Add sonarlint fixes

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

@@ -0,0 +1,18 @@
+package gov.cdc.usds.simplereport.api.converter;
+
+import java.time.ZonedDateTime;
+import lombok.Builder;
+import lombok.Getter;
+
+@Builder
+@Getter
+public class ConvertToSpecimenProps {
+  private String specimenCode;
+  private String specimenName;
+  private String collectionCode;
+  private String collectionName;
+  private String id;
+  private String identifier;
+  private ZonedDateTime collectionDate;
+  private ZonedDateTime receivedTime;
+}

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

@@ -73,7 +73,6 @@
 import java.util.TimeZone;
 import java.util.UUID;
 import java.util.function.Function;
-import java.util.stream.Collectors;
 import javax.validation.constraints.NotNull;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
@@ -158,7 +157,7 @@ public HumanName convertToHumanName(String first, String middle, String last, St
 
   public List<ContactPoint> convertPhoneNumbersToContactPoint(
       @NotNull List<PhoneNumber> phoneNumber) {
-    return phoneNumber.stream().map(this::convertToContactPoint).collect(Collectors.toList());
+    return phoneNumber.stream().map(this::convertToContactPoint).toList();
   }
 
   public ContactPoint convertToContactPoint(@NotNull PhoneNumber phoneNumber) {
@@ -187,9 +186,7 @@ public ContactPoint convertToContactPoint(ContactPointUse contactPointUse, Strin
   }
 
   public List<ContactPoint> convertEmailsToContactPoint(ContactPointUse use, List<String> emails) {
-    return emails.stream()
-        .map(email -> convertEmailToContactPoint(use, email))
-        .collect(Collectors.toList());
+    return emails.stream().map(email -> convertEmailToContactPoint(use, email)).toList();
   }
 
   public ContactPoint convertEmailToContactPoint(ContactPointUse use, @NotNull String email) {
@@ -203,11 +200,9 @@ public ContactPoint convertToContactPoint(
 
   public AdministrativeGender convertToAdministrativeGender(@NotNull String gender) {
     switch (gender.toLowerCase()) {
-      case "male":
-      case "m":
+      case "male", "m":
         return AdministrativeGender.MALE;
-      case "female":
-      case "f":
+      case "female", "f":
         return AdministrativeGender.FEMALE;
       default:
         return AdministrativeGender.UNKNOWN;
@@ -496,41 +491,33 @@ public Device convertToDevice(String manufacturer, @NotNull String model, String
     return device;
   }
 
-  public Specimen convertToSpecimen(
-      String specimenCode,
-      String specimenName,
-      String collectionCode,
-      String collectionName,
-      String id,
-      String identifier,
-      ZonedDateTime collectionDate,
-      ZonedDateTime receivedTime) {
+  public Specimen convertToSpecimen(ConvertToSpecimenProps props) {
     var specimen = new Specimen();
-    specimen.setId(id);
-    specimen.addIdentifier().setValue(identifier);
-    if (StringUtils.isNotBlank(specimenCode)) {
+    specimen.setId(props.getId());
+    specimen.addIdentifier().setValue(props.getIdentifier());
+    if (StringUtils.isNotBlank(props.getSpecimenCode())) {
       var codeableConcept = specimen.getType();
       var coding = codeableConcept.addCoding();
       coding.setSystem(SNOMED_CODE_SYSTEM);
-      coding.setCode(specimenCode);
-      codeableConcept.setText(specimenName);
+      coding.setCode(props.getSpecimenCode());
+      codeableConcept.setText(props.getSpecimenName());
     }
-    if (StringUtils.isNotBlank(collectionCode)) {
+    if (StringUtils.isNotBlank(props.getCollectionCode())) {
       var collection = specimen.getCollection();
       var codeableConcept = collection.getBodySite();
       var coding = codeableConcept.addCoding();
       coding.setSystem(SNOMED_CODE_SYSTEM);
-      coding.setCode(collectionCode);
-      codeableConcept.setText(collectionName);
+      coding.setCode(props.getCollectionCode());
+      codeableConcept.setText(props.getCollectionName());
     }
 
-    if (collectionDate != null) {
+    if (props.getCollectionDate() != null) {
       var collection = specimen.getCollection();
-      collection.setCollected(convertToDateTimeType(collectionDate));
+      collection.setCollected(convertToDateTimeType(props.getCollectionDate()));
     }
 
-    if (receivedTime != null) {
-      specimen.setReceivedTimeElement(convertToDateTimeType(receivedTime));
+    if (props.getReceivedTime() != null) {
+      specimen.setReceivedTimeElement(convertToDateTimeType(props.getReceivedTime()));
     }
 
     return specimen;
@@ -542,14 +529,16 @@ public Specimen convertToSpecimen(
       ZonedDateTime collectionDate,
       ZonedDateTime receivedTime) {
     return convertToSpecimen(
-        specimenType.getTypeCode(),
-        specimenType.getName(),
-        specimenType.getCollectionLocationCode(),
-        specimenType.getCollectionLocationName(),
-        specimenType.getInternalId().toString(),
-        specimenIdentifier.toString(),
-        collectionDate,
-        receivedTime);
+        ConvertToSpecimenProps.builder()
+            .specimenCode(specimenType.getTypeCode())
+            .specimenName(specimenType.getName())
+            .collectionCode(specimenType.getCollectionLocationCode())
+            .collectionName(specimenType.getCollectionLocationName())
+            .id(specimenType.getInternalId().toString())
+            .identifier(specimenIdentifier.toString())
+            .collectionDate(collectionDate)
+            .receivedTime(receivedTime)
+            .build());
   }
 
   public List<Observation> convertToObservation(
@@ -586,7 +575,7 @@ public List<Observation> convertToObservation(
                   deviceType.getModel(),
                   resultDate);
             })
-        .collect(Collectors.toList());
+        .toList();
   }
 
   public String getCommonDiseaseValue(
@@ -728,7 +717,7 @@ public Set<Observation> convertToAOEObservation(
 
   public Set<Observation> convertToAOEObservations(String eventId, AskOnEntrySurvey surveyData) {
     Boolean symptomatic = null;
-    if (surveyData.getNoSymptoms()) {
+    if (Boolean.TRUE.equals(surveyData.getNoSymptoms())) {
       symptomatic = false;
     } else if (surveyData.getSymptoms().containsValue(Boolean.TRUE)) {
       symptomatic = true;

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

@@ -31,12 +31,17 @@ public class ResultsUploaderCachingService {
   private final SpecimenTypeRepository specimenTypeRepository;
   private final AddressValidationService addressValidationService;
 
+  private static final String NASAL_SWAB_SNOMED = "445297001";
+  private static final String NASAL_THROAT_SWAB_SNOMED = "433801000124107";
+  private static final String BRONCHOALVEOLAR_LAVAGE = "258607008";
+  private static final String DRIED_BLOOD_SPOT = "440500007";
+
   private static final Map<String, String> specimenSNOMEDMap =
       Map.ofEntries(
-          Map.entry("swab of internal nose", "445297001"),
-          Map.entry("nasal swab", "445297001"),
-          Map.entry("nasal", "445297001"),
-          Map.entry("varied", "445297001"),
+          Map.entry("swab of internal nose", NASAL_SWAB_SNOMED),
+          Map.entry("nasal swab", NASAL_SWAB_SNOMED),
+          Map.entry("nasal", NASAL_SWAB_SNOMED),
+          Map.entry("varied", NASAL_SWAB_SNOMED),
           Map.entry("nasopharyngeal swab", "258500001"),
           Map.entry("mid-turbinate nasal swab", "871810001"),
           Map.entry("anterior nares swab", "697989009"),
@@ -64,17 +69,17 @@ public class ResultsUploaderCachingService {
           Map.entry("blood specimen", "119297000"),
           Map.entry("capillary blood specimen", "122554006"),
           Map.entry("fingerstick whole blood", "122554006"),
-          Map.entry("dried blood spot specimen", "440500007"),
-          Map.entry("dried blood spot", "440500007"),
-          Map.entry("fingerstick blood dried blood spot", "440500007"),
-          Map.entry("nasopharyngeal and oropharyngeal swab", "433801000124107"),
-          Map.entry("nasal and throat swab combination", "433801000124107"),
-          Map.entry("nasal and throat swab", "433801000124107"),
+          Map.entry("dried blood spot specimen", DRIED_BLOOD_SPOT),
+          Map.entry("dried blood spot", DRIED_BLOOD_SPOT),
+          Map.entry("fingerstick blood dried blood spot", DRIED_BLOOD_SPOT),
+          Map.entry("nasopharyngeal and oropharyngeal swab", NASAL_THROAT_SWAB_SNOMED),
+          Map.entry("nasal and throat swab combination", NASAL_THROAT_SWAB_SNOMED),
+          Map.entry("nasal and throat swab", NASAL_THROAT_SWAB_SNOMED),
           Map.entry("lower respiratory fluid sample", "309171007"),
           Map.entry("lower respiratory tract aspirates", "309171007"),
-          Map.entry("bronchoalveolar lavage fluid sample", "258607008"),
-          Map.entry("bronchoalveolar lavage fluid", "258607008"),
-          Map.entry("bronchoalveolar lavage", "258607008"));
+          Map.entry("bronchoalveolar lavage fluid sample", BRONCHOALVEOLAR_LAVAGE),
+          Map.entry("bronchoalveolar lavage fluid", BRONCHOALVEOLAR_LAVAGE),
+          Map.entry("bronchoalveolar lavage", BRONCHOALVEOLAR_LAVAGE));
 
   @Cacheable(DEVICE_MODEL_AND_TEST_PERFORMED_CODE_MAP)
   public Map<String, DeviceType> getModelAndTestPerformedCodeToDeviceMap() {

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

@@ -13,6 +13,7 @@
 import gov.cdc.usds.simplereport.api.Translators;
 import gov.cdc.usds.simplereport.api.converter.ConvertToObservationProps;
 import gov.cdc.usds.simplereport.api.converter.ConvertToPatientProps;
+import gov.cdc.usds.simplereport.api.converter.ConvertToSpecimenProps;
 import gov.cdc.usds.simplereport.api.converter.CreateFhirBundleProps;
 import gov.cdc.usds.simplereport.api.converter.FhirConverter;
 import gov.cdc.usds.simplereport.api.model.errors.CsvProcessingException;
@@ -37,7 +38,6 @@
 import java.util.UUID;
 import java.util.concurrent.CompletableFuture;
 import java.util.concurrent.ExecutionException;
-import java.util.stream.Collectors;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.lang3.StringUtils;
@@ -121,7 +121,7 @@ public List<String> convertToFhirBundles(InputStream csvStream, UUID orgId) {
                     throw new CsvProcessingException("Unable to process file.");
                   }
                 })
-            .collect(Collectors.toList());
+            .toList();
 
     // Clear cache to free memory
     resultsUploaderCachingService.clearAddressTimezoneLookupCache();
@@ -331,14 +331,16 @@ private Bundle convertRowToFhirBundle(TestResultRow row, UUID orgId) {
 
     var specimen =
         fhirConverter.convertToSpecimen(
-            getSpecimenTypeSnomed(row.getSpecimenType().getValue()),
-            getDescriptionValue(row.getSpecimenType().getValue()),
-            null,
-            null,
-            uuidGenerator.randomUUID().toString(),
-            uuidGenerator.randomUUID().toString(),
-            specimenCollectionDate,
-            testingLabSpecimenReceivedDate);
+            ConvertToSpecimenProps.builder()
+                .specimenCode(getSpecimenTypeSnomed(row.getSpecimenType().getValue()))
+                .specimenName(getDescriptionValue(row.getSpecimenType().getValue()))
+                .collectionCode(null)
+                .collectionName(null)
+                .id(uuidGenerator.randomUUID().toString())
+                .identifier(uuidGenerator.randomUUID().toString())
+                .collectionDate(specimenCollectionDate)
+                .receivedTime(testingLabSpecimenReceivedDate)
+                .build());
 
     var observation =
         List.of(

backend/src/test/java/gov/cdc/usds/simplereport/api/converter/FhirConverterTest.java

@@ -513,17 +513,22 @@ void convertToDevice_DeviceType_matchesJson() throws IOException {
 
   @Test
   void convertToSpecimen_Strings_valid() {
+    var collectionDate =
+        ZonedDateTime.ofInstant(Instant.parse("2023-06-22T16:38:00.000Z"), DEFAULT_TIME_ZONE_ID);
+    var receivedTime = ZonedDateTime.of(2023, 6, 23, 12, 0, 0, 0, ZoneId.of("US/Eastern"));
+
     var actual =
         fhirConverter.convertToSpecimen(
-            "258500001",
-            "Nasopharyngeal swab",
-            "53342003",
-            "Internal nose structure (body structure)",
-            "id-123",
-            "uuid-123",
-            ZonedDateTime.ofInstant(
-                Instant.parse("2023-06-22T16:38:00.000Z"), DEFAULT_TIME_ZONE_ID),
-            ZonedDateTime.of(2023, 6, 23, 12, 0, 0, 0, ZoneId.of("US/Eastern")));
+            ConvertToSpecimenProps.builder()
+                .specimenCode("258500001")
+                .specimenName("Nasopharyngeal swab")
+                .collectionCode("53342003")
+                .collectionName("Internal nose structure (body structure)")
+                .id("id-123")
+                .identifier("uuid-123")
+                .collectionDate(collectionDate)
+                .receivedTime(receivedTime)
+                .build());
 
     assertThat(actual.getId()).isEqualTo("id-123");
     assertThat(actual.getIdentifierFirstRep().getValue()).isEqualTo("uuid-123");
@@ -545,7 +550,7 @@ void convertToSpecimen_Strings_valid() {
 
   @Test
   void convertToSpecimen_Strings_null() {
-    var actual = fhirConverter.convertToSpecimen(null, null, null, null, null, null, null, null);
+    var actual = fhirConverter.convertToSpecimen(ConvertToSpecimenProps.builder().build());
 
     assertThat(actual.getId()).isNull();
     assertThat(actual.getType().getText()).isNull();