Add patient gender identity to bulk upload

backend/src/main/java/gov/cdc/usds/simplereport/api/model/filerow/TestResultRow.java

@@ -14,6 +14,7 @@
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateEmail;
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateEthnicity;
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateGendersOfSexualPartners;
+import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validatePatientGenderIdentity;
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validatePhoneNumber;
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateRace;
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateRequiredFieldsForPositiveResult;
@@ -54,7 +55,17 @@ public class TestResultRow implements FileRow {
   final ValueOrError patientCounty;
   final ValueOrError patientPhoneNumber;
   final ValueOrError patientDob;
+
+  /**
+   * This field "patient_gender" refers to the patient's sex assigned at birth. <br>
+   *
+   * <p>When "patient_gender_identity" was added as a field in 2024, the team decided to keep this
+   * current column name of "patient_gender" instead of changing the header to something like
+   * "patient_sex_assigned_at_birth". This decision was made to maintain compatibility for existing
+   * bulk upload users.
+   */
   final ValueOrError patientGender;
+
   final ValueOrError patientRace;
   final ValueOrError patientEthnicity;
   final ValueOrError patientPreferredLanguage;
@@ -107,6 +118,7 @@ public class TestResultRow implements FileRow {
   final ValueOrError testOrderedCode;
   final ValueOrError gendersOfSexualPartners;
   final ValueOrError syphilisHistory;
+  final ValueOrError patientGenderIdentity;
 
   static final String PATIENT_LAST_NAME = "patient_last_name";
   static final String PATIENT_FIRST_NAME = "patient_first_name";
@@ -152,6 +164,7 @@ public class TestResultRow implements FileRow {
   public static final String ORDERING_FACILITY_PHONE_NUMBER = "ordering_facility_phone_number";
   public static final String GENDERS_OF_SEXUAL_PARTNERS = "genders_of_sexual_partners";
   public static final String SYPHILIS_HISTORY = "syphilis_history";
+  public static final String PATIENT_GENDER_IDENTITY = "patient_gender_identity";
 
   public static final ImmutableMap<String, String> diseaseSpecificLoincMap =
       new ImmutableMap.Builder<String, String>()
@@ -456,6 +469,8 @@ public TestResultRow(Map<String, String> rawRow) {
     gendersOfSexualPartners =
         getValue(rawRow, GENDERS_OF_SEXUAL_PARTNERS, isRequired(GENDERS_OF_SEXUAL_PARTNERS));
     syphilisHistory = getValue(rawRow, SYPHILIS_HISTORY, isRequired(SYPHILIS_HISTORY));
+    patientGenderIdentity =
+        getValue(rawRow, PATIENT_GENDER_IDENTITY, isRequired(PATIENT_GENDER_IDENTITY));
   }
 
   private List<FeedbackMessage> validateDeviceModelAndTestPerformedCode(
@@ -612,6 +627,8 @@ public List<FeedbackMessage> validateIndividualValues() {
 
     errors.addAll(validateGendersOfSexualPartners(gendersOfSexualPartners));
 
+    errors.addAll(validatePatientGenderIdentity(patientGenderIdentity));
+
     if (isHivResult()) {
       errors.addAll(
           validateRequiredFieldsForPositiveResult(

backend/src/main/java/gov/cdc/usds/simplereport/db/model/PersonUtils.java

@@ -843,6 +843,7 @@ public static Map<String, String> getGenderIdentityAbbreviationMap() {
     genderMap.put("M", MALE);
     genderMap.put("MALE", MALE);
     genderMap.put("NB", NON_BINARY);
+    genderMap.put("NON BINARY", NON_BINARY);
     genderMap.put("NONBINARY", NON_BINARY);
     genderMap.put("TM", TRANS_MAN);
     genderMap.put("TRANS MAN", TRANS_MAN);

backend/src/main/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhir.java

@@ -528,6 +528,16 @@ private Bundle convertRowToFhirBundle(TestResultRow row, UUID orgId) {
           fhirConverter.convertToAOEGenderOfSexualPartnersObservation(abbrConvertedGenders));
     }
 
+    String patientGenderIdentity = row.getPatientGenderIdentity().getValue();
+    if (StringUtils.isNotBlank(patientGenderIdentity)) {
+      Map<String, String> genderAbbreviationMap = getGenderIdentityAbbreviationMap();
+      String abbrConvertedGenderIdentity =
+          genderAbbreviationMap.get(patientGenderIdentity.toUpperCase());
+      aoeObservations.addAll(
+          fhirConverter.convertToAOEGenderIdentityObservation(
+              testEventId, abbrConvertedGenderIdentity));
+    }
+
     var serviceRequest =
         fhirConverter.convertToServiceRequest(
             ServiceRequest.ServiceRequestStatus.COMPLETED,

backend/src/main/java/gov/cdc/usds/simplereport/validators/CsvValidatorUtils.java

@@ -660,6 +660,26 @@ public static List<FeedbackMessage> validateGendersOfSexualPartners(ValueOrError
     return errors;
   }
 
+  public static List<FeedbackMessage> validatePatientGenderIdentity(ValueOrError input) {
+    List<FeedbackMessage> errors = new ArrayList<>();
+    String value = parseString(input.getValue());
+    if (value == null) {
+      return errors;
+    }
+    if (!getGenderIdentityAbbreviationMap().containsKey(value.toUpperCase())) {
+      errors.add(
+          FeedbackMessage.builder()
+              .scope(ITEM_SCOPE)
+              .fieldHeader(input.getHeader())
+              .source(ResultUploadErrorSource.SIMPLE_REPORT)
+              .message(getInvalidValueErrorMessage(input.getValue(), input.getHeader()))
+              .errorType(ResultUploadErrorType.INVALID_DATA)
+              .fieldRequired(input.isRequired())
+              .build());
+    }
+    return errors;
+  }
+
   public static List<FeedbackMessage> validateRequiredFieldsForPositiveResult(
       ValueOrError testResult, String diseaseName, List<ValueOrError> fields) {
     List<FeedbackMessage> errors = new ArrayList<>();

backend/src/test/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhirTest.java

@@ -214,7 +214,7 @@ void convertExistingCsv_aoeQuestionsMapped() {
             .filter(
                 observation -> observation.getResource().getNamedProperty("identifier").hasValues())
             .toList();
-    assertThat(asymptomaticNotCongregateAOE).hasSize(11);
+    assertThat(asymptomaticNotCongregateAOE).hasSize(12);
 
     var symptomaticCongregateSettingEntry = serializedBundles.get(1);
     var deserializedSymptomaticCongregateEntry =
@@ -227,7 +227,7 @@ void convertExistingCsv_aoeQuestionsMapped() {
         symptomaticCongregateObservations.stream()
             .filter(obs -> obs.getResource().getNamedProperty("identifier").hasValues())
             .toList();
-    assertThat(symptomaticCongregateAOE).hasSize(10);
+    assertThat(symptomaticCongregateAOE).hasSize(11);
   }
 
   private InputStream loadCsv(String csvFile) {

backend/src/test/java/gov/cdc/usds/simplereport/validators/CsvValidatorUtilsTest.java

@@ -10,6 +10,7 @@
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateFlexibleDate;
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateGendersOfSexualPartners;
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validatePartialUnkAddress;
+import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validatePatientGenderIdentity;
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validatePhoneNumber;
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateRequiredFieldsForPositiveResult;
 import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateSpecimenType;
@@ -290,6 +291,61 @@ void invalidGendersOfSexualPartners() {
     assertThat(validateGendersOfSexualPartners(genders)).hasSize(1);
   }
 
+  @Test
+  void validPatientGenderIdentity() {
+    assertThat(validatePatientGenderIdentity(new ValueOrError("f", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(validatePatientGenderIdentity(new ValueOrError("m", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(validatePatientGenderIdentity(new ValueOrError("nb", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(validatePatientGenderIdentity(new ValueOrError("tm", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(validatePatientGenderIdentity(new ValueOrError("tw", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(validatePatientGenderIdentity(new ValueOrError("o", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(validatePatientGenderIdentity(new ValueOrError("r", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(validatePatientGenderIdentity(new ValueOrError("female", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(validatePatientGenderIdentity(new ValueOrError("male", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(
+            validatePatientGenderIdentity(
+                new ValueOrError("non binary", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(
+            validatePatientGenderIdentity(new ValueOrError("nonbinary", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(
+            validatePatientGenderIdentity(new ValueOrError("trans man", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(
+            validatePatientGenderIdentity(
+                new ValueOrError("trans woman", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(validatePatientGenderIdentity(new ValueOrError("other", "patient_gender_identity")))
+        .isEmpty();
+    assertThat(
+            validatePatientGenderIdentity(new ValueOrError("refused", "patient_gender_identity")))
+        .isEmpty();
+  }
+
+  @Test
+  void invalidPatientGenderIdentity() {
+    assertThat(validatePatientGenderIdentity(new ValueOrError("t", "patient_gender_identity")))
+        .hasSize(1);
+    assertThat(validatePatientGenderIdentity(new ValueOrError("n", "patient_gender_identity")))
+        .hasSize(1);
+    assertThat(validatePatientGenderIdentity(new ValueOrError("ma", "patient_gender_identity")))
+        .hasSize(1);
+    assertThat(validatePatientGenderIdentity(new ValueOrError("fe", "patient_gender_identity")))
+        .hasSize(1);
+    assertThat(validatePatientGenderIdentity(new ValueOrError(" ", "patient_gender_identity")))
+        .hasSize(1);
+  }
+
   @Test
   void validNegativeHIVNoRequiredAOEFields() {
     ValueOrError testResult = new ValueOrError("negative", "test_result");

backend/src/test/java/gov/cdc/usds/simplereport/validators/TestResultRowTest.java

@@ -96,7 +96,8 @@ class TestResultRowTest {
           "test_result_status",
           "specimen_type",
           "testing_lab_clia",
-          "genders_of_sexual_partners");
+          "genders_of_sexual_partners",
+          "patient_gender_identity");
 
   @BeforeEach
   public void init() {
@@ -164,6 +165,7 @@ public void init() {
     validRowMap.put("comment", "Test Comment");
     validRowMap.put("test_result_status", "");
     validRowMap.put("genders_of_sexual_partners", "M, F, TM, TW");
+    validRowMap.put("patient_gender_identity", "F");
   }
 
   @Test
@@ -358,7 +360,10 @@ void processRowSetsAllValues() {
             from(TestResultRow::getTestResultStatus).andThen(ValueOrError::getValue))
         .returns(
             validRowMap.get("genders_of_sexual_partners"),
-            from(TestResultRow::getGendersOfSexualPartners).andThen(ValueOrError::getValue));
+            from(TestResultRow::getGendersOfSexualPartners).andThen(ValueOrError::getValue))
+        .returns(
+            validRowMap.get("patient_gender_identity"),
+            from(TestResultRow::getPatientGenderIdentity).andThen(ValueOrError::getValue));
   }
 
   @Test
@@ -412,6 +417,7 @@ void validateIndividualFields() {
     invalidIndividualFields.put("specimen_type", "100");
     invalidIndividualFields.put("testing_lab_clia", "à");
     invalidIndividualFields.put("genders_of_sexual_partners", "ma, f");
+    invalidIndividualFields.put("patient_gender_identity", "fe");
     var testResultRow =
         new TestResultRow(
             invalidIndividualFields,

backend/src/test/resources/testResultUpload/test-results-upload-all-fields.csv

@@ -1,3 +1,3 @@
-patient_id,patient_last_name,patient_first_name,patient_middle_name,patient_street,patient_street2,patient_city,patient_state,patient_zip_code,patient_county,patient_phone_number,patient_dob,patient_gender,patient_race,patient_ethnicity,patient_preferred_language,patient_email,accession_number,equipment_model_name,test_performed_code,test_result,order_test_date,specimen_collection_date,testing_lab_specimen_received_date,test_result_date,date_result_released,specimen_type,ordering_provider_id,ordering_provider_last_name,ordering_provider_first_name,ordering_provider_middle_name,ordering_provider_street,ordering_provider_street2,ordering_provider_city,ordering_provider_state,ordering_provider_zip_code,ordering_provider_phone_number,testing_lab_clia,testing_lab_name,testing_lab_street,testing_lab_street2,testing_lab_city,testing_lab_state,testing_lab_zip_code,testing_lab_phone_number,pregnant,employed_in_healthcare,symptomatic_for_disease,illness_onset_date,resident_congregate_setting,residence_type,hospitalized,icu,ordering_facility_name,ordering_facility_street,ordering_facility_street2,ordering_facility_city,ordering_facility_state,ordering_facility_zip_code,ordering_facility_phone_number,comment,test_result_status,test_ordered_code,genders_of_sexual_partners,syphilis_history
-1234,Doe,Jane,Jingleheimer,123 Main St,Suite 401,Birmingham,AL,35226,Jefferson,205-999-2800,1/20/1962,F,White,Not Hispanic or Latino,Eng,[email protected],123,ID NOW,94534-5,Detected,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,Nasal Swab,1013012657,Smith MD,John,Smitty,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,01D1058442,My Urgent Care,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,N,N,N,01/01/1901,N,22232009,N,N,My Urgent Care,400 Main Street,Suite 100,Birmingham,AL,35228,205-888-2000,Test Comment,C,94534-1,"M, F, trans man, TW, nonbinary",""
-5678,Doe,John,Jingleheimer,333 Elm St,Suite 401,Hoover,AL,35244,Shelby,205-222-2000,11/1/2001,MALE,BLACK OR AFRICAN AMERICAN,NOT HISPANIC OR LATINO,Spa,[email protected],05be96ef-949f-4f46-9c07-2675e8abf412,BD Veritor System for Rapid Detection of SARS-CoV-2*,94558-4,NOT DETECTED,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,ANTERIOR NARES SWAB,1013012657,Smith MD,John,Smitty,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,01D1058442,My Urgent Care,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,NO,YES,Y,01/01/2020,Y,HOSTEL,NO,NO,My Urgent Care,400 Main Street,Suite 100,Birmingham,AL,35228,205-888-2000,testy mctesterson,F,94534-2,"Male, NB",""
+patient_id,patient_last_name,patient_first_name,patient_middle_name,patient_street,patient_street2,patient_city,patient_state,patient_zip_code,patient_county,patient_phone_number,patient_dob,patient_gender,patient_race,patient_ethnicity,patient_preferred_language,patient_email,accession_number,equipment_model_name,test_performed_code,test_result,order_test_date,specimen_collection_date,testing_lab_specimen_received_date,test_result_date,date_result_released,specimen_type,ordering_provider_id,ordering_provider_last_name,ordering_provider_first_name,ordering_provider_middle_name,ordering_provider_street,ordering_provider_street2,ordering_provider_city,ordering_provider_state,ordering_provider_zip_code,ordering_provider_phone_number,testing_lab_clia,testing_lab_name,testing_lab_street,testing_lab_street2,testing_lab_city,testing_lab_state,testing_lab_zip_code,testing_lab_phone_number,pregnant,employed_in_healthcare,symptomatic_for_disease,illness_onset_date,resident_congregate_setting,residence_type,hospitalized,icu,ordering_facility_name,ordering_facility_street,ordering_facility_street2,ordering_facility_city,ordering_facility_state,ordering_facility_zip_code,ordering_facility_phone_number,comment,test_result_status,test_ordered_code,genders_of_sexual_partners,syphilis_history,patient_gender_identity
+1234,Doe,Jane,Jingleheimer,123 Main St,Suite 401,Birmingham,AL,35226,Jefferson,205-999-2800,1/20/1962,F,White,Not Hispanic or Latino,Eng,[email protected],123,ID NOW,94534-5,Detected,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,Nasal Swab,1013012657,Smith MD,John,Smitty,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,01D1058442,My Urgent Care,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,N,N,N,01/01/1901,N,22232009,N,N,My Urgent Care,400 Main Street,Suite 100,Birmingham,AL,35228,205-888-2000,Test Comment,C,94534-1,"M, F, trans man, TW, nonbinary","",m
+5678,Doe,John,Jingleheimer,333 Elm St,Suite 401,Hoover,AL,35244,Shelby,205-222-2000,11/1/2001,MALE,BLACK OR AFRICAN AMERICAN,NOT HISPANIC OR LATINO,Spa,[email protected],05be96ef-949f-4f46-9c07-2675e8abf412,BD Veritor System for Rapid Detection of SARS-CoV-2*,94558-4,NOT DETECTED,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,ANTERIOR NARES SWAB,1013012657,Smith MD,John,Smitty,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,01D1058442,My Urgent Care,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,NO,YES,Y,01/01/2020,Y,HOSTEL,NO,NO,My Urgent Care,400 Main Street,Suite 100,Birmingham,AL,35228,205-888-2000,testy mctesterson,F,94534-2,"Male, NB","",f