Map syphilis history to FHIR

CDCgov · Sep 30, 2024 · 3060e88 · 3060e88
1 parent 00710d9
commit 3060e88
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Showing 10 changed files with 328 additions and 13 deletions.
diff --git a/backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConverter.java b/backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConverter.java
@@ -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;
@@ -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 =
@@ -991,6 +1007,10 @@ public Set<Observation> convertToAOEObservations(
       observations.addAll(convertToAOEGenderOfSexualPartnersObservation(sexualPartners));
     }
 
+    if (surveyData.getSyphilisHistory() != null) {
+      observations.add(convertToAOESyphilisHistoryObservation(surveyData.getSyphilisHistory()));
+    }
+
     return observations;
   }
 
@@ -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);

diff --git a/backend/src/main/java/gov/cdc/usds/simplereport/api/model/filerow/TestResultRow.java b/backend/src/main/java/gov/cdc/usds/simplereport/api/model/filerow/TestResultRow.java
@@ -618,6 +618,7 @@ public List<FeedbackMessage> validateIndividualValues() {
               testResult, DiseaseService.HIV_NAME, List.of(gendersOfSexualPartners, pregnant)));
     }
 
+    errors.addAll(validateYesNoAnswer(syphilisHistory));
     if (isSyphilisResult()) {
       errors.addAll(
           validateRequiredFieldsForPositiveResult(

diff --git a/backend/src/main/java/gov/cdc/usds/simplereport/db/model/PersonUtils.java b/backend/src/main/java/gov/cdc/usds/simplereport/db/model/PersonUtils.java
@@ -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);
 }
diff --git a/backend/src/main/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhir.java b/backend/src/main/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhir.java
@@ -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;
@@ -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());
@@ -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());

diff --git a/backend/src/test/java/gov/cdc/usds/simplereport/api/converter/FhirConverterTest.java b/backend/src/test/java/gov/cdc/usds/simplereport/api/converter/FhirConverterTest.java
@@ -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;
@@ -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,
@@ -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")),

diff --git a/backend/src/test/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhirTest.java b/backend/src/test/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhirTest.java
@@ -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"));
@@ -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"));
+  }
 }
diff --git a/backend/src/test/resources/fhir/observationAllAoe.json b/backend/src/test/resources/fhir/observationAllAoe.json
@@ -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",
@@ -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",