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[APHL-798][APHL-799] Condition useContext management (#752)
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* [APHL-300] valueset interceptor initial implementation

* [APHL-300] preserve useContext extensions when releasing

* [APHL-300] package is aware of useContext

* [APHL-300] updated to use vsm-specific extension

* [APHL-300] fix test

* [APHL-300][APHL-798][APHL-799] updates to package and release

* [APHL-799] update package validation test for depends-on relatedArtifact

* remove interceptor

* [APHL-799] update package test data

* [APHL-798] preserve all RelatedArtifact extensions to keep it generic

* [APHL-799] replace existing useContexts for condition and priority

* comments

* cleanup

* fix bad assignment

* simplify

* cleanup

* [APHL-300] forgot to update reference

---------

Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com>
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@TahaAttari
TahaAttari and taha.attari@smilecdr.com authored Nov 27, 2023
1 parent 3d39ec9 commit b38a07c
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Showing 8 changed files with 11,485 additions and 10,733 deletions.
4 changes: 2 additions & 2 deletions plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/CrConfig.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
package org.opencds.cqf.ruler.cr;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import org.cqframework.cql.cql2elm.LibraryManager;
import org.cqframework.cql.cql2elm.LibrarySourceProvider;
import org.cqframework.cql.cql2elm.ModelManager;
Expand All @@ -14,8 +12,10 @@
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.cr.common.ILibraryManagerFactory;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;

@Configuration
@ConditionalOnProperty(prefix = "hapi.fhir.rulercr", name = "enabled", havingValue = "true", matchIfMissing = true)
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173 changes: 128 additions & 45 deletions plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/KnowledgeArtifactProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,15 @@ public class KnowledgeArtifactProcessor {
public static final String releaseLabelUrl = "http://hl7.org/fhir/StructureDefinition/artifact-releaseLabel";
public static final String releaseDescriptionUrl = "http://hl7.org/fhir/StructureDefinition/artifact-releaseDescription";
public static final String valueSetPriorityUrl = "http://aphl.org/fhir/vsm/StructureDefinition/vsm-valueset-priority";
public static final String contextTypeUrl = "http://hl7.org/fhir/us/ecr/CodeSystem/us-ph-usage-context-type";
public static final String valueSetConditionUrl = "http://aphl.org/fhir/vsm/StructureDefinition/vsm-valueset-condition";
public static final String valueSetPriorityCode = "priority";
public static final String valueSetConditionCode = "focus";
public final List<String> preservedExtensionUrls = List.of(
valueSetPriorityUrl,
valueSetConditionUrl
);
public static final String usPhContextTypeUrl = "http://hl7.org/fhir/us/ecr/CodeSystem/us-ph-usage-context-type";
public static final String contextTypeUrl = "http://terminology.hl7.org/CodeSystem/usage-context-type";
public static final String contextUrl = "http://hl7.org/fhir/us/ecr/CodeSystem/us-ph-usage-context";

// as per http://hl7.org/fhir/R4/resource.html#canonical
Expand Down Expand Up @@ -504,7 +512,8 @@ public Bundle createReleaseBundle(IdType idType, String releaseLabel, String ver
List<MetadataResource> releasedResources = internalRelease(rootArtifactAdapter, releaseVersion, rootEffectivePeriod, versionBehavior, latestFromTxServer, experimentalBehavior, fhirDal);
updateReleaseLabel(rootArtifact, releaseLabel);
List<RelatedArtifact> rootArtifactOriginalDependencies = new ArrayList<RelatedArtifact>(rootArtifactAdapter.getDependencies());
List<RelatedArtifact> originalDependenciesWithPriorityExtension = rootArtifactOriginalDependencies.stream().filter(ra -> ra.getExtensionByUrl(valueSetPriorityUrl) != null).collect(Collectors.toList());
// Get list of extensions which need to be preserved
List<RelatedArtifact> originalDependenciesWithExtensions = rootArtifactOriginalDependencies.stream().filter(dep -> dep.getExtension() != null && dep.getExtension().size() > 0).collect(Collectors.toList());
// once iteration is complete, delete all depends-on RAs in the root artifact
rootArtifactAdapter.getRelatedArtifact().removeIf(ra -> ra.getType() == RelatedArtifact.RelatedArtifactType.DEPENDSON);

Expand Down Expand Up @@ -562,12 +571,15 @@ public Bundle createReleaseBundle(IdType idType, String releaseLabel, String ver
for (RelatedArtifact resolvedRelatedArtifact: rootArtifactAdapter.getRelatedArtifact()) {
if (!distinctResolvedRelatedArtifacts.stream().anyMatch(distinctRelatedArtifact -> distinctRelatedArtifact.getResource().equals(resolvedRelatedArtifact.getResource()) && distinctRelatedArtifact.getType().equals(resolvedRelatedArtifact.getType()))) {
distinctResolvedRelatedArtifacts.add(resolvedRelatedArtifact);
// add priority Extension if found
originalDependenciesWithPriorityExtension.stream()
// preserve Extensions if found
originalDependenciesWithExtensions
.stream()
.filter(originalDep -> originalDep.getResource().equals(resolvedRelatedArtifact.getResource()))
.map(originalDep -> originalDep.getExtensionByUrl(valueSetPriorityUrl))
.findFirst()
.ifPresent(priorityExt -> resolvedRelatedArtifact.addExtension(priorityExt));
.ifPresent(dep -> {
resolvedRelatedArtifact.getExtension().addAll(dep.getExtension());
originalDependenciesWithExtensions.removeIf(ra -> ra.getResource().equals(resolvedRelatedArtifact.getResource()));
});
}
}
// update ArtifactComments referencing the old Canonical Reference
Expand All @@ -576,6 +588,13 @@ public Bundle createReleaseBundle(IdType idType, String releaseLabel, String ver

return transactionBundle;
}
private List<RelatedArtifact> getRelatedArtifactsWithPreservedExtensions(List<RelatedArtifact> deps) {
return deps.stream()
.filter(ra -> preservedExtensionUrls
.stream().anyMatch(url -> ra.getExtension()
.stream().anyMatch(ext -> ext.getUrl().equalsIgnoreCase(url))))
.collect(Collectors.toList());
}
private List<BundleEntryComponent> findArtifactCommentsToUpdate(MetadataResource rootArtifact,String releaseVersion, FhirDal fhirDal){
List<BundleEntryComponent> returnEntries = new ArrayList<BundleEntryComponent>();
// find any artifact assessments and update those as part of the bundle
Expand Down Expand Up @@ -604,7 +623,7 @@ private List<BundleEntryComponent> findArtifactCommentsToUpdate(MetadataResource
});
return returnEntries;
}
private void updateReleaseLabel(MetadataResource artifact,String releaseLabel) {
private void updateReleaseLabel(MetadataResource artifact,String releaseLabel) throws IllegalArgumentException {
if (releaseLabel != null) {
Extension releaseLabelExtension = artifact.getExtensionByUrl(releaseLabel);
if (releaseLabelExtension == null) {
Expand Down Expand Up @@ -759,7 +778,7 @@ private void checkNonExperimental(MetadataResource resource, CRMIReleaseExperime
}

/* $package */
public Bundle createPackageBundle(IdType id, FhirDal fhirDal, List<String> capability, List<String> include, List<CanonicalType> canonicalVersion, List<CanonicalType> checkCanonicalVersion, List<CanonicalType> forceCanonicalVersion, Integer count, Integer offset, Endpoint contentEndpoint, Endpoint terminologyEndpoint, Boolean packageOnly) throws NotImplementedOperationException, UnprocessableEntityException {
public Bundle createPackageBundle(IdType id, FhirDal fhirDal, List<String> capability, List<String> include, List<CanonicalType> canonicalVersion, List<CanonicalType> checkCanonicalVersion, List<CanonicalType> forceCanonicalVersion, Integer count, Integer offset, Endpoint contentEndpoint, Endpoint terminologyEndpoint, Boolean packageOnly) throws NotImplementedOperationException, UnprocessableEntityException, IllegalArgumentException {
if (contentEndpoint != null || terminologyEndpoint != null) {
throw new NotImplementedOperationException("This repository is not implementing custom Content and Terminology endpoints at this time");
}
Expand Down Expand Up @@ -789,10 +808,15 @@ public Bundle createPackageBundle(IdType id, FhirDal fhirDal, List<String> capab
}
setCorrectBundleType(count,offset,packagedBundle);
pageBundleBasedOnCountAndOffset(count, offset, packagedBundle);
handlePriority(resource, packagedBundle.getEntry());
handleValueSetReferenceExtensions(resource, packagedBundle.getEntry());
return packagedBundle;
}

/**
* $crmi.package allows for a bundle to be paged
* @param count the maximum number of resources to be returned
* @param offset the number of resources to skip beginning from the start of the bundle (starts from 1)
* @param bundle the bundle to page
*/
private void pageBundleBasedOnCountAndOffset(Integer count, Integer offset, Bundle bundle) {
if (offset != null) {
List<BundleEntryComponent> entries = bundle.getEntry();
Expand Down Expand Up @@ -837,44 +861,103 @@ private void setCorrectBundleType(Integer count, Integer offset, Bundle bundle)
bundle.setType(BundleType.TRANSACTION);
}
}

private void handlePriority(MetadataResource resource, List<BundleEntryComponent> bundleEntries) {
KnowledgeArtifactAdapter<MetadataResource> adapter = new KnowledgeArtifactAdapter<MetadataResource>(resource);
List<ValueSet> valueSets = bundleEntries.stream()
.filter(entry -> entry.getResource().getResourceType().equals(ResourceType.ValueSet))
.map(entry -> (ValueSet) entry.getResource())
.collect(Collectors.toList());
List<RelatedArtifact> relatedArtifactsWithPriorityExtension = adapter.getDependencies().stream()
.filter(ra -> ra.getExtensionByUrl(valueSetPriorityUrl) != null)
.collect(Collectors.toList());
valueSets.stream().forEach(valueSet -> {
UsageContext priority = valueSet.getUseContext().stream()
.filter(useContext -> useContext.getCode().getSystem().equals(contextTypeUrl) && useContext.getCode().getCode().equals("priority"))
.findFirst().orElseGet(()-> {
// create the priority UseContext if it doesn't exist
Coding contextType = new Coding(contextTypeUrl, "priority", null);
UsageContext newPriority = new UsageContext(contextType, null);
// add it to the ValueSet before returning
valueSet.getUseContext().add(newPriority);
return newPriority;
});
relatedArtifactsWithPriorityExtension.stream()
.filter(relatedArtifactWithPriorityExtension -> valueSet.getUrl().equals(Canonicals.getUrl(relatedArtifactWithPriorityExtension.getResource())) && valueSet.getVersion().equals(Canonicals.getVersion(relatedArtifactWithPriorityExtension.getResource())))
.findFirst()
.ifPresentOrElse(
// set priority to author-assigned value if possible
relatedArtifactWithPriorityExtension -> {
priority.setValue(relatedArtifactWithPriorityExtension.getExtensionByUrl(valueSetPriorityUrl).getValue());
},
// otherwise set it to routine
() -> {
CodeableConcept routine = new CodeableConcept(new Coding(contextUrl, "routine", null)).setText("Routine");
priority.setValue(routine);
/**
* ValueSets can be part of multiple artifacts at the same time. Certain properties are tracked/managed in the manifest to avoid conflicts with other artifacts. This function sets those properties on the ValueSets themselves at export / $crmi.package time
* @param manifest the resource containing all RelatedArtifact references
* @param bundleEntries the list of packaged resources to modify according to the extensions on the manifest relatedArtifact references
*/
private void handleValueSetReferenceExtensions(MetadataResource manifest, List<BundleEntryComponent> bundleEntries) throws UnprocessableEntityException, IllegalArgumentException {
KnowledgeArtifactAdapter<MetadataResource> adapter = new KnowledgeArtifactAdapter<MetadataResource>(manifest);
List<RelatedArtifact> relatedArtifactsWithPreservedExtension = getRelatedArtifactsWithPreservedExtensions(adapter.getDependencies());
bundleEntries.stream()
.forEach(entry -> {
if (entry.getResource().getResourceType().equals(ResourceType.ValueSet)) {
ValueSet valueSet = (ValueSet) entry.getResource();
// remove any existing Priority and Conditions
List<UsageContext> usageContexts = removeExistingReferenceExtensionData(valueSet.getUseContext());
valueSet.setUseContext(usageContexts);
// List<UsageContext> usageContexts = valueSet.getUseContext();
Optional<RelatedArtifact> maybeVSRelatedArtifact = relatedArtifactsWithPreservedExtension.stream().filter(ra -> Canonicals.getUrl(ra.getResource()).equals(valueSet.getUrl())).findFirst();
// If leaf valueset
if (!valueSet.hasCompose()
|| (valueSet.hasCompose() && valueSet.getCompose().getIncludeFirstRep().getValueSet().size() == 0)) {
// If Condition extension is present
maybeVSRelatedArtifact
.map(ra -> ra.getExtension())
.ifPresentOrElse(
// add Conditions
exts -> {
exts.stream()
.filter(ext -> ext.getUrl().equalsIgnoreCase(valueSetConditionUrl))
.forEach(ext -> tryAddCondition(usageContexts, (CodeableConcept) ext.getValue()));
},
// else throw error
() -> {
throw new UnprocessableEntityException("Missing condition for ValueSet : " + valueSet.getUrl());
});
}
);
});
// update Priority
UsageContext priority = getOrCreateUsageContext(usageContexts, usPhContextTypeUrl, valueSetPriorityCode);
maybeVSRelatedArtifact
.map(ra -> ra.getExtensionByUrl(valueSetPriorityUrl))
.ifPresentOrElse(
// set value as per extension
ext -> priority.setValue(ext.getValue()),
// set to "routine" if missing
() -> {
CodeableConcept routine = new CodeableConcept(new Coding(contextUrl, "routine", null)).setText("Routine");
priority.setValue(routine);
});
}
});
}
/**
* Removes any existing UsageContexts corresponding the the VSM specific extensions
* @param usageContexts the list of usage contexts to modify
*/
private List<UsageContext> removeExistingReferenceExtensionData(List<UsageContext> usageContexts) {
List<String> useContextCodesToReplace = List.of(valueSetConditionCode,valueSetPriorityCode);
return usageContexts.stream()
// remove any useContexts which need to be replaced
.filter(useContext -> !useContextCodesToReplace.stream()
.anyMatch(code -> useContext.getCode().getCode().equals(code)))
.collect(Collectors.toList());
}

private void tryAddCondition(List<UsageContext> usageContexts, CodeableConcept condition) {
boolean focusAlreadyExists = usageContexts.stream().anyMatch(u ->
u.getCode().getSystem().equals(contextTypeUrl)
&& u.getCode().getCode().equals(valueSetConditionCode)
&& u.getValueCodeableConcept().hasCoding(condition.getCoding().get(0).getSystem(), condition.getCoding().get(0).getCode())
);
if (!focusAlreadyExists) {
UsageContext newFocus = new UsageContext(new Coding(contextTypeUrl,valueSetConditionCode,null),condition);
newFocus.setValue(condition);
usageContexts.add(newFocus);
}
}
/**
*
* Either finds a usageContext with the same system and code or creates an empty one
* and appends it
*
* @param usageContexts the list of usageContexts to search and/or append to
* @param system the usageContext.code.system to find / create
* @param code the usage.code.code to find / create
* @return the found / created usageContext
*/
private UsageContext getOrCreateUsageContext(List<UsageContext> usageContexts, String system, String code) {
return usageContexts.stream()
.filter(useContext -> useContext.getCode().getSystem().equals(system) && useContext.getCode().getCode().equals(code))
.findFirst().orElseGet(()-> {
// create the UseContext if it doesn't exist
Coding c = new Coding(system, code, null);
UsageContext n = new UsageContext(c, null);
// add it to the ValueSet before returning
usageContexts.add(n);
return n;
});
}
void recursivePackage(
MetadataResource resource,
Bundle bundle,
Expand Down
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