eRSD Transformer Enhancements for eRSD V3 (#592)

* Updates to eRSD Transformer for manifest parameters and other V3 improvements

* Updated test cases

* Remove eRSDGrouperComposeFixer

* Created constants for frequently-used system url

Author: sliver007

tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/OperationFactory.java

@@ -15,8 +15,6 @@
 import org.opencds.cqf.tooling.acceleratorkit.DTProcessor;
 import org.opencds.cqf.tooling.acceleratorkit.Processor;
 import org.opencds.cqf.tooling.casereporting.tes.TESPackageGenerator;
-import org.opencds.cqf.tooling.casereporting.transformer.ErsdTransformer;
-import org.opencds.cqf.tooling.dateroller.DataDateRollerOperation;
 import org.opencds.cqf.tooling.exception.InvalidOperationArgs;
 import org.opencds.cqf.tooling.exception.OperationNotFound;
 import org.opencds.cqf.tooling.library.r4.LibraryGenerator;

tooling/src/main/java/org/opencds/cqf/tooling/casereporting/transformer/ErsdTransformer.java

@@ -4,6 +4,9 @@
 import ca.uhn.fhir.context.FhirVersionEnum;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.CanonicalType;
+import org.hl7.fhir.r4.model.ResourceType;
+import org.hl7.fhir.r4.model.ValueSet;
 import org.opencds.cqf.tooling.Operation;
 
 import java.io.*;
@@ -15,6 +18,7 @@ public class BundleToTransactionOperation extends Operation {
     private String encoding; // -encoding (-e)
     private String path; // -path (-p)
     private String version; // -version (-v) Can be dstu2, stu3, or r4
+    private Boolean relativeRequestUrls; // -relativerequesturls (-rru_
 
     private IBaseResource theResource;
     private List<IBaseResource> theResources = new ArrayList<>();
@@ -49,6 +53,8 @@ public void execute(String[] args) {
                 case "version": case "v":
                     version = value;
                     break;
+                case "relativerequesturls": case "rru":
+                    relativeRequestUrls = Boolean.parseBoolean(value); break; // -relativerequesturls (-rru)
                 default: throw new IllegalArgumentException("Unknown flag: " + flag);
             }
         }
@@ -112,7 +118,32 @@ else if (context.getVersion().getVersion() == FhirVersionEnum.R4) {
                     org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle)resource;
                     for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
                         if (entry.getResource() != null) {
-                            entry.setRequest(new org.hl7.fhir.r4.model.Bundle.BundleEntryRequestComponent().setUrl(entry.getResource().getId()).setMethod(org.hl7.fhir.r4.model.Bundle.HTTPVerb.PUT));
+                            if (entry.getResource().getResourceType().compareTo(ResourceType.ValueSet) == 0) {
+                                var valueSet = (org.hl7.fhir.r4.model.ValueSet)entry.getResource();
+                                ValueSet.ValueSetComposeComponent compose = valueSet.getCompose();
+                                ValueSet.ValueSetComposeComponent newCompose = new ValueSet.ValueSetComposeComponent();
+                                List<ValueSet.ConceptSetComponent> concepts = compose.getInclude();
+                                for (ValueSet.ConceptSetComponent concept : concepts) {
+                                    if (concept.hasValueSet()) {
+                                        List<CanonicalType> referencedValueSets = concept.getValueSet();
+                                        if (referencedValueSets.size() > 1) {
+
+                                            for (CanonicalType reference : referencedValueSets) {
+                                                List<CanonicalType> newInclude = new ArrayList<>();
+                                                newInclude.add(reference);
+                                                newCompose.addInclude(new ValueSet.ConceptSetComponent().setValueSet(newInclude));
+                                            }
+                                        }
+                                    }
+                                }
+                                valueSet.setCompose(newCompose);
+                            }
+
+                            entry.setRequest(
+                                    new org.hl7.fhir.r4.model.Bundle.BundleEntryRequestComponent()
+                                            .setUrl(entry.getResource().getResourceType() + "/" + entry.getResource().getIdPart())
+                                            .setMethod(org.hl7.fhir.r4.model.Bundle.HTTPVerb.PUT)
+                            );
                         }
                     }
                     bundle.setType(org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION);

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

@@ -45,4 +45,39 @@ public void testExecute_BundleDecomposition() {
         }
         Assert.assertTrue(found, "Expected file not found: " + expectedFile);
     }
+
+    @Test
+    public void testExecute_CollectionToTransaction() {
+        String projectPath = System.getProperty("user.dir");
+
+        String relativeJsonPath = "src/main/resources/eRSDv2_specification_bundle.json";
+        String jsonFilePath = projectPath + File.separator + relativeJsonPath;
+
+        String relativePath = "target/test-output/bundleTransactionResults";
+
+        String[] args = new String[4];
+        args[0] = "-MakeTransaction";
+        args[1] = PATH_ARGUMENT + jsonFilePath;
+        args[2] = ENCODING_ARGUMENT + "json";
+        args[3] = OUTPUT_PATH_ARGUMENT + projectPath + File.separator + relativePath;
+        bundleToTransactionOperation.execute(args);
+
+        File resultDir = new File(projectPath + File.separator + relativePath);
+
+        Assert.assertTrue(resultDir.exists() && resultDir.isDirectory(), "Result directory does not exist.");
+
+        String expectedFile = "Bundle-rctc-release-1.2.4.0-Bundle-rctc.json";
+
+        File[] actualFiles = resultDir.listFiles((dir, name) -> name.endsWith(".json"));
+        Assert.assertNotNull(actualFiles, "Bundle resource folder should not be null.");
+
+        boolean found = false;
+        for (File file : actualFiles) {
+            if (file.getName().equals(expectedFile)) {
+                found = true;
+                break;
+            }
+        }
+        Assert.assertTrue(found, "Expected file not found: " + expectedFile);
+    }
 }