Update various dependency versions (#1220)

Author: labkey-susanh

build.gradle

@@ -252,6 +252,8 @@ allprojects {
                     force "org.eclipse.angus:angus-activation:${angusActivationVersion}"
                     // force Jakarta Activation API version used by our Angus Activation implementation
                     force "jakarta.activation:jakarta.activation-api:${jakartaActivationApiVersion}"
+                    // SequenceAnalysis brings in an older version via biojava-genome 7.1.1
+                    force "jakarta.xml.bind:jakarta.xml.bind-api:${jaxbApiVersion}"
                     // force version for accounts, api, query
                     force "javax.validation:validation-api:${validationApiVersion}"
                     // force version for accounts, docker, api, workflow
@@ -299,7 +301,7 @@ allprojects {
                     force "io.grpc:grpc-stub:${grpcVersion}"
                     force "io.grpc:grpc-xds:${grpcVersion}"
 
-                    // workflow (Activiti) brings in older versions of these libraries, so we need to force these versions
+                    // tcrdb, cloud, SequenceAnalysis, recipe mfa, pipeline, fileTransfer, docker mcc, DiscvrLabKeyModules:Studies and api have differnet versions of these libraries, so we need to force these versions
                     force "com.fasterxml.jackson.core:jackson-core:${jacksonVersion}"
                     force "com.fasterxml.jackson.core:jackson-databind:${jacksonDatabindVersion}"
                     // The version of picard we depend on brings in an older version of htsjdk, but SequenceAnalysis depends on a later version
@@ -557,6 +559,6 @@ project.tasks.register('ijConfigure') {
 project.tasks.register('purgeNpmAlphaVersions', PurgeNpmAlphaVersions) {
     group = GroupNames.NPM_RUN
     description = "Given an alpha version prefix for npm packages via the property -P${PurgeNpmAlphaVersions.ALPHA_PREFIX_PROPERTY}=yourPrefix, " +
-            "removes all packages with versions that match that prefix from Artifactory (e.g., @labkey/components-1.2.3-yourPrefix.0 and @labkey/workflow-0.3.4-yourPrefix.1). " +
+            "removes all packages with versions that match that prefix from Artifactory (e.g., @labkey/components-1.2.3-yourPrefix.0 and @labkey/premium-0.3.4-yourPrefix.1). " +
             " Use -PdryRun to see what versions would be deleted without actually doing the deletion."
 }

gradle.properties

@@ -60,7 +60,7 @@ windowsProteomicsBinariesVersion=1.0
 artifactoryPluginVersion=5.2.5
 gradleNodePluginVersion=7.1.0
 gradlePluginsVersion=7.1.0
-owaspDependencyCheckPluginVersion=12.1.8
+owaspDependencyCheckPluginVersion=12.1.9
 versioningPluginVersion=1.1.3
 
 # Versions of node and npm to use during the build. If set, these versions
@@ -99,7 +99,7 @@ apacheDirectoryVersion=2.1.7
 apacheMinaVersion=2.2.4
 
 # Usually matches the version specified as a Spring Boot dependency (see springBootVersion below)
-apacheTomcatVersion=10.1.48
+apacheTomcatVersion=10.1.49
 
 # (mothership) -> json-path -> json-smart -> accessor-smart
 # (core) -> graalvm
@@ -122,24 +122,24 @@ commonmarkVersion=0.27.0
 # the beanutils version is not the default version brought from commons-validator and/or commons-digester
 # in the :server:api module but is required for some of our code to compile
 commonsBeanutilsVersion=1.11.0
-commonsCodecVersion=1.19.0
+commonsCodecVersion=1.20.0
 commonsCollections4Version=4.5.0
 commonsCollectionsVersion=3.2.2
 commonsCompressVersion=1.28.0
 commonsDbcpVersion=1.4
 commonsDigesterVersion=1.8.1
 commonsDiscoveryVersion=0.2
-commonsIoVersion=2.20.0
-commonsLang3Version=3.19.0
+commonsIoVersion=2.21.0
+commonsLang3Version=3.20.0
 commonsLangVersion=2.6
 commonsLoggingVersion=1.3.5
 commonsMath3Version=3.6.1
 commonsPoolVersion=1.6
 commonsTextVersion=1.14.0
-commonsValidatorVersion=1.10.0
+commonsValidatorVersion=1.10.1
 commonsVfs2Version=2.10.0
 
-datadogVersion=1.54.0
+datadogVersion=1.55.0
 
 dom4jVersion=2.1.4
 
@@ -155,7 +155,7 @@ fopVersion=2.11
 
 # Force latest for consistency
 googleAutoValueAnnotationsVersion=1.10.4
-googleErrorProneAnnotationsVersion=2.42.0
+googleErrorProneAnnotationsVersion=2.44.0
 googleHttpClientVersion=2.0.2
 googleOauthClientVersion=1.39.0
 googleProtocolBufVersion=3.25.8
@@ -166,7 +166,7 @@ googleProtocolBufVersion=3.25.8
 # "java.lang.NoSuchMethodError: 'void com.google.gson.internal.ConstructorConstructor.<init>(java.util.Map)'" errors
 gsonVersion=2.8.9
 
-grpcVersion=1.76.0
+grpcVersion=1.77.0
 
 guavaVersion=33.5.0-jre
 
@@ -212,7 +212,7 @@ jaxbApiOldVersion=2.3.1
 jaxbOldVersion=2.3.3
 
 # All other direct and indirect uses of JAXB use the current, jakarta-packaged versions
-jaxbApiVersion=4.0.2
+jaxbApiVersion=4.0.4
 jaxbVersion=4.0.5
 
 jaxrpcVersion=1.1
@@ -267,7 +267,7 @@ pollingWatchVersion=0.2.0
 # Newer versions of the driver have a perf degradation that's important for us. https://github.com/pgjdbc/pgjdbc/issues/3505
 postgresqlDriverVersion=42.7.8
 
-quartzVersion=2.5.0
+quartzVersion=2.5.1
 
 reflectionsVersion=0.10.2
 
@@ -290,9 +290,9 @@ snappyJavaVersion=1.1.10.8
 # Also, update apacheTomcatVersion above to match Spring Boot's Tomcat dependency version
 springBootVersion=3.5.7
 # This usually matches the Spring Framework version dictated by springBootVersion
-springVersion=6.2.12
+springVersion=6.2.13
 
-sqliteJdbcVersion=3.50.3.0
+sqliteJdbcVersion=3.51.0.0
 
 # NLP and SAML bring stax2-api in as a transitive dependency but with very different versions. We force the later version.
 stax2ApiVersion=4.2.2