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BS 290 | Dosage Validation (IHTSDO#12)
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* added route and dose unti check

* updated roa dosage flow

* updated message template and other feedback comments

* Added dosage route and dose unit cdss card flow and misconfigured medications flow

Updated test cases for the same

* BS-290 | Mani | Updated test method names suggested in review
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@manimaarans
manimaarans committed Nov 16, 2023
1 parent 304c361 commit 098ea49
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86 changes: 63 additions & 23 deletions ...rg/snomed/cdsservice/service/medication/dose/SnomedMedicationDefinedDailyDoseService.java
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Expand Up @@ -2,6 +2,7 @@

import jakarta.annotation.PostConstruct;
import net.steppschuh.markdowngenerator.list.UnorderedList;
import net.steppschuh.markdowngenerator.list.UnorderedListItem;
import net.steppschuh.markdowngenerator.text.Text;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.Coding;
Expand Down Expand Up @@ -38,7 +39,6 @@
import java.io.FileReader;
import java.math.BigDecimal;
import java.math.RoundingMode;
import java.text.DecimalFormat;
import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.Collections;
Expand Down Expand Up @@ -72,6 +72,9 @@ public class SnomedMedicationDefinedDailyDoseService {
public static final String INFO = "info";
private static final String NEW_LINE = "\n";
private static final String HIGH_DOSAGE_ALERT_TYPE = "High Dosage";
private static final String INVALID_DOSAGE_ALERT_TYPE = "Validation Error";
private static final String DOSAGE_EXCEPTION_DOSE_INPUT = "dose unit";
private static final String DOSAGE_EXCEPTION_ROUTE_INPUT = "dose route";

@Autowired
private FHIRTerminologyServerClient tsClient;
Expand Down Expand Up @@ -147,8 +150,18 @@ public List<CDSCard> checkMedications(List<MedicationRequest> medicationRequests
if (snomedMedication.isPresent()) {
String snomedMedicationCode = snomedMedication.get().getCode();
String snomedMedicationLabel = snomedMedication.get().getDisplay();

ConceptParameters conceptParameters = tsClient.lookup(SNOMEDCT_SYSTEM, snomedMedicationCode);
if ("NA".equals(doseQuantity.getUnit())) {
logger.debug("Prescribed dosage could not be validated for {}. Reason: Dose unit unknown to CDSS.", snomedMedicationLabel);
continue;
}
ConceptParameters conceptParameters = null;
try {
conceptParameters = tsClient.lookup(SNOMEDCT_SYSTEM, snomedMedicationCode);
} catch (Exception e) {
String errorMessage = String.format("Bahmni->SNOMED mapping is misconfigured for medication %s.", snomedMedicationLabel);
logger.error(errorMessage);
throw new ResponseStatusException(HttpStatus.PRECONDITION_FAILED, errorMessage, null);
}
if (conceptParameters == null) {
logger.debug("No SNOMED concept found for code {}, ignoring.", snomedMedicationCode);
continue;
Expand Down Expand Up @@ -176,7 +189,13 @@ public List<CDSCard> checkMedications(List<MedicationRequest> medicationRequests
logger.info("SNOMED dose form {} is not covered by the route of administration dynamic map, skipping", manufacturedDoseForm);
continue;
}
aggregateMedicationsBySubstance(aggregatedMedicationsBySubstanceMap, prescribedDailyDose, codingList, snomedMedicationLabel, atcRouteOfAdministrationCode, routeOfAdministrationLabel, normalForm);
if (!(dosage.getRoute() != null && atcRouteOfAdministrationCode.equals(dosage.getRoute().getText()))) {
String expectedUnit = atcRouteOfAdministrationCode + (routeOfAdministrationLabel.equals(atcRouteOfAdministrationCode) ? "" : " (" + routeOfAdministrationLabel.trim() + ")" );
logger.info("Expected route {} for medication {}", expectedUnit, snomedMedicationLabel);
composeCdssCardForDosageMismatch(cards, snomedMedicationLabel, codingList, expectedUnit, false);
continue;
}
aggregateMedicationsBySubstance(aggregatedMedicationsBySubstanceMap, prescribedDailyDose, codingList, snomedMedicationLabel, atcRouteOfAdministrationCode, routeOfAdministrationLabel, normalForm, cards);
}
}
composeDosageAlerts(aggregatedMedicationsBySubstanceMap, cards);
Expand Down Expand Up @@ -241,7 +260,7 @@ private void updateTotalPrescribedDailyDose(AggregatedMedicationsBySubstance agg
}
}

private void aggregateMedicationsBySubstance(Map<String, AggregatedMedicationsBySubstance> aggregatedMedicationsBySubstanceMap, PrescribedDailyDose prescribedDailyDose, List<Coding> codingList, String snomedMedicationLabel, String atcRouteOfAdministrationCode, String routeOfAdministrationLabel, SnomedConceptNormalForm normalForm) {
private void aggregateMedicationsBySubstance(Map<String, AggregatedMedicationsBySubstance> aggregatedMedicationsBySubstanceMap, PrescribedDailyDose prescribedDailyDose, List<Coding> codingList, String snomedMedicationLabel, String atcRouteOfAdministrationCode, String routeOfAdministrationLabel, SnomedConceptNormalForm normalForm, List<CDSCard> cards) {
// The substances within the clinical drug concepts are contained within attribute groups
for (Map<String, String> attributeGroup : normalForm.getAttributeGroups()) {
String substance = attributeGroup.get(ATTRIBUTE_HAS_BASIS_OF_STRENGTH_SUBSTANCE);
Expand Down Expand Up @@ -287,10 +306,11 @@ private void aggregateMedicationsBySubstance(Map<String, AggregatedMedicationsBy
PrescribedDailyDose prescribedDailyDoseInUnitOfSubstanceStrength;
PrescribedDailyDose prescribedDailyDoseInUnitOfDDD;
try {
prescribedDailyDoseInUnitOfSubstanceStrength = getPrescribedDailyDoseInUnitOfSubstanceStrength(prescribedDailyDose, strengthValue, strengthUnit, denominatorValue, denominatorUnit);
prescribedDailyDoseInUnitOfDDD = getPrescribedDailyDoseInUnitOfDDD(prescribedDailyDoseInUnitOfSubstanceStrength.getQuantity(), prescribedDailyDoseInUnitOfSubstanceStrength.getUnit(), substanceDefinedDailyDose.unit());
prescribedDailyDoseInUnitOfSubstanceStrength = getPrescribedDailyDoseInUnitOfSubstanceStrength(prescribedDailyDose, strengthValue, strengthUnit, denominatorValue, denominatorUnit, cards, snomedMedicationLabel, codingList);
prescribedDailyDoseInUnitOfDDD = getPrescribedDailyDoseInUnitOfDDD(prescribedDailyDoseInUnitOfSubstanceStrength.getQuantity(), prescribedDailyDoseInUnitOfSubstanceStrength.getUnit(), substanceDefinedDailyDose.unit(), cards, snomedMedicationLabel, codingList);
} catch (Exception e) {
throw new ResponseStatusException(HttpStatus.PRECONDITION_FAILED, String.format("Prescribed dosage could not be validated for %s. Reason: Invalid dose unit.", snomedMedicationLabel), null);
logger.debug(String.format("Prescribed dosage could not be validated for %s. Reason: Invalid dose unit.", snomedMedicationLabel));
continue;
}
AggregatedMedicationsBySubstance aggregatedMedicationsBySubstance = aggregatedMedicationsBySubstanceMap.get(substance);
if (aggregatedMedicationsBySubstance == null) {
Expand All @@ -305,6 +325,25 @@ private void aggregateMedicationsBySubstance(Map<String, AggregatedMedicationsBy
}
}

private void composeCdssCardForDosageMismatch(List<CDSCard> cards, String medicationLabel, List<Coding> codingList, String expectedUnit, boolean isDoseUnit) {
UUID randomUuid = UUID.fromString(UUID.nameUUIDFromBytes(medicationLabel.getBytes()).toString());
String invalidMessage = isDoseUnit ? DOSAGE_EXCEPTION_DOSE_INPUT : DOSAGE_EXCEPTION_ROUTE_INPUT;
Optional<CDSCard> optionalCard = cards.stream().filter(cdsCard -> cdsCard.getUuid().equals(randomUuid.toString())).findFirst();
String cardDetailMsg = "Expected %s for %s";
cardDetailMsg = new UnorderedListItem(String.format(cardDetailMsg, expectedUnit, invalidMessage)).toString();
String cardSummaryMessage = String.format("One or more dose Inputs are invalid for %s", medicationLabel);
if(optionalCard.isEmpty()) {
CDSCard cdsCard = new CDSCard(randomUuid.toString(), cardSummaryMessage, NEW_LINE + cardDetailMsg, CDSIndicator.valueOf(WARNING), new CDSSource("DummyService", null), Collections.singletonList(new CDSReference(getCodings(codingList))), null, INVALID_DOSAGE_ALERT_TYPE);
cards.add(cdsCard);
return;
}
CDSCard card = optionalCard.get();
if(!card.getDetail().contains(invalidMessage)) {
card.setDetail(card.getDetail() + NEW_LINE + cardDetailMsg);
}

}

void composeDosageAlerts(Map<String, AggregatedMedicationsBySubstance> aggregatedMedicationsBySubstanceMap, List<CDSCard> cards) {
for (var aggregatedMedicationsBySubstanceEntry : aggregatedMedicationsBySubstanceMap.entrySet()) {
String substanceName = aggregatedMedicationsBySubstanceEntry.getValue().getSubstanceShortName();
Expand Down Expand Up @@ -360,24 +399,34 @@ private void addMedications(AggregatedMedicationsBySubstance aggregatedMedicatio
}
}

private PrescribedDailyDose getPrescribedDailyDoseInUnitOfSubstanceStrength(PrescribedDailyDose prescribedDailyDose, String strengthValue, String strengthUnit, String denominatorValue, String denominatorUnit) {
private PrescribedDailyDose getPrescribedDailyDoseInUnitOfSubstanceStrength(PrescribedDailyDose prescribedDailyDose, String strengthValue, String strengthUnit, String denominatorValue, String denominatorUnit, List<CDSCard> cards, String medicationLabel, List<Coding> codingList) {
BigDecimal prescribedDoseQuantity = prescribedDailyDose.getQuantity();
String prescribedDisplayUnit = prescribedDailyDose.getUnit();

String strengthDisplayUnit = getSnomedParameterValue(strengthUnit, "display");
String denominatorDisplayUnit = getSnomedParameterValue(denominatorUnit, "display");
BigDecimal prescribedDoseQuantityInUnitOfSubstanceStrength = prescribedDoseQuantity.multiply((new BigDecimal(strengthValue)).divide(new BigDecimal(denominatorValue))).multiply(new BigDecimal(UnitConversion.factorOfConversion(prescribedDisplayUnit, denominatorDisplayUnit)));
return new PrescribedDailyDose(prescribedDoseQuantityInUnitOfSubstanceStrength, strengthDisplayUnit);
try {
BigDecimal prescribedDoseQuantityInUnitOfSubstanceStrength = prescribedDoseQuantity.multiply((new BigDecimal(strengthValue)).divide(new BigDecimal(denominatorValue))).multiply(new BigDecimal(UnitConversion.factorOfConversion(prescribedDisplayUnit, denominatorDisplayUnit)));
return new PrescribedDailyDose(prescribedDoseQuantityInUnitOfSubstanceStrength, strengthDisplayUnit);
} catch (Exception e) {
composeCdssCardForDosageMismatch(cards, medicationLabel, codingList, denominatorDisplayUnit, true);
throw new RuntimeException(e);
}
}

private String getSnomedParameterValue(String snomedCode, String parameterName) {
ConceptParameters conceptParameters = tsClient.lookup(SNOMEDCT_SYSTEM, snomedCode);
return conceptParameters.getParameter(parameterName).getValue().toString();
}

private PrescribedDailyDose getPrescribedDailyDoseInUnitOfDDD(BigDecimal inputStrengthValue, String inputStrengthUnit, String targetStrengthUnit) {
BigDecimal prescribedDailyDoseQuantity = inputStrengthValue.multiply(new BigDecimal(UnitConversion.factorOfConversion(inputStrengthUnit, targetStrengthUnit)));
return new PrescribedDailyDose(prescribedDailyDoseQuantity, targetStrengthUnit);
private PrescribedDailyDose getPrescribedDailyDoseInUnitOfDDD(BigDecimal inputStrengthValue, String inputStrengthUnit, String targetStrengthUnit, List<CDSCard> cards, String medicationLabel, List<Coding> codingList) {
try {
BigDecimal prescribedDailyDoseQuantity = inputStrengthValue.multiply(new BigDecimal(UnitConversion.factorOfConversion(inputStrengthUnit, targetStrengthUnit)));
return new PrescribedDailyDose(prescribedDailyDoseQuantity, targetStrengthUnit);
} catch (Exception e) {
composeCdssCardForDosageMismatch(cards, medicationLabel, codingList, targetStrengthUnit, true);
throw new RuntimeException(e);
}
}

private String getCardSummaryTemplate() {
Expand Down Expand Up @@ -409,15 +458,6 @@ private List<CDSCoding> getCodings(List<Coding> codings) {
return codings.stream().map(coding -> new CDSCoding(coding.getSystem(), coding.getCode(), coding.getDisplay())).collect(Collectors.toList());
}

private String getDecimalPlace(Double value) {
return String.format("%.2f", value);
}

private String getDynamicDecimalPlace(Double value) {
DecimalFormat decimalFormat = new DecimalFormat("#.##");
return decimalFormat.format(value);
}

private BigDecimal formatToTwoDecimalPlaces(BigDecimal value){
return value.setScale(2, RoundingMode.HALF_UP);
}
Expand Down
28 changes: 25 additions & 3 deletions src/test/java/org/snomed/cdsservice/service/MedicationOrderSelectCDSServiceTest.java
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Expand Up @@ -50,7 +50,9 @@ class MedicationOrderSelectCDSServiceTest {
public static final String SNOMEDCT_SYSTEM = "http://snomed.info/sct";
private static final String CONTRAINDICATION_ALERT_TYPE = "Contraindication";
private static final String HIGH_DOSAGE_ALERT_TYPE = "High Dosage";
@Autowired
private static final String INVALID_DOSAGE_ALERT_TYPE = "Validation Error";

@Autowired
SnomedMedicationDefinedDailyDoseService snomedMedicationDefinedDailyDoseService;
@MockBean
private MedicationConditionRuleLoaderService ruleLoaderService;
Expand Down Expand Up @@ -96,6 +98,7 @@ void setMockOutput() throws ServiceException {
when(mockTsClient.lookup(eq(SNOMEDCT_SYSTEM), eq("387365004"))).thenReturn(getConceptParamsForSubstanceProbenecid());
when(mockTsClient.lookup(eq(SNOMEDCT_SYSTEM), eq("258685003"))).thenReturn(getConceptParamsForDoseUnitMcg());
when(mockTsClient.lookup(eq(SNOMEDCT_SYSTEM), eq("387413002"))).thenReturn(getConceptParamsForSubstanceColchicine());
when(mockTsClient.lookup(eq(SNOMEDCT_SYSTEM), eq("dummyCode"))).thenThrow(new RuntimeException("dummy exception"));
when(mockDoseFormsLoaderService.loadDoseFormMap()).thenReturn(getMockMapList());
snomedMedicationDefinedDailyDoseService.setDoseFormsManySnomedToOneAtcCodeMap(getMockMapList());
}
Expand Down Expand Up @@ -387,12 +390,31 @@ public void shouldReturnOverDoseAlert_WhenPrescribedDailyDoseExceedsThresholdFac
}

@Test
public void shouldThrowException_WhenRequestBundleContainsMismatchedDoseUnits() throws IOException {
public void shouldCreateInvalidDosageCdssAlerts_WhenRequestBundleContainsMismatchedDoseUnitsAndRoutes() throws IOException {
CDSRequest cdsRequest = new CDSRequest();
cdsRequest.setPrefetchStrings(Map.of(
"patient", StreamUtils.copyToString(getClass().getResourceAsStream("/medication-order-select/PatientResource.json"), StandardCharsets.UTF_8),
"conditions", StreamUtils.copyToString(getClass().getResourceAsStream("/medication-order-select/ConditionBundle.json"), StandardCharsets.UTF_8),
"draftMedicationRequests", StreamUtils.copyToString(getClass().getResourceAsStream("/medication-order-select/MedicationRequestBundleWithMismatchedDoseUnitsAndRoutes.json"), StandardCharsets.UTF_8)
));
List<CDSCard> cards = service.call(cdsRequest);
CDSCard cdsCard1 = cards.get(0);
CDSCard cdsCard2 = cards.get(1);
CDSCard cdsCard3 = cards.get(2);
assertEquals(3, cards.size());
assertEquals(CONTRAINDICATION_ALERT_TYPE, cdsCard1.getAlertType());
assertEquals(INVALID_DOSAGE_ALERT_TYPE, cdsCard2.getAlertType());
assertEquals(INVALID_DOSAGE_ALERT_TYPE, cdsCard3.getAlertType());
assertTrue(cdsCard2.getDetail().contains("dose unit"));
assertTrue(cdsCard3.getDetail().contains("dose route"));
}
@Test
public void shouldThrowException_WhenRequestBundleContainsInvalidMedicationCode() throws IOException {
CDSRequest cdsRequest = new CDSRequest();
cdsRequest.setPrefetchStrings(Map.of(
"patient", StreamUtils.copyToString(getClass().getResourceAsStream("/medication-order-select/PatientResource.json"), StandardCharsets.UTF_8),
"conditions", StreamUtils.copyToString(getClass().getResourceAsStream("/medication-order-select/ConditionBundle.json"), StandardCharsets.UTF_8),
"draftMedicationRequests", StreamUtils.copyToString(getClass().getResourceAsStream("/medication-order-select/MedicationRequestBundleWithMismatchedDoseUnits"), StandardCharsets.UTF_8)
"draftMedicationRequests", StreamUtils.copyToString(getClass().getResourceAsStream("/medication-order-select/MedicationRequestBundleWithInvalidMedicationCode.json"), StandardCharsets.UTF_8)
));
assertThrows(ResponseStatusException.class, () ->service.call(cdsRequest) );
}
Expand Down
11 changes: 10 additions & 1 deletion src/test/resources/medication-order-select/MedicationRequestBundle.json
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,16 @@
"unit": "Tablet"
}
}
]
],
"route": {
"coding": [
{
"code": "",
"display": "O"
}
],
"text": "O"
}
}
]
},
Expand Down
11 changes: 10 additions & 1 deletion src/test/resources/medication-order-select/MedicationRequestBundleWithCombinatorialDrug.json
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,16 @@
"unit": "Tablet"
}
}
]
],
"route": {
"coding": [
{
"code": "",
"display": "O"
}
],
"text": "O"
}
}
]
},
Expand Down
22 changes: 20 additions & 2 deletions ...ionRequestBundleWithDifferentManufacturedDosageFormAndDifferentRouteOfAdministration.json
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,16 @@
"unit": "Tablet"
}
}
]
],
"route": {
"coding": [
{
"code": "",
"display": "O"
}
],
"text": "O"
}
}
]
},
Expand Down Expand Up @@ -132,7 +141,16 @@
"unit": "mL"
}
}
]
],
"route": {
"coding": [
{
"code": "",
"display": "P"
}
],
"text": "P"
}
}
]
},
Expand Down
22 changes: 20 additions & 2 deletions src/test/resources/medication-order-select/MedicationRequestBundleWithDosageAndUnits.json
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,16 @@
"unit": "Tablet"
}
}
]
],
"route": {
"coding": [
{
"code": "",
"display": "O"
}
],
"text": "O"
}
}
]
},
Expand Down Expand Up @@ -132,7 +141,16 @@
"unit": "mL"
}
}
]
],
"route": {
"coding": [
{
"code": "",
"display": "P"
}
],
"text": "P"
}
}
]
},
Expand Down
11 changes: 10 additions & 1 deletion ...sources/medication-order-select/MedicationRequestBundleWithFrequencyPeriodUnitInDays.json
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Expand Up @@ -66,7 +66,16 @@
"unit": "Tablet"
}
}
]
],
"route": {
"coding": [
{
"code": "",
"display": "O"
}
],
"text": "O"
}
}
]
},
Expand Down
11 changes: 10 additions & 1 deletion ...ources/medication-order-select/MedicationRequestBundleWithFrequencyPeriodUnitInHours.json
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,16 @@
"unit": "Tablet"
}
}
]
],
"route": {
"coding": [
{
"code": "",
"display": "O"
}
],
"text": "O"
}
}
]
},
Expand Down
11 changes: 10 additions & 1 deletion ...urces/medication-order-select/MedicationRequestBundleWithFrequencyPeriodUnitInMonths.json
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,16 @@
"unit": "Tablet"
}
}
]
],
"route": {
"coding": [
{
"code": "",
"display": "O"
}
],
"text": "O"
}
}
]
},
Expand Down
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