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raleigh-g-thompsonc-schuler
raleigh-g-thompson
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c-schuler
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Feature/convert r5 to r4 (#589)
* adds convert r5 to r4 operation * adds r5 to r4 operation tests * change default bundle type to transaction * adds ConvertR5toR4 command to operation factory * updates based on PR feedback * Improve ConvertR5toR4 CLI conversion tests and modernize implementation - Keeps the runtime behavior of ConvertR5toR4 intact. - Significantly strengthens the test suite by asserting that: - All CLI conversions produce R4 Bundles. - Entry counts match the number of source resources for both single and multiple inputs. - Error paths for invalid encoding and invalid directories are enforced. - Cleans up test code style and ensures no test artifacts persist on disk after execution. - Removed operations/convert/ConvertR5toR4 class --------- Co-authored-by: c-schuler <hoofschu@gmail.com>
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‎tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/OperationFactory.java‎

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@@ -223,6 +223,8 @@ static Operation createOperation(String operationName) {
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return new StripGeneratedContentOperation();
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case "SpreadsheetValidateVSandCS":
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return new SpreadsheetValidateVSandCS();
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case "ConvertR5toR4":
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return new ConvertR5toR4();
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default:
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throw new IllegalArgumentException("Invalid operation: " + operationName);
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}

‎tooling/src/main/java/org/opencds/cqf/tooling/operation/ConvertR5toR4.java‎

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package org.opencds.cqf.tooling.operation;
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import ca.uhn.fhir.model.valueset.BundleTypeEnum;
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import ca.uhn.fhir.util.BundleBuilder;
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import jakarta.annotation.Nonnull;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.opencds.cqf.tooling.Operation;
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import org.opencds.cqf.tooling.utilities.BundleUtils;
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import org.opencds.cqf.tooling.utilities.FhirContextCache;
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import org.opencds.cqf.tooling.utilities.IOUtils;
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import org.opencds.cqf.tooling.utilities.converters.ResourceAndTypeConverter;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.UUID;
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import java.util.stream.Collectors;
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public class ConvertR5toR4 extends Operation {
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public static final List<BundleTypeEnum> ALLOWED_BUNDLE_TYPES = List.of(
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BundleTypeEnum.COLLECTION,
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BundleTypeEnum.TRANSACTION
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);
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public static Boolean isBundleTypeAllowed(String bundleType) {
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if (bundleType == null) {
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return false;
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}
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return ALLOWED_BUNDLE_TYPES.stream()
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.anyMatch(bt -> bt.name().equalsIgnoreCase(bundleType));
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}
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public static List<String> allowedBundleTypes() {
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return ALLOWED_BUNDLE_TYPES.stream()
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.map(Enum::name)
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.map(String::toLowerCase)
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.collect(Collectors.toList());
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}
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private static final Logger logger = LoggerFactory.getLogger(ConvertR5toR4.class);
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// COMMAND LINE ARGUMENTS - REQUIRED
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private String pathToDirectory; // -pathtodir (-ptd)
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// COMMAND LINE ARGUMENTS - OPTIONAL
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private String encoding = "json"; // -encoding (-e)
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private String bundleId = UUID.randomUUID().toString(); // -bundleid (-bid)
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private String bundleType = "transaction"; // -type (-t)
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private String outputFileName = null; // -outputfilename (-ofn)
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private void extractOptionsFromArgs(String[] args) {
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for (String arg : args) {
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if (arg.equals("-ConvertR5toR4")) continue;
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var flagAndValue = arg.split("=");
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if (flagAndValue.length < 2) {
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throw new IllegalArgumentException("Invalid argument: " + arg);
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}
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var flag = flagAndValue[0];
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var value = flagAndValue[1];
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switch (flag.replace("-", "").toLowerCase()) {
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case "bundleid":
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case "bid":
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bundleId = value;
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break;
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case "bundletype":
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case "bt":
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bundleType = value;
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break;
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case "encoding":
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case "e":
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encoding = value.toLowerCase();
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break;
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case "outputfilename":
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case "ofn":
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outputFileName = value;
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break;
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case "outputpath":
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case "op":
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setOutputPath(value);
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break;
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case "pathtodir":
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case "ptd":
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pathToDirectory = value;
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break;
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default: throw new IllegalArgumentException("Unknown flag: " + flag);
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}
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}
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}
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private void validateBundleType() {
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if (bundleType == null) {
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throw new IllegalArgumentException("BundleType cannot be null");
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}
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if (!isBundleTypeAllowed(bundleType)) {
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throw new IllegalArgumentException(String.format("The bundle type [%s] is invalid. Allowed Types: %s", bundleType, String.join(", ",allowedBundleTypes())));
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}
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}
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private void validateEncoding() {
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if (encoding == null || encoding.isEmpty()) {
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encoding = "json";
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} else {
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if (!encoding.equalsIgnoreCase("xml") && !encoding.equalsIgnoreCase("json")) {
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throw new IllegalArgumentException(String.format("Unsupported encoding: %s. Allowed encodings { json, xml }", encoding));
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}
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}
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}
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private void validatePathToDirectory() {
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if (pathToDirectory == null) {
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throw new IllegalArgumentException(String.format("The path [%s] to the resource directory is required", pathToDirectory));
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}
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var resourceDirectory = new File(pathToDirectory);
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if (!resourceDirectory.isDirectory()) {
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throw new RuntimeException(String.format("The specified path [%s] to resource files is not a directory", pathToDirectory));
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}
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var resources = resourceDirectory.listFiles();
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if (resources == null || resources.length == 0) {
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throw new RuntimeException(String.format("The specified path [%s] to resource files is empty", pathToDirectory));
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}
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}
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@Override
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public void execute(String[] args) {
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setOutputPath("src/main/resources/org/opencds/cqf/tooling/convert/output"); // default
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extractOptionsFromArgs(args);
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validateEncoding();
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validatePathToDirectory();
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validateBundleType();
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var bundleType = BundleUtils.getBundleType(this.bundleType);
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if (bundleType == null) {
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logger.error("Invalid bundle type: {}", this.bundleType);
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}
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else {
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var bundle = convertResources(
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bundleId,
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bundleType,
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IOUtils.readResources(
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IOUtils.getFilePaths(pathToDirectory, true),
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FhirContextCache.getContext("r5")));
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IOUtils.writeResource(
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bundle,
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getOutputPath(),
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IOUtils.Encoding.parse(encoding),
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FhirContextCache.getContext("r4"),
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true,
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outputFileName != null ? outputFileName : bundleId);
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}
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}
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private IBaseBundle convertResources(String bundleId, BundleTypeEnum type,
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@Nonnull List<IBaseResource> resourcesToConvert) {
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var convertedResources = new ArrayList<org.hl7.fhir.r4.model.Resource>();
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for (var resource : resourcesToConvert){
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if (resource instanceof org.hl7.fhir.r5.model.Resource) {
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convertedResources.add(ResourceAndTypeConverter.r5ToR4Resource(resource));
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}
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}
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var context = FhirContextCache.getContext("r4");
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var builder = new BundleBuilder(context);
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if (type == BundleTypeEnum.COLLECTION) {
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convertedResources.forEach(builder::addCollectionEntry);
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}
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else {
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convertedResources.forEach(builder::addTransactionUpdateEntry);
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}
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var bundle = builder.getBundle();
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bundle.setId(bundleId == null ? UUID.randomUUID().toString() : bundleId);
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return bundle;
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}
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}

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