Examples with FINAL org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL used on opensource projects

Example 76 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL 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;
}

Example 77 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project pathling by aehrc.

the class UpdateProvider method update.

/**
 * Implements the update operation.
 *
 * @param id the id of the resource to be updated
 * @param resource the resource to be updated
 * @return a {@link MethodOutcome} describing the result of the operation
 * @see <a href="https://hl7.org/fhir/R4/http.html#update">update</a>
 */
@Update
@OperationAccess("update")
@SuppressWarnings("UnusedReturnValue")
public MethodOutcome update(@Nullable @IdParam final IdType id, @Nullable @ResourceParam final IBaseResource resource) {
    checkUserInput(id != null && !id.isEmpty(), "ID must be supplied");
    checkUserInput(resource != null, "Resource must be supplied");
    final String resourceId = id.getIdPart();
    final IBaseResource preparedResource = prepareResourceForUpdate(resource, resourceId);
    database.merge(resourceType, preparedResource);
    final MethodOutcome outcome = new MethodOutcome();
    outcome.setId(resource.getIdElement());
    outcome.setResource(preparedResource);
    return outcome;
}

Example 78 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project pathling by aehrc.

the class AggregateExecutorTest method assertResponse.

void assertResponse(@Nonnull final String expectedPath, @Nonnull final AggregateResponse response) {
    final Parameters parameters = response.toParameters();
    final String actualJson = jsonParser.encodeResourceToString(parameters);
    assertJson("responses/" + expectedPath, actualJson);
}

Example 79 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project pathling by aehrc.

the class BaseMapping method checkResponseEntry.

/**
 * Ensures that the bundle-response entry contains a successful response or otherwise throws the
 * appropriate subclass of {@link BaseServerResponseException}  capturing the error information
 * returned from the terminology server.
 *
 * <p>
 * This is adapted from HAPI: `ca.uhn.fhir.rest.client.impl.BaseClient#invokeClient(...)`.
 *
 * @param entry the bundle entry.
 * @param fhirContext the Fhir context to use.
 * @throws BaseServerResponseException then the entry status code is not 2xx.
 */
private static void checkResponseEntry(@Nonnull final BundleEntryComponent entry, @Nonnull final FhirContext fhirContext) {
    final BundleEntryResponseComponent response = entry.getResponse();
    final int statusCode = Integer.parseInt(response.getStatus());
    if (statusCode < 200 || statusCode > 299) {
        String message = "Error in response entry : HTTP " + response.getStatus();
        final IBaseOperationOutcome oo = (IBaseOperationOutcome) entry.getResource();
        final String details = OperationOutcomeUtil.getFirstIssueDetails(fhirContext, oo);
        if (StringUtils.isNotBlank(details)) {
            message = message + " : " + details;
        }
        final BaseServerResponseException exception = BaseServerResponseException.newInstance(statusCode, message);
        exception.setOperationOutcome(oo);
        throw exception;
    }
}

Example 80 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL 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;
}