$care-gaps functionality integration (#4561)

* care gaps integration

* fix review comments.

* Clean up for HAPI Conventions

* More cleanup to share constants

* More cleanup of tests

* More cleanup

* Update CQL versions

* Added changelog

* fix failing test cases for care gaps.

* WIP care-gaps tests

* implementation of end to end care gaps test case.

* addressing the code review comments.

* addressing comments to bring to hapi-fhir standards.

* added the docs required.

* Adding hapi-fhir-storage-cr module for test coverage inclusion.

* Addressing the comments.

* addressing comments and updated with master.

* Addressing comments for minor changes requested.

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4562-care-gaps.yaml

@@ -0,0 +1,4 @@
+---
+type: add
+issue: 4562
+title: "Added support for the $care-gaps operation defined by the DaVinci DEQM IG"

hapi-fhir-jacoco/pom.xml

@@ -197,6 +197,11 @@
 					<artifactId>hapi-fhir-storage</artifactId>
 					<version>${project.version}</version>
 				</dependency>
+				<dependency>
+					<groupId>ca.uhn.hapi.fhir</groupId>
+					<artifactId>hapi-fhir-storage-cr</artifactId>
+					<version>${project.version}</version>
+				</dependency>
 			</dependencies>
 		</profile>
 	</profiles>

hapi-fhir-storage-cr/pom.xml

@@ -71,6 +71,11 @@
 				<artifactId>hapi-fhir-structures-dstu3</artifactId>
 				<version>${project.version}</version>
 			</dependency>
+			<dependency>
+				<groupId>ca.uhn.hapi.fhir</groupId>
+				<artifactId>hapi-fhir-base</artifactId>
+				<version>${project.version}</version>
+			</dependency>
 		</dependencies>
 	</dependencyManagement>
 

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/BaseClinicalReasoningConfig.java

@@ -69,7 +69,6 @@ import org.opencds.cqf.cql.evaluator.engine.model.CachingModelResolverDecorator;
 import org.opencds.cqf.cql.evaluator.engine.retrieve.BundleRetrieveProvider;
 import org.opencds.cqf.cql.evaluator.fhir.Constants;
 import org.opencds.cqf.cql.evaluator.fhir.adapter.AdapterFactory;
-import org.opencds.cqf.cql.evaluator.fhir.Constants;
 import org.opencds.cqf.cql.evaluator.measure.MeasureEvaluationOptions;
 import org.opencds.cqf.cql.evaluator.spring.fhir.adapter.AdapterConfiguration;
 import org.slf4j.Logger;
@@ -111,26 +110,22 @@ public abstract class BaseClinicalReasoningConfig {
 
 	@Bean
 	public CrProperties.CqlProperties cqlProperties(CrProperties theCrProperties) {
-		return theCrProperties.getCql();
+		return theCrProperties.getCqlProperties();
 	}
 
 	@Bean
 	public CrProperties.MeasureProperties measureProperties(CrProperties theCrProperties) {
-		return theCrProperties.getMeasure();
+		return theCrProperties.getMeasureProperties();
 	}
 
 	@Bean
 	public MeasureEvaluationOptions measureEvaluationOptions(CrProperties theCrProperties) {
-		theCrProperties.getMeasure();
+		return theCrProperties.getMeasureProperties().getMeasureEvaluationOptions();
-		MeasureEvaluationOptions measureEvaluation = theCrProperties.getMeasure().getMeasureEvaluation();
-		return measureEvaluation;
 	}
 
-
-
 	@Bean
 	public CqlOptions cqlOptions(CrProperties theCrProperties) {
-		return theCrProperties.getCql().getOptions();
+		return theCrProperties.getCqlProperties().getCqlOptions();
 	}
 
 	@Bean
@@ -140,7 +135,7 @@ public abstract class BaseClinicalReasoningConfig {
 
 	@Bean
 	public CqlTranslatorOptions cqlTranslatorOptions(FhirContext theFhirContext, CrProperties.CqlProperties theCqlProperties) {
-		CqlTranslatorOptions options = theCqlProperties.getOptions().getCqlTranslatorOptions();
+		CqlTranslatorOptions options = theCqlProperties.getCqlOptions().getCqlTranslatorOptions();
 
 		if (theFhirContext.getVersion().getVersion().isOlderThan(FhirVersionEnum.R4)
 			&& (options.getCompatibilityLevel().equals("1.5") || options.getCompatibilityLevel().equals("1.4"))) {
@@ -239,7 +234,7 @@ public abstract class BaseClinicalReasoningConfig {
 		ModelManager theModelManager, CqlTranslatorOptions theCqlTranslatorOptions, CrProperties.CqlProperties theCqlProperties) {
 		return lcp -> {
 
-			if (theCqlProperties.getOptions().useEmbeddedLibraries()) {
+			if (theCqlProperties.getCqlOptions().useEmbeddedLibraries()) {
 				lcp.add(new FhirLibrarySourceProvider());
 			}
 

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/CrProperties.java

@@ -26,80 +26,87 @@ import org.opencds.cqf.cql.evaluator.measure.MeasureEvaluationOptions;
 
 public class CrProperties {
 
-	private boolean enabled = true;
+	private boolean myCqlEnabled = true;
-	private MeasureProperties measureProperties;
+	private MeasureProperties myMeasureProperties;
-	private CqlProperties cqlProperties = new CqlProperties();
+	private CqlProperties myCqlProperties = new CqlProperties();
 
 	public CrProperties () {
-		this.measureProperties = new MeasureProperties();
+		this.myMeasureProperties = new MeasureProperties();
 	};
 
 
-	public boolean isEnabled() {
+	public boolean isCqlEnabled() {
-		return enabled;
+		return myCqlEnabled;
 	}
 
-	public void setEnabled(boolean enabled) {
+	public void setCqlEnabled(boolean theCqlEnabled) {
-		this.enabled = enabled;
+		this.myCqlEnabled = theCqlEnabled;
 	}
 
-	public MeasureProperties getMeasure() {
+	public MeasureProperties getMeasureProperties() {
-		return measureProperties;
+		return myMeasureProperties;
 	}
 
-	public void setMeasure(MeasureProperties measureProperties) {
+	public void setMeasureProperties(MeasureProperties theMeasureProperties) {
-		this.measureProperties = measureProperties;
+		this.myMeasureProperties = theMeasureProperties;
 	}
 
-	public CqlProperties getCql() {
+	public CqlProperties getCqlProperties() {
-		return cqlProperties;
+		return myCqlProperties;
 	}
 
-	public void setCql(CqlProperties cqlProperties) {
+	public void setCqlProperties(CqlProperties theCqlProperties) {
-		this.cqlProperties = cqlProperties;
+		this.myCqlProperties = theCqlProperties;
 	}
 
 	public static class MeasureProperties {
 
-		private boolean threadedCareGapsEnabled = true;
+		private boolean myThreadedCareGapsEnabled = true;
-		private MeasureReportConfiguration measureReportConfiguration;
+		private MeasureReportConfiguration myMeasureReportConfiguration;
-		private MeasureEvaluationOptions measureEvaluationOptions;
+		private MeasureEvaluationOptions myMeasureEvaluationOptions;
+
+		public static final int DEFAULT_THREADS_FOR_MEASURE_EVAL = 4;
+		public static final int DEFAULT_THREADS_BATCH_SIZE = 250;
+		public static final boolean DEFAULT_THREADS_ENABLED_FOR_MEASURE_EVAL = true;
 
 		public MeasureProperties() {
-			measureEvaluationOptions = MeasureEvaluationOptions.defaultOptions();
+			myMeasureEvaluationOptions = MeasureEvaluationOptions.defaultOptions();
-			measureEvaluationOptions.setNumThreads(4);
+			myMeasureEvaluationOptions.setNumThreads(DEFAULT_THREADS_FOR_MEASURE_EVAL);
-			measureEvaluationOptions.setThreadedBatchSize(250);
+			myMeasureEvaluationOptions.setThreadedBatchSize(DEFAULT_THREADS_BATCH_SIZE);
-			measureEvaluationOptions.setThreadedEnabled(true);
+			myMeasureEvaluationOptions.setThreadedEnabled(DEFAULT_THREADS_ENABLED_FOR_MEASURE_EVAL);
 		};
 
-		//eval options
-		public MeasureEvaluationOptions getMeasureEvaluation() {
-			return this.measureEvaluationOptions;
-		}
-
-		public void setMeasureEvaluation(MeasureEvaluationOptions measureEvaluation) {
-			this.measureEvaluationOptions = measureEvaluation;
-		}
 
 		//care gaps
 		public boolean getThreadedCareGapsEnabled() {
-			return threadedCareGapsEnabled;
+			return myThreadedCareGapsEnabled;
 		}
 
-		public void setThreadedCareGapsEnabled(boolean enabled) {
+		public void setThreadedCareGapsEnabled(boolean theThreadedCareGapsEnabled) {
-			this.threadedCareGapsEnabled = enabled;
+			myThreadedCareGapsEnabled = theThreadedCareGapsEnabled;
+		}
+		public boolean isThreadedCareGapsEnabled() {
+			return myThreadedCareGapsEnabled;
 		}
 
 		//report configuration
-		public MeasureReportConfiguration getMeasureReport() {
+		public MeasureReportConfiguration getMeasureReportConfiguration() {
-			return this.measureReportConfiguration;
+			return myMeasureReportConfiguration;
 		}
 
-		public void setMeasureReport(MeasureReportConfiguration measureReport) {
+		public void setMeasureReportConfiguration(MeasureReportConfiguration theMeasureReport) {
-			this.measureReportConfiguration = measureReport;
+			myMeasureReportConfiguration = theMeasureReport;
 		}
 
 
+		//measure evaluations
+		public void setMeasureEvaluationOptions(MeasureEvaluationOptions theMeasureEvaluation) {
+			myMeasureEvaluationOptions = theMeasureEvaluation;
+		}
+
+		public MeasureEvaluationOptions getMeasureEvaluationOptions() {
+			return myMeasureEvaluationOptions;
+		}
 
 		public static class MeasureReportConfiguration {
 			/**
@@ -112,7 +119,7 @@ public class CrProperties {
 			 * <a href="http://build.fhir.org/ig/HL7/davinci-deqm/index.html">Da Vinci DEQM
 			 * FHIR Implementation Guide</a>.
 			 **/
-			private String careGapsReporter;
+			private String myCareGapsReporter;
 			/**
 			 * Implements the author element of the <a href=
 			 * "http://www.hl7.org/fhir/composition.html">Composition</a> FHIR
@@ -123,22 +130,22 @@ public class CrProperties {
 			 * <a href="http://build.fhir.org/ig/HL7/davinci-deqm/index.html">Da Vinci DEQM
 			 * FHIR Implementation Guide</a>.
 			 **/
-			private String careGapsCompositionSectionAuthor;
+			private String myCareGapsCompositionSectionAuthor;
 
-			public String getReporter() {
+			public String getCareGapsReporter() {
-				return careGapsReporter;
+				return myCareGapsReporter;
 			}
 
-			public void setCareGapsReporter(String careGapsReporter) {
+			public void setCareGapsReporter(String theCareGapsReporter) {
-				this.careGapsReporter = null;// ResourceBuilder.ensureOrganizationReference(careGapsReporter);
+				myCareGapsReporter = theCareGapsReporter;
 			}
 
-			public String getCompositionAuthor() {
+			public String getCareGapsCompositionSectionAuthor() {
-				return careGapsCompositionSectionAuthor;
+				return myCareGapsCompositionSectionAuthor;
 			}
 
-			public void setCareGapsCompositionSectionAuthor(String careGapsCompositionSectionAuthor) {
+			public void setCareGapsCompositionSectionAuthor(String theCareGapsCompositionSectionAuthor) {
-				this.careGapsCompositionSectionAuthor = careGapsCompositionSectionAuthor;
+				myCareGapsCompositionSectionAuthor = theCareGapsCompositionSectionAuthor;
 			}
 		}
 
@@ -147,41 +154,41 @@ public class CrProperties {
 
 	public static class CqlProperties {
 
-		private boolean useEmbeddedLibraries = true;
+		private boolean myCqlUseOfEmbeddedLibraries = true;
 
-		private CqlEngineOptions runtimeOptions = CqlEngineOptions.defaultOptions();
+		private CqlEngineOptions myCqlRuntimeOptions = CqlEngineOptions.defaultOptions();
-		private CqlTranslatorOptions compilerOptions = CqlTranslatorOptions.defaultOptions();
+		private CqlTranslatorOptions myCqlTranslatorOptions = CqlTranslatorOptions.defaultOptions();
 
 
-		public boolean useEmbeddedLibraries() {
+		public boolean isCqlUseOfEmbeddedLibraries() {
-			return this.useEmbeddedLibraries;
+			return myCqlUseOfEmbeddedLibraries;
 		}
 
-		public void setUseEmbeddedLibraries(boolean useEmbeddedLibraries) {
+		public void setCqlUseOfEmbeddedLibraries(boolean theCqlUseOfEmbeddedLibraries) {
-			this.useEmbeddedLibraries = useEmbeddedLibraries;
+			myCqlUseOfEmbeddedLibraries = theCqlUseOfEmbeddedLibraries;
 		}
 
-		public CqlEngineOptions getRuntime() {
+		public CqlEngineOptions getCqlRuntimeOptions() {
-			return this.runtimeOptions;
+			return myCqlRuntimeOptions;
 		}
 
-		public void setRuntime(CqlEngineOptions runtime) {
+		public void setCqlRuntimeOptions(CqlEngineOptions theRuntime) {
-			this.runtimeOptions = runtime;
+			myCqlRuntimeOptions = theRuntime;
 		}
 
-		public CqlTranslatorOptions getCompiler() {
+		public CqlTranslatorOptions getCqlTranslatorOptions() {
-			return this.compilerOptions;
+			return myCqlTranslatorOptions;
 		}
 
-		public void setCompiler(CqlTranslatorOptions compiler) {
+		public void setCqlTranslatorOptions(CqlTranslatorOptions theCqlTranslatorOptions) {
-			this.compilerOptions = compiler;
+			myCqlTranslatorOptions = theCqlTranslatorOptions;
 		}
 
-		public CqlOptions getOptions() {
+		public CqlOptions getCqlOptions() {
 			CqlOptions cqlOptions = new CqlOptions();
-			cqlOptions.setUseEmbeddedLibraries(this.useEmbeddedLibraries());
+			cqlOptions.setUseEmbeddedLibraries(isCqlUseOfEmbeddedLibraries());
-			cqlOptions.setCqlEngineOptions(this.getRuntime());
+			cqlOptions.setCqlEngineOptions(getCqlRuntimeOptions());
-			cqlOptions.setCqlTranslatorOptions(this.getCompiler());
+			cqlOptions.setCqlTranslatorOptions(getCqlTranslatorOptions());
 			return cqlOptions;
 		}
 	}

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/CrR4Config.java

@@ -19,8 +19,14 @@
  */
 package ca.uhn.fhir.cr.config;
 
+import ca.uhn.fhir.cr.r4.measure.CareGapsOperationProvider;
+import ca.uhn.fhir.cr.r4.measure.CareGapsService;
+import ca.uhn.fhir.cr.r4.measure.ISubmitDataService;
 import ca.uhn.fhir.cr.r4.measure.MeasureOperationsProvider;
 import ca.uhn.fhir.cr.r4.measure.MeasureService;
+import ca.uhn.fhir.cr.r4.measure.SubmitDataProvider;
+import ca.uhn.fhir.cr.r4.measure.SubmitDataService;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
@@ -51,4 +57,31 @@ public class CrR4Config extends BaseClinicalReasoningConfig {
 	public MeasureOperationsProvider r4measureOperationsProvider() {
 		return new MeasureOperationsProvider();
 	}
+
+	@Bean
+	public Function<RequestDetails, CareGapsService> r4CareGapsServiceFactory(Function<RequestDetails, MeasureService> theR4MeasureServiceFactory,
+																									  CrProperties theCrProperties,
+																									  DaoRegistry theDaoRegistry) {
+		return r -> {
+			var ms = theR4MeasureServiceFactory.apply(r);
+			var cs = new CareGapsService(theCrProperties, ms, theDaoRegistry, cqlExecutor(), r);
+			return cs;
+		};
+	}
+
+	@Bean
+	public CareGapsOperationProvider r4CareGapsProvider(Function<RequestDetails, CareGapsService> theCareGapsServiceFunction){
+		return new CareGapsOperationProvider(theCareGapsServiceFunction);
+	}
+
+	@Bean
+	public ISubmitDataService r4SubmitDataService(DaoRegistry theDaoRegistry){
+		return requestDetails -> new SubmitDataService(theDaoRegistry, requestDetails);
+	}
+
+	@Bean
+	public SubmitDataProvider r4SubmitDataProvider(ISubmitDataService theSubmitDataService){
+		return new SubmitDataProvider(theSubmitDataService);
+	}
+
 }

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/constant/CareCapsConstants.java

@@ -0,0 +1,12 @@
+package ca.uhn.fhir.cr.constant;
+
+public class CareCapsConstants {
+	private CareCapsConstants(){}
+	public static final String CARE_GAPS_REPORT_PROFILE = "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/indv-measurereport-deqm";
+	public static final String CARE_GAPS_BUNDLE_PROFILE = "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/gaps-bundle-deqm";
+	public static final String CARE_GAPS_COMPOSITION_PROFILE = "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/gaps-composition-deqm";
+	public static final String CARE_GAPS_DETECTED_ISSUE_PROFILE = "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/gaps-detectedissue-deqm";
+	public static final String CARE_GAPS_GAP_STATUS_EXTENSION = "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/extension-gapStatus";
+	public static final String CARE_GAPS_GAP_STATUS_SYSTEM = "http://hl7.org/fhir/us/davinci-deqm/CodeSystem/gaps-status";
+
+}

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/constant/HtmlConstants.java

@@ -0,0 +1,9 @@
+package ca.uhn.fhir.cr.constant;
+
+public class HtmlConstants {
+
+	private HtmlConstants(){}
+	public static final String HTML_DIV_CONTENT = "<div xmlns=\"http://www.w3.org/1999/xhtml\">%s</div>";
+	public static final String HTML_PARAGRAPH_CONTENT = "<p>%s</p>";
+	public static final String HTML_DIV_PARAGRAPH_CONTENT = String.format(HTML_DIV_CONTENT, HTML_PARAGRAPH_CONTENT);
+}

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/constant/MeasureReportConstants.java

@@ -17,13 +17,24 @@
  * limitations under the License.
  * #L%
  */
-package ca.uhn.fhir.cr.common;
+package ca.uhn.fhir.cr.constant;
 
-public class SupplementalDataConstants {
+import java.sql.Date;
+import java.time.LocalDate;
 
-	private SupplementalDataConstants() {}
+public class MeasureReportConstants {
+
+	private MeasureReportConstants() {}
+
+	public static final String MEASUREREPORT_IMPROVEMENT_NOTATION_SYSTEM = "http://terminology.hl7.org/CodeSystem/measure-improvement-notation";
+	public static final String MEASUREREPORT_MEASURE_POPULATION_SYSTEM = "http://terminology.hl7.org/CodeSystem/measure-population";
 	public static final String MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION = "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/extension-supplementalData";
 	public static final String MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL = "http://hl7.org/fhir/us/davinci-deqm/SearchParameter/measurereport-supplemental-data";
 	public static final String MEASUREREPORT_PRODUCT_LINE_EXT_URL = "http://hl7.org/fhir/us/cqframework/cqfmeasures/StructureDefinition/cqfm-productLine";
 	public static final String MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION = "0.1.0";
+	public static final Date MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_DEFINITION_DATE = Date.valueOf(LocalDate.of(2022, 7, 20));
+	public static final String COUNTRY_CODING_SYSTEM_CODE = "urn:iso:std:iso:3166";
+	public static final String US_COUNTRY_CODE = "US";
+	public static final String US_COUNTRY_DISPLAY = "United States of America";
+
 }

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/dstu3/ISupplementalDataSearchParamUser.java

@@ -1,100 +0,0 @@
-/*-
- * #%L
- * HAPI FHIR - Clinical Reasoning
- * %%
- * Copyright (C) 2014 - 2023 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-package ca.uhn.fhir.cr.dstu3;
-
-import ca.uhn.fhir.cr.common.IDaoRegistryUser;
-import ca.uhn.fhir.cr.common.Searches;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import org.hl7.fhir.dstu3.model.CodeableConcept;
-import org.hl7.fhir.dstu3.model.Coding;
-import org.hl7.fhir.dstu3.model.ContactDetail;
-import org.hl7.fhir.dstu3.model.ContactPoint;
-import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
-import org.hl7.fhir.dstu3.model.Enumerations.SearchParamType;
-import org.hl7.fhir.dstu3.model.SearchParameter;
-import org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType;
-
-import java.util.Calendar;
-import java.util.Collections;
-import java.util.List;
-
-import static ca.uhn.fhir.cr.common.SupplementalDataConstants.MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION;
-import static ca.uhn.fhir.cr.common.SupplementalDataConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL;
-import static ca.uhn.fhir.cr.common.SupplementalDataConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION;
-
-public interface ISupplementalDataSearchParamUser extends IDaoRegistryUser {
-
-	List<ContactDetail> CQI_CONTACT_DETAIL = Collections.singletonList(
-		new ContactDetail()
-			.addTelecom(
-				new ContactPoint()
-					.setSystem(ContactPoint.ContactPointSystem.URL)
-					.setValue("http://www.hl7.org/Special/committees/cqi/index.cfm")));
-
-	static String CODING_SYSTEM_CODE = "urn:iso:std:iso:3166";
-	static String CODING_COUNTRY_CODE = "US";
-	static String CODING_COUNTRY_DISPLAY = "United States of America";
-	List<CodeableConcept> US_JURISDICTION_CODING =  Collections.singletonList(
-				new CodeableConcept()
-					.addCoding(
-						new Coding(CODING_SYSTEM_CODE, CODING_COUNTRY_CODE, CODING_COUNTRY_DISPLAY)));
-
-	default void ensureSupplementalDataElementSearchParameter(RequestDetails theRequestDetails) {
-		if (search(SearchParameter.class,
-			Searches.byUrlAndVersion(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL,
-				MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION),
-			theRequestDetails).iterator().hasNext()) {
-			return;
-		}
-
-		Calendar calendar = Calendar.getInstance();
-		calendar.clear();
-		calendar.set(2022, 7, 20);
-
-		SearchParameter searchParameter = new SearchParameter()
-			.setUrl(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL)
-			.setVersion(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION)
-			.setName("DEQMMeasureReportSupplementalData")
-			.setStatus(PublicationStatus.ACTIVE)
-			.setDate(calendar.getTime())
-			.setPublisher("HL7 International - Clinical Quality Information Work Group")
-			.setContact(CQI_CONTACT_DETAIL)
-			.setDescription(
-				String.format(
-					"Returns resources (supplemental data) from references on extensions on the MeasureReport with urls matching %s.",
-					MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
-			.setJurisdiction(US_JURISDICTION_CODING)
-			.addBase("MeasureReport")
-			.setCode("supplemental-data")
-			.setType(SearchParamType.REFERENCE)
-			.setExpression(
-				String.format("MeasureReport.extension('%s').value",
-					MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
-			.setXpath(
-				String.format("f:MeasureReport/f:extension[@url='%s'].value",
-					MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
-			.setXpathUsage(XPathUsageType.NORMAL);
-
-		searchParameter.setId("deqm-measurereport-supplemental-data");
-		searchParameter.setTitle("Supplemental Data");
-
-		create(searchParameter, theRequestDetails);
-	}
-}

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/dstu3/measure/MeasureService.java

@@ -19,21 +19,28 @@
  */
 package ca.uhn.fhir.cr.dstu3.measure;
 
+import ca.uhn.fhir.cr.common.IDaoRegistryUser;
 import ca.uhn.fhir.cr.common.IDataProviderFactory;
 import ca.uhn.fhir.cr.common.IFhirDalFactory;
 import ca.uhn.fhir.cr.common.ILibrarySourceProviderFactory;
 import ca.uhn.fhir.cr.common.ITerminologyProviderFactory;
-import ca.uhn.fhir.cr.dstu3.ISupplementalDataSearchParamUser;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.util.BundleBuilder;
 import org.cqframework.cql.cql2elm.LibrarySourceProvider;
 import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.CodeableConcept;
+import org.hl7.fhir.dstu3.model.Coding;
+import org.hl7.fhir.dstu3.model.ContactDetail;
+import org.hl7.fhir.dstu3.model.ContactPoint;
 import org.hl7.fhir.dstu3.model.Endpoint;
+import org.hl7.fhir.dstu3.model.Enumerations;
 import org.hl7.fhir.dstu3.model.Extension;
 import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.Measure;
 import org.hl7.fhir.dstu3.model.MeasureReport;
+import org.hl7.fhir.dstu3.model.SearchParameter;
 import org.hl7.fhir.dstu3.model.StringType;
 import org.opencds.cqf.cql.engine.data.DataProvider;
 import org.opencds.cqf.cql.engine.fhir.terminology.Dstu3FhirTerminologyProvider;
@@ -44,9 +51,57 @@ import org.opencds.cqf.cql.evaluator.fhir.util.Clients;
 import org.opencds.cqf.cql.evaluator.measure.MeasureEvaluationOptions;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.util.Collections;
+import java.util.List;
 import java.util.Map;
 
-public class MeasureService implements ISupplementalDataSearchParamUser {
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.COUNTRY_CODING_SYSTEM_CODE;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_DEFINITION_DATE;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.US_COUNTRY_CODE;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.US_COUNTRY_DISPLAY;
+
+public class MeasureService implements IDaoRegistryUser {
+
+	public static final List<ContactDetail> CQI_CONTACT_DETAIL = Collections.singletonList(
+		new ContactDetail()
+			.addTelecom(
+				new ContactPoint()
+					.setSystem(ContactPoint.ContactPointSystem.URL)
+					.setValue("http://www.hl7.org/Special/committees/cqi/index.cfm")));
+
+	public static final List<CodeableConcept> US_JURISDICTION_CODING =  Collections.singletonList(
+		new CodeableConcept()
+			.addCoding(
+				new Coding(COUNTRY_CODING_SYSTEM_CODE, US_COUNTRY_CODE, US_COUNTRY_DISPLAY)));
+
+	public static final SearchParameter SUPPLEMENTAL_DATA_SEARCHPARAMETER = (SearchParameter) new SearchParameter()
+		.setUrl(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL)
+		.setVersion(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION)
+		.setName("DEQMMeasureReportSupplementalData")
+		.setStatus(Enumerations.PublicationStatus.ACTIVE)
+		.setDate(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_DEFINITION_DATE)
+		.setPublisher("HL7 International - Clinical Quality Information Work Group")
+		.setContact(CQI_CONTACT_DETAIL)
+		.setDescription(
+			String.format(
+				"Returns resources (supplemental data) from references on extensions on the MeasureReport with urls matching %s.",
+				MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
+		.setJurisdiction(US_JURISDICTION_CODING)
+		.addBase("MeasureReport")
+		.setCode("supplemental-data")
+		.setType(Enumerations.SearchParamType.REFERENCE)
+		.setExpression(
+			String.format("MeasureReport.extension('%s').value",
+				MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
+		.setXpath(
+			String.format("f:MeasureReport/f:extension[@url='%s'].value",
+				MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
+		.setXpathUsage(SearchParameter.XPathUsageType.NORMAL)
+		.setTitle("Supplemental Data")
+		.setId("deqm-measurereport-supplemental-data");
 
 	@Autowired
 	protected ITerminologyProviderFactory myTerminologyProviderFactory;
@@ -121,7 +176,7 @@ public class MeasureService implements ISupplementalDataSearchParamUser {
 													 Bundle theAdditionalData,
 													 Endpoint theTerminologyEndpoint) {
 
-		ensureSupplementalDataElementSearchParameter(myRequestDetails);
+		ensureSupplementalDataElementSearchParameter();
 
 		Measure measure = read(theId, myRequestDetails);
 
@@ -161,4 +216,12 @@ public class MeasureService implements ISupplementalDataSearchParamUser {
 		return this.myDaoRegistry;
 	}
 
+	protected void ensureSupplementalDataElementSearchParameter() {
+		//create a transaction bundle
+		BundleBuilder builder = new BundleBuilder(getFhirContext());
+
+		//set the request to be condition on code == supplemental data
+		builder.addTransactionCreateEntry(SUPPLEMENTAL_DATA_SEARCHPARAMETER).conditional("code=supplemental-data");
+		transaction(builder.getBundle(), this.myRequestDetails);
+	}
 }

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/enumeration/CareGapsStatusCode.java

@@ -0,0 +1,34 @@
+package ca.uhn.fhir.cr.enumeration;
+
+import ca.uhn.fhir.i18n.Msg;
+
+public enum CareGapsStatusCode {
+	OPEN_GAP("open-gap"), CLOSED_GAP("closed-gap"), NOT_APPLICABLE("not-applicable");
+
+	private final String myValue;
+
+	CareGapsStatusCode(final String theValue) {
+		myValue = theValue;
+	}
+
+	@Override
+	public String toString() {
+		return myValue;
+	}
+
+	public String toDisplayString() {
+		if (myValue.equals("open-gap")) {
+			return "Open Gap";
+		}
+
+		if (myValue.equals("closed-gap")) {
+			return "Closed Gap";
+		}
+
+		if (myValue.equals("not-applicable")) {
+			return "Not Applicable";
+		}
+
+		throw new RuntimeException(Msg.code(2301) + "Error getting display strings for care gaps status codes");
+	}
+}

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/ISupplementalDataSearchParamUser.java

@@ -1,97 +0,0 @@
-/*-
- * #%L
- * HAPI FHIR - Clinical Reasoning
- * %%
- * Copyright (C) 2014 - 2023 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-package ca.uhn.fhir.cr.r4;
-
-import ca.uhn.fhir.cr.common.IDaoRegistryUser;
-import ca.uhn.fhir.cr.common.Searches;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import org.hl7.fhir.r4.model.CodeableConcept;
-import org.hl7.fhir.r4.model.Coding;
-import org.hl7.fhir.r4.model.ContactDetail;
-import org.hl7.fhir.r4.model.ContactPoint;
-import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
-import org.hl7.fhir.r4.model.Enumerations.SearchParamType;
-import org.hl7.fhir.r4.model.SearchParameter;
-import org.hl7.fhir.r4.model.SearchParameter.XPathUsageType;
-
-import java.util.Calendar;
-import java.util.Collections;
-import java.util.List;
-
-import static ca.uhn.fhir.cr.common.SupplementalDataConstants.MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION;
-import static ca.uhn.fhir.cr.common.SupplementalDataConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL;
-import static ca.uhn.fhir.cr.common.SupplementalDataConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION;
-
-public interface ISupplementalDataSearchParamUser extends IDaoRegistryUser {
-
-	List<ContactDetail> CQI_CONTACTDETAIL = Collections.singletonList(
-		new ContactDetail()
-			.addTelecom(
-				new ContactPoint()
-					.setSystem(ContactPoint.ContactPointSystem.URL)
-					.setValue("http://www.hl7.org/Special/committees/cqi/index.cfm")));
-
-	List<CodeableConcept> US_JURISDICTION_CODING = Collections.singletonList(
-		new CodeableConcept()
-			.addCoding(
-				new Coding("urn:iso:std:iso:3166", "US", "United States of America")));
-
-	default void ensureSupplementalDataElementSearchParameter(RequestDetails theRequestDetails) {
-		if (search(SearchParameter.class,
-			Searches.byUrlAndVersion(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL,
-				MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION),
-			theRequestDetails).iterator().hasNext()) {
-			return;
-		}
-
-		Calendar calendar = Calendar.getInstance();
-		calendar.clear();
-		calendar.set(2022, 7, 20);
-
-		SearchParameter searchParameter = new SearchParameter()
-			.setUrl(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL)
-			.setVersion(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION)
-			.setName("DEQMMeasureReportSupplementalData")
-			.setStatus(PublicationStatus.ACTIVE)
-			.setDate(calendar.getTime())
-			.setPublisher("HL7 International - Clinical Quality Information Work Group")
-			.setContact(CQI_CONTACTDETAIL)
-			.setDescription(
-				String.format(
-					"Returns resources (supplemental data) from references on extensions on the MeasureReport with urls matching %s.",
-					MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
-			.setJurisdiction(US_JURISDICTION_CODING)
-			.addBase("MeasureReport")
-			.setCode("supplemental-data")
-			.setType(SearchParamType.REFERENCE)
-			.setExpression(
-				String.format("MeasureReport.extension('%s').value",
-					MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
-			.setXpath(
-				String.format("f:MeasureReport/f:extension[@url='%s'].value",
-					MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
-			.setXpathUsage(XPathUsageType.NORMAL);
-
-		searchParameter.setId("deqm-measurereport-supplemental-data");
-		searchParameter.setTitle("Supplemental Data");
-
-		create(searchParameter, theRequestDetails);
-	}
-}

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/measure/CareGapsOperationProvider.java

@@ -0,0 +1,108 @@
+package ca.uhn.fhir.cr.r4.measure;
+
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.CanonicalType;
+import org.hl7.fhir.r4.model.Measure;
+import org.hl7.fhir.r4.model.Parameters;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
+
+import java.util.Date;
+import java.util.List;
+import java.util.function.Function;
+
+public class CareGapsOperationProvider {
+	private static final Logger ourLog = LoggerFactory.getLogger(CareGapsOperationProvider.class);
+
+	Function<RequestDetails, CareGapsService> myCareGapsServiceFunction;
+
+	public CareGapsOperationProvider(Function<RequestDetails, CareGapsService> theCareGapsServiceFunction) {
+		this.myCareGapsServiceFunction = theCareGapsServiceFunction;
+	}
+
+	/**
+	 * Implements the <a href=
+	 * "http://build.fhir.org/ig/HL7/davinci-deqm/OperationDefinition-care-gaps.html">$care-gaps</a>
+	 * operation found in the
+	 * <a href="http://build.fhir.org/ig/HL7/davinci-deqm/index.html">Da Vinci DEQM
+	 * FHIR Implementation Guide</a> that overrides the <a href=
+	 * "http://build.fhir.org/operation-measure-care-gaps.html">$care-gaps</a>
+	 * operation found in the
+	 * <a href="http://hl7.org/fhir/R4/clinicalreasoning-module.html">FHIR Clinical
+	 * Reasoning Module</a>.
+	 *
+	 * The operation calculates measures describing gaps in care. For more details,
+	 * reference the <a href=
+	 * "http://build.fhir.org/ig/HL7/davinci-deqm/gaps-in-care-reporting.html">Gaps
+	 * in Care Reporting</a> section of the
+	 * <a href="http://build.fhir.org/ig/HL7/davinci-deqm/index.html">Da Vinci DEQM
+	 * FHIR Implementation Guide</a>.
+	 *
+	 * A Parameters resource that includes zero to many document bundles that
+	 * include Care Gap Measure Reports will be returned.
+	 *
+	 * Usage:
+	 * URL: [base]/Measure/$care-gaps
+	 *
+	 * @param theRequestDetails generally auto-populated by the HAPI server
+	 *                          framework.
+	 * @param thePeriodStart       the start of the gaps through period
+	 * @param thePeriodEnd         the end of the gaps through period
+	 * @param theTopic             the category of the measures that is of interest for
+	 *                          the care gaps report
+	 * @param theSubject           a reference to either a Patient or Group for which
+	 *                          the gaps in care report(s) will be generated
+	 * @param thePractitioner      a reference to a Practitioner for which the gaps in
+	 *                          care report(s) will be generated
+	 * @param theOrganization      a reference to an Organization for which the gaps in
+	 *                          care report(s) will be generated
+	 * @param theStatus            the status code of gaps in care reports that will be
+	 *                          included in the result
+	 * @param theMeasureId         the id of Measure(s) for which the gaps in care
+	 *                          report(s) will be calculated
+	 * @param theMeasureIdentifier the identifier of Measure(s) for which the gaps in
+	 *                          care report(s) will be calculated
+	 * @param theMeasureUrl        the canonical URL of Measure(s) for which the gaps
+	 *                          in care report(s) will be calculated
+	 * @param theProgram           the program that a provider (either clinician or
+	 *                          clinical organization) participates in
+	 * @return Parameters of bundles of Care Gap Measure Reports
+	 */
+	@Description(shortDefinition = "$care-gaps operation", value = "Implements the <a href=\"http://build.fhir.org/ig/HL7/davinci-deqm/OperationDefinition-care-gaps.html\">$care-gaps</a> operation found in the <a href=\"http://build.fhir.org/ig/HL7/davinci-deqm/index.html\">Da Vinci DEQM FHIR Implementation Guide</a> which is an extension of the <a href=\"http://build.fhir.org/operation-measure-care-gaps.html\">$care-gaps</a> operation found in the <a href=\"http://hl7.org/fhir/R4/clinicalreasoning-module.html\">FHIR Clinical Reasoning Module</a>.")
+	@Operation(name = "$care-gaps", idempotent = false, type = Measure.class)
+	public Parameters careGapsReport(
+		RequestDetails theRequestDetails,
+		@OperationParam(name = "periodStart", typeName = "date") IPrimitiveType<Date> thePeriodStart,
+		@OperationParam(name = "periodEnd", typeName = "date") IPrimitiveType<Date> thePeriodEnd,
+		@OperationParam(name = "topic") List<String> theTopic,
+		@OperationParam(name = "subject") String theSubject,
+		@OperationParam(name = "practitioner") String thePractitioner,
+		@OperationParam(name = "organization") String theOrganization,
+		@OperationParam(name = "status") List<String> theStatus,
+		@OperationParam(name = "measureId") List<String> theMeasureId,
+		@OperationParam(name = "measureIdentifier") List<String> theMeasureIdentifier,
+		@OperationParam(name = "measureUrl") List<CanonicalType> theMeasureUrl,
+		@OperationParam(name = "program") List<String> theProgram) {
+
+		return myCareGapsServiceFunction
+			.apply(theRequestDetails)
+					.getCareGapsReport(
+						thePeriodStart,
+						thePeriodEnd,
+						theTopic,
+						theSubject,
+						thePractitioner,
+						theOrganization,
+						theStatus,
+						theMeasureId,
+						theMeasureIdentifier,
+						theMeasureUrl,
+						theProgram
+					);
+	}
+}

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/measure/CareGapsService.java

@@ -0,0 +1,521 @@
+package ca.uhn.fhir.cr.r4.measure;
+
+import ca.uhn.fhir.cr.enumeration.CareGapsStatusCode;
+import ca.uhn.fhir.cr.common.IDaoRegistryUser;
+import ca.uhn.fhir.cr.common.Searches;
+import ca.uhn.fhir.cr.config.CrProperties;
+import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
+import com.google.common.base.Strings;
+import org.apache.commons.lang3.tuple.ImmutablePair;
+import org.apache.commons.lang3.tuple.MutablePair;
+import org.apache.commons.lang3.tuple.Pair;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.CanonicalType;
+import org.hl7.fhir.r4.model.Composition;
+import org.hl7.fhir.r4.model.DetectedIssue;
+import org.hl7.fhir.r4.model.Extension;
+import org.hl7.fhir.r4.model.Group;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Measure;
+import org.hl7.fhir.r4.model.MeasureReport;
+import org.hl7.fhir.r4.model.Meta;
+import org.hl7.fhir.r4.model.Organization;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.Resource;
+import org.opencds.cqf.cql.evaluator.fhir.builder.BundleBuilder;
+import org.opencds.cqf.cql.evaluator.fhir.builder.CodeableConceptSettings;
+import org.opencds.cqf.cql.evaluator.fhir.builder.CompositionBuilder;
+import org.opencds.cqf.cql.evaluator.fhir.builder.CompositionSectionComponentBuilder;
+import org.opencds.cqf.cql.evaluator.fhir.builder.DetectedIssueBuilder;
+import org.opencds.cqf.cql.evaluator.fhir.builder.NarrativeSettings;
+import org.opencds.cqf.cql.evaluator.fhir.util.Ids;
+import org.opencds.cqf.cql.evaluator.fhir.util.Resources;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
+
+import java.util.AbstractMap;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.UUID;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.Executor;
+
+import static ca.uhn.fhir.cr.constant.CareCapsConstants.CARE_GAPS_BUNDLE_PROFILE;
+import static ca.uhn.fhir.cr.constant.CareCapsConstants.CARE_GAPS_COMPOSITION_PROFILE;
+import static ca.uhn.fhir.cr.constant.CareCapsConstants.CARE_GAPS_DETECTED_ISSUE_PROFILE;
+import static ca.uhn.fhir.cr.constant.CareCapsConstants.CARE_GAPS_GAP_STATUS_EXTENSION;
+import static ca.uhn.fhir.cr.constant.CareCapsConstants.CARE_GAPS_GAP_STATUS_SYSTEM;
+import static ca.uhn.fhir.cr.constant.CareCapsConstants.CARE_GAPS_REPORT_PROFILE;
+import static ca.uhn.fhir.cr.constant.HtmlConstants.HTML_DIV_PARAGRAPH_CONTENT;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_IMPROVEMENT_NOTATION_SYSTEM;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_MEASURE_POPULATION_SYSTEM;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION;
+import static com.google.common.base.Preconditions.checkArgument;
+import static com.google.common.base.Preconditions.checkNotNull;
+import static java.util.Map.ofEntries;
+import static org.hl7.fhir.r4.model.Factory.newId;
+import static org.opencds.cqf.cql.evaluator.fhir.util.Resources.newResource;
+
+public class CareGapsService implements IDaoRegistryUser {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(CareGapsService.class);
+	public static final Map<String, CodeableConceptSettings> CARE_GAPS_CODES = ofEntries(
+		new AbstractMap.SimpleEntry<>("http://loinc.org/96315-7",
+			new CodeableConceptSettings().add(
+				"http://loinc.org", "96315-7", "Gaps in care report")),
+		new AbstractMap.SimpleEntry<>("http://terminology.hl7.org/CodeSystem/v3-ActCode/CAREGAP",
+			new CodeableConceptSettings().add(
+				"http://terminology.hl7.org/CodeSystem/v3-ActCode", "CAREGAP", "Care Gaps")));
+
+	private RequestDetails myRequestDetails;
+
+	private CrProperties myCrProperties;
+
+	private MeasureService myR4MeasureService;
+
+	private Executor myCqlExecutor;
+
+	private DaoRegistry myDaoRegistry;
+
+	private final Map<String, Resource> myConfiguredResources = new HashMap<>();
+
+	public CareGapsService(CrProperties theCrProperties,
+								  MeasureService theMeasureService,
+								  DaoRegistry theDaoRegistry,
+								  Executor theExecutor,
+								  RequestDetails theRequestDetails){
+		this.myDaoRegistry = theDaoRegistry;
+		this.myCrProperties = theCrProperties;
+		this.myR4MeasureService = theMeasureService;
+		this.myCqlExecutor = theExecutor;
+		this.myRequestDetails = theRequestDetails;
+	}
+
+	/**
+	 * Calculate measures describing gaps in care
+	 * @param thePeriodStart
+	 * @param thePeriodEnd
+	 * @param theTopic
+	 * @param theSubject
+	 * @param thePractitioner
+	 * @param theOrganization
+	 * @param theStatuses
+	 * @param theMeasureIds
+	 * @param theMeasureIdentifiers
+	 * @param theMeasureUrls
+	 * @param thePrograms
+	 * @return Parameters that includes zero to many document bundles that
+	 * include Care Gap Measure Reports will be returned.
+	 */
+	public Parameters getCareGapsReport(IPrimitiveType<Date> thePeriodStart,
+													IPrimitiveType<Date> thePeriodEnd,
+													List<String> theTopic,
+													String theSubject,
+													String thePractitioner,
+													String theOrganization,
+													List<String> theStatuses,
+													List<String> theMeasureIds,
+													List<String> theMeasureIdentifiers,
+													List<CanonicalType> theMeasureUrls,
+													List<String> thePrograms) {
+
+		validateConfiguration();
+
+		List<Measure> measures = ensureMeasures(getMeasures(theMeasureIds, theMeasureIdentifiers, theMeasureUrls, myRequestDetails));
+
+		List<Patient> patients;
+		if (!Strings.isNullOrEmpty(theSubject)) {
+			patients = getPatientListFromSubject(theSubject);
+		} else {
+			throw new NotImplementedOperationException(Msg.code(2275) + "Only the subject parameter has been implemented.");
+		}
+
+		List<CompletableFuture<Parameters.ParametersParameterComponent>> futures = new ArrayList<>();
+		Parameters result = initializeResult();
+		if (myCrProperties.getMeasureProperties().getThreadedCareGapsEnabled()) {
+			patients
+				.forEach(
+					patient -> {
+						Parameters.ParametersParameterComponent patientReports = patientReports(myRequestDetails,
+							thePeriodStart.getValueAsString(), thePeriodEnd.getValueAsString(), patient, theStatuses, measures,
+							theOrganization);
+						futures.add(CompletableFuture.supplyAsync(() -> patientReports, myCqlExecutor));
+					});
+
+			futures.forEach(x -> result.addParameter(x.join()));
+		} else {
+			patients.forEach(
+				patient -> {
+					Parameters.ParametersParameterComponent patientReports = patientReports(myRequestDetails,
+						thePeriodStart.getValueAsString(), thePeriodEnd.getValueAsString(), patient, theStatuses, measures,
+						theOrganization);
+					if (patientReports != null) {
+						result.addParameter(patientReports);
+					}
+				});
+		}
+		return result;
+	}
+
+	public void validateConfiguration() {
+		checkNotNull(myCrProperties.getMeasureProperties(),
+			"The measure_report setting properties are required for the $care-gaps operation.");
+		checkNotNull(myCrProperties.getMeasureProperties().getMeasureReportConfiguration(),
+			"The measure_report setting is required for the $care-gaps operation.");
+		checkArgument(!Strings.isNullOrEmpty(myCrProperties.getMeasureProperties().getMeasureReportConfiguration().getCareGapsReporter()),
+			"The measure_report.care_gaps_reporter setting is required for the $care-gaps operation.");
+		checkArgument(!Strings.isNullOrEmpty(myCrProperties.getMeasureProperties().getMeasureReportConfiguration().getCareGapsCompositionSectionAuthor()),
+			"The measure_report.care_gaps_composition_section_author setting is required for the $care-gaps operation.");
+
+		Resource configuredReporter = addConfiguredResource(Organization.class,
+			myCrProperties.getMeasureProperties().getMeasureReportConfiguration().getCareGapsReporter(), "care_gaps_reporter");
+		Resource configuredAuthor = addConfiguredResource(Organization.class,
+			myCrProperties.getMeasureProperties().getMeasureReportConfiguration().getCareGapsCompositionSectionAuthor(),
+								"care_gaps_composition_section_author");
+
+		checkNotNull(configuredReporter, String.format(
+			"The %s Resource is configured as the measure_report.care_gaps_reporter but the Resource could not be read.",
+			myCrProperties.getMeasureProperties().getMeasureReportConfiguration().getCareGapsReporter()));
+		checkNotNull(configuredAuthor, String.format(
+			"The %s Resource is configured as the measure_report.care_gaps_composition_section_author but the Resource could not be read.",
+			myCrProperties.getMeasureProperties().getMeasureReportConfiguration().getCareGapsCompositionSectionAuthor()));
+	}
+	List<Patient> getPatientListFromSubject(String theSubject) {
+		if (theSubject.startsWith("Patient/")) {
+			return Collections.singletonList(validatePatientExists(theSubject));
+		} else if (theSubject.startsWith("Group/")) {
+			return getPatientListFromGroup(theSubject);
+		}
+
+		ourLog.info("Subject member was not a Patient or a Group, so skipping. \n{}", theSubject);
+		return Collections.emptyList();
+	}
+
+	List<Patient> getPatientListFromGroup(String theSubjectGroupId) {
+		List<Patient> patientList = new ArrayList<>();
+
+		Group group = read(newId(theSubjectGroupId));
+		if (group == null) {
+			throw new IllegalArgumentException(Msg.code(2276) + "Could not find Group: " + theSubjectGroupId);
+		}
+
+		group.getMember().forEach(member -> {
+			Reference reference = member.getEntity();
+			if (reference.getReferenceElement().getResourceType().equals("Patient")) {
+				Patient patient = validatePatientExists(reference.getReference());
+				patientList.add(patient);
+			} else if (reference.getReferenceElement().getResourceType().equals("Group")) {
+				patientList.addAll(getPatientListFromGroup(reference.getReference()));
+			} else {
+				ourLog.info("Group member was not a Patient or a Group, so skipping. \n{}", reference.getReference());
+			}
+		});
+
+		return patientList;
+	}
+
+	Patient validatePatientExists(String thePatientRef) {
+		Patient patient = read(newId(thePatientRef));
+		if (patient == null) {
+			throw new IllegalArgumentException(Msg.code(2277) + "Could not find Patient: " + thePatientRef);
+		}
+
+		return patient;
+	}
+
+	List<Measure> getMeasures(List<String> theMeasureIds, List<String> theMeasureIdentifiers,
+									  List<CanonicalType> theMeasureCanonicals, RequestDetails theRequestDetails) {
+		boolean hasMeasureIds = theMeasureIds != null && !theMeasureIds.isEmpty();
+		boolean hasMeasureIdentifiers = theMeasureIdentifiers != null && !theMeasureIdentifiers.isEmpty();
+		boolean hasMeasureUrls = theMeasureCanonicals != null && !theMeasureCanonicals.isEmpty();
+		if (!hasMeasureIds && !hasMeasureIdentifiers && !hasMeasureUrls) {
+			return Collections.emptyList();
+		}
+
+		List<Measure> measureList = new ArrayList<>();
+		Iterable<IBaseResource> measureSearchResults;
+		if (hasMeasureIds) {
+			measureSearchResults = search(Measure.class, Searches.byIds(theMeasureIds), theRequestDetails);
+			populateMeasures(measureList, measureSearchResults);
+		}
+
+		if(hasMeasureUrls) {
+			measureSearchResults = search(Measure.class, Searches.byCanonicals(theMeasureCanonicals), theRequestDetails);
+			populateMeasures(measureList, measureSearchResults);
+		}
+
+		// TODO: implement searching by measure identifiers
+		if (hasMeasureIdentifiers) {
+			throw new NotImplementedOperationException(Msg.code(2278) + "Measure identifiers have not yet been implemented.");
+		}
+
+		Map<String, Measure> result = new HashMap<>();
+		measureList.forEach(measure -> result.putIfAbsent(measure.getUrl(), measure));
+
+		return new ArrayList<>(result.values());
+	}
+
+	private void populateMeasures(List<Measure> measureList, Iterable<IBaseResource> measureSearchResults) {
+		if(measureSearchResults != null){
+			Iterator<IBaseResource> measures = measureSearchResults.iterator();
+			while(measures.hasNext()){
+				measureList.add((Measure)measures.next());
+			}
+		}
+	}
+
+	private <T extends Resource> T addConfiguredResource(Class<T> theResourceClass, String theId, String theKey) {
+		//T resource = repo.search(theResourceClass, Searches.byId(theId)).firstOrNull();
+		Iterable<IBaseResource> resourceResult = search(theResourceClass, Searches.byId(theId), myRequestDetails);
+		T resource = null;
+		if(resourceResult != null){
+			Iterator<IBaseResource> resources = resourceResult.iterator();
+			while(resources.hasNext()){
+				resource = (T) resources.next();
+				break;
+			}
+			if (resource != null) {
+				myConfiguredResources.put(theKey, resource);
+			}
+		}
+		return resource;
+	}
+
+	private List<Measure> ensureMeasures(List<Measure> theMeasures) {
+		theMeasures.forEach(measure -> {
+			if (!measure.hasScoring()) {
+				ourLog.info("Measure does not specify a scoring so skipping: {}.", measure.getId());
+				theMeasures.remove(measure);
+			}
+			if (!measure.hasImprovementNotation()) {
+				ourLog.info("Measure does not specify an improvement notation so skipping: {}.", measure.getId());
+				theMeasures.remove(measure);
+			}
+		});
+		return theMeasures;
+	}
+
+	private Parameters.ParametersParameterComponent patientReports(RequestDetails theRequestDetails, String thePeriodStart,
+																						String thePeriodEnd, Patient thePatient, List<String> theStatuses, List<Measure> theMeasures, String theOrganization) {
+		// TODO: add organization to report, if it exists.
+		Composition composition = getComposition(thePatient);
+		List<DetectedIssue> detectedIssues = new ArrayList<>();
+		Map<String, Resource> evalPlusSDE = new HashMap<>();
+		List<MeasureReport> reports = getReports(theRequestDetails, thePeriodStart, thePeriodEnd, thePatient, theStatuses, theMeasures,
+			composition, detectedIssues, evalPlusSDE);
+
+		if (reports.isEmpty()) {
+			return null;
+		}
+
+		return initializePatientParameter(thePatient).setResource(
+			addBundleEntries(theRequestDetails.getFhirServerBase(), composition, detectedIssues, reports, evalPlusSDE));
+	}
+
+	private List<MeasureReport> getReports(RequestDetails theRequestDetails, String thePeriodStart, String thePeriodEnd,
+														Patient thePatient, List<String> theStatuses, List<Measure> theMeasures, Composition theComposition,
+														List<DetectedIssue> theDetectedIssues, Map<String, Resource> theEvalPlusSDEs) {
+		List<MeasureReport> reports = new ArrayList<>();
+		MeasureReport report;
+		for (Measure measure : theMeasures) {
+			report = myR4MeasureService.evaluateMeasure(measure.getIdElement(), thePeriodStart,
+				thePeriodEnd, "patient", Ids.simple(thePatient), null, null, null, null, null);
+			if (!report.hasGroup()) {
+				ourLog.info("Report does not include a group so skipping.\nSubject: {}\nMeasure: {}",
+					Ids.simple(thePatient),
+					Ids.simplePart(measure));
+				continue;
+			}
+
+			initializeReport(report);
+
+			CareGapsStatusCode gapStatus = getGapStatus(measure, report);
+			if (!theStatuses.contains(gapStatus.toString())) {
+				continue;
+			}
+
+			DetectedIssue detectedIssue = getDetectedIssue(thePatient, report, gapStatus);
+			theDetectedIssues.add(detectedIssue);
+			theComposition.addSection(getSection(measure, report, detectedIssue, gapStatus));
+			populateEvaluatedResources(report, theEvalPlusSDEs);
+			populateSDEResources(report, theEvalPlusSDEs);
+			reports.add(report);
+		}
+
+		return reports;
+	}
+
+	private void initializeReport(MeasureReport theMeasureReport) {
+		if (Strings.isNullOrEmpty(theMeasureReport.getId())) {
+			IIdType id = Ids.newId(MeasureReport.class, UUID.randomUUID().toString());
+			theMeasureReport.setId(id);
+		}
+		Reference reporter = new Reference().setReference(myCrProperties.getMeasureProperties().getMeasureReportConfiguration().getCareGapsReporter());
+		// TODO: figure out what this extension is for
+		// reporter.addExtension(new
+		// Extension().setUrl(CARE_GAPS_MEASUREREPORT_REPORTER_EXTENSION));
+		theMeasureReport.setReporter(reporter);
+		if (theMeasureReport.hasMeta()) {
+			theMeasureReport.getMeta().addProfile(CARE_GAPS_REPORT_PROFILE);
+		} else {
+			theMeasureReport.setMeta(new Meta().addProfile(CARE_GAPS_REPORT_PROFILE));
+		}
+	}
+
+	private Parameters.ParametersParameterComponent initializePatientParameter(Patient thePatient) {
+		Parameters.ParametersParameterComponent patientParameter = Resources
+			.newBackboneElement(Parameters.ParametersParameterComponent.class)
+			.setName("return");
+		patientParameter.setId("subject-" + Ids.simplePart(thePatient));
+		return patientParameter;
+	}
+
+	private Bundle addBundleEntries(String theServerBase, Composition theComposition, List<DetectedIssue> theDetectedIssues,
+											  List<MeasureReport> theMeasureReports, Map<String, Resource> theEvalPlusSDEs) {
+		Bundle reportBundle = getBundle();
+		reportBundle.addEntry(getBundleEntry(theServerBase, theComposition));
+		theMeasureReports.forEach(report -> reportBundle.addEntry(getBundleEntry(theServerBase, report)));
+		theDetectedIssues.forEach(detectedIssue -> reportBundle.addEntry(getBundleEntry(theServerBase, detectedIssue)));
+		myConfiguredResources.values().forEach(resource -> reportBundle.addEntry(getBundleEntry(theServerBase, resource)));
+		theEvalPlusSDEs.values().forEach(resource -> reportBundle.addEntry(getBundleEntry(theServerBase, resource)));
+		return reportBundle;
+	}
+
+	private CareGapsStatusCode getGapStatus(Measure theMeasure, MeasureReport theMeasureReport) {
+		Pair<String, Boolean> inNumerator = new MutablePair<>("numerator", false);
+		theMeasureReport.getGroup().forEach(group -> group.getPopulation().forEach(population -> {
+			if (population.hasCode()
+				&& population.getCode().hasCoding(MEASUREREPORT_MEASURE_POPULATION_SYSTEM, inNumerator.getKey())
+				&& population.getCount() == 1) {
+				inNumerator.setValue(true);
+			}
+		}));
+
+		boolean isPositive = theMeasure.getImprovementNotation().hasCoding(MEASUREREPORT_IMPROVEMENT_NOTATION_SYSTEM,
+			"increase");
+
+		if ((isPositive && !inNumerator.getValue()) || (!isPositive && inNumerator.getValue())) {
+			return CareGapsStatusCode.OPEN_GAP;
+		}
+
+		return CareGapsStatusCode.CLOSED_GAP;
+	}
+
+	private Bundle.BundleEntryComponent getBundleEntry(String theServerBase, Resource theResource) {
+		return new Bundle.BundleEntryComponent().setResource(theResource)
+			.setFullUrl(getFullUrl(theServerBase, theResource));
+	}
+
+	private Composition.SectionComponent getSection(Measure theMeasure, MeasureReport theMeasureReport, DetectedIssue theDetectedIssue,
+																	CareGapsStatusCode theGapStatus) {
+		String narrative = String.format(HTML_DIV_PARAGRAPH_CONTENT,
+			theGapStatus == CareGapsStatusCode.CLOSED_GAP ? "No detected issues."
+				: String.format("Issues detected.  See %s for details.", Ids.simple(theDetectedIssue)));
+		return new CompositionSectionComponentBuilder<>(Composition.SectionComponent.class)
+			.withTitle(theMeasure.hasTitle() ? theMeasure.getTitle() : theMeasure.getUrl())
+			.withFocus(Ids.simple(theMeasureReport))
+			.withText(new NarrativeSettings(narrative))
+			.withEntry(Ids.simple(theDetectedIssue))
+			.build();
+	}
+
+	private Bundle getBundle() {
+		return new BundleBuilder<>(Bundle.class)
+			.withProfile(CARE_GAPS_BUNDLE_PROFILE)
+			.withType(Bundle.BundleType.DOCUMENT.toString())
+			.build();
+	}
+
+	private Composition getComposition(Patient thePatient) {
+		return new CompositionBuilder<>(Composition.class)
+			.withProfile(CARE_GAPS_COMPOSITION_PROFILE)
+			.withType(CARE_GAPS_CODES.get("http://loinc.org/96315-7"))
+			.withStatus(Composition.CompositionStatus.FINAL.toString())
+			.withTitle("Care Gap Report for " + Ids.simplePart(thePatient))
+			.withSubject(Ids.simple(thePatient))
+			.withAuthor(Ids.simple(myConfiguredResources.get("care_gaps_composition_section_author")))
+			// .withCustodian(organization) // TODO: Optional: identifies the organization
+			// who is responsible for ongoing maintenance of and accessing to this gaps in
+			// care report. Add as a setting and optionally read if it's there.
+			.build();
+	}
+
+	private DetectedIssue getDetectedIssue(Patient thePatient, MeasureReport theMeasureReport, CareGapsStatusCode theCareGapStatusCode) {
+		return new DetectedIssueBuilder<>(DetectedIssue.class)
+			.withProfile(CARE_GAPS_DETECTED_ISSUE_PROFILE)
+			.withStatus(DetectedIssue.DetectedIssueStatus.FINAL.toString())
+			.withCode(CARE_GAPS_CODES.get("http://terminology.hl7.org/CodeSystem/v3-ActCode/CAREGAP"))
+			.withPatient(Ids.simple(thePatient))
+			.withEvidenceDetail(Ids.simple(theMeasureReport))
+			.withModifierExtension(new ImmutablePair<>(
+				CARE_GAPS_GAP_STATUS_EXTENSION,
+				new CodeableConceptSettings().add(CARE_GAPS_GAP_STATUS_SYSTEM, theCareGapStatusCode.toString(),
+					theCareGapStatusCode.toDisplayString())))
+			.build();
+	}
+
+	protected void populateEvaluatedResources(MeasureReport theMeasureReport, Map<String, Resource> theResources) {
+		theMeasureReport.getEvaluatedResource().forEach(evaluatedResource -> {
+			IIdType resourceId = evaluatedResource.getReferenceElement();
+			if (resourceId.getResourceType() == null || theResources.containsKey(Ids.simple(resourceId))) {
+				return;
+			}
+			IBaseResource resourceBase = this.read(resourceId);
+			if (resourceBase instanceof Resource) {
+				Resource resource = (Resource) resourceBase;
+				theResources.put(Ids.simple(resourceId), resource);
+			}
+		});
+	}
+
+	protected void populateSDEResources(MeasureReport theMeasureReport, Map<String, Resource> theResources) {
+		if (theMeasureReport.hasExtension()) {
+			for (Extension extension : theMeasureReport.getExtension()) {
+				if (extension.hasUrl() && extension.getUrl().equals(MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION)) {
+					Reference sdeRef = extension.hasValue() && extension.getValue() instanceof Reference
+						? (Reference) extension.getValue()
+						: null;
+					if (sdeRef != null && sdeRef.hasReference() && !sdeRef.getReference().startsWith("#")) {
+						IdType sdeId = new IdType(sdeRef.getReference());
+						if (!theResources.containsKey(Ids.simple(sdeId))) {
+							theResources.put(Ids.simple(sdeId), read(sdeId));
+						}
+					}
+				}
+			}
+		}
+	}
+	private Parameters initializeResult() {
+		return newResource(Parameters.class, "care-gaps-report-" + UUID.randomUUID());
+	}
+
+	public static String getFullUrl(String theServerAddress, IBaseResource theResource) {
+		checkArgument(theResource.getIdElement().hasIdPart(),
+			"Cannot generate a fullUrl because the resource does not have an id.");
+		return getFullUrl(theServerAddress, theResource.fhirType(), Ids.simplePart(theResource));
+	}
+
+	public static String getFullUrl(String theServerAddress, String theFhirType, String theElementId) {
+		return String.format("%s%s/%s", theServerAddress + (theServerAddress.endsWith("/") ? "" : "/"), theFhirType,
+			theElementId);
+	}
+
+	@Override
+	public DaoRegistry getDaoRegistry() {
+		return myDaoRegistry;
+	}
+}

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/measure/ISubmitDataService.java

@@ -0,0 +1,8 @@
+package ca.uhn.fhir.cr.r4.measure;
+
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+
+import java.util.function.Function;
+
+public interface ISubmitDataService extends Function<RequestDetails, SubmitDataService> {
+}

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/measure/MeasureOperationsProvider.java

@@ -36,7 +36,6 @@ import org.springframework.stereotype.Component;
 
 import java.util.function.Function;
 
-@Component
 public class MeasureOperationsProvider {
 	@Autowired
 	Function<RequestDetails, MeasureService> myR4MeasureServiceFactory;

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/measure/MeasureService.java

@@ -19,27 +19,34 @@
  */
 package ca.uhn.fhir.cr.r4.measure;
 
+import ca.uhn.fhir.cr.common.IDaoRegistryUser;
 import ca.uhn.fhir.cr.common.IDataProviderFactory;
 import ca.uhn.fhir.cr.common.IFhirDalFactory;
 import ca.uhn.fhir.cr.common.ILibrarySourceProviderFactory;
 import ca.uhn.fhir.cr.common.ITerminologyProviderFactory;
-import ca.uhn.fhir.cr.common.SupplementalDataConstants;
+import ca.uhn.fhir.cr.constant.MeasureReportConstants;
-import ca.uhn.fhir.cr.r4.ISupplementalDataSearchParamUser;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.param.ReferenceParam;
+import ca.uhn.fhir.util.BundleBuilder;
 import org.apache.commons.lang3.StringUtils;
 import org.cqframework.cql.cql2elm.LibrarySourceProvider;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.ContactDetail;
+import org.hl7.fhir.r4.model.ContactPoint;
 import org.hl7.fhir.r4.model.Endpoint;
+import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Measure;
 import org.hl7.fhir.r4.model.MeasureReport;
+import org.hl7.fhir.r4.model.SearchParameter;
 import org.hl7.fhir.r4.model.StringType;
 import org.opencds.cqf.cql.engine.data.DataProvider;
 import org.opencds.cqf.cql.engine.fhir.terminology.R4FhirTerminologyProvider;
@@ -48,13 +55,64 @@ import org.opencds.cqf.cql.evaluator.CqlOptions;
 import org.opencds.cqf.cql.evaluator.fhir.dal.FhirDal;
 import org.opencds.cqf.cql.evaluator.fhir.util.Clients;
 import org.opencds.cqf.cql.evaluator.measure.MeasureEvaluationOptions;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 
-public class MeasureService implements ISupplementalDataSearchParamUser {
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.COUNTRY_CODING_SYSTEM_CODE;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_DEFINITION_DATE;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.US_COUNTRY_CODE;
+import static ca.uhn.fhir.cr.constant.MeasureReportConstants.US_COUNTRY_DISPLAY;
+
+public class MeasureService implements IDaoRegistryUser {
+
+	private Logger ourLogger = LoggerFactory.getLogger(MeasureService.class);
+
+	public static final List<ContactDetail> CQI_CONTACTDETAIL = Collections.singletonList(
+		new ContactDetail()
+			.addTelecom(
+				new ContactPoint()
+					.setSystem(ContactPoint.ContactPointSystem.URL)
+					.setValue("http://www.hl7.org/Special/committees/cqi/index.cfm")));
+
+	public static final List<CodeableConcept> US_JURISDICTION_CODING =  Collections.singletonList(
+		new CodeableConcept()
+			.addCoding(
+				new Coding(COUNTRY_CODING_SYSTEM_CODE, US_COUNTRY_CODE, US_COUNTRY_DISPLAY)));
+
+	public static final SearchParameter SUPPLEMENTAL_DATA_SEARCHPARAMETER = (SearchParameter) new SearchParameter()
+		.setUrl(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_URL)
+		.setVersion(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_VERSION)
+		.setName("DEQMMeasureReportSupplementalData")
+		.setStatus(Enumerations.PublicationStatus.ACTIVE)
+		.setDate(MEASUREREPORT_SUPPLEMENTALDATA_SEARCHPARAMETER_DEFINITION_DATE)
+		.setPublisher("HL7 International - Clinical Quality Information Work Group")
+		.setContact(CQI_CONTACTDETAIL)
+		.setDescription(
+			String.format(
+				"Returns resources (supplemental data) from references on extensions on the MeasureReport with urls matching %s.",
+				MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
+		.setJurisdiction(US_JURISDICTION_CODING)
+		.addBase("MeasureReport")
+		.setCode("supplemental-data")
+		.setType(Enumerations.SearchParamType.REFERENCE)
+		.setExpression(
+			String.format("MeasureReport.extension('%s').value",
+				MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
+		.setXpath(
+			String.format("f:MeasureReport/f:extension[@url='%s'].value",
+				MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION))
+		.setXpathUsage(SearchParameter.XPathUsageType.NORMAL)
+		.setTitle("Supplemental Data")
+		.setId("deqm-measurereport-supplemental-data");
 
 	@Autowired
 	protected ITerminologyProviderFactory myTerminologyProviderFactory;
@@ -130,7 +188,7 @@ public class MeasureService implements ISupplementalDataSearchParamUser {
 													 Bundle theAdditionalData,
 													 Endpoint theTerminologyEndpoint) {
 
-		ensureSupplementalDataElementSearchParameter(myRequestDetails);
+		ensureSupplementalDataElementSearchParameter();
 
 		Measure measure = read(theId, myRequestDetails);
 
@@ -171,10 +229,10 @@ public class MeasureService implements ISupplementalDataSearchParamUser {
 		return measureReport;
 	}
 
-	private List<String> getPractitionerPatients(String practitioner, RequestDetails theRequestDetails) {
+	private List<String> getPractitionerPatients(String thePractitioner, RequestDetails theRequestDetails) {
 		SearchParameterMap map = SearchParameterMap.newSynchronous();
 		map.add("general-practitioner", new ReferenceParam(
-			practitioner.startsWith("Practitioner/") ? practitioner : "Practitioner/" + practitioner));
+			thePractitioner.startsWith("Practitioner/") ? thePractitioner : "Practitioner/" + thePractitioner));
 		List<String> patients = new ArrayList<>();
 		IBundleProvider patientProvider = myDaoRegistry.getResourceDao("Patient").search(map, theRequestDetails);
 		List<IBaseResource> patientList = patientProvider.getAllResources();
@@ -182,12 +240,12 @@ public class MeasureService implements ISupplementalDataSearchParamUser {
 		return patients;
 	}
 
-	private void addProductLineExtension(MeasureReport measureReport, String productLine) {
+	private void addProductLineExtension(MeasureReport theMeasureReport, String theProductLine) {
-		if (productLine != null) {
+		if (theProductLine != null) {
 			Extension ext = new Extension();
-			ext.setUrl(SupplementalDataConstants.MEASUREREPORT_PRODUCT_LINE_EXT_URL);
+			ext.setUrl(MeasureReportConstants.MEASUREREPORT_PRODUCT_LINE_EXT_URL);
-			ext.setValue(new StringType(productLine));
+			ext.setValue(new StringType(theProductLine));
-			measureReport.addExtension(ext);
+			theMeasureReport.addExtension(ext);
 		}
 	}
 
@@ -196,4 +254,12 @@ public class MeasureService implements ISupplementalDataSearchParamUser {
 		return this.myDaoRegistry;
 	}
 
+	protected void ensureSupplementalDataElementSearchParameter() {
+		//create a transaction bundle
+		BundleBuilder builder = new BundleBuilder(getFhirContext());
+
+		//set the request to be condition on code == supplemental data
+		builder.addTransactionCreateEntry(SUPPLEMENTAL_DATA_SEARCHPARAMETER).conditional("code=supplemental-data");
+		transaction(builder.getBundle(), this.myRequestDetails);
+	}
 }

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/measure/SubmitDataProvider.java

@@ -0,0 +1,61 @@
+package ca.uhn.fhir.cr.r4.measure;
+
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Measure;
+import org.hl7.fhir.r4.model.MeasureReport;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
+
+import java.util.List;
+import java.util.function.Function;
+
+public class SubmitDataProvider {
+	private static final Logger ourLog = LoggerFactory.getLogger(SubmitDataProvider.class);
+
+	Function<RequestDetails, SubmitDataService> mySubmitDataServiceFunction;
+
+	public SubmitDataProvider(Function<RequestDetails, SubmitDataService> submitDataServiceFunction) {
+		this.mySubmitDataServiceFunction = submitDataServiceFunction;
+	}
+	/**
+	 * Implements the <a href=
+	 * "http://hl7.org/fhir/R4/measure-operation-submit-data.html">$submit-data</a>
+	 * operation found in the
+	 * <a href="http://hl7.org/fhir/R4/clinicalreasoning-module.html">FHIR Clinical
+	 * Reasoning Module</a> per the
+	 * <a href="http://build.fhir.org/ig/HL7/davinci-deqm/datax.html#submit-data">Da
+	 * Vinci DEQM FHIR Implementation Guide</a>.
+	 * 
+	 * 
+	 * The submitted MeasureReport and Resources will be saved to the local server.
+	 * A Bundle reporting the result of the transaction will be returned.
+	 * 
+	 * Usage:
+	 * URL: [base]/Measure/$submit-data
+	 * URL: [base]/Measure/[id]/$submit-data
+	 * 
+	 * @param theRequestDetails generally auto-populated by the HAPI server
+	 *                          framework.
+	 * @param theId             the Id of the Measure to submit data for
+	 * @param theReport         the MeasureReport to be submitted
+	 * @param theResources      the resources to be submitted
+	 * @return Bundle the transaction result
+	 */
+	@Description(shortDefinition = "$submit-data", value = "Implements the <a href=\"http://hl7.org/fhir/R4/measure-operation-submit-data.html\">$submit-data</a> operation found in the <a href=\"http://hl7.org/fhir/R4/clinicalreasoning-module.html\">FHIR Clinical Reasoning Module</a> per the <a href=\"http://build.fhir.org/ig/HL7/davinci-deqm/datax.html#submit-data\">Da Vinci DEQM FHIR Implementation Guide</a>.")
+	@Operation(name = "$submit-data", type = Measure.class)
+	public Bundle submitData(RequestDetails theRequestDetails,
+			@IdParam IdType theId,
+			@OperationParam(name = "measureReport", min = 1, max = 1) MeasureReport theReport,
+			@OperationParam(name = "resource") List<IBaseResource> theResources) {
+		return mySubmitDataServiceFunction.apply(theRequestDetails)
+									.submitData(theId, theReport, theResources);
+	}
+}

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/measure/SubmitDataService.java

@@ -0,0 +1,83 @@
+package ca.uhn.fhir.cr.r4.measure;
+
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.MeasureReport;
+import org.hl7.fhir.r4.model.Resource;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.List;
+
+public class SubmitDataService{
+	private static final Logger ourLogger = LoggerFactory.getLogger(SubmitDataService.class);
+
+	private final DaoRegistry myDaoRegistry;
+
+	private final RequestDetails myRequestDetails;
+
+	public SubmitDataService(DaoRegistry theDaoRegistry, RequestDetails theRequestDetails){
+		this.myDaoRegistry = theDaoRegistry;
+		this.myRequestDetails = theRequestDetails;
+	}
+
+	/**
+	 * Save measure report and resources to the local repository
+	 * @param theId
+	 * @param theReport
+	 * @param theResources
+	 * @return Bundle transaction result
+	 */
+	public Bundle submitData(IdType theId, MeasureReport theReport, List<IBaseResource> theResources) {
+		/*
+		 * TODO - resource validation using $data-requirements operation (params are the
+		 * provided id and the measurement period from the MeasureReport)
+		 *
+		 * TODO - profile validation ... not sure how that would work ... (get
+		 * StructureDefinition from URL or must it be stored in Ruler?)
+		 */
+
+		Bundle transactionBundle = new Bundle()
+			.setType(Bundle.BundleType.TRANSACTION)
+			.addEntry(createEntry(theReport));
+
+		if (theResources != null) {
+			for (IBaseResource res : theResources) {
+				// Unpack nested Bundles
+				if (res instanceof Bundle) {
+					Bundle nestedBundle = (Bundle) res;
+					for (Bundle.BundleEntryComponent entry : nestedBundle.getEntry()) {
+						transactionBundle.addEntry(createEntry(entry.getResource()));
+					}
+				} else {
+					transactionBundle.addEntry(createEntry(res));
+				}
+			}
+		}
+		return (Bundle) myDaoRegistry.getSystemDao().transaction(myRequestDetails, transactionBundle);
+	}
+
+	private Bundle.BundleEntryComponent createEntry(IBaseResource theResource) {
+		return new Bundle.BundleEntryComponent()
+			.setResource((Resource) theResource)
+			.setRequest(createRequest(theResource));
+	}
+
+	private Bundle.BundleEntryRequestComponent createRequest(IBaseResource theResource) {
+		Bundle.BundleEntryRequestComponent request = new Bundle.BundleEntryRequestComponent();
+		if (theResource.getIdElement().hasValue()) {
+			request
+				.setMethod(Bundle.HTTPVerb.PUT)
+				.setUrl(theResource.getIdElement().getValue());
+		} else {
+			request
+				.setMethod(Bundle.HTTPVerb.POST)
+				.setUrl(theResource.fhirType());
+		}
+
+		return request;
+	}
+}

hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/BaseCrDstu3Test.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.cr.config.CrDstu3Config;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.test.BaseJpaDstu3Test;
 import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import io.specto.hoverfly.junit.dsl.HoverflyDsl;
 import io.specto.hoverfly.junit.dsl.StubServiceBuilder;
 import io.specto.hoverfly.junit.rule.HoverflyRule;
@@ -14,6 +15,7 @@ import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.OperationOutcome;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.dstu3.model.ValueSet;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.junit.ClassRule;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.test.context.ContextConfiguration;
@@ -55,14 +57,6 @@ public abstract class BaseCrDstu3Test extends BaseJpaDstu3Test implements IResou
 		return ourFhirContext;
 	}
 
-	public Bundle loadBundle(String theLocation) {
-		return loadBundle(Bundle.class, theLocation);
-	}
-
-	public IParser getFhirParser() {
-		return ourParser;
-	}
-
 	public StubServiceBuilder mockNotFound(String theResource) {
 		OperationOutcome outcome = new OperationOutcome();
 		outcome.getText().setStatusAsString("generated");
@@ -106,10 +100,6 @@ public abstract class BaseCrDstu3Test extends BaseJpaDstu3Test implements IResou
 			.willReturn(success());
 	}
 
-	public Bundle makeBundle(List<? extends Resource> theResources) {
-		return makeBundle(theResources.toArray(new Resource[theResources.size()]));
-	}
-
 	public Bundle makeBundle(Resource... theResources) {
 		Bundle bundle = new Bundle();
 		bundle.setType(Bundle.BundleType.SEARCHSET);
@@ -121,4 +111,8 @@ public abstract class BaseCrDstu3Test extends BaseJpaDstu3Test implements IResou
 		}
 		return bundle;
 	}
+
+	public Bundle loadBundle(String theLocation) {
+		return loadBundle(Bundle.class, theLocation);
+	}
 }

hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/BaseCrR4Test.java

@@ -32,11 +32,11 @@ import static io.specto.hoverfly.junit.dsl.ResponseCreators.success;
 public abstract class BaseCrR4Test extends BaseResourceProviderR4Test implements IResourceLoader {
 	protected static final FhirContext ourFhirContext = FhirContext.forR4Cached();
 	private static final IParser ourParser = ourFhirContext.newJsonParser().setPrettyPrint(true);
-	private static final String TEST_ADDRESS = "test-address.com";
+	protected static final String TEST_ADDRESS = "http://test:9001/fhir";
 	@ClassRule
 	public static HoverflyRule hoverflyRule = HoverflyRule.inSimulationMode(dsl(
 		service(TEST_ADDRESS)
-			.get("/fhir/metadata")
+			.get("/metadata")
 			.willReturn(success(getCapabilityStatement().toString(), "application/json"))
 	));
 

hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/IResourceLoader.java

@@ -1,11 +1,26 @@
 package ca.uhn.fhir.cr;
 
 import ca.uhn.fhir.cr.common.IDaoRegistryUser;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.util.ClasspathUtil;
+import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Resource;
+import org.opencds.cqf.cql.evaluator.fhir.util.Ids;
+import org.springframework.core.io.DefaultResourceLoader;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import static com.google.common.base.Preconditions.checkNotNull;
 
 /**
  * This is a utility interface that allows a class that has a DaoRegistry to load Bundles and read Resources.
@@ -51,4 +66,103 @@ public interface IResourceLoader extends IDaoRegistryUser {
 
 		return resource;
 	}
+
+	default public IBaseResource readResource(String theLocation) {
+		String resourceString = stringFromResource(theLocation);
+		return EncodingEnum.detectEncoding(resourceString).newParser(getFhirContext()).parseResource(resourceString);
+	}
+
+	default public IBaseResource readAndLoadResource(String theLocation) {
+		String resourceString = stringFromResource(theLocation);
+		if (theLocation.endsWith("json")) {
+			return loadResource(parseResource("json", resourceString));
+		} else {
+			return loadResource(parseResource("xml", resourceString));
+		}
+	}
+
+	default public IBaseResource loadResource(IBaseResource theResource) {
+		if (getDaoRegistry() == null) {
+			return theResource;
+		}
+
+		update(theResource);
+		return theResource;
+	}
+
+	default public IBaseResource parseResource(String theEncoding, String theResourceString) {
+		IParser parser;
+		switch (theEncoding.toLowerCase()) {
+			case "json":
+				parser = getFhirContext().newJsonParser();
+				break;
+			case "xml":
+				parser = getFhirContext().newXmlParser();
+				break;
+			default:
+				throw new IllegalArgumentException(
+					String.format("Expected encoding xml, or json.  %s is not a valid encoding", theEncoding));
+		}
+
+		return parser.parseResource(theResourceString);
+	}
+
+	default public String stringFromResource(String theLocation) {
+		InputStream is = null;
+		try {
+			if (theLocation.startsWith(File.separator)) {
+				is = new FileInputStream(theLocation);
+			} else {
+				DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
+				org.springframework.core.io.Resource resource = resourceLoader.getResource(theLocation);
+				is = resource.getInputStream();
+			}
+			return IOUtils.toString(is, StandardCharsets.UTF_8);
+		} catch (Exception e) {
+			throw new RuntimeException(String.format("Error loading resource from %s", theLocation), e);
+		}
+	}
+
+	default Object loadTransaction(String theLocation) {
+		IBaseBundle resource = (IBaseBundle) readResource(theLocation);
+		return transaction(resource, new SystemRequestDetails());
+	}
+
+	private Bundle.BundleEntryComponent createEntry(IBaseResource theResource) {
+		return new Bundle.BundleEntryComponent()
+			.setResource((Resource) theResource)
+			.setRequest(createRequest(theResource));
+	}
+
+	private Bundle.BundleEntryRequestComponent createRequest(IBaseResource theResource) {
+		Bundle.BundleEntryRequestComponent request = new Bundle.BundleEntryRequestComponent();
+		if (theResource.getIdElement().hasValue()) {
+			request
+				.setMethod(Bundle.HTTPVerb.PUT)
+				.setUrl(theResource.getIdElement().getValue());
+		} else {
+			request
+				.setMethod(Bundle.HTTPVerb.POST)
+				.setUrl(theResource.fhirType());
+		}
+
+		return request;
+	}
+
+	default <T extends IBaseResource> T newResource(Class<T> theResourceClass, String theIdPart) {
+		checkNotNull(theResourceClass);
+		checkNotNull(theIdPart);
+
+		T newResource = newResource(theResourceClass);
+		newResource.setId((IIdType) Ids.newId(getFhirContext(), newResource.fhirType(), theIdPart));
+
+		return newResource;
+	}
+
+	@SuppressWarnings("unchecked")
+	default <T extends IBaseResource> T newResource(Class<T> theResourceClass) {
+		checkNotNull(theResourceClass);
+
+		return (T) this.getFhirContext().getResourceDefinition(theResourceClass).newInstance();
+	}
 }

hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/dstu3/CrProviderDstu3Test.java

@@ -21,12 +21,11 @@ import org.springframework.beans.factory.annotation.Autowired;
 import java.io.IOException;
 import java.util.List;
 
-import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.hamcrest.Matchers.hasSize;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
-public class CrProviderDstu3Test extends BaseCrDstu3Test {
+public class 	CrProviderDstu3Test extends BaseCrDstu3Test {
 	private static final Logger ourLog = LoggerFactory.getLogger(CrProviderDstu3Test.class);
 	protected final RequestDetails myRequestDetails = RequestDetailsHelper.newServletRequestDetails();
 
@@ -77,12 +76,10 @@ public class CrProviderDstu3Test extends BaseCrDstu3Test {
 		loadResource(Library.class, "ca/uhn/fhir/cr/dstu3/hedis-ig/library/library-asf-logic.json", myRequestDetails);
 		// Load the measure for ASF: Unhealthy Alcohol Use Screening and Follow-up (ASF)
 		loadResource(Measure.class,"ca/uhn/fhir/cr/dstu3/hedis-ig/measure-asf.json", myRequestDetails);
-		var result = loadBundle("ca/uhn/fhir/cr/dstu3/hedis-ig/test-patient-6529-data.json");
+		Bundle result = loadBundle("ca/uhn/fhir/cr/dstu3/hedis-ig/test-patient-6529-data.json");
 		assertNotNull(result);
 		List<Bundle.BundleEntryComponent> entries = result.getEntry();
-		assertThat(entries, hasSize(22));
+		assertEquals(entries.size(), 22);
-//		assertEquals(entries.get(0).getResponse().getStatus(), "201 Created");
-//		assertEquals(entries.get(21).getResponse().getStatus(), "201 Created");
 
 		IdType measureId = new IdType("Measure", "measure-asf");
 		String patient = "Patient/Patient-6529";
@@ -104,8 +101,8 @@ public class CrProviderDstu3Test extends BaseCrDstu3Test {
 			null,
 			myRequestDetails);
 		// Assert it worked
-		assertThat(report.getGroup(), hasSize(2));
+		assertEquals(report.getGroup().size(), 2);
-		assertThat(report.getGroup().get(0).getPopulation(), hasSize(3));
+		assertEquals(report.getGroup().get(0).getPopulation().size(), 3);
 		ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(report));
 
 		// Now timed runs
@@ -147,8 +144,8 @@ public class CrProviderDstu3Test extends BaseCrDstu3Test {
 		MeasureReport report = myMeasureOperationsProvider.evaluateMeasure(measureId, periodStart, periodEnd, "population",
 			null, null, null, null, null, null, myRequestDetails);
 		// Assert it worked
-		assertThat(report.getGroup(), hasSize(2));
+		assertEquals(report.getGroup().size(), 2);
-		assertThat(report.getGroup().get(0).getPopulation(), hasSize(3));
+		assertEquals(report.getGroup().get(0).getPopulation().size(), 3);
 		ourLog.debug(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(report));
 
 		// Now timed runs

hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/dstu3/MeasureOperationsProviderTest.java

@@ -70,17 +70,17 @@ class MeasureOperationsProviderTest extends BaseCrDstu3Test {
 	}
 
 	@Test
-	void testMeasureEvaluateWithTerminology(Hoverfly hoverfly) throws IOException {
+	void testMeasureEvaluateWithTerminology() throws IOException {
 		loadBundle("Exm105Fhir3Measure.json");
 
 		var returnMeasureReport = this.myMeasureOperationsProvider.evaluateMeasure(
 			new IdType("Measure", "measure-EXM105-FHIR3-8.0.000"),
 			"2019-01-01",
 			"2020-01-01",
-			"individual",
+			"patient",
 			"Patient/denom-EXM105-FHIR3",
 			null,
-			"2019-12-12",
+			null,
 			null,
 			null,
 			null,

hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/r4/CareGapsOperationProviderIT.java

@@ -0,0 +1,213 @@
+package ca.uhn.fhir.cr.r4;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.cr.IResourceLoader;
+import ca.uhn.fhir.cr.config.CrProperties;
+import ca.uhn.fhir.cr.config.CrR4Config;
+import ca.uhn.fhir.cr.r4.measure.CareGapsOperationProvider;
+import ca.uhn.fhir.cr.r4.measure.SubmitDataProvider;
+import ca.uhn.fhir.cr.r4.measure.SubmitDataService;
+import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.test.utilities.JettyUtil;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.DateType;
+import org.hl7.fhir.r4.model.Extension;
+import org.hl7.fhir.r4.model.Measure;
+import org.hl7.fhir.r4.model.Parameters;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.ContextConfiguration;
+
+import java.util.Optional;
+import java.util.concurrent.TimeUnit;
+
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+/**
+ * End to end test for care gaps functionality
+ * Scenario is that we have a Provider that is transmitting data to a Payer to validate that
+ * no gaps in care exist (a "gap in care" means that a Patient is not conformant with best practices for a given pathology).
+ * Specifically, for this test, we're checking to ensure that a Patient has had the appropriate colorectal cancer screenings.
+ *
+ * So, it's expected that the Payer already has the relevant quality measure content loaded. The first two steps here are initializing the Payer
+ * by loading Measure content, and by setting up a reporting Organization resource (IOW, the Payer's identify to associate with the care-gaps report).
+ *
+ * The next step is for the Provider to submit data to the Payer for review. That's the submit data operation.
+ *
+ * After that, the Provider can invoke $care-gaps to check for any issues, which are reported.
+ *
+ * The Provider can then resolve those issues, submit additional data, and then check to see if the gaps are closed.
+ *
+ * 1. Initialize Payer with Measure content
+ * 2. Initialize Payer with Organization info
+ * 3. Provider submits Patient data
+ * 4. Provider invokes care-gaps (and discovers issues)
+ * 5. (not included in test, since it's done out of bad) Provider closes gap (by having the Procedure done on the Patient).
+ * 6. Provider submits additional Patient data
+ * 7. Provider invokes care-gaps (and discovers issues are closed).
+ */
+@ContextConfiguration(classes = CrR4Config.class)
+class CareGapsOperationProviderIT extends BaseJpaR4Test implements IResourceLoader {
+
+	private static RestfulServer ourRestServer;
+	private static IGenericClient ourClient;
+	private static FhirContext ourCtx;
+	private static CloseableHttpClient ourHttpClient;
+	private static Server ourServer;
+	private static String ourServerBase;
+	@Autowired
+	CareGapsOperationProvider myCareGapsOperationProvider;
+
+	@Autowired
+	CrProperties myCrProperties;
+
+	SubmitDataProvider mySubmitDataProvider;
+	private SimpleRequestHeaderInterceptor mySimpleHeaderInterceptor;
+
+	@SuppressWarnings("deprecation")
+	@AfterEach
+	public void after() {
+		ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
+		myStorageSettings.setIndexMissingFields(new JpaStorageSettings().getIndexMissingFields());
+	}
+
+	@BeforeEach
+	public void beforeStartServer() throws Exception {
+		if (ourRestServer == null) {
+			RestfulServer restServer = new RestfulServer(ourCtx);
+
+			mySubmitDataProvider = new SubmitDataProvider(requestDetails -> {
+				return new SubmitDataService(getDaoRegistry(), requestDetails);
+			});
+			restServer.setPlainProviders(mySystemProvider, myCareGapsOperationProvider, mySubmitDataProvider);
+
+			ourServer = new Server(0);
+
+			ServletContextHandler proxyHandler = new ServletContextHandler();
+			proxyHandler.setContextPath("/");
+
+			ServletHolder servletHolder = new ServletHolder();
+			servletHolder.setServlet(restServer);
+			proxyHandler.addServlet(servletHolder, "/fhir/*");
+
+			ourCtx = FhirContext.forR4Cached();
+			restServer.setFhirContext(ourCtx);
+
+			ourServer.setHandler(proxyHandler);
+			JettyUtil.startServer(ourServer);
+			int myPort = JettyUtil.getPortForStartedServer(ourServer);
+			ourServerBase = "http://localhost:" + myPort + "/fhir";
+
+			PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+			HttpClientBuilder builder = HttpClientBuilder.create();
+			builder.setConnectionManager(connectionManager);
+			ourHttpClient = builder.build();
+
+			ourCtx.getRestfulClientFactory().setSocketTimeout(600 * 1000);
+			ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
+			ourClient.setLogRequestAndResponse(true);
+			ourRestServer = restServer;
+		}
+
+		ourRestServer.setDefaultResponseEncoding(EncodingEnum.XML);
+		ourRestServer.setPagingProvider(myPagingProvider);
+
+		mySimpleHeaderInterceptor = new SimpleRequestHeaderInterceptor();
+		ourClient.registerInterceptor(mySimpleHeaderInterceptor);
+		myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
+
+		// Set properties
+		CrProperties.MeasureProperties measureProperties = new CrProperties.MeasureProperties();
+		CrProperties.MeasureProperties.MeasureReportConfiguration measureReportConfiguration = new CrProperties.MeasureProperties.MeasureReportConfiguration();
+		measureReportConfiguration.setCareGapsReporter("Organization/alphora");
+		measureReportConfiguration.setCareGapsCompositionSectionAuthor("Organization/alphora-author");
+		measureProperties.setMeasureReportConfiguration(measureReportConfiguration);
+		myCrProperties.setMeasureProperties(measureProperties);
+	}
+
+	@Test
+	public void careGapsEndToEnd(){
+
+		// 1. Initialize Payer content
+		var measureBundle = (Bundle) readResource("CaregapsColorectalCancerScreeningsFHIR-bundle.json");
+		ourClient.transaction().withBundle(measureBundle).execute();
+
+		// 2. Initialize Payer org data
+		var orgData = (Bundle) readResource("CaregapsAuthorAndReporter.json");
+		ourClient.transaction().withBundle(orgData).execute();
+
+		// 3. Provider submits Patient data
+		var patientData = (Parameters) readResource("CaregapsPatientData.json");
+		ourClient.operation().onInstance("Measure/ColorectalCancerScreeningsFHIR").named("submit-data")
+			.withParameters(patientData).execute();
+
+		// 4. Provider runs $care-gaps
+		var parameters = new Parameters();
+		parameters.addParameter("status", "open-gap");
+		parameters.addParameter("status", "closed-gap");
+		parameters.addParameter("periodStart", new DateType("2020-01-01"));
+		parameters.addParameter("periodEnd", new DateType("2020-12-31"));
+		parameters.addParameter("subject", "Patient/end-to-end-EXM130");
+		parameters.addParameter("measureId", "ColorectalCancerScreeningsFHIR");
+
+		var result = ourClient.operation().onType(Measure.class)
+			.named("$care-gaps")
+			.withParameters(parameters)
+			.returnResourceType(Parameters.class)
+			.execute();
+
+		// assert open-gap
+		assertForGaps(result);
+
+		// 5. (out of band) Provider fixes gaps
+		var newData = (Parameters) readResource("CaregapsSubmitDataCloseGap.json");
+		// 6. Provider submits additional Patient data showing that they did another procedure that was needed.
+		ourClient.operation().onInstance("Measure/ColorectalCancerScreeningsFHIR").named("submit-data").withParameters(newData).execute();
+
+		// 7. Provider runs care-gaps again
+		result = ourClient.operation().onType("Measure")
+			.named("care-gaps")
+			.withParameters(parameters)
+			.execute();
+
+		// assert closed-gap
+		assertForGaps(result);
+	}
+
+	private void assertForGaps(Parameters theResult) {
+		assertNotNull(theResult);
+		var dataBundle = (Bundle) theResult.getParameter().get(0).getResource();
+		var detectedIssue = dataBundle.getEntry()
+																.stream()
+											.filter(bundleEntryComponent -> "DetectedIssue".equalsIgnoreCase(bundleEntryComponent.getResource().getResourceType().name())).findFirst().get();
+		var extension = (Extension) detectedIssue.getResource().getChildByName("modifierExtension").getValues().get(0);
+
+		var codeableConcept = (CodeableConcept) extension.getValue();
+		Optional<Coding> coding = codeableConcept.getCoding()
+																.stream()
+											.filter(code -> "open-gap".equalsIgnoreCase(code.getCode()) || "closed-gap".equalsIgnoreCase(code.getCode())).findFirst();
+		assertTrue(!coding.isEmpty());
+	}
+
+	@Override
+	public DaoRegistry getDaoRegistry() {
+		return myDaoRegistry;
+	}
+}

hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/r4/CareGapsServiceR4Test.java

@@ -0,0 +1,502 @@
+package ca.uhn.fhir.cr.r4;
+
+import ca.uhn.fhir.cr.BaseCrR4Test;
+import ca.uhn.fhir.cr.config.CrProperties;
+import ca.uhn.fhir.cr.r4.measure.CareGapsService;
+import ca.uhn.fhir.cr.r4.measure.MeasureService;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.model.primitive.DateDt;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.CanonicalType;
+import org.hl7.fhir.r4.model.Parameters;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.concurrent.Executor;
+import java.util.concurrent.Executors;
+import java.util.function.Function;
+
+import static javolution.testing.TestContext.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+@ExtendWith(SpringExtension.class)
+public class CareGapsServiceR4Test extends BaseCrR4Test {
+	private static final String ourPeriodStartValid = "2019-01-01";
+	private static IPrimitiveType<Date> ourPeriodStart = new DateDt("2019-01-01");
+	private static final String ourPeriodEndValid = "2019-12-31";
+	private static IPrimitiveType<Date> ourPeriodEnd = new DateDt("2019-12-31");
+	private static final String ourSubjectPatientValid = "Patient/numer-EXM125";
+	private static final String ourSubjectGroupValid = "Group/gic-gr-1";
+	private static final String ourSubjectGroupParallelValid = "Group/gic-gr-parallel";
+	private static final String ourStatusValid = "open-gap";
+	private List<String> myStatuses;
+
+	private List<CanonicalType> myMeasureUrls;
+	private static final String ourStatusValidSecond = "closed-gap";
+
+	private List<String> myMeasures;
+	private static final String ourMeasureIdValid = "BreastCancerScreeningFHIR";
+	private static final String ourMeasureUrlValid = "http://ecqi.healthit.gov/ecqms/Measure/BreastCancerScreeningFHIR";
+	private static final String ourPractitionerValid = "gic-pra-1";
+	private static final String ourOrganizationValid = "gic-org-1";
+	private static final String ourDateInvalid = "bad-date";
+	private static final String ourSubjectInvalid = "bad-subject";
+	private static final String ourStatusInvalid = "bad-status";
+	private static final String ourSubjectReferenceInvalid = "Measure/gic-sub-1";
+
+	Function<RequestDetails, CareGapsService> myCareGapsService;
+
+	CrProperties myCrProperties;
+	@Autowired
+	MeasureService myMeasureService;
+	Executor myExecutor;
+
+	@BeforeEach
+	public void beforeEach() {
+		loadBundle(Bundle.class, "CaregapsAuthorAndReporter.json");
+		readAndLoadResource("numer-EXM125-patient.json");
+		myStatuses = new ArrayList<>();
+		myMeasures = new ArrayList<>();
+		myMeasureUrls = new ArrayList<>();
+
+		myCrProperties = new CrProperties();
+		CrProperties.MeasureProperties measureProperties = new CrProperties.MeasureProperties();
+		CrProperties.MeasureProperties.MeasureReportConfiguration measureReportConfiguration = new CrProperties.MeasureProperties.MeasureReportConfiguration();
+		measureReportConfiguration.setCareGapsReporter("Organization/alphora");
+		measureReportConfiguration.setCareGapsCompositionSectionAuthor("Organization/alphora-author");
+		measureProperties.setMeasureReportConfiguration(measureReportConfiguration);
+		myCrProperties.setMeasureProperties(measureProperties);
+
+		myExecutor = Executors.newSingleThreadExecutor();
+
+		//measureService = new MeasureService();
+
+		myCareGapsService = requestDetails -> {
+			CareGapsService careGapsService = new CareGapsService(myCrProperties, myMeasureService, getDaoRegistry(), myExecutor, requestDetails);
+			return careGapsService;
+		};
+
+	}
+
+	private void beforeEachMeasure() {
+		loadBundle("BreastCancerScreeningFHIR-bundle.json");
+	}
+	private void beforeEachMultipleMeasures() {
+		loadBundle("BreastCancerScreeningFHIR-bundle.json");
+		loadBundle("ColorectalCancerScreeningsFHIR-bundle.json");
+	}
+
+	@Test
+	void testMinimalParametersValid() {
+		beforeEachMeasure();
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		Parameters result = myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, ourSubjectPatientValid
+			, null
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		);
+
+		assertNotNull(result);
+	}
+
+	@Test
+	void testPeriodStartNull() {
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		assertThrows(Exception.class, () -> myCareGapsService.apply(requestDetails).getCareGapsReport(null, ourPeriodEnd
+			, null
+			, ourSubjectPatientValid
+			, null
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		));
+	}
+
+	@Test
+	void testPeriodStartInvalid() {
+		beforeEachMeasure();
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		assertThrows(Exception.class, () -> myCareGapsService.apply(requestDetails).getCareGapsReport(new DateDt("12-21-2025"), ourPeriodEnd
+			, null
+			, ourSubjectPatientValid
+			, null
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		));
+	}
+
+	@Test
+	void testPeriodEndNull() {
+		beforeEachMeasure();
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		assertThrows(Exception.class, () -> myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, null
+			, null
+			, ourSubjectPatientValid
+			, null
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		));
+	}
+
+	@Test
+	void testPeriodEndInvalid() {
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		assertThrows(Exception.class, () -> myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, new DateDt("12-21-2025")
+			, null
+			, ourSubjectPatientValid
+			, null
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		));
+	}
+
+	@Test
+	void testSubjectGroupValid() {
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		readAndLoadResource("gic-gr-1.json");
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		assertDoesNotThrow(() -> {
+			 myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+				, null
+				, ourSubjectGroupValid
+				, null
+				, null
+				, myStatuses
+				, myMeasures
+				, null
+				, null
+				, null
+			);
+		});
+	}
+
+	@Test
+	void testSubjectInvalid() {
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		Parameters result = myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, ourSubjectInvalid
+			, null
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		);
+		assertTrue(result.getParameter().isEmpty());
+	}
+
+	@Test
+	void testSubjectReferenceInvalid() {
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		Parameters result = myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, ourSubjectReferenceInvalid
+			, null
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		);
+		assertTrue(result.getParameter().isEmpty());
+	}
+
+	@Test
+	void testSubjectAndPractitioner() {
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		Parameters result = myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, ourSubjectPatientValid
+			, ourPractitionerValid
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		);
+		assertTrue(result.getParameter().isEmpty());
+	}
+
+	@Test
+	void testSubjectAndOrganization() {
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		Parameters result = myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, ourSubjectPatientValid
+			, null
+			, ourOrganizationValid
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		);
+		assertTrue(result.getParameter().isEmpty());
+	}
+
+	@Test
+	void testOrganizationOnly() {
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		assertThrows(NotImplementedOperationException.class, () -> myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, null
+			, null
+			, ourOrganizationValid
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		));
+	}
+
+	@Test
+	void testPractitionerAndOrganization() {
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		assertThrows(NotImplementedOperationException.class, () -> myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, null
+			, ourPractitionerValid
+			, ourOrganizationValid
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		));
+	}
+
+	@Test
+	void testPractitionerOnly() {
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		assertThrows(NotImplementedOperationException.class, () ->  myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, null
+			, ourPractitionerValid
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		));
+	}
+
+	@Test
+	void testNoMeasure() {
+		myStatuses.add(ourStatusValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		var result = myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, ourSubjectPatientValid
+			, null
+			, null
+			, myStatuses
+			, null
+			, null
+			, null
+			, null
+		);
+
+		assertTrue(result.getParameter().isEmpty());
+	}
+
+	@Test
+	void testStatusInvalid() {
+		myStatuses.add(ourStatusInvalid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		Parameters result = myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, ourSubjectPatientValid
+			, null
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		);
+		assertTrue(result.getParameter().isEmpty());
+	}
+
+	@Test
+	void testStatusNull() {
+		myStatuses.add(ourStatusInvalid);
+		myMeasures.add(ourMeasureIdValid);
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		var result = myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, ourSubjectPatientValid
+			, null
+			, null
+			, null
+			, myMeasures
+			, null
+			, null
+			, null
+		);
+
+		assertTrue(result.getParameter().isEmpty());
+	}
+
+	@Test
+	public void testMeasures() {
+		beforeEachMultipleMeasures();
+		myStatuses.add(ourStatusValid);
+		ourPeriodStart = new DateDt("2019-01-01");
+		myMeasures.add("ColorectalCancerScreeningsFHIR");
+		myMeasureUrls.add(new CanonicalType(ourMeasureUrlValid));
+
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		Parameters result = myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, ourSubjectPatientValid
+			, null
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, myMeasureUrls
+			, null
+		);
+
+		assertNotNull(result);
+
+		//Test to search for how many search parameters are created.
+		//only 1 should be created.
+		var searchParams = this.myDaoRegistry.getResourceDao("SearchParameter")
+			.search(new SearchParameterMap(), requestDetails);
+
+		assertNotNull(searchParams);
+
+		assertEquals(searchParams.getAllResources().size(), 1);
+	}
+
+	@Test
+	void testParallelMultiSubject() {
+		beforeEachParallelMeasure();
+		myStatuses.add(ourStatusValid);
+		myMeasures.add(ourMeasureIdValid);
+
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		requestDetails.setFhirServerBase("test.com");
+		Parameters result = myCareGapsService.apply(requestDetails).getCareGapsReport(ourPeriodStart, ourPeriodEnd
+			, null
+			, ourSubjectGroupParallelValid
+			, null
+			, null
+			, myStatuses
+			, myMeasures
+			, null
+			, null
+			, null
+		);
+
+		assertNotNull(result);
+	}
+
+	private void beforeEachParallelMeasure() {
+		readAndLoadResource("gic-gr-parallel.json");
+		loadBundle("BreastCancerScreeningFHIR-bundle.json");
+	}
+}

hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/r4/SubmitDataServiceR4Test.java

@@ -0,0 +1,68 @@
+package ca.uhn.fhir.cr.r4;
+
+import ca.uhn.fhir.cr.BaseCrR4Test;
+import ca.uhn.fhir.cr.common.Searches;
+import ca.uhn.fhir.cr.r4.measure.SubmitDataService;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import com.google.common.collect.Lists;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.MeasureReport;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.StringType;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+
+import java.util.Iterator;
+import java.util.function.Function;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+@ExtendWith(SpringExtension.class)
+public class SubmitDataServiceR4Test extends BaseCrR4Test {
+
+	Function<RequestDetails, SubmitDataService> mySubmitDataServiceFunction;
+
+	@BeforeEach
+	public void beforeEach() {
+		mySubmitDataServiceFunction = rs -> {
+			return new SubmitDataService(getDaoRegistry(), new SystemRequestDetails());
+		};
+	}
+
+	@Test
+	public void submitDataTest(){
+		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setFhirContext(getFhirContext());
+		MeasureReport mr = newResource(MeasureReport.class).setMeasure("Measure/A123");
+		Observation obs = newResource(Observation.class).setValue(new StringType("ABC"));
+		mySubmitDataServiceFunction.apply(requestDetails)
+			.submitData(new IdType("Measure", "A123"), mr,
+				Lists.newArrayList(obs));
+
+		Iterable<IBaseResource> resourcesResult = search(Observation.class, Searches.all());
+		Observation savedObs = null;
+		Iterator<IBaseResource> iterator = resourcesResult.iterator();
+		while(iterator.hasNext()){
+			savedObs = (Observation) iterator.next();
+			break;
+		}
+		assertNotNull(savedObs);
+		assertEquals("ABC", savedObs.getValue().primitiveValue());
+
+		resourcesResult = search(MeasureReport.class, Searches.all());
+		MeasureReport savedMr = null;
+		iterator = resourcesResult.iterator();
+		while(iterator.hasNext()){
+			savedMr = (MeasureReport) iterator.next();
+			break;
+		}
+		assertNotNull(savedMr);
+		assertEquals("Measure/A123", savedMr.getMeasure());
+	}
+
+}

hapi-fhir-storage-cr/src/test/resources/Alphora-organization.json

@@ -0,0 +1,58 @@
+{
+	"resourceType": "Organization",
+	"id": "alphora",
+	"meta": {
+		"profile": [
+			"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
+		]
+	},
+	"identifier": [
+		{
+			"use": "official",
+			"type": {
+				"coding": [
+					{
+						"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+						"code": "TAX",
+						"display": "Tax ID number"
+					}
+				]
+			},
+			"system": "urn:oid:2.16.840.1.113883.4.4",
+			"value": "123456789",
+			"assigner": {
+				"display": "www.irs.gov"
+			}
+		}
+	],
+	"active": true,
+	"type": [
+		{
+			"coding": [
+				{
+					"system": "http://terminology.hl7.org/CodeSystem/organization-type",
+					"code": "prov",
+					"display": "Healthcare Provider"
+				}
+			]
+		}
+	],
+	"name": "alphora",
+	"telecom": [
+		{
+			"system": "phone",
+			"value": "(+1) 401-555-1212"
+		}
+	],
+	"address": [
+		{
+			"line": [
+				"73 Lakewood Street"
+			],
+			"city": "Warwick",
+			"state": "RI",
+			"postalCode": "02886",
+			"country": "USA"
+		}
+	]
+}

hapi-fhir-storage-cr/src/test/resources/AlphoraAuthor-organization.json

@@ -0,0 +1,58 @@
+{
+	"resourceType": "Organization",
+	"id": "alphora-author",
+	"meta": {
+		"profile": [
+			"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
+		]
+	},
+	"identifier": [
+		{
+			"use": "official",
+			"type": {
+				"coding": [
+					{
+						"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+						"code": "TAX",
+						"display": "Tax ID number"
+					}
+				]
+			},
+			"system": "urn:oid:2.16.840.1.113883.4.4",
+			"value": "12345678910",
+			"assigner": {
+				"display": "www.irs.gov"
+			}
+		}
+	],
+	"active": true,
+	"type": [
+		{
+			"coding": [
+				{
+					"system": "http://terminology.hl7.org/CodeSystem/organization-type",
+					"code": "prov",
+					"display": "Healthcare Provider"
+				}
+			]
+		}
+	],
+	"name": "alphora-author",
+	"telecom": [
+		{
+			"system": "phone",
+			"value": "(+1) 401-555-1313"
+		}
+	],
+	"address": [
+		{
+			"line": [
+				"737 Lakewood Street"
+			],
+			"city": "Warwick",
+			"state": "RI",
+			"postalCode": "02886",
+			"country": "USA"
+		}
+	]
+}

hapi-fhir-storage-cr/src/test/resources/CaregapsAuthorAndReporter.json

@@ -0,0 +1,135 @@
+{
+	"resourceType": "Bundle",
+	"id": "gic-configuration",
+	"type": "transaction",
+	"entry": [
+		{
+			"resource": {
+				"resourceType": "Organization",
+				"id": "alphora",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
+					]
+				},
+				"identifier": [
+					{
+						"use": "official",
+						"type": {
+							"coding": [
+								{
+									"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+									"code": "TAX",
+									"display": "Tax ID number"
+								}
+							]
+						},
+						"system": "urn:oid:2.16.840.1.113883.4.4",
+						"value": "123456789",
+						"assigner": {
+							"display": "www.irs.gov"
+						}
+					}
+				],
+				"active": true,
+				"type": [
+					{
+						"coding": [
+							{
+								"system": "http://terminology.hl7.org/CodeSystem/organization-type",
+								"code": "prov",
+								"display": "Healthcare Provider"
+							}
+						]
+					}
+				],
+				"name": "alphora",
+				"telecom": [
+					{
+						"system": "phone",
+						"value": "(+1) 401-555-1212"
+					}
+				],
+				"address": [
+					{
+						"line": [
+							"73 Lakewood Street"
+						],
+						"city": "Warwick",
+						"state": "RI",
+						"postalCode": "02886",
+						"country": "USA"
+					}
+				]
+			},
+			"request": {
+				"method": "PUT",
+				"url": "Organization/alphora"
+			}
+		},
+		{
+			"resource": {
+				"resourceType": "Organization",
+				"id": "alphora-author",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
+					]
+				},
+				"identifier": [
+					{
+						"use": "official",
+						"type": {
+							"coding": [
+								{
+									"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+									"code": "TAX",
+									"display": "Tax ID number"
+								}
+							]
+						},
+						"system": "urn:oid:2.16.840.1.113883.4.4",
+						"value": "12345678910",
+						"assigner": {
+							"display": "www.irs.gov"
+						}
+					}
+				],
+				"active": true,
+				"type": [
+					{
+						"coding": [
+							{
+								"system": "http://terminology.hl7.org/CodeSystem/organization-type",
+								"code": "prov",
+								"display": "Healthcare Provider"
+							}
+						]
+					}
+				],
+				"name": "alphora-author",
+				"telecom": [
+					{
+						"system": "phone",
+						"value": "(+1) 401-555-1313"
+					}
+				],
+				"address": [
+					{
+						"line": [
+							"737 Lakewood Street"
+						],
+						"city": "Warwick",
+						"state": "RI",
+						"postalCode": "02886",
+						"country": "USA"
+					}
+				]
+			},
+			"request": {
+				"method": "PUT",
+				"url": "Organization/alphora-author"
+			}
+		}
+	]
+}

hapi-fhir-storage-cr/src/test/resources/CaregapsNumerator.json

@@ -0,0 +1,277 @@
+{
+	"resourceType": "Parameters",
+	"id": "EXM130-7.3.000-end-to-end-submit-data-bundle",
+	"parameter": [
+		{
+			"name": "measureReport",
+			"resource": {
+				"resourceType": "MeasureReport",
+				"id": "col-measurereport",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/datax-measurereport-deqm"
+					]
+				},
+				"extension": [
+					{
+						"url": "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/extension-submitDataUpdateType",
+						"valueCode": "incremental"
+					}
+				],
+				"status": "complete",
+				"type": "data-collection",
+				"measure": "http://ecqi.healthit.gov/ecqms/Measure/ColorectalCancerScreeningsFHIR",
+				"subject": {
+					"reference": "Patient/numer-EXM130"
+				},
+				"date": "2021-01-01T16:59:52.404Z",
+				"reporter": {
+					"reference": "Organization/organization03"
+				},
+				"period": {
+					"start": "2019-01-01",
+					"end": "2019-12-31"
+				},
+				"evaluatedResource": [
+					{
+						"reference": "Procedure/numer-EXM130-2"
+					}
+				]
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Patient",
+				"id": "numer-EXM130",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"
+					]
+				},
+				"extension": [
+					{
+						"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+						"extension": [
+							{
+								"url": "ombCategory",
+								"valueCoding": {
+									"system": "urn:oid:2.16.840.1.113883.6.238",
+									"code": "2028-9",
+									"display": "Asian"
+								}
+							}
+						]
+					},
+					{
+						"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+						"extension": [
+							{
+								"url": "ombCategory",
+								"valueCoding": {
+									"system": "urn:oid:2.16.840.1.113883.6.238",
+									"code": "2135-2",
+									"display": "Hispanic or Latino"
+								}
+							}
+						]
+					}
+				],
+				"identifier": [
+					{
+						"use": "usual",
+						"type": {
+							"coding": [
+								{
+									"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+									"code": "MR",
+									"display": "Medical Record Number"
+								}
+							]
+						},
+						"system": "http://hospital.smarthealthit.org",
+						"value": "999999992"
+					}
+				],
+				"name": [
+					{
+						"family": "Blitz",
+						"given": [
+							"Don"
+						]
+					}
+				],
+				"gender": "male",
+				"birthDate": "1965-01-01"
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Encounter",
+				"id": "numer-EXM130-2",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter"
+					]
+				},
+				"status": "finished",
+				"class": {
+					"system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+					"code": "AMB",
+					"display": "ambulatory"
+				},
+				"type": [
+					{
+						"coding": [
+							{
+								"system": "http://www.ama-assn.org/go/cpt",
+								"code": "99201",
+								"display": "Office or other outpatient visit for the evaluation and management of a new patient, which requires these 3 key components: A problem focused history; A problem focused examination; Straightforward medical decision making. Counseling and/or coordination of care with other physicians, other qualified health care professionals, or agencies are provided consistent with the nature of the problem(s) and the patient's and/or family's needs. Usually, the presenting problem(s) are self limited or minor. Typically, 10 minutes are spent face-to-face with the patient and/or family."
+							}
+						]
+					}
+				],
+				"subject": {
+					"reference": "Patient/numer-EXM130"
+				},
+				"period": {
+					"start": "2020-05-01T09:00:00-06:00",
+					"end": "2020-05-01T14:00:00-06:00"
+				}
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Procedure",
+				"id": "numer-EXM130-2",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure"
+					]
+				},
+				"status": "completed",
+				"code": {
+					"coding": [
+						{
+							"system": "http://www.ama-assn.org/go/cpt",
+							"code": "44388",
+							"display": "Colonoscopy through stoma; with ablation of tumor(s), polyp(s), or other lesion(s) not amenable to removal by hot biopsy forceps, bipolar cautery or snare technique"
+						}
+					]
+				},
+				"subject": {
+					"reference": "Patient/numer-EXM130"
+				},
+				"performedPeriod": {
+					"start": "2020-05-01T10:00:00-06:00",
+					"end": "2020-05-01T12:00:00-06:00"
+				}
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Practitioner",
+				"id": "practitioner01",
+				"meta": {
+					"source": "http://example.org/fhir/server",
+					"profile": [
+						"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/practitioner-deqm"
+					]
+				},
+				"identifier": [
+					{
+						"use": "official",
+						"type": {
+							"coding": [
+								{
+									"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+									"code": "PRN",
+									"display": "Provider number"
+								}
+							]
+						},
+						"system": "http://hl7.org/fhir/sid/us-npi",
+						"value": "456789123"
+					}
+				],
+				"active": true,
+				"name": [
+					{
+						"family": "Hale",
+						"given": [
+							"Cody"
+						],
+						"suffix": [
+							"MD"
+						]
+					}
+				],
+				"gender": "male"
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Organization",
+				"id": "organization03",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
+					]
+				},
+				"identifier": [
+					{
+						"use": "official",
+						"type": {
+							"coding": [
+								{
+									"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+									"code": "PRN",
+									"display": "Provider number"
+								}
+							]
+						},
+						"system": "http://hl7.org/fhir/sid/us-npi",
+						"value": "345678912",
+						"assigner": {
+							"display": "www.cms.gov"
+						}
+					}
+				],
+				"active": true,
+				"type": [
+					{
+						"coding": [
+							{
+								"system": "http://terminology.hl7.org/CodeSystem/organization-type",
+								"code": "prov",
+								"display": "Healthcare Provider"
+							}
+						]
+					}
+				],
+				"name": "DaVinciHospital03",
+				"telecom": [
+					{
+						"system": "phone",
+						"value": "(+1) 201-555-1212"
+					}
+				],
+				"address": [
+					{
+						"line": [
+							"94 Olive Ave."
+						],
+						"city": "Union City",
+						"state": "NJ",
+						"postalCode": "07087",
+						"country": "USA"
+					}
+				]
+			}
+		}
+	]
+}

hapi-fhir-storage-cr/src/test/resources/CaregapsPatientData.json

@@ -0,0 +1,278 @@
+{
+	"resourceType": "Parameters",
+	"id": "EXM130-7.3.000-end-to-end-submit-data-bundle",
+	"parameter": [
+		{
+			"name": "measureReport",
+			"resource": {
+				"resourceType": "MeasureReport",
+				"id": "col-measurereport",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/datax-measurereport-deqm"
+					]
+				},
+				"extension": [
+					{
+						"url": "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/extension-submitDataUpdateType",
+						"valueCode": "incremental"
+					}
+				],
+				"status": "complete",
+				"type": "data-collection",
+				"measure": "http://ecqi.healthit.gov/ecqms/Measure/ColorectalCancerScreeningsFHIR",
+				"subject": {
+					"reference": "Patient/end-to-end-EXM130"
+				},
+				"date": "2021-01-01T16:59:52.404Z",
+				"reporter": {
+					"reference": "Organization/organization03"
+				},
+				"period": {
+					"start": "2019-01-01",
+					"end": "2019-12-31"
+				},
+				"evaluatedResource": [
+					{
+						"reference": "Encounter/end-to-end-EXM130-1",
+						"reference": "Procedure/end-to-end-EXM130-1"
+					}
+				]
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Patient",
+				"id": "end-to-end-EXM130",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"
+					]
+				},
+				"extension": [
+					{
+						"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+						"extension": [
+							{
+								"url": "ombCategory",
+								"valueCoding": {
+									"system": "urn:oid:2.16.840.1.113883.6.238",
+									"code": "2028-9",
+									"display": "Asian"
+								}
+							}
+						]
+					},
+					{
+						"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+						"extension": [
+							{
+								"url": "ombCategory",
+								"valueCoding": {
+									"system": "urn:oid:2.16.840.1.113883.6.238",
+									"code": "2135-2",
+									"display": "Hispanic or Latino"
+								}
+							}
+						]
+					}
+				],
+				"identifier": [
+					{
+						"use": "usual",
+						"type": {
+							"coding": [
+								{
+									"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+									"code": "MR",
+									"display": "Medical Record Number"
+								}
+							]
+						},
+						"system": "http://hospital.smarthealthit.org",
+						"value": "999999992"
+					}
+				],
+				"name": [
+					{
+						"family": "Blitz",
+						"given": [
+							"Don"
+						]
+					}
+				],
+				"gender": "male",
+				"birthDate": "1965-01-01"
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Practitioner",
+				"id": "practitioner01",
+				"meta": {
+					"source": "http://example.org/fhir/server",
+					"profile": [
+						"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/practitioner-deqm"
+					]
+				},
+				"identifier": [
+					{
+						"use": "official",
+						"type": {
+							"coding": [
+								{
+									"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+									"code": "PRN",
+									"display": "Provider number"
+								}
+							]
+						},
+						"system": "http://hl7.org/fhir/sid/us-npi",
+						"value": "456789123"
+					}
+				],
+				"active": true,
+				"name": [
+					{
+						"family": "Hale",
+						"given": [
+							"Cody"
+						],
+						"suffix": [
+							"MD"
+						]
+					}
+				],
+				"gender": "male"
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Organization",
+				"id": "organization03",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
+					]
+				},
+				"identifier": [
+					{
+						"use": "official",
+						"type": {
+							"coding": [
+								{
+									"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+									"code": "PRN",
+									"display": "Provider number"
+								}
+							]
+						},
+						"system": "http://hl7.org/fhir/sid/us-npi",
+						"value": "345678912",
+						"assigner": {
+							"display": "www.cms.gov"
+						}
+					}
+				],
+				"active": true,
+				"type": [
+					{
+						"coding": [
+							{
+								"system": "http://terminology.hl7.org/CodeSystem/organization-type",
+								"code": "prov",
+								"display": "Healthcare Provider"
+							}
+						]
+					}
+				],
+				"name": "DaVinciHospital03",
+				"telecom": [
+					{
+						"system": "phone",
+						"value": "(+1) 201-555-1212"
+					}
+				],
+				"address": [
+					{
+						"line": [
+							"94 Olive Ave."
+						],
+						"city": "Union City",
+						"state": "NJ",
+						"postalCode": "07087",
+						"country": "USA"
+					}
+				]
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Encounter",
+				"id": "end-to-end-EXM130-1",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter"
+					]
+				},
+				"status": "finished",
+				"class": {
+					"system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+					"code": "AMB",
+					"display": "ambulatory"
+				},
+				"type": [
+					{
+						"coding": [
+							{
+								"system": "http://www.ama-assn.org/go/cpt",
+								"code": "99201",
+								"display": "Office or other outpatient visit for the evaluation and management of a new patient, which requires these 3 key components: A problem focused history; A problem focused examination; Straightforward medical decision making. Counseling and/or coordination of care with other physicians, other qualified health care professionals, or agencies are provided consistent with the nature of the problem(s) and the patient's and/or family's needs. Usually, the presenting problem(s) are self limited or minor. Typically, 10 minutes are spent face-to-face with the patient and/or family."
+							}
+						]
+					}
+				],
+				"subject": {
+					"reference": "Patient/end-to-end-EXM130"
+				},
+				"period": {
+					"start": "2020-01-01T09:00:00-06:00",
+					"end": "2020-01-01T14:00:00-06:00"
+				}
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Procedure",
+				"id": "end-to-end-EXM130-2",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure"
+					]
+				},
+				"status": "completed",
+				"code": {
+					"coding": [
+						{
+							"system": "http://www.ama-assn.org/go/cpt",
+							"code": "33120",
+							"display": "Colonoscopy through stoma; with ablation of tumor(s), polyp(s), or other lesion(s) not amenable to removal by hot biopsy forceps, bipolar cautery or snare technique"
+						}
+					]
+				},
+				"subject": {
+					"reference": "Patient/end-to-end-EXM130"
+				},
+				"performedPeriod": {
+					"start": "2020-01-01T10:00:00-06:00",
+					"end": "2020-01-01T12:00:00-06:00"
+				}
+			}
+		}
+	]
+}

hapi-fhir-storage-cr/src/test/resources/CaregapsSubmitDataCloseGap.json

@@ -0,0 +1,108 @@
+{
+	"resourceType": "Parameters",
+	"id": "EXM130-7.3.000-end-to-end-submit-data-bundle",
+	"parameter": [
+		{
+			"name": "measureReport",
+			"resource": {
+				"resourceType": "MeasureReport",
+				"id": "col-measurereport-submit-data",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/datax-measurereport-deqm"
+					]
+				},
+				"extension": [
+					{
+						"url": "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/extension-submitDataUpdateType",
+						"valueCode": "incremental"
+					}
+				],
+				"status": "complete",
+				"type": "data-collection",
+				"measure": "http://ecqi.healthit.gov/ecqms/Measure/ColorectalCancerScreeningsFHIR",
+				"subject": {
+					"reference": "Patient/end-to-end-EXM130"
+				},
+				"date": "2021-01-01T16:59:52.404Z",
+				"reporter": {
+					"reference": "Organization/organization03"
+				},
+				"period": {
+					"start": "2019-01-01",
+					"end": "2019-12-31"
+				},
+				"evaluatedResource": [
+					{
+						"reference": "Procedure/end-to-end-EXM130-2"
+					}
+				]
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Encounter",
+				"id": "end-to-end-EXM130-2",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter"
+					]
+				},
+				"status": "finished",
+				"class": {
+					"system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+					"code": "AMB",
+					"display": "ambulatory"
+				},
+				"type": [
+					{
+						"coding": [
+							{
+								"system": "http://www.ama-assn.org/go/cpt",
+								"code": "99201",
+								"display": "Office or other outpatient visit for the evaluation and management of a new patient, which requires these 3 key components: A problem focused history; A problem focused examination; Straightforward medical decision making. Counseling and/or coordination of care with other physicians, other qualified health care professionals, or agencies are provided consistent with the nature of the problem(s) and the patient's and/or family's needs. Usually, the presenting problem(s) are self limited or minor. Typically, 10 minutes are spent face-to-face with the patient and/or family."
+							}
+						]
+					}
+				],
+				"subject": {
+					"reference": "Patient/end-to-end-EXM130"
+				},
+				"period": {
+					"start": "2020-05-01T09:00:00-06:00",
+					"end": "2020-05-01T14:00:00-06:00"
+				}
+			}
+		},
+		{
+			"name": "resource",
+			"resource": {
+				"resourceType": "Procedure",
+				"id": "end-to-end-EXM130-2",
+				"meta": {
+					"profile": [
+						"http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure"
+					]
+				},
+				"status": "completed",
+				"code": {
+					"coding": [
+						{
+							"system": "http://www.ama-assn.org/go/cpt",
+							"code": "44388",
+							"display": "Colonoscopy through stoma; with ablation of tumor(s), polyp(s), or other lesion(s) not amenable to removal by hot biopsy forceps, bipolar cautery or snare technique"
+						}
+					]
+				},
+				"subject": {
+					"reference": "Patient/end-to-end-EXM130"
+				},
+				"performedPeriod": {
+					"start": "2020-05-01T10:00:00-06:00",
+					"end": "2020-05-01T12:00:00-06:00"
+				}
+			}
+		}
+	]
+}

hapi-fhir-storage-cr/src/test/resources/gic-gr-1.json

@@ -0,0 +1,18 @@
+{
+	"resourceType": "Group",
+	"id": "gic-gr-1",
+	"meta": {
+		"profile": [
+			"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/gaps-group-deqm"
+		]
+	},
+	"type": "person",
+	"actual": true,
+	"member": [
+		{
+			"entity": {
+				"reference": "Patient/numer-EXM125"
+			}
+		}
+	]
+}

hapi-fhir-storage-cr/src/test/resources/gic-gr-parallel.json

@@ -0,0 +1,23 @@
+{
+	"resourceType": "Group",
+	"id": "gic-gr-parallel",
+	"meta": {
+		"profile": [
+			"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/gaps-group-deqm"
+		]
+	},
+	"type": "person",
+	"actual": true,
+	"member": [
+		{
+			"entity": {
+				"reference": "Patient/numer-EXM125"
+			}
+		},
+		{
+			"entity": {
+				"reference": "Patient/denom-EXM125"
+			}
+		}
+	]
+}

hapi-fhir-storage-cr/src/test/resources/numer-EXM125-patient.json

@@ -0,0 +1,63 @@
+{
+	"resourceType": "Patient",
+	"id": "numer-EXM125",
+	"meta": {
+		"profile": [
+			"http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"
+		]
+	},
+	"extension": [
+		{
+			"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+			"extension": [
+				{
+					"url": "ombCategory",
+					"valueCoding": {
+						"system": "urn:oid:2.16.840.1.113883.6.238",
+						"code": "2028-9",
+						"display": "Asian"
+					}
+				}
+			]
+		},
+		{
+			"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+			"extension": [
+				{
+					"url": "ombCategory",
+					"valueCoding": {
+						"system": "urn:oid:2.16.840.1.113883.6.238",
+						"code": "2135-2",
+						"display": "Hispanic or Latino"
+					}
+				}
+			]
+		}
+	],
+	"identifier": [
+		{
+			"use": "usual",
+			"type": {
+				"coding": [
+					{
+						"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+						"code": "MR",
+						"display": "Medical Record Number"
+					}
+				]
+			},
+			"system": "http://hospital.smarthealthit.org",
+			"value": "999999995"
+		}
+	],
+	"name": [
+		{
+			"family": "McCarren",
+			"given": [
+				"Karen"
+			]
+		}
+	],
+	"gender": "female",
+	"birthDate": "1965-01-01"
+}