Merge branch 'master' into 2566_update_s13n_and_validation_handling

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties

@@ -70,6 +70,9 @@ page.server_jpa_mdm.mdm_operations=MDM Operations
 page.server_jpa_mdm.mdm_details=MDM Technical Details
 page.server_jpa_mdm.mdm_expansion=MDM Search Expansion
 
+section.server_jpa_cql.title=JPA Server: CQL
+page.server_jpa_cql.cql=CQL Getting Started
+
 section.server_jpa_partitioning.title=JPA Server: Partitioning and Multitenancy
 page.server_jpa_partitioning.partitioning=Partitioning and Multitenancy
 page.server_jpa_partitioning.partition_interceptor_examples=Partition Interceptor Examples

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_cql/cql.md

@@ -0,0 +1,38 @@
+# CQL Getting Started
+
+## Introduction
+
+Clinical Quality Language (CQL) is a high-level, domain-specific language focused on clinical quality and targeted at measure and decision support artifact authors. HAPI embeds a [CQL engine](https://github.com/DBCG/cql_engine) allowing the evaluation of clinical knowledge artifacts that use CQL to describe their logic.
+
+A more detailed description of CQL is available at the [CQL Specification Implementation Guide](https://cql.hl7.org/)
+
+The FHIR [Clinical Reasoning module](http://www.hl7.org/fhir/clinicalreasoning-module.html) defines a set of resources, profiles, operations, etc. that can be used to work with clinical knowledge within FHIR. HAPI provides implementation for some of those operations, described in more detail below.
+
+## Working Example
+
+A complete working example of HAPI CQL can be found in the [JPA Server Starter](/hapi-fhir/docs/server_jpa/get_started.html) project. You may wish to browse its source to see how it is set up.
+
+## Overview
+
+To get up and running with HAPI CQL, you can enable it using the `hapi.properties` file in the JPA Server Starter by setting `hapi.fhir.enable_cql` key to `true`. If you are running your own server follow the instructions below to [enable it in HAPI FHIR directly](#cql-settings).
+
+Once you've enabled CQL processing, the next step is to load the appropriate knowledge artifact resources into your server.
+
+## CQL Settings
+
+There are two Spring beans available that add CQL processing to HAPI. You can enable CQL processing by importing the appropriate version for your server configuration.
+
+* `ca.uhn.fhir.cql.config.CqlDstu3Config`
+* `ca.uhn.fhir.cql.config.CqlR4Config`
+
+## Operations
+
+HAPI provides implementations for some Measure operations for DSTU3 and R4
+
+### $evaluate-measure
+
+The [$evaluate-measure](http://hl7.org/fhir/measure-operation-evaluate-measure.html) operation allows the evaluation of a clinical quality measure. This operation is invoked on an instance of a Measure resource:
+
+`http://base/Measure/measureId/$evaluate-measure?subject=124&periodStart=2014-01&periodend=2014-03`
+
+The Measure will be evaluated, including any CQL that is referenced. The CQL evaluation requires that all the supporting knowledge artifacts for a given Measure be loaded on the HAPI server, including `Libaries` and `ValueSets`.

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -437,25 +437,25 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
 		obs.getCode().getCodingFirstRep().setSystem("http://loinc.org").setCode("non-existing-code").setDisplay("Display 3");
 		oo = validateAndReturnOutcome(obs);
-		assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://loinc.org#non-existing-code)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
+		assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://loinc.org#non-existing-code)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
 
 		// Valid code with no system
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
 		obs.getCode().getCodingFirstRep().setSystem(null).setCode("CODE3").setDisplay("Display 3");
 		oo = validateAndReturnOutcome(obs);
-		assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = null#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
+		assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = null#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
 
 		// Valid code with wrong system
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
 		obs.getCode().getCodingFirstRep().setSystem("http://foo").setCode("CODE3").setDisplay("Display 3");
 		oo = validateAndReturnOutcome(obs);
-		assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://foo#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
+		assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://foo#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
 
 		// Code that exists but isn't in the valueset
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
 		obs.getCode().getCodingFirstRep().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs").setDisplay("Display 3");
 		oo = validateAndReturnOutcome(obs);
-		assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://terminology.hl7.org/CodeSystem/observation-category#vital-signs)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
+		assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://terminology.hl7.org/CodeSystem/observation-category#vital-signs)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
 
 		// Invalid code in built-in VS/CS
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
@@ -813,7 +813,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		} catch (PreconditionFailedException e) {
 			outcome = (OperationOutcome) e.getOperationOutcome();
 			ourLog.info("Outcome: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
-			assertEquals("None of the codes provided are in the value set http://example.com/valueset (http://example.com/valueset), and a code from this value set is required) (codes = http://example.com/foo-foo#some-code)", outcome.getIssueFirstRep().getDiagnostics());
+			assertEquals("None of the codings provided are in the value set http://example.com/valueset (http://example.com/valueset), and a coding from this value set is required) (codes = http://example.com/foo-foo#some-code)", outcome.getIssueFirstRep().getDiagnostics());
 			assertEquals(OperationOutcome.IssueSeverity.ERROR, outcome.getIssueFirstRep().getSeverity());
 		}
 	}
@@ -872,25 +872,25 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
 		obs.getCode().getCodingFirstRep().setSystem("http://loinc.org").setCode("non-existing-code").setDisplay("Display 3");
 		oo = validateAndReturnOutcome(obs);
-		assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://loinc.org#non-existing-code)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
+		assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://loinc.org#non-existing-code)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
 
 		// Valid code with no system
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
 		obs.getCode().getCodingFirstRep().setSystem(null).setCode("CODE3").setDisplay("Display 3");
 		oo = validateAndReturnOutcome(obs);
-		assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = null#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
+		assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = null#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
 
 		// Valid code with wrong system
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
 		obs.getCode().getCodingFirstRep().setSystem("http://foo").setCode("CODE3").setDisplay("Display 3");
 		oo = validateAndReturnOutcome(obs);
-		assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://foo#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
+		assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://foo#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
 
 		// Code that exists but isn't in the valueset
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
 		obs.getCode().getCodingFirstRep().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs").setDisplay("Display 3");
 		oo = validateAndReturnOutcome(obs);
-		assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://terminology.hl7.org/CodeSystem/observation-category#vital-signs)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
+		assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://terminology.hl7.org/CodeSystem/observation-category#vital-signs)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
 
 		// Invalid code in built-in VS/CS
 		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
@@ -1028,7 +1028,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		ourLog.info(myFhirCtx.newJsonParser().encodeResourceToString(allergy));
 
 		OperationOutcome oo = validateAndReturnOutcome(allergy);
-		assertThat(encode(oo), containsString("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/allergyintolerance-clinical"));
+		assertThat(encode(oo), containsString("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/allergyintolerance-clinical"));
 	}
 
 	@SuppressWarnings("unchecked")
@@ -1138,7 +1138,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 
 		// It would be ok for this to produce 0 issues, or just an information message too
 		assertEquals(1, OperationOutcomeUtil.getIssueCount(myFhirCtx, oo));
-		assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type), and a code should come from this value set unless it has no suitable code and the validator cannot judge what is suitable) (codes = http://foo#bar)", OperationOutcomeUtil.getFirstIssueDetails(myFhirCtx, oo));
+		assertEquals("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type), and a coding should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) (codes = http://foo#bar)", OperationOutcomeUtil.getFirstIssueDetails(myFhirCtx, oo));
 
 	}
 
@@ -1630,7 +1630,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		} catch (PreconditionFailedException e) {
 			OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
 			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
-			assertThat(oo.getIssueFirstRep().getDiagnostics(), containsString("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-clinical"));
+			assertThat(oo.getIssueFirstRep().getDiagnostics(), containsString("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/condition-clinical"));
 		}
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ConceptMapTest.java

@@ -26,7 +26,6 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
 
 	@Test
 	public void testTranslateWithConceptMapUrlAndVersion() {
-		
 		//- conceptMap1 v1
 		ConceptMap conceptMap1 = new ConceptMap();
 		conceptMap1.setUrl(CM_URL).setVersion("v1").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
@@ -63,7 +62,6 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
 		
 		ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap2));
 
-		
 		Parameters inParams = new Parameters();
 		inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
 		inParams.addParameter().setName("conceptMapVersion").setValue(new StringType("v2"));
@@ -73,7 +71,6 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
 
 		ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
 
-		
 		Parameters respParams = myClient
 			.operation()
 			.onType(ConceptMap.class)
@@ -82,8 +79,7 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
 			.execute();
 
 		ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
-		
+
-		
 		ParametersParameterComponent param = getParameterByName(respParams, "result");
 		assertTrue(((BooleanType) param.getValue()).booleanValue());
 
@@ -92,7 +88,8 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
 
 		assertEquals(1, getNumberOfParametersByName(respParams, "match"));
 		param = getParametersByName(respParams, "match").get(0);
-		assertEquals(2, param.getPart().size());
+
+		assertEquals(3, param.getPart().size());
 		
 		ParametersParameterComponent part = getPartByName(param, "concept");
 		Coding coding = (Coding) part.getValue();
@@ -104,7 +101,9 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
 		
 		part = getPartByName(param, "source");
 		assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
-	
+
+		part = getPartByName(param, "equivalence");
+		assertEquals("relatedto", part.getValue().toString());
 	}
 	
 	@Test

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/common/provider/LibraryContentProvider.java

@@ -22,14 +22,15 @@ package ca.uhn.fhir.cql.common.provider;
 
 import org.cqframework.cql.cql2elm.FhirLibrarySourceProvider;
 import org.hl7.elm.r1.VersionedIdentifier;
+import org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentType;
 
 import java.io.ByteArrayInputStream;
 import java.io.InputStream;
 import java.util.function.Function;
 
-public class LibrarySourceProvider<LibraryType, AttachmentType>
+public class LibraryContentProvider<LibraryType, AttachmentType>
-	implements org.cqframework.cql.cql2elm.LibrarySourceProvider {
+	implements org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(LibrarySourceProvider.class);
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(LibraryContentProvider.class);
 
 	private FhirLibrarySourceProvider innerProvider;
 	private LibraryResolutionProvider<LibraryType> provider;
@@ -37,7 +38,7 @@ public class LibrarySourceProvider<LibraryType, AttachmentType>
 	private Function<AttachmentType, String> getContentType;
 	private Function<AttachmentType, byte[]> getContent;
 
-	public LibrarySourceProvider(LibraryResolutionProvider<LibraryType> provider,
+	public LibraryContentProvider(LibraryResolutionProvider<LibraryType> provider,
 										  Function<LibraryType, Iterable<AttachmentType>> getAttachments,
 										  Function<AttachmentType, String> getContentType, Function<AttachmentType, byte[]> getContent) {
 
@@ -50,7 +51,13 @@ public class LibrarySourceProvider<LibraryType, AttachmentType>
 	}
 
 	@Override
-	public InputStream getLibrarySource(VersionedIdentifier versionedIdentifier) {
+	public InputStream getLibraryContent(VersionedIdentifier versionedIdentifier, LibraryContentType libraryContentType){
+
+		// TODO: Support loading ELM
+		if (libraryContentType != LibraryContentType.CQL) {
+			return null;
+		}
+
 		try {
 			LibraryType lib = this.provider.resolveLibraryByName(versionedIdentifier.getId(),
 				versionedIdentifier.getVersion());

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/config/BaseCqlConfig.java

@@ -27,6 +27,7 @@ import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
 
 import org.cqframework.cql.cql2elm.model.Model;
+import org.cqframework.cql.elm.execution.Library;
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.springframework.context.annotation.Bean;
 
@@ -46,4 +47,9 @@ public abstract class BaseCqlConfig {
 	Map<VersionedIdentifier, Model> globalModelCache() {
 		return new ConcurrentHashMap<VersionedIdentifier, Model>();
 	}
+
+	@Bean(name="globalLibraryCache") 
+	Map<org.cqframework.cql.elm.execution.VersionedIdentifier, Library> globalLibraryCache() {
+		return new ConcurrentHashMap<org.cqframework.cql.elm.execution.VersionedIdentifier, Library>();
+	} 
 }

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/config/CqlDstu3Config.java

@@ -26,12 +26,20 @@ import ca.uhn.fhir.cql.common.provider.EvaluationProviderFactory;
 import ca.uhn.fhir.cql.common.provider.LibraryResolutionProvider;
 import ca.uhn.fhir.cql.dstu3.evaluation.ProviderFactory;
 import ca.uhn.fhir.cql.dstu3.helper.LibraryHelper;
+import ca.uhn.fhir.cql.dstu3.listener.ElmCacheResourceChangeListener;
 import ca.uhn.fhir.cql.dstu3.provider.JpaTerminologyProvider;
 import ca.uhn.fhir.cql.dstu3.provider.LibraryResolutionProviderImpl;
 import ca.uhn.fhir.cql.dstu3.provider.MeasureOperationsProvider;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
+
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
 import org.cqframework.cql.cql2elm.model.Model;
+import org.cqframework.cql.elm.execution.Library;
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.opencds.cqf.cql.engine.fhir.model.Dstu3FhirModelResolver;
 import org.opencds.cqf.cql.engine.model.ModelResolver;
@@ -60,7 +68,7 @@ public class CqlDstu3Config extends BaseCqlConfig {
 
 	@Lazy
 	@Bean
-	LibraryResolutionProvider libraryResolutionProvider() {
+	LibraryResolutionProvider<org.hl7.fhir.dstu3.model.Library> libraryResolutionProvider() {
 		return new LibraryResolutionProviderImpl();
 	}
 
@@ -70,13 +78,28 @@ public class CqlDstu3Config extends BaseCqlConfig {
 		return new MeasureOperationsProvider();
 	}
 
+	@Lazy
 	@Bean
 	public ModelResolver fhirModelResolver() {
 		return new CachingModelResolverDecorator(new Dstu3FhirModelResolver());
 	}
 
+	@Lazy
 	@Bean
-	public LibraryHelper libraryHelper(Map<VersionedIdentifier, Model> globalModelCache) {
+	public LibraryHelper libraryHelper(Map<VersionedIdentifier, Model> globalModelCache, Map<org.cqframework.cql.elm.execution.VersionedIdentifier, Library> globalLibraryCache, CqlTranslatorOptions cqlTranslatorOptions) {
-		return new LibraryHelper(globalModelCache);
+		return new LibraryHelper(globalModelCache, globalLibraryCache, cqlTranslatorOptions);
+	}
+
+
+	@Bean
+	public CqlTranslatorOptions cqlTranslatorOptions() {
+		return CqlTranslatorOptions.defaultOptions().withCompatibilityLevel("1.3");
+	}
+
+	@Bean
+	public ElmCacheResourceChangeListener elmCacheResourceChangeListener(IResourceChangeListenerRegistry resourceChangeListenerRegistry, IFhirResourceDao<org.hl7.fhir.dstu3.model.Library> libraryDao,  Map<org.cqframework.cql.elm.execution.VersionedIdentifier, Library> globalLibraryCache) {
+		ElmCacheResourceChangeListener listener = new ElmCacheResourceChangeListener(libraryDao, globalLibraryCache);
+		resourceChangeListenerRegistry.registerResourceResourceChangeListener("Library", new SearchParameterMap(), listener, 1000);
+		return listener;
 	}
 }

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/config/CqlR4Config.java

@@ -27,12 +27,20 @@ import ca.uhn.fhir.cql.common.provider.EvaluationProviderFactory;
 import ca.uhn.fhir.cql.common.provider.LibraryResolutionProvider;
 import ca.uhn.fhir.cql.r4.evaluation.ProviderFactory;
 import ca.uhn.fhir.cql.r4.helper.LibraryHelper;
+import ca.uhn.fhir.cql.r4.listener.ElmCacheResourceChangeListener;
 import ca.uhn.fhir.cql.r4.provider.JpaTerminologyProvider;
 import ca.uhn.fhir.cql.r4.provider.LibraryResolutionProviderImpl;
 import ca.uhn.fhir.cql.r4.provider.MeasureOperationsProvider;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
+
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
 import org.cqframework.cql.cql2elm.model.Model;
+import org.cqframework.cql.elm.execution.Library;
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.opencds.cqf.cql.engine.fhir.model.R4FhirModelResolver;
 import org.opencds.cqf.cql.engine.model.ModelResolver;
@@ -55,19 +63,21 @@ public class CqlR4Config extends BaseCqlConfig {
 
 	@Lazy
 	@Bean
-	TerminologyProvider terminologyProvider(ITermReadSvcR4 theITermReadSvc, DaoRegistry theDaoRegistry, IValidationSupport theValidationSupport) {
+	TerminologyProvider terminologyProvider(ITermReadSvcR4 theITermReadSvc, DaoRegistry theDaoRegistry,
+			IValidationSupport theValidationSupport) {
 		return new JpaTerminologyProvider(theITermReadSvc, theDaoRegistry, theValidationSupport);
 	}
 
 	@Lazy
 	@Bean
-	EvaluationProviderFactory evaluationProviderFactory(FhirContext theFhirContext, DaoRegistry theDaoRegistry, TerminologyProvider theLocalSystemTerminologyProvider, ModelResolver modelResolver) {
+	EvaluationProviderFactory evaluationProviderFactory(FhirContext theFhirContext, DaoRegistry theDaoRegistry,
+			TerminologyProvider theLocalSystemTerminologyProvider, ModelResolver modelResolver) {
 		return new ProviderFactory(theFhirContext, theDaoRegistry, theLocalSystemTerminologyProvider, modelResolver);
 	}
 
 	@Lazy
 	@Bean
-	LibraryResolutionProvider libraryResolutionProvider() {
+	LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResolutionProvider() {
 		return new LibraryResolutionProviderImpl();
 	}
 
@@ -77,13 +87,30 @@ public class CqlR4Config extends BaseCqlConfig {
 		return new MeasureOperationsProvider();
 	}
 
+	@Lazy
 	@Bean
 	public ModelResolver fhirModelResolver() {
 		return new CachingModelResolverDecorator(new R4FhirModelResolver());
 	}
 
+	@Lazy
 	@Bean
-	public LibraryHelper libraryHelper(Map<VersionedIdentifier, Model> globalModelCache) {
+	public LibraryHelper libraryHelper(Map<VersionedIdentifier, Model> globalModelCache,
-		return new LibraryHelper(globalModelCache);
+			Map<org.cqframework.cql.elm.execution.VersionedIdentifier, Library> globalLibraryCache,
+			CqlTranslatorOptions cqlTranslatorOptions) {
+		return new LibraryHelper(globalModelCache, globalLibraryCache, cqlTranslatorOptions);
+	}
+
+	@Lazy
+	@Bean
+	public CqlTranslatorOptions cqlTranslatorOptions() {
+		return CqlTranslatorOptions.defaultOptions();
+	}
+
+	@Bean
+	public ElmCacheResourceChangeListener elmCacheResourceChangeListener(IResourceChangeListenerRegistry resourceChangeListenerRegistry, IFhirResourceDao<org.hl7.fhir.r4.model.Library> libraryDao,  Map<org.cqframework.cql.elm.execution.VersionedIdentifier, Library> globalLibraryCache) {
+		ElmCacheResourceChangeListener listener = new ElmCacheResourceChangeListener(libraryDao, globalLibraryCache);
+		resourceChangeListenerRegistry.registerResourceResourceChangeListener("Library", new SearchParameterMap(), listener, 1000);
+		return listener;
 	}
 }

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/dstu3/evaluation/MeasureEvaluation.java

@@ -39,6 +39,7 @@ import org.hl7.fhir.dstu3.model.Measure;
 import org.hl7.fhir.dstu3.model.MeasureReport;
 import org.hl7.fhir.dstu3.model.Observation;
 import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.Quantity;
 import org.hl7.fhir.dstu3.model.Reference;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.dstu3.model.StringType;
@@ -677,7 +678,7 @@ public class MeasureEvaluation {
                         .setValue(new StringType(sdeKey));
                 obsExtension.addExtension(extExtPop);
                 obs.addExtension(obsExtension);
-                obs.setValue(new IntegerType(sdeAccumulatorValue));
+                obs.setValue(new Quantity(sdeAccumulatorValue));
                 if(!isSingle) {
                     valueCoding.setCode(sdeAccumulatorKey);
                     obsCodeableConcept.setCoding(Collections.singletonList(valueCoding));

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/dstu3/helper/LibraryHelper.java

@@ -20,11 +20,12 @@ package ca.uhn.fhir.cql.dstu3.helper;
  * #L%
  */
 
-import ca.uhn.fhir.cql.common.evaluation.LibraryLoader;
 import ca.uhn.fhir.cql.common.provider.LibraryResolutionProvider;
-import ca.uhn.fhir.cql.common.provider.LibrarySourceProvider;
 import org.apache.commons.lang3.StringUtils;
 import org.cqframework.cql.cql2elm.LibraryManager;
+import ca.uhn.fhir.cql.common.provider.LibraryContentProvider;
+
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
 import org.cqframework.cql.cql2elm.ModelManager;
 import org.cqframework.cql.cql2elm.model.Model;
 import org.cqframework.cql.elm.execution.Library;
@@ -36,11 +37,13 @@ import org.hl7.fhir.dstu3.model.Reference;
 import org.hl7.fhir.dstu3.model.RelatedArtifact;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.opencds.cqf.cql.evaluator.cql2elm.model.CacheAwareModelManager;
-import org.opencds.cqf.cql.evaluator.engine.execution.PrivateCachingLibraryLoaderDecorator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.opencds.cqf.cql.evaluator.engine.execution.CacheAwareLibraryLoaderDecorator;
+import org.opencds.cqf.cql.evaluator.engine.execution.TranslatingLibraryLoader;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 
@@ -48,22 +51,24 @@ public class LibraryHelper {
 	private static final Logger ourLog = LoggerFactory.getLogger(LibraryHelper.class);
 
 	private final Map<org.hl7.elm.r1.VersionedIdentifier, Model> modelCache;
+	private Map<VersionedIdentifier, Library> libraryCache;
+	private CqlTranslatorOptions translatorOptions; 
 
-	public LibraryHelper(Map<org.hl7.elm.r1.VersionedIdentifier, Model> modelCache) {
+
+	public LibraryHelper(Map<org.hl7.elm.r1.VersionedIdentifier, Model> modelCache, Map<VersionedIdentifier, Library> libraryCache, CqlTranslatorOptions translatorOptions) {
 		this.modelCache = modelCache;
+		this.libraryCache = libraryCache;
+		this.translatorOptions = translatorOptions;
 	}
 
 	public org.opencds.cqf.cql.engine.execution.LibraryLoader createLibraryLoader(
 		LibraryResolutionProvider<org.hl7.fhir.dstu3.model.Library> provider) {
 		ModelManager modelManager = new CacheAwareModelManager(this.modelCache);
-		LibraryManager libraryManager = new LibraryManager(modelManager);
-		libraryManager.getLibrarySourceLoader().clearProviders();
 
-		libraryManager.getLibrarySourceLoader().registerProvider(
+		List<org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider> contentProviders = Collections.singletonList(new LibraryContentProvider<org.hl7.fhir.dstu3.model.Library, Attachment>(
-			new LibrarySourceProvider<org.hl7.fhir.dstu3.model.Library, Attachment>(
+			provider, x -> x.getContent(), x -> x.getContentType(), x -> x.getData()));
-				provider, x -> x.getContent(), x -> x.getContentType(), x -> x.getData()));
 
-		return new PrivateCachingLibraryLoaderDecorator(new LibraryLoader(libraryManager, modelManager));
+		return new CacheAwareLibraryLoaderDecorator(new TranslatingLibraryLoader(modelManager, contentProviders, translatorOptions), libraryCache);
 	}
 
 	public List<Library> loadLibraries(Measure measure,
@@ -115,11 +120,13 @@ public class LibraryHelper {
 			if (artifact.hasType() && artifact.getType().equals(RelatedArtifact.RelatedArtifactType.DEPENDSON) && artifact.hasResource() && artifact.getResource().hasReference()) {
 				if (artifact.getResource().getReferenceElement().getResourceType().equals("Library")) {
 					org.hl7.fhir.dstu3.model.Library library = libraryResourceProvider.resolveLibraryById(artifact.getResource().getReferenceElement().getIdPart());
-
+					if (library != null) {
-					if (library != null && isLogicLibrary(library)) {
+						if (isLogicLibrary(library)) {
-						libraries.add(
+							libraries.add(libraryLoader
-							libraryLoader.load(new VersionedIdentifier().withId(library.getName()).withVersion(library.getVersion()))
+									.load(new VersionedIdentifier().withId(library.getName()).withVersion(library.getVersion())));
-						);
+						} else {
+							ourLog.warn("Library {} not included as part of evaluation context. Only Libraries with the 'logic-library' type are included.", library.getId());
+						}
 					}
 				}
 			}

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/dstu3/listener/ElmCacheResourceChangeListener.java

@@ -0,0 +1,72 @@
+package ca.uhn.fhir.cql.dstu3.listener;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import org.cqframework.cql.elm.execution.Library;
+import org.cqframework.cql.elm.execution.VersionedIdentifier;
+import org.hl7.fhir.instance.model.api.IIdType;
+
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.cache.IResourceChangeEvent;
+import ca.uhn.fhir.jpa.cache.IResourceChangeListener;
+
+public class ElmCacheResourceChangeListener implements IResourceChangeListener {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ElmCacheResourceChangeListener.class);
+
+	private IFhirResourceDao<org.hl7.fhir.dstu3.model.Library> libraryDao;
+	private Map<VersionedIdentifier, Library> globalLibraryCache;
+
+	public ElmCacheResourceChangeListener(IFhirResourceDao<org.hl7.fhir.dstu3.model.Library> libraryDao, Map<VersionedIdentifier, Library> globalLibraryCache) {
+		this.libraryDao = libraryDao;
+		this.globalLibraryCache = globalLibraryCache;
+	}
+
+	@Override
+	public void handleInit(Collection<IIdType> theResourceIds) {
+		// Intentionally empty. Only cache ELM on eval request
+	}
+
+	@Override
+	public void handleChange(IResourceChangeEvent theResourceChangeEvent) {
+		if (theResourceChangeEvent == null) {
+			return;
+		}
+
+		this.invalidateCacheByIds(theResourceChangeEvent.getDeletedResourceIds());
+		this.invalidateCacheByIds(theResourceChangeEvent.getUpdatedResourceIds());
+	}
+
+	private void invalidateCacheByIds(List<IIdType> theIds) {
+		if (theIds == null) {
+			return;
+		}
+
+		for (IIdType id : theIds) {
+			this.invalidateCacheById(id);
+		}
+	}
+
+	private void invalidateCacheById(IIdType theId) {
+		if (!theId.getResourceType().equals("Library"))  {
+			return;
+		}
+
+		try {
+			org.hl7.fhir.dstu3.model.Library library = this.libraryDao.read(theId);
+
+			this.globalLibraryCache.remove(new VersionedIdentifier().withId(library.getName()).withVersion(library.getVersion()));
+		}
+		// This happens when a Library is deleted entirely so it's impossible to look up name and version.
+		catch (Exception e) {
+			// TODO: This needs to be smarter... the issue is that ELM is cached with library name and version as the key since
+			// that's the access path the CQL engine uses, but change notifications occur with the resource Id, which is not
+			// necessarily tied to the resource name. In any event, if a unknown resource is deleted, clear all libraries as a workaround.
+			// One option is to maintain a cache with multiple indices.
+			ourLog.debug("Failed to locate resource {} to look up name and version. Clearing all libraries from cache.", theId.getValueAsString());
+			this.globalLibraryCache.clear();
+	}
+	}
+}

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/dstu3/provider/MeasureOperationsProvider.java

@@ -40,8 +40,6 @@ import org.hl7.fhir.dstu3.model.MeasureReport;
 import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.opencds.cqf.cql.engine.execution.LibraryLoader;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
@@ -54,8 +52,6 @@ import org.springframework.stereotype.Component;
  */
 @Component
 public class MeasureOperationsProvider {
-	private static final Logger logger = LoggerFactory.getLogger(MeasureOperationsProvider.class);
-
 	@Autowired
 	private LibraryResolutionProvider<Library> libraryResolutionProvider;
 	@Autowired

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/r4/helper/LibraryHelper.java

@@ -20,10 +20,11 @@ package ca.uhn.fhir.cql.r4.helper;
  * #L%
  */
 
-import ca.uhn.fhir.cql.common.evaluation.LibraryLoader;
 import ca.uhn.fhir.cql.common.provider.LibraryResolutionProvider;
-import ca.uhn.fhir.cql.common.provider.LibrarySourceProvider;
 import org.apache.commons.lang3.StringUtils;
+import ca.uhn.fhir.cql.common.provider.LibraryContentProvider;
+
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
 import org.cqframework.cql.cql2elm.LibraryManager;
 import org.cqframework.cql.cql2elm.ModelManager;
 import org.cqframework.cql.cql2elm.model.Model;
@@ -33,14 +34,16 @@ import org.hl7.fhir.r4.model.Attachment;
 import org.hl7.fhir.r4.model.CanonicalType;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Measure;
+import org.hl7.fhir.r4.model.PlanDefinition;
 import org.hl7.fhir.r4.model.RelatedArtifact;
 import org.hl7.fhir.r4.model.Resource;
 import org.opencds.cqf.cql.evaluator.cql2elm.model.CacheAwareModelManager;
-import org.opencds.cqf.cql.evaluator.engine.execution.PrivateCachingLibraryLoaderDecorator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-
+import org.opencds.cqf.cql.evaluator.engine.execution.CacheAwareLibraryLoaderDecorator;
+import org.opencds.cqf.cql.evaluator.engine.execution.TranslatingLibraryLoader;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 
@@ -51,34 +54,43 @@ public class LibraryHelper {
 	private static final Logger ourLog = LoggerFactory.getLogger(LibraryHelper.class);
 
 	private final Map<org.hl7.elm.r1.VersionedIdentifier, Model> modelCache;
+	private Map<VersionedIdentifier, Library> libraryCache;
+	private CqlTranslatorOptions translatorOptions;
 
-	public LibraryHelper(Map<org.hl7.elm.r1.VersionedIdentifier, Model> modelCache) {
+	public LibraryHelper(Map<org.hl7.elm.r1.VersionedIdentifier, Model> modelCache,
+			Map<VersionedIdentifier, Library> libraryCache, CqlTranslatorOptions translatorOptions) {
 		this.modelCache = modelCache;
+		this.libraryCache = libraryCache;
+		this.translatorOptions = translatorOptions;
 	}
 
-	public org.opencds.cqf.cql.engine.execution.LibraryLoader createLibraryLoader(LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> provider) {
+	public org.opencds.cqf.cql.engine.execution.LibraryLoader createLibraryLoader(
+			LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> provider) {
 		ModelManager modelManager = new CacheAwareModelManager(this.modelCache);
 		LibraryManager libraryManager = new LibraryManager(modelManager);
 		libraryManager.getLibrarySourceLoader().clearProviders();
+		List<org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider> contentProviders = Collections
+				.singletonList(new LibraryContentProvider<org.hl7.fhir.r4.model.Library, Attachment>(provider,
+						x -> x.getContent(), x -> x.getContentType(), x -> x.getData()));
 
-		libraryManager.getLibrarySourceLoader().registerProvider(
+		return new CacheAwareLibraryLoaderDecorator(
-			new LibrarySourceProvider<org.hl7.fhir.r4.model.Library, Attachment>(provider,
+				new TranslatingLibraryLoader(modelManager, contentProviders, translatorOptions), libraryCache);
-				x -> x.getContent(), x -> x.getContentType(), x -> x.getData()));
-
-		return new PrivateCachingLibraryLoaderDecorator(new LibraryLoader(libraryManager, modelManager));
 	}
 
-	public org.opencds.cqf.cql.engine.execution.LibraryLoader createLibraryLoader(org.cqframework.cql.cql2elm.LibrarySourceProvider provider) {
+	public org.opencds.cqf.cql.engine.execution.LibraryLoader createLibraryLoader(
+			org.cqframework.cql.cql2elm.LibrarySourceProvider provider) {
 		ModelManager modelManager = new CacheAwareModelManager(this.modelCache);
 		LibraryManager libraryManager = new LibraryManager(modelManager);
 		libraryManager.getLibrarySourceLoader().clearProviders();
 
 		libraryManager.getLibrarySourceLoader().registerProvider(provider);
 
-		return new PrivateCachingLibraryLoaderDecorator(new LibraryLoader(libraryManager, modelManager));
+		return new CacheAwareLibraryLoaderDecorator(new TranslatingLibraryLoader(modelManager, null, translatorOptions),
+				libraryCache);
 	}
 
-	public org.hl7.fhir.r4.model.Library resolveLibraryReference(LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResourceProvider, String reference) {
+	public org.hl7.fhir.r4.model.Library resolveLibraryReference(
+			LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResourceProvider, String reference) {
 		// Raw references to Library/libraryId or libraryId
 		if (reference.startsWith("Library/") || !reference.contains("/")) {
 			return libraryResourceProvider.resolveLibraryById(reference.replace("Library/", ""));
@@ -92,30 +104,21 @@ public class LibraryHelper {
 	}
 
 	public List<org.cqframework.cql.elm.execution.Library> loadLibraries(Measure measure,
-																								org.opencds.cqf.cql.engine.execution.LibraryLoader libraryLoader,
+			org.opencds.cqf.cql.engine.execution.LibraryLoader libraryLoader,
-																								LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResourceProvider) {
+			LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResourceProvider) {
 		List<org.cqframework.cql.elm.execution.Library> libraries = new ArrayList<org.cqframework.cql.elm.execution.Library>();
 
-		List<String> messages = new ArrayList<>();
-
 		// load libraries
-		//TODO: if there's a bad measure argument, this blows up for an obscure error
+		// TODO: if there's a bad measure argument, this blows up for an obscure error
 		org.hl7.fhir.r4.model.Library primaryLibrary = null;
-
+		for (CanonicalType ref : measure.getLibrary()) {
-		List<CanonicalType> measureLibraries = measure.getLibrary();
-		if (measureLibraries.isEmpty()) {
-			String message = "No libraries found on " + measure.getId() + ".  Did you perhaps load a DSTU3 Measure onto an R4 server?";
-			messages.add(message);
-			ourLog.warn(message);
-		}
-		for (CanonicalType ref : measureLibraries) {
 			// if library is contained in measure, load it into server
-			String id = ref.getValue(); //CanonicalHelper.getId(ref);
+			String id = ref.getValue(); // CanonicalHelper.getId(ref);
 			if (id.startsWith("#")) {
 				id = id.substring(1);
 				for (Resource resource : measure.getContained()) {
 					if (resource instanceof org.hl7.fhir.r4.model.Library
-						&& resource.getIdElement().getIdPart().equals(id)) {
+							&& resource.getIdElement().getIdPart().equals(id)) {
 						libraryResourceProvider.update((org.hl7.fhir.r4.model.Library) resource);
 					}
 				}
@@ -127,34 +130,30 @@ public class LibraryHelper {
 				primaryLibrary = library;
 			}
 
-
+			if (library != null && isLogicLibrary(library)) {
-			if (library != null) {
+				libraries.add(libraryLoader
-				if (isLogicLibrary(library)) {
+						.load(new VersionedIdentifier().withId(library.getName()).withVersion(library.getVersion())));
-					libraries.add(
-						libraryLoader.load(new VersionedIdentifier().withId(library.getName()).withVersion(library.getVersion()))
-					);
-				} else {
-					String message = "Skipping library " + library.getId() + " is not a logic library.  Probably missing type.coding.system=\"http://terminology.hl7.org/CodeSystem/library-type\"";
-					messages.add(message);
-					ourLog.warn(message);
-				}
 			}
 		}
 
 		if (libraries.isEmpty()) {
-			throw new IllegalArgumentException(String
+			throw new IllegalArgumentException(
-				.format("Could not load library source for libraries referenced in %s:\n%s", measure.getId(), StringUtils.join("\n", messages)));
+					String.format("Could not load library source for libraries referenced in %s.", measure.getId()));
 		}
 
 		for (RelatedArtifact artifact : primaryLibrary.getRelatedArtifact()) {
-			if (artifact.hasType() && artifact.getType().equals(RelatedArtifact.RelatedArtifactType.DEPENDSON) && artifact.hasResource()) {
+			if (artifact.hasType() && artifact.getType().equals(RelatedArtifact.RelatedArtifactType.DEPENDSON)
+					&& artifact.hasResource()) {
 				org.hl7.fhir.r4.model.Library library = null;
 				library = resolveLibraryReference(libraryResourceProvider, artifact.getResource());
 
-				if (library != null && isLogicLibrary(library)) {
+				if (library != null) {
-					libraries.add(
+					if (isLogicLibrary(library)) {
-						libraryLoader.load(new VersionedIdentifier().withId(library.getName()).withVersion(library.getVersion()))
+						libraries.add(libraryLoader
-					);
+								.load(new VersionedIdentifier().withId(library.getName()).withVersion(library.getVersion())));
+					} else {
+						ourLog.warn("Library {} not included as part of evaluation context. Only Libraries with the 'logic-library' type are included.", library.getId());
+					}
 				}
 			}
 		}
@@ -168,12 +167,13 @@ public class LibraryHelper {
 		}
 
 		if (!library.hasType()) {
-			// If no type is specified, assume it is a logic library based on whether there is a CQL content element.
+			// If no type is specified, assume it is a logic library based on whether there
+			// is a CQL content element.
 			if (library.hasContent()) {
 				for (Attachment a : library.getContent()) {
-					if (a.hasContentType() && (a.getContentType().equals("text/cql")
+					if (a.hasContentType()
-						|| a.getContentType().equals("application/elm+xml")
+							&& (a.getContentType().equals("text/cql") || a.getContentType().equals("application/elm+xml")
-						|| a.getContentType().equals("application/elm+json"))) {
+									|| a.getContentType().equals("application/elm+json"))) {
 						return true;
 					}
 				}
@@ -186,8 +186,8 @@ public class LibraryHelper {
 		}
 
 		for (Coding c : library.getType().getCoding()) {
-			if (c.hasSystem() && c.getSystem().equals("http://terminology.hl7.org/CodeSystem/library-type")
+			if (c.hasSystem() && c.getSystem().equals("http://terminology.hl7.org/CodeSystem/library-type") && c.hasCode()
-				&& c.hasCode() && c.getCode().equals("logic-library")) {
+					&& c.getCode().equals("logic-library")) {
 				return true;
 			}
 		}
@@ -195,27 +195,40 @@ public class LibraryHelper {
 		return false;
 	}
 
-	public Library resolveLibraryById(String libraryId,
+	public Library resolveLibraryById(String libraryId, org.opencds.cqf.cql.engine.execution.LibraryLoader libraryLoader,
-												 org.opencds.cqf.cql.engine.execution.LibraryLoader libraryLoader,
+			LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResourceProvider) {
-												 LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResourceProvider) {
-		// Library library = null;
 
 		org.hl7.fhir.r4.model.Library fhirLibrary = libraryResourceProvider.resolveLibraryById(libraryId);
 		return libraryLoader
-			.load(new VersionedIdentifier().withId(fhirLibrary.getName()).withVersion(fhirLibrary.getVersion()));
+				.load(new VersionedIdentifier().withId(fhirLibrary.getName()).withVersion(fhirLibrary.getVersion()));
 	}
 
 	public Library resolvePrimaryLibrary(Measure measure,
-													 org.opencds.cqf.cql.engine.execution.LibraryLoader libraryLoader,
+			org.opencds.cqf.cql.engine.execution.LibraryLoader libraryLoader,
-													 LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResourceProvider) {
+			LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResourceProvider) {
 		// default is the first library reference
 		String id = CanonicalHelper.getId(measure.getLibrary().get(0));
 
 		Library library = resolveLibraryById(id, libraryLoader, libraryResourceProvider);
 
 		if (library == null) {
-			throw new IllegalArgumentException(String.format("Could not resolve primary library for Measure/%s.",
+			throw new IllegalArgumentException(
-				measure.getIdElement().getIdPart()));
+					String.format("Could not resolve primary library for Measure/%s.", measure.getIdElement().getIdPart()));
+		}
+
+		return library;
+	}
+
+	public Library resolvePrimaryLibrary(PlanDefinition planDefinition,
+			org.opencds.cqf.cql.engine.execution.LibraryLoader libraryLoader,
+			LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResourceProvider) {
+		String id = CanonicalHelper.getId(planDefinition.getLibrary().get(0));
+
+		Library library = resolveLibraryById(id, libraryLoader, libraryResourceProvider);
+
+		if (library == null) {
+			throw new IllegalArgumentException(String.format("Could not resolve primary library for PlanDefinition/%s",
+					planDefinition.getIdElement().getIdPart()));
 		}
 
 		return library;

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/r4/listener/ElmCacheResourceChangeListener.java

@@ -0,0 +1,72 @@
+package ca.uhn.fhir.cql.r4.listener;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import org.cqframework.cql.elm.execution.Library;
+import org.cqframework.cql.elm.execution.VersionedIdentifier;
+import org.hl7.fhir.instance.model.api.IIdType;
+
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.cache.IResourceChangeEvent;
+import ca.uhn.fhir.jpa.cache.IResourceChangeListener;
+
+public class ElmCacheResourceChangeListener implements IResourceChangeListener {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ElmCacheResourceChangeListener.class);
+
+	private IFhirResourceDao<org.hl7.fhir.r4.model.Library> libraryDao;
+	private Map<VersionedIdentifier, Library> globalLibraryCache;
+
+	public ElmCacheResourceChangeListener(IFhirResourceDao<org.hl7.fhir.r4.model.Library> libraryDao, Map<VersionedIdentifier, Library> globalLibraryCache) {
+		this.libraryDao = libraryDao;
+		this.globalLibraryCache = globalLibraryCache;
+	}
+
+	@Override
+	public void handleInit(Collection<IIdType> theResourceIds) {
+		// Intentionally empty. Only cache ELM on eval request
+	}
+
+	@Override
+	public void handleChange(IResourceChangeEvent theResourceChangeEvent) {
+		if (theResourceChangeEvent == null) {
+			return;
+		}
+
+		this.invalidateCacheByIds(theResourceChangeEvent.getDeletedResourceIds());
+		this.invalidateCacheByIds(theResourceChangeEvent.getUpdatedResourceIds());
+	}
+
+	private void invalidateCacheByIds(List<IIdType> theIds) {
+		if (theIds == null) {
+			return;
+		}
+
+		for (IIdType id : theIds) {
+			this.invalidateCacheById(id);
+		}
+	}
+
+	private void invalidateCacheById(IIdType theId) {
+		if (!theId.getResourceType().equals("Library"))  {
+			return;
+		}
+
+		try {
+			org.hl7.fhir.r4.model.Library library = this.libraryDao.read(theId);
+
+			this.globalLibraryCache.remove(new VersionedIdentifier().withId(library.getName()).withVersion(library.getVersion()));
+		}
+		// This happens when a Library is deleted entirely so it's impossible to look up name and version.
+		catch (Exception e) {
+			// TODO: This needs to be smarter... the issue is that ELM is cached with library name and version as the key since
+			// that's the access path the CQL engine uses, but change notifications occur with the resource Id, which is not
+			// necessarily tied to the resource name. In any event, if a unknown resource is deleted, clear all libraries as a workaround.
+			// One option is to maintain a cache with multiple indices.
+			ourLog.debug("Failed to locate resource {} to look up name and version. Clearing all libraries from cache.", theId.getValueAsString());
+			this.globalLibraryCache.clear();
+		}
+	}
+}

hapi-fhir-jpaserver-cql/src/test/java/ca/uhn/fhir/cql/config/TestCqlConfig.java

@@ -1,15 +1,23 @@
 package ca.uhn.fhir.cql.config;
 
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Primary;
-
-
 
 @Configuration
 @Import({SubscriptionSubmitterConfig.class, SubscriptionChannelConfig.class})
 public class TestCqlConfig {
+
+	@Bean
+	public DaoConfig daoConfig() {
+		DaoConfig daoConfig = new DaoConfig();
+		daoConfig.setAllowExternalReferences(true);
+		daoConfig.setEnforceReferentialIntegrityOnWrite(false);
+		daoConfig.setEnforceReferenceTargetTypes(false);
+
+		return daoConfig;
+	}
 }

hapi-fhir-jpaserver-cql/src/test/java/ca/uhn/fhir/cql/dstu3/CqlMeasureEvaluationDstu3Test.java

@@ -75,7 +75,7 @@ public class CqlMeasureEvaluationDstu3Test extends BaseCqlDstu3Test {
 		assertNotNull("expected MeasureReport can not be null", expected);
 		assertNotNull("actual MeasureReport can not be null", actual);
 
-		String errorLocator = String.format("Measure: %s, Subject: %s", expected.getMeasure(),
+		String errorLocator = String.format("Measure: %s, Subject: %s", expected.getMeasure().getReference(),
 				expected.getPatient().getReference());
 
 		assertEquals(expected.hasGroup(), actual.hasGroup(), errorLocator);
@@ -83,10 +83,10 @@ public class CqlMeasureEvaluationDstu3Test extends BaseCqlDstu3Test {
 
 		for (MeasureReportGroupComponent mrgcExpected : expected.getGroup()) {
 			Optional<MeasureReportGroupComponent> mrgcActualOptional = actual.getGroup().stream()
-					.filter(x -> x.getId().equals(mrgcExpected.getId())).findFirst();
+					.filter(x -> x.getIdentifier() != null && x.getIdentifier().getValue().equals(mrgcExpected.getIdentifier().getValue())).findFirst();
 
-			errorLocator = String.format("Measure: %s, Subject: %s, Group: %s", expected.getMeasure(),
+			errorLocator = String.format("Measure: %s, Subject: %s, Group: %s", expected.getMeasure().getReference(),
-					expected.getPatient().getReference(), mrgcExpected.getId());
+					expected.getPatient().getReference(), mrgcExpected.getIdentifier().getValue());
 			assertTrue(errorLocator, mrgcActualOptional.isPresent());
 
 			MeasureReportGroupComponent mrgcActual = mrgcActualOptional.get();
@@ -94,7 +94,7 @@ public class CqlMeasureEvaluationDstu3Test extends BaseCqlDstu3Test {
 			if (mrgcExpected.getMeasureScore() == null) {
 				assertNull(mrgcActual.getMeasureScore(), errorLocator);
 			} else {
-				assertNotNull(mrgcActual.getMeasureScore());
+				assertNotNull(errorLocator, mrgcActual.getMeasureScore());
 				BigDecimal decimalExpected = mrgcExpected.getMeasureScore();
 				BigDecimal decimalActual = mrgcActual.getMeasureScore();
 
@@ -135,10 +135,13 @@ public class CqlMeasureEvaluationDstu3Test extends BaseCqlDstu3Test {
 		return new DateTimeType(date).getValueAsString();
 	}
 
-	// As of 2/11/2021, all the DSTU3 bundles in the Connectathon IG are out of date
+	@Test
-	// and can't be posted
+	public void test_EXM124_FHIR3_72000() throws IOException {
-	// @Test
+		this.testMeasureBundle("dstu3/connectathon/EXM124-FHIR3-7.2.000-bundle.json");
-	// public void test_EXM117_83000() throws IOException {
+	}
-	// 	this.testMeasureBundle("dstu3/connectathon/EXM117_FHIR3-8.3.000-bundle.json");
+
-	// }
+	@Test
+	public void test_EXM104_FHIR3_81000() throws IOException {
+		this.testMeasureBundle("dstu3/connectathon/EXM104-FHIR3-8.1.000-bundle.json");
+	}
 }

hapi-fhir-jpaserver-cql/src/test/java/ca/uhn/fhir/cql/r4/CqlMeasureEvaluationR4Test.java

@@ -83,7 +83,7 @@ public class CqlMeasureEvaluationR4Test extends BaseCqlR4Test {
 
 		for (MeasureReportGroupComponent mrgcExpected : expected.getGroup()) {
 			Optional<MeasureReportGroupComponent> mrgcActualOptional = actual.getGroup().stream()
-					.filter(x -> x.getId().equals(mrgcExpected.getId())).findFirst();
+			.filter(x -> x.getId() != null && x.getId().equals(mrgcExpected.getId())).findFirst();
 
 			errorLocator = String.format("Measure: %s, Subject: %s, Group: %s", expected.getMeasure(),
 					expected.getSubject().getReference(), mrgcExpected.getId());

hapi-fhir-validation/pom.xml

@@ -63,6 +63,10 @@
 					<groupId>junit</groupId>
 					<artifactId>junit</artifactId>
 				</exclusion>
+				<exclusion>
+					<groupId>org.apache.commons</groupId>
+					<artifactId>commons-collections4</artifactId>
+				</exclusion>
 			</exclusions>
 		</dependency>
 		<dependency>

hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidatorDstu3Test.java

@@ -596,7 +596,7 @@ public class FhirInstanceValidatorDstu3Test {
 		ValidationResult output = myVal.validateWithResult(input);
 		List<SingleValidationMessage> issues = logResultsAndReturnNonInformationalOnes(output);
 
-		assertThat(issues.toString(), containsString("None of the codes provided are in the value set http://phr.kanta.fi/ValueSet/fiphr-vs-medicationcontext"));
+		assertThat(issues.toString(), containsString("None of the codings provided are in the value set http://phr.kanta.fi/ValueSet/fiphr-vs-medicationcontext"));
 	}
 
 	@Test
@@ -1278,7 +1278,7 @@ public class FhirInstanceValidatorDstu3Test {
 		assertEquals(1, all.size());
 		assertEquals("Patient.identifier[0].type", all.get(0).getLocationString());
 		assertEquals(
-			"None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type), and a code should come from this value set unless it has no suitable code and the validator cannot judge what is suitable) (codes = http://example.com/foo/bar#bar)",
+			"None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type), and a coding should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) (codes = http://example.com/foo/bar#bar)",
 			all.get(0).getMessage());
 		assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
 

hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/QuestionnaireValidatorDstu3Test.java

@@ -118,7 +118,7 @@ public class QuestionnaireValidatorDstu3Test {
 			ValidationResult errors = myVal.validateWithResult(q);
 			ourLog.info(errors.toString());
 			assertThat(errors.isSuccessful(), Matchers.is(true));
-			assertThat(errors.getMessages().get(0).getMessage(), containsString("and a code should come from this value set unless it has no suitable code and the validator cannot judge what is suitable) (codes = null#text-box)"));
+			assertThat(errors.getMessages().get(0).getMessage(), containsString("and a coding should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) (codes = null#text-box)"));
 		}
 	}
 

hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/ResourceValidatorDstu3Test.java

@@ -165,7 +165,7 @@ public class ResourceValidatorDstu3Test {
 		ValidationResult output = val.validateWithResult(p);
 		List<SingleValidationMessage> all = logResultsAndReturnNonInformationalOnes(output);
 
-		assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/marital-status (http://hl7.org/fhir/ValueSet/marital-status), and a code should come from this value set unless it has no suitable code and the validator cannot judge what is suitable) (codes = http://hl7.org/fhir/v3/MaritalStatus#FOO)", output.getMessages().get(0).getMessage());
+		assertEquals("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/marital-status (http://hl7.org/fhir/ValueSet/marital-status), and a coding should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) (codes = http://hl7.org/fhir/v3/MaritalStatus#FOO)", output.getMessages().get(0).getMessage());
 		assertEquals(ResultSeverityEnum.WARNING, output.getMessages().get(0).getSeverity());
 	}
 

hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

@@ -628,7 +628,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
 		ValidationResult output = myVal.validateWithResult(input);
 		List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
 		assertEquals(1, errors.size());
-		assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/report-codes (http://hl7.org/fhir/ValueSet/report-codes), and a code is recommended to come from this value set) (codes = http://loinc.org#1-8)", errors.get(0).getMessage());
+		assertEquals("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/report-codes (http://hl7.org/fhir/ValueSet/report-codes), and a coding is recommended to come from this value set) (codes = http://loinc.org#1-8)", errors.get(0).getMessage());
 	}
 
 	@Test
@@ -1333,7 +1333,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
 		List<SingleValidationMessage> all = logResultsAndReturnAll(output);
 		assertEquals(1, all.size());
 		assertEquals("Patient.identifier[0].type", all.get(0).getLocationString());
-		assertThat(all.get(0).getMessage(), containsString("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type"));
+		assertThat(all.get(0).getMessage(), containsString("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type"));
 		assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
 
 	}

hapi-fhir-validation/src/test/java/org/hl7/fhir/r5/validation/FhirInstanceValidatorR5Test.java

@@ -945,7 +945,7 @@ public class FhirInstanceValidatorR5Test {
 		assertEquals(1, all.size());
 		assertEquals("Patient.identifier[0].type", all.get(0).getLocationString());
 		assertEquals(
-			"None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type), and a code should come from this value set unless it has no suitable code and the validator cannot judge what is suitable) (codes = http://example.com/foo/bar#bar)",
+			"None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type), and a coding should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) (codes = http://example.com/foo/bar#bar)",
 			all.get(0).getMessage());
 		assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
 

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/ResourceValidatorDstu3FeatureTest.java

@@ -142,7 +142,7 @@ public class ResourceValidatorDstu3FeatureTest {
 		ValidationResult output = val.validateWithResult(p);
 		List<SingleValidationMessage> all = logResultsAndReturnNonInformationalOnes(output);
 
-		assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/marital-status (http://hl7.org/fhir/ValueSet/marital-status, and a code should come from this value set unless it has no suitable code) (codes = http://hl7.org/fhir/v3/MaritalStatus#FOO)", output.getMessages().get(0).getMessage());
+		assertEquals("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/marital-status (http://hl7.org/fhir/ValueSet/marital-status, and a coding should come from this value set unless it has no suitable code) (codes = http://hl7.org/fhir/v3/MaritalStatus#FOO)", output.getMessages().get(0).getMessage());
 		assertEquals(ResultSeverityEnum.WARNING, output.getMessages().get(0).getSeverity());
 	}
 

pom.xml

@@ -743,7 +743,7 @@
 
 	<properties>
 
-		<fhir_core_version>5.3.0</fhir_core_version>
+		<fhir_core_version>5.3.10</fhir_core_version>
 		<ucum_version>1.0.3</ucum_version>
 
 		<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>
@@ -829,8 +829,8 @@
 		<elastic_apm_version>1.13.0</elastic_apm_version>
 		<!-- CQL Support -->
 		<cql-engine.version>1.5.1</cql-engine.version>
-		<cql-evaluator.version>1.1.0</cql-evaluator.version>
+		<cql-evaluator.version>1.2.0</cql-evaluator.version>
-		<cqframework.version>1.5.1</cqframework.version>
+		<cqframework.version>1.5.2</cqframework.version>
 
 		<!-- Site properties -->
 		<fontawesomeVersion>5.4.1</fontawesomeVersion>