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Merged
brynrhodes merged 4 commits into from
Sep 9, 2025
Merged

Br connectathon fixes #584

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cc93f1e
Do not report dependencies on model info that is loaded from the tran…
brynrhodes Sep 7, 2025
9795070
Fix attachment URL preventing CQL source file information lookup
brynrhodes Sep 7, 2025
95dae4f
Fixed measure packages not including Group resource
brynrhodes Sep 7, 2025
d807c4f
Fixed test case
brynrhodes Sep 8, 2025
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7 changes: 4 additions & 3 deletions tooling/src/main/java/org/opencds/cqf/tooling/library/LibraryProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -236,6 +236,9 @@ protected Library refreshGeneratedContent(Library sourceLibrary) {
var translatorOptions = getCqlProcessor().getCqlTranslatorOptions();
var formats = translatorOptions.getFormats();
CqlProcessor.CqlSourceFileInformation info = getCqlProcessor().getFileInformation(attachment.getUrl());
if (this.parentContext != null && this.parentContext.getCanonicalBase() != null) {
attachment.setUrl(this.parentContext.getCanonicalBase() + "/" + fileName);
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}
if (info != null) {
if (info.getElm() != null && emptyIfNull(formats).contains(Format.XML)) {
sourceLibrary.addContent().setContentType("application/elm+xml").setData(info.getElm());
Expand Down Expand Up @@ -379,9 +382,7 @@ private Attachment loadFile(String fn) throws IOException {
Attachment att = new Attachment();
att.setContentType("text/cql");
att.setData(TextFile.fileToBytes(f));
if (this.parentContext != null && this.parentContext.getCanonicalBase() != null) {
att.setUrl(this.parentContext.getCanonicalBase() + "/Library-" + f.getName());
}
att.setUrl(f.getAbsolutePath());
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return att;
}
}
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19 changes: 19 additions & 0 deletions tooling/src/main/java/org/opencds/cqf/tooling/measure/MeasureRefreshProcessor.java
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Expand Up @@ -38,6 +38,7 @@ public Measure refreshMeasure(Measure measureToUse, LibraryManager libraryManage
clearRelatedArtifacts(measureToUse);

Library moduleDefinitionLibrary = getModuleDefinitionLibrary(measureToUse, libraryManager, compiledLibrary, options);
removeModelInfoDependencies(moduleDefinitionLibrary);
measureToUse.setDate(new Date());
// http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/measure-cqfm
setMeta(measureToUse, moduleDefinitionLibrary);
Expand All @@ -51,6 +52,24 @@ public Measure refreshMeasure(Measure measureToUse, LibraryManager libraryManage
return measureToUse;
}

private void removeModelInfoDependencies(Library moduleDefinitionLibrary) {
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// NOTE: see similar logic in CqlProcessor.translateFile
if (moduleDefinitionLibrary.hasRelatedArtifact()) {
for (int i = moduleDefinitionLibrary.getRelatedArtifact().size() - 1; i >= 0; i--) {
RelatedArtifact relatedArtifact = moduleDefinitionLibrary.getRelatedArtifact().get(i);
if (relatedArtifact != null && relatedArtifact.hasResource() && (
relatedArtifact.getResource().startsWith("http://hl7.org/fhir/Library/QICore-ModelInfo")
|| relatedArtifact.getResource().startsWith("http://fhir.org/guides/cqf/common/Library/FHIR-ModelInfo")
|| relatedArtifact.getResource().startsWith("http://hl7.org/fhir/Library/USCore-ModelInfo")
)) {
// Do not report dependencies on model info loaded from the translator, or
// from CQF Common (because these should be loaded from Using CQL now)
moduleDefinitionLibrary.getRelatedArtifact().remove(i);
}
}
}
}

private Library getModuleDefinitionLibrary(Measure measureToUse, LibraryManager libraryManager, CompiledLibrary compiledLibrary, CqlCompilerOptions options){
Set<String> expressionList = getExpressions(measureToUse);
DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
Expand Down
9 changes: 5 additions & 4 deletions tooling/src/main/java/org/opencds/cqf/tooling/packaging/r4/PackageMeasure.java
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Expand Up @@ -140,17 +140,18 @@ public void output() {

if (isIncludeTests() && testPackage != null) {
logger.info("Packaging {} Tests...", testPackage.getTests().size());
if (testPackage.getGroup() != null) {
IOUtils.writeResource(testPackage.getGroup(), measureFilesOutputPath, IOUtils.Encoding.JSON, getFhirContext(),
true, "Group-" + testPackage.getGroup().getIdElement().getIdPart());
}
testPackage.getTests().forEach(
test -> {
dependencies.addAll(BundleUtils.getR4ResourcesFromBundle((Bundle) test));
IOUtils.writeBundle(test, measureFilesOutputPath, IOUtils.Encoding.JSON,
getFhirContext(), test.getIdElement().getIdPart());
}
);
if (testPackage.getGroup() != null) {
dependencies.add(testPackage.getGroup());
IOUtils.writeResource(testPackage.getGroup(), measureFilesOutputPath, IOUtils.Encoding.JSON, getFhirContext(),
true, "Group-" + testPackage.getGroup().getIdElement().getIdPart());
}
}

dependencies.add(mainArtifact);
Expand Down
15 changes: 14 additions & 1 deletion tooling/src/main/java/org/opencds/cqf/tooling/processor/CqlProcessor.java
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Expand Up @@ -432,7 +432,20 @@ private void translateFile(LibraryManager libraryManager, File file, CqlCompiler
//result.extension.addAll(requirementsLibrary.getExtensionsByUrl("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"));

// Extract relatedArtifact data (models, libraries, code systems, and value sets)
result.relatedArtifacts.addAll(requirementsLibrary.getRelatedArtifact());
for (RelatedArtifact relatedArtifact : requirementsLibrary.getRelatedArtifact()) {
// NOTE: see similar logic in MeasureRefreshProcessor.removeModelInfoDependencies
if (relatedArtifact.hasResource() && (
relatedArtifact.getResource().startsWith("http://hl7.org/fhir/Library/QICore-ModelInfo")
|| relatedArtifact.getResource().startsWith("http://fhir.org/guides/cqf/common/Library/FHIR-ModelInfo")
|| relatedArtifact.getResource().startsWith("http://hl7.org/fhir/Library/USCore-ModelInfo")
)) {
// Do not report dependencies on model info loaded from the translator, or
// from CQF Common (because these should be loaded from Using CQL now)
continue;
}

result.relatedArtifacts.add(relatedArtifact);
}

// Extract parameter data and validate result types are supported types
result.parameters.addAll(requirementsLibrary.getParameter());
Expand Down
4 changes: 3 additions & 1 deletion tooling/src/test/java/org/opencds/cqf/tooling/processor/IGProcessorTest.java
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Expand Up @@ -61,6 +61,7 @@ public class IGProcessorTest extends RefreshTest {
private final String BUNDLE_TYPE = "Bundle";
private final String LIB_TYPE = "Library";
private final String MEASURE_TYPE = "Measure";
private final String GROUP_TYPE = "Group";

private final String INI_LOC = "target" + separator + "refreshIG" + separator + "ig.ini";

Expand Down Expand Up @@ -136,10 +137,11 @@ void testRefreshIG() throws Exception {
// ensure "resourceType" exists
if (map.containsKey(RESOURCE_TYPE)) {
String parentResourceType = (String) map.get(RESOURCE_TYPE);
// if Library, resource will produce a "Measure" in main bundled file:
// if Library, resource will produce a "Measure" and a "Group" in main bundled file:
if (parentResourceType.equalsIgnoreCase(LIB_TYPE)) {
resourceTypeMap.put(MEASURE_TYPE + "_" + map.get(ID), MEASURE_TYPE);
resourceTypeMap.put(LIB_TYPE + "_" + map.get(ID), LIB_TYPE);
resourceTypeMap.put(GROUP_TYPE + "_" + map.get(ID), GROUP_TYPE);
} else if (parentResourceType.equalsIgnoreCase(BUNDLE_TYPE)) {
// file is a bundle type, loop through resources in entry list, build up map of
// <id, resourceType>:
Expand Down
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