Examples with Identifier org.hl7.fhir.r4b.model.Identifier used on opensource projects

Example 86 with Identifier

use of org.hl7.fhir.r4b.model.Identifier in project quality-measure-and-cohort-service by Alvearie.

the class ValueSetUtil method createArtifact.

public static ValueSetArtifact createArtifact(InputStream is, Map<String, String> customCodeSystem) throws IOException {
    XSSFSheet informationSheet;
    try (XSSFWorkbook wb = new XSSFWorkbook(is)) {
        informationSheet = wb.getSheetAt(wb.getSheetIndex("Expansion List"));
    } catch (IllegalArgumentException e) {
        throw new RuntimeException("Spreadsheet is missing required sheet \"Expansion List\"", e);
    }
    ValueSet valueSet = new ValueSet();
    boolean inCodesSection = false;
    valueSet.setStatus(Enumerations.PublicationStatus.ACTIVE);
    HashMap<CodeSystemKey, List<ValueSet.ConceptReferenceComponent>> codeSystemToCodes = new HashMap<>();
    String url = "http://cts.nlm.nih.gov/fhir/ValueSet/";
    String identifier = null;
    for (Row currentRow : informationSheet) {
        String code = currentRow.getCell(0) == null ? "" : currentRow.getCell(0).getStringCellValue();
        if (!code.equals("") && currentRow.getCell(1) != null && !inCodesSection) {
            String value;
            switch(currentRow.getCell(1).getCellType()) {
                case NUMERIC:
                    value = Double.toString(currentRow.getCell(1).getNumericCellValue());
                    break;
                case STRING:
                    value = currentRow.getCell(1).getStringCellValue();
                    break;
                default:
                    throw new RuntimeException("Cell type does not match either String or Numeric for key " + code);
            }
            switch(currentRow.getCell(0).getStringCellValue().toLowerCase()) {
                case "value set name":
                    valueSet.setName(value);
                    valueSet.setTitle(value);
                    break;
                case "id":
                    valueSet.setId(value);
                    identifier = value;
                    break;
                case "oid":
                    if (valueSet.getId() == null) {
                        valueSet.setId(value);
                        identifier = value;
                    }
                    break;
                case "url":
                    // fallthrough
                    url = value.endsWith("/") ? value : value + "/";
                case "definition version":
                    valueSet.setVersion(value);
                    break;
                case "code":
                    inCodesSection = true;
                    break;
                default:
                    break;
            }
        } else if (inCodesSection) {
            String display = currentRow.getCell(1).getStringCellValue();
            String codeSystemEntry = currentRow.getCell(2).getStringCellValue();
            String codeSystemVersion = currentRow.getCell(3).getStringCellValue();
            String codeSystem;
            if (codeSystemEntry.startsWith("http://") || codeSystemEntry.startsWith("https://")) {
                codeSystem = codeSystemEntry;
            } else if (customCodeSystem != null && customCodeSystem.get(codeSystemEntry) != null) {
                codeSystem = customCodeSystem.get(codeSystemEntry);
            } else {
                codeSystem = CodeSystemLookup.getUrlFromName(codeSystemEntry);
            }
            if (codeSystem == null) {
                throw new IllegalArgumentException("Unmatched Code System! " + codeSystemEntry + " not found!");
            }
            ValueSet.ConceptReferenceComponent concept = new ValueSet.ConceptReferenceComponent();
            concept.setCode(code);
            concept.setDisplay(display);
            List<ValueSet.ConceptReferenceComponent> conceptsSoFar = codeSystemToCodes.computeIfAbsent(new CodeSystemKey(codeSystem, codeSystemVersion), x -> new ArrayList<>());
            conceptsSoFar.add(concept);
        }
    }
    if (identifier == null || identifier.equals("")) {
        throw new RuntimeException("There must be an Identifier specified! Please populate the ID field");
    }
    valueSet.setUrl(url + identifier);
    valueSet.setId(identifier);
    ValueSet.ValueSetComposeComponent compose = new ValueSet.ValueSetComposeComponent();
    for (Entry<CodeSystemKey, List<ConceptReferenceComponent>> singleInclude : codeSystemToCodes.entrySet()) {
        ValueSet.ConceptSetComponent component = new ValueSet.ConceptSetComponent();
        component.setSystem(singleInclude.getKey().getCodeSystem());
        component.setVersion(singleInclude.getKey().getCodeSystemVersion());
        component.setConcept(singleInclude.getValue());
        compose.addInclude(component);
    }
    valueSet.setCompose(compose);
    ValueSetArtifact artifact = new ValueSetArtifact();
    artifact.setName(valueSet.getName());
    artifact.setFhirResource(valueSet);
    artifact.setUrl(valueSet.getUrl());
    return artifact;
}

Example 87 with Identifier

use of org.hl7.fhir.r4b.model.Identifier in project summary-care-record-api by NHSDigital.

the class AgentPersonSdsMapper method mapPractitionerRole.

private PractitionerRole mapPractitionerRole(Node agentPersonSds) {
    var role = new PractitionerRole();
    var roleProfileId = xmlUtils.getValueByXPath(agentPersonSds, ID_EXTENSION_XPATH);
    role.setId(randomUUID());
    role.addIdentifier(new Identifier().setSystem(SDS_ROLE_PROFILE_ID).setValue(roleProfileId));
    return role;
}

Example 88 with Identifier

use of org.hl7.fhir.r4b.model.Identifier in project summary-care-record-api by NHSDigital.

the class GpSummaryMapper method map.

@SneakyThrows
public List<Resource> map(Node document) {
    var gpSummaryId = xmlUtils.getValueByXPath(document, GP_SUMMARY_ID_XPATH);
    var gpSummaryCodeCode = xmlUtils.getValueByXPath(document, GP_SUMMARY_CODE_CODE_XPATH);
    var gpSummaryCodeDisplayName = xmlUtils.getValueByXPath(document, GP_SUMMARY_CODE_DISPLAY_NAME_XPATH);
    var gpSummaryStatusCode = xmlUtils.getValueByXPath(document, GP_SUMMARY_STATUS_CODE_XPATH);
    var gpSummaryEffectiveTime = parseDate(xmlUtils.getValueByXPath(document, GP_SUMMARY_EFFECTIVE_TIME_XPATH), InstantType.class);
    var authorTime = parseDate(xmlUtils.getValueByXPath(document, GP_SUMMARY_AUTHOR_TIME_XPATH), DateTimeType.class);
    var replacementOfPriorMessageRefIdRoot = xmlUtils.getOptionalValueByXPath(document, REPLACEMENT_OF_PRIOR_MESSAGE_REF_ID_ROOT_XPATH);
    var pertinentRootCreTypeCodeCode = xmlUtils.getValueByXPath(document, PERTINENT_ROOT_CRE_TYPE_CODE_CODE_XPATH);
    var pertinentRootCreTypeCodeDisplayName = xmlUtils.getValueByXPath(document, PERTINENT_ROOT_CRE_TYPE_CODE_DISPLAY_NAME_XPATH);
    var presentationTextValue = xmlUtils.detachOptionalNodeByXPath(document, PRESENTATION_TEXT_VALUE);
    var eventId = xmlUtils.getValueByXPath(document, EVENT_ID_XPATH);
    List<Resource> resources = new ArrayList<>();
    var composition = new Composition();
    composition.setId(eventId);
    composition.setIdentifier(new Identifier().setValue(gpSummaryId).setSystem("https://tools.ietf.org/html/rfc4122"));
    composition.setType(new CodeableConcept().addCoding(new Coding().setCode(gpSummaryCodeCode).setSystem(SNOMED_SYSTEM).setDisplay(gpSummaryCodeDisplayName)));
    composition.setMeta(new Meta().setLastUpdatedElement(gpSummaryEffectiveTime));
    composition.setStatus(mapCompositionStatus(gpSummaryStatusCode));
    composition.setDateElement(authorTime);
    replacementOfPriorMessageRefIdRoot.ifPresent(val -> composition.addRelatesTo(new Composition.CompositionRelatesToComponent().setTarget(new Identifier().setValue(val)).setCode(REPLACES)));
    composition.addCategory(new CodeableConcept().addCoding(new Coding().setCode(pertinentRootCreTypeCodeCode).setSystem(SNOMED_SYSTEM).setDisplay(pertinentRootCreTypeCodeDisplayName)));
    Map<String, List<String>> references = sectionReferences(document);
    presentationTextValue.map(htmlParser::parse).map(Collection::stream).ifPresent(it -> it.forEach(section -> {
        if (section.getTitle() != null && CODED_ENTRY_RESOURCE_MAP.keySet().contains(section.getTitle()) && references.containsKey(section.getTitle())) {
            for (String codedEntryId : references.get(section.getTitle())) {
                section.addEntry(new Reference(CODED_ENTRY_RESOURCE_MAP.get(section.getTitle()) + "/" + codedEntryId));
            }
        }
        composition.addSection(section);
    }));
    resources.add(composition);
    addAuthor(document, resources, composition);
    return resources;
}

Example 89 with Identifier

use of org.hl7.fhir.r4b.model.Identifier in project summary-care-record-api by NHSDigital.

the class GetScrService method buildPatientResource.

private Patient buildPatientResource(String nhsNumber) {
    Patient patient = new Patient();
    String patientResourceId = randomUUID();
    patient.setId(patientResourceId);
    patient.setIdentifier(asList(new Identifier().setSystem(NHS_ID_SYSTEM).setValue(nhsNumber)));
    return patient;
}

Example 90 with Identifier

use of org.hl7.fhir.r4b.model.Identifier in project summary-care-record-api by NHSDigital.

the class OrganisationSdsMapper method mapOrganizationSds.

public Organization mapOrganizationSds(Node organisationSds) {
    var org = new Organization();
    org.setId(randomUUID());
    var orgIdentifier = new Identifier().setValue(xmlUtils.getValueByXPath(organisationSds, ORG_SDS_ID_XPATH));
    var rootId = xmlUtils.getValueByXPath(organisationSds, ORG_SDS_ID_ROOT_XPATH);
    if (HL7_ORG_OID.equals(rootId)) {
        orgIdentifier.setSystem(ORG_SDS_SYSTEM);
    }
    org.addIdentifier(orgIdentifier);
    xmlUtils.detachOptionalNodeByXPath(organisationSds, ORG_NAME_XPATH).ifPresent(nameNode -> org.setName(nameNode.getTextContent()));
    return org;
}