Examples with Coding org.hl7.fhir.dstu3.model.Coding used on opensource projects

Example 11 with Coding

use of org.hl7.fhir.dstu3.model.Coding in project bunsen by cerner.

the class FhirEncodersTest method coding.

@Test
public void coding() {
    Coding expectedCoding = condition.getSeverity().getCodingFirstRep();
    Coding actualCoding = decodedCondition.getSeverity().getCodingFirstRep();
    // Codings are a nested array, so we explode them into a table of the coding
    // fields so we can easily select and compare individual fields.
    Dataset<Row> severityCodings = conditionsDataset.select(functions.explode(conditionsDataset.col("severity.coding")).alias("coding")).select(// Pull all fields in the coding to the top level.
    "coding.*").cache();
    Assert.assertEquals(expectedCoding.getCode(), severityCodings.select("code").head().get(0));
    Assert.assertEquals(expectedCoding.getCode(), actualCoding.getCode());
    Assert.assertEquals(expectedCoding.getSystem(), severityCodings.select("system").head().get(0));
    Assert.assertEquals(expectedCoding.getSystem(), actualCoding.getSystem());
    Assert.assertEquals(expectedCoding.getUserSelected(), severityCodings.select("userSelected").head().get(0));
    Assert.assertEquals(expectedCoding.getUserSelected(), actualCoding.getUserSelected());
    Assert.assertEquals(expectedCoding.getDisplay(), severityCodings.select("display").head().get(0));
    Assert.assertEquals(expectedCoding.getDisplay(), actualCoding.getDisplay());
}

Example 12 with Coding

use of org.hl7.fhir.dstu3.model.Coding in project loinc2hpo by monarch-initiative.

the class FhirObservationAnalyzer method getHPO4ObservationOutcome.

/**
 * A core function that tries three ways to return a LabTestResultInHPO object:
 * first, it tries to return the result through the interpretation field. If it fails,
 * second, it tries to return the result through the quantative value, or
 * third, it tries to return the retult through the coded value (ordinal Loinc)
 * @param loinc2HPOannotationMap
 * @param loincIds
 * @return
 */
public static LabTestResultInHPO getHPO4ObservationOutcome(HashSet<LoincId> loincIds, Map<LoincId, UniversalLoinc2HPOAnnotation> loinc2HPOannotationMap) {
    // first make sure the observation has a valid loinc code; otherwise, we cannot handle it
    if (!hasValidLoincCode(loincIds)) {
        // TODO: consider handling this as a future project
        return null;
    }
    LoincId loincId = null;
    try {
        loincId = getLoincIdOfObservation();
    } catch (MalformedLoincCodeException e) {
        logger.error("malformed loinc code; should never happen");
        return null;
    } catch (LoincCodeNotFoundException e) {
        logger.error("No loinc code was found in the observation; should never happen");
        return null;
    } catch (UnsupportedCodingSystemException e) {
        logger.error("coding system not recognized");
        return null;
    }
    if (!loinc2HPOannotationMap.containsKey(loincId)) {
        return null;
    }
    if (observation.hasInterpretation()) {
        logger.debug("enter analyzer using the interpretation field");
        try {
            // return getHPOFromInterpretation(observation.getInterpretation(), loinc2HPOannotationMap);
            HpoTermId4LoincTest hpoterm = new ObservationAnalysisFromInterpretation(getLoincIdOfObservation(), observation.getInterpretation(), loinc2HPOannotationMap).getHPOforObservation();
            return new BasicLabTestResultInHPO(hpoterm, null);
        } catch (UnrecognizedCodeException e) {
            // this means the interpretation code is not recognized
            logger.info("The interpretation codes for this loinc code is not annotated; system will try using raw values");
        } catch (MalformedLoincCodeException e1) {
            // not going to happen
            logger.error("malformed loinc code.");
            return null;
        } catch (LoincCodeNotFoundException e2) {
            // not going to happen
            logger.error("no loinc code is found in the observation");
            return null;
        } catch (UnsupportedCodingSystemException e3) {
            // not going to happen
            logger.error("The interpretation coding system cannot be recognized.");
            return null;
        } catch (AmbiguousResultsFoundException e) {
            logger.error("The observation has conflicting interpretation codes.");
            return null;
        } catch (AnnotationNotFoundException e) {
            logger.error("There is no annotation for the loinc code used in the observation");
        }
    }
    // Qn will have a value field
    if (observation.hasValueQuantity()) {
        try {
            HpoTermId4LoincTest hpoterm = new ObservationAnalysisFromQnValue(loincId, observation, loinc2HPOannotationMap).getHPOforObservation();
            if (hpoterm != null)
                return new BasicLabTestResultInHPO(hpoterm, null);
        } catch (ReferenceNotFoundException e) {
            // if there is no reference
            logger.error("The observation has no reference field.");
        // TODO: make a list of our own references
        } catch (AmbiguousReferenceException e) {
            logger.info("There are two reference ranges or more");
        } catch (UnrecognizedCodeException e) {
            logger.error("uncognized coding system");
        }
    }
    // Ord will have a ValueCodeableConcept field
    if (observation.hasValueCodeableConcept()) {
        try {
            HpoTermId4LoincTest hpoterm = null;
            hpoterm = new ObservationAnalysisFromCodedValues(loincId, observation.getValueCodeableConcept(), loinc2HPOannotationMap).getHPOforObservation();
            if (hpoterm != null)
                return new BasicLabTestResultInHPO(hpoterm, null);
        } catch (AmbiguousResultsFoundException e) {
            logger.error("multiple results are found");
        } catch (UnrecognizedCodeException e) {
            logger.error("unrecognized codes");
        } catch (FHIRException e) {
            // not going to happen
            logger.error("Could not get HPO term from coded value");
        } catch (AnnotationNotFoundException e) {
            logger.error("There is no annotation for the loinc code used in the observation");
        }
    }
    // if all the above fails, we cannot do nothing
    logger.error("Could not return HPO for observation: " + observation.getId());
    return null;
}

Example 13 with Coding

use of org.hl7.fhir.dstu3.model.Coding in project gpconnect-demonstrator by nhsconnect.

the class LocationResourceProvider method locationDetailsToLocation.

/**
 * convert locationDetails to fhir resource
 * @param locationDetails
 * @return Location resource
 */
private Location locationDetailsToLocation(LocationDetails locationDetails) {
    Location location = new Location();
    String resourceId = String.valueOf(locationDetails.getId());
    String versionId = String.valueOf(locationDetails.getLastUpdated().getTime());
    String resourceType = location.getResourceType().toString();
    IdType id = new IdType(resourceType, resourceId, versionId);
    location.setId(id);
    location.getMeta().setVersionId(versionId);
    location.getMeta().setLastUpdated(locationDetails.getLastUpdated());
    location.getMeta().addProfile(SystemURL.SD_GPC_LOCATION);
    location.setName(locationDetails.getName());
    // #207 no site code
    // location.setIdentifier(Collections.singletonList(new Identifier().setSystem(SystemURL.ID_ODS_SITE_CODE).setValue(locationDetails.getSiteOdsCode())));
    // #246 remove type element
    // Coding locationCommTypeCode = new Coding();
    // locationCommTypeCode.setCode("COMM");
    // locationCommTypeCode.setSystem(SystemURL.VS_CC_SER_DEL_LOCROLETYPE);
    // locationCommTypeCode.setDisplay("Community Location");
    // 
    // Coding locationGachTypeCode = new Coding();
    // locationGachTypeCode.setCode("GACH");
    // locationGachTypeCode.setSystem(SystemURL.VS_CC_SER_DEL_LOCROLETYPE);
    // locationGachTypeCode.setDisplay("Hospitals; General Acute Care Hospital");
    // 
    // @SuppressWarnings("deprecation")
    // CodeableConcept locationType = new CodeableConcept();
    // locationType.addCoding(locationCommTypeCode);
    // locationType.addCoding(locationGachTypeCode);
    // location.setType(locationType);
    Organization orgz = FindOrganization(locationDetails.getOrgOdsCode());
    if (orgz != null) {
        Reference mngOrg = new Reference();
        mngOrg.setReference(orgz.getId());
        // #246 remove display element
        // mngOrg.setDisplay(orgz.getName());
        location.setManagingOrganization(mngOrg);
    }
    EnumSet<LocationStatus> statusList = EnumSet.allOf(LocationStatus.class);
    LocationStatus locationStatus = null;
    String status = locationDetails.getStatus();
    if (status != null) {
        for (LocationStatus statusItem : statusList) {
            if (statusItem.toCode().equalsIgnoreCase(status)) {
                locationStatus = statusItem;
                break;
            }
        }
    }
    location.setAddress(createAddress(locationDetails));
    location.setStatus(locationStatus);
    return location;
}

Example 14 with Coding

use of org.hl7.fhir.dstu3.model.Coding in project gpconnect-demonstrator by nhsconnect.

the class MedicationStatementResourceProvider method getMedicationStatementResource.

public MedicationStatement getMedicationStatementResource(MedicationStatementDetail statementDetail) {
    MedicationStatement medicationStatement = new MedicationStatement();
    medicationStatement.setId(statementDetail.getId().toString());
    List<Identifier> identifiers = new ArrayList<>();
    Identifier identifier = new Identifier().setSystem("https://fhir.nhs.uk/Id/cross-care-setting-identifier").setValue(statementDetail.getGuid());
    identifiers.add(identifier);
    medicationStatement.setIdentifier(identifiers);
    medicationStatement.setMeta(new Meta().addProfile(SystemURL.SD_GPC_MEDICATION_STATEMENT));
    medicationStatement.addExtension(new Extension(SystemURL.SD_CC_EXT_MEDICATION_STATEMENT_LAST_ISSUE, new DateTimeType(statementDetail.getLastIssueDate(), TemporalPrecisionEnum.DAY)));
    if (statementDetail.getMedicationRequestPlanId() != null) {
        medicationStatement.addBasedOn(new Reference(new IdType("MedicationRequest", statementDetail.getMedicationRequestPlanId())));
    }
    try {
        medicationStatement.setStatus(MedicationStatementStatus.fromCode(statementDetail.getStatusCode()));
    } catch (FHIRException e) {
        throw new UnprocessableEntityException(e.getMessage());
    }
    if (statementDetail.getMedicationId() != null) {
        medicationStatement.setMedication(new Reference(new IdType("Medication", statementDetail.getMedicationId())));
    }
    medicationStatement.setEffective(new Period().setStart(statementDetail.getStartDate()).setEnd(statementDetail.getEndDate()));
    medicationStatement.setDateAsserted(statementDetail.getDateAsserted());
    if (statementDetail.getPatientId() != null)
        medicationStatement.setSubject(new Reference(new IdType("Patient", statementDetail.getPatientId())));
    try {
        medicationStatement.setTaken(statementDetail.getTakenCode() != null ? MedicationStatementTaken.fromCode(statementDetail.getTakenCode()) : MedicationStatementTaken.UNK);
    } catch (FHIRException e) {
        throw new UnprocessableEntityException(e.getMessage());
    }
    setReasonCodes(medicationStatement, statementDetail);
    setNotes(medicationStatement, statementDetail);
    String dosageText = statementDetail.getDosageText();
    medicationStatement.addDosage(new Dosage().setText(dosageText == null || dosageText.trim().isEmpty() ? NO_INFORMATION_AVAILABLE : dosageText).setPatientInstruction(statementDetail.getDosagePatientInstruction()));
    String prescribingAgency = statementDetail.getPrescribingAgency();
    if (prescribingAgency != null && !prescribingAgency.trim().isEmpty()) {
        String prescribingAgencyDisplay = "";
        if (prescribingAgency.equalsIgnoreCase("prescribed-at-gp-practice")) {
            prescribingAgencyDisplay = "Prescribed at GP practice";
        } else if (prescribingAgency.equalsIgnoreCase("prescribed-by-another-organisation")) {
            prescribingAgencyDisplay = "Prescribed by another organisation";
        }
        Coding coding = new Coding(SystemURL.CS_CC_PRESCRIBING_AGENCY_STU3, prescribingAgency, prescribingAgencyDisplay);
        CodeableConcept codeableConcept = new CodeableConcept().addCoding(coding);
        medicationStatement.addExtension(new Extension(SystemURL.SD_EXTENSION_CC_PRESCRIBING_AGENCY, codeableConcept));
    }
    // #281 1.2.5 add dosageLastChanged
    Date dosageLastChanged = statementDetail.getDosageLastChanged();
    if (dosageLastChanged != null) {
        medicationStatement.addExtension(new Extension(SystemURL.SD_EXTENSION_CC_DOSAGE_LAST_CHANGED, new DateTimeType(dosageLastChanged)));
    }
    return medicationStatement;
}

Example 15 with Coding

use of org.hl7.fhir.dstu3.model.Coding in project gpconnect-demonstrator by nhsconnect.

the class PatientResourceProvider method addWarningIssue.

/**
 * see
 * https://gpconnect-1-2-4.netlify.com/accessrecord_structured_development_version_compatibility.html
 * add an issue to the OperationOutcome to be returned in a successful
 * response bundle this is for forward compatibility as specified in 1.2.4
 *
 * @param param
 * @param paramPart
 * @param issueType
 * @param details lower level details to be added to the text element
 */
private void addWarningIssue(ParametersParameterComponent param, ParametersParameterComponent paramPart, IssueType issueType, String details) {
    if (operationOutcome == null) {
        createOperationOutcome();
    }
    OperationOutcomeIssueComponent issue = new OperationOutcomeIssueComponent();
    issue.setSeverity(OperationOutcome.IssueSeverity.WARNING);
    CodeableConcept codeableConcept = new CodeableConcept();
    Coding coding = new Coding();
    coding.setSystem(VS_GPC_ERROR_WARNING_CODE);
    switch(issueType) {
        case NOTSUPPORTED:
            issue.setCode(issueType);
            coding.setCode(SystemCode.NOT_IMPLEMENTED);
            coding.setDisplay("Not implemented");
            break;
        case REQUIRED:
            issue.setCode(issueType);
            coding.setCode(SystemCode.PARAMETER_NOT_FOUND);
            coding.setDisplay("Parameter not found");
            break;
        case INVALID:
            issue.setCode(issueType);
            coding.setCode(SystemCode.INVALID_PARAMETER);
            coding.setDisplay("Invalid Parameter");
            break;
    }
    codeableConcept.addCoding(coding);
    issue.setDetails(codeableConcept);
    String locus = paramPart != null ? "." + paramPart.getName() : "";
    issue.setDiagnostics(param.getName() + locus);
    if (details == null) {
        // mod to remove more informative text which was off spec
        codeableConcept.setText(param.getName() + locus + " is an unrecognised parameter");
    } else {
        codeableConcept.setText(details);
    }
    operationOutcome.addIssue(issue);
}