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Merge branch 'master' into br-fix-dupliate-namespace
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@JPercival
JPercival authored Sep 27, 2024
2 parents be89809 + 6e14c44 commit f3d2dba
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Showing 33 changed files with 26,353 additions and 109 deletions.
2 changes: 2 additions & 0 deletions cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/constant/CareGapsConstants.java
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Expand Up @@ -17,6 +17,8 @@ private CareGapsConstants() {
"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_DETECTED_ISSUE_MR_GROUP_ID =
"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/gaps-detectedissue-mr-group-id-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 =
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3 changes: 3 additions & 0 deletions ...hir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/constant/MeasureReportConstants.java
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Expand Up @@ -10,6 +10,9 @@ private MeasureReportConstants() {}

public static final String MEASUREREPORT_IMPROVEMENT_NOTATION_SYSTEM =
"http://terminology.hl7.org/CodeSystem/measure-improvement-notation";

public static final String MEASUREREPORT_IMPROVEMENT_NOTATION_EXTENSION =
"http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-improvementNotation";
public static final String MEASUREREPORT_MEASURE_POPULATION_SYSTEM =
"http://terminology.hl7.org/CodeSystem/measure-population";
public static final String MEASUREREPORT_MEASURE_SUPPLEMENTALDATA_EXTENSION =
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44 changes: 38 additions & 6 deletions cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4CareGapStatusEvaluator.java
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Expand Up @@ -3,10 +3,13 @@
import static org.opencds.cqf.fhir.cr.measure.constant.MeasureReportConstants.MEASUREREPORT_IMPROVEMENT_NOTATION_SYSTEM;
import static org.opencds.cqf.fhir.cr.measure.constant.MeasureReportConstants.MEASUREREPORT_MEASURE_POPULATION_SYSTEM;

import java.util.HashMap;
import java.util.Map;
import org.apache.commons.lang3.tuple.MutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.r4.model.Measure;
import org.hl7.fhir.r4.model.MeasureReport;
import org.hl7.fhir.r4.model.MeasureReport.MeasureReportGroupComponent;
import org.opencds.cqf.fhir.cr.measure.enumeration.CareGapsStatusCode;

/**
Expand All @@ -28,8 +31,8 @@ public class R4CareGapStatusEvaluator {
* Improvement Notation of Scoring Algorithm indicates whether the ratio of Numerator over Denominator populations represents a scenario to increase the Numerator to improve outcomes, or to decrease the Numerator count. If this value is not set on a Measure resource, then it is defaulted to 'Increase' under the IsPositive variable.
* </p>
* <ul>
* <li>ex: 1/10 with improvementNotation "decrease" means that the measureScore is 90%, therefore absense from 'Numerator' means criteria for care was met</li>
* <li>ex: 1/10 with improvementNotation "increase" means that the measureScore is 10%, therefore absense from 'Numerator' means criteria for care was NOT met.</li>
* <li>ex: 1/10 with improvementNotation "decrease" means that the measureScore is 90%, therefore absence from 'Numerator' means criteria for care was met</li>
* <li>ex: 1/10 with improvementNotation "increase" means that the measureScore is 10%, therefore absence from 'Numerator' means criteria for care was NOT met.</li>
* </ul>
* <ul>
* <li>'open-gap': if in 'Denominator' & NOT in 'Numerator', where 'improvement notation' = increase. Then the subject is 'open-gap'</li>
Expand All @@ -38,10 +41,23 @@ public class R4CareGapStatusEvaluator {
* <li>'closed-gap': if in 'Denominator' & in 'Numerator', where 'improvement notation' = increase. Then the subject is 'closed-gap'</li>
* </ul>
*/
public CareGapsStatusCode getGapStatus(Measure measure, MeasureReport measureReport) {
public Map<String, CareGapsStatusCode> getGroupGapStatus(Measure measure, MeasureReport measureReport) {
Map<String, CareGapsStatusCode> groupStatus = new HashMap<>();

for (MeasureReportGroupComponent group : measureReport.getGroup()) {
var groupId = group.getId();
var gapStatus = getGapStatus(measure, group);

groupStatus.put(groupId, gapStatus);
}
return groupStatus;
}

private CareGapsStatusCode getGapStatus(Measure measure, MeasureReportGroupComponent measureReportGroup) {
Pair<String, Boolean> inNumerator = new MutablePair<>("numerator", false);
Pair<String, Boolean> inDenominator = new MutablePair<>("denominator", false);
measureReport.getGroup().forEach(group -> group.getPopulation().forEach(population -> {
// get Numerator and Denominator membership
measureReportGroup.getPopulation().forEach(population -> {
if (population.hasCode()
&& population.getCode().hasCoding(MEASUREREPORT_MEASURE_POPULATION_SYSTEM, inNumerator.getKey())
&& population.getCount() == 1) {
Expand All @@ -52,12 +68,15 @@ public CareGapsStatusCode getGapStatus(Measure measure, MeasureReport measureRep
&& population.getCount() == 1) {
inDenominator.setValue(true);
}
}));
});

// default improvementNotation
boolean isPositive = true;

// if value is present, set value from measure if populated
// TODO: look for group specified 'improvement notation', if missing, then look on measure
/*if (groupHasImprovementNotation(measureReportGroup)) {
isPositive = groupImprovementNotationIsPositive(measureReportGroup);
} else if (measure.hasImprovementNotation()) {*/
if (measure.hasImprovementNotation()) {
isPositive =
measure.getImprovementNotation().hasCoding(MEASUREREPORT_IMPROVEMENT_NOTATION_SYSTEM, "increase");
Expand All @@ -75,4 +94,17 @@ public CareGapsStatusCode getGapStatus(Measure measure, MeasureReport measureRep

return CareGapsStatusCode.CLOSED_GAP;
}

/*
// TODO implement Measure Group Level improvement notation extension
private boolean groupHasImprovementNotation(MeasureReportGroupComponent groupComponent) {
return groupComponent.getExtensionByUrl(MEASUREREPORT_IMPROVEMENT_NOTATION_EXTENSION) != null;
}
private boolean groupImprovementNotationIsPositive(MeasureReportGroupComponent groupComponent) {
var code = (CodeableConcept) groupComponent
.getExtensionByUrl(MEASUREREPORT_IMPROVEMENT_NOTATION_EXTENSION)
.getValue();
return code.hasCoding(MEASUREREPORT_IMPROVEMENT_NOTATION_SYSTEM, "increase");
}*/
}
64 changes: 53 additions & 11 deletions cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4CareGapsBundleBuilder.java
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Expand Up @@ -3,6 +3,7 @@
import static org.opencds.cqf.fhir.cr.measure.common.MeasureConstants.EXT_SDE_REFERENCE_URL;
import static org.opencds.cqf.fhir.cr.measure.constant.CareGapsConstants.CARE_GAPS_BUNDLE_PROFILE;
import static org.opencds.cqf.fhir.cr.measure.constant.CareGapsConstants.CARE_GAPS_COMPOSITION_PROFILE;
import static org.opencds.cqf.fhir.cr.measure.constant.CareGapsConstants.CARE_GAPS_DETECTED_ISSUE_MR_GROUP_ID;
import static org.opencds.cqf.fhir.cr.measure.constant.CareGapsConstants.CARE_GAPS_DETECTED_ISSUE_PROFILE;
import static org.opencds.cqf.fhir.cr.measure.constant.CareGapsConstants.CARE_GAPS_GAP_STATUS_EXTENSION;
import static org.opencds.cqf.fhir.cr.measure.constant.CareGapsConstants.CARE_GAPS_GAP_STATUS_SYSTEM;
Expand All @@ -17,6 +18,7 @@
import com.google.common.collect.ImmutableMap;
import jakarta.annotation.Nullable;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
Expand All @@ -40,6 +42,7 @@
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.StringType;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cr.measure.CareGapsProperties;
import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
Expand Down Expand Up @@ -146,15 +149,22 @@ public Bundle makePatientBundle(Bundle bundle, List<String> statuses, Patient pa
addResourceId(mr);
Measure measure = r4MeasureServiceUtils.resolveByUrl(mr.getMeasure());
// Applicable Reports per Gap-Status
var gapStatus = gapEvaluator.getGapStatus(measure, mr);
boolean keepResult = statuses.contains(gapStatus.toString());
if (keepResult) {
var gapStatus = gapEvaluator.getGroupGapStatus(measure, mr);
var filteredGapStatus = filteredGapStatus(gapStatus, statuses);
if (!filteredGapStatus.isEmpty()) {
// add Report to final Care-gap report
measureReports.add(mr);
// Issue Detected for Report
DetectedIssue detectedIssue = getDetectedIssue(patient, mr, gapStatus);
detectedIssues.add(getDetectedIssue(patient, mr, gapStatus));
composition.addSection(getSection(measure, mr, detectedIssue, gapStatus));
// Issue(s) Detected from MeasureReport
for (Map.Entry<String, CareGapsStatusCode> item : filteredGapStatus.entrySet()) {
String groupId = item.getKey();
CareGapsStatusCode careGapsStatusCode = item.getValue();
// create DetectedIssue per gap-status and MeasureReport.groupId
DetectedIssue issue = getDetectedIssue(patient, mr, groupId, careGapsStatusCode);
// add DetectedIssue list to set on Bundle
detectedIssues.add(issue);
// add sections for DetectedIssues created
composition.addSection(getSection(measure, mr, issue, careGapsStatusCode));
}
// Track evaluated Resources
populateEvaluatedResources(mr, evalPlusSDE);
populateSDEResources(mr, evalPlusSDE);
Expand All @@ -170,6 +180,20 @@ public Bundle makePatientBundle(Bundle bundle, List<String> statuses, Patient pa
}
}

private Map<String, CareGapsStatusCode> filteredGapStatus(
Map<String, CareGapsStatusCode> careGapStatusPerGroupId, List<String> statuses) {
Map<String, CareGapsStatusCode> filtered = new HashMap<>();
for (Map.Entry<String, CareGapsStatusCode> entry : careGapStatusPerGroupId.entrySet()) {
String groupId = entry.getKey();
CareGapsStatusCode careGapsStatusCode = entry.getValue();
// check resulting status for report groups is in operation request 'statuses'
if (statuses.contains(careGapsStatusCode.toString())) {
filtered.put(groupId, careGapsStatusCode);
}
}
return filtered;
}

private Bundle.BundleEntryComponent getBundleEntry(String serverBase, Resource resource) {
return new Bundle.BundleEntryComponent().setResource(resource).setFullUrl(getFullUrl(serverBase, resource));
}
Expand Down Expand Up @@ -203,9 +227,17 @@ private Composition getComposition(Patient patient) {
.build();
}

private boolean isMultiRateMeasure(MeasureReport measureReport) {
return measureReport.getGroup().size() > 1;
}

private DetectedIssue getDetectedIssue(
Patient patient, MeasureReport measureReport, CareGapsStatusCode careGapStatusCode) {
return new DetectedIssueBuilder<>(DetectedIssue.class)
Patient patient,
MeasureReport measureReport,
String measureReportGroupId,
CareGapsStatusCode careGapsStatusCode) {

var detectedIssue = 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"))
Expand All @@ -216,9 +248,19 @@ private DetectedIssue getDetectedIssue(
new CodeableConceptSettings()
.add(
CARE_GAPS_GAP_STATUS_SYSTEM,
careGapStatusCode.toString(),
careGapStatusCode.toDisplayString())))
careGapsStatusCode.toString(),
careGapsStatusCode.toDisplayString())))
.build();

if (measureReportGroupId != null && isMultiRateMeasure(measureReport)) {
// MeasureReportGroupComponent.id value set here to differentiate between DetectedIssue resources for the
// same MeasureReport
Extension groupIdExt = new Extension();
groupIdExt.setUrl(CARE_GAPS_DETECTED_ISSUE_MR_GROUP_ID);
groupIdExt.setValue(new StringType(measureReportGroupId));
detectedIssue.setExtension(Collections.singletonList(groupIdExt));
}
return detectedIssue;
}

private void populateEvaluatedResources(MeasureReport measureReport, Map<String, Resource> resources) {
Expand Down
29 changes: 29 additions & 0 deletions cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4CareGapsProcessor.java
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Expand Up @@ -14,6 +14,7 @@
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Measure;
import org.hl7.fhir.r4.model.Measure.MeasureGroupComponent;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.PrimitiveType;
Expand Down Expand Up @@ -154,6 +155,34 @@ private void measureCompatibilityCheck(List<Measure> measures) {
for (Measure measure : measures) {
checkMeasureScoringType(measure);
checkMeasureImprovementNotation(measure);
checkMeasureBasis(measure);
checkMeasureGroupComponents(measure);
}
}

private void checkMeasureBasis(Measure measure) {
R4MeasureBasisDef measureDef = new R4MeasureBasisDef();
if (!measureDef.isBooleanBasis(measure)) {
throw new IllegalArgumentException(
String.format("CareGaps can't process Measure: %s, it is not Boolean basis.", measure.getIdPart()));
}
}

/**
* MultiRate Measures require a unique 'id' per GroupComponent to uniquely identify results in Measure Report.
* This is helpful when creating DetectedIssues per GroupComponent so endUsers can attribute evidence of a Care-Gap to the specific MeasureReport result
* @param measure Measure resource
*/
private void checkMeasureGroupComponents(Measure measure) {
// if a Multi-rate Measure, enforce groupId to be populated
if (measure.getGroup().size() > 1) {
for (MeasureGroupComponent group : measure.getGroup()) {
if (measure.getGroup().size() > 1
&& (group.getId() == null || group.getId().isEmpty())) {
throw new IllegalArgumentException(
"Multi-rate Measure resources require unique 'id' for GroupComponents to be populated.");
}
}
}
}

Expand Down
2 changes: 1 addition & 1 deletion cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/measure/r4/DataRequirementsTest.java
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Expand Up @@ -56,7 +56,7 @@ void dataRequirements_booleanBasisMeasure_noPeriod() {
.DataRequirements()
.then()
.hasDataRequirementCount(1)
.hasParameterDefCount(11)
.hasParameterDefCount(13)
.hasRelatedArtifactCount(1)
.report();
}
Expand Down
103 changes: 103 additions & 0 deletions cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/measure/r4/R4CareGapsTest.java
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Expand Up @@ -507,4 +507,107 @@ void ContinuousVariable_ScoringTypeError() {
"MeasureScoring type: Continuous Variable, is not an accepted Type for care-gaps service"));
}
}

// MinimalProportionResourceBasisSingleGroup
@Test
void MinimalProportionResourceBasisSingleGroup_Subject() {
try {
GIVEN_REPO
.when()
.subject("Patient/female-1988")
.periodStart("2024-01-01")
.periodEnd("2024-12-31")
.measureIds("MinimalProportionResourceBasisSingleGroup")
.statuses("closed-gap")
.statuses("open-gap")
.getCareGapsReport()
.then()
.hasBundleCount(1);
fail("resource based measures should fail");
} catch (IllegalArgumentException e) {
Assertions.assertTrue(
e.getMessage()
.contains(
"CareGaps can't process Measure: MinimalProportionResourceBasisSingleGroup, it is not Boolean basis"));
}
}

@Test
void MinimalProportionBooleanBasisMultiGroup() {
GIVEN_REPO
.when()
.subject("Patient/female-1988")
.periodStart("2019-01-01")
.periodEnd("2019-12-31")
.measureIds("MinimalProportionBooleanBasisMultiGroup")
.statuses("closed-gap")
.statuses("open-gap")
.statuses("not-applicable")
.getCareGapsReport()
.then()
.hasBundleCount(1)
.firstParameter()
.detectedIssueCount(2); // 1 Detected issue per groupId
}

@Test
void MinimalProportionBooleanBasisMultiGroupDifferentStatus() {
GIVEN_REPO
.when()
.subject("Patient/female-1988")
.periodStart("2019-01-01")
.periodEnd("2019-12-31")
.measureIds("MinimalProportionBooleanBasisMultiGroupDifferentStatus")
.statuses("closed-gap")
.getCareGapsReport()
.then()
.hasBundleCount(1)
.firstParameter()
.detectedIssueCount(
1); // 2 Detected issue per groupId, 1 open-gap, 1 closed-gap. Only "closed-gap" should show
}

@Test
void MinimalProportionBooleanBasisMultiGroup_NoId() {
try {
GIVEN_REPO
.when()
.subject("Patient/female-1988")
.periodStart("2019-01-01")
.periodEnd("2019-12-31")
.measureIds("MinimalProportionBooleanBasisMultiGroupNoGroupId")
.statuses("closed-gap")
.statuses("open-gap")
.statuses("not-applicable")
.getCareGapsReport()
.then()
.hasBundleCount(1)
.firstParameter()
.detectedIssueCount(2); // 1 Detected issue per groupId
fail("this should fail without a groupId");
} catch (IllegalArgumentException e) {
Assertions.assertTrue(e.getMessage()
.contains("Multi-rate Measure resources require unique 'id' for GroupComponents to be populated."));
}
}

/*
// TODO implement Measure Group Level improvement notation extension
@Test
void MinimalProportionBooleanBasisMultiGroupGroupImpNotation() {
GIVEN_REPO
.when()
.subject("Patient/female-1988")
.periodStart("2019-01-01")
.periodEnd("2019-12-31")
.measureIds("MinimalProportionBooleanBasisMultiGroupGroupImpNotation")
.statuses("closed-gap")
.getCareGapsReport()
.then()
.hasBundleCount(1)
.firstParameter()
.detectedIssueCount(
2); // 2 Detected issue per groupId, one is decrease, the other increase improvement Notation. Both should be closed-gap
}
*/
}
8 changes: 7 additions & 1 deletion ...r/cr/measure/r4/MinimalMeasureEvaluation/cql/MinimalProportionBooleanBasisSingleGroup.cql
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Expand Up @@ -32,4 +32,10 @@ define "Measure Population":
"Denominator"

define "date of compliance":
"Measurement Period"
"Measurement Period"

define "always false":
false

define "always true":
true
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