diff --git a/modules/nextflow/build.gradle b/modules/nextflow/build.gradle index de5240774c..0b5a7eeb3c 100644 --- a/modules/nextflow/build.gradle +++ b/modules/nextflow/build.gradle @@ -76,7 +76,7 @@ dependencies { testImplementation 'org.subethamail:subethasmtp:3.1.7' testImplementation (project(':nf-lineage')) - testImplementation 'org.wiremock:wiremock:3.13.1' + testImplementation 'org.wiremock:wiremock:3.13.2' // test configuration testFixturesApi ("org.apache.groovy:groovy-test:4.0.31") { exclude group: 'org.apache.groovy' } testFixturesApi ("org.objenesis:objenesis:3.4") diff --git a/modules/nf-commons/build.gradle b/modules/nf-commons/build.gradle index ef1a429896..9d8eb460ca 100644 --- a/modules/nf-commons/build.gradle +++ b/modules/nf-commons/build.gradle @@ -45,6 +45,6 @@ dependencies { testFixturesImplementation(project(":nextflow")) testImplementation "org.apache.groovy:groovy-json:4.0.31" // needed by wiremock - testImplementation ('org.wiremock:wiremock:3.13.1') { exclude module: 'groovy-all' } + testImplementation ('org.wiremock:wiremock:3.13.2') { exclude module: 'groovy-all' } } diff --git a/modules/nf-httpfs/build.gradle b/modules/nf-httpfs/build.gradle index 1ead9cc6cb..98e46c1c6d 100644 --- a/modules/nf-httpfs/build.gradle +++ b/modules/nf-httpfs/build.gradle @@ -36,7 +36,7 @@ dependencies { /* testImplementation inherited from top gradle build file */ testImplementation "org.apache.groovy:groovy-json:4.0.31" // needed by wiremock - testImplementation ('org.wiremock:wiremock:3.13.1') { exclude module: 'groovy-all' } + testImplementation ('org.wiremock:wiremock:3.13.2') { exclude module: 'groovy-all' } testImplementation(testFixtures(project(":nextflow"))) } diff --git a/plugins/nf-amazon/build.gradle b/plugins/nf-amazon/build.gradle index b5da009fd1..f9b30f74f0 100644 --- a/plugins/nf-amazon/build.gradle +++ b/plugins/nf-amazon/build.gradle @@ -48,6 +48,7 @@ sourceSets { configurations { // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api' + testRuntimeClasspath.exclude group: 'io.micronaut', module: 'micronaut-core-bom' } dependencies { @@ -56,25 +57,20 @@ dependencies { compileOnly 'org.pf4j:pf4j:3.14.1' api ('javax.xml.bind:jaxb-api:2.4.0-b180830.0359') - api ('software.amazon.awssdk:s3:2.33.2') - api ('software.amazon.awssdk:ec2:2.33.2') - api ('software.amazon.awssdk:batch:2.33.2') - api ('software.amazon.awssdk:iam:2.33.2') - api ('software.amazon.awssdk:ecs:2.33.2') - api ('software.amazon.awssdk:cloudwatchlogs:2.33.2') - api ('software.amazon.awssdk:codecommit:2.33.2') - api ('software.amazon.awssdk:sts:2.33.2') - api ('software.amazon.awssdk:ses:2.33.2') - api ('software.amazon.awssdk:sso:2.33.2') - api ('software.amazon.awssdk:ssooidc:2.33.2') - api ('software.amazon.awssdk:s3-transfer-manager:2.33.2') - api ('software.amazon.awssdk:apache-client:2.33.2') - api ('software.amazon.awssdk:aws-crt-client:2.33.2') - - // address security vulnerabilities - implementation 'io.netty:netty-common:4.1.133.Final' - implementation 'io.netty:netty-handler:4.1.133.Final' - implementation 'io.netty:netty-codec-http2:4.1.133.Final' + api ('software.amazon.awssdk:s3:2.44.3') + api ('software.amazon.awssdk:ec2:2.44.3') + api ('software.amazon.awssdk:batch:2.44.3') + api ('software.amazon.awssdk:iam:2.44.3') + api ('software.amazon.awssdk:ecs:2.44.3') + api ('software.amazon.awssdk:cloudwatchlogs:2.44.3') + api ('software.amazon.awssdk:codecommit:2.44.3') + api ('software.amazon.awssdk:sts:2.44.3') + api ('software.amazon.awssdk:ses:2.44.3') + api ('software.amazon.awssdk:sso:2.44.3') + api ('software.amazon.awssdk:ssooidc:2.44.3') + api ('software.amazon.awssdk:s3-transfer-manager:2.44.3') + api ('software.amazon.awssdk:apache-client:2.44.3') + api ('software.amazon.awssdk:aws-crt-client:2.44.3') testImplementation(testFixtures(project(":nextflow"))) testImplementation project(':nextflow') diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java index 5a59b61c2a..205a16de35 100644 --- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java +++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java @@ -21,6 +21,7 @@ import java.io.InputStream; import java.io.InterruptedIOException; import java.nio.file.*; +import java.nio.file.AccessDeniedException; import java.nio.file.attribute.BasicFileAttributes; import java.util.EnumSet; import java.util.Queue; diff --git a/plugins/nf-azure/build.gradle b/plugins/nf-azure/build.gradle index 63371d193a..49e1e4e37b 100644 --- a/plugins/nf-azure/build.gradle +++ b/plugins/nf-azure/build.gradle @@ -47,20 +47,21 @@ sourceSets { configurations { // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api' + testRuntimeClasspath.exclude group: 'io.micronaut', module: 'micronaut-core-bom' } dependencies { compileOnly project(':nextflow') compileOnly 'org.slf4j:slf4j-api:2.0.17' compileOnly 'org.pf4j:pf4j:3.14.1' - api('com.azure:azure-storage-blob:12.33.2') { + api('com.azure:azure-storage-blob:12.33.3') { exclude group: 'org.slf4j', module: 'slf4j-api' } api('com.azure:azure-compute-batch:1.0.0-beta.3') { exclude group: 'org.slf4j', module: 'slf4j-api' exclude group: 'com.google.guava', module: 'guava' } - api('com.azure:azure-identity:1.18.2') { + api('com.azure:azure-identity:1.18.3') { exclude group: 'org.slf4j', module: 'slf4j-api' } diff --git a/plugins/nf-codecommit/build.gradle b/plugins/nf-codecommit/build.gradle index d1127bd5ca..b9ab6d22db 100644 --- a/plugins/nf-codecommit/build.gradle +++ b/plugins/nf-codecommit/build.gradle @@ -43,6 +43,7 @@ sourceSets { configurations { // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api' + testRuntimeClasspath.exclude group: 'io.micronaut', module: 'micronaut-core-bom' } dependencies { @@ -51,12 +52,9 @@ dependencies { compileOnly 'org.pf4j:pf4j:3.14.1' api ('javax.xml.bind:jaxb-api:2.4.0-b180830.0359') - api ('software.amazon.awssdk:codecommit:2.31.64') - api ('software.amazon.awssdk:sso:2.31.64') - api ('software.amazon.awssdk:ssooidc:2.31.64') - - // address security vulnerabilities - runtimeOnly 'io.netty:netty-codec-http:4.1.133.Final' + api ('software.amazon.awssdk:codecommit:2.44.3') + api ('software.amazon.awssdk:sso:2.44.3') + api ('software.amazon.awssdk:ssooidc:2.44.3') testImplementation(testFixtures(project(":nextflow"))) testImplementation project(':nextflow') diff --git a/plugins/nf-tower/build.gradle b/plugins/nf-tower/build.gradle index 7b63a2f57d..5aefac4f66 100644 --- a/plugins/nf-tower/build.gradle +++ b/plugins/nf-tower/build.gradle @@ -69,7 +69,7 @@ dependencies { testImplementation "org.apache.groovy:groovy-nio:4.0.31" testImplementation "org.apache.groovy:groovy-json:4.0.31" // wiremock required by TowerFusionEnvTest - testImplementation "org.wiremock:wiremock:3.13.1" + testImplementation "org.wiremock:wiremock:3.13.2" // Address security vulnerabilities CVE-2022-45688 and CVE-2023-5072 testImplementation 'org.json:json:20240303' }