AgeAndBirthDateDto.class, caze.getAgeAndBirthDate(), isInJurisdiction, null));
    }
    return cases;
}

Example 2 with CaseIndexDto

use of de.symeda.sormas.api.caze.CaseIndexDto in project SORMAS-Project by hzi-braunschweig.

the class CaseService method getCasesForDuplicateMerging.

public List<CaseIndexDto[]> getCasesForDuplicateMerging(CaseCriteria criteria, boolean ignoreRegion, double nameSimilarityThreshold) {
    CriteriaBuilder cb = em.getCriteriaBuilder();
    CriteriaQuery<Object[]> cq = cb.createQuery(Object[].class);
    Root<Case> root = cq.from(Case.class);
    final CaseQueryContext caseQueryContext = new CaseQueryContext(cb, cq, root);
    final CaseJoins<Case> joins = (CaseJoins<Case>) caseQueryContext.getJoins();
    Root<Case> root2 = cq.from(Case.class);
    Join<Case, Person> person = joins.getPerson();
    Join<Case, Person> person2 = root2.join(Case.PERSON, JoinType.LEFT);
    Join<Case, Region> responsibleRegion = joins.getResponsibleRegion();
    Join<Case, Region> responsibleRegion2 = root2.join(Case.RESPONSIBLE_REGION, JoinType.LEFT);
    Join<Case, Region> region = joins.getRegion();
    Join<Case, Region> region2 = root2.join(Case.REGION, JoinType.LEFT);
    Join<Case, Symptoms> symptoms = joins.getSymptoms();
    Join<Case, Symptoms> symptoms2 = root2.join(Case.SYMPTOMS, JoinType.LEFT);
    cq.distinct(true);
    // similarity:
    // * first & last name concatenated with whitespace. Similarity function with default threshold of 0.65D
    // uses postgres pg_trgm: https://www.postgresql.org/docs/9.6/pgtrgm.html
    // * same disease
    // * same region (optional)
    // * report date within 30 days of each other
    // * same sex or same birth date (when defined)
    // * same birth date (when fully defined)
    // * onset date within 30 days of each other (when defined)
    Predicate userFilter = createUserFilter(cb, cq, root);
    Predicate criteriaFilter = criteria != null ? createCriteriaFilter(criteria, caseQueryContext) : null;
    Expression<String> nameSimilarityExpr = cb.concat(person.get(Person.FIRST_NAME), " ");
    nameSimilarityExpr = cb.concat(nameSimilarityExpr, person.get(Person.LAST_NAME));
    Expression<String> nameSimilarityExpr2 = cb.concat(person2.get(Person.FIRST_NAME), " ");
    nameSimilarityExpr2 = cb.concat(nameSimilarityExpr2, person2.get(Person.LAST_NAME));
    Predicate nameSimilarityFilter = cb.gt(cb.function("similarity", double.class, nameSimilarityExpr, nameSimilarityExpr2), nameSimilarityThreshold);
    Predicate diseaseFilter = cb.equal(root.get(Case.DISEASE), root2.get(Case.DISEASE));
    Predicate regionFilter = cb.and(cb.equal(responsibleRegion.get(Region.ID), responsibleRegion2.get(Region.ID)), cb.or(cb.and(cb.isNull(region)), cb.equal(region.get(Region.ID), region2.get(Region.ID))));
    Predicate reportDateFilter = cb.lessThanOrEqualTo(cb.abs(cb.diff(cb.function("date_part", Long.class, cb.parameter(String.class, "date_type"), root.get(Case.REPORT_DATE)), cb.function("date_part", Long.class, cb.parameter(String.class, "date_type"), root2.get(Case.REPORT_DATE)))), SECONDS_30_DAYS);
    // // todo this should use PersonService.buildSimilarityCriteriaFilter
    // Sex filter: only when sex is filled in for both cases
    Predicate sexFilter = cb.or(cb.or(cb.isNull(person.get(Person.SEX)), cb.isNull(person2.get(Person.SEX))), cb.or(cb.equal(person.get(Person.SEX), Sex.UNKNOWN), cb.equal(person2.get(Person.SEX), Sex.UNKNOWN)), cb.equal(person.get(Person.SEX), person2.get(Person.SEX)));
    // Birth date filter: only when birth date is filled in for both cases
    Predicate birthDateFilter = cb.or(cb.or(cb.isNull(person.get(Person.BIRTHDATE_DD)), cb.isNull(person.get(Person.BIRTHDATE_MM)), cb.isNull(person.get(Person.BIRTHDATE_YYYY)), cb.isNull(person2.get(Person.BIRTHDATE_DD)), cb.isNull(person2.get(Person.BIRTHDATE_MM)), cb.isNull(person2.get(Person.BIRTHDATE_YYYY))), cb.and(cb.equal(person.get(Person.BIRTHDATE_DD), person2.get(Person.BIRTHDATE_DD)), cb.equal(person.get(Person.BIRTHDATE_MM), person2.get(Person.BIRTHDATE_MM)), cb.equal(person.get(Person.BIRTHDATE_YYYY), person2.get(Person.BIRTHDATE_YYYY))));
    // Onset date filter: only when onset date is filled in for both cases
    Predicate onsetDateFilter = cb.or(cb.or(cb.isNull(symptoms.get(Symptoms.ONSET_DATE)), cb.isNull(symptoms2.get(Symptoms.ONSET_DATE))), cb.lessThanOrEqualTo(cb.abs(cb.diff(cb.function("date_part", Long.class, cb.parameter(String.class, "date_type"), symptoms.get(Symptoms.ONSET_DATE)), cb.function("date_part", Long.class, cb.parameter(String.class, "date_type"), symptoms2.get(Symptoms.ONSET_DATE)))), SECONDS_30_DAYS));
    Predicate creationDateFilter = cb.or(cb.lessThan(root.get(Case.CREATION_DATE), root2.get(Case.CREATION_DATE)), cb.or(cb.lessThanOrEqualTo(root2.get(Case.CREATION_DATE), DateHelper.getStartOfDay(criteria.getCreationDateFrom())), cb.greaterThanOrEqualTo(root2.get(Case.CREATION_DATE), DateHelper.getEndOfDay(criteria.getCreationDateTo()))));
    Predicate filter = cb.and(createDefaultFilter(cb, root), createDefaultFilter(cb, root2));
    if (userFilter != null) {
        filter = cb.and(filter, userFilter);
    }
    if (filter != null) {
        filter = cb.and(filter, criteriaFilter);
    } else {
        filter = criteriaFilter;
    }
    if (filter != null) {
        filter = cb.and(filter, nameSimilarityFilter);
    } else {
        filter = nameSimilarityFilter;
    }
    filter = cb.and(filter, diseaseFilter);
    if (!ignoreRegion) {
        filter = cb.and(filter, regionFilter);
    }
    filter = cb.and(filter, reportDateFilter);
    filter = cb.and(filter, cb.and(sexFilter, birthDateFilter));
    filter = cb.and(filter, onsetDateFilter);
    filter = cb.and(filter, creationDateFilter);
    filter = cb.and(filter, cb.notEqual(root.get(Case.ID), root2.get(Case.ID)));
    cq.where(filter);
    cq.multiselect(root.get(Case.ID), root2.get(Case.ID), root.get(Case.CREATION_DATE));
    cq.orderBy(cb.desc(root.get(Case.CREATION_DATE)));
    List<Object[]> foundIds = em.createQuery(cq).setParameter("date_type", "epoch").getResultList();
    List<CaseIndexDto[]> resultList = new ArrayList<>();
    if (!foundIds.isEmpty()) {
        CriteriaQuery<CaseIndexDto> indexCasesCq = cb.createQuery(CaseIndexDto.class);
        Root<Case> indexRoot = indexCasesCq.from(Case.class);
        selectIndexDtoFields(new CaseQueryContext(cb, indexCasesCq, indexRoot));
        indexCasesCq.where(indexRoot.get(Case.ID).in(foundIds.stream().map(a -> Arrays.copyOf(a, 2)).flatMap(Arrays::stream).collect(Collectors.toSet())));
        Map<Long, CaseIndexDto> indexCases = em.createQuery(indexCasesCq).getResultStream().collect(Collectors.toMap(c -> c.getId(), Function.identity()));
        for (Object[] idPair : foundIds) {
            try {
                // Cloning is necessary here to allow us to add the same CaseIndexDto to the grid multiple times
                CaseIndexDto parent = (CaseIndexDto) indexCases.get(idPair[0]).clone();
                CaseIndexDto child = (CaseIndexDto) indexCases.get(idPair[1]).clone();
                if (parent.getCompleteness() == null && child.getCompleteness() == null || parent.getCompleteness() != null && (child.getCompleteness() == null || (parent.getCompleteness() >= child.getCompleteness()))) {
                    resultList.add(new CaseIndexDto[] { parent, child });
                } else {
                    resultList.add(new CaseIndexDto[] { child, parent });
                }
            } catch (CloneNotSupportedException e) {
                throw new RuntimeException(e);
            }
        }
    }
    return resultList;
}

Example 3 with CaseIndexDto

use of de.symeda.sormas.api.caze.CaseIndexDto in project SORMAS-Project by hzi-braunschweig.

the class CaseFacadeEjbTest method testGetIndexList.

@Test
public void testGetIndexList() {
    String districtName = "District";
    RDCF rdcf = creator.createRDCF("Region", districtName, "Community", "Facility");
    useSurveillanceOfficerLogin(rdcf);
    UserDto user = creator.createUser(rdcf.region.getUuid(), rdcf.district.getUuid(), rdcf.facility.getUuid(), "Surv", "Sup", UserRole.SURVEILLANCE_SUPERVISOR);
    String lastName = "Person";
    PersonDto cazePerson = creator.createPerson("Case", lastName);
    creator.createCase(user.toReference(), cazePerson.toReference(), Disease.EVD, CaseClassification.PROBABLE, InvestigationStatus.PENDING, new Date(), rdcf);
    creator.createCase(user.toReference(), cazePerson.toReference(), Disease.EVD, CaseClassification.PROBABLE, InvestigationStatus.PENDING, new Date(), rdcf, c -> c.setHealthFacilityDetails("abc"));
    creator.createCase(user.toReference(), cazePerson.toReference(), Disease.EVD, CaseClassification.PROBABLE, InvestigationStatus.PENDING, new Date(), rdcf, c -> c.setHealthFacilityDetails("xyz"));
    List<CaseIndexDto> results = getCaseFacade().getIndexList(null, 0, 100, Arrays.asList(new SortProperty(CaseIndexDto.DISEASE), new SortProperty(CaseIndexDto.PERSON_FIRST_NAME), new SortProperty(CaseIndexDto.RESPONSIBLE_DISTRICT_NAME), new SortProperty(CaseIndexDto.HEALTH_FACILITY_NAME, false), new SortProperty(CaseIndexDto.SURVEILLANCE_OFFICER_UUID)));
    // List should have one entry
    assertEquals(3, results.size());
    assertEquals(districtName, results.get(0).getResponsibleDistrictName());
    assertEquals(lastName, results.get(0).getPersonLastName());
    assertEquals("Facility - xyz", results.get(0).getHealthFacilityName());
    assertEquals("Facility - abc", results.get(1).getHealthFacilityName());
    assertEquals("Facility", results.get(2).getHealthFacilityName());
}

Example 4 with CaseIndexDto

use of de.symeda.sormas.api.caze.CaseIndexDto in project SORMAS-Project by hzi-braunschweig.

the class CaseFacadeEjbTest method testSearchCasesFreetext.

@Test
public void testSearchCasesFreetext() {
    RDCF rdcf = creator.createRDCF();
    final UserReferenceDto user = creator.createUser(rdcf, UserRole.SURVEILLANCE_OFFICER).toReference();
    CaseDataDto caze = creator.createCase(user, creator.createPerson().toReference(), rdcf);
    caze.setInternalToken("internalToken");
    caze.setExternalToken("externalToken");
    caze.setExternalID("externalID");
    getCaseFacade().save(caze);
    CaseDataDto secondCaze = creator.createCase(user, creator.createPerson().toReference(), rdcf);
    secondCaze.setInternalToken("internalToken2");
    getCaseFacade().save(secondCaze);
    List<CaseIndexDto> indexList = getCaseFacade().getIndexList(new CaseCriteria(), 0, 100, Collections.emptyList());
    // test several freetext variations
    assertEquals(2, indexList.size());
    CaseCriteria caseCriteria = new CaseCriteria();
    caseCriteria.setCaseLike("internal");
    List<CaseIndexDto> indexListFiltered = getCaseFacade().getIndexList(caseCriteria, 0, 100, Collections.emptyList());
    assertEquals(2, indexListFiltered.size());
    caseCriteria.setCaseLike("Token");
    indexListFiltered = getCaseFacade().getIndexList(caseCriteria, 0, 100, Collections.emptyList());
    assertEquals(2, indexListFiltered.size());
    caseCriteria.setCaseLike("externalToken");
    indexListFiltered = getCaseFacade().getIndexList(caseCriteria, 0, 100, Collections.emptyList());
    assertEquals(1, indexListFiltered.size());
    assertThat(indexListFiltered.get(0).getUuid(), is(caze.getUuid()));
    caseCriteria.setCaseLike("externalID");
    indexListFiltered = getCaseFacade().getIndexList(caseCriteria, 0, 100, Collections.emptyList());
    assertEquals(1, indexListFiltered.size());
    assertThat(indexListFiltered.get(0).getUuid(), is(caze.getUuid()));
    caseCriteria.setCaseLike("unmatchableString");
    indexListFiltered = getCaseFacade().getIndexList(caseCriteria, 0, 100, Collections.emptyList());
    assertEquals(0, indexListFiltered.size());
    caseCriteria.setCaseLike(caze.getUuid());
    indexListFiltered = getCaseFacade().getIndexList(caseCriteria, 0, 100, Collections.emptyList());
    assertEquals(1, indexListFiltered.size());
    assertThat(indexListFiltered.get(0).getUuid(), is(caze.getUuid()));
}

Example 5 with CaseIndexDto

use of de.symeda.sormas.api.caze.CaseIndexDto in project SORMAS-Project by hzi-braunschweig.

the class CaseFacadeEjbTest method testSearchCasesWithReducedQuarantine.

@Test
public void testSearchCasesWithReducedQuarantine() {
    RDCF rdcf = creator.createRDCF();
    CaseDataDto caze = creator.createCase(creator.createUser(rdcf, UserRole.SURVEILLANCE_OFFICER).toReference(), creator.createPerson().toReference(), rdcf);
    caze.setQuarantineReduced(true);
    getCaseFacade().save(caze);
    List<CaseIndexDto> indexList = getCaseFacade().getIndexList(new CaseCriteria(), 0, 100, Collections.emptyList());
    assertThat(indexList.get(0).getUuid(), is(caze.getUuid()));
    CaseCriteria caseCriteria = new CaseCriteria();
    caseCriteria.setWithReducedQuarantine(true);
    List<CaseIndexDto> indexListFiltered = getCaseFacade().getIndexList(caseCriteria, 0, 100, Collections.emptyList());
    assertThat(indexListFiltered.get(0).getUuid(), is(caze.getUuid()));
}