Examples with Section org.hl7.fhir.r4.utils.formats.Turtle.Section used on opensource projects

Example 26 with Section

use of org.hl7.fhir.r4.utils.formats.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class TurtleParser method composeElement.

private void composeElement(Section section, Complex ctxt, Element element, Element parent) throws FHIRException {
    // "Extension".equals(element.getType())?
    // (element.getProperty().getDefinition().getIsModifier()? "modifierExtension" : "extension") ;
    String en = getFormalName(element);
    Complex t;
    if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY && parent != null && parent.getNamedChildValue("fullUrl") != null) {
        String url = "<" + parent.getNamedChildValue("fullUrl") + ">";
        ctxt.linkedPredicate("fhir:" + en, url, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()));
        t = section.subject(url);
    } else {
        t = ctxt.linkedPredicate("fhir:" + en, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()));
    }
    if (element.getSpecial() != null)
        t.linkedPredicate("a", "fhir:" + element.fhirType(), linkResolver == null ? null : linkResolver.resolveType(element.fhirType()));
    if (element.hasValue())
        t.linkedPredicate("fhir:value", ttlLiteral(element.getValue(), element.getType()), linkResolver == null ? null : linkResolver.resolveType(element.getType()));
    if (element.getProperty().isList() && (!element.isResource() || element.getSpecial() == SpecialElement.CONTAINED))
        t.linkedPredicate("fhir:index", Integer.toString(element.getIndex()), linkResolver == null ? null : linkResolver.resolvePage("rdf.html#index"));
    if ("Coding".equals(element.getType()))
        decorateCoding(t, element, section);
    if (Utilities.existsInList(element.getType(), "Reference"))
        decorateReference(t, element);
    else if (Utilities.existsInList(element.getType(), "canonical"))
        decorateCanonical(t, element);
    if ("canonical".equals(element.getType())) {
        String refURI = element.primitiveValue();
        if (refURI != null) {
            String uriType = getURIType(refURI);
            if (uriType != null && !section.hasSubject(refURI))
                section.triple(refURI, "a", "fhir:" + uriType);
        }
    }
    if ("Reference".equals(element.getType())) {
        String refURI = getReferenceURI(element.getChildValue("reference"));
        if (refURI != null) {
            String uriType = getURIType(refURI);
            if (uriType != null && !section.hasSubject(refURI))
                section.triple(refURI, "a", "fhir:" + uriType);
        }
    }
    for (Element child : element.getChildren()) {
        if ("xhtml".equals(child.getType())) {
            String childfn = getFormalName(child);
            t.predicate("fhir:" + childfn, ttlLiteral(child.getValue(), child.getType()));
        } else
            composeElement(section, t, child, element);
    }
}

Example 27 with Section

use of org.hl7.fhir.r4.utils.formats.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class RdfParserBase method compose.

@Override
public void compose(OutputStream stream, Resource resource) throws IOException {
    Turtle ttl = new Turtle();
    // ttl.setFormat(FFormat);
    ttl.prefix("fhir", "http://hl7.org/fhir/");
    ttl.prefix("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
    Section section = ttl.section("resource");
    Subject subject;
    if (url != null)
        subject = section.triple("<" + url + ">", "a", "fhir:" + resource.getResourceType().toString());
    else
        subject = section.triple("[]", "a", "fhir:" + resource.getResourceType().toString());
    composeResource(subject, resource);
    try {
        ttl.commit(stream, false);
    } catch (Exception e) {
        throw new IOException(e);
    }
}

Example 28 with Section

use of org.hl7.fhir.r4.utils.formats.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class RdfParserBase method compose.

@Override
public void compose(OutputStream stream, Resource resource) throws IOException {
    Turtle ttl = new Turtle();
    // ttl.setFormat(FFormat);
    ttl.prefix("fhir", "http://hl7.org/fhir/");
    ttl.prefix("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
    Section section = ttl.section("resource");
    Subject subject;
    if (url != null)
        subject = section.triple("<" + url + ">", "a", "fhir:" + resource.getResourceType().toString());
    else
        subject = section.triple("[]", "a", "fhir:" + resource.getResourceType().toString());
    composeResource(subject, resource);
    try {
        ttl.commit(stream, false);
    } catch (Exception e) {
        throw new IOException(e);
    }
}

Example 29 with Section

use of org.hl7.fhir.r4.utils.formats.Turtle.Section in project pathling by aehrc.

the class ValueSetMapping method toIntersection.

/**
 * Constructs a {@link ValueSet} representing the intersection of a set of codings and a server
 *
 * @param valueSetUri the server defined value set.
 * @param codings the set of codings to intersect.
 * @return the intersection value set.
 */
@Nonnull
public static ValueSet toIntersection(@Nonnull final String valueSetUri, @Nonnull final Collection<SimpleCoding> codings) {
    final Set<CodeSystemReference> validCodeSystems = codings.stream().filter(SimpleCoding::isDefined).map(coding -> new CodeSystemReference(Optional.ofNullable(coding.getSystem()), Optional.ofNullable(coding.getVersion()))).collect(Collectors.toUnmodifiableSet());
    // Create a ValueSet to represent the intersection of the input codings and the ValueSet
    // described by the URI in the argument.
    final ValueSet intersection = new ValueSet();
    final ValueSetComposeComponent compose = new ValueSetComposeComponent();
    final List<ConceptSetComponent> includes = new ArrayList<>();
    // Create an include section for each unique code system present within the input codings.
    for (final CodeSystemReference codeSystem : validCodeSystems) {
        final ConceptSetComponent include = new ConceptSetComponent();
        include.setValueSet(Collections.singletonList(new CanonicalType(valueSetUri)));
        // noinspection OptionalGetWithoutIsPresent
        include.setSystem(codeSystem.getSystem().get());
        codeSystem.getVersion().ifPresent(include::setVersion);
        // Add the codings that match the current code system.
        final List<ConceptReferenceComponent> concepts = codings.stream().filter(codeSystem::matchesCoding).map(SimpleCoding::getCode).filter(Objects::nonNull).distinct().map(code -> {
            final ConceptReferenceComponent concept = new ConceptReferenceComponent();
            concept.setCode(code);
            return concept;
        }).collect(Collectors.toList());
        if (!concepts.isEmpty()) {
            include.setConcept(concepts);
            includes.add(include);
        }
    }
    compose.setInclude(includes);
    intersection.setCompose(compose);
    return intersection;
}

Example 30 with Section

use of org.hl7.fhir.r4.utils.formats.Turtle.Section in project eCRNow by drajer-health.

the class CdaHistoryOfPresentIllnessGenerator method generateHistoryOfPresentIllnessSection.

public static String generateHistoryOfPresentIllnessSection(R4FhirData data) {
    StringBuilder sb = new StringBuilder(2000);
    // Will have to wait to discuss with vendors on History of Present Illness and how to obtain
    // that information reliably..
    // Then we can generate better text.
    sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.COMP_EL_NAME));
    sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.SECTION_EL_NAME));
    sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.HISTORY_OF_PRESENT_ILLNESS_SEC_TEMPLATE_ID));
    sb.append(CdaGeneratorUtils.getXmlForCD(CdaGeneratorConstants.CODE_EL_NAME, CdaGeneratorConstants.HISTORY_OF_PRESENT_ILLNESS_SEC_CODE, CdaGeneratorConstants.LOINC_CODESYSTEM_OID, CdaGeneratorConstants.LOINC_CODESYSTEM_NAME, CdaGeneratorConstants.HISTORY_OF_PRESENT_ILLNESS_SEC_CODE_NAME));
    // Add Title
    sb.append(CdaGeneratorUtils.getXmlForText(CdaGeneratorConstants.TITLE_EL_NAME, CdaGeneratorConstants.HISTORY_OF_PRESENT_ILLNESS_SEC_TITLE));
    // Add Narrative Text
    sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.TEXT_EL_NAME));
    List<Condition> conds = data.getEncounterDiagnosisConditions();
    // Create Table Header.
    List<String> list = new ArrayList<>();
    list.add(CdaGeneratorConstants.NARRATIVE_TEXT_EL_NAME);
    sb.append(CdaGeneratorUtils.getXmlForTableHeader(list, CdaGeneratorConstants.TABLE_BORDER, CdaGeneratorConstants.TABLE_WIDTH));
    // Add Table Body
    sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.TABLE_BODY_EL_NAME));
    String text = CdaGeneratorConstants.UNKNOWN_HISTORY_OF_PRESENT_ILLNESS;
    int rowNum = 1;
    if (conds != null && !conds.isEmpty()) {
        // Add Body Rows
        for (Condition prob : conds) {
            String probDisplayName = CdaGeneratorConstants.UNKNOWN_VALUE;
            if (prob.getCode() != null && !StringUtils.isEmpty(prob.getCode().getText())) {
                probDisplayName = prob.getCode().getText();
            } else if (prob.getCode().getCodingFirstRep() != null && !StringUtils.isEmpty(prob.getCode().getCodingFirstRep().getDisplay())) {
                probDisplayName = prob.getCode().getCodingFirstRep().getDisplay();
            }
            Map<String, String> bodyvals = new LinkedHashMap<>();
            bodyvals.put(CdaGeneratorConstants.HISTORY_OF_PRESENT_ILLNESS_BODY_CONTENT, probDisplayName);
            sb.append(CdaGeneratorUtils.addTableRow(bodyvals, rowNum));
            ++rowNum;
        }
    } else {
        Map<String, String> bodyvals = new HashMap<>();
        bodyvals.put(CdaGeneratorConstants.HISTORY_OF_PRESENT_ILLNESS_BODY_CONTENT, text);
        sb.append(CdaGeneratorUtils.addTableRow(bodyvals, rowNum));
    }
    sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.TABLE_BODY_EL_NAME));
    // End Table.
    sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.TABLE_EL_NAME));
    sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.TEXT_EL_NAME));
    // Complete the section end tags.
    sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.SECTION_EL_NAME));
    sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.COMP_EL_NAME));
    return sb.toString();
}