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
@@ -97,22 +97,22 @@ 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
 
@@ -140,7 +140,7 @@ commonsTextVersion=1.15.0
 commonsValidatorVersion=1.10.1
 commonsVfs2Version=2.10.0
 
-datadogVersion=1.56.3
+datadogVersion=1.58.2
 
 dom4jVersion=2.1.4
 
@@ -158,8 +158,8 @@ fopVersion=2.11
 googleApiVersion=2.47.0
 googleAuthVersion=1.33.0
 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
 
@@ -186,7 +186,7 @@ hamcrestVersion=2.2
 htsjdkVersion=4.3.0
 
 httpclient5Version=5.5.1
-httpcore5Version=5.3.6
+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
 
@@ -289,9 +289,9 @@ 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