[DCJ-400-gradle]: Bump the minor-patch-dependencies group with 45 updates

.github/workflows/trivy.yml

@@ -33,7 +33,7 @@ jobs:
           # Enable pipefail so a gradle build failure fails this step.
           set -o pipefail
           # build sources and store the plain log without colors
-          ./gradlew jibDockerBuild --console=plain \
+          ./gradlew jibDockerBuild --stacktrace --scan --console=plain \
             | perl -pe 's/\x1b\[[0-9;]*[mG]//g' | tee build.log
 
           # export image name from the log

build.gradle

@@ -20,25 +20,25 @@ buildscript {
         mavenCentral()
     }
     dependencies {
-        classpath('io.swagger.codegen.v3:swagger-codegen:3.0.52')
+        classpath('io.swagger.codegen.v3:swagger-codegen:3.0.56')
     }
 }
 
 plugins {
-    id 'com.google.cloud.tools.jib' version '3.2.0'
+    id 'com.google.cloud.tools.jib' version '3.4.3'
     id 'org.liquibase.gradle' version '2.2.1'
-    id 'org.gradle.test-retry' version '1.5.8'
+    id 'org.gradle.test-retry' version '1.5.10'
     id 'antlr'
     id 'org.hidetake.swagger.generator' version '2.19.2'
-    id 'org.springframework.boot' version '3.2.4'
+    id 'org.springframework.boot' version '3.3.2'
     id 'idea'
     id 'java'
-    id 'io.spring.dependency-management' version '1.1.4'
+    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 '2.1.0'
     // enables release info in sentry events
-    id 'com.gorylenko.gradle-git-properties' version '2.4.1'
+    id 'com.gorylenko.gradle-git-properties' version '2.4.2'
     id 'org.sonarqube' version '4.2.1.3168'
     id 'com.srcclr.gradle' version '3.1.12'
 }
@@ -58,8 +58,8 @@ allprojects {
             mavenBom SpringBootPlugin.BOM_COORDINATES
         }
         dependencies {
-            dependency 'io.swagger.core.v3:swagger-annotations:2.2.20'
-            dependency 'io.swagger.codegen.v3:swagger-codegen-cli:3.0.51'
+            dependency 'io.swagger.core.v3:swagger-annotations:2.2.22'
+            dependency 'io.swagger.codegen.v3:swagger-codegen-cli:3.0.56'
         }
     }
 }
@@ -172,7 +172,7 @@ dependencies {
     implementation 'com.google.apis:google-api-services-oauth2:v2-rev20200213-2.0.0'
     implementation 'com.google.apis:google-api-services-iam:v1-rev20230209-2.0.0'
 
-    implementation platform('com.google.cloud:libraries-bom:26.30.0')
+    implementation platform('com.google.cloud:libraries-bom:26.43.0')
     implementation 'com.google.cloud:google-cloud-billing'
     implementation 'com.google.cloud:google-cloud-resourcemanager'
     implementation 'com.google.cloud:google-cloud-bigquery'
@@ -188,7 +188,7 @@ dependencies {
     implementation 'org.apache.directory.studio:org.apache.commons.io:2.4'
     implementation 'org.apache.httpcomponents.client5:httpclient5'
 
-    implementation 'org.liquibase:liquibase-core:4.26.0'
+    implementation 'org.liquibase:liquibase-core:4.29.1'
 
     implementation 'org.codehaus.janino:janino'           // Provides if/else xml parsing for logback config
     implementation 'org.springframework.boot:spring-boot-starter-web'
@@ -199,90 +199,89 @@ dependencies {
     swaggerCodegen 'io.swagger.codegen.v3:swagger-codegen-cli'
 
     implementation 'org.springframework:spring-jdbc'
-    implementation 'org.antlr:ST4:4.3'                          // String templating
+    implementation 'org.antlr:ST4:4.3.4'                          // String templating
 
     implementation 'org.springframework.boot:spring-boot-starter-thymeleaf'
     implementation 'jakarta.servlet.jsp.jstl:jakarta.servlet.jsp.jstl-api'
 
     implementation 'com.microsoft.sqlserver:mssql-jdbc:11.2.3.jre17'
 
     // For distributed locking of Spring @Scheduled tasks across multiple instances
-    implementation 'net.javacrumbs.shedlock:shedlock-provider-jdbc-template:5.2.0'
-    implementation 'net.javacrumbs.shedlock:shedlock-spring:5.2.0'
+    implementation 'net.javacrumbs.shedlock:shedlock-provider-jdbc-template:5.14.0'
+    implementation 'net.javacrumbs.shedlock:shedlock-spring:5.14.0'
 
     implementation 'bio.terra:terra-common-lib:1.1.17-SNAPSHOT'
     implementation 'org.broadinstitute.dsde.workbench:sam-client_2.13:v0.0.241'
-    implementation 'bio.terra:terra-policy-client:1.0.11-SNAPSHOT'
+    implementation 'bio.terra:terra-policy-client:1.0.15-SNAPSHOT'
     implementation 'bio.terra:terra-resource-buffer-client:0.198.42-SNAPSHOT'
-    implementation 'bio.terra:externalcreds-client-resttemplate:1.3.0-SNAPSHOT'
+    implementation 'bio.terra:externalcreds-client-resttemplate:1.45.0-SNAPSHOT'
 
     implementation 'org.glassfish.jersey.inject:jersey-hk2'
 
     implementation 'com.squareup.okhttp3:okhttp'
     implementation 'org.springframework.boot:spring-boot-starter-actuator'
     implementation 'io.micrometer:micrometer-registry-prometheus'
 
-    implementation 'com.fasterxml.jackson.core:jackson-core:2.15.3'
-    implementation 'com.fasterxml.jackson.core:jackson-annotations:2.15.3'
-    implementation 'com.fasterxml.jackson.core:jackson-databind:2.15.3'
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.17.2'
+    implementation 'com.fasterxml.jackson.core:jackson-annotations:2.17.2'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.17.2'
 
     // Azure related dependencies
-    implementation 'com.azure:azure-identity:1.11.1'
-    implementation 'com.azure.resourcemanager:azure-resourcemanager:2.34.0'
+    implementation 'com.azure:azure-identity:1.13.2'
+    implementation 'com.azure.resourcemanager:azure-resourcemanager:2.41.0'
     implementation 'com.azure.resourcemanager:azure-resourcemanager-loganalytics:1.0.0'
     implementation 'com.azure.resourcemanager:azure-resourcemanager-securityinsights:1.0.0-beta.4'
-    implementation 'com.azure:azure-storage-common:12.24.1'
-    implementation 'com.azure:azure-storage-file-datalake:12.18.1'
-    implementation 'com.azure:azure-data-tables:12.3.18'
+    implementation 'com.azure:azure-storage-common:12.26.0'
+    implementation 'com.azure:azure-storage-file-datalake:12.20.0'
+    implementation 'com.azure:azure-data-tables:12.4.3'
 
     implementation platform('io.sentry:sentry-bom:6.25.0') //import bom
     implementation('io.sentry:sentry-spring-boot-starter')
     implementation('io.sentry:sentry-logback')
 
     // OpenTelemetry @WithSpan annotations:
-    implementation 'io.opentelemetry.instrumentation:opentelemetry-instrumentation-annotations:2.2.0'
-
-    testImplementation 'org.apache.parquet:parquet-common:1.12.0'
-    testImplementation 'org.apache.parquet:parquet-hadoop:1.12.0'
-    testImplementation 'org.apache.parquet:parquet-hadoop-bundle:1.12.0'
-    testImplementation 'org.apache.parquet:parquet-encoding:1.12.0'
-    testImplementation 'org.apache.parquet:parquet-column:1.12.0'
-    testImplementation ('org.apache.hadoop:hadoop-common:3.3.1')  {
+    implementation 'io.opentelemetry.instrumentation:opentelemetry-instrumentation-annotations:2.6.0'
+
+    testImplementation 'org.apache.parquet:parquet-common:1.14.1'
+    testImplementation 'org.apache.parquet:parquet-hadoop:1.14.1'
+    testImplementation 'org.apache.parquet:parquet-hadoop-bundle:1.14.1'
+    testImplementation 'org.apache.parquet:parquet-encoding:1.14.1'
+    testImplementation 'org.apache.parquet:parquet-column:1.14.1'
+    testImplementation ('org.apache.hadoop:hadoop-common:3.4.0')  {
         exclude group: 'com.sun.jersey', module: 'jersey-core'
         exclude group: 'com.sun.jersey', module: 'jersey-servlet'
         exclude group: 'com.sun.jersey', module: 'jersey-json'
         exclude group: 'com.sun.jersey', module: 'jersey-server'
+        exclude group: 'org.slf4j', module: 'slf4j-reload4j'
     }
-    testImplementation ('org.apache.hadoop:hadoop-azure:3.3.1') {
+    testImplementation ('org.apache.hadoop:hadoop-azure:3.4.0') {
         exclude group: 'com.sun.jersey', module: 'jersey-core'
         exclude group: 'com.sun.jersey', module: 'jersey-servlet'
         exclude group: 'com.sun.jersey', module: 'jersey-json'
         exclude group: 'com.sun.jersey', module: 'jersey-server'
+        exclude group: 'org.slf4j', module: 'slf4j-reload4j'
     }
-    testImplementation('org.apache.hadoop:hadoop-mapreduce-client-core:3.3.1') {
+    testImplementation('org.apache.hadoop:hadoop-mapreduce-client-core:3.4.0') {
         exclude group: 'com.sun.jersey', module: 'jersey-core'
         exclude group: 'com.sun.jersey', module: 'jersey-servlet'
         exclude group: 'com.sun.jersey', module: 'jersey-json'
         exclude group: 'com.sun.jersey', module: 'jersey-server'
+        exclude group: 'org.slf4j', module: 'slf4j-reload4j'
     }
 
-    testImplementation 'au.com.dius.pact.provider:junit5:4.3.19'
-    testImplementation 'au.com.dius.pact.provider:junit5spring:4.3.19'
+    testImplementation 'au.com.dius.pact.provider:junit5:4.6.12'
+    testImplementation 'au.com.dius.pact.provider:junit5spring:4.6.12'
 
-    antlr 'org.antlr:antlr4:4.8'
-
-    // Need groovy on the class path for the logback config. Could use XML and skip this dependency,
-    // but the groovy config is... well... groovy.
-    runtimeOnly 'org.codehaus.groovy:groovy:3.0.7'
+    antlr 'org.antlr:antlr4:4.13.2'
 
     liquibaseRuntime 'org.liquibase:liquibase-core'
     liquibaseRuntime 'org.postgresql:postgresql'
-    liquibaseRuntime 'info.picocli:picocli:4.7.5'
+    liquibaseRuntime 'info.picocli:picocli:4.7.6'
 
     testImplementation 'org.junit.vintage:junit-vintage-engine'
     testImplementation 'org.springframework.boot:spring-boot-starter-test'
-    testImplementation 'io.zonky.test:embedded-database-spring-test:2.5.0'
-    testImplementation 'io.zonky.test:embedded-postgres:2.0.6'
+    testImplementation 'io.zonky.test:embedded-database-spring-test:2.5.1'
+    testImplementation 'io.zonky.test:embedded-postgres:2.0.7'
     implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:12.8.0')
 
     generatedCompile 'org.springframework.boot:spring-boot-starter-web'

datarepo-client/build.gradle

@@ -29,9 +29,9 @@ repositories {
 
 dependencies {
     ext {
-        jersey = "3.1.2"
-        jackson = "2.16.0"
-        swaggerAnnotations = "2.1.12"
+        jersey = "3.1.8"
+        jackson = "2.17.2"
+        swaggerAnnotations = "2.2.22"
 
     }
 

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/auth/ras/EcmService.java

@@ -5,6 +5,7 @@
 import bio.terra.common.iam.AuthenticatedUserRequest;
 import bio.terra.externalcreds.api.PassportApi;
 import bio.terra.externalcreds.client.ApiClient;
+import bio.terra.externalcreds.model.PassportProvider;
 import bio.terra.externalcreds.model.RASv1Dot1VisaCriterion;
 import bio.terra.externalcreds.model.ValidatePassportRequest;
 import bio.terra.externalcreds.model.ValidatePassportResult;
@@ -37,7 +38,6 @@ public class EcmService {
   private final ObjectMapper objectMapper;
   private final OidcApiService oidcApiService;
 
-  private static final String RAS_PROVIDER = "ras";
   @VisibleForTesting public static final String GA4GH_PASSPORT_V1_CLAIM = "ga4gh_passport_v1";
   private static final String RAS_DBGAP_PERMISSIONS_CLAIM = "ras_dbgap_permissions";
   private static final String RAS_CRITERIA_TYPE = "RASv1Dot1VisaCriterion";
@@ -98,7 +98,7 @@ public ValidatePassportResult validatePassport(ValidatePassportRequest validateP
    */
   public String getRasProviderPassport(AuthenticatedUserRequest userReq) {
     try {
-      return oidcApiService.getOidcApi(userReq).getProviderPassport(RAS_PROVIDER);
+      return oidcApiService.getOidcApi(userReq).getProviderPassport(PassportProvider.RAS);
     } catch (HttpClientErrorException ex) {
       if (ex.getStatusCode() == HttpStatus.NOT_FOUND) {
         return null;

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;