From 72c02183da250ea366ce9ebaa70be7a93f21847e Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 31 Jul 2025 13:57:54 -0700 Subject: [PATCH 1/4] Update HTSJDK and picard versions (#1139) --- gradle.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gradle.properties b/gradle.properties index 28f5f3cba4..2dd52ce211 100644 --- a/gradle.properties +++ b/gradle.properties @@ -180,7 +180,7 @@ hadoopHdfsClientVersion=3.4.1 hamcrestVersion=2.2 # Note: if changing this, we might need to match with the picard version in the SequenceAnalysis module build.gradle -htsjdkVersion=4.0.0 +htsjdkVersion=4.3.0 httpclient5Version=5.4.3 httpcore5Version=5.3.4 From 57d4e0c3e38652516cc2fecf365b47813660d826 Mon Sep 17 00:00:00 2001 From: Marty Pradere Date: Mon, 18 Aug 2025 15:30:43 -0700 Subject: [PATCH 2/4] Tomcat version bump (#1151) --- gradle.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gradle.properties b/gradle.properties index 2dd52ce211..052f7ad2c8 100644 --- a/gradle.properties +++ b/gradle.properties @@ -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=10.1.43 +apacheTomcatVersion=10.1.44 # (mothership) -> json-path -> json-smart -> accessor-smart # (core) -> graalvm From 3c19124643bb7fb4703ae8f68ed9514b99913826 Mon Sep 17 00:00:00 2001 From: Marty Pradere Date: Wed, 20 Aug 2025 11:58:44 -0700 Subject: [PATCH 3/4] update spring version (#1153) --- gradle.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gradle.properties b/gradle.properties index 052f7ad2c8..af769e688a 100644 --- a/gradle.properties +++ b/gradle.properties @@ -292,7 +292,7 @@ snappyJavaVersion=1.1.10.7 # Also, update apacheTomcatVersion above to match Spring Boot's Tomcat dependency version springBootVersion=3.5.3 # This usually matches the Spring Framework version dictated by springBootVersion -springVersion=6.2.8 +springVersion=6.2.10 sqliteJdbcVersion=3.49.1.0 From b2aa5a6c41dcb58496a561c5993cdd7e736c02df Mon Sep 17 00:00:00 2001 From: Josh Eckels Date: Mon, 1 Sep 2025 16:55:59 -0700 Subject: [PATCH 4/4] Update tika version (#1163) * Resolve Tika backport conflicts * More dependency version bumps * New JSoup needed for correct HTML indexing --------- Co-authored-by: Marty Pradere --- gradle.properties | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gradle.properties b/gradle.properties index af769e688a..2d202c4458 100644 --- a/gradle.properties +++ b/gradle.properties @@ -104,7 +104,7 @@ apacheTomcatVersion=10.1.44 # (mothership) -> json-path -> json-smart -> accessor-smart # (core) -> graalvm # tika -asmVersion=9.7.1 +asmVersion=9.8 # Apache Batik -- Batik version needs to be compatible with Apache FOP, but we need to pull in batik-codec separately batikVersion=1.18 @@ -125,7 +125,7 @@ commonsBeanutilsVersion=1.11.0 commonsCodecVersion=1.17.1 commonsCollections4Version=4.4 commonsCollectionsVersion=3.2.2 -commonsCompressVersion=1.27.1 +commonsCompressVersion=1.28.0 commonsDbcpVersion=1.4 commonsDigesterVersion=1.8.1 commonsDiscoveryVersion=0.2 @@ -230,7 +230,7 @@ jsr305Version=3.0.2 orgJsonVersion=20250107 -jsoupVersion=1.18.3 +jsoupVersion=1.21.1 junitVersion=4.13.2 @@ -259,7 +259,7 @@ opencsvVersion=2.3 openTracingVersion=0.33.0 # sync with version Tika ships -pdfboxVersion=3.0.3 +pdfboxVersion=3.0.4 # sync with version Tika ships poiVersion=5.4.0 @@ -282,9 +282,9 @@ romeVersion=2.1.0 servletApiVersion=6.0.0 # this version is forced for compatibility with pipeline and tika -slf4jLog4j12Version=2.0.16 +slf4jLog4j12Version=2.0.17 # this version is forced for compatibility with api, LDK, and workflow -slf4jLog4jApiVersion=2.0.16 +slf4jLog4jApiVersion=2.0.17 # This is a dependency for HTSJDK. Force version for CVE-2023-43642 snappyJavaVersion=1.1.10.7 @@ -302,7 +302,7 @@ stax2ApiVersion=4.2.2 thumbnailatorVersion=0.4.20 # used for tika-core in API and tika-parsers in search -tikaVersion=3.0.0 +tikaVersion=3.2.2 # sync with Tika tukaaniXZVersion=1.10