Examples with UriType org.hl7.fhir.r5.model.UriType used on opensource projects

Example 21 with UriType

use of org.hl7.fhir.r5.model.UriType in project org.hl7.fhir.core by hapifhir.

the class R5ToR5Loader method loadBundle.

@Override
public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
    Resource r5 = null;
    if (isJson)
        r5 = new JsonParser().parse(stream);
    else
        r5 = new XmlParser().parse(stream);
    Bundle b;
    if (r5 instanceof Bundle)
        b = (Bundle) r5;
    else {
        b = new Bundle();
        b.setId(UUID.randomUUID().toString().toLowerCase());
        b.setType(BundleType.COLLECTION);
        b.addEntry().setResource(r5).setFullUrl(r5 instanceof CanonicalResource ? ((CanonicalResource) r5).getUrl() : null);
    }
    for (CodeSystem cs : cslist) {
        BundleEntryComponent be = b.addEntry();
        be.setFullUrl(cs.getUrl());
        be.setResource(cs);
    }
    if (killPrimitives) {
        List<BundleEntryComponent> remove = new ArrayList<BundleEntryComponent>();
        for (BundleEntryComponent be : b.getEntry()) {
            if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
                StructureDefinition sd = (StructureDefinition) be.getResource();
                if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)
                    remove.add(be);
            }
        }
        b.getEntry().removeAll(remove);
    }
    if (patchUrls) {
        for (BundleEntryComponent be : b.getEntry()) {
            if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
                StructureDefinition sd = (StructureDefinition) be.getResource();
                sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
                sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
                for (ElementDefinition ed : sd.getSnapshot().getElement()) patchUrl(ed);
                for (ElementDefinition ed : sd.getDifferential().getElement()) patchUrl(ed);
            }
        }
    }
    return b;
}

Example 22 with UriType

use of org.hl7.fhir.r5.model.UriType in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method renderLeaf.

private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints) throws FHIRException, UnsupportedEncodingException, IOException {
    if (ew == null)
        return;
    Base e = ew.getBase();
    if (e instanceof StringType)
        x.addText(((StringType) e).getValue());
    else if (e instanceof CodeType)
        x.addText(((CodeType) e).getValue());
    else if (e instanceof IdType)
        x.addText(((IdType) e).getValue());
    else if (e instanceof Extension)
        x.addText("Extensions: Todo");
    else if (e instanceof InstantType)
        x.addText(((InstantType) e).toHumanDisplay());
    else if (e instanceof DateTimeType)
        x.addText(((DateTimeType) e).toHumanDisplay());
    else if (e instanceof Base64BinaryType)
        x.addText(new Base64().encodeAsString(((Base64BinaryType) e).getValue()));
    else if (e instanceof org.hl7.fhir.dstu2.model.DateType)
        x.addText(((org.hl7.fhir.dstu2.model.DateType) e).toHumanDisplay());
    else if (e instanceof Enumeration) {
        Object ev = ((Enumeration<?>) e).getValue();
        // todo: look up a display name if there is one
        x.addText(ev == null ? "" : ev.toString());
    } else if (e instanceof BooleanType)
        x.addText(((BooleanType) e).getValue().toString());
    else if (e instanceof CodeableConcept) {
        renderCodeableConcept((CodeableConcept) e, x, showCodeDetails);
    } else if (e instanceof Coding) {
        renderCoding((Coding) e, x, showCodeDetails);
    } else if (e instanceof Annotation) {
        renderAnnotation((Annotation) e, x);
    } else if (e instanceof Identifier) {
        renderIdentifier((Identifier) e, x);
    } else if (e instanceof org.hl7.fhir.dstu2.model.IntegerType) {
        x.addText(Integer.toString(((org.hl7.fhir.dstu2.model.IntegerType) e).getValue()));
    } else if (e instanceof org.hl7.fhir.dstu2.model.DecimalType) {
        x.addText(((org.hl7.fhir.dstu2.model.DecimalType) e).getValue().toString());
    } else if (e instanceof HumanName) {
        renderHumanName((HumanName) e, x);
    } else if (e instanceof SampledData) {
        renderSampledData((SampledData) e, x);
    } else if (e instanceof Address) {
        renderAddress((Address) e, x);
    } else if (e instanceof ContactPoint) {
        renderContactPoint((ContactPoint) e, x);
    } else if (e instanceof UriType) {
        renderUri((UriType) e, x);
    } else if (e instanceof Timing) {
        renderTiming((Timing) e, x);
    } else if (e instanceof Range) {
        renderRange((Range) e, x);
    } else if (e instanceof Quantity) {
        renderQuantity((Quantity) e, x, showCodeDetails);
    } else if (e instanceof Ratio) {
        renderQuantity(((Ratio) e).getNumerator(), x, showCodeDetails);
        x.addText("/");
        renderQuantity(((Ratio) e).getDenominator(), x, showCodeDetails);
    } else if (e instanceof Period) {
        Period p = (Period) e;
        x.addText(!p.hasStart() ? "??" : p.getStartElement().toHumanDisplay());
        x.addText(" --> ");
        x.addText(!p.hasEnd() ? "(ongoing)" : p.getEndElement().toHumanDisplay());
    } else if (e instanceof Reference) {
        Reference r = (Reference) e;
        XhtmlNode c = x;
        ResourceWithReference tr = null;
        if (r.hasReferenceElement()) {
            tr = resolveReference(res, r.getReference());
            if (!r.getReference().startsWith("#")) {
                if (tr != null && tr.getReference() != null)
                    c = x.addTag("a").attribute("href", tr.getReference());
                else
                    c = x.addTag("a").attribute("href", r.getReference());
            }
        }
        // what to display: if text is provided, then that. if the reference was resolved, then show the generated narrative
        if (r.hasDisplayElement()) {
            c.addText(r.getDisplay());
            if (tr != null) {
                c.addText(". Generated Summary: ");
                generateResourceSummary(c, tr.getResource(), true, r.getReference().startsWith("#"));
            }
        } else if (tr != null) {
            generateResourceSummary(c, tr.getResource(), r.getReference().startsWith("#"), r.getReference().startsWith("#"));
        } else {
            c.addText(r.getReference());
        }
    } else if (e instanceof Resource) {
        return;
    } else if (e instanceof ElementDefinition) {
        x.addText("todo-bundle");
    } else if (e != null && !(e instanceof Attachment) && !(e instanceof Narrative) && !(e instanceof Meta))
        throw new NotImplementedException("type " + e.getClass().getName() + " not handled yet");
}

Example 23 with UriType

use of org.hl7.fhir.r5.model.UriType in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method generateComposition.

private boolean generateComposition(XhtmlNode x, ValueSet vs, boolean header) {
    boolean hasExtensions = false;
    if (!vs.hasCodeSystem()) {
        if (header) {
            XhtmlNode h = x.addTag("h2");
            h.addText(vs.getName());
            XhtmlNode p = x.addTag("p");
            smartAddText(p, vs.getDescription());
            if (vs.hasCopyrightElement())
                generateCopyright(x, vs);
        }
        XhtmlNode p = x.addTag("p");
        p.addText("This value set includes codes from the following code systems:");
    } else {
        XhtmlNode p = x.addTag("p");
        p.addText("In addition, this value set includes codes from other code systems:");
    }
    XhtmlNode ul = x.addTag("ul");
    XhtmlNode li;
    for (UriType imp : vs.getCompose().getImport()) {
        li = ul.addTag("li");
        li.addText("Import all the codes that are contained in ");
        AddVsRef(imp.getValue(), li);
    }
    for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
        hasExtensions = genInclude(ul, inc, "Include") || hasExtensions;
    }
    for (ConceptSetComponent exc : vs.getCompose().getExclude()) {
        hasExtensions = genInclude(ul, exc, "Exclude") || hasExtensions;
    }
    return hasExtensions;
}

Example 24 with UriType

use of org.hl7.fhir.r5.model.UriType in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpanderSimple method includeCodes.

private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params) throws TerminologyServiceException, ETooCostly {
    if (context.supportsSystem(inc.getSystem())) {
        addCodes(context.expandVS(inc), params);
        return;
    }
    ValueSet cs = context.fetchCodeSystem(inc.getSystem());
    if (cs == null)
        throw new TerminologyServiceException("unable to find code system " + inc.getSystem().toString());
    if (cs.hasVersion())
        if (!existsInParams(params, "version", new UriType(cs.getUrl() + "?version=" + cs.getVersion())))
            params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "?version=" + cs.getVersion())));
    if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
        // special case - add all the code system
        for (ConceptDefinitionComponent def : cs.getCodeSystem().getConcept()) {
            addCodeAndDescendents(inc.getSystem(), def);
        }
    }
    for (ConceptReferenceComponent c : inc.getConcept()) {
        addCode(inc.getSystem(), c.getCode(), Utilities.noString(c.getDisplay()) ? getCodeDisplay(cs, c.getCode()) : c.getDisplay());
    }
    if (inc.getFilter().size() > 1)
        // need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
        throw new TerminologyServiceException("Multiple filters not handled yet");
    if (inc.getFilter().size() == 1) {
        ConceptSetFilterComponent fc = inc.getFilter().get(0);
        if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
            // special: all non-abstract codes in the target code system under the value
            ConceptDefinitionComponent def = getConceptForCode(cs.getCodeSystem().getConcept(), fc.getValue());
            if (def == null)
                throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
            addCodeAndDescendents(inc.getSystem(), def);
        } else
            throw new NotImplementedException("not done yet");
    }
}

Example 25 with UriType

use of org.hl7.fhir.r5.model.UriType in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpanderSimple method importValueSet.

private void importValueSet(String value, List<ValueSetExpansionParameterComponent> params) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException {
    if (value == null)
        throw new TerminologyServiceException("unable to find value set with no identity");
    ValueSet vs = context.fetchResource(ValueSet.class, value);
    if (vs == null)
        throw new TerminologyServiceException("Unable to find imported value set " + value);
    ValueSetExpansionOutcome vso = factory.getExpander().expand(vs);
    if (vso.getService() != null)
        throw new TerminologyServiceException("Unable to expand imported value set " + value);
    if (vs.hasVersion())
        if (!existsInParams(params, "version", new UriType(vs.getUrl() + "?version=" + vs.getVersion())))
            params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "?version=" + vs.getVersion())));
    for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
        if (!existsInParams(params, p.getName(), p.getValue()))
            params.add(p);
    }
    for (ValueSetExpansionContainsComponent c : vso.getValueset().getExpansion().getContains()) {
        addCode(c.getSystem(), c.getCode(), c.getDisplay());
    }
}