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[DCJ-400] Upgrade com.diffplug.spotless 6.7.1 -> 6.25.0 (#1771)
* [DCJ-400] Upgrade com.diffplug.spotless 6.7.1 -> 6.25.0 Ran `./gradlew spotlessApply` to pull in new changes.
1 parent 895c3a6 commit 99e385b

29 files changed

+98
-70
lines changed

‎build.gradle

+1-1
Original file line numberDiff line numberDiff line change
@@ -37,7 +37,7 @@ plugins {
3737
id 'java'
3838
id 'io.spring.dependency-management' version '1.1.6'
3939
id 'jacoco'
40-
id 'com.diffplug.spotless' version '6.7.1'
40+
id 'com.diffplug.spotless' version '6.25.0'
4141
id 'com.dorongold.task-tree' version '4.0.0'
4242
// enables release info in sentry events
4343
id 'com.gorylenko.gradle-git-properties' version '2.4.2'

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

+4
Original file line numberDiff line numberDiff line change
@@ -49,14 +49,18 @@ public class ApplicationConfiguration {
4949
private String dnsName;
5050
private String resourceId;
5151
private String userId;
52+
5253
/**
5354
* Size of the Stairway thread pool. The pool is consumed by requests and by file load threads.
5455
*/
5556
private int maxStairwayThreads;
57+
5658
/** Maximum number of file loads allowed in the input array in a bulk file load */
5759
private int maxBulkFileLoadArray;
60+
5861
/** Number of file loads to run concurrently in a bulk file load */
5962
private int loadConcurrentFiles;
63+
6064
/**
6165
* Number of file loads to run concurrently. NOTE: the maximum number of threads used for load is
6266
* one for the driver flight and N for the number of concurrent files: {@code

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

+1
Original file line numberDiff line numberDiff line change
@@ -18,6 +18,7 @@ public class JdbcConfiguration {
1818
private String username;
1919
private String password;
2020
private String changesetFile;
21+
2122
/**
2223
* Maximum number of database connections in the connection pool; -1 means no limit The goal of
2324
* these parameters is to prevent waiting for a database connection.

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

+1
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@ public enum LockOperation {
2222
LockOperation(boolean isLock) {
2323
this(isLock, null, null);
2424
}
25+
2526
/**
2627
* @return additional guidance for users investigating a failed lock operation, usually as part of
2728
* a failed job / flight.

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

+2-2
Original file line numberDiff line numberDiff line change
@@ -98,8 +98,8 @@ public static String translateDataType(
9898
case TIME -> "time";
9999
// Data of type RECORD contains table-like that can be nested or repeated
100100
// It's provided in JSON format, making it hard to parse from inside a CSV/JSON ingest
101-
case RECORD -> throw new NotSupportedException(
102-
"RECORD type is not yet supported for synapse");
101+
case RECORD ->
102+
throw new NotSupportedException("RECORD type is not yet supported for synapse");
103103
};
104104
}
105105

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

+1
Original file line numberDiff line numberDiff line change
@@ -275,6 +275,7 @@ void overwriteGroupPolicyEmailsIncludeRequestingUser(
275275
String policyName,
276276
List<String> emailAddresses)
277277
throws InterruptedException;
278+
278279
/**
279280
* @param accessToken valid oauth token for the account modifying the group policy members
280281
* @param groupName name of Firecloud managed group

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

+1
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,7 @@ public class SamApiService {
2424

2525
private final SamConfiguration samConfig;
2626
private final ConfigurationService configurationService;
27+
2728
/** OkHttpClients should be shared among requests to reduce latency and save memory * */
2829
private final OkHttpClient sharedHttpClient;
2930

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

+6-4
Original file line numberDiff line numberDiff line change
@@ -121,10 +121,12 @@ public DuosDatasetApprovedUsers getApprovedUsers(String duosId) {
121121
static ErrorReportException convertToDataRepoException(
122122
HttpStatusCodeException duosEx, String duosId) {
123123
return switch (HttpStatus.valueOf(duosEx.getStatusCode().value())) {
124-
case BAD_REQUEST -> new DuosDatasetBadRequestException(
125-
"DUOS dataset identifier %s is malformed".formatted(duosId), duosEx);
126-
case NOT_FOUND -> new DuosDatasetNotFoundException(
127-
"Could not find DUOS dataset for identifier %s".formatted(duosId), duosEx);
124+
case BAD_REQUEST ->
125+
new DuosDatasetBadRequestException(
126+
"DUOS dataset identifier %s is malformed".formatted(duosId), duosEx);
127+
case NOT_FOUND ->
128+
new DuosDatasetNotFoundException(
129+
"Could not find DUOS dataset for identifier %s".formatted(duosId), duosEx);
128130
default -> new DuosInternalServerErrorException("Unexpected error from DUOS", duosEx);
129131
};
130132
}

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

+8-14
Original file line numberDiff line numberDiff line change
@@ -1462,16 +1462,16 @@ private Object extractValue(ResultSet resultSet, Column column) {
14621462
return switch (column.getType()) {
14631463
case BOOLEAN -> resultSet.getBoolean(column.getName());
14641464
case BYTES -> resultSet.getBytes(column.getName());
1465-
case DIRREF, FILEREF, STRING, TEXT, DATE, DATETIME, TIMESTAMP -> resultSet.getString(
1466-
column.getName());
1465+
case DIRREF, FILEREF, STRING, TEXT, DATE, DATETIME, TIMESTAMP ->
1466+
resultSet.getString(column.getName());
14671467
case FLOAT -> resultSet.getFloat(column.getName());
14681468
case FLOAT64 -> resultSet.getDouble(column.getName());
14691469
case INTEGER -> resultSet.getInt(column.getName());
14701470
case INT64 -> resultSet.getLong(column.getName());
14711471
case NUMERIC -> resultSet.getFloat(column.getName());
14721472
case TIME -> resultSet.getTime(column.getName());
1473-
default -> throw new IllegalArgumentException(
1474-
"Unknown datatype '" + column.getType() + "'");
1473+
default ->
1474+
throw new IllegalArgumentException("Unknown datatype '" + column.getType() + "'");
14751475
};
14761476
} catch (SQLException e) {
14771477
throw new PdaoException("Error reading data", e);
@@ -1492,17 +1492,11 @@ private Object extractValue(ResultSet resultSet, Column column) {
14921492
TypeReference<?> targetType =
14931493
switch (column.getType()) {
14941494
case BOOLEAN -> new TypeReference<List<Boolean>>() {};
1495-
case DATE,
1496-
DATETIME,
1497-
DIRREF,
1498-
FILEREF,
1499-
STRING,
1500-
TEXT,
1501-
TIME,
1502-
TIMESTAMP -> new TypeReference<List<String>>() {};
1495+
case DATE, DATETIME, DIRREF, FILEREF, STRING, TEXT, TIME, TIMESTAMP ->
1496+
new TypeReference<List<String>>() {};
15031497
case FLOAT, FLOAT64, INTEGER, INT64, NUMERIC -> new TypeReference<List<Number>>() {};
1504-
default -> throw new IllegalArgumentException(
1505-
"Unknown datatype '" + column.getType() + "'");
1498+
default ->
1499+
throw new IllegalArgumentException("Unknown datatype '" + column.getType() + "'");
15061500
};
15071501
try {
15081502
return objectMapper.readValue(rawValue, targetType);

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

+2
Original file line numberDiff line numberDiff line change
@@ -6,10 +6,12 @@ private AzureConstants() {}
66

77
/** The code that the Azure resource management APIs found when a resource is not found */
88
public static final String RESOURCE_NOT_FOUND_CODE = "ResourceNotFound";
9+
910
/**
1011
* The code that the Azure security insights management APIs found when a resource is not found
1112
*/
1213
public static final String NOT_FOUND_CODE = "NotFound";
14+
1315
/**
1416
* The code that the Azure resource management APIs found when an invalid request is sent. This
1517
* can sometimes be equivalent to a 404

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

+1
Original file line numberDiff line numberDiff line change
@@ -332,6 +332,7 @@ public List<FireStoreDirectoryEntry> enumerateAll(Firestore firestore, String co
332332
CollectionReference dirColl = firestore.collection(collectionId);
333333
return query(dirColl.orderBy("path"));
334334
}
335+
335336
// -- private methods --
336337

337338
List<FireStoreDirectoryEntry> enumerateDirectory(

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

+1
Original file line numberDiff line numberDiff line change
@@ -243,6 +243,7 @@ public void writeListToCloudFile(String path, List<String> contentsToWrite, Stri
243243
writeStreamToCloudFile(path, stream, projectId);
244244
}
245245
}
246+
246247
/**
247248
* Write a {@link Stream} to a GCS file separated by newlines
248249
*

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

+1
Original file line numberDiff line numberDiff line change
@@ -125,6 +125,7 @@ public LoadHistoryIterator loadHistoryIterator(
125125
List<BulkLoadHistoryModel> backingList, int chunkSize) {
126126
return new LoadHistoryIterator(backingList, chunkSize);
127127
}
128+
128129
/**
129130
* A convenience class wrapping the getting of load history table rows in an Iterator. The
130131
* Iterator's elements are a list of BulkLoadHistoryModel chunk of the full results retrieved from

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

+1
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,7 @@
1414
@Service
1515
public class PolicyApiService {
1616
private final PolicyServiceConfiguration policyServiceConfiguration;
17+
1718
/** Clients should be shared among requests to reduce latency and save memory * */
1819
private final Client sharedHttpClient;
1920

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

+7-6
Original file line numberDiff line numberDiff line change
@@ -131,10 +131,11 @@ public void deletePaoIfExists(UUID resourceId) {
131131
@VisibleForTesting
132132
static RuntimeException convertApiException(ApiException ex) {
133133
return switch (ex.getCode()) {
134-
case HttpStatus.SC_UNAUTHORIZED -> new PolicyServiceAuthorizationException(
135-
"Not authorized to access Terra Policy Service", ex.getCause());
136-
case HttpStatus.SC_NOT_FOUND -> new PolicyServiceNotFoundException(
137-
"Policy access object not found", ex);
134+
case HttpStatus.SC_UNAUTHORIZED ->
135+
new PolicyServiceAuthorizationException(
136+
"Not authorized to access Terra Policy Service", ex.getCause());
137+
case HttpStatus.SC_NOT_FOUND ->
138+
new PolicyServiceNotFoundException("Policy access object not found", ex);
138139
case HttpStatus.SC_BAD_REQUEST -> {
139140
if (StringUtils.containsIgnoreCase(ex.getMessage(), "duplicate")) {
140141
// TODO - this special handling may be removed once
@@ -146,8 +147,8 @@ yield new PolicyServiceDuplicateException(
146147
yield new PolicyServiceApiException(ex);
147148
}
148149
}
149-
case HttpStatus.SC_CONFLICT -> new PolicyConflictException(
150-
"Policy access object already exists", ex);
150+
case HttpStatus.SC_CONFLICT ->
151+
new PolicyConflictException("Policy access object already exists", ex);
151152
default -> new PolicyServiceApiException(ex);
152153
};
153154
}

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

+1
Original file line numberDiff line numberDiff line change
@@ -38,6 +38,7 @@ public class BufferService {
3838
private final ResourceBufferServiceConfiguration bufferServiceConfiguration;
3939
private final GoogleResourceConfiguration googleConfig;
4040
private final GoogleResourceManagerService googleResourceManagerService;
41+
4142
/** Clients should be shared among requests to reduce latency and save memory * */
4243
private final Client sharedHttpClient;
4344

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

+1
Original file line numberDiff line numberDiff line change
@@ -84,6 +84,7 @@ public AccessInfoModel accessInfoFromSnapshot(
8484
final Snapshot snapshot, final AuthenticatedUserRequest userRequest) {
8585
return accessInfoFromSnapshot(snapshot, userRequest, null);
8686
}
87+
8788
/** Generate an {@link AccessInfoModel} from a Snapshot */
8889
public AccessInfoModel accessInfoFromSnapshot(
8990
final Snapshot snapshot, final AuthenticatedUserRequest userRequest, String forTable) {

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

+1
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@ public class DatasetProject {
88
private UUID profileId;
99
private String
1010
dataProject; // Project id of the snapshot data project--which is a string and feels like a
11+
1112
// name
1213

1314
public UUID getId() {

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

+2-2
Original file line numberDiff line numberDiff line change
@@ -67,8 +67,8 @@ private void validateSnapshotContents(
6767
}
6868
case BYQUERY -> validateSnapshotQuerySpec(contents.getQuerySpec(), errors);
6969
case BYROWID -> validateSnapshotRowIdSpec(contents.getRowIdSpec(), errors);
70-
case BYREQUESTID -> validateSnapshotRequestIdSpec(
71-
contents.getRequestIdSpec(), errors);
70+
case BYREQUESTID ->
71+
validateSnapshotRequestIdSpec(contents.getRequestIdSpec(), errors);
7272
}
7373
});
7474
}

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

+22-20
Original file line numberDiff line numberDiff line change
@@ -219,18 +219,19 @@ public SnapshotCreateFlight(FlightMap inputParameters, Object applicationContext
219219
new CreateSnapshotByAssetParquetFilesAzureStep(
220220
azureSynapsePdao, snapshotService, snapshotReq, snapshotId)));
221221
}
222-
case BYFULLVIEW -> addStep(
223-
platform.choose(
224-
() ->
225-
new CreateSnapshotPrimaryDataFullViewGcpStep(
226-
bigQuerySnapshotPdao,
227-
snapshotDao,
228-
snapshotService,
229-
snapshotReq,
230-
sourceDataset),
231-
() ->
232-
new CreateSnapshotByFullViewParquetFilesAzureStep(
233-
azureSynapsePdao, snapshotService, snapshotReq, snapshotId)));
222+
case BYFULLVIEW ->
223+
addStep(
224+
platform.choose(
225+
() ->
226+
new CreateSnapshotPrimaryDataFullViewGcpStep(
227+
bigQuerySnapshotPdao,
228+
snapshotDao,
229+
snapshotService,
230+
snapshotReq,
231+
sourceDataset),
232+
() ->
233+
new CreateSnapshotByFullViewParquetFilesAzureStep(
234+
azureSynapsePdao, snapshotService, snapshotReq, snapshotId)));
234235
case BYQUERY -> {
235236
addStep(new CreateSnapshotValidateQueryStep(datasetService, snapshotReq));
236237
addStep(
@@ -255,14 +256,15 @@ public SnapshotCreateFlight(FlightMap inputParameters, Object applicationContext
255256
snapshotId,
256257
sourceDataset)));
257258
}
258-
case BYROWID -> addStep(
259-
platform.choose(
260-
() ->
261-
new CreateSnapshotPrimaryDataRowIdsStep(
262-
bigQuerySnapshotPdao, snapshotDao, snapshotService, snapshotReq),
263-
() ->
264-
new CreateSnapshotByRowIdParquetFilesAzureStep(
265-
azureSynapsePdao, snapshotService, snapshotReq, snapshotId)));
259+
case BYROWID ->
260+
addStep(
261+
platform.choose(
262+
() ->
263+
new CreateSnapshotPrimaryDataRowIdsStep(
264+
bigQuerySnapshotPdao, snapshotDao, snapshotService, snapshotReq),
265+
() ->
266+
new CreateSnapshotByRowIdParquetFilesAzureStep(
267+
azureSynapsePdao, snapshotService, snapshotReq, snapshotId)));
266268
case BYREQUESTID -> {
267269
addStep(new CreateSnapshotSamGroupNameStep(snapshotId, iamService));
268270
addStep(new CreateSnapshotSamGroupStep(iamService));

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

+9-6
Original file line numberDiff line numberDiff line change
@@ -86,12 +86,15 @@ static String generateSummaryForCriteriaGroup(
8686
.map(
8787
criteria ->
8888
switch (criteria.getKind()) {
89-
case LIST -> generateSummaryForCriteria(
90-
(SnapshotBuilderProgramDataListCriteria) criteria, settings);
91-
case RANGE -> generateSummaryForCriteria(
92-
(SnapshotBuilderProgramDataRangeCriteria) criteria, settings);
93-
case DOMAIN -> generateSummaryForCriteria(
94-
(SnapshotBuilderDomainCriteria) criteria, settings);
89+
case LIST ->
90+
generateSummaryForCriteria(
91+
(SnapshotBuilderProgramDataListCriteria) criteria, settings);
92+
case RANGE ->
93+
generateSummaryForCriteria(
94+
(SnapshotBuilderProgramDataRangeCriteria) criteria, settings);
95+
case DOMAIN ->
96+
generateSummaryForCriteria(
97+
(SnapshotBuilderDomainCriteria) criteria, settings);
9598
})
9699
.collect(Collectors.joining("\n")));
97100
}

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

+6-5
Original file line numberDiff line numberDiff line change
@@ -70,11 +70,12 @@ public String renderSQL(SqlRenderContext context) {
7070
return switch (dataType) {
7171
case STRING -> stringVal == null ? "NULL" : "'" + sqlEscape(stringVal) + "'";
7272
case INT64 -> String.valueOf(int64Val);
73-
case BOOLEAN -> context
74-
.getPlatform()
75-
// In T-SQL, TRUE is not a keyword, so we need to use 1 instead. The JDBC API converts
76-
// the 1 to a boolean TRUE when the query result is processed.
77-
.choose(() -> String.valueOf(booleanVal), () -> booleanVal ? "1" : "0");
73+
case BOOLEAN ->
74+
context
75+
.getPlatform()
76+
// In T-SQL, TRUE is not a keyword, so we need to use 1 instead. The JDBC API converts
77+
// the 1 to a boolean TRUE when the query result is processed.
78+
.choose(() -> String.valueOf(booleanVal), () -> booleanVal ? "1" : "0");
7879
case DATE -> "DATE('" + dateVal.toString() + "')";
7980
case DOUBLE -> "FLOAT('" + doubleVal + "')";
8081
};

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

+1
Original file line numberDiff line numberDiff line change
@@ -85,6 +85,7 @@ public Query generateQuery(SnapshotBuilderDomainOption domainOption, int concept
8585
.orderBy(List.of(new OrderByVariable(conceptName, OrderByDirection.ASCENDING)))
8686
.build();
8787
}
88+
8889
/**
8990
* Filter concept to only allow standard concepts. See <a
9091
* 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

+1
Original file line numberDiff line numberDiff line change
@@ -181,6 +181,7 @@ public static int getTableTotalRowCount(FSContainerInterface tdrResource, String
181181
return 0;
182182
}
183183
}
184+
184185
/*
185186
* WARNING: Ensure input parameters are validated before executing this method!
186187
*/

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

+1
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,7 @@ public static List<Map<String, Object>> readGcsParquetRecords(
3737
throw new RuntimeException("Could not write " + url + " to local temp file", e);
3838
}
3939
}
40+
4041
/**
4142
* Given a signed Azure URL, this method will read through the parquet data specified as list of
4243
* maps that are keyed on column name and whose values are string representations of the parquet

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

+9-6
Original file line numberDiff line numberDiff line change
@@ -567,8 +567,9 @@ public DataRepoResponse<Object> addPolicyMemberRaw(
567567
case DATASET -> "/api/repository/v1/datasets/";
568568
case DATASNAPSHOT -> "/api/repository/v1/snapshots/";
569569
case SPEND_PROFILE -> "/api/resources/v1/profiles/";
570-
default -> throw new IllegalArgumentException(
571-
"Policy member addition undefined for IamResourceType " + iamResourceType);
570+
default ->
571+
throw new IllegalArgumentException(
572+
"Policy member addition undefined for IamResourceType " + iamResourceType);
572573
};
573574
String path = pathPrefix + resourceId + "/policies/" + role.toString() + "/members";
574575
return dataRepoClient.post(user, path, TestUtils.mapToJson(req), new TypeReference<>() {});
@@ -604,8 +605,9 @@ public DataRepoResponse<List<String>> retrieveUserRolesRaw(
604605
switch (iamResourceType) {
605606
case DATASET -> "/api/repository/v1/datasets/";
606607
case DATASNAPSHOT -> "/api/repository/v1/snapshots/";
607-
default -> throw new IllegalArgumentException(
608-
"Role fetch undefined for IamResourceType " + iamResourceType);
608+
default ->
609+
throw new IllegalArgumentException(
610+
"Role fetch undefined for IamResourceType " + iamResourceType);
609611
};
610612
String path = pathPrefix + resourceId + "/roles";
611613

@@ -628,8 +630,9 @@ public DataRepoResponse<PolicyResponse> retrievePoliciesRaw(
628630
case DATASET -> "/api/repository/v1/datasets/";
629631
case DATASNAPSHOT -> "/api/repository/v1/snapshots/";
630632
case SPEND_PROFILE -> "/api/resources/v1/profiles/";
631-
default -> throw new IllegalArgumentException(
632-
"Policy fetch undefined for IamResourceType " + iamResourceType);
633+
default ->
634+
throw new IllegalArgumentException(
635+
"Policy fetch undefined for IamResourceType " + iamResourceType);
633636
};
634637
String path = pathPrefix + resourceId + "/policies";
635638

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