Examples with Section org.hl7.fhir.utilities.turtle.Turtle.Section used on opensource projects

Example 66 with Section

use of org.hl7.fhir.utilities.turtle.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class CCDAConverter method processVitalSignsSection.

protected SectionComponent processVitalSignsSection(Element section) throws Exception {
    ListResource list = new ListResource();
    for (Element entry : cda.getChildren(section, "entry")) {
        Element organizer = cda.getlastChild(entry);
        if (cda.hasTemplateId(organizer, "2.16.840.1.113883.10.20.22.4.26")) {
            processVitalSignsOrganizer(list, organizer);
        } else
            throw new Exception("Unhandled Section template ids: " + cda.showTemplateIds(organizer));
    }
    // todo: text
    SectionComponent s = new Composition.SectionComponent();
    s.setCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")));
    // todo: check subject
    s.addEntry(Factory.makeReference(addReference(list, "Vital Signs", makeUUIDReference())));
    return s;
}

Example 67 with Section

use of org.hl7.fhir.utilities.turtle.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class CCDAConverter method convert.

public Bundle convert(InputStream stream) throws Exception {
    cda = new CDAUtilities(stream);
    doc = cda.getElement();
    cda.checkTemplateId(doc, "2.16.840.1.113883.10.20.22.1.1");
    convert = new Convert(cda, ucumSvc, "Z");
    // check it's a CDA/CCD
    feed = new Bundle();
    feed.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));
    feed.setId(makeUUIDReference());
    // todo-bundle  ("http://hl7.org/fhir/tag", "http://hl7.org/fhir/tag/document", "Document"));
    feed.getMeta().getTag().add(new Coding());
    // process the header
    makeDocument();
    composition.setSubject(Factory.makeReference(makeSubject()));
    for (Element e : cda.getChildren(doc, "author")) composition.getAuthor().add(Factory.makeReference(makeAuthor(e)));
    // todo: data enterer & informant goes in provenance
    composition.setCustodian(Factory.makeReference(makeOrganization(cda.getDescendent(doc, "custodian/assignedCustodian/representedCustodianOrganization"), "Custodian")));
    // todo: informationRecipient
    for (Element e : cda.getChildren(doc, "legalAuthenticator")) composition.getAttester().add(makeAttester(e, CompositionAttestationMode.LEGAL, "Legal Authenticator"));
    for (Element e : cda.getChildren(doc, "authenticator")) composition.getAttester().add(makeAttester(e, CompositionAttestationMode.PROFESSIONAL, "Authenticator"));
    // process the contents
    // we do this by section - keep the original section order
    Element body = cda.getDescendent(doc, "component/structuredBody");
    processComponentSections(composition.getSection(), body);
    return feed;
}

Example 68 with Section

use of org.hl7.fhir.utilities.turtle.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class CCDAConverter method processAdverseReactionsSection.

protected SectionComponent processAdverseReactionsSection(Element section) throws Exception {
    ListResource list = new ListResource();
    for (Element entry : cda.getChildren(section, "entry")) {
        Element concern = cda.getChild(entry, "act");
        if (cda.hasTemplateId(concern, "2.16.840.1.113883.10.20.22.4.30")) {
            processAllergyProblemAct(list, concern);
        } else
            throw new Exception("Unhandled Section template ids: " + cda.showTemplateIds(concern));
    }
    // todo: text
    SectionComponent s = new Composition.SectionComponent();
    s.setCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")));
    // todo: check subject
    s.addEntry(Factory.makeReference(addReference(list, "Allergies, Adverse Reactions, Alerts", makeUUIDReference())));
    return s;
}

Example 69 with Section

use of org.hl7.fhir.utilities.turtle.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilities method generateForChildren.

private void generateForChildren(SchematronWriter sch, String xpath, ElementDefinition ed, StructureDefinition structure, StructureDefinition base) throws IOException {
    // generateForChild(txt, structure, child);
    List<ElementDefinition> children = getChildList(structure, ed);
    String sliceName = null;
    ElementDefinitionSlicingComponent slicing = null;
    for (ElementDefinition child : children) {
        String name = tail(child.getPath());
        if (child.hasSlicing()) {
            sliceName = name;
            slicing = child.getSlicing();
        } else if (!name.equals(sliceName))
            slicing = null;
        ElementDefinition based = getByPath(base, child.getPath());
        boolean doMin = (child.getMin() > 0) && (based == null || (child.getMin() != based.getMin()));
        boolean doMax = child.hasMax() && !child.getMax().equals("*") && (based == null || (!child.getMax().equals(based.getMax())));
        Slicer slicer = slicing == null ? new Slicer(true) : generateSlicer(child, slicing, structure);
        if (slicer.check) {
            if (doMin || doMax) {
                Section s = sch.section(xpath);
                Rule r = s.rule(xpath);
                if (doMin)
                    r.assrt("count(f:" + name + slicer.criteria + ") >= " + Integer.toString(child.getMin()), name + slicer.name + ": minimum cardinality of '" + name + "' is " + Integer.toString(child.getMin()));
                if (doMax)
                    r.assrt("count(f:" + name + slicer.criteria + ") <= " + child.getMax(), name + slicer.name + ": maximum cardinality of '" + name + "' is " + child.getMax());
            }
        }
    }
    for (ElementDefinitionConstraintComponent inv : ed.getConstraint()) {
        if (inv.hasXpath()) {
            Section s = sch.section(ed.getPath());
            Rule r = s.rule(xpath);
            r.assrt(inv.getXpath(), (inv.hasId() ? inv.getId() + ": " : "") + inv.getHuman() + (inv.hasUserData(IS_DERIVED) ? " (inherited)" : ""));
        }
    }
    for (ElementDefinition child : children) {
        String name = tail(child.getPath());
        generateForChildren(sch, xpath + "/f:" + name, child, structure, base);
    }
}

Example 70 with Section

use of org.hl7.fhir.utilities.turtle.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) {
    // "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 ("Reference".equals(element.getType()))
        decorateReference(t, element);
    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);
    }
}