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Merged
barhodes merged 5 commits into from
May 16, 2025
Merged

Add direct reference codes to manifest during $release #665

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051b0f5
Add direct reference codes to manifest during $release
Chris0296 May 13, 2025
4a7fe1d
Fix sonar issues
Chris0296 May 13, 2025
5f2ff0a
Update cqf-directReference URL constant and tests to reflect
Chris0296 May 14, 2025
56b7a2e
Move constants from MeasureConstants to Constants class
Chris0296 May 15, 2025
f528e81
Merge branch 'master' into cor-add-direct-references-codes
barhodes May 16, 2025
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13 changes: 13 additions & 0 deletions cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/visitor/ReleaseVisitor.java
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Expand Up @@ -376,6 +376,19 @@ private void gatherDependencies(
rootAdapter.setRelatedArtifact(updatedRelatedArtifacts);
}
}

extractMeasureDirectReferenceCodes(rootAdapter, artifactAdapter);
}
}

private void extractMeasureDirectReferenceCodes(
IKnowledgeArtifactAdapter rootAdapter, IKnowledgeArtifactAdapter artifactAdapter) {
if (artifactAdapter instanceof org.opencds.cqf.fhir.utility.adapter.r4.MeasureAdapter measureAdapter) {
org.opencds.cqf.fhir.cr.visitor.r4.ReleaseVisitor.extractDirectReferenceCodes(
rootAdapter, measureAdapter.get());
} else if (artifactAdapter instanceof org.opencds.cqf.fhir.utility.adapter.r5.MeasureAdapter measureAdapter) {
org.opencds.cqf.fhir.cr.visitor.r5.ReleaseVisitor.extractDirectReferenceCodes(
rootAdapter, measureAdapter.get());
}
}

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20 changes: 20 additions & 0 deletions cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/visitor/r4/ReleaseVisitor.java
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Expand Up @@ -16,14 +16,18 @@
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.Library;
import org.hl7.fhir.r4.model.Measure;
import org.hl7.fhir.r4.model.MetadataResource;
import org.hl7.fhir.r4.model.Period;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.ResourceType;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.ValueSet;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cr.visitor.r4.CRMIReleaseExperimentalBehavior.CRMIReleaseExperimentalBehaviorCodes;
import org.opencds.cqf.fhir.cr.visitor.r4.CRMIReleaseVersionBehavior.CRMIReleaseVersionBehaviorCodes;
import org.opencds.cqf.fhir.utility.Constants;
import org.opencds.cqf.fhir.utility.PackageHelper;
import org.opencds.cqf.fhir.utility.SearchHelper;
import org.opencds.cqf.fhir.utility.adapter.IKnowledgeArtifactAdapter;
Expand Down Expand Up @@ -156,4 +160,20 @@ public static List<BundleEntryComponent> findArtifactCommentsToUpdate(
});
return returnEntries;
}

public static void extractDirectReferenceCodes(IKnowledgeArtifactAdapter rootAdapter, Measure measure) {
Optional<Extension> effectiveDataRequirementsExt = measure.getExtension().stream()
.filter(ext -> ext.getUrl().equals(Constants.CQFM_EFFECTIVE_DATA_REQUIREMENTS))
.findFirst();
if (effectiveDataRequirementsExt.isPresent()) {
Reference ref = (Reference) effectiveDataRequirementsExt.get().getValue();
Library effectiveDataRequirementsLib = (Library) measure.getContained("#" + ref.getReference());
if (effectiveDataRequirementsLib != null) {
effectiveDataRequirementsLib.getExtension().stream()
.filter(ext -> ext.getUrl().equals(Constants.CQFM_DIRECT_REFERENCE_EXTENSION))
.map(ext -> ext.setUrl(Constants.CQF_DIRECT_REFERENCE_EXTENSION))
.forEach(rootAdapter::addExtension);
}
}
}
}
19 changes: 19 additions & 0 deletions cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/visitor/r5/ReleaseVisitor.java
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Expand Up @@ -16,15 +16,19 @@
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.Library;
import org.hl7.fhir.r5.model.Measure;
import org.hl7.fhir.r5.model.MetadataResource;
import org.hl7.fhir.r5.model.Period;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.model.RelatedArtifact.RelatedArtifactType;
import org.hl7.fhir.r5.model.ResourceType;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.ValueSet;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cr.visitor.r5.CRMIReleaseExperimentalBehavior.CRMIReleaseExperimentalBehaviorCodes;
import org.opencds.cqf.fhir.cr.visitor.r5.CRMIReleaseVersionBehavior.CRMIReleaseVersionBehaviorCodes;
import org.opencds.cqf.fhir.utility.Constants;
import org.opencds.cqf.fhir.utility.PackageHelper;
import org.opencds.cqf.fhir.utility.SearchHelper;
import org.opencds.cqf.fhir.utility.adapter.IKnowledgeArtifactAdapter;
Expand Down Expand Up @@ -143,4 +147,19 @@ public static List<BundleEntryComponent> findArtifactCommentsToUpdate(
});
return returnEntries;
}

public static void extractDirectReferenceCodes(IKnowledgeArtifactAdapter rootAdapter, Measure measure) {
Optional<Extension> effectiveDataRequirementsExt = measure.getExtension().stream()
.filter(ext -> ext.getUrl().equals(Constants.CQFM_EFFECTIVE_DATA_REQUIREMENTS))
.findFirst();
if (effectiveDataRequirementsExt.isPresent()) {
Reference ref = effectiveDataRequirementsExt.get().getValueReference();
Library effectiveDataRequirementsLib = (Library) measure.getContained("#" + ref.getReference());
if (effectiveDataRequirementsLib != null) {
effectiveDataRequirementsLib.getExtension().stream()
.filter(ext -> ext.getUrl().equals(Constants.CQF_DIRECT_REFERENCE_EXTENSION))
.forEach(rootAdapter::addExtension);
}
}
}
}
34 changes: 34 additions & 0 deletions cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/visitor/r4/ReleaseVisitorTests.java
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Expand Up @@ -252,6 +252,40 @@ void bothCRMIandCQFMEffectiveDataRequirementsTest() {
assertEquals(2, componentsOnReleasedArtifact.size());
}

@Test
void measureDirectReferenceCodesIncludedInReleaseTest() {
Bundle bundle = (Bundle) jsonParser.parseResource(
ReleaseVisitorTests.class.getResourceAsStream("Bundle-ecqm-qicore-2024-simplified.json"));
repo.transaction(bundle);
Library library = repo.read(Library.class, new IdType("Library/ecqm-update-2024-05-02"))
.copy();
ILibraryAdapter libraryAdapter = new AdapterFactory().createLibrary(library);
Parameters params = new Parameters();
params.addParameter("version", "1.0.0");
params.addParameter("versionBehavior", new CodeType("default"));
var crmiEDRId = "exp-params-crmi-test";
var crmiEDRExtension = new Extension();
crmiEDRExtension.setUrl(Constants.CRMI_EFFECTIVE_DATA_REQUIREMENTS);
crmiEDRExtension.setValue(new CanonicalType("#" + crmiEDRId));
ReleaseVisitor releaseVisitor = new ReleaseVisitor(repo);
// Approval date is required to release an artifact
library.setApprovalDateElement(new DateType("2024-04-23"));

Bundle returnResource = (Bundle) libraryAdapter.accept(releaseVisitor, params);
assertNotNull(returnResource);
Optional<BundleEntryComponent> maybeLib = returnResource.getEntry().stream()
.filter(entry -> entry.getResponse().getLocation().contains("Library"))
.findFirst();
assertTrue(maybeLib.isPresent());
Library releasedLibrary =
repo.read(Library.class, new IdType(maybeLib.get().getResponse().getLocation()));
var directReferenceExtensions = releasedLibrary.getExtension().stream()
.filter(ext -> ext.getUrl().equals(Constants.CQF_DIRECT_REFERENCE_EXTENSION))
.toList();

assertEquals(18, directReferenceExtensions.size());
}

@Test
void visitLibraryTest() {
Bundle bundle = (Bundle) jsonParser.parseResource(
Expand Down
35 changes: 35 additions & 0 deletions cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/visitor/r5/ReleaseVisitorTests.java
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Expand Up @@ -252,6 +252,41 @@ void bothCRMIandCQFMEffectiveDataRequirementsTest() {
assertEquals(2, componentsOnReleasedArtifact.size());
}

@Test
void measureDirectReferenceCodesIncludedInReleaseTest() {
Bundle bundle = (Bundle) jsonParser.parseResource(
org.opencds.cqf.fhir.cr.visitor.r5.ReleaseVisitorTests.class.getResourceAsStream(
"Bundle-ecqm-qicore-2024-simplified.json"));
repo.transaction(bundle);
Library library = repo.read(Library.class, new IdType("Library/ecqm-update-2024-05-02"))
.copy();
ILibraryAdapter libraryAdapter = new AdapterFactory().createLibrary(library);
Parameters params = new Parameters();
params.addParameter("version", "1.0.0");
params.addParameter("versionBehavior", new CodeType("default"));
var crmiEDRId = "exp-params-crmi-test";
var crmiEDRExtension = new Extension();
crmiEDRExtension.setUrl(Constants.CRMI_EFFECTIVE_DATA_REQUIREMENTS);
crmiEDRExtension.setValue(new CanonicalType("#" + crmiEDRId));
ReleaseVisitor releaseVisitor = new ReleaseVisitor(repo);
// Approval date is required to release an artifact
library.setApprovalDateElement(new DateType("2024-04-23"));

Bundle returnResource = (Bundle) libraryAdapter.accept(releaseVisitor, params);
assertNotNull(returnResource);
Optional<Bundle.BundleEntryComponent> maybeLib = returnResource.getEntry().stream()
.filter(entry -> entry.getResponse().getLocation().contains("Library"))
.findFirst();
assertTrue(maybeLib.isPresent());
Library releasedLibrary =
repo.read(Library.class, new IdType(maybeLib.get().getResponse().getLocation()));
var directReferenceExtensions = releasedLibrary.getExtension().stream()
.filter(ext -> ext.getUrl().equals(Constants.CQF_DIRECT_REFERENCE_EXTENSION))
.toList();

assertEquals(18, directReferenceExtensions.size());
}

@Test
void visitLibraryTest() {
Bundle bundle = (Bundle) jsonParser.parseResource(
Expand Down
36 changes: 18 additions & 18 deletions ...test/resources/org/opencds/cqf/fhir/cr/visitor/r5/Bundle-ecqm-qicore-2024-simplified.json
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Expand Up @@ -209,55 +209,55 @@
"id": "effective-data-requirements",
"extension": [
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory",
"display": "laboratory"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://snomed.info/sct",
"code": "428361000124107",
"display": "Discharge to home for hospice care (procedure)"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://snomed.info/sct",
"code": "428371000124100",
"display": "Discharge to healthcare facility for hospice care (procedure)"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "survey",
"display": "survey"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://snomed.info/sct",
"code": "373066001",
"display": "Yes (qualifier value)"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://loinc.org",
"code": "45755-6",
"display": "Hospice care [Minimum Data Set]"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://loinc.org",
"code": "71007-9",
Expand Down Expand Up @@ -2145,87 +2145,87 @@
"id": "effective-data-requirements",
"extension": [
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://snomed.info/sct",
"code": "428361000124107",
"display": "Discharge to home for hospice care (procedure)"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://snomed.info/sct",
"code": "428371000124100",
"display": "Discharge to healthcare facility for hospice care (procedure)"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "survey",
"display": "survey"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://snomed.info/sct",
"code": "373066001",
"display": "Yes (qualifier value)"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://loinc.org",
"code": "45755-6",
"display": "Hospice care [Minimum Data Set]"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://snomed.info/sct",
"code": "24028007",
"display": "Right (qualifier value)"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://snomed.info/sct",
"code": "7771000",
"display": "Left (qualifier value)"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://loinc.org",
"code": "98181-1",
"display": "Medical equipment used"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://loinc.org",
"code": "71802-3",
"display": "Housing status"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://snomed.info/sct",
"code": "160734000",
"display": "Lives in a nursing home (finding)"
}
},
{
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
"url": "http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode",
"valueCoding": {
"system": "http://loinc.org",
"code": "71007-9",
Expand Down
5 changes: 4 additions & 1 deletion cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/Constants.java
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Expand Up @@ -88,6 +88,8 @@ public enum CqfApplicabilityBehavior {
public static final String CQF_LIBRARY = "http://hl7.org/fhir/StructureDefinition/cqf-library";
public static final String CQF_CALCULATED_VALUE = "http://hl7.org/fhir/StructureDefinition/cqf-calculatedValue";
public static final String CQF_FHIR_QUERY_PATTERN = "http://hl7.org/fhir/StructureDefinition/cqf-fhirQueryPattern";
public static final String CQF_DIRECT_REFERENCE_EXTENSION =
"http://hl7.org/fhir/StructureDefinition/cqf-directReferenceCode";

public static final String CQFM_EFFECTIVE_DATA_REQUIREMENTS =
"http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-effectiveDataRequirements";
Expand All @@ -98,7 +100,8 @@ public enum CqfApplicabilityBehavior {
public static final String CQFM_INPUT_PARAMETERS =
"http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-inputParameters";
public static final String CQFM_COMPONENT = "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-component";

public static final String CQFM_DIRECT_REFERENCE_EXTENSION =
"http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode";
public static final String CRMI_EFFECTIVE_DATA_REQUIREMENTS =
"http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-effectiveDataRequirements";

Expand Down