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

Example 46 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project cqf-ruler by DBCG.

the class DiscoveryResolutionStu3 method resolveValueSetCodes.

public List<String> resolveValueSetCodes(String valueSetId) {
    ValueSet valueSet = this.search(ValueSet.class, Searches.byCanonical(valueSetId)).firstOrNull();
    List<String> result = new ArrayList<>();
    StringBuilder codes = new StringBuilder();
    if (valueSet.hasExpansion() && valueSet.getExpansion().hasContains()) {
        for (ValueSet.ValueSetExpansionContainsComponent contains : valueSet.getExpansion().getContains()) {
            String system = contains.getSystem();
            String code = contains.getCode();
            codes = getCodesStringBuilder(result, codes, system, code);
        }
    } else if (valueSet.hasCompose() && valueSet.getCompose().hasInclude()) {
        for (ValueSet.ConceptSetComponent concepts : valueSet.getCompose().getInclude()) {
            String system = concepts.getSystem();
            if (concepts.hasConcept()) {
                for (ValueSet.ConceptReferenceComponent concept : concepts.getConcept()) {
                    String code = concept.getCode();
                    codes = getCodesStringBuilder(result, codes, system, code);
                }
            }
        }
    }
    result.add(codes.toString());
    return result;
}

Example 47 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project cqf-ruler by DBCG.

the class CacheValueSetsProvider method cacheValuesets.

/**
 * Using basic authentication this {@link Operation Operation} will update
 * any {@link ValueSet Valueset} listed given the {@link Endpoint Endpoint}
 * provided.
 * Any Valuesets that require expansion will be expanded.
 *
 * @param details    the {@link RequestDetails RequestDetails}
 * @param endpointId the {@link Endpoint Endpoint} id
 * @param valuesets  the {@link StringAndListParam list} of {@link ValueSet
 *                   Valueset} ids
 * @param userName   the userName
 * @param password   the password
 * @return the {@link OperationOutcome OperationOutcome} or the resulting
 *         {@link Bundle Bundle}
 */
@Description(shortDefinition = "$cache-valuesets", value = "Using basic authentication this Operation will update any Valueset listed given the Endpoint provided. Any Valuesets that require expansion will be expanded.", example = "Endpoint/example-id/$cache-valuesets?valuesets=valuesetId1&valuesets=valuesetId2&user=user&password=password")
@Operation(name = "$cache-valuesets", idempotent = true, type = Endpoint.class)
public Resource cacheValuesets(RequestDetails details, @IdParam IdType endpointId, @OperationParam(name = "valuesets") StringAndListParam valuesets, @OperationParam(name = "user") String userName, @OperationParam(name = "pass") String password) {
    Endpoint endpoint = null;
    try {
        endpoint = this.endpointDao.read(endpointId);
        if (endpoint == null) {
            return createErrorOutcome("Could not find Endpoint/" + endpointId);
        }
    } catch (Exception e) {
        return createErrorOutcome("Could not find Endpoint/" + endpointId + "\n" + e);
    }
    IGenericClient client = Clients.forEndpoint(ourCtx, endpoint);
    if (userName != null || password != null) {
        if (userName == null) {
            return createErrorOutcome("Password was provided, but not a user name.");
        } else if (password == null) {
            return createErrorOutcome("User name was provided, but not a password.");
        }
        BasicAuthInterceptor basicAuth = new BasicAuthInterceptor(userName, password);
        client.registerInterceptor(basicAuth);
    // TODO - more advanced security like bearer tokens, etc...
    }
    try {
        Bundle bundleToPost = new Bundle();
        for (StringOrListParam params : valuesets.getValuesAsQueryTokens()) {
            for (StringParam valuesetId : params.getValuesAsQueryTokens()) {
                bundleToPost.addEntry().setRequest(new Bundle.BundleEntryRequestComponent().setMethod(Bundle.HTTPVerb.PUT).setUrl("ValueSet/" + valuesetId.getValue())).setResource(resolveValueSet(client, valuesetId.getValue()));
            }
        }
        return (Resource) systemDao.transaction(details, bundleToPost);
    } catch (Exception e) {
        return createErrorOutcome(e.getMessage());
    }
}

Example 48 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project cqf-ruler by DBCG.

the class CacheValueSetsProvider method getCachedValueSet.

private ValueSet getCachedValueSet(ValueSet expandedValueSet) {
    ValueSet clean = expandedValueSet.copy().setExpansion(null);
    Map<String, ValueSet.ConceptSetComponent> concepts = new HashMap<>();
    for (ValueSet.ValueSetExpansionContainsComponent expansion : expandedValueSet.getExpansion().getContains()) {
        if (!expansion.hasSystem()) {
            continue;
        }
        if (concepts.containsKey(expansion.getSystem())) {
            concepts.get(expansion.getSystem()).addConcept(new ValueSet.ConceptReferenceComponent().setCode(expansion.hasCode() ? expansion.getCode() : null).setDisplay(expansion.hasDisplay() ? expansion.getDisplay() : null));
        } else {
            concepts.put(expansion.getSystem(), new ValueSet.ConceptSetComponent().setSystem(expansion.getSystem()).addConcept(new ValueSet.ConceptReferenceComponent().setCode(expansion.hasCode() ? expansion.getCode() : null).setDisplay(expansion.hasDisplay() ? expansion.getDisplay() : null)));
        }
    }
    clean.setCompose(new ValueSet.ValueSetComposeComponent().setInclude(new ArrayList<>(concepts.values())));
    return clean;
}

Example 49 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project cqf-ruler by DBCG.

the class CodeSystemUpdateProvider method performCodeSystemUpdate.

public OperationOutcome performCodeSystemUpdate(List<ValueSet> valueSets) {
    OperationOutcome response = new OperationOutcome();
    List<String> codeSystems = new ArrayList<>();
    // Possible for this to run out of memory with really large ValueSets and
    // CodeSystems.
    Map<String, Set<String>> codesBySystem = new HashMap<>();
    for (ValueSet vs : valueSets) {
        if (vs.hasCompose() && vs.getCompose().hasInclude()) {
            for (ValueSet.ConceptSetComponent csc : vs.getCompose().getInclude()) {
                if (!csc.hasSystem() || !csc.hasConcept()) {
                    continue;
                }
                String system = csc.getSystem();
                if (!codesBySystem.containsKey(system)) {
                    codesBySystem.put(system, new HashSet<>());
                }
                Set<String> codes = codesBySystem.get(system);
                codes.addAll(csc.getConcept().stream().map(ValueSet.ConceptReferenceComponent::getCode).collect(Collectors.toList()));
            }
        }
    }
    for (Map.Entry<String, Set<String>> entry : codesBySystem.entrySet()) {
        String system = entry.getKey();
        CodeSystem codeSystem = getCodeSystemByUrl(system);
        updateCodeSystem(codeSystem.setUrl(system), getUnionDistinctCodes(entry.getValue(), codeSystem));
        codeSystems.add(codeSystem.getUrl());
    }
    if (codeSystems.size() > 0) {
        return buildIssue(response, "information", "informational", "Successfully updated the following CodeSystems: " + String.join(", ", codeSystems));
    } else {
        return buildIssue(response, "information", "informational", "No code systems were updated");
    }
}

Example 50 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project cqf-ruler by DBCG.

the class CodeSystemUpdateProvider method updateCodeSystems.

/**
 * Update existing {@link CodeSystem CodeSystems} with the codes in all
 * {@link ValueSet ValueSet} resources.
 * System level CodeSystem update operation
 *
 * @return FHIR {@link OperationOutcome OperationOutcome} detailing the success
 *         or failure of the
 *         operation
 */
@Description(shortDefinition = "$updateCodeSystems", value = "Update existing CodeSystems with the codes in all ValueSet resources. System level CodeSystem update operation", example = "$updateCodeSystems")
@Operation(name = "$updateCodeSystems", idempotent = true)
public OperationOutcome updateCodeSystems() {
    IBundleProvider valuesets = this.myValueSetDaoDSTU3.search(SearchParameterMap.newSynchronous());
    List<ValueSet> valueSets = valuesets.getAllResources().stream().map(x -> (ValueSet) x).collect(Collectors.toList());
    OperationOutcome outcome = this.performCodeSystemUpdate(valueSets);
    OperationOutcome response = new OperationOutcome();
    if (outcome.hasIssue()) {
        for (OperationOutcome.OperationOutcomeIssueComponent issue : outcome.getIssue()) {
            response.addIssue(issue);
        }
    }
    return response;
}