Examples with CodeType org.hl7.fhir.r4.model.CodeType used on opensource projects

Example 66 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project org.hl7.fhir.core by hapifhir.

the class CodeTypeNullTest method equalsShallow.

@Test
@DisplayName("Test null value equalsShallow()")
void equalsShallow() {
    CodeType nullCode = new CodeType();
    CodeType validCode = new CodeType("theValue");
    Assertions.assertFalse(nullCode.equalsShallow(validCode));
}

Example 67 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project org.hl7.fhir.core by hapifhir.

the class ProfileDrivenRenderer method renderLeaf.

private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode parent, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints, String path, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
    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)
        return;
    else if (e instanceof InstantType)
        x.addText(((InstantType) e).toHumanDisplay());
    else if (e instanceof DateTimeType) {
        renderDateTime(x, e);
    } else if (e instanceof Base64BinaryType)
        x.addText(new Base64().encodeAsString(((Base64BinaryType) e).getValue()));
    else if (e instanceof org.hl7.fhir.r5.model.DateType) {
        org.hl7.fhir.r5.model.DateType dt = ((org.hl7.fhir.r5.model.DateType) e);
        renderDate(x, dt);
    } 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(x, (CodeableConcept) e, showCodeDetails);
    } else if (e instanceof Coding) {
        renderCoding(x, (Coding) e, showCodeDetails);
    } else if (e instanceof CodeableReference) {
        renderCodeableReference(x, (CodeableReference) e, showCodeDetails);
    } else if (e instanceof Annotation) {
        renderAnnotation(x, (Annotation) e);
    } else if (e instanceof Identifier) {
        renderIdentifier(x, (Identifier) e);
    } else if (e instanceof org.hl7.fhir.r5.model.IntegerType) {
        if (((org.hl7.fhir.r5.model.IntegerType) e).hasValue()) {
            x.addText(Integer.toString(((org.hl7.fhir.r5.model.IntegerType) e).getValue()));
        } else {
            x.addText("??");
        }
    } else if (e instanceof org.hl7.fhir.r5.model.Integer64Type) {
        if (((org.hl7.fhir.r5.model.Integer64Type) e).hasValue()) {
            x.addText(Long.toString(((org.hl7.fhir.r5.model.Integer64Type) e).getValue()));
        } else {
            x.addText("??");
        }
    } else if (e instanceof org.hl7.fhir.r5.model.DecimalType) {
        x.addText(((org.hl7.fhir.r5.model.DecimalType) e).getValue().toString());
    } else if (e instanceof HumanName) {
        renderHumanName(x, (HumanName) e);
    } else if (e instanceof SampledData) {
        renderSampledData(x, (SampledData) e);
    } else if (e instanceof Address) {
        renderAddress(x, (Address) e);
    } else if (e instanceof ContactPoint) {
        renderContactPoint(x, (ContactPoint) e);
    } else if (e instanceof Expression) {
        renderExpression(x, (Expression) e);
    } else if (e instanceof Money) {
        renderMoney(x, (Money) e);
    } else if (e instanceof ContactDetail) {
        ContactDetail cd = (ContactDetail) e;
        if (cd.hasName()) {
            x.tx(cd.getName() + ": ");
        }
        boolean first = true;
        for (ContactPoint c : cd.getTelecom()) {
            if (first)
                first = false;
            else
                x.tx(",");
            renderContactPoint(x, c);
        }
    } else if (e instanceof UriType) {
        renderUri(x, (UriType) e, defn.getPath(), rcontext != null && rcontext.getResourceResource() != null ? rcontext.getResourceResource().getId() : null);
    } else if (e instanceof Timing) {
        renderTiming(x, (Timing) e);
    } else if (e instanceof Range) {
        renderRange(x, (Range) e);
    } else if (e instanceof Quantity) {
        renderQuantity(x, (Quantity) e, showCodeDetails);
    } else if (e instanceof Ratio) {
        renderQuantity(x, ((Ratio) e).getNumerator(), showCodeDetails);
        x.tx("/");
        renderQuantity(x, ((Ratio) e).getDenominator(), showCodeDetails);
    } else if (e instanceof Period) {
        Period p = (Period) e;
        renderPeriod(x, p);
    } else if (e instanceof Reference) {
        Reference r = (Reference) e;
        if (r.getReference() != null && r.getReference().contains("#")) {
            if (containedIds.contains(r.getReference().substring(1))) {
                x.ah(r.getReference()).tx("See " + r.getReference());
            } else {
                // in this case, we render the resource in line
                ResourceWrapper rw = null;
                for (ResourceWrapper t : res.getContained()) {
                    if (r.getReference().substring(1).equals(t.getId())) {
                        rw = t;
                    }
                }
                if (rw == null) {
                    renderReference(res, x, r);
                } else {
                    x.an(rw.getId());
                    ResourceRenderer rr = RendererFactory.factory(rw, context.copy().setAddGeneratedNarrativeHeader(false));
                    rr.render(parent.blockquote(), rw);
                }
            }
        } else {
            renderReference(res, x, r);
        }
    } else if (e instanceof Resource) {
        return;
    } else if (e instanceof DataRequirement) {
        DataRequirement p = (DataRequirement) e;
        renderDataRequirement(x, p);
    } else if (e instanceof PrimitiveType) {
        x.tx(((PrimitiveType) e).primitiveValue());
    } else if (e instanceof ElementDefinition) {
        x.tx("todo-bundle");
    } else if (e != null && !(e instanceof Attachment) && !(e instanceof Narrative) && !(e instanceof Meta)) {
        throw new NotImplementedException("type " + e.getClass().getName() + " not handled - should not be here");
    }
}

Example 68 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project org.hl7.fhir.core by hapifhir.

the class SearchParameterRenderer method render.

public boolean render(XhtmlNode x, SearchParameter spd) throws IOException, FHIRException, EOperationOutcome {
    x.h2().addText(spd.getName());
    XhtmlNode p = x.para();
    p.tx("Parameter ");
    p.code().tx(spd.getCode());
    p.tx(":");
    p.code().tx(spd.getType().toCode());
    addMarkdown(x, spd.getDescription());
    XhtmlNode tbl = x.table("grid");
    XhtmlNode tr = tbl.tr();
    tr.td().tx(Utilities.pluralize("Resource", spd.getBase().size()));
    XhtmlNode td = tr.td();
    for (CodeType t : spd.getBase()) {
        StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
        if (sd != null && sd.hasUserData("path")) {
            td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
        } else {
            td.sep(", ").tx(t.getCode());
        }
    }
    tr = tbl.tr();
    tr.td().tx("Expression");
    if (spd.hasExpression()) {
        tr.td().code().tx(spd.getExpression());
    } else {
        tr.td().tx("(none)");
    }
    if (spd.hasXpathUsage()) {
        tr = tbl.tr();
        tr.td().tx("Usage");
        tr.td().tx(spd.getXpathUsage().getDisplay());
    }
    if (spd.hasXpath()) {
        tr = tbl.tr();
        tr.td().tx("XPath");
        tr.td().code().tx(spd.getXpath());
    }
    if (spd.hasTarget()) {
        tr = tbl.tr();
        tr.td().tx(Utilities.pluralize("Target Resources", spd.getTarget().size()));
        td = tr.td();
        for (CodeType t : spd.getTarget()) {
            StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
            if (sd != null && sd.hasUserData("path")) {
                td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
            } else {
                td.sep(", ").tx(t.getCode());
            }
        }
    }
    tr = tbl.tr();
    tr.td().tx("Multiples");
    if (spd.getMultipleAnd() && spd.getMultipleOr()) {
        tr.td().tx("The parameter can repeat (and) and can have repeating values (or)");
    } else if (spd.getMultipleOr()) {
        tr.td().tx("The parameter can repeat (and) but each repeat can only have one value");
    } else if (spd.getMultipleAnd()) {
        tr.td().tx("The parameter cannot repeat (and) but the single parameter can have multiple values (or)");
    } else {
        tr.td().tx("The parameter cannot repeat or have multiple values");
    }
    if (spd.hasComparator()) {
        tr = tbl.tr();
        tr.td().tx("Comparators");
        td = tr.td().tx("Allowed: ");
        for (Enumeration<SearchComparator> t : spd.getComparator()) {
            td.sep(", ").tx(t.asStringValue());
        }
    }
    if (spd.hasModifier()) {
        tr = tbl.tr();
        tr.td().tx("Modifiers");
        td = tr.td().tx("Allowed: ");
        for (Enumeration<SearchModifierCode> t : spd.getModifier()) {
            td.sep(", ").tx(t.asStringValue());
        }
    }
    if (spd.hasChain()) {
        tr = tbl.tr();
        tr.td().tx("Chains");
        td = tr.td().tx("Allowed: ");
        for (StringType t : spd.getChain()) {
            td.sep(", ").tx(t.asStringValue());
        }
    }
    if (spd.hasComponent()) {
        x.para().b().tx("Components");
        tbl = x.table("grid");
        for (SearchParameterComponentComponent t : spd.getComponent()) {
            tr = tbl.tr();
            SearchParameter tsp = context.getWorker().fetchResource(SearchParameter.class, t.getDefinition());
            if (tsp != null && tsp.hasUserData("path")) {
                tr.td().ah(tsp.getUserString("path")).tx(tsp.present());
            } else {
                tr.td().tx(t.getDefinition());
            }
            tr.td().code().tx(t.getExpression());
        }
    }
    return false;
}

Example 69 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project org.hl7.fhir.core by hapifhir.

the class StructureMapUtilities method translate.

public Base translate(TransformContext context, StructureMap map, Base source, String conceptMapUrl, String fieldToReturn) throws FHIRException {
    Coding src = new Coding();
    if (source.isPrimitive()) {
        src.setCode(source.primitiveValue());
    } else if ("Coding".equals(source.fhirType())) {
        Base[] b = source.getProperty("system".hashCode(), "system", true);
        if (b.length == 1)
            src.setSystem(b[0].primitiveValue());
        b = source.getProperty("code".hashCode(), "code", true);
        if (b.length == 1)
            src.setCode(b[0].primitiveValue());
    } else if ("CE".equals(source.fhirType())) {
        Base[] b = source.getProperty("codeSystem".hashCode(), "codeSystem", true);
        if (b.length == 1)
            src.setSystem(b[0].primitiveValue());
        b = source.getProperty("code".hashCode(), "code", true);
        if (b.length == 1)
            src.setCode(b[0].primitiveValue());
    } else
        throw new FHIRException("Unable to translate source " + source.fhirType());
    String su = conceptMapUrl;
    if (conceptMapUrl.equals("http://hl7.org/fhir/ConceptMap/special-oid2uri")) {
        String uri = worker.oid2Uri(src.getCode());
        if (uri == null)
            uri = "urn:oid:" + src.getCode();
        if ("uri".equals(fieldToReturn))
            return new UriType(uri);
        else
            throw new FHIRException("Error in return code");
    } else {
        ConceptMap cmap = null;
        if (conceptMapUrl.startsWith("#")) {
            for (Resource r : map.getContained()) {
                if (r instanceof ConceptMap && r.getId().equals(conceptMapUrl.substring(1))) {
                    cmap = (ConceptMap) r;
                    su = map.getUrl() + "#" + conceptMapUrl;
                }
            }
            if (cmap == null)
                throw new FHIRException("Unable to translate - cannot find map " + conceptMapUrl);
        } else {
            if (conceptMapUrl.contains("#")) {
                String[] p = conceptMapUrl.split("\\#");
                StructureMap mapU = worker.fetchResource(StructureMap.class, p[0]);
                for (Resource r : mapU.getContained()) {
                    if (r instanceof ConceptMap && r.getId().equals(p[1])) {
                        cmap = (ConceptMap) r;
                        su = conceptMapUrl;
                    }
                }
            }
            if (cmap == null)
                cmap = worker.fetchResource(ConceptMap.class, conceptMapUrl);
        }
        Coding outcome = null;
        boolean done = false;
        String message = null;
        if (cmap == null) {
            if (services == null)
                message = "No map found for " + conceptMapUrl;
            else {
                outcome = services.translate(context.getAppInfo(), src, conceptMapUrl);
                done = true;
            }
        } else {
            List<SourceElementComponentWrapper> list = new ArrayList<SourceElementComponentWrapper>();
            for (ConceptMapGroupComponent g : cmap.getGroup()) {
                for (SourceElementComponent e : g.getElement()) {
                    if (!src.hasSystem() && src.getCode().equals(e.getCode()))
                        list.add(new SourceElementComponentWrapper(g, e));
                    else if (src.hasSystem() && src.getSystem().equals(g.getSource()) && src.getCode().equals(e.getCode()))
                        list.add(new SourceElementComponentWrapper(g, e));
                }
            }
            if (list.size() == 0)
                done = true;
            else if (list.get(0).getComp().getTarget().size() == 0)
                message = "Concept map " + su + " found no translation for " + src.getCode();
            else {
                for (TargetElementComponent tgt : list.get(0).getComp().getTarget()) {
                    if (tgt.getRelationship() == null || EnumSet.of(ConceptMapRelationship.RELATEDTO, ConceptMapRelationship.EQUIVALENT, ConceptMapRelationship.SOURCEISNARROWERTHANTARGET).contains(tgt.getRelationship())) {
                        if (done) {
                            message = "Concept map " + su + " found multiple matches for " + src.getCode();
                            done = false;
                        } else {
                            done = true;
                            outcome = new Coding().setCode(tgt.getCode()).setSystem(list.get(0).getGroup().getTarget());
                        }
                    }
                }
                if (!done)
                    message = "Concept map " + su + " found no usable translation for " + src.getCode();
            }
        }
        if (!done)
            throw new FHIRException(message);
        if (outcome == null)
            return null;
        if ("code".equals(fieldToReturn))
            return new CodeType(outcome.getCode());
        else
            return outcome;
    }
}

Example 70 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project pathling by aehrc.

the class ImportExecutor method execute.

/**
 * Executes an import request.
 *
 * @param inParams a FHIR {@link Parameters} object describing the import request
 * @return a FHIR {@link OperationOutcome} resource describing the result
 */
@Nonnull
public OperationOutcome execute(@Nonnull @ResourceParam final Parameters inParams) {
    // Parse and validate the JSON request.
    final List<ParametersParameterComponent> sourceParams = inParams.getParameter().stream().filter(param -> "source".equals(param.getName())).collect(Collectors.toList());
    if (sourceParams.isEmpty()) {
        throw new InvalidUserInputError("Must provide at least one source parameter");
    }
    log.info("Received $import request");
    // the corresponding table in the warehouse.
    for (final ParametersParameterComponent sourceParam : sourceParams) {
        final ParametersParameterComponent resourceTypeParam = sourceParam.getPart().stream().filter(param -> "resourceType".equals(param.getName())).findFirst().orElseThrow(() -> new InvalidUserInputError("Must provide resourceType for each source"));
        final ParametersParameterComponent urlParam = sourceParam.getPart().stream().filter(param -> "url".equals(param.getName())).findFirst().orElseThrow(() -> new InvalidUserInputError("Must provide url for each source"));
        // The mode parameter defaults to 'overwrite'.
        final ImportMode importMode = sourceParam.getPart().stream().filter(param -> "mode".equals(param.getName()) && param.getValue() instanceof CodeType).findFirst().map(param -> ImportMode.fromCode(((CodeType) param.getValue()).asStringValue())).orElse(ImportMode.OVERWRITE);
        final String resourceCode = ((CodeType) resourceTypeParam.getValue()).getCode();
        final ResourceType resourceType = ResourceType.fromCode(resourceCode);
        // Get an encoder based on the declared resource type within the source parameter.
        final ExpressionEncoder<IBaseResource> fhirEncoder;
        try {
            fhirEncoder = fhirEncoders.of(resourceType.toCode());
        } catch (final UnsupportedResourceError e) {
            throw new InvalidUserInputError("Unsupported resource type: " + resourceCode);
        }
        // Read the resources from the source URL into a dataset of strings.
        final Dataset<String> jsonStrings = readStringsFromUrl(urlParam);
        // Parse each line into a HAPI FHIR object, then encode to a Spark dataset.
        final Dataset<IBaseResource> resources = jsonStrings.map(jsonToResourceConverter(), fhirEncoder);
        log.info("Importing {} resources (mode: {})", resourceType.toCode(), importMode.getCode());
        if (importMode == ImportMode.OVERWRITE) {
            database.overwrite(resourceType, resources.toDF());
        } else {
            database.merge(resourceType, resources.toDF());
        }
    }
    // We return 200, as this operation is currently synchronous.
    log.info("Import complete");
    // Construct a response.
    final OperationOutcome opOutcome = new OperationOutcome();
    final OperationOutcomeIssueComponent issue = new OperationOutcomeIssueComponent();
    issue.setSeverity(IssueSeverity.INFORMATION);
    issue.setCode(IssueType.INFORMATIONAL);
    issue.setDiagnostics("Data import completed successfully");
    opOutcome.getIssue().add(issue);
    return opOutcome;
}