[DCJ-400] Upgrade com.diffplug.spotless 6.7.1 -> 6.25.0

build.gradle

@@ -37,7 +37,7 @@ plugins {
     id 'java'
     id 'io.spring.dependency-management' version '1.1.6'
     id 'jacoco'
-    id 'com.diffplug.spotless' version '6.7.1'
+    id 'com.diffplug.spotless' version '6.25.0'
     id 'com.dorongold.task-tree' version '4.0.0'
     // enables release info in sentry events
     id 'com.gorylenko.gradle-git-properties' version '2.4.2'

src/main/java/bio/terra/app/configuration/ApplicationConfiguration.java

@@ -49,14 +49,18 @@ public class ApplicationConfiguration {
   private String dnsName;
   private String resourceId;
   private String userId;
+
   /**
    * Size of the Stairway thread pool. The pool is consumed by requests and by file load threads.
    */
   private int maxStairwayThreads;
+
   /** Maximum number of file loads allowed in the input array in a bulk file load */
   private int maxBulkFileLoadArray;
+
   /** Number of file loads to run concurrently in a bulk file load */
   private int loadConcurrentFiles;
+
   /**
    * Number of file loads to run concurrently. NOTE: the maximum number of threads used for load is
    * one for the driver flight and N for the number of concurrent files: {@code

src/main/java/bio/terra/app/configuration/JdbcConfiguration.java

@@ -18,6 +18,7 @@ public class JdbcConfiguration {
   private String username;
   private String password;
   private String changesetFile;
+
   /**
    * Maximum number of database connections in the connection pool; -1 means no limit The goal of
    * these parameters is to prevent waiting for a database connection.

src/main/java/bio/terra/common/LockOperation.java

@@ -22,6 +22,7 @@ public enum LockOperation {
   LockOperation(boolean isLock) {
     this(isLock, null, null);
   }
+
   /**
    * @return additional guidance for users investigating a failed lock operation, usually as part of
    *     a failed job / flight.

src/main/java/bio/terra/common/SynapseColumn.java

@@ -98,8 +98,8 @@ public static String translateDataType(
       case TIME -> "time";
         // Data of type RECORD contains table-like that can be nested or repeated
         // It's provided in JSON format, making it hard to parse from inside a CSV/JSON ingest
-      case RECORD -> throw new NotSupportedException(
-          "RECORD type is not yet supported for synapse");
+      case RECORD ->
+          throw new NotSupportedException("RECORD type is not yet supported for synapse");
     };
   }
 

src/main/java/bio/terra/service/auth/iam/IamProviderInterface.java

@@ -275,6 +275,7 @@ void overwriteGroupPolicyEmailsIncludeRequestingUser(
       String policyName,
       List<String> emailAddresses)
       throws InterruptedException;
+
   /**
    * @param accessToken valid oauth token for the account modifying the group policy members
    * @param groupName name of Firecloud managed group

src/main/java/bio/terra/service/auth/iam/sam/SamApiService.java

@@ -24,6 +24,7 @@ public class SamApiService {
 
   private final SamConfiguration samConfig;
   private final ConfigurationService configurationService;
+
   /** OkHttpClients should be shared among requests to reduce latency and save memory * */
   private final OkHttpClient sharedHttpClient;
 

src/main/java/bio/terra/service/duos/DuosClient.java

@@ -121,10 +121,12 @@ public DuosDatasetApprovedUsers getApprovedUsers(String duosId) {
   static ErrorReportException convertToDataRepoException(
       HttpStatusCodeException duosEx, String duosId) {
     return switch (HttpStatus.valueOf(duosEx.getStatusCode().value())) {
-      case BAD_REQUEST -> new DuosDatasetBadRequestException(
-          "DUOS dataset identifier %s is malformed".formatted(duosId), duosEx);
-      case NOT_FOUND -> new DuosDatasetNotFoundException(
-          "Could not find DUOS dataset for identifier %s".formatted(duosId), duosEx);
+      case BAD_REQUEST ->
+          new DuosDatasetBadRequestException(
+              "DUOS dataset identifier %s is malformed".formatted(duosId), duosEx);
+      case NOT_FOUND ->
+          new DuosDatasetNotFoundException(
+              "Could not find DUOS dataset for identifier %s".formatted(duosId), duosEx);
       default -> new DuosInternalServerErrorException("Unexpected error from DUOS", duosEx);
     };
   }

src/main/java/bio/terra/service/filedata/azure/AzureSynapsePdao.java

@@ -1462,16 +1462,16 @@ private Object extractValue(ResultSet resultSet, Column column) {
         return switch (column.getType()) {
           case BOOLEAN -> resultSet.getBoolean(column.getName());
           case BYTES -> resultSet.getBytes(column.getName());
-          case DIRREF, FILEREF, STRING, TEXT, DATE, DATETIME, TIMESTAMP -> resultSet.getString(
-              column.getName());
+          case DIRREF, FILEREF, STRING, TEXT, DATE, DATETIME, TIMESTAMP ->
+              resultSet.getString(column.getName());
           case FLOAT -> resultSet.getFloat(column.getName());
           case FLOAT64 -> resultSet.getDouble(column.getName());
           case INTEGER -> resultSet.getInt(column.getName());
           case INT64 -> resultSet.getLong(column.getName());
           case NUMERIC -> resultSet.getFloat(column.getName());
           case TIME -> resultSet.getTime(column.getName());
-          default -> throw new IllegalArgumentException(
-              "Unknown datatype '" + column.getType() + "'");
+          default ->
+              throw new IllegalArgumentException("Unknown datatype '" + column.getType() + "'");
         };
       } catch (SQLException e) {
         throw new PdaoException("Error reading data", e);
@@ -1492,17 +1492,11 @@ private Object extractValue(ResultSet resultSet, Column column) {
       TypeReference<?> targetType =
           switch (column.getType()) {
             case BOOLEAN -> new TypeReference<List<Boolean>>() {};
-            case DATE,
-                DATETIME,
-                DIRREF,
-                FILEREF,
-                STRING,
-                TEXT,
-                TIME,
-                TIMESTAMP -> new TypeReference<List<String>>() {};
+            case DATE, DATETIME, DIRREF, FILEREF, STRING, TEXT, TIME, TIMESTAMP ->
+                new TypeReference<List<String>>() {};
             case FLOAT, FLOAT64, INTEGER, INT64, NUMERIC -> new TypeReference<List<Number>>() {};
-            default -> throw new IllegalArgumentException(
-                "Unknown datatype '" + column.getType() + "'");
+            default ->
+                throw new IllegalArgumentException("Unknown datatype '" + column.getType() + "'");
           };
       try {
         return objectMapper.readValue(rawValue, targetType);

src/main/java/bio/terra/service/filedata/azure/util/AzureConstants.java

@@ -6,10 +6,12 @@ private AzureConstants() {}
 
   /** The code that the Azure resource management APIs found when a resource is not found */
   public static final String RESOURCE_NOT_FOUND_CODE = "ResourceNotFound";
+
   /**
    * The code that the Azure security insights management APIs found when a resource is not found
    */
   public static final String NOT_FOUND_CODE = "NotFound";
+
   /**
    * The code that the Azure resource management APIs found when an invalid request is sent. This
    * can sometimes be equivalent to a 404

src/main/java/bio/terra/service/filedata/google/firestore/FireStoreDirectoryDao.java

@@ -332,6 +332,7 @@ public List<FireStoreDirectoryEntry> enumerateAll(Firestore firestore, String co
     CollectionReference dirColl = firestore.collection(collectionId);
     return query(dirColl.orderBy("path"));
   }
+
   // -- private methods --
 
   List<FireStoreDirectoryEntry> enumerateDirectory(

src/main/java/bio/terra/service/filedata/google/gcs/GcsPdao.java

@@ -243,6 +243,7 @@ public void writeListToCloudFile(String path, List<String> contentsToWrite, Stri
       writeStreamToCloudFile(path, stream, projectId);
     }
   }
+
   /**
    * Write a {@link Stream} to a GCS file separated by newlines
    *

src/main/java/bio/terra/service/load/LoadService.java

@@ -125,6 +125,7 @@ public LoadHistoryIterator loadHistoryIterator(
       List<BulkLoadHistoryModel> backingList, int chunkSize) {
     return new LoadHistoryIterator(backingList, chunkSize);
   }
+
   /**
    * A convenience class wrapping the getting of load history table rows in an Iterator. The
    * Iterator's elements are a list of BulkLoadHistoryModel chunk of the full results retrieved from

src/main/java/bio/terra/service/policy/PolicyApiService.java

@@ -14,6 +14,7 @@
 @Service
 public class PolicyApiService {
   private final PolicyServiceConfiguration policyServiceConfiguration;
+
   /** Clients should be shared among requests to reduce latency and save memory * */
   private final Client sharedHttpClient;
 

src/main/java/bio/terra/service/policy/PolicyService.java

@@ -131,10 +131,11 @@ public void deletePaoIfExists(UUID resourceId) {
   @VisibleForTesting
   static RuntimeException convertApiException(ApiException ex) {
     return switch (ex.getCode()) {
-      case HttpStatus.SC_UNAUTHORIZED -> new PolicyServiceAuthorizationException(
-          "Not authorized to access Terra Policy Service", ex.getCause());
-      case HttpStatus.SC_NOT_FOUND -> new PolicyServiceNotFoundException(
-          "Policy access object not found", ex);
+      case HttpStatus.SC_UNAUTHORIZED ->
+          new PolicyServiceAuthorizationException(
+              "Not authorized to access Terra Policy Service", ex.getCause());
+      case HttpStatus.SC_NOT_FOUND ->
+          new PolicyServiceNotFoundException("Policy access object not found", ex);
       case HttpStatus.SC_BAD_REQUEST -> {
         if (StringUtils.containsIgnoreCase(ex.getMessage(), "duplicate")) {
           // TODO - this special handling may be removed once
@@ -146,8 +147,8 @@ yield new PolicyServiceDuplicateException(
           yield new PolicyServiceApiException(ex);
         }
       }
-      case HttpStatus.SC_CONFLICT -> new PolicyConflictException(
-          "Policy access object already exists", ex);
+      case HttpStatus.SC_CONFLICT ->
+          new PolicyConflictException("Policy access object already exists", ex);
       default -> new PolicyServiceApiException(ex);
     };
   }

src/main/java/bio/terra/service/resourcemanagement/BufferService.java

@@ -38,6 +38,7 @@ public class BufferService {
   private final ResourceBufferServiceConfiguration bufferServiceConfiguration;
   private final GoogleResourceConfiguration googleConfig;
   private final GoogleResourceManagerService googleResourceManagerService;
+
   /** Clients should be shared among requests to reduce latency and save memory * */
   private final Client sharedHttpClient;
 

src/main/java/bio/terra/service/resourcemanagement/MetadataDataAccessUtils.java

@@ -84,6 +84,7 @@ public AccessInfoModel accessInfoFromSnapshot(
       final Snapshot snapshot, final AuthenticatedUserRequest userRequest) {
     return accessInfoFromSnapshot(snapshot, userRequest, null);
   }
+
   /** Generate an {@link AccessInfoModel} from a Snapshot */
   public AccessInfoModel accessInfoFromSnapshot(
       final Snapshot snapshot, final AuthenticatedUserRequest userRequest, String forTable) {

src/main/java/bio/terra/service/snapshot/DatasetProject.java

@@ -8,6 +8,7 @@ public class DatasetProject {
   private UUID profileId;
   private String
       dataProject; // Project id of the snapshot data project--which is a string and feels like a
+
   // name
 
   public UUID getId() {

src/main/java/bio/terra/service/snapshot/SnapshotRequestValidator.java

@@ -67,8 +67,8 @@ private void validateSnapshotContents(
               }
               case BYQUERY -> validateSnapshotQuerySpec(contents.getQuerySpec(), errors);
               case BYROWID -> validateSnapshotRowIdSpec(contents.getRowIdSpec(), errors);
-              case BYREQUESTID -> validateSnapshotRequestIdSpec(
-                  contents.getRequestIdSpec(), errors);
+              case BYREQUESTID ->
+                  validateSnapshotRequestIdSpec(contents.getRequestIdSpec(), errors);
             }
           });
     }

src/main/java/bio/terra/service/snapshot/flight/create/SnapshotCreateFlight.java

@@ -219,18 +219,19 @@ public SnapshotCreateFlight(FlightMap inputParameters, Object applicationContext
                     new CreateSnapshotByAssetParquetFilesAzureStep(
                         azureSynapsePdao, snapshotService, snapshotReq, snapshotId)));
       }
-      case BYFULLVIEW -> addStep(
-          platform.choose(
-              () ->
-                  new CreateSnapshotPrimaryDataFullViewGcpStep(
-                      bigQuerySnapshotPdao,
-                      snapshotDao,
-                      snapshotService,
-                      snapshotReq,
-                      sourceDataset),
-              () ->
-                  new CreateSnapshotByFullViewParquetFilesAzureStep(
-                      azureSynapsePdao, snapshotService, snapshotReq, snapshotId)));
+      case BYFULLVIEW ->
+          addStep(
+              platform.choose(
+                  () ->
+                      new CreateSnapshotPrimaryDataFullViewGcpStep(
+                          bigQuerySnapshotPdao,
+                          snapshotDao,
+                          snapshotService,
+                          snapshotReq,
+                          sourceDataset),
+                  () ->
+                      new CreateSnapshotByFullViewParquetFilesAzureStep(
+                          azureSynapsePdao, snapshotService, snapshotReq, snapshotId)));
       case BYQUERY -> {
         addStep(new CreateSnapshotValidateQueryStep(datasetService, snapshotReq));
         addStep(
@@ -255,14 +256,15 @@ public SnapshotCreateFlight(FlightMap inputParameters, Object applicationContext
                         snapshotId,
                         sourceDataset)));
       }
-      case BYROWID -> addStep(
-          platform.choose(
-              () ->
-                  new CreateSnapshotPrimaryDataRowIdsStep(
-                      bigQuerySnapshotPdao, snapshotDao, snapshotService, snapshotReq),
-              () ->
-                  new CreateSnapshotByRowIdParquetFilesAzureStep(
-                      azureSynapsePdao, snapshotService, snapshotReq, snapshotId)));
+      case BYROWID ->
+          addStep(
+              platform.choose(
+                  () ->
+                      new CreateSnapshotPrimaryDataRowIdsStep(
+                          bigQuerySnapshotPdao, snapshotDao, snapshotService, snapshotReq),
+                  () ->
+                      new CreateSnapshotByRowIdParquetFilesAzureStep(
+                          azureSynapsePdao, snapshotService, snapshotReq, snapshotId)));
       case BYREQUESTID -> {
         addStep(new CreateSnapshotSamGroupNameStep(snapshotId, iamService));
         addStep(new CreateSnapshotSamGroupStep(iamService));

src/main/java/bio/terra/service/snapshotbuilder/SnapshotAccessRequestModel.java

@@ -86,12 +86,15 @@ static String generateSummaryForCriteriaGroup(
             .map(
                 criteria ->
                     switch (criteria.getKind()) {
-                      case LIST -> generateSummaryForCriteria(
-                          (SnapshotBuilderProgramDataListCriteria) criteria, settings);
-                      case RANGE -> generateSummaryForCriteria(
-                          (SnapshotBuilderProgramDataRangeCriteria) criteria, settings);
-                      case DOMAIN -> generateSummaryForCriteria(
-                          (SnapshotBuilderDomainCriteria) criteria, settings);
+                      case LIST ->
+                          generateSummaryForCriteria(
+                              (SnapshotBuilderProgramDataListCriteria) criteria, settings);
+                      case RANGE ->
+                          generateSummaryForCriteria(
+                              (SnapshotBuilderProgramDataRangeCriteria) criteria, settings);
+                      case DOMAIN ->
+                          generateSummaryForCriteria(
+                              (SnapshotBuilderDomainCriteria) criteria, settings);
                     })
             .collect(Collectors.joining("\n")));
   }

src/main/java/bio/terra/service/snapshotbuilder/query/Literal.java

@@ -70,11 +70,12 @@ public String renderSQL(SqlRenderContext context) {
     return switch (dataType) {
       case STRING -> stringVal == null ? "NULL" : "'" + sqlEscape(stringVal) + "'";
       case INT64 -> String.valueOf(int64Val);
-      case BOOLEAN -> context
-          .getPlatform()
-          // In T-SQL, TRUE is not a keyword, so we need to use 1 instead. The JDBC API converts
-          // the 1 to a boolean TRUE when the query result is processed.
-          .choose(() -> String.valueOf(booleanVal), () -> booleanVal ? "1" : "0");
+      case BOOLEAN ->
+          context
+              .getPlatform()
+              // In T-SQL, TRUE is not a keyword, so we need to use 1 instead. The JDBC API converts
+              // the 1 to a boolean TRUE when the query result is processed.
+              .choose(() -> String.valueOf(booleanVal), () -> booleanVal ? "1" : "0");
       case DATE -> "DATE('" + dateVal.toString() + "')";
       case DOUBLE -> "FLOAT('" + doubleVal + "')";
     };

src/main/java/bio/terra/service/snapshotbuilder/utils/HierarchyQueryBuilder.java

@@ -85,6 +85,7 @@ public Query generateQuery(SnapshotBuilderDomainOption domainOption, int concept
         .orderBy(List.of(new OrderByVariable(conceptName, OrderByDirection.ASCENDING)))
         .build();
   }
+
   /**
    * Filter concept to only allow standard concepts. See <a
    * href="https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:standard_classification_and_source_concepts">Standard,

src/main/java/bio/terra/service/tabulardata/google/bigquery/BigQueryPdao.java

@@ -181,6 +181,7 @@ public static int getTableTotalRowCount(FSContainerInterface tdrResource, String
       return 0;
     }
   }
+
   /*
    * WARNING: Ensure input parameters are validated before executing this method!
    */

src/test/java/bio/terra/common/ParquetUtils.java

@@ -37,6 +37,7 @@ public static List<Map<String, Object>> readGcsParquetRecords(
       throw new RuntimeException("Could not write " + url + " to local temp file", e);
     }
   }
+
   /**
    * Given a signed Azure URL, this method will read through the parquet data specified as list of
    * maps that are keyed on column name and whose values are string representations of the parquet

src/test/java/bio/terra/integration/DataRepoFixtures.java

@@ -567,8 +567,9 @@ public DataRepoResponse<Object> addPolicyMemberRaw(
           case DATASET -> "/api/repository/v1/datasets/";
           case DATASNAPSHOT -> "/api/repository/v1/snapshots/";
           case SPEND_PROFILE -> "/api/resources/v1/profiles/";
-          default -> throw new IllegalArgumentException(
-              "Policy member addition undefined for IamResourceType " + iamResourceType);
+          default ->
+              throw new IllegalArgumentException(
+                  "Policy member addition undefined for IamResourceType " + iamResourceType);
         };
     String path = pathPrefix + resourceId + "/policies/" + role.toString() + "/members";
     return dataRepoClient.post(user, path, TestUtils.mapToJson(req), new TypeReference<>() {});
@@ -604,8 +605,9 @@ public DataRepoResponse<List<String>> retrieveUserRolesRaw(
         switch (iamResourceType) {
           case DATASET -> "/api/repository/v1/datasets/";
           case DATASNAPSHOT -> "/api/repository/v1/snapshots/";
-          default -> throw new IllegalArgumentException(
-              "Role fetch undefined for IamResourceType " + iamResourceType);
+          default ->
+              throw new IllegalArgumentException(
+                  "Role fetch undefined for IamResourceType " + iamResourceType);
         };
     String path = pathPrefix + resourceId + "/roles";
 
@@ -628,8 +630,9 @@ public DataRepoResponse<PolicyResponse> retrievePoliciesRaw(
           case DATASET -> "/api/repository/v1/datasets/";
           case DATASNAPSHOT -> "/api/repository/v1/snapshots/";
           case SPEND_PROFILE -> "/api/resources/v1/profiles/";
-          default -> throw new IllegalArgumentException(
-              "Policy fetch undefined for IamResourceType " + iamResourceType);
+          default ->
+              throw new IllegalArgumentException(
+                  "Policy fetch undefined for IamResourceType " + iamResourceType);
         };
     String path = pathPrefix + resourceId + "/policies";