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labkey-adamlabkey-adam
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Update dependencies (#1401)
1 parent f412646 commit b897894

2 files changed

Lines changed: 27 additions & 36 deletions

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‎build.gradle‎

Lines changed: 10 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -224,9 +224,9 @@ allprojects {
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// brought in by SequenceAnalysis, jbrowse
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force "org.apache.logging.log4j:log4j-slf4j-impl:${log4j2Version}"
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force "org.apache.commons:commons-vfs2:${commonsVfs2Version}"
227-
// force version for consistency with saml, query, LDK, and pipeline
227+
// force version for consistency with query, LDK, and pipeline
228228
force "commons-lang:commons-lang:${commonsLangVersion}"
229-
// force version for consistency with workflow, api, SequenceAnalysis
229+
// force version for consistency with api, SequenceAnalysis
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force "org.apache.commons:commons-lang3:${commonsLang3Version}"
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force "commons-dbcp:commons-dbcp:${commonsDbcpVersion}"
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force "commons-io:commons-io:${commonsIoVersion}"
@@ -236,9 +236,9 @@ allprojects {
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force "org.apache.commons:commons-text:${commonsTextVersion}"
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// force version for consistency with search, premium, api
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force "org.apache.commons:commons-collections4:${commonsCollections4Version}"
239-
// force version for consistency with query, saml, LDK, api
239+
// force version for consistency with LDK, api
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force "commons-collections:commons-collections:${commonsCollectionsVersion}"
241-
// force version for ms2, saml, fileTransfer, harvest, api, accounts, docker
241+
// force version for ms2, fileTransfer, harvest, api, accounts, docker
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force "commons-codec:commons-codec:${commonsCodecVersion}"
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// force version consistency in TCRdb, SequenceAnalysis, API
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force "org.apache.commons:commons-math3:${commonsMath3Version}"
@@ -249,7 +249,7 @@ allprojects {
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// force version for cloud, docker, fileTransfer, googledrive, tcrb, wnprc_ehr
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force "org.apache.httpcomponents:httpclient:${httpclientVersion}"
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force "org.apache.httpcomponents.client5:httpclient5:${httpclient5Version}"
252-
// force version for postgresql jdbc, cloud, docker, fileTransfer, saml, query, GoogleDrive, WNPRC_EHR
252+
// force version for postgresql jdbc, cloud, docker, fileTransfer, GoogleDrive, WNPRC_EHR
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force "org.checkerframework:checker-qual:${checkerQualVersion}"
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// force version for SequenceAnalysis, api, cloud
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force "com.google.guava:guava:${guavaVersion}"
@@ -266,17 +266,15 @@ allprojects {
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force "jakarta.xml.bind:jakarta.xml.bind-api:${jaxbApiVersion}"
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// force version for accounts, api, query
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force "javax.validation:validation-api:${validationApiVersion}"
269-
// force version for accounts, docker, api, workflow
269+
// force version for accounts, docker, api
270270
force "com.fasterxml.jackson.core:jackson-annotations:${jacksonAnnotationsVersion}"
271-
// saml and query bring in different versions transitively; we force the later one
272-
force "xalan:xalan:${xalanVersion}"
273271
// genotyping brings in a much older version of this, so we force a newer version for compatibility
274272
force "org.apache.commons:commons-compress:${commonsCompressVersion}"
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// Force ant to be a newer version (transitive dependency of query > eigenbase-resgen > eigenbase-xom)
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force "org.apache.ant:ant:${antVersion}"
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// Transitive dependency of commons-compress -- Transitive dependency com.github.samtools:htsjdk which references an older version
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force "org.tukaani:xz:${tukaaniXZVersion}"
279-
// force version for api, LDK, pipeline, query, saml, but not for the xsdDoc configuration, which requires
277+
// force version for api and LDK, but not for the xsdDoc configuration, which requires
280278
// an older version for the docflex library we use
281279
if (!config.name.equals('xsdDoc'))
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force "xml-apis:xml-apis:${xmlApisVersion}"
@@ -350,9 +348,6 @@ allprojects {
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force "org.apache.tika:tika-core:${tikaVersion}"
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// OpenLDAPSync and premium have transitive dependency on a broken version of MINA
352350
force "org.apache.mina:mina-core:${apacheMinaVersion}"
353-
// saml has transitive dependencies on old versions of batik and xmlgraphics-commons, which conflict with more recent versions in api
354-
force "org.apache.xmlgraphics:batik-css:${batikVersion}"
355-
force "org.apache.xmlgraphics:xmlgraphics-commons:${fopVersion}"
356351
// force consistency in TCRdb, WNPRC
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force "org.javassist:javassist:${javassistVersion}"
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force "org.jetbrains:annotations:${annotationsVersion}"
@@ -365,12 +360,11 @@ allprojects {
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// The hamcrest dependencies come through transitively from jackson, junit, jmock
366361
force "org.hamcrest:hamcrest:${hamcrestVersion}"
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force "junit:junit:${junitVersion}"
368-
// force consistency in nlp and saml that bring these in transitively
363+
// SAML brings these in transitively
369364
force "org.codehaus.woodstox:stax2-api:${stax2ApiVersion}"
370365
force "com.fasterxml.woodstox:woodstox-core:${woodstoxCoreVersion}"
371-
// force consistency in docker and connectors, saml, nlp
366+
// force consistency in docker, connectors, and saml
372367
force "org.bouncycastle:bcprov-jdk18on:${bouncycastleVersion}"
373-
// force consistency in docker and connectors and saml
374368
force "org.bouncycastle:bcpkix-jdk18on:${bouncycastleVersion}"
375369

376370
// Force consistency for dependencies from pipeline and query
@@ -387,7 +381,7 @@ allprojects {
387381
// Force snappy-java version for CVE-2023-43642. Remove once HTSJDK bumps its preferred version.
388382
force "org.xerial.snappy:snappy-java:${snappyJavaVersion}"
389383

390-
// Consistency between cloud, pipeline, and query
384+
// Consistency between cloud, pipeline
391385
force "javax.xml.bind:jaxb-api:${jaxbApiOldVersion}"
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393387
// Force consistency for dependencies from cloud

‎gradle.properties‎

Lines changed: 17 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -102,7 +102,7 @@ apacheTomcatVersion=11.0.22
102102
# (mothership) -> json-path -> json-smart -> accessor-smart
103103
# (core) -> graalvm
104104
# tika
105-
asmVersion=9.9.1
105+
asmVersion=9.10
106106

107107
awsSdkVersion=2.29.50
108108

@@ -194,15 +194,15 @@ httpcoreVersion=4.4.16
194194
intellijKotlinVersion=2.3.10
195195

196196
# Update the three Jackson dependency versions below in tandem, unless one gets a patch release out-of-sync with the others
197-
jacksonVersion=2.21.3
198-
jacksonDatabindVersion=2.21.3
199-
jacksonJaxrsBaseVersion=2.21.3
197+
jacksonVersion=2.21.4
198+
jacksonDatabindVersion=2.21.4
199+
jacksonJaxrsBaseVersion=2.21.4
200200

201201
# Note the inconsistent version numbering for "annotations"... it no longer matches the above
202202
jacksonAnnotationsVersion=2.21
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204204
# Spring Boot brings in a transitive dependency on Jackson 3.x. It has changed package names and can coexist with Jackson 2.x.
205-
jackson3Version=3.1.3
205+
jackson3Version=3.1.4
206206

207207
# The Jakarta Activation API version that Angus Activation implements. Keep in sync with angusActivationVersion (above).
208208
jakartaActivationApiVersion=2.1.4
@@ -219,7 +219,7 @@ jaxbOldVersion=2.3.3
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220220
# All other direct and indirect uses of JAXB use the current, jakarta-packaged versions
221221
jaxbApiVersion=4.0.5
222-
jaxbVersion=4.0.7
222+
jaxbVersion=4.0.8
223223

224224
jaxrpcVersion=1.1
225225

@@ -233,12 +233,12 @@ jmockVersion=2.6.0
233233
# Transitive dependency via azure-identity and docker; force for consistency
234234
jnaVersion=5.18.1
235235

236-
jodaTimeVersion=2.14.1
236+
jodaTimeVersion=2.14.2
237237

238238
# brought in transitively by Cloud, FileTransfer, SequenceAnalysis, etc. Need to resolve consistently
239239
jsr305Version=3.0.2
240240

241-
orgJsonVersion=20251224
241+
orgJsonVersion=20260522
242242

243243
jsoupVersion=1.22.2
244244

@@ -255,12 +255,12 @@ lombokVersion=1.18.46
255255
luceneVersion=10.4.0
256256

257257
# Microsoft library for sending OAuth2-authenticated notification emails via the Microsoft Graph API
258-
microsoftGraphVersion=6.59.0
258+
microsoftGraphVersion=6.65.0
259259

260260
mssqlJdbcVersion=13.4.0.jre11
261261

262262
# Netty - transitive dependency via azure-core-http-netty; force for CVE-2026-33871, CVE-2026-33870
263-
nettyVersion=4.2.13.Final
263+
nettyVersion=4.2.14.Final
264264
# Reactor - transitive dependency via azure-core; force for version consistency across modules
265265
reactorCoreVersion=3.8.1
266266

@@ -293,9 +293,9 @@ romeVersion=2.1.0
293293
servletApiVersion=6.1.0
294294

295295
# this version is forced for compatibility with pipeline and tika
296-
slf4jLog4j12Version=2.0.17
296+
slf4jLog4j12Version=2.0.18
297297
# this version is forced for compatibility with api, LDK, and workflow
298-
slf4jLog4jApiVersion=2.0.17
298+
slf4jLog4jApiVersion=2.0.18
299299

300300
# This is a dependency for HTSJDK. Force version for CVE-2023-43642
301301
snappyJavaVersion=1.1.10.8
@@ -306,26 +306,23 @@ springBootVersion=4.0.6
306306
springVersion=7.0.7
307307
springAiVersion=2.0.0-M6
308308

309-
sqliteJdbcVersion=3.53.0.0
309+
sqliteJdbcVersion=3.53.1.0
310310

311-
# NLP and SAML bring stax2-api in as a transitive dependency but with very different versions. We force the later version.
311+
# SAML brings stax2-api in as a transitive dependency. We force the latest version.
312312
stax2ApiVersion=4.2.2
313313

314314
thumbnailatorVersion=0.4.21
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316316
# used for tika-core in API and tika-parsers in search
317-
tikaVersion=3.3.0
317+
tikaVersion=3.3.1
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319319
# sync with Tika
320320
tukaaniXZVersion=1.12
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322322
validationApiVersion=1.1.0.Final
323323

324-
# NLP and SAML bring woodstox-core in as a transitive dependency but with very different versions. We force the later version.
325-
woodstoxCoreVersion=7.1.1
326-
327-
# saml and query bring in different versions transitively; we force the later one
328-
xalanVersion=2.7.2
324+
# SAML brings woodstox-core in as a transitive dependency. We force the latest version.
325+
woodstoxCoreVersion=7.2.0
329326

330327
# sync with Tika
331328
xercesImplVersion=2.12.2

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