Examples with UnsupportedResourceError au.csiro.pathling.encoders.UnsupportedResourceError used on opensource projects

Example 1 with UnsupportedResourceError

use of au.csiro.pathling.encoders.UnsupportedResourceError 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;
}