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jorgeejorgee
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alternatice to version pinning
Signed-off-by: jorgee <jorge.ejarque@seqera.io>
1 parent f02ea8b commit 6308e6e

7 files changed

Lines changed: 24 additions & 55 deletions

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‎modules/nextflow/build.gradle‎

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@@ -76,7 +76,7 @@ dependencies {
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testImplementation 'org.subethamail:subethasmtp:3.1.7'
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testImplementation (project(':nf-lineage'))
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testImplementation 'org.wiremock:wiremock:3.13.1'
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testImplementation 'org.wiremock:wiremock:3.13.2'
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// test configuration
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testFixturesApi ("org.apache.groovy:groovy-test:4.0.31") { exclude group: 'org.apache.groovy' }
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testFixturesApi ("org.objenesis:objenesis:3.4")

‎modules/nf-commons/build.gradle‎

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@@ -45,6 +45,6 @@ dependencies {
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testFixturesImplementation(project(":nextflow"))
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testImplementation "org.apache.groovy:groovy-json:4.0.31" // needed by wiremock
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testImplementation ('org.wiremock:wiremock:3.13.1') { exclude module: 'groovy-all' }
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testImplementation ('org.wiremock:wiremock:3.13.2') { exclude module: 'groovy-all' }
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}
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‎modules/nf-httpfs/build.gradle‎

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@@ -36,7 +36,7 @@ dependencies {
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/* testImplementation inherited from top gradle build file */
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testImplementation "org.apache.groovy:groovy-json:4.0.31" // needed by wiremock
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testImplementation ('org.wiremock:wiremock:3.13.1') { exclude module: 'groovy-all' }
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testImplementation ('org.wiremock:wiremock:3.13.2') { exclude module: 'groovy-all' }
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testImplementation(testFixtures(project(":nextflow")))
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}

‎plugins/nf-amazon/build.gradle‎

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@@ -48,40 +48,30 @@ sourceSets {
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configurations {
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// see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
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runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
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testRuntimeClasspath.exclude group: 'io.micronaut', module: 'micronaut-core-bom'
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}
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dependencies {
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// Force patched Netty across all configurations (incl. testRuntimeClasspath, where
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// a transitive fixture would otherwise escalate to 4.2.x).
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// Addresses GHSA-pwqr-wmgm-9rr8 (netty-codec-http HTTP Request Smuggling)
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// and GHSA-w9fj-cfpg-grvv (netty-codec-http2 CONTINUATION Frame Flood DoS).
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constraints {
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implementation('io.netty:netty-buffer') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-common') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-handler') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-codec-http') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-codec-http2') { version { strictly '4.1.132.Final' } }
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}
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compileOnly project(':nextflow')
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compileOnly 'org.slf4j:slf4j-api:2.0.17'
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compileOnly 'org.pf4j:pf4j:3.14.1'
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api ('javax.xml.bind:jaxb-api:2.4.0-b180830.0359')
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api ('software.amazon.awssdk:s3:2.33.2')
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api ('software.amazon.awssdk:ec2:2.33.2')
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api ('software.amazon.awssdk:batch:2.33.2')
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api ('software.amazon.awssdk:iam:2.33.2')
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api ('software.amazon.awssdk:ecs:2.33.2')
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api ('software.amazon.awssdk:cloudwatchlogs:2.33.2')
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api ('software.amazon.awssdk:codecommit:2.33.2')
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api ('software.amazon.awssdk:sts:2.33.2')
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api ('software.amazon.awssdk:ses:2.33.2')
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api ('software.amazon.awssdk:sso:2.33.2')
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api ('software.amazon.awssdk:ssooidc:2.33.2')
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api ('software.amazon.awssdk:s3-transfer-manager:2.33.2')
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api ('software.amazon.awssdk:apache-client:2.33.2')
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api ('software.amazon.awssdk:aws-crt-client:2.33.2')
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api ('software.amazon.awssdk:s3:2.42.41')
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api ('software.amazon.awssdk:ec2:2.42.41')
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api ('software.amazon.awssdk:batch:2.42.41')
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api ('software.amazon.awssdk:iam:2.42.41')
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api ('software.amazon.awssdk:ecs:2.42.41')
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api ('software.amazon.awssdk:cloudwatchlogs:2.42.41')
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api ('software.amazon.awssdk:codecommit:2.42.41')
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api ('software.amazon.awssdk:sts:2.42.41')
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api ('software.amazon.awssdk:ses:2.42.41')
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api ('software.amazon.awssdk:sso:2.42.41')
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api ('software.amazon.awssdk:ssooidc:2.42.41')
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api ('software.amazon.awssdk:s3-transfer-manager:2.42.41')
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api ('software.amazon.awssdk:apache-client:2.42.41')
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api ('software.amazon.awssdk:aws-crt-client:2.42.41')
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testImplementation(testFixtures(project(":nextflow")))
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testImplementation project(':nextflow')

‎plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java‎

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@@ -21,6 +21,7 @@
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import java.io.InputStream;
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import java.io.InterruptedIOException;
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import java.nio.file.*;
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import java.nio.file.AccessDeniedException;
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import java.nio.file.attribute.BasicFileAttributes;
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import java.util.EnumSet;
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import java.util.Queue;

‎plugins/nf-azure/build.gradle‎

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Original file line numberDiff line numberDiff line change
@@ -47,22 +47,10 @@ sourceSets {
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configurations {
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// see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
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runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
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testRuntimeClasspath.exclude group: 'io.micronaut', module: 'micronaut-core-bom'
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}
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dependencies {
53-
// Force patched Netty across all configurations (incl. testRuntimeClasspath, where
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// a transitive fixture would otherwise escalate to 4.2.x).
55-
// Addresses GHSA-pwqr-wmgm-9rr8 (netty-codec-http HTTP Request Smuggling)
56-
// and GHSA-w9fj-cfpg-grvv (netty-codec-http2 CONTINUATION Frame Flood DoS).
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// netty-buffer must be pinned alongside the rest -- leaving it at 4.2.x
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// (via Micronaut BOM) causes ABI mismatch in AbstractByteBufAllocator.
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constraints {
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implementation('io.netty:netty-buffer') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-common') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-handler') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-codec-http') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-codec-http2') { version { strictly '4.1.132.Final' } }
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}
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compileOnly project(':nextflow')
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compileOnly 'org.slf4j:slf4j-api:2.0.17'

‎plugins/nf-codecommit/build.gradle‎

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Original file line numberDiff line numberDiff line change
@@ -43,29 +43,19 @@ sourceSets {
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configurations {
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// see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
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runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
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testRuntimeClasspath.exclude group: 'io.micronaut', module: 'micronaut-core-bom'
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}
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dependencies {
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// Force patched Netty across all configurations (incl. testRuntimeClasspath, where
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// a transitive fixture would otherwise escalate to 4.2.x).
51-
// Addresses GHSA-pwqr-wmgm-9rr8 (netty-codec-http HTTP Request Smuggling)
52-
// and GHSA-w9fj-cfpg-grvv (netty-codec-http2 CONTINUATION Frame Flood DoS).
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constraints {
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implementation('io.netty:netty-buffer') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-common') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-handler') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-codec-http') { version { strictly '4.1.132.Final' } }
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implementation('io.netty:netty-codec-http2') { version { strictly '4.1.132.Final' } }
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}
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compileOnly project(':nextflow')
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compileOnly 'org.slf4j:slf4j-api:2.0.17'
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compileOnly 'org.pf4j:pf4j:3.14.1'
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api ('javax.xml.bind:jaxb-api:2.4.0-b180830.0359')
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api ('software.amazon.awssdk:codecommit:2.31.64')
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api ('software.amazon.awssdk:sso:2.31.64')
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api ('software.amazon.awssdk:ssooidc:2.31.64')
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api ('software.amazon.awssdk:codecommit:2.42.41')
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api ('software.amazon.awssdk:sso:2.42.41')
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api ('software.amazon.awssdk:ssooidc:2.42.41')
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testImplementation(testFixtures(project(":nextflow")))
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testImplementation project(':nextflow')

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