Java dependency updates

gradle.properties

@@ -60,7 +60,7 @@ windowsProteomicsBinariesVersion=1.0
 artifactoryPluginVersion=5.2.5
 gradleNodePluginVersion=7.1.0
 gradlePluginsVersion=7.3.0
-owaspDependencyCheckPluginVersion=12.1.9
+owaspDependencyCheckPluginVersion=12.2.0
 
 # Versions of node and npm to use during the build. If set, these versions
 # will be downloaded and used. If not set, the existing local installations will be used
@@ -90,35 +90,35 @@ angusMailVersion=2.0.5
 
 annotationsVersion=15.0
 
-antVersion=1.10.13
+antVersion=1.10.15
 
 antlrST4Version=4.3.4
 
 #Unifying version used by DISCVR and Premium
 apacheDirectoryVersion=2.1.7
 #Transitive dependency of Apache directory: 2.0.18 contains some regressions
-apacheMinaVersion=2.2.4
+apacheMinaVersion=2.2.5
 
 # Usually matches the version specified as a Spring Boot dependency (see springBootVersion below)
-apacheTomcatVersion=11.0.15
+apacheTomcatVersion=11.0.18
 
 # (mothership) -> json-path -> json-smart -> accessor-smart
 # (core) -> graalvm
 # tika
-asmVersion=9.9
+asmVersion=9.9.1
 
 # Apache Batik -- Batik version needs to be compatible with Apache FOP, but we need to pull in batik-codec separately
 batikVersion=1.19
 
 # sync with Tika version (or later)
-bouncycastlePgpVersion=1.82
-bouncycastleVersion=1.82
+bouncycastlePgpVersion=1.83
+bouncycastleVersion=1.83
 
 cglibNodepVersion=2.2.3
 
-checkerQualVersion=3.31.0
+checkerQualVersion=3.53.0
 
-commonmarkVersion=0.27.0
+commonmarkVersion=0.27.1
 
 # 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
@@ -140,9 +140,9 @@ commonsTextVersion=1.15.0
 commonsValidatorVersion=1.10.1
 commonsVfs2Version=2.10.0
 
-datadogVersion=1.56.3
+datadogVersion=1.58.2
 
-dom4jVersion=2.1.4
+dom4jVersion=2.2.0
 
 ehcacheCoreVersion=2.6.8
 eigenbasePropertiesVersion=1.1.6
@@ -156,10 +156,10 @@ fopVersion=2.11
 
 # Force latest for consistency
 googleApiVersion=2.47.0
-googleAuthVersion=1.33.0
+googleAuthVersion=1.40.0
 googleAutoValueAnnotationsVersion=1.10.4
-googleErrorProneAnnotationsVersion=2.45.0
-googleHttpClientVersion=2.0.2
+googleErrorProneAnnotationsVersion=2.46.0
+googleHttpClientVersion=2.1.0
 googleOauthClientVersion=1.39.0
 googleProtocolBufVersion=3.25.8
 
@@ -169,7 +169,7 @@ googleProtocolBufVersion=3.25.8
 # "java.lang.NoSuchMethodError: 'void com.google.gson.internal.ConstructorConstructor.<init>(java.util.Map)'" errors
 gsonVersion=2.8.9
 
-grpcVersion=1.77.0
+grpcVersion=1.78.0
 
 guavaVersion=33.5.0-jre
 
@@ -185,8 +185,8 @@ hamcrestVersion=2.2
 # Note: if changing this, we might need to match with the picard version in the SequenceAnalysis module build.gradle
 htsjdkVersion=4.3.0
 
-httpclient5Version=5.5.1
-httpcore5Version=5.3.6
+httpclient5Version=5.5.2
+httpcore5Version=5.4
 
 # Not used directly, but these are widely used transitive dependencies
 httpclientVersion=4.5.14
@@ -195,12 +195,12 @@ httpcoreVersion=4.4.16
 intellijKotlinVersion=1.9.10
 
 # Update the three Jackson dependency versions below in tandem, unless one gets a patch release out-of-sync with the others
-jacksonVersion=2.20.1
-jacksonDatabindVersion=2.20.1
-jacksonJaxrsBaseVersion=2.20.1
+jacksonVersion=2.21.0
+jacksonDatabindVersion=2.21.0
+jacksonJaxrsBaseVersion=2.21.0
 
 # Note the inconsistent version numbering for "annotations"... it no longer matches the above
-jacksonAnnotationsVersion=2.20
+jacksonAnnotationsVersion=2.21
 
 # The Jakarta Activation API version that Angus Activation implements. Keep in sync with angusActivationVersion (above).
 jakartaActivationApiVersion=2.1.4
@@ -217,7 +217,7 @@ jaxbOldVersion=2.3.3
 
 # All other direct and indirect uses of JAXB use the current, jakarta-packaged versions
 jaxbApiVersion=4.0.4
-jaxbVersion=4.0.5
+jaxbVersion=4.0.6
 
 jaxrpcVersion=1.1
 
@@ -233,9 +233,9 @@ jodaTimeVersion=2.14.0
 # brought in transitively by Cloud, FileTransfer, SequenceAnalysis, etc. Need to resolve consistently
 jsr305Version=3.0.2
 
-orgJsonVersion=20250517
+orgJsonVersion=20251224
 
-jsoupVersion=1.21.2
+jsoupVersion=1.22.1
 
 junitVersion=4.13.2
 
@@ -266,7 +266,7 @@ poiVersion=5.4.0
 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
+postgresqlDriverVersion=42.7.9
 
 quartzVersion=2.5.2
 
@@ -289,17 +289,17 @@ slf4jLog4jApiVersion=2.0.17
 snappyJavaVersion=1.1.10.8
 
 # Also, update apacheTomcatVersion above to match Spring Boot's Tomcat dependency version
-springBootVersion=4.0.1
+springBootVersion=4.0.2
 # This usually matches the Spring Framework version dictated by springBootVersion
-springVersion=7.0.2
+springVersion=7.0.3
 springAiVersion=1.1.2
 
 sqliteJdbcVersion=3.51.1.0
 
 # 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
 
-thumbnailatorVersion=0.4.20
+thumbnailatorVersion=0.4.21
 
 # used for tika-core in API and tika-parsers in search
 tikaVersion=3.2.3