Add more measure testing infrastructure, test cases for 104,105,108,124,125 (#2379)

hapi-fhir-jpaserver-cql/src/test/java/ca/uhn/fhir/cql/BaseCqlDstu3Test.java

@@ -73,10 +73,18 @@ public class BaseCqlDstu3Test extends BaseJpaDstu3Test implements CqlProviderTes
 		return count;
 	}
 
-	protected Bundle loadBundle(String theLocation) throws IOException {
+	protected Bundle parseBundle(String theLocation) throws IOException  {
 		String json = stringFromResource(theLocation);
 		Bundle bundle = (Bundle) myFhirContext.newJsonParser().parseResource(json);
-		Bundle result = (Bundle) mySystemDao.transaction(null, bundle);
-		return result;
+		return bundle;
+	}
+
+	protected Bundle loadBundle(Bundle bundle) {
+		return (Bundle) mySystemDao.transaction(null, bundle);
+	}
+ 
+	protected Bundle loadBundle(String theLocation) throws IOException {
+		Bundle bundle = parseBundle(theLocation);
+		return loadBundle(bundle);
 	}
 }

hapi-fhir-jpaserver-cql/src/test/java/ca/uhn/fhir/cql/BaseCqlR4Test.java

@@ -8,8 +8,11 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
 import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
+import ca.uhn.fhir.util.BundleUtil;
+
 import org.apache.commons.io.FileUtils;
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.MeasureReport;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -21,6 +24,7 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
 import java.io.File;
 import java.io.IOException;
 import java.util.Collection;
+import java.util.List;
 
 @ExtendWith(SpringExtension.class)
 @ContextConfiguration(classes = {CqlR4Config.class, TestCqlConfig.class, SubscriptionProcessorConfig.class})
@@ -72,11 +76,18 @@ public class BaseCqlR4Test extends BaseJpaR4Test implements CqlProviderTestBase
 		return count;
 	}
 
-	protected Bundle loadBundle(String theLocation) throws IOException {
+	protected Bundle parseBundle(String theLocation) throws IOException  {
 		String json = stringFromResource(theLocation);
 		Bundle bundle = (Bundle) myFhirContext.newJsonParser().parseResource(json);
-		Bundle result = (Bundle) mySystemDao.transaction(null, bundle);
-		return result;
+		return bundle;
 	}
 
+	protected Bundle loadBundle(Bundle bundle) {
+		return (Bundle) mySystemDao.transaction(null, bundle);
+	}
+ 
+	protected Bundle loadBundle(String theLocation) throws IOException {
+		Bundle bundle = parseBundle(theLocation);
+		return loadBundle(bundle);
+	}
 }

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

@@ -0,0 +1,144 @@
+package ca.uhn.fhir.cql.dstu3;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNull;
+
+import java.io.IOException;
+import java.math.BigDecimal;
+import java.util.Date;
+import java.util.List;
+import java.util.Optional;
+
+import org.hamcrest.Matchers;
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.DateTimeType;
+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.MeasureReport.MeasureReportGroupComponent;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import ca.uhn.fhir.cql.BaseCqlDstu3Test;
+import ca.uhn.fhir.cql.dstu3.provider.MeasureOperationsProvider;
+import ca.uhn.fhir.util.BundleUtil;
+
+public class CqlMeasureEvaluationDstu3Test extends BaseCqlDstu3Test {
+	Logger ourLog = LoggerFactory.getLogger(CqlMeasureEvaluationDstu3Test.class);
+
+	@Autowired
+	MeasureOperationsProvider myMeasureOperationsProvider;
+
+	protected void testMeasureBundle(String theLocation) throws IOException {
+		Bundle bundle = parseBundle(theLocation);
+		loadBundle(bundle);
+
+		List<Measure> measures = BundleUtil.toListOfResourcesOfType(myFhirContext, bundle, Measure.class);
+		if (measures == null || measures.isEmpty()) {
+			throw new IllegalArgumentException(String.format("No measures found for Bundle %s", theLocation));
+		}
+
+		List<MeasureReport> reports = BundleUtil.toListOfResourcesOfType(myFhirContext, bundle, MeasureReport.class);
+		if (reports == null || reports.isEmpty()) {
+			throw new IllegalArgumentException(String.format("No measure reports found for Bundle %s", theLocation));
+		}
+
+		for (MeasureReport report : reports) {
+			testMeasureReport(report);
+		}
+	}
+
+	protected void testMeasureReport(MeasureReport expected) {
+		String measureId = this.getMeasureId(expected);
+		String patientId = this.getPatientId(expected);
+		String periodStart = this.getPeriodStart(expected);
+		String periodEnd = this.getPeriodEnd(expected);
+
+		this.ourLog.info("Measure: %s, Patient: %s, Start: %s, End: %s", measureId, patientId, periodStart, periodEnd);
+
+		MeasureReport actual = this.myMeasureOperationsProvider.evaluateMeasure(new IdType("Measure", measureId),
+				periodStart, periodEnd, null,
+				// TODO: These are all individual reports
+				"patient", patientId,
+				// TODO: Generalize these parameters into a Parameters resource
+				null, null, null, null, null, null);
+
+		compareMeasureReport(expected, actual);
+	}
+
+	protected void compareMeasureReport(MeasureReport expected, MeasureReport actual) {
+		assertNotNull("expected MeasureReport can not be null", expected);
+		assertNotNull("actual MeasureReport can not be null", actual);
+
+		String errorLocator = String.format("Measure: %s, Subject: %s", expected.getMeasure(),
+				expected.getPatient().getReference());
+
+		assertEquals(expected.hasGroup(), actual.hasGroup(), errorLocator);
+		assertEquals(expected.getGroup().size(), actual.getGroup().size(), errorLocator);
+
+		for (MeasureReportGroupComponent mrgcExpected : expected.getGroup()) {
+			Optional<MeasureReportGroupComponent> mrgcActualOptional = actual.getGroup().stream()
+					.filter(x -> x.getId().equals(mrgcExpected.getId())).findFirst();
+
+			errorLocator = String.format("Measure: %s, Subject: %s, Group: %s", expected.getMeasure(),
+					expected.getPatient().getReference(), mrgcExpected.getId());
+			assertTrue(errorLocator, mrgcActualOptional.isPresent());
+
+			MeasureReportGroupComponent mrgcActual = mrgcActualOptional.get();
+
+			if (mrgcExpected.getMeasureScore() == null) {
+				assertNull(mrgcActual.getMeasureScore(), errorLocator);
+			} else {
+				assertNotNull(mrgcActual.getMeasureScore());
+				BigDecimal decimalExpected = mrgcExpected.getMeasureScore();
+				BigDecimal decimalActual = mrgcActual.getMeasureScore();
+
+				assertThat(errorLocator, decimalActual, Matchers.comparesEqualTo(decimalExpected));
+			}
+		}
+	}
+
+	public String getPatientId(MeasureReport measureReport) {
+		String[] subjectRefParts = measureReport.getPatient().getReference().split("/");
+		String patientId = subjectRefParts[subjectRefParts.length - 1];
+		return patientId;
+	}
+
+	public String getMeasureId(MeasureReport measureReport) {
+		String[] measureRefParts = measureReport.getMeasure().getReference().split("/");
+		String measureId = measureRefParts[measureRefParts.length - 1];
+		return measureId;
+	}
+
+	public String getPeriodStart(MeasureReport measureReport) {
+		Date periodStart = measureReport.getPeriod().getStart();
+		if (periodStart != null) {
+			return toDateString(periodStart);
+		}
+		return null;
+	}
+
+	public String getPeriodEnd(MeasureReport measureReport) {
+		Date periodEnd = measureReport.getPeriod().getEnd();
+		if (periodEnd != null) {
+			return toDateString(periodEnd);
+		}
+		return null;
+	}
+
+	public String toDateString(Date date) {
+		return new DateTimeType(date).getValueAsString();
+	}
+
+	// As of 2/11/2021, all the DSTU3 bundles in the Connectathon IG are out of date
+	// and can't be posted
+	// @Test
+	// public void test_EXM117_83000() throws IOException {
+	// 	this.testMeasureBundle("dstu3/connectathon/EXM117_FHIR3-8.3.000-bundle.json");
+	// }
+}

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

@@ -1,54 +1,208 @@
 package ca.uhn.fhir.cql.r4;
 
 import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.hasSize;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNull;
 
 import java.io.IOException;
-import java.math.BigDecimal;
+import java.util.Date;
+import java.util.List;
+import java.util.Optional;
 
+import org.hamcrest.Matchers;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.DateTimeType;
 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.MeasureReport.MeasureReportGroupComponent;
 import org.hl7.fhir.r4.model.Quantity;
-import org.hl7.fhir.r4.model.MeasureReport.MeasureReportGroupPopulationComponent;
-import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import ca.uhn.fhir.cql.BaseCqlR4Test;
-import ca.uhn.fhir.cql.common.provider.CqlProviderTestBase;
 import ca.uhn.fhir.cql.r4.provider.MeasureOperationsProvider;
+import ca.uhn.fhir.util.BundleUtil;
 
-public class CqlMeasureEvaluationR4Test extends BaseCqlR4Test implements CqlProviderTestBase {
-
-	private static final IdType measureId = new IdType("Measure", "measure-EXM130-7.3.000");
-	private static final String periodStart = "2019-01-01";
-	private static final String periodEnd = "2019-12-31";
+public class CqlMeasureEvaluationR4Test extends BaseCqlR4Test {
+	Logger ourLog = LoggerFactory.getLogger(CqlMeasureEvaluationR4Test.class);
 
 	@Autowired
 	MeasureOperationsProvider myMeasureOperationsProvider;
 
-	public void loadBundles() throws IOException {
-		loadBundle("r4/connectathon/EXM130-7.3.000-bundle.json");
+	protected void testMeasureBundle(String theLocation) throws IOException {
+		Bundle bundle = parseBundle(theLocation);
+		loadBundle(bundle);
+
+		List<Measure> measures = BundleUtil.toListOfResourcesOfType(myFhirContext, bundle, Measure.class);
+		if (measures == null || measures.isEmpty()) {
+			throw new IllegalArgumentException(String.format("No measures found for Bundle %s", theLocation));
+		}
+
+		List<MeasureReport> reports = BundleUtil.toListOfResourcesOfType(myFhirContext, bundle, MeasureReport.class);
+		if (reports == null || reports.isEmpty()) {
+			throw new IllegalArgumentException(String.format("No measure reports found for Bundle %s", theLocation));
+		}
+
+		for (MeasureReport report : reports) {
+			testMeasureReport(report);
+		}
+	}
+
+	protected void testMeasureReport(MeasureReport expected) {
+		String measureId = this.getMeasureId(expected);
+		String patientId = this.getPatientId(expected);
+		String periodStart = this.getPeriodStart(expected);
+		String periodEnd = this.getPeriodEnd(expected);
+
+		this.ourLog.info("Measure: %s, Patient: %s, Start: %s, End: %s", measureId, patientId, periodStart, periodEnd);
+
+		MeasureReport actual = this.myMeasureOperationsProvider.evaluateMeasure(new IdType("Measure", measureId),
+				periodStart, periodEnd, null,
+				// TODO: These are all individual reports
+				"patient", patientId,
+				// TODO: Generalize these parameters into a Parameters resource
+				null, null, null, null, null, null);
+
+		compareMeasureReport(expected, actual);
+	}
+
+	protected void compareMeasureReport(MeasureReport expected, MeasureReport actual) {
+		assertNotNull("expected MeasureReport can not be null", expected);
+		assertNotNull("actual MeasureReport can not be null", actual);
+
+		String errorLocator = String.format("Measure: %s, Subject: %s", expected.getMeasure(),
+				expected.getSubject().getReference());
+
+		assertEquals(expected.hasGroup(), actual.hasGroup(), errorLocator);
+		assertEquals(expected.getGroup().size(), actual.getGroup().size(), errorLocator);
+
+		for (MeasureReportGroupComponent mrgcExpected : expected.getGroup()) {
+			Optional<MeasureReportGroupComponent> mrgcActualOptional = actual.getGroup().stream()
+					.filter(x -> x.getId().equals(mrgcExpected.getId())).findFirst();
+
+			errorLocator = String.format("Measure: %s, Subject: %s, Group: %s", expected.getMeasure(),
+					expected.getSubject().getReference(), mrgcExpected.getId());
+			assertTrue(errorLocator, mrgcActualOptional.isPresent());
+
+			MeasureReportGroupComponent mrgcActual = mrgcActualOptional.get();
+
+			if (mrgcExpected.getMeasureScore() == null) {
+				assertNull(mrgcActual.getMeasureScore(), errorLocator);
+			} else {
+				assertNotNull(mrgcActual.getMeasureScore());
+				Quantity quantityExpected = mrgcExpected.getMeasureScore();
+				Quantity quantityActual = mrgcActual.getMeasureScore();
+
+				assertThat(errorLocator, quantityActual.getValue(), Matchers.comparesEqualTo(quantityExpected.getValue()));
+			}
+		}
+	}
+
+	// TODO: In R4 the Subject will not necessarily be a Patient.
+	public String getPatientId(MeasureReport measureReport) {
+		String[] subjectRefParts = measureReport.getSubject().getReference().split("/");
+		String patientId = subjectRefParts[subjectRefParts.length - 1];
+		return patientId;
+	}
+
+	public String getMeasureId(MeasureReport measureReport) {
+		String[] measureRefParts = measureReport.getMeasure().split("/");
+		String measureId = measureRefParts[measureRefParts.length - 1];
+		return measureId;
+	}
+
+	public String getPeriodStart(MeasureReport measureReport) {
+		Date periodStart = measureReport.getPeriod().getStart();
+		if (periodStart != null) {
+			return toDateString(periodStart);
+		}
+		return null;
+	}
+
+	public String getPeriodEnd(MeasureReport measureReport) {
+		Date periodEnd = measureReport.getPeriod().getEnd();
+		if (periodEnd != null) {
+			return toDateString(periodEnd);
+		}
+		return null;
+	}
+
+	public String toDateString(Date date) {
+		return new DateTimeType(date).getValueAsString();
+	}
+
+	// @Test - No test results in this bundle yet
+	// public void test_EXM74_102000() throws IOException {
+	// 	this.testMeasureBundle("r4/connectathon/EXM74-10.2.000-bundle.json");
+	// }
+
+	@Test
+	public void test_EXM105_82000() throws IOException {
+		this.testMeasureBundle("r4/connectathon/EXM105-8.2.000-bundle.json");
 	}
 
 	@Test
-	public void testExm130PatientNumerator() throws IOException {
-		loadBundles();
-		MeasureReport report = myMeasureOperationsProvider.evaluateMeasure(measureId, periodStart, periodEnd, null, "patient",
-			"numer-EXM130", null, null, null, null, null, null);
-		// Assert it worked
-		assertThat(report.getGroup(), hasSize(1));
-		assertEquals(new BigDecimal("1.0"), report.getGroupFirstRep().getMeasureScore().getValue());
+	public void test_EXM108_83000() throws IOException {
+		this.testMeasureBundle("r4/connectathon/EXM108-8.3.000-bundle.json");
+	}
+
+	// @Test - No test results in this bundle yet
+	// public void test_EXM111_91000() throws IOException {
+	// 	this.testMeasureBundle("r4/connectathon/EXM111-9.1.000-bundle.json");
+	// }
+
+	// @Test - The test data for the denominator exclusion appears to be invalid
+	// public void test_EXM124_82000() throws IOException {
+	// 	this.testMeasureBundle("r4/connectathon/EXM124-8.2.000-bundle.json");
+	// }
+
+	@Test
+	public void test_EXM124_90000() throws IOException {
+		this.testMeasureBundle("r4/connectathon/EXM124-9.0.000-bundle.json");
 	}
 
 	@Test
-	public void testExm130PatientDenominator() throws IOException {
-		loadBundles();
-		MeasureReport report = myMeasureOperationsProvider.evaluateMeasure(measureId, periodStart, periodEnd, null, "patient",
-			"denom-EXM130", null, null, null, null, null, null);
-		// Assert it worked
-		assertThat(report.getGroup(), hasSize(1));
-		assertEquals(new BigDecimal("0.0"), report.getGroupFirstRep().getMeasureScore().getValue());
+	public void test_EXM125_73000() throws IOException {
+		this.testMeasureBundle("r4/connectathon/EXM125-7.3.000-bundle.json");
 	}
+
+	@Test
+	public void test_EXM130_73000() throws IOException {
+		this.testMeasureBundle("r4/connectathon/EXM130-7.3.000-bundle.json");
+	}
+
+	// @Test - No test results in this bundle yet
+	// public void test_EXM149_92000() throws IOException {
+	// 	this.testMeasureBundle("r4/connectathon/EXM149-9.2.000-bundle.json");
+	// }
+
+	// @Test - Missing Adult outpatient encounters Library
+	// public void test_EXM153_92000() throws IOException {
+	// 	this.testMeasureBundle("r4/connectathon/EXM153-9.2.000-bundle.json");
+	// }
+
+	// @Test - Missing Encounter data for Numerator test
+	// public void test_EXM347_43000() throws IOException {
+	// 	this.testMeasureBundle("r4/connectathon/EXM347-4.3.000-bundle.json");
+	// }
+
+	// @Test - No test results in this bundle yet
+	// public void test_EXM349_210000() throws IOException {
+	// 	this.testMeasureBundle("r4/connectathon/EXM349-2.10.000-bundle.json");
+	// }
+
+	// @Test - No test results in this bundle yet
+	// public void test_EXM506_22000() throws IOException {
+	// 	this.testMeasureBundle("r4/connectathon/EXM506-2.2.000-bundle.json");
+	// }
+
+	// @Test - No test results in this bundle yet
+	// public void test_EXM529_10000() throws IOException {
+	// 	this.testMeasureBundle("r4/connectathon/EXM529-1.0.000-bundle.json");
+	// }
 }