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Map syphilis history to FHIR
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@emyl3
emyl3 committed Sep 30, 2024
1 parent 00710d9 commit 302abfb
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Showing 10 changed files with 330 additions and 15 deletions.
34 changes: 32 additions & 2 deletions backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConverter.java
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Expand Up @@ -66,6 +66,8 @@
import static gov.cdc.usds.simplereport.api.model.TestEventExport.DEFAULT_LOCATION_NAME;
import static gov.cdc.usds.simplereport.api.model.TestEventExport.FALLBACK_DEFAULT_TEST_MINUTES;
import static gov.cdc.usds.simplereport.api.model.TestEventExport.UNKNOWN_ADDRESS_INDICATOR;
import static gov.cdc.usds.simplereport.db.model.PersonUtils.NO_SYPHILIS_HISTORY_SNOMED;
import static gov.cdc.usds.simplereport.db.model.PersonUtils.YES_SYPHILIS_HISTORY_SNOMED;
import static gov.cdc.usds.simplereport.db.model.PersonUtils.genderIdentityDisplaySet;
import static gov.cdc.usds.simplereport.db.model.PersonUtils.genderIdentitySnomedSet;
import static gov.cdc.usds.simplereport.db.model.PersonUtils.getResidenceTypeMap;
Expand Down Expand Up @@ -865,6 +867,20 @@ public Observation convertToAOEPregnancyObservation(String pregnancyStatusSnomed
pregnancyStatusValueCode);
}

public Observation convertToAOESyphilisHistoryObservation(String syphilisHistory) {
CodeableConcept observationCode =
createSNOMEDConcept(
YES_SYPHILIS_HISTORY_SNOMED, "History of syphilis", "History of syphilis");
Boolean hasHistory = null;
if (syphilisHistory.equalsIgnoreCase(YES_SYPHILIS_HISTORY_SNOMED)) {
hasHistory = true;
} else if (syphilisHistory.equalsIgnoreCase(NO_SYPHILIS_HISTORY_SNOMED)) {
hasHistory = false;
}
return createAOEObservation(
uuidGenerator.randomUUID().toString(), observationCode, createYesNoUnkConcept(hasHistory));
}

public Observation convertToAOEYesNoUnkObservation(
Boolean isObserved, String observationLoinc, String observationDisplayText) {
CodeableConcept observationCode =
Expand Down Expand Up @@ -991,6 +1007,10 @@ public Set<Observation> convertToAOEObservations(
observations.addAll(convertToAOEGenderOfSexualPartnersObservation(sexualPartners));
}

if (surveyData.getSyphilisHistory() != null) {
observations.add(convertToAOESyphilisHistoryObservation(surveyData.getSyphilisHistory()));
}

return observations;
}

Expand Down Expand Up @@ -1050,7 +1070,17 @@ private CodeableConcept createYesNoUnkConcept(Boolean val) {
}

private CodeableConcept createSNOMEDConcept(String resultCode, String resultDisplay) {
return createSNOMEDConcept(resultCode, resultDisplay, null);
}

private CodeableConcept createSNOMEDConcept(
String resultCode, String resultDisplay, String resultText) {
CodeableConcept concept = new CodeableConcept();

if (StringUtils.isNotBlank(resultText)) {
concept.setText(resultText);
}

Coding coding = concept.addCoding();
coding.setSystem(SNOMED_CODE_SYSTEM);
coding.setCode(resultCode);
Expand Down Expand Up @@ -1629,7 +1659,7 @@ public Bundle createFhirBundle(ConditionAgnosticCreateFhirBundleProps props) {

var bundle =
new Bundle()
.setType(Bundle.BundleType.MESSAGE)
.setType(BundleType.MESSAGE)
.setTimestamp(currentDate)
.setIdentifier(new Identifier().setValue(props.getDiagnosticReport().getId()));

Expand All @@ -1638,7 +1668,7 @@ public Bundle createFhirBundle(ConditionAgnosticCreateFhirBundleProps props) {
entryList.forEach(
pair ->
bundle.addEntry(
new Bundle.BundleEntryComponent()
new BundleEntryComponent()
.setFullUrl(pair.getFirst())
.setResource(pair.getSecond())));

Expand Down
1 change: 1 addition & 0 deletions backend/src/main/java/gov/cdc/usds/simplereport/api/model/filerow/TestResultRow.java
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Expand Up @@ -624,6 +624,7 @@ public List<FeedbackMessage> validateIndividualValues() {
testResult,
DiseaseService.SYPHILIS_NAME,
List.of(gendersOfSexualPartners, pregnant, syphilisHistory, symptomaticForDisease)));
errors.addAll(validateYesNoAnswer(syphilisHistory));
}

return errors;
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9 changes: 9 additions & 0 deletions backend/src/main/java/gov/cdc/usds/simplereport/db/model/PersonUtils.java
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Expand Up @@ -855,4 +855,13 @@ public static Map<String, String> getGenderIdentityAbbreviationMap() {

return genderMap;
}

public static final Map<String, String> syphilisHistorySnomedMap =
Map.of(
"YES".toLowerCase(), YES_SYPHILIS_HISTORY_SNOMED,
"Y".toLowerCase(), YES_SYPHILIS_HISTORY_SNOMED,
"NO".toLowerCase(), NO_SYPHILIS_HISTORY_SNOMED,
"N".toLowerCase(), NO_SYPHILIS_HISTORY_SNOMED,
"UNK".toLowerCase(), UNKNOWN_SYPHILIS_HISTORY_SNOMED,
"U".toLowerCase(), UNKNOWN_SYPHILIS_HISTORY_SNOMED);
}
15 changes: 15 additions & 0 deletions backend/src/main/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhir.java
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Expand Up @@ -8,6 +8,7 @@
import static gov.cdc.usds.simplereport.api.model.filerow.TestResultRow.diseaseSpecificLoincMap;
import static gov.cdc.usds.simplereport.db.model.PersonUtils.getGenderIdentityAbbreviationMap;
import static gov.cdc.usds.simplereport.db.model.PersonUtils.getResidenceTypeMap;
import static gov.cdc.usds.simplereport.db.model.PersonUtils.syphilisHistorySnomedMap;
import static gov.cdc.usds.simplereport.utils.DateTimeUtils.DATE_TIME_FORMATTER;
import static gov.cdc.usds.simplereport.utils.DateTimeUtils.convertToZonedDateTime;
import static gov.cdc.usds.simplereport.utils.ResultUtils.mapTestResultStatusToSRValue;
Expand Down Expand Up @@ -475,6 +476,13 @@ private Bundle convertRowToFhirBundle(TestResultRow row, UUID orgId) {
AOE_EMPLOYED_IN_HEALTHCARE_DISPLAY));
}

String syphilisHistory = row.getSyphilisHistory().getValue();
if (StringUtils.isNotBlank(syphilisHistory)) {
String syphilisHistorySnomed = getSyphilisHistorySnomed(syphilisHistory);
aoeObservations.add(
fhirConverter.convertToAOESyphilisHistoryObservation(syphilisHistorySnomed));
}

String hospitalizedValue = row.getHospitalized().getValue();
if (StringUtils.isNotBlank(hospitalizedValue)) {
Boolean hospitalized = yesNoToBooleanMap.get(hospitalizedValue.toLowerCase());
Expand Down Expand Up @@ -601,6 +609,13 @@ private String getPregnancyStatusSnomed(String input) {
return null;
}

private String getSyphilisHistorySnomed(String input) {
if (input != null && input.matches(ALPHABET_REGEX)) {
return syphilisHistorySnomedMap.get(input.toLowerCase());
}
return null;
}

private String getResidenceTypeSnomed(String input) {
if (input != null && input.matches(ALPHABET_REGEX)) {
return getResidenceTypeMap().get(input.toLowerCase());
Expand Down
45 changes: 39 additions & 6 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 @@ -5,7 +5,9 @@
import static gov.cdc.usds.simplereport.api.model.TestEventExport.DEFAULT_LOCATION_CODE;
import static gov.cdc.usds.simplereport.api.model.TestEventExport.DEFAULT_LOCATION_NAME;
import static gov.cdc.usds.simplereport.api.model.TestEventExport.UNKNOWN_ADDRESS_INDICATOR;
import static gov.cdc.usds.simplereport.db.model.PersonUtils.NO_SYPHILIS_HISTORY_SNOMED;
import static gov.cdc.usds.simplereport.db.model.PersonUtils.PREGNANT_UNKNOWN_SNOMED;
import static gov.cdc.usds.simplereport.db.model.PersonUtils.YES_SYPHILIS_HISTORY_SNOMED;
import static org.assertj.core.api.Assertions.assertThat;
import static org.assertj.core.api.Assertions.from;
import static org.junit.jupiter.params.provider.Arguments.arguments;
Expand Down Expand Up @@ -1238,22 +1240,53 @@ void convertToAoeObservation_genderOfSexualPartners_matchesJson() throws IOExcep
JSONAssert.assertEquals(expectedSerialized, actualSerialized, true);
}

@Test
void convertToAoeObservation_syphilisHistory_matchesJson() throws IOException {
AskOnEntrySurvey answers =
AskOnEntrySurvey.builder()
.pregnancy(null)
.syphilisHistory(YES_SYPHILIS_HISTORY_SNOMED)
.symptoms(null)
.genderOfSexualPartners(null)
.symptomOnsetDate(null)
.noSymptoms(false)
.build();

String testId = "fakeId";

Set<Observation> actual =
fhirConverter.convertToAOEObservations(
testId, answers, new Person("first", "last", "middle", "suffix", null));

String actualSerialized =
actual.stream().map(parser::encodeResourceToString).collect(Collectors.toSet()).toString();
String expectedSerialized =
IOUtils.toString(
Objects.requireNonNull(
getClass()
.getClassLoader()
.getResourceAsStream("fhir/observationSyphilisHistory.json")),
StandardCharsets.UTF_8);
JSONAssert.assertEquals(expectedSerialized, actualSerialized, true);
}

@Test
void convertToAoeObservation_allAOE_matchesJson() throws IOException {
List<String> sexualPartners = List.of("male", "female");
AskOnEntrySurvey answers =
AskOnEntrySurvey.builder()
.pregnancy(PREGNANT_UNKNOWN_SNOMED)
.syphilisHistory(null)
.syphilisHistory(NO_SYPHILIS_HISTORY_SNOMED)
.symptoms(Map.of("fake", true))
.symptomOnsetDate(LocalDate.of(2023, 3, 4))
.genderOfSexualPartners(null)
.genderOfSexualPartners(sexualPartners)
.noSymptoms(false)
.build();

String testId = "fakeId";

var birthDate = LocalDate.of(2022, 12, 13);
var person =
LocalDate birthDate = LocalDate.of(2022, 12, 13);
Person person =
new Person(
null,
null,
Expand All @@ -1277,11 +1310,11 @@ void convertToAoeObservation_allAOE_matchesJson() throws IOException {
"English",
null);

var actual = fhirConverter.convertToAOEObservations(testId, answers, person);
Set<Observation> actual = fhirConverter.convertToAOEObservations(testId, answers, person);

String actualSerialized =
actual.stream().map(parser::encodeResourceToString).collect(Collectors.toSet()).toString();
var expectedSerialized =
String expectedSerialized =
IOUtils.toString(
Objects.requireNonNull(
getClass().getClassLoader().getResourceAsStream("fhir/observationAllAoe.json")),
Expand Down
41 changes: 37 additions & 4 deletions backend/src/test/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhirTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -77,14 +77,22 @@ public void beforeEach() {
when(resultsUploaderCachingService.getSpecimenTypeNameToSNOMEDMap())
.thenReturn(
Map.of(
"Nasal swab".toLowerCase(), "445297001",
"Anterior nares swab".toLowerCase(), "697989009"));
"Nasal swab".toLowerCase(),
"445297001",
"Anterior nares swab".toLowerCase(),
"697989009",
"Venous blood specimen".toLowerCase(),
"122555007"));

when(resultsUploaderCachingService.getSNOMEDToSpecimenTypeNameMap())
.thenReturn(
Map.of(
"445297001", "Nasal swab",
"697989009", "Anterior nares swab"));
"445297001",
"Nasal swab",
"697989009",
"Anterior nares swab",
"122555007",
"Venous blood specimen"));

when(resultsUploaderCachingService.getZoneIdByAddress(any()))
.thenReturn(ZoneId.of("US/Central"));
Expand Down Expand Up @@ -650,4 +658,29 @@ void convertExistingCsv_validHivPositive_withAOEdataColumns() {
assertThat(gendersOfSexualPartnersObservations).hasSize(5);
assertThat(codeableConceptValues).containsExactlyInAnyOrderElementsOf(expectedGenders);
}

@Test
void convertExistingCsv_validSyphilisPositive_withAOEdataColumns() {
InputStream input = loadCsv("testResultUpload/test-results-upload-valid-syphilis-only.csv");

FHIRBundleRecord bundleRecord = sut.convertToFhirBundles(input, UUID.randomUUID());
List<String> serializedBundles = bundleRecord.serializedBundle();
String first = serializedBundles.get(0);
Bundle deserializedBundle = (Bundle) parser.parseResource(first);

List<Observation> syphilisHistoryObservations =
deserializedBundle.getEntry().stream()
.filter(entry -> entry.getFullUrl().contains("Observation/"))
.map(x -> (Observation) x.getResource())
.filter(x -> Objects.equals(x.getCode().getText(), "History of syphilis"))
.collect(Collectors.toList());

List<String> codeableConceptValues =
syphilisHistoryObservations.stream()
.map(x -> x.getValueCodeableConcept().getCoding().get(0).getDisplay())
.collect(Collectors.toList());

assertThat(syphilisHistoryObservations).hasSize(1);
assertThat(codeableConceptValues).isEqualTo(List.of("unknown"));
}
}
114 changes: 114 additions & 0 deletions backend/src/test/resources/fhir/observationAllAoe.json
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@@ -1,4 +1,42 @@
[
{
"resourceType": "Observation",
"id": "8526bd3b-42e4-3a6f-88ff-3fc43b69dc20",
"identifier": [
{
"use": "official",
"type": {
"coding": [
{
"system": "http://loinc.org",
"code": "81959-9",
"display": "Public health laboratory ask at order entry panel"
}
]
}
}
],
"status": "final",
"code": {
"coding": [
{
"system": "http://simplereport.gov/",
"code": "SR0001",
"display": "What is the gender of their sexual partners"
}
],
"text": "What is the gender of their sexual partners"
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "446151000124109",
"display": "Male gender identity"
}
]
}
},
{
"resourceType": "Observation",
"id": "5f3026ea-845b-3649-8b62-d3dbfd3e7b62",
Expand Down Expand Up @@ -37,6 +75,82 @@
]
}
},
{
"resourceType": "Observation",
"id": "8526bd3b-42e4-3a6f-88ff-3fc43b69dc20",
"identifier": [
{
"use": "official",
"type": {
"coding": [
{
"system": "http://loinc.org",
"code": "81959-9",
"display": "Public health laboratory ask at order entry panel"
}
]
}
}
],
"status": "final",
"code": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "1087151000119108",
"display": "History of syphilis"
}
],
"text": "History of syphilis"
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://terminology.hl7.org/ValueSet/v2-0136",
"code": "N",
"display": "No"
}
]
}
},
{
"resourceType": "Observation",
"id": "8526bd3b-42e4-3a6f-88ff-3fc43b69dc20",
"identifier": [
{
"use": "official",
"type": {
"coding": [
{
"system": "http://loinc.org",
"code": "81959-9",
"display": "Public health laboratory ask at order entry panel"
}
]
}
}
],
"status": "final",
"code": {
"coding": [
{
"system": "http://simplereport.gov/",
"code": "SR0001",
"display": "What is the gender of their sexual partners"
}
],
"text": "What is the gender of their sexual partners"
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "446141000124107",
"display": "Female gender identity"
}
]
}
},
{
"resourceType": "Observation",
"id": "07099f95-8754-3317-8e87-e1c4717c1af1",
Expand Down
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