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

Example 41 with ResourceType

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

the class ManifestConverterTest method convertsManifest.

@Test
void convertsManifest() {
    database = new Database(configuration, spark, fhirEncoders, executor);
    final PassportScope passportScope = new PassportScope();
    final VisaManifest manifest = new VisaManifest();
    manifest.setPatientIds(Arrays.asList(PATIENT_ID_1, PATIENT_ID_2, PATIENT_ID_3, PATIENT_ID_4));
    final ManifestConverter manifestConverter = new ManifestConverter(configuration, fhirContext);
    manifestConverter.populateScope(passportScope, manifest);
    // Convert the scope to JSON and compare it to a test fixture.
    final Gson gson = new GsonBuilder().create();
    final String json = gson.toJson(passportScope);
    assertJson("responses/ManifestConverterTest/convertsManifest.json", json);
    // our test patients.
    for (final ResourceType resourceType : passportScope.keySet()) {
        if (AVAILABLE_RESOURCE_TYPES.contains(resourceType)) {
            boolean found = false;
            for (final String filter : passportScope.get(resourceType)) {
                final Dataset<Row> dataset = assertThatResultOf(resourceType, filter).isElementPath(BooleanPath.class).selectResult().apply(result -> result.filter(result.columns()[1])).getDataset();
                if (dataset.count() > 0) {
                    found = true;
                }
            }
            assertTrue(found, "No results found for " + resourceType.toCode());
        }
    }
}

Example 42 with ResourceType

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

the class AbstractParserTest method mockResource.

void mockResource(final ResourceType... resourceTypes) {
    for (final ResourceType resourceType : resourceTypes) {
        final Dataset<Row> dataset = TestHelpers.getDatasetForResourceType(spark, resourceType);
        when(database.read(resourceType)).thenReturn(dataset);
    }
}

Example 43 with ResourceType

use of org.hl7.fhir.r4.model.ResourceType 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 44 with ResourceType

use of org.hl7.fhir.r4.model.ResourceType 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 45 with ResourceType

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

the class BatchProvider method batch.

@Transaction
@OperationAccess("batch")
public Bundle batch(@Nullable @TransactionParam final Bundle bundle) {
    checkUserInput(bundle != null, "Bundle must be provided");
    final Map<ResourceType, List<IBaseResource>> resourcesForUpdate = new EnumMap<>(ResourceType.class);
    final Bundle response = new Bundle();
    response.setType(BATCHRESPONSE);
    // the responses should these operations be successful.
    for (final Bundle.BundleEntryComponent entry : bundle.getEntry()) {
        processEntry(resourcesForUpdate, response, entry);
    }
    if (!resourcesForUpdate.isEmpty()) {
        // Merge in any updated resources into their respective tables.
        update(resourcesForUpdate);
    }
    return response;
}