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Add NPM package loader classes as a first step to introducing wider NPM functionality #724

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d2f0b73
Add all utilities classes as well as tests to support NPM. Test tgzs…
lukedegruchy Aug 29, 2025
533dba6
All R4 tests working.
lukedegruchy Aug 29, 2025
008137c
Start setting up R5.
lukedegruchy Aug 29, 2025
b9a2fa5
More R5 done.
lukedegruchy Aug 29, 2025
49d391a
All NPM tests working.
lukedegruchy Aug 29, 2025
3cfeec3
Delete tgzs that on normal OSs are mixed case instead of the lowercas…
lukedegruchy Aug 29, 2025
4cebd93
Add back files in lowercase.
lukedegruchy Aug 29, 2025
52cc66d
Address sonar feedback.
lukedegruchy Aug 29, 2025
7704709
Increase test coverage.
lukedegruchy Sep 2, 2025
fbc36c2
More test coverage.
lukedegruchy Sep 2, 2025
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132 changes: 54 additions & 78 deletions cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/adapter/IAdapter.java
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The changes in this file seem like formatting changes? Do we really need to make these changes as part of this PR?

Original file line number Diff line number Diff line change
Expand Up @@ -32,11 +32,11 @@ public interface IAdapter<T extends IBase> {
*/
T get();

public FhirContext fhirContext();
FhirContext fhirContext();

public ModelResolver getModelResolver();
ModelResolver getModelResolver();

public default void setExtension(List<? extends IBaseExtension<?, ?>> extensions) {
default void setExtension(List<? extends IBaseExtension<?, ?>> extensions) {
try {
getModelResolver().setValue(get(), "extension", null);
getModelResolver().setValue(get(), "extension", extensions);
Expand All @@ -46,7 +46,7 @@ public default void setExtension(List<? extends IBaseExtension<?, ?>> extensions
}
}

public default <E extends IBaseExtension<?, ?>> void addExtension(E extension) {
default <E extends IBaseExtension<?, ?>> void addExtension(E extension) {
try {
getModelResolver().setValue(get(), "extension", Collections.singletonList(extension));
} catch (Exception e) {
Expand All @@ -55,63 +55,63 @@ public default void setExtension(List<? extends IBaseExtension<?, ?>> extensions
}
}

public default boolean hasExtension() {
default boolean hasExtension() {
return !getExtension().isEmpty();
}

public default boolean hasExtension(String url) {
default boolean hasExtension(String url) {
return hasExtension(get(), url);
}

public default <E extends IBaseExtension<?, ?>> List<E> getExtension() {
default <E extends IBaseExtension<?, ?>> List<E> getExtension() {
return getExtension(get());
}

public default <E extends IBaseExtension<?, ?>> E getExtensionByUrl(String url) {
default <E extends IBaseExtension<?, ?>> E getExtensionByUrl(String url) {
return getExtensionByUrl(get(), url);
}

public default <E extends IBaseExtension<?, ?>> List<E> getExtensionsByUrl(String url) {
default <E extends IBaseExtension<?, ?>> List<E> getExtensionsByUrl(String url) {
return getExtensionsByUrl(get(), url);
}

@SuppressWarnings("unchecked")
public default <E extends IBaseExtension<?, ?>> List<E> getExtension(IBase base) {
default <E extends IBaseExtension<?, ?>> List<E> getExtension(IBase base) {
return resolvePathList(base, "extension").stream().map(e -> (E) e).collect(Collectors.toList());
}

@SuppressWarnings("unchecked")
public default <E extends IBaseExtension<?, ?>> List<E> getExtensionsByUrl(IBase base, String url) {
default <E extends IBaseExtension<?, ?>> List<E> getExtensionsByUrl(IBase base, String url) {
return getExtension(base).stream()
.filter(e -> e.getUrl().equals(url))
.map(e -> (E) e)
.collect(Collectors.toList());
}

@SuppressWarnings("unchecked")
public default <E extends IBaseExtension<?, ?>> E getExtensionByUrl(IBase base, String url) {
default <E extends IBaseExtension<?, ?>> E getExtensionByUrl(IBase base, String url) {
return getExtensionsByUrl(base, url).stream()
.map(e -> (E) e)
.findFirst()
.orElse(null);
}

public default Boolean hasExtension(IBase base, String url) {
default Boolean hasExtension(IBase base, String url) {
return getExtension(base).stream().anyMatch(e -> e.getUrl().equals(url));
}

@SuppressWarnings("unchecked")
public default List<IBase> resolvePathList(IBase base, String path) {
default List<IBase> resolvePathList(IBase base, String path) {
var pathResult = getModelResolver().resolvePath(base, path);
return pathResult instanceof List ? (List<IBase>) pathResult : new ArrayList<>();
}

@SuppressWarnings("unchecked")
public default <B extends IBase> List<B> resolvePathList(IBase base, String path, Class<B> clazz) {
default <B extends IBase> List<B> resolvePathList(IBase base, String path, Class<B> clazz) {
return resolvePathList(base, path).stream().map(i -> (B) i).collect(Collectors.toList());
}

public default String resolvePathString(IBase base, String path) {
default String resolvePathString(IBase base, String path) {
var result = resolvePath(base, path);
if (result == null) {
return null;
Expand All @@ -127,96 +127,72 @@ public default String resolvePathString(IBase base, String path) {
}
}

public default IBase resolvePath(IBase base, String path) {
default IBase resolvePath(IBase base, String path) {
return (IBase) getModelResolver().resolvePath(base, path);
}

@SuppressWarnings("unchecked")
public default <B extends IBase> B resolvePath(IBase base, String path, Class<B> clazz) {
default <B extends IBase> B resolvePath(IBase base, String path, Class<B> clazz) {
return (B) resolvePath(base, path);
}

@SuppressWarnings("unchecked")
static <T extends ICompositeType> T newPeriod(FhirVersionEnum version) {
switch (version) {
case DSTU3:
return (T) new org.hl7.fhir.dstu3.model.Period();
case R4:
return (T) new org.hl7.fhir.r4.model.Period();
case R5:
return (T) new org.hl7.fhir.r5.model.Period();
default:
throw new UnprocessableEntityException(UNSUPPORTED_VERSION.formatted(version.toString()));
}
return switch (version) {
case DSTU3 -> (T) new org.hl7.fhir.dstu3.model.Period();
case R4 -> (T) new org.hl7.fhir.r4.model.Period();
case R5 -> (T) new org.hl7.fhir.r5.model.Period();
default -> throw new UnprocessableEntityException(String.format(UNSUPPORTED_VERSION, version.toString()));
};
}

@SuppressWarnings("unchecked")
static <T extends IPrimitiveType<String>> T newStringType(FhirVersionEnum version, String string) {
switch (version) {
case DSTU3:
return (T) new org.hl7.fhir.dstu3.model.StringType(string);
case R4:
return (T) new org.hl7.fhir.r4.model.StringType(string);
case R5:
return (T) new org.hl7.fhir.r5.model.StringType(string);
default:
throw new UnprocessableEntityException(UNSUPPORTED_VERSION.formatted(version.toString()));
}
return switch (version) {
case DSTU3 -> (T) new org.hl7.fhir.dstu3.model.StringType(string);
case R4 -> (T) new org.hl7.fhir.r4.model.StringType(string);
case R5 -> (T) new org.hl7.fhir.r5.model.StringType(string);
default -> throw new UnprocessableEntityException(String.format(UNSUPPORTED_VERSION, version.toString()));
};
}

@SuppressWarnings("unchecked")
static <T extends IPrimitiveType<String>> T newUriType(FhirVersionEnum version, String string) {
switch (version) {
case DSTU3:
return (T) new org.hl7.fhir.dstu3.model.UriType(string);
case R4:
return (T) new org.hl7.fhir.r4.model.UriType(string);
case R5:
return (T) new org.hl7.fhir.r5.model.UriType(string);
default:
throw new UnprocessableEntityException(UNSUPPORTED_VERSION.formatted(version.toString()));
}
return switch (version) {
case DSTU3 -> (T) new org.hl7.fhir.dstu3.model.UriType(string);
case R4 -> (T) new org.hl7.fhir.r4.model.UriType(string);
case R5 -> (T) new org.hl7.fhir.r5.model.UriType(string);
default -> throw new UnprocessableEntityException(String.format(UNSUPPORTED_VERSION, version.toString()));
};
}

@SuppressWarnings("unchecked")
static <T extends IPrimitiveType<String>> T newUrlType(FhirVersionEnum version, String string) {
switch (version) {
case DSTU3:
return (T) new org.hl7.fhir.dstu3.model.UriType(string);
case R4:
return (T) new org.hl7.fhir.r4.model.UrlType(string);
case R5:
return (T) new org.hl7.fhir.r5.model.UrlType(string);
default:
throw new UnprocessableEntityException(UNSUPPORTED_VERSION.formatted(version.toString()));
}
return switch (version) {
case DSTU3 -> (T) new org.hl7.fhir.dstu3.model.UriType(string);
case R4 -> (T) new org.hl7.fhir.r4.model.UrlType(string);
case R5 -> (T) new org.hl7.fhir.r5.model.UrlType(string);
default -> throw new UnprocessableEntityException(String.format(UNSUPPORTED_VERSION, version.toString()));
};
}

@SuppressWarnings("unchecked")
static <T extends IPrimitiveType<Date>> T newDateType(FhirVersionEnum version, Date date) {
switch (version) {
case DSTU3:
return (T) new org.hl7.fhir.dstu3.model.DateType(date);
case R4:
return (T) new org.hl7.fhir.r4.model.DateType(date);
case R5:
return (T) new org.hl7.fhir.r5.model.DateType(date);
default:
throw new UnprocessableEntityException(UNSUPPORTED_VERSION.formatted(version.toString()));
}
return switch (version) {
case DSTU3 -> (T) new org.hl7.fhir.dstu3.model.DateType(date);
case R4 -> (T) new org.hl7.fhir.r4.model.DateType(date);
case R5 -> (T) new org.hl7.fhir.r5.model.DateType(date);
default -> throw new UnprocessableEntityException(String.format(UNSUPPORTED_VERSION, version.toString()));
};
}

@SuppressWarnings("unchecked")
static <T extends IPrimitiveType<Date>> T newDateTimeType(FhirVersionEnum version, Date date) {
switch (version) {
case DSTU3:
return (T) new org.hl7.fhir.dstu3.model.DateTimeType(date);
case R4:
return (T) new org.hl7.fhir.r4.model.DateTimeType(date);
case R5:
return (T) new org.hl7.fhir.r5.model.DateTimeType(date);
default:
throw new UnprocessableEntityException(UNSUPPORTED_VERSION.formatted(version.toString()));
}
return switch (version) {
case DSTU3 -> (T) new org.hl7.fhir.dstu3.model.DateTimeType(date);
case R4 -> (T) new org.hl7.fhir.r4.model.DateTimeType(date);
case R5 -> (T) new org.hl7.fhir.r5.model.DateTimeType(date);
default -> throw new UnprocessableEntityException(String.format(UNSUPPORTED_VERSION, version.toString()));
};
}
}
8 changes: 8 additions & 0 deletions cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/adapter/IAdapterFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,14 @@ static IResourceAdapter createAdapterForResource(IBaseResource resource) {
*/
ILibraryAdapter createLibrary(IBaseResource library);

/**
* Creates an adapter that exposes common Measure operations across multiple versions of FHIR
*
* @param measure a FHIR Measure Resource
* @return an adapter exposing common api calls
*/
IMeasureAdapter createMeasure(IBaseResource measure);

/**
* Creates an adapter that exposes common PlanDefinition operations across multiple versions of FHIR
*
Expand Down
5 changes: 2 additions & 3 deletions ...utility/src/main/java/org/opencds/cqf/fhir/utility/adapter/IKnowledgeArtifactAdapter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,8 @@
import org.opencds.cqf.fhir.utility.Canonicals;
import org.opencds.cqf.fhir.utility.Constants;
import org.opencds.cqf.fhir.utility.SearchHelper;
import org.opencds.cqf.fhir.utility.VersionComparator;
import org.opencds.cqf.fhir.utility.VersionUtilities;
import org.opencds.cqf.fhir.utility.Versions;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand Down Expand Up @@ -338,12 +338,11 @@ static boolean isSupportedMetadataResource(IBaseResource resource) {
}

static Optional<IDomainResource> findLatestVersion(IBaseBundle bundle) {
var versionComparator = new VersionComparator();
var sorted = BundleHelper.getEntryResources(bundle).stream()
.filter(IKnowledgeArtifactAdapter::isSupportedMetadataResource)
.map(r -> (IKnowledgeArtifactAdapter) IAdapterFactory.forFhirVersion(r.getStructureFhirVersionEnum())
.createResource(r))
.sorted((a, b) -> versionComparator.compare(a.getVersion(), b.getVersion()))
.sorted((a, b) -> Versions.compareVersions(a.getVersion(), b.getVersion()))
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Similar question, is this change needed by this PR?

.toList();
if (!sorted.isEmpty()) {
return Optional.of(sorted.get(sorted.size() - 1).get());
Expand Down
6 changes: 5 additions & 1 deletion cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/adapter/IMeasureAdapter.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
package org.opencds.cqf.fhir.utility.adapter;

import java.util.List;

/**
* This interface exposes common functionality across all FHIR Questionnaire versions.
*/
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Comment seems wrong?

public interface IMeasureAdapter extends IKnowledgeArtifactAdapter {}
public interface IMeasureAdapter extends IKnowledgeArtifactAdapter {
List<String> getLibrary();
}
6 changes: 6 additions & 0 deletions ...fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/adapter/dstu3/AdapterFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
import org.opencds.cqf.fhir.utility.adapter.IEndpointAdapter;
import org.opencds.cqf.fhir.utility.adapter.IKnowledgeArtifactAdapter;
import org.opencds.cqf.fhir.utility.adapter.ILibraryAdapter;
import org.opencds.cqf.fhir.utility.adapter.IMeasureAdapter;
import org.opencds.cqf.fhir.utility.adapter.IParametersAdapter;
import org.opencds.cqf.fhir.utility.adapter.IParametersParameterComponentAdapter;
import org.opencds.cqf.fhir.utility.adapter.IPlanDefinitionAdapter;
Expand Down Expand Up @@ -82,6 +83,11 @@ public ILibraryAdapter createLibrary(IBaseResource library) {
return new LibraryAdapter((IDomainResource) library);
}

@Override
public IMeasureAdapter createMeasure(IBaseResource measure) {
return new MeasureAdapter((IDomainResource) measure);
}

@Override
public IAttachmentAdapter createAttachment(ICompositeType attachment) {
return new AttachmentAdapter(attachment);
Expand Down
5 changes: 5 additions & 0 deletions ...fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/adapter/dstu3/MeasureAdapter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,11 @@ public Measure copy() {
private Library effectiveDataRequirements;
private LibraryAdapter effectiveDataRequirementsAdapter;

@Override
public List<String> getLibrary() {
return getMeasure().getLibrary().stream().map(Reference::getReference).toList();
}

private String getEdrReferenceString(Extension edrExtension) {
return edrExtension.getUrl().contains("cqfm")
? ((Reference) edrExtension.getValue()).getReference()
Expand Down
6 changes: 6 additions & 0 deletions cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/adapter/r4/AdapterFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
import org.opencds.cqf.fhir.utility.adapter.IEndpointAdapter;
import org.opencds.cqf.fhir.utility.adapter.IKnowledgeArtifactAdapter;
import org.opencds.cqf.fhir.utility.adapter.ILibraryAdapter;
import org.opencds.cqf.fhir.utility.adapter.IMeasureAdapter;
import org.opencds.cqf.fhir.utility.adapter.IParametersAdapter;
import org.opencds.cqf.fhir.utility.adapter.IParametersParameterComponentAdapter;
import org.opencds.cqf.fhir.utility.adapter.IPlanDefinitionAdapter;
Expand Down Expand Up @@ -82,6 +83,11 @@ public ILibraryAdapter createLibrary(IBaseResource library) {
return new LibraryAdapter((IDomainResource) library);
}

@Override
public IMeasureAdapter createMeasure(IBaseResource measure) {
return new MeasureAdapter((IDomainResource) measure);
}

@Override
public IAttachmentAdapter createAttachment(ICompositeType attachment) {
return new AttachmentAdapter(attachment);
Expand Down
8 changes: 8 additions & 0 deletions cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/adapter/r4/MeasureAdapter.java
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Should we have a PR that is just for the Measure adapter?

Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
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.PrimitiveType;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.RelatedArtifact;
import org.hl7.fhir.r4.model.UriType;
Expand Down Expand Up @@ -50,6 +51,13 @@ public Measure copy() {
private Library effectiveDataRequirements;
private LibraryAdapter effectiveDataRequirementsAdapter;

@Override
public List<String> getLibrary() {
return getMeasure().getLibrary().stream()
.map(PrimitiveType::getValueAsString)
.toList();
}

private String getEdrReferenceString(Extension edrExtension) {
return edrExtension.getUrl().contains("cqfm")
? ((Reference) edrExtension.getValue()).getReference()
Expand Down
6 changes: 6 additions & 0 deletions cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/adapter/r5/AdapterFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
import org.opencds.cqf.fhir.utility.adapter.IEndpointAdapter;
import org.opencds.cqf.fhir.utility.adapter.IKnowledgeArtifactAdapter;
import org.opencds.cqf.fhir.utility.adapter.ILibraryAdapter;
import org.opencds.cqf.fhir.utility.adapter.IMeasureAdapter;
import org.opencds.cqf.fhir.utility.adapter.IParametersAdapter;
import org.opencds.cqf.fhir.utility.adapter.IParametersParameterComponentAdapter;
import org.opencds.cqf.fhir.utility.adapter.IPlanDefinitionAdapter;
Expand Down Expand Up @@ -82,6 +83,11 @@ public ILibraryAdapter createLibrary(IBaseResource library) {
return new LibraryAdapter((IDomainResource) library);
}

@Override
public IMeasureAdapter createMeasure(IBaseResource measure) {
return new MeasureAdapter((IDomainResource) measure);
}

@Override
public IAttachmentAdapter createAttachment(ICompositeType attachment) {
return new AttachmentAdapter(attachment);
Expand Down
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