Examples with System org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System used on opensource projects

Example 91 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project openmrs-module-fhir2 by openmrs.

the class ConceptTranslatorImplTest method shouldNotTranslateUnknownMappingCode.

@Test
public void shouldNotTranslateUnknownMappingCode() {
    Collection<ConceptMap> conceptMaps = new ArrayList<>();
    ConceptMap conceptMap = mock(ConceptMap.class);
    conceptMaps.add(conceptMap);
    ConceptMapType conceptMapType = mock(ConceptMapType.class);
    conceptMapType.setName("SAME-AS");
    conceptMap.setConceptMapType(conceptMapType);
    ConceptSource conceptSource = mock(ConceptSource.class);
    when(concept.getConceptMappings()).thenReturn(conceptMaps);
    CodeableConcept result = conceptTranslator.toFhirResource(concept);
    assertThat(result, notNullValue());
    assertThat(result.getCoding(), hasSize(1));
    assertThat(result.getCoding(), not(hasItem(hasProperty("system", notNullValue()))));
}

Example 92 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project openmrs-module-fhir2 by openmrs.

the class ConditionTranslatorImplTest method shouldTranslateConditionCodeToOpenMrsConcept.

@Test
public void shouldTranslateConditionCodeToOpenMrsConcept() {
    CodeableConcept codeableConcept = new CodeableConcept();
    Coding coding = new Coding();
    coding.setCode(CODE.toString());
    coding.setSystem(SYSTEM);
    codeableConcept.addCoding(coding);
    fhirCondition.setCode(codeableConcept);
    Concept concept = new Concept();
    concept.setUuid(CONCEPT_UUID);
    concept.setConceptId(CODE);
    when(conceptService.getConceptByUuid(FhirConstants.CONDITION_OBSERVATION_CONCEPT_UUID)).thenReturn(concept);
    when(conceptTranslator.toOpenmrsType(codeableConcept)).thenReturn(concept);
    Obs condition = conditionTranslator.toOpenmrsType(fhirCondition);
    assertThat(condition, notNullValue());
    assertThat(condition.getValueCoded(), notNullValue());
    assertThat(condition.getValueCoded().getConceptId(), equalTo(CODE));
}

Example 93 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project openmrs-module-fhir2 by openmrs.

the class ConditionTranslatorImplTest method shouldTranslateConditionConceptToFhirType.

@Test
public void shouldTranslateConditionConceptToFhirType() {
    Concept concept = new Concept();
    concept.setUuid(CONCEPT_UUID);
    concept.setConceptId(CODE);
    CodeableConcept codeableConcept = new CodeableConcept();
    Coding coding = new Coding();
    coding.setCode(CODE.toString());
    coding.setSystem(SYSTEM);
    codeableConcept.addCoding(coding);
    openmrsCondition.setValueCoded(concept);
    when(conceptTranslator.toFhirResource(concept)).thenReturn(codeableConcept);
    org.hl7.fhir.r4.model.Condition condition = conditionTranslator.toFhirResource(openmrsCondition);
    assertThat(condition, notNullValue());
    assertThat(condition.getCode(), notNullValue());
    assertThat(condition.getCode().getCoding(), not(Collections.emptyList()));
    assertThat(condition.getCode().getCoding().get(0).getCode(), equalTo(CODE.toString()));
    assertThat(condition.getCode().getCoding().get(0).getSystem(), equalTo(SYSTEM));
}

Example 94 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project openmrs-module-fhir2 by openmrs.

the class ImmunizationTranslatorImpl method toOpenmrsType.

@Override
public Obs toOpenmrsType(@Nonnull Obs openmrsImmunization, @Nonnull Immunization fhirImmunization) {
    if (openmrsImmunization == null) {
        return null;
    }
    if (fhirImmunization == null) {
        return openmrsImmunization;
    }
    Patient patient = patientReferenceTranslator.toOpenmrsType(fhirImmunization.getPatient());
    if (patient == null) {
        final String errMsg;
        if (fhirImmunization.getPatient().hasReference()) {
            errMsg = "Could not find patient matching " + fhirImmunization.getPatient().getReference();
        } else {
            errMsg = "No patient was specified for this request";
        }
        throw createImmunizationRequestValidationError(errMsg);
    }
    List<ImmunizationPerformerComponent> performers = fhirImmunization.getPerformer();
    Provider provider = null;
    if (performers.size() > 1) {
        throw createImmunizationRequestValidationError("More than one performer was specified. Only a single performer is currently supported for each immunization.");
    } else if (performers.size() == 1) {
        ImmunizationPerformerComponent performer = performers.get(0);
        if (performer != null && performer.hasActor()) {
            provider = practitionerReferenceTranslator.toOpenmrsType(performer.getActor());
        }
    }
    final Visit visit;
    if (fhirImmunization.hasEncounter()) {
        visit = visitReferenceTranslator.toOpenmrsType(fhirImmunization.getEncounter());
    } else {
        visit = null;
    }
    if (visit == null) {
        final String errMsg;
        if (fhirImmunization.getEncounter().hasReference()) {
            errMsg = "Could not find visit matching " + fhirImmunization.getEncounter().getReference();
        } else {
            errMsg = "No encounter was specified for this request";
        }
        throw createImmunizationRequestValidationError(errMsg);
    }
    Location location = visit.getLocation();
    if (fhirImmunization.hasLocation()) {
        Location recordedLocation = locationReferenceTranslator.toOpenmrsType(fhirImmunization.getLocation());
        if (recordedLocation != null) {
            location = recordedLocation;
        }
    }
    if (!patient.equals(visit.getPatient())) {
        throw createImmunizationRequestValidationError("The visit '" + visit.getUuid() + "' does not belong to patient '" + patient.getUuid() + "'.");
    }
    EncounterType encounterType = helper.getImmunizationsEncounterType();
    // taking the visit's most recent immunization encounter
    Optional<Encounter> existingEncounter = visit.getEncounters().stream().filter(e -> encounterType.equals(e.getEncounterType())).max(Comparator.comparing(Encounter::getEncounterDatetime));
    final Provider encounterProvider = provider;
    final Location finalLocation = location;
    Encounter encounter = existingEncounter.orElseGet(() -> {
        final EncounterRole encounterRole = helper.getAdministeringEncounterRole();
        final Encounter newEncounter = new Encounter();
        newEncounter.setVisit(visit);
        newEncounter.setLocation(finalLocation);
        newEncounter.setEncounterType(encounterType);
        newEncounter.setPatient(patient);
        if (encounterProvider != null) {
            newEncounter.setProvider(encounterRole, encounterProvider);
        }
        if (visit.getStopDatetime() != null) {
            newEncounter.setEncounterDatetime(visit.getStopDatetime());
        } else {
            newEncounter.setEncounterDatetime(openmrsImmunization.getObsDatetime());
        }
        return newEncounter;
    });
    openmrsImmunization.setPerson(patient);
    openmrsImmunization.setLocation(location);
    openmrsImmunization.setEncounter(encounter);
    openmrsImmunization.getGroupMembers().forEach(obs -> {
        obs.setPerson(patient);
        obs.setLocation(finalLocation);
        obs.setEncounter(encounter);
    });
    Map<String, Obs> members = helper.getObsMembersMap(openmrsImmunization);
    Coding coding = fhirImmunization.getVaccineCode().getCoding().stream().filter(code -> StringUtils.isEmpty(code.getSystem())).reduce((code1, code2) -> {
        throw createImmunizationRequestValidationError("Multiple system-less coding found for the immunization's vaccine: " + code1.getCode() + " and " + code2.getCode() + ". No unique system concept could be identified as the coded answer.");
    }).orElseThrow(() -> createImmunizationRequestValidationError("Could not find a valid coding could be identified for this immunization."));
    {
        Obs obs = members.get(CIEL_984);
        if (obs == null) {
            obs = helper.addNewObs(openmrsImmunization, CIEL_984);
            members.put(CIEL_984, obs);
            obs.setValueCoded(conceptService.getConceptByUuid(coding.getCode()));
        } else if (obs.getId() == null) {
            obs.setValueCoded(conceptService.getConceptByUuid(coding.getCode()));
        } else {
            Concept newValue = conceptService.getConceptByUuid(coding.getCode());
            Concept prevValue = obs.getValueCoded();
            if (!newValue.equals(prevValue)) {
                obs = helper.replaceObs(openmrsImmunization, obs);
                obs.setValueCoded(newValue);
            }
        }
    }
    if (!fhirImmunization.hasOccurrenceDateTimeType() || !fhirImmunization.getOccurrenceDateTimeType().hasValue()) {
        throw createImmunizationRequestValidationError("An Immunization must have a valid occurrenceDateTime value");
    }
    {
        Obs obs = members.get(CIEL_1410);
        if (obs == null) {
            obs = helper.addNewObs(openmrsImmunization, CIEL_1410);
            members.put(CIEL_1410, obs);
            obs.setValueDatetime(fhirImmunization.getOccurrenceDateTimeType().getValue());
        } else if (obs.getId() == null) {
            obs.setValueDatetime(fhirImmunization.getOccurrenceDateTimeType().getValue());
        } else {
            Date newValue = fhirImmunization.getOccurrenceDateTimeType().getValue();
            Date prevValue = obs.getValueDatetime();
            if (!newValue.equals(prevValue)) {
                obs = helper.replaceObs(openmrsImmunization, obs);
                obs.setValueDatetime(newValue);
            }
        }
    }
    if (fhirImmunization.hasProtocolApplied()) {
        if (fhirImmunization.getProtocolApplied().size() != 1) {
            throw createImmunizationRequestValidationError("Either no protocol applied was found or multiple protocols applied were found. " + "Only one protocol is currently supported for each immunization.");
        }
        ImmunizationProtocolAppliedComponent protocolApplied = fhirImmunization.getProtocolApplied().get(0);
        if (protocolApplied.hasDoseNumber()) {
            {
                Obs obs = members.get(CIEL_1418);
                if (obs == null) {
                    obs = helper.addNewObs(openmrsImmunization, CIEL_1418);
                    members.put(CIEL_1418, obs);
                    obs.setValueNumeric(protocolApplied.getDoseNumberPositiveIntType().getValue().doubleValue());
                } else if (obs.getId() == null) {
                    obs.setValueNumeric(protocolApplied.getDoseNumberPositiveIntType().getValue().doubleValue());
                } else {
                    double newValue = protocolApplied.getDoseNumberPositiveIntType().getValue().doubleValue();
                    Double updatedValue = obs.getValueNumeric();
                    if (updatedValue != null && newValue != updatedValue) {
                        obs = helper.replaceObs(openmrsImmunization, obs);
                        obs.setValueNumeric(newValue);
                    }
                }
            }
        }
    } else {
        openmrsImmunization.removeGroupMember(members.get(CIEL_1418));
    }
    if (fhirImmunization.hasManufacturer() && fhirImmunization.getManufacturer().hasDisplay()) {
        {
            Obs obs = members.get(CIEL_1419);
            if (obs == null) {
                obs = helper.addNewObs(openmrsImmunization, CIEL_1419);
                members.put(CIEL_1419, obs);
                obs.setValueText(fhirImmunization.getManufacturer().getDisplay());
            } else if (obs.getId() == null) {
                obs.setValueText(fhirImmunization.getManufacturer().getDisplay());
            } else {
                String newValue = fhirImmunization.getManufacturer().getDisplay();
                String prevValue = obs.getValueText();
                if (!newValue.equals(prevValue)) {
                    obs = helper.replaceObs(openmrsImmunization, obs);
                    obs.setValueText(newValue);
                }
            }
        }
    } else {
        openmrsImmunization.removeGroupMember(members.get(CIEL_1419));
    }
    if (fhirImmunization.hasLotNumber()) {
        {
            Obs obs = members.get(CIEL_1420);
            if (obs == null) {
                obs = helper.addNewObs(openmrsImmunization, CIEL_1420);
                members.put(CIEL_1420, obs);
                obs.setValueText(fhirImmunization.getLotNumber());
            } else if (obs.getId() == null) {
                obs.setValueText(fhirImmunization.getLotNumber());
            } else {
                String newValue = fhirImmunization.getLotNumber();
                String prevValue = obs.getValueText();
                if (!newValue.equals(prevValue)) {
                    obs = helper.replaceObs(openmrsImmunization, obs);
                    obs.setValueText(newValue);
                }
            }
        }
    } else {
        openmrsImmunization.removeGroupMember(members.get(CIEL_1420));
    }
    if (fhirImmunization.hasExpirationDate()) {
        {
            Obs obs = members.get(CIEL_165907);
            if (obs == null) {
                obs = helper.addNewObs(openmrsImmunization, CIEL_165907);
                members.put(CIEL_165907, obs);
                obs.setValueDate(fhirImmunization.getExpirationDate());
            } else if (obs.getId() == null) {
                obs.setValueDate(fhirImmunization.getExpirationDate());
            } else {
                Date newValue = fhirImmunization.getExpirationDate();
                Date prevValue = obs.getValueDate();
                if (!newValue.equals(prevValue)) {
                    obs = helper.replaceObs(openmrsImmunization, obs);
                    obs.setValueDate(newValue);
                }
            }
        }
    } else {
        openmrsImmunization.removeGroupMember(members.get(CIEL_165907));
    }
    return openmrsImmunization;
}

Example 95 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project openmrs-module-fhir2 by openmrs.

the class ConditionTranslatorImpl_2_2Test method shouldTranslateConditionCodeToOpenMrsConcept.

@Test
public void shouldTranslateConditionCodeToOpenMrsConcept() {
    CodeableConcept codeableConcept = new CodeableConcept();
    Coding coding = new Coding();
    coding.setCode(CODE.toString());
    coding.setSystem(SYSTEM);
    codeableConcept.addCoding(coding);
    fhirCondition.setCode(codeableConcept);
    Concept concept = new Concept();
    concept.setUuid(CONCEPT_UUID);
    concept.setConceptId(CODE);
    when(conceptTranslator.toOpenmrsType(codeableConcept)).thenReturn(concept);
    org.openmrs.Condition condition = conditionTranslator.toOpenmrsType(fhirCondition);
    assertThat(condition, notNullValue());
    assertThat(condition.getCondition(), notNullValue());
    assertThat(condition.getCondition().getCoded().getConceptId(), equalTo(CODE));
}