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c-schulerc-schuler
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Bringing back BundleToTransaction operation
1 parent 37a4a89 commit c65d3c5

3 files changed

Lines changed: 244 additions & 0 deletions

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‎tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/command/BundleCommand.java‎

Lines changed: 14 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,7 @@
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BundleCommand.Resources.class,
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BundleCommand.ToResources.class,
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BundleCommand.ToTransaction.class,
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BundleCommand.Transaction.class,
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BundleCommand.Post.class,
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BundleCommand.Publish.class,
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})
@@ -60,6 +61,19 @@ protected String getOperationName() {
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return "MakeTransaction";
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}
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@Override
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protected Operation createOperation() {
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return new ExecutableOperationAdapter(new org.opencds.cqf.tooling.operations.bundle.BundleToTransaction());
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}
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}
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@Command(name = "transaction", description = "Execute Bundles as transactions on a FHIR server")
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static class Transaction extends OperationCommand {
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@Override
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protected String getOperationName() {
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return "BundleTransaction";
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}
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@Override
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protected Operation createOperation() {
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return new ExecutableOperationAdapter(new org.opencds.cqf.tooling.operations.bundle.BundleTransaction());

‎tooling-ig/src/main/java/org/opencds/cqf/tooling/operations/bundle/BundleToTransaction.java‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,186 @@
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package org.opencds.cqf.tooling.operations.bundle;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.FileReader;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.opencds.cqf.tooling.operations.ExecutableOperation;
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import org.opencds.cqf.tooling.operations.Operation;
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import org.opencds.cqf.tooling.operations.OperationParam;
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import org.opencds.cqf.tooling.utilities.FhirContextCache;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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@Operation(name = "MakeTransaction")
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public class BundleToTransaction implements ExecutableOperation {
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private static final Logger logger = LoggerFactory.getLogger(BundleToTransaction.class);
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private static final String DEFAULT_OUTPUT_PATH =
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"src/main/resources/org/opencds/cqf/tooling/bundle/output";
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@OperationParam(
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alias = {"e", "encoding"},
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setter = "setEncoding",
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defaultValue = "json",
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description = "Output encoding { json, xml } (default json)")
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private String encoding;
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@OperationParam(
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alias = {"p", "path"},
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setter = "setPath",
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required = true,
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description = "Path to a Bundle file or directory of Bundles (required)")
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private String path;
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@OperationParam(
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alias = {"op", "outputpath"},
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setter = "setOutputPath",
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description = "Output directory for the converted transaction Bundles")
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private String outputPath;
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@OperationParam(
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alias = {"v", "version"},
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setter = "setVersion",
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defaultValue = "r4",
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description = "FHIR version { dstu2, stu3, r4 } (default r4)")
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private String version;
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@Override
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public void execute() {
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if (path == null) {
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throw new IllegalArgumentException("The path to a Bundle or directory of resources is required");
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}
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if (outputPath == null) {
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outputPath = DEFAULT_OUTPUT_PATH;
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}
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File outputDir = new File(outputPath);
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if (!outputDir.exists()) {
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outputDir.mkdirs();
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}
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if (encoding == null) {
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encoding = "json";
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}
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FhirContext context = FhirContextCache.getContext(version);
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File file = new File(path);
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File[] bundles;
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if (file.isDirectory()) {
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bundles = file.listFiles();
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} else {
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bundles = new File[] {file};
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}
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List<IBaseResource> resources = getResources(bundles, context);
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convertToTransaction(resources, context);
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}
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private void convertToTransaction(List<IBaseResource> resources, FhirContext context) {
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if (context.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
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for (IBaseResource resource : resources) {
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if (resource instanceof org.hl7.fhir.dstu3.model.Bundle) {
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org.hl7.fhir.dstu3.model.Bundle bundle = (org.hl7.fhir.dstu3.model.Bundle) resource;
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for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
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if (entry.getResource() != null) {
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entry.setRequest(new org.hl7.fhir.dstu3.model.Bundle.BundleEntryRequestComponent()
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.setUrl(entry.getResource().getId())
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.setMethod(org.hl7.fhir.dstu3.model.Bundle.HTTPVerb.PUT));
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}
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}
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bundle.setType(org.hl7.fhir.dstu3.model.Bundle.BundleType.TRANSACTION);
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writeResource(bundle, context);
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}
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}
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} else if (context.getVersion().getVersion() == FhirVersionEnum.R4) {
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for (IBaseResource resource : resources) {
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if (resource instanceof org.hl7.fhir.r4.model.Bundle) {
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org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) resource;
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for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
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if (entry.getResource() != null) {
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entry.setRequest(new org.hl7.fhir.r4.model.Bundle.BundleEntryRequestComponent()
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.setUrl(entry.getResource().getId())
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.setMethod(org.hl7.fhir.r4.model.Bundle.HTTPVerb.PUT));
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}
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}
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bundle.setType(org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION);
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writeResource(bundle, context);
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}
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}
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}
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}
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private List<IBaseResource> getResources(File[] files, FhirContext context) {
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List<IBaseResource> resources = new ArrayList<>();
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for (File file : files) {
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if (file.isDirectory()) {
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resources.addAll(getResources(file.listFiles(), context));
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continue;
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}
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IBaseResource resource = null;
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if (file.getPath().endsWith(".xml")) {
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try {
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resource = context.newXmlParser().parseResource(new FileReader(file));
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} catch (FileNotFoundException e) {
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throw new RuntimeException(e.getMessage(), e);
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} catch (Exception e) {
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logger.debug("Skipping non-parseable file: {}", file.getName());
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continue;
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}
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} else if (file.getPath().endsWith(".json")) {
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try {
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resource = context.newJsonParser().parseResource(new FileReader(file));
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} catch (FileNotFoundException e) {
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throw new RuntimeException(e.getMessage(), e);
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} catch (Exception e) {
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logger.debug("Skipping non-parseable file: {}", file.getName());
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continue;
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}
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} else {
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continue;
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}
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resources.add(resource);
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}
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return resources;
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}
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private void writeResource(IBaseResource resource, FhirContext context) {
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String fileName = resource.getIdElement().getResourceType() + "-"
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+ resource.getIdElement().getIdPart() + "." + encoding;
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File outputFile = new File(outputPath, fileName);
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try (FileOutputStream writer = new FileOutputStream(outputFile)) {
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String encoded = encoding.equals("json")
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? context.newJsonParser().setPrettyPrint(true).encodeResourceToString(resource)
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: context.newXmlParser().setPrettyPrint(true).encodeResourceToString(resource);
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writer.write(encoded.getBytes());
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writer.flush();
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} catch (IOException e) {
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throw new RuntimeException(e.getMessage(), e);
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}
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}
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public void setEncoding(String encoding) {
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this.encoding = encoding;
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}
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public void setPath(String path) {
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this.path = path;
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}
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public void setOutputPath(String outputPath) {
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this.outputPath = outputPath;
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}
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public void setVersion(String version) {
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this.version = version;
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}
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}

‎tooling-ig/src/test/java/org/opencds/cqf/tooling/operation/BundleToTransactionTest.java‎

Lines changed: 44 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,44 @@
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package org.opencds.cqf.tooling.operation;
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import java.io.File;
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import org.opencds.cqf.tooling.Operation;
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import org.opencds.cqf.tooling.operations.ExecutableOperationAdapter;
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import org.opencds.cqf.tooling.operations.bundle.BundleToTransaction;
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import org.testng.Assert;
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import org.testng.annotations.Test;
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public class BundleToTransactionTest {
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@Test
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public void testExecute_BundleDecomposition() {
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String projectPath = System.getProperty("user.dir");
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String relativeJsonPath = "src/main/resources/libraryevaluationtest-bundle.json";
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String jsonFilePath = projectPath + File.separator + relativeJsonPath;
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String relativePath = "target/test-output/bundleToTransactionResults";
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Operation operation = new ExecutableOperationAdapter(new BundleToTransaction());
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String[] args = new String[] {
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"-MakeTransaction",
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"-p=" + jsonFilePath,
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"-e=json",
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"-op=" + projectPath + File.separator + relativePath
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};
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operation.execute(args);
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File resultDir = new File(projectPath + File.separator + relativePath);
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Assert.assertTrue(resultDir.exists() && resultDir.isDirectory(), "Result directory does not exist.");
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String expectedFile = "Bundle-libraryevaluationtest-bundle.json";
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File[] actualFiles = resultDir.listFiles((dir, name) -> name.endsWith(".json"));
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Assert.assertNotNull(actualFiles, "Bundle resource folder should not be null.");
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boolean found = false;
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for (File file : actualFiles) {
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if (file.getName().equals(expectedFile)) {
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found = true;
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break;
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}
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}
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Assert.assertTrue(found, "Expected file not found: " + expectedFile);
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}
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}

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