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Merge pull request #259 from MeasureAuthoringTool/MAT-5932/addStratif…
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…icationtoQICoreTestCaseExportPatientBases

MAT-5932,MAT-7781 add stratification to QI Core testcase export
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@sb-prateekkeerthi
sb-prateekkeerthi authored Nov 20, 2024
2 parents 75fa6f5 + 2726e26 commit 44e23e6
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Showing 3 changed files with 316 additions and 42 deletions.
155 changes: 118 additions & 37 deletions src/main/java/gov/cms/madie/madiefhirservice/services/TestCaseBundleService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,19 +23,14 @@
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import gov.cms.madie.models.dto.TestCaseExportMetaData;
import gov.cms.madie.models.measure.*;
import gov.cms.madie.models.measure.Group;
import gov.cms.madie.models.measure.Measure;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DateFormatUtils;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Bundle;

import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.MarkdownType;
import org.hl7.fhir.r4.model.MeasureReport;
import org.hl7.fhir.r4.model.Meta;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.*;

import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.StringType;
import org.springframework.stereotype.Service;
import org.springframework.util.CollectionUtils;
import org.springframework.web.client.RestClientException;
Expand All @@ -51,8 +46,6 @@
import gov.cms.madie.madiefhirservice.utils.FhirResourceHelpers;
import gov.cms.madie.models.common.BundleType;
import gov.cms.madie.models.dto.ExportDTO;
import gov.cms.madie.models.measure.Measure;
import gov.cms.madie.models.measure.TestCase;
import gov.cms.madie.packaging.utils.PackagingUtility;
import gov.cms.madie.packaging.utils.PackagingUtilityFactory;
import lombok.RequiredArgsConstructor;
Expand Down Expand Up @@ -179,7 +172,7 @@ private MeasureReport buildMeasureReport(
getUTCDates(measure.getMeasurementPeriodStart()),
getUTCDates(measure.getMeasurementPeriodEnd())));

measureReport.setGroup(buildMeasureReportGroupComponents(testCase));
measureReport.setGroup(buildMeasureReportGroupComponents(testCase, measure.getGroups()));
measureReport.setEvaluatedResource(buildEvaluatedResource(testCaseBundle));
return measureReport;
}
Expand Down Expand Up @@ -241,53 +234,141 @@ private List<Extension> buildModifierExtension() {
}

private List<MeasureReport.MeasureReportGroupComponent> buildMeasureReportGroupComponents(
TestCase testCase) {
TestCase testCase, List<Group> groups) {
if (CollectionUtils.isEmpty(testCase.getGroupPopulations())) {
return List.of();
}
return testCase.getGroupPopulations().stream()
.map(
population -> {
var measureReportGroupComponent = new MeasureReport.MeasureReportGroupComponent();

measureReportGroupComponent.setId(population.getGroupId());
// adding populations
if (population.getPopulationValues() != null) {
var measureReportGroupPopulationComponents =
population.getPopulationValues().stream()
.map(
testCasePopulationValue -> {
String populationCode = testCasePopulationValue.getName().toCode();
String populationDisplay =
testCasePopulationValue.getName().getDisplay();
int expectedValue =
getExpectedValue(testCasePopulationValue.getExpected());
return (new MeasureReport.MeasureReportGroupPopulationComponent())
.setCode(
FhirResourceHelpers.buildCodeableConcept(
populationCode,
UriConstants.POPULATION_SYSTEM_URI,
populationDisplay))
.setCount(expectedValue);
var groupComponent =
(new MeasureReport.MeasureReportGroupPopulationComponent())
.setCode(
FhirResourceHelpers.buildCodeableConcept(
testCasePopulationValue.getName().toCode(),
UriConstants.POPULATION_SYSTEM_URI,
testCasePopulationValue.getName().getDisplay()))
.setCount(
FhirResourceHelpers.getExpectedValue(
testCasePopulationValue.getExpected()));
groupComponent.setId(testCasePopulationValue.getId());
return groupComponent;
})
.collect(Collectors.toList());
measureReportGroupComponent.setPopulation(measureReportGroupPopulationComponents);
}
// adding measure score
measureReportGroupComponent.setMeasureScore(
new Quantity()
.setValue(
StringUtils.equalsIgnoreCase("boolean", population.getPopulationBasis())
? 1.0
: 0));
// adding stratification for patient basis
if (population.getStratificationValues() != null) {
if (StringUtils.equalsIgnoreCase("boolean", population.getPopulationBasis())) {
measureReportGroupComponent.setStratifier(
buildGroupStratifierComponent(
population, groups, population.getGroupId(), true));
} else {
measureReportGroupComponent.setStratifier(
buildGroupStratifierComponent(population, null, null, false));
}
}
return measureReportGroupComponent;
})
.collect(Collectors.toList());
}

/**
* @param expectedValue expected value for a population, can be a string or boolean
* @return an equivalent integer
*/
private int getExpectedValue(Object expectedValue) {
if (expectedValue == null || StringUtils.isBlank(expectedValue.toString())) {
return 0;
} else if (expectedValue instanceof Boolean) {
return (Boolean) expectedValue ? 1 : 0;
private List<MeasureReport.MeasureReportGroupStratifierComponent> buildGroupStratifierComponent(
TestCaseGroupPopulation population,
List<Group> groups,
String populationGroupId,
boolean isPatientBased) {
return population.getStratificationValues().stream()
.map(
testCaseStratificationValue -> {
List<CodeableConcept> code = new ArrayList<CodeableConcept>();
var codeText =
isPatientBased
? getStratificationDefinition(
groups, populationGroupId, testCaseStratificationValue.getId())
: testCaseStratificationValue.getName();
code.add(new CodeableConcept().setText(codeText));

var stratifierComponent =
new MeasureReport.MeasureReportGroupStratifierComponent()
.setCode(code)
.setStratum(
buildStratum(
testCaseStratificationValue,
isPatientBased,
testCaseStratificationValue.getName()));
stratifierComponent.setId(testCaseStratificationValue.getId());
return stratifierComponent;
})
.collect(Collectors.toList());
}

private String getStratificationDefinition(
List<Group> groups, String populationId, String testCaseStratificationId) {
Group filteredGroup =
groups.stream()
.filter(group -> group.getId().equals(populationId))
.findFirst()
.orElse(null);
if (filteredGroup != null) {
return filteredGroup.getStratifications().stream()
.filter(stratification -> stratification.getId().equals(testCaseStratificationId))
.map(selectedStratification -> selectedStratification.getCqlDefinition())
.findFirst()
.orElse(null);
}
return null;
}

private List<MeasureReport.StratifierGroupComponent> buildStratum(
TestCaseStratificationValue testCaseStratificationValue,
boolean isPatientBased,
String testCaseStratificationName) {

// stratum
List<MeasureReport.StratifierGroupComponent> stratum =
new ArrayList<MeasureReport.StratifierGroupComponent>();

MeasureReport.StratifierGroupComponent stratifierGroupComponent =
new MeasureReport.StratifierGroupComponent();

if (isPatientBased) {
// when value is true
stratifierGroupComponent.setValue(new CodeableConcept().setText("true"));
stratifierGroupComponent.setPopulation(
FhirResourceHelpers.buildStratumPopulation(testCaseStratificationValue, true, true));
stratum.add(stratifierGroupComponent);

// when value is false (i.e., inverted )
MeasureReport.StratifierGroupComponent stratifierGroupComponentForInvertedValue =
new MeasureReport.StratifierGroupComponent();
stratifierGroupComponentForInvertedValue.setValue(new CodeableConcept().setText("false"));
stratifierGroupComponentForInvertedValue.setPopulation(
FhirResourceHelpers.buildStratumPopulation(testCaseStratificationValue, false, true));
stratum.add(stratifierGroupComponentForInvertedValue);
} else {
return Integer.parseInt(expectedValue.toString());
// Non-patient based measures
stratifierGroupComponent.setValue(new CodeableConcept().setText(testCaseStratificationName));
stratifierGroupComponent.setPopulation(
FhirResourceHelpers.buildStratumPopulation(testCaseStratificationValue, null, false));
stratum.add(stratifierGroupComponent);
}
return stratum;
}

/**
Expand Down
64 changes: 59 additions & 5 deletions src/main/java/gov/cms/madie/madiefhirservice/utils/FhirResourceHelpers.java
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Original file line number Diff line number Diff line change
@@ -1,16 +1,17 @@
package gov.cms.madie.madiefhirservice.utils;

import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
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.Period;
import org.hl7.fhir.r4.model.Resource;
import gov.cms.madie.madiefhirservice.constants.UriConstants;
import gov.cms.madie.models.measure.TestCaseStratificationValue;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.*;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Component;

import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.stream.Collectors;

@Component
public class FhirResourceHelpers {
Expand Down Expand Up @@ -62,6 +63,59 @@ public static CodeableConcept buildCodeableConcept(String code, String system, S
return codeableConcept;
}

/**
* @param expectedValue expected value for a population, can be a string or boolean
* @return an equivalent integer
*/
public static int getExpectedValue(Object expectedValue) {
if (expectedValue == null || StringUtils.isBlank(expectedValue.toString())) {
return 0;
} else if (expectedValue instanceof Boolean) {
return (Boolean) expectedValue ? 1 : 0;
} else {
return Integer.parseInt(expectedValue.toString());
}
}

public static int getExpectedInverseValue(int expectedValue) {
if (expectedValue == 0) {
return 1;
}
return 0;
}

public static List<MeasureReport.StratifierGroupPopulationComponent> buildStratumPopulation(
TestCaseStratificationValue testCaseStratificationValue,
Boolean valueIndex,
boolean isPatientBased) {
var measureTestCaseStratificationComponents =
testCaseStratificationValue.getPopulationValues().stream()
.map(
populationValue -> {
MeasureReport.StratifierGroupPopulationComponent
stratifierGroupPopulationComponent =
new MeasureReport.StratifierGroupPopulationComponent();

stratifierGroupPopulationComponent.setId(populationValue.getId());
stratifierGroupPopulationComponent.setCode(
buildCodeableConcept(
populationValue.getName().toCode(),
UriConstants.POPULATION_SYSTEM_URI,
populationValue.getName().getDisplay()));

stratifierGroupPopulationComponent.setCount(
isPatientBased
? (valueIndex
? getExpectedValue(populationValue.getExpected())
: getExpectedInverseValue(
getExpectedValue(populationValue.getExpected())))
: Integer.parseInt(populationValue.getExpected().toString()));
return stratifierGroupPopulationComponent;
})
.collect(Collectors.toList());
return measureTestCaseStratificationComponents;
}

public static Coding buildCoding(String code, String system, String display) {
return new Coding().setCode(code).setSystem(system).setDisplay(display);
}
Expand Down
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