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Adjust abnormal flag mapping #7903

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merged 2 commits into from
Jul 12, 2024
Merged

Adjust abnormal flag mapping #7903

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770ac2f
Adjust abnormal flag mapping
emyl3 Jul 11, 2024
f1d0934
Only add abnormal flag interpretation if value present
emyl3 Jul 12, 2024
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58 changes: 55 additions & 3 deletions backend/src/main/java/gov/cdc/usds/simplereport/api/Translators.java
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Original file line number Diff line number Diff line change
Expand Up @@ -441,12 +441,64 @@ public static PersonName consolidateNameArguments(
Map.entry(OTHER, "Other"));
private static final Set<String> ORGANIZATION_TYPE_KEYS = ORGANIZATION_TYPES.keySet();

private static final String DETECTED_SNOMED = "260373001";
private static final String NOT_DETECTED_SNOMED = "260415000";
private static final String INVALID_SNOMED = "455371000124106";
public static final Map<String, SnomedConceptRecord> ABNORMAL_SNOMEDS =
Map.ofEntries(
Map.entry(
DETECTED_SNOMED,
new SnomedConceptRecord("Detected", DETECTED_SNOMED, TestResult.POSITIVE)),
Map.entry(
"720735008",
new SnomedConceptRecord("Presumptive positive", "720735008", TestResult.POSITIVE)),
Map.entry(
"10828004", new SnomedConceptRecord("Positive", "10828004", TestResult.POSITIVE)),
Map.entry(
"11214006", new SnomedConceptRecord("Reactive", "11214006", TestResult.POSITIVE)));

public static final Map<String, SnomedConceptRecord> NORMAL_SNOMEDS =
Map.ofEntries(
Map.entry(
NOT_DETECTED_SNOMED,
new SnomedConceptRecord("Not detected", NOT_DETECTED_SNOMED, TestResult.NEGATIVE)),
Map.entry(
"260385009", new SnomedConceptRecord("Negative", "260385009", TestResult.NEGATIVE)),
Map.entry(
"895231008",
new SnomedConceptRecord(
"Not detected in pooled specimen", "895231008", TestResult.NEGATIVE)),
Map.entry(
"131194007",
new SnomedConceptRecord("Non-Reactive", "131194007", TestResult.NEGATIVE)),
// certain UNDETERMINED codes are also flagged as normal
// https://github.com/CDCgov/prime-reportstream/blob/1ffae4ca0b04cd0aa9f169e26813ecd86df71bb5/prime-router/src/main/kotlin/metadata/Mappers.kt#L768
Map.entry(
"419984006",
new SnomedConceptRecord("Inconclusive", "419984006", TestResult.UNDETERMINED)),
Map.entry(
"42425007",
new SnomedConceptRecord("Equivocal", "42425007", TestResult.UNDETERMINED)),
Map.entry(
"82334004",
new SnomedConceptRecord("Indeterminate", "82334004", TestResult.UNDETERMINED)),
Map.entry(
"373121007",
new SnomedConceptRecord("Test not done", "373121007", TestResult.UNDETERMINED)),
Map.entry(
INVALID_SNOMED,
new SnomedConceptRecord("Invalid result", INVALID_SNOMED, TestResult.UNDETERMINED)),
Map.entry(
"125154007",
new SnomedConceptRecord(
"Specimen unsatisfactory for evaluation", "125154007", TestResult.UNDETERMINED)));

public static final SnomedConceptRecord DETECTED_SNOMED_CONCEPT =
new SnomedConceptRecord("Detected", "260373001", TestResult.POSITIVE);
ABNORMAL_SNOMEDS.get(DETECTED_SNOMED);
private static final SnomedConceptRecord NOT_DETECTED_SNOMED_CONCEPT =
new SnomedConceptRecord("Not detected", "260415000", TestResult.NEGATIVE);
NORMAL_SNOMEDS.get(NOT_DETECTED_SNOMED);
private static final SnomedConceptRecord INVALID_SNOMED_CONCEPT =
new SnomedConceptRecord("Invalid result", "455371000124106", TestResult.UNDETERMINED);
NORMAL_SNOMEDS.get(INVALID_SNOMED);
private static final List<SnomedConceptRecord> RESULTS_SNOMED_CONCEPTS =
List.of(DETECTED_SNOMED_CONCEPT, NOT_DETECTED_SNOMED_CONCEPT, INVALID_SNOMED_CONCEPT);

Expand Down
14 changes: 9 additions & 5 deletions backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConverter.java
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
package gov.cdc.usds.simplereport.api.converter;

import static gov.cdc.usds.simplereport.api.Translators.DETECTED_SNOMED_CONCEPT;
import static gov.cdc.usds.simplereport.api.Translators.ABNORMAL_SNOMEDS;
import static gov.cdc.usds.simplereport.api.Translators.FEMALE;
import static gov.cdc.usds.simplereport.api.Translators.GENDER_IDENTITIES;
import static gov.cdc.usds.simplereport.api.Translators.MALE;
import static gov.cdc.usds.simplereport.api.Translators.NON_BINARY;
import static gov.cdc.usds.simplereport.api.Translators.NORMAL_SNOMEDS;
import static gov.cdc.usds.simplereport.api.Translators.OTHER;
import static gov.cdc.usds.simplereport.api.Translators.REFUSED;
import static gov.cdc.usds.simplereport.api.Translators.TRANS_MAN;
Expand Down Expand Up @@ -159,6 +160,7 @@
import org.hl7.fhir.r4.model.Specimen;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.Type;
import org.owasp.encoder.Encode;
import org.springframework.boot.info.GitProperties;
import org.springframework.data.util.Pair;
import org.springframework.stereotype.Component;
Expand Down Expand Up @@ -753,19 +755,21 @@ public Observation convertToObservation(ConvertToObservationProps props) {
return observation;
}

private Coding convertToAbnormalFlagInterpretation(String resultCode) {
public Coding convertToAbnormalFlagInterpretation(String resultCode) {
Coding abnormalFlag = new Coding();

abnormalFlag.setSystem(ABNORMAL_FLAGS_CODE_SYSTEM);

if (resultCode.equals(DETECTED_SNOMED_CONCEPT.code())) {
if (ABNORMAL_SNOMEDS.keySet().contains(resultCode)) {
abnormalFlag.setCode(ABNORMAL_FLAG_ABNORMAL.code());
abnormalFlag.setDisplay(ABNORMAL_FLAG_ABNORMAL.displayName());
} else {
} else if (NORMAL_SNOMEDS.keySet().contains(resultCode)) {
abnormalFlag.setCode(ABNORMAL_FLAG_NORMAL.code());
abnormalFlag.setDisplay(ABNORMAL_FLAG_NORMAL.displayName());
} else {
log.info("Unsupported SNOMED result code: {}", Encode.forJava(resultCode));
return null;
Comment on lines +770 to +772
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I think it also makes sense to adjust this bit to not add the interpretation that the abnormal flag coding lives inside. (otherwise it will just be an empty interpretation)

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+1 agree that makes sense to omit the interpretation if it'll be empty anyway

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OO good catch -- thank you!

}

return abnormalFlag;
}

Expand Down
24 changes: 24 additions & 0 deletions backend/src/test/java/gov/cdc/usds/simplereport/api/converter/FhirConverterTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ContactPoint;
import org.hl7.fhir.r4.model.ContactPoint.ContactPointSystem;
import org.hl7.fhir.r4.model.ContactPoint.ContactPointUse;
Expand Down Expand Up @@ -2045,4 +2046,27 @@ void convertToSpecimen_withoutCollectionCodeAndName_useDefaults() {
.isEqualTo(DEFAULT_LOCATION_CODE);
assertThat(specimen.getCollection().getBodySite().getText()).isEqualTo(DEFAULT_LOCATION_NAME);
}

@Test
void convertToAbnormalFlagInterpretation_withUnsupportedSnomed_returnsNull() {
String snomed = "1111";
Coding actual = fhirConverter.convertToAbnormalFlagInterpretation(snomed);
assertThat(actual).isNull();
}

@ParameterizedTest
@MethodSource("snomedArgs")
void convertToAbnormalFlagInterpretation_matches(
String snomed, String expectedCode, String expectedCodeName) {
Coding actual = fhirConverter.convertToAbnormalFlagInterpretation(snomed);
assertThat(actual.getCode()).isEqualTo(expectedCode);
assertThat(actual.getDisplay()).isEqualTo(expectedCodeName);
}

private static Stream<Arguments> snomedArgs() {
return Stream.of(
arguments("10828004", "A", "Abnormal"),
arguments("131194007", "N", "Normal"),
arguments("455371000124106", "N", "Normal"));
}
}
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