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latest from Tx Server #621

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77baf99
[APHL-1326] latest from Tx Server
Dec 21, 2024
36c56a4
[APHL-1326] latest from Tx Server is now supported
Dec 21, 2024
b436298
spotless
Dec 21, 2024
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151 changes: 98 additions & 53 deletions cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/visitor/ReleaseVisitor.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
package org.opencds.cqf.fhir.cr.visitor;

import static org.opencds.cqf.fhir.utility.adapter.IAdapterFactory.createAdapterForResource;

import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
Expand Down Expand Up @@ -31,8 +33,10 @@
import org.opencds.cqf.fhir.utility.SearchHelper;
import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
import org.opencds.cqf.fhir.utility.adapter.IDependencyInfo;
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.client.TerminologyServerClient;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand All @@ -41,19 +45,23 @@ public class ReleaseVisitor extends BaseKnowledgeArtifactVisitor {
private static final String ACTIVE = "active";
private Logger logger = LoggerFactory.getLogger(ReleaseVisitor.class);
private static final String DEPENDSON = "depends-on";
protected final TerminologyServerClient terminologyServerClient;

public ReleaseVisitor(Repository repository) {
super(repository);
terminologyServerClient = new TerminologyServerClient(fhirContext());
}

@SuppressWarnings("unchecked")
@Override
public IBase visit(IKnowledgeArtifactAdapter rootAdapter, IBaseParameters operationParameters) {
Optional<Boolean> latestFromTxServer =
VisitorHelper.getBooleanParameter("latestFromTxServer", operationParameters);
// This check is to avoid partial releases and should be removed once the argument is supported.
if (latestFromTxServer.isPresent()) {
throw new NotImplementedOperationException("Support for 'latestFromTxServer' is not yet implemented.");
var latestFromTxServer = VisitorHelper.getBooleanParameter("latestFromTxServer", operationParameters)
.orElse(false);
Optional<IEndpointAdapter> terminologyEndpoint = VisitorHelper.getResourceParameter(
"terminologyEndpoint", operationParameters)
.map(r -> (IEndpointAdapter) createAdapterForResource(r));
if (latestFromTxServer && !terminologyEndpoint.isPresent()) {
throw new UnprocessableEntityException("latestFromTxServer = true but no terminologyEndpoint is available");
}
var version = VisitorHelper.getStringParameter("version", operationParameters)
.orElseThrow(() -> new UnprocessableEntityException("Version must be present"));
Expand Down Expand Up @@ -81,10 +89,11 @@ public IBase visit(IKnowledgeArtifactAdapter rootAdapter, IBaseParameters operat
rootAdapter,
releaseVersion,
rootEffectivePeriod,
latestFromTxServer.orElse(false),
latestFromTxServer,
requireNonExperimental,
new Date(),
new HashSet<>());
new HashSet<>(),
terminologyEndpoint.orElse(null));
var rootArtifactOriginalDependencies = new ArrayList<IDependencyInfo>(rootAdapter.getDependencies());
// Get list of extensions which need to be preserved
var originalDependenciesWithExtensions = rootArtifactOriginalDependencies.stream()
Expand Down Expand Up @@ -114,7 +123,9 @@ public IBase visit(IKnowledgeArtifactAdapter rootAdapter, IBaseParameters operat
releasedResources,
new HashMap<>(),
systemVersionParams,
canonicalVersionParams);
canonicalVersionParams,
latestFromTxServer,
terminologyEndpoint.orElse(null));
if (rootAdapter.get().fhirType().equals("Library")) {
((ILibraryAdapter) rootAdapter).setExpansionParameters(systemVersionParams, canonicalVersionParams);
}
Expand Down Expand Up @@ -184,7 +195,8 @@ private List<IDomainResource> internalRelease(
boolean latestFromTxServer,
Optional<String> experimentalBehavior,
Date current,
Set<String> releasedResources)
Set<String> releasedResources,
IEndpointAdapter endpoint)
throws NotImplementedOperationException, ResourceNotFoundException {
var resourcesToUpdate = new ArrayList<IDomainResource>();
if (releasedResources.contains(artifactAdapter.getCanonical())) {
Expand All @@ -205,32 +217,52 @@ private List<IDomainResource> internalRelease(
// If a version IS specified then `tryGetLatestVersion`
// will return that version.
var alreadyUpdated = checkIfReferenceInList(preReleaseReference, resourcesToUpdate);
if (IKnowledgeArtifactAdapter.checkIfRelatedArtifactIsOwned(component) && !alreadyUpdated.isPresent()) {
// get the latest version regardless of status because it's owned and we're releasing it
var latest = VisitorHelper.tryGetLatestVersion(preReleaseReference, repository);
if (latest.isPresent()) {
checkNonExperimental(latest.get().get(), experimentalBehavior, repository);
// release components recursively
resourcesToUpdate.addAll(internalRelease(
latest.get(),
version,
rootEffectivePeriod,
latestFromTxServer,
experimentalBehavior,
current,
releasedResources));
if (!alreadyUpdated.isPresent()) {
var resourceType = Canonicals.getResourceType(preReleaseReference);
var prereleaseReferenceVersion = Canonicals.getVersion(preReleaseReference);
if (resourceType != null
&& resourceType.equals("ValueSet")
&& prereleaseReferenceVersion == null
&& latestFromTxServer) {
var latest =
terminologyServerClient.getResource(endpoint, preReleaseReference, this.fhirVersion());
if (latest.isPresent()) {
checkNonExperimental(latest.get(), experimentalBehavior, repository);
// release components recursively
resourcesToUpdate.addAll(internalRelease(
IAdapterFactory.forFhirVersion(fhirVersion())
.createKnowledgeArtifactAdapter(latest.get()),
version,
rootEffectivePeriod,
latestFromTxServer,
experimentalBehavior,
current,
releasedResources,
endpoint));
}
} else if (IKnowledgeArtifactAdapter.checkIfRelatedArtifactIsOwned(component)) {
// get the latest version regardless of status because it's owned and we're releasing it
var latest = VisitorHelper.tryGetLatestVersion(preReleaseReference, repository);
if (latest.isPresent()) {
checkNonExperimental(latest.get().get(), experimentalBehavior, repository);
// release components recursively
resourcesToUpdate.addAll(internalRelease(
latest.get(),
version,
rootEffectivePeriod,
latestFromTxServer,
experimentalBehavior,
current,
releasedResources,
endpoint));
}
} else {
// if missing throw because it's an owned resource
throw new ResourceNotFoundException(String.format(
"Resource with URL '%s' is Owned by this repository and referenced by resource '%s', but no active version was found on the server.",
preReleaseReference, artifactAdapter.getUrl()));
// if it's a not-owned component just try to get the latest active version
VisitorHelper.tryGetLatestVersionWithStatus(preReleaseReference, repository, ACTIVE)
.ifPresent(latestActive ->
// check if it's experimental
checkNonExperimental(latestActive.get(), experimentalBehavior, repository));
}
} else if (!alreadyUpdated.isPresent()) {
// if it's a not-owned component just try to get the latest active version
VisitorHelper.tryGetLatestVersionWithStatus(preReleaseReference, repository, ACTIVE)
.ifPresent(latestActive ->
// check if it's experimental
checkNonExperimental(latestActive.get(), experimentalBehavior, repository));
}
}
}
Expand All @@ -245,7 +277,9 @@ private void gatherDependencies(
List<IDomainResource> releasedResources,
Map<String, IDomainResource> alreadyUpdatedDependencies,
List<String> systemVersionExpansionParameters,
List<String> canonicalVersionExpansionParameters) {
List<String> canonicalVersionExpansionParameters,
Boolean latestFromTxServer,
IEndpointAdapter endpoint) {
if (artifactAdapter == null) {
return;
}
Expand Down Expand Up @@ -317,23 +351,23 @@ private void gatherDependencies(
releasedResources,
alreadyUpdatedDependencies,
systemVersionExpansionParameters,
canonicalVersionExpansionParameters);
canonicalVersionExpansionParameters,
latestFromTxServer,
endpoint);
} else {
// try to get versions from expansion parameters if they are available
var resourceType = Canonicals.getResourceType(dependency.getReference()) == null
? null
: SearchHelper.getResourceType(repository, dependency);
String resourceType = getResourceType(dependency);
if (StringUtils.isBlank(Canonicals.getVersion(dependency.getReference()))) {
// This needs to be updated once we support requireVersionedDependencies
Optional<String> expansionParametersVersion = Optional.empty();
// assume if we can't figure out the resource type it's a CodeSystem
if (resourceType == null || resourceType.getSimpleName().equals("CodeSystem")) {
if (resourceType == null || resourceType.equals("CodeSystem")) {
expansionParametersVersion = systemVersionExpansionParameters.stream()
.filter(canonical -> !StringUtils.isBlank(Canonicals.getUrl(canonical)))
.filter(canonical ->
Canonicals.getUrl(canonical).equals(dependency.getReference()))
.findAny();
} else if (resourceType.getSimpleName().equals("ValueSet")) {
} else if (resourceType.equals("ValueSet")) {
expansionParametersVersion = canonicalVersionExpansionParameters.stream()
.filter(canonical ->
Canonicals.getUrl(canonical).equals(dependency.getReference()))
Expand All @@ -350,15 +384,19 @@ private void gatherDependencies(
// dependency
if (StringUtils.isBlank(Canonicals.getVersion(dependency.getReference()))) {
final var url = dependencyUrl;
maybeAdapter = VisitorHelper.tryGetLatestVersionWithStatus(
dependency.getReference(), repository, ACTIVE)
.map(adapter -> {
String versionedReference =
addVersionToReference(dependency.getReference(), adapter);
dependency.setReference(versionedReference);
alreadyUpdatedDependencies.put(url, adapter.get());
return adapter;
});
if (resourceType != null && resourceType.equals("ValueSet") && latestFromTxServer) {
maybeAdapter = terminologyServerClient
.getResource(endpoint, dependency.getReference(), this.fhirVersion())
.map(r -> (IKnowledgeArtifactAdapter) createAdapterForResource(r));
} else {
maybeAdapter = VisitorHelper.tryGetLatestVersionWithStatus(
dependency.getReference(), repository, ACTIVE);
}
maybeAdapter.ifPresent(adapter -> {
String versionedReference = addVersionToReference(dependency.getReference(), adapter);
dependency.setReference(versionedReference);
alreadyUpdatedDependencies.put(url, adapter.get());
});
} else {
// This is a versioned reference, just get the dependency
maybeAdapter =
Expand All @@ -374,7 +412,9 @@ private void gatherDependencies(
releasedResources,
alreadyUpdatedDependencies,
systemVersionExpansionParameters,
canonicalVersionExpansionParameters);
canonicalVersionExpansionParameters,
latestFromTxServer,
endpoint);
} else {
alreadyUpdatedDependencies.put(dependencyUrl, null);
}
Expand All @@ -394,6 +434,12 @@ private void gatherDependencies(
}
}

private String getResourceType(IDependencyInfo dependency) {
return Canonicals.getResourceType(dependency.getReference()) == null
? null
: SearchHelper.getResourceType(repository, dependency).getSimpleName();
}

private void checkNonExperimental(
IDomainResource resource, Optional<String> experimentalBehavior, Repository repository)
throws UnprocessableEntityException {
Expand Down Expand Up @@ -447,15 +493,14 @@ private IKnowledgeArtifactAdapter getArtifactByCanonical(String inputReference,
List<IKnowledgeArtifactAdapter> matchingResources = VisitorHelper.getMetadataResourcesFromBundle(
SearchHelper.searchRepositoryByCanonicalWithPaging(repository, inputReference))
.stream()
.map(r -> IAdapterFactory.forFhirVersion(r.getStructureFhirVersionEnum())
.createKnowledgeArtifactAdapter(r))
.map(r -> (IKnowledgeArtifactAdapter) createAdapterForResource(r))
.collect(Collectors.toList());
if (matchingResources.isEmpty()) {
return null;
} else if (matchingResources.size() == 1) {
return matchingResources.get(0);
} else {
logger.info("Multiple resources found matching {}", inputReference);
logger.info("Multiple resources found matching {}, used the first one", inputReference);
return matchingResources.get(0);
}
}
Expand Down
26 changes: 0 additions & 26 deletions cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/visitor/dstu3/ReleaseVisitorTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,6 @@
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.CodeType;
Expand Down Expand Up @@ -484,31 +483,6 @@ void releaseResource_propagate_effective_period() {
repo);
}

@Test
void releaseResource_latestFromTx_NotSupported_test() {
Bundle bundle = (Bundle) jsonParser.parseResource(
ReleaseVisitorTests.class.getResourceAsStream("Bundle-small-approved-draft.json"));
repo.transaction(bundle);

String actualErrorMessage = "";

Parameters params = parameters(
part("version", "1.2.3"),
part("versionBehavior", new CodeType("default")),
part("latestFromTxServer", new BooleanType(true)));
var releaseVisitor = new ReleaseVisitor(repo);
Library library = repo.read(Library.class, new IdType("Library/SpecificationLibrary"))
.copy();
ILibraryAdapter libraryAdapter = new AdapterFactory().createLibrary(library);

try {
libraryAdapter.accept(releaseVisitor, params);
} catch (Exception e) {
actualErrorMessage = e.getMessage();
}
assertTrue(actualErrorMessage.contains("not yet implemented"));
}

@Test
void release_missing_approvalDate_validation_test() {
Bundle bundle = (Bundle) jsonParser.parseResource(
Expand Down
26 changes: 0 additions & 26 deletions cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/visitor/r4/ReleaseVisitorTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
import java.util.Optional;
import java.util.stream.Collectors;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.CanonicalType;
Expand Down Expand Up @@ -459,31 +458,6 @@ void releaseResource_propagate_effective_period() {
repo);
}

@Test
void releaseResource_latestFromTx_NotSupported_test() {
Bundle bundle = (Bundle) jsonParser.parseResource(
ReleaseVisitorTests.class.getResourceAsStream("Bundle-small-approved-draft.json"));
repo.transaction(bundle);

String actualErrorMessage = "";

Parameters params = parameters(
part("version", "1.2.3"),
part("versionBehavior", new CodeType("default")),
part("latestFromTxServer", new BooleanType(true)));
ReleaseVisitor releaseVisitor = new ReleaseVisitor(repo);
Library library = repo.read(Library.class, new IdType("Library/SpecificationLibrary"))
.copy();
ILibraryAdapter libraryAdapter = new AdapterFactory().createLibrary(library);

try {
libraryAdapter.accept(releaseVisitor, params);
} catch (Exception e) {
actualErrorMessage = e.getMessage();
}
assertTrue(actualErrorMessage.contains("not yet implemented"));
}

@Test
void release_missing_approvalDate_validation_test() {
Bundle bundle = (Bundle) jsonParser.parseResource(
Expand Down
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