Merge branch 'main' into bobby/MOP-backend

backend/build.gradle

@@ -31,7 +31,7 @@ jar {
 
 dependencies {
     // core infrastructure
-    implementation 'org.springframework.boot:spring-boot-starter-web:3.2.0'
+    implementation 'org.springframework.boot:spring-boot-starter-web:3.3.4'
     implementation 'org.springframework.boot:spring-boot-starter-cache'
     implementation 'org.springframework.boot:spring-boot-actuator'
     implementation 'org.springframework.boot:spring-boot-actuator-autoconfigure'
@@ -61,7 +61,7 @@ dependencies {
      *
      * DevSecOps verifies these packages at least once per month. LAST VERIFIED: 10 July 2024.
      */
-    implementation 'com.squareup.okio:okio:3.9.0'
+    implementation 'com.squareup.okio:okio:3.9.1'
     implementation 'org.springframework:spring-core:6.0.16'
     implementation 'org.springframework.security:spring-security-core:6.1.8'
     implementation 'org.springframework.security:spring-security-oauth2-client:6.3.1'

backend/gradle.lockfile

@@ -61,8 +61,8 @@ com.sendgrid:java-http-client:4.5.0=compileClasspath,runtimeClasspath
 com.sendgrid:sendgrid-java:4.10.3=compileClasspath,runtimeClasspath
 com.smartystreets.api:smartystreets-java-sdk:3.18.0=compileClasspath,runtimeClasspath
 com.squareup.okhttp3:okhttp:4.10.0=compileClasspath,runtimeClasspath
-com.squareup.okio:okio-jvm:3.9.0=compileClasspath,runtimeClasspath
-com.squareup.okio:okio:3.9.0=compileClasspath,runtimeClasspath
+com.squareup.okio:okio-jvm:3.9.1=compileClasspath,runtimeClasspath
+com.squareup.okio:okio:3.9.1=compileClasspath,runtimeClasspath
 com.stoyanr:evictor:1.0.0=compileClasspath,runtimeClasspath
 com.sun.istack:istack-commons-runtime:4.1.2=runtimeClasspath
 com.twilio.sdk:twilio:10.1.0=compileClasspath,runtimeClasspath
@@ -204,7 +204,7 @@ org.springframework.boot:spring-boot-starter-security:3.1.7=compileClasspath,run
 org.springframework.boot:spring-boot-starter-thymeleaf:3.1.7=compileClasspath,runtimeClasspath
 org.springframework.boot:spring-boot-starter-tomcat:3.1.7=compileClasspath,runtimeClasspath
 org.springframework.boot:spring-boot-starter-validation:3.1.7=compileClasspath,runtimeClasspath
-org.springframework.boot:spring-boot-starter-web:3.2.0=compileClasspath,runtimeClasspath
+org.springframework.boot:spring-boot-starter-web:3.3.4=compileClasspath,runtimeClasspath
 org.springframework.boot:spring-boot-starter:3.1.7=compileClasspath,runtimeClasspath
 org.springframework.boot:spring-boot:3.1.7=compileClasspath,runtimeClasspath
 org.springframework.cloud:spring-cloud-commons:4.0.4=compileClasspath,runtimeClasspath

backend/src/main/java/gov/cdc/usds/simplereport/api/Translators.java

@@ -378,6 +378,51 @@ public static String parseState(String s) {
     throw IllegalGraphqlArgumentException.invalidInput(s, "state");
   }
 
+  private static final Map<String, String> RESPIRATORY_SYMPTOMS =
+      Map.ofEntries(
+          Map.entry("426000000", "Fever over 100.4F"),
+          Map.entry("103001002", "Feeling feverish"),
+          Map.entry("43724002", "Chills"),
+          Map.entry("49727002", "Cough"),
+          Map.entry("267036007", "Shortness of breath"),
+          Map.entry("230145002", "Difficulty breathing"),
+          Map.entry("84229001", "Fatigue"),
+          Map.entry("68962001", "Muscle or body aches"),
+          Map.entry("25064002", "Headache"),
+          Map.entry("36955009", "New loss of taste"),
+          Map.entry("44169009", "New loss of smell"),
+          Map.entry("162397003", "Sore throat"),
+          Map.entry("68235000", "Nasal congestion"),
+          Map.entry("64531003", "Runny nose"),
+          Map.entry("422587007", "Nausea"),
+          Map.entry("422400008", "Vomiting"),
+          Map.entry("62315008", "Diarrhea"),
+          Map.entry("261665006", "Other symptom not listed"));
+
+  private static final Map<String, String> SYPHILIS_SYMPTOMS =
+      Map.ofEntries(
+          Map.entry("724386005", "Genital sore/lesion"),
+          Map.entry("195469007", "Anal sore/lesion"),
+          Map.entry("26284000", "Sore(s) in mouth/lips"),
+          Map.entry("266128007", "Body Rash"),
+          Map.entry("56940005", "Palmar (hand)/plantar (foot) rash"),
+          Map.entry("91554004", "Flat white warts"),
+          Map.entry("15188001", "Hearing loss"),
+          Map.entry("246636008", "Blurred vision"),
+          Map.entry("56317004", "Alopecia"));
+
+  private static Map<String, String> getSupportedSymptoms() {
+    Map<String, String> supportedSymptoms = new HashMap<>();
+    supportedSymptoms.putAll(RESPIRATORY_SYMPTOMS);
+    supportedSymptoms.putAll(SYPHILIS_SYMPTOMS);
+    return supportedSymptoms;
+  }
+
+  public static String getSymptomName(String snomedCode) {
+    Map<String, String> supportedSymptoms = getSupportedSymptoms();
+    return supportedSymptoms.get(snomedCode);
+  }
+
   public static Map<String, Boolean> parseSymptoms(String symptoms) {
     if (symptoms == null) {
       return Collections.emptyMap();

backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConstants.java

@@ -51,6 +51,8 @@ private FhirConstants() {
 
   public static final String LOINC_AOE_IDENTIFIER = "81959-9";
   public static final String LOINC_AOE_SYMPTOMATIC = "95419-8";
+  public static final String LOINC_SYMPTOM_TIMING_PANEL = "99582-9";
+  public static final String LOINC_SYMPTOM = "75325-1";
   public static final String LOINC_AOE_SYMPTOM_ONSET = "11368-8";
   public static final String LOINC_AOE_PREGNANCY_STATUS = "82810-3";
   public static final String LOINC_AOE_EMPLOYED_IN_HEALTHCARE = "95418-0";

backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConverter.java

@@ -10,6 +10,7 @@
 import static gov.cdc.usds.simplereport.api.Translators.REFUSED;
 import static gov.cdc.usds.simplereport.api.Translators.TRANS_MAN;
 import static gov.cdc.usds.simplereport.api.Translators.TRANS_WOMAN;
+import static gov.cdc.usds.simplereport.api.Translators.getSymptomName;
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.ABNORMAL_FLAGS_CODE_SYSTEM;
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.ABNORMAL_FLAG_ABNORMAL;
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.ABNORMAL_FLAG_NORMAL;
@@ -34,6 +35,8 @@
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.LOINC_AOE_SYMPTOM_ONSET;
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.LOINC_CODE_SYSTEM;
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.LOINC_GENDER_IDENTITY;
+import static gov.cdc.usds.simplereport.api.converter.FhirConstants.LOINC_SYMPTOM;
+import static gov.cdc.usds.simplereport.api.converter.FhirConstants.LOINC_SYMPTOM_TIMING_PANEL;
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.NOTE_TYPE_CODING_SYSTEM;
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.NOTE_TYPE_CODING_SYSTEM_CODE;
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.NOTE_TYPE_CODING_SYSTEM_CODE_INDEX_EXTENSION_URL;
@@ -114,12 +117,15 @@
 import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.Set;
 import java.util.TimeZone;
 import java.util.UUID;
 import java.util.function.Function;
+import java.util.stream.Collectors;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.lang3.StringUtils;
@@ -802,7 +808,7 @@ private void addCorrectionNote(
     }
   }
 
-  public Set<Observation> convertToAOESymptomObservation(
+  public Set<Observation> convertToAOESymptomaticObservation(
       String eventId, Boolean symptomatic, LocalDate symptomOnsetDate) {
     var observations = new LinkedHashSet<Observation>();
     var symptomaticCode =
@@ -827,6 +833,33 @@ public Set<Observation> convertToAOESymptomObservation(
     return observations;
   }
 
+  public Observation createSymptomObservation(CodeableConcept code, Type value) {
+    Observation observation =
+        new Observation().setStatus(ObservationStatus.FINAL).setCode(code).setValue(value);
+    observation.setId(uuidGenerator.randomUUID().toString());
+    observation
+        .addIdentifier()
+        .setUse(IdentifierUse.OFFICIAL)
+        .setType(createLoincConcept(LOINC_SYMPTOM_TIMING_PANEL, "Symptom and timing panel", null));
+    return observation;
+  }
+
+  public Set<Observation> convertToSymptomsObservations(List<String> symptoms) {
+    HashSet<Observation> observations = new HashSet<>();
+
+    CodeableConcept symptomStatusCode = createLoincConcept(LOINC_SYMPTOM, "Symptom", "Symptom");
+
+    symptoms.forEach(
+        symptom -> {
+          String symptomName = getSymptomName(symptom);
+          if (symptomName != null && !symptomName.isBlank()) {
+            CodeableConcept symptomValueCode = createSNOMEDConcept(symptom, symptomName, null);
+            observations.add(createSymptomObservation(symptomStatusCode, symptomValueCode));
+          }
+        });
+    return observations;
+  }
+
   public Set<Observation> convertToAOEGenderOfSexualPartnersObservation(
       Set<String> sexualPartners) {
     HashSet<Observation> observations = new LinkedHashSet<>();
@@ -972,10 +1005,12 @@ public Set<Observation> convertToAOEObservations(
     } else if (surveyData.getSymptoms() != null
         && surveyData.getSymptoms().containsValue(Boolean.TRUE)) {
       symptomatic = true;
+      List<String> symptomsPresent = getFilteredSymptomsPresent(surveyData.getSymptoms());
+      observations.addAll(convertToSymptomsObservations(symptomsPresent));
     } // implied else: AoE form was not completed. Symptomatic set to null
 
     var symptomOnsetDate = surveyData.getSymptomOnsetDate();
-    observations.addAll(convertToAOESymptomObservation(eventId, symptomatic, symptomOnsetDate));
+    observations.addAll(convertToAOESymptomaticObservation(eventId, symptomatic, symptomOnsetDate));
 
     String pregnancyStatus = surveyData.getPregnancy();
     if (pregnancyStatus != null && pregnancyStatusSnomedMap.values().contains(pregnancyStatus)) {
@@ -1195,15 +1230,18 @@ public ServiceRequest convertToServiceRequest(
    */
   public DiagnosticReport convertToDiagnosticReport(TestEvent testEvent, Date currentDate) {
     DiagnosticReportStatus status = null;
+    String id = Objects.toString(testEvent.getInternalId(), "");
     switch (testEvent.getCorrectionStatus()) {
       case ORIGINAL:
         status = (DiagnosticReportStatus.FINAL);
         break;
       case CORRECTED:
         status = (DiagnosticReportStatus.CORRECTED);
+        id = testEvent.getPriorCorrectedTestEventId().toString();
         break;
       case REMOVED:
         status = (DiagnosticReportStatus.ENTEREDINERROR);
+        id = testEvent.getPriorCorrectedTestEventId().toString();
         break;
     }
 
@@ -1241,12 +1279,7 @@ public DiagnosticReport convertToDiagnosticReport(TestEvent testEvent, Date curr
       dateIssued = ZonedDateTime.ofInstant(currentDate.toInstant(), ZoneOffset.UTC);
 
     return convertToDiagnosticReport(
-        status,
-        testOrderLoinc,
-        testOrderLoincLongName,
-        Objects.toString(testEvent.getInternalId(), ""),
-        dateTested,
-        dateIssued);
+        status, testOrderLoinc, testOrderLoincLongName, id, dateTested, dateIssued);
   }
 
   /**
@@ -1616,6 +1649,13 @@ private Patient assignPotentiallyAbsentName(
     return patient;
   }
 
+  private List<String> getFilteredSymptomsPresent(Map<String, Boolean> symptomsMap) {
+    return symptomsMap.entrySet().stream()
+        .filter(symptom -> Boolean.TRUE.equals(symptom.getValue()))
+        .map(Entry::getKey)
+        .collect(Collectors.toList());
+  }
+
   public Bundle createFhirBundle(ConditionAgnosticCreateFhirBundleProps props) {
 
     var patientFullUrl = ResourceType.Patient + "/" + props.getPatient().getId();

backend/src/main/java/gov/cdc/usds/simplereport/config/FeatureFlagsConfig.java

@@ -25,6 +25,7 @@ public class FeatureFlagsConfig {
   private final FeatureFlagRepository _repo;
 
   private boolean oktaMigrationEnabled;
+  private boolean hepatitisCEnabled;
   private boolean syphilisEnabled;
   private boolean hivBulkUploadEnabled;
   private boolean hivEnabled;
@@ -40,6 +41,7 @@ private void loadFeatureFlagsFromDB() {
   private void flagMapping(String flagName, Boolean flagValue) {
     switch (flagName) {
       case "oktaMigrationEnabled" -> setOktaMigrationEnabled(flagValue);
+      case "hepatitisCEnabled" -> setHepatitisCEnabled(flagValue);
       case "syphilisEnabled" -> setSyphilisEnabled(flagValue);
       case "hivBulkUploadEnabled" -> setHivBulkUploadEnabled(flagValue);
       case "hivEnabled" -> setHivEnabled(flagValue);

backend/src/main/java/gov/cdc/usds/simplereport/service/ApiUserService.java

@@ -721,6 +721,10 @@ private UserInfo consolidateUser(ApiUser apiUser, PartialOktaUser oktaUser) {
     OrganizationRoles orgRoles =
         getOrganizationRoles(Optional.ofNullable(oktaClaims), apiUser, isSiteAdmin);
 
+    _dbOrgRoleClaimsService.checkOrgRoleClaimsEquality(
+        List.of(oktaClaims),
+        List.of(_dbOrgRoleClaimsService.getOrganizationRoleClaims(apiUser)),
+        apiUser.getLoginEmail());
     return new UserInfo(apiUser, Optional.of(orgRoles), isSiteAdmin, userStatus);
   }
 

backend/src/main/java/gov/cdc/usds/simplereport/service/DbOrgRoleClaimsService.java

@@ -67,7 +67,9 @@ public OrganizationRoleClaims getOrganizationRoleClaims(ApiUser user) {
    * @return boolean
    */
   public boolean checkOrgRoleClaimsEquality(
-      List<OrganizationRoleClaims> oktaClaims, List<OrganizationRoleClaims> dbClaims) {
+      List<OrganizationRoleClaims> oktaClaims,
+      List<OrganizationRoleClaims> dbClaims,
+      String username) {
     boolean hasEqualRoleClaims = false;
     if (oktaClaims.size() == dbClaims.size()) {
       List<OrganizationRoleClaims> sanitizedOktaClaims = sanitizeOktaOrgRoleClaims(oktaClaims);
@@ -79,17 +81,18 @@ public boolean checkOrgRoleClaimsEquality(
                           .anyMatch(dbClaim -> equalOrgRoleClaim(sanitizedOktaClaim, dbClaim)));
     }
     if (!hasEqualRoleClaims) {
-      logUnequalClaims();
+      logUnequalClaims(username);
     }
 
     return hasEqualRoleClaims;
   }
 
-  /** Logs a message saying OrganizationRoleClaims are unequal with the affected User ID */
-  private void logUnequalClaims() {
-    // WIP: Currently assumes check is for the current user
-    // This may change based on where checkOrgRoleClaimsEquality is called
-    String username = _getCurrentUser.get().getUsername();
+  /**
+   * Logs a message saying OrganizationRoleClaims are unequal with the affected User ID *
+   *
+   * @param username - String user login email
+   */
+  private void logUnequalClaims(String username) {
     ApiUser user = _userRepo.findByLoginEmail(username).orElseThrow(NonexistentUserException::new);
     log.error(
         "Okta OrganizationRoleClaims do not match database OrganizationRoleClaims for User ID: {}",

backend/src/main/java/gov/cdc/usds/simplereport/service/LoggedInAuthorizationService.java

@@ -60,6 +60,8 @@ public List<OrganizationRoleClaims> findAllOrganizationRoles() {
       String username = currentAuth.getName();
       List<OrganizationRoleClaims> dbOrgRoleClaims =
           _dbOrgRoleClaimsService.getOrganizationRoleClaims(username);
+      _dbOrgRoleClaimsService.checkOrgRoleClaimsEquality(
+          oktaOrgRoleClaims, dbOrgRoleClaims, username);
       if (_featureFlagsConfig.isOktaMigrationEnabled()) {
         return dbOrgRoleClaims;
       }

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

@@ -458,7 +458,8 @@ private Bundle convertRowToFhirBundle(TestResultRow row, UUID orgId) {
     }
 
     aoeObservations.addAll(
-        fhirConverter.convertToAOESymptomObservation(testEventId, symptomatic, symptomOnsetDate));
+        fhirConverter.convertToAOESymptomaticObservation(
+            testEventId, symptomatic, symptomOnsetDate));
 
     String pregnancyValue = row.getPregnant().getValue();
     if (StringUtils.isNotBlank(pregnancyValue)) {

backend/src/main/resources/application-azure-prod.yaml

@@ -22,6 +22,7 @@ twilio:
   from-number: "+14045312484"
 features:
   oktaMigrationEnabled: false
+  hepatitisCEnabled: false
   syphilisEnabled: false
   hivBulkUploadEnabled: true
   hivEnabled: true

backend/src/main/resources/application.yaml

@@ -175,6 +175,7 @@ datahub:
   csv-upload-api-fhir-client: "simple_report.fullelr"
 features:
   oktaMigrationEnabled: false
+  hepatitisCEnabled: true
   syphilisEnabled: true
   hivBulkUploadEnabled: true
   hivEnabled: true

backend/src/main/resources/db/changelog/db.changelog-master.yaml

@@ -5634,7 +5634,7 @@ databaseChangeLog:
         - addColumn:
             tableName: test_order
             columns:
-              - column:
+            - column:
                   name: timer_started_at
                   type: text
                   constraints:
@@ -5644,6 +5644,25 @@ databaseChangeLog:
             tableName: test_order
             columnName: timer_started_at
 
+  - changeSet:
+      id: add-hepatitis-c-to-supported_disease-table
+      author: [email protected]
+      comment: Add Hepatitis-C to the supported_disease table.
+      changes:
+        - tagDatabase:
+            tag: add-hepatitis-c-to-supported_disease-table
+        - sql:
+            sql: |
+              INSERT INTO ${database.defaultSchemaName}.supported_disease (
+                   internal_id,
+                   name,
+                   loinc)
+              VALUES
+                   (gen_random_uuid(), 'Hepatitis-C', 'LP14400-3')
+      rollback:
+        - sql:
+            sql: DELETE FROM ${database.defaultSchemaName}.supported_disease WHERE name = 'Hepatitis-C';
+
   - changeSet:
       id: create-facility_providers-table
       author: [email protected]