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edmundmilleredmundmiller
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build: Use nextflow gradle plugin
1 parent 0cca8fa commit 57e06ee

23 files changed

+103
-297
lines changed

‎Makefile

+11-61
Original file line numberDiff line numberDiff line change
@@ -1,71 +1,21 @@
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config ?= compileClasspath
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ifdef module
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mm = :${module}:
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else
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mm =
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endif
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# Build the plugin
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assemble:
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./gradlew assemble
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clean:
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rm -rf .nextflow*
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rm -rf work
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rm -rf build
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rm -rf plugins/*/build
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./gradlew clean
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compile:
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./gradlew compileGroovy
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@echo "DONE `date`"
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check:
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./gradlew check
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#
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# Show dependencies try `make deps config=runtime`, `make deps config=google`
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#
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deps:
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./gradlew -q ${mm}dependencies --configuration ${config}
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deps-all:
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./gradlew -q dependencyInsight --configuration ${config} --dependency ${module}
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#
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# Refresh SNAPSHOTs dependencies
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#
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refresh:
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./gradlew --refresh-dependencies
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#
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# Run all tests or selected ones
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#
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# Run plugin unit tests
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test:
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ifndef class
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./gradlew ${mm}test
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else
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./gradlew ${mm}test --tests ${class}
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endif
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assemble:
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./gradlew assemble
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#
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# generate build zips under build/plugins
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# you can install the plugin copying manually these files to $HOME/.nextflow/plugins
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#
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buildPlugins:
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./gradlew copyPluginZip
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#
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# Upload JAR artifacts to Maven Central
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#
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upload:
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./gradlew upload
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./gradlew test
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upload-plugins:
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./gradlew plugins:upload
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# Install the plugin into local nextflow plugins dir
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install:
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./gradlew install
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publish-index:
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./gradlew plugins:publishIndex
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# Publish the plugin
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release:
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./gradlew releasePlugin

‎plugins/nf-sqldb/build.gradle renamed to ‎build.gradle

+84-56
Original file line numberDiff line numberDiff line change
@@ -14,19 +14,34 @@
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* limitations under the License.
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*/
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plugins {
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// Apply the groovy plugin to add support for Groovy
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id 'io.nextflow.groovy-library-conventions'
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id 'idea'
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id 'de.undercouch.download' version '4.1.2'
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// Add the download plugin
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buildscript {
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repositories {
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mavenCentral()
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}
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dependencies {
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classpath 'de.undercouch:gradle-download-task:4.1.2'
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}
2225
}
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group = 'io.nextflow'
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// DO NOT SET THE VERSION HERE
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// THE VERSION FOR PLUGINS IS DEFINED IN THE `/resources/META-INF/MANIFEST.NF` file
27+
plugins {
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id 'io.nextflow.nextflow-plugin' version '0.0.1-alpha'
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}
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idea {
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module.inheritOutputDirs = true
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sourceSets {
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main {
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groovy {
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srcDirs = ['src/main/groovy']
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}
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resources {
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srcDirs = ['src/main/resources']
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}
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}
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test {
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groovy {
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srcDirs = ['src/test/groovy']
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}
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}
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}
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repositories {
@@ -36,75 +51,86 @@ repositories {
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maven { url = 'https://s3-eu-west-1.amazonaws.com/maven.seqera.io/snapshots' }
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}
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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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}
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sourceSets {
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main.java.srcDirs = []
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main.groovy.srcDirs = ['src/main']
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main.resources.srcDirs = ['src/resources']
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test.groovy.srcDirs = ['src/test']
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test.java.srcDirs = []
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test.resources.srcDirs = []
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}
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ext{
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nextflowVersion = '24.04.0'
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}
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dependencies {
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compileOnly "io.nextflow:nextflow:$nextflowVersion"
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compileOnly 'org.slf4j:slf4j-api:2.0.7'
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compileOnly 'org.pf4j:pf4j:3.12.0'
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// API dependencies from the original build.gradle
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api("org.apache.groovy:groovy-sql:4.0.23") { transitive = false }
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api 'com.h2database:h2:1.4.200'
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api 'mysql:mysql-connector-java:8.0.33'
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api 'org.mariadb.jdbc:mariadb-java-client:2.7.0'
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api 'org.postgresql:postgresql:42.7.4'
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api 'org.xerial:sqlite-jdbc:3.47.0.0'
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api 'org.duckdb:duckdb_jdbc:0.10.2'
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// JDBC driver setup for AWS Athena - the 3rd party JAR are being downloaded and setup as gradle tasks below.
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// Reference https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html
63+
64+
// Replace commons-logging with jcl-over-slf4j
65+
implementation 'org.slf4j:jcl-over-slf4j:2.0.7'
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// JDBC driver for AWS Athena
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api files('src/dist/lib/AthenaJDBC42_2.0.25.1001.jar')
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//NOTE: Had to remove the slf4j jar due to a conflict
7669
implementation fileTree(dir: 'src/dist/lib/libs', include: '*.jar')
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// test configuration
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// Test dependencies
7972
testImplementation "org.apache.groovy:groovy:4.0.23"
8073
testImplementation "org.apache.groovy:groovy-nio:4.0.23"
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testImplementation "io.nextflow:nextflow:$nextflowVersion"
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testImplementation ("org.apache.groovy:groovy-test:4.0.23") { exclude group: 'org.apache.groovy' }
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testImplementation ("cglib:cglib-nodep:3.3.0")
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testImplementation ("org.objenesis:objenesis:3.1")
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testImplementation ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
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testImplementation ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
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testImplementation ('com.google.jimfs:jimfs:1.1')
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89-
testImplementation(testFixtures("io.nextflow:nextflow:$nextflowVersion"))
90-
testImplementation(testFixtures("io.nextflow:nf-commons:$nextflowVersion"))
81+
// Add back Nextflow test dependencies
82+
testImplementation "io.nextflow:nextflow:${nextflowPlugin.nextflowVersion}"
83+
testImplementation(testFixtures("io.nextflow:nextflow:${nextflowPlugin.nextflowVersion}"))
84+
testImplementation(testFixtures("io.nextflow:nf-commons:${nextflowPlugin.nextflowVersion}"))
85+
}
86+
87+
configurations {
88+
// see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
89+
runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
90+
}
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92-
// see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
93-
modules {
94-
module("commons-logging:commons-logging") { replacedBy("org.slf4j:jcl-over-slf4j") }
92+
// Use the version from the MANIFEST.MF
93+
version = '0.6.0'
94+
95+
nextflowPlugin {
96+
// From the MANIFEST.MF
97+
nextflowVersion = '24.04.0'
98+
99+
provider = 'Seqera Labs'
100+
className = 'nextflow.sql.SqlPlugin'
101+
extensionPoints = [
102+
'nextflow.sql.ChannelSqlExtension'
103+
]
104+
105+
publishing {
106+
github {
107+
repository = 'seqera/nf-sqldb'
108+
userName = project.findProperty('github_username')
109+
authToken = project.findProperty('github_access_token')
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email = project.findProperty('github_commit_email')
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// You may need to adjust this URL if the central plugin index is different
113+
indexUrl = 'https://github.com/nextflow-io/plugins/main/plugins.json'
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}
95115
}
96116
}
97117

118+
// Configure the packagePlugin task to handle duplicates
119+
tasks.named('packagePlugin') {
120+
duplicatesStrategy = DuplicatesStrategy.EXCLUDE
121+
}
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123+
// Add test configuration for Java modules
98124
test {
99125
useJUnitPlatform()
126+
jvmArgs = ['--add-opens=java.base/java.lang=ALL-UNNAMED',
127+
'--add-opens=java.base/java.util=ALL-UNNAMED',
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'--add-opens=java.base/java.lang.reflect=ALL-UNNAMED']
100129
}
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/**
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* AWS Athena
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* The following tasks download and confirm the MD5 checksum of the ZIP archive
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* for Simba Athena JDBC driver and extract its contents to the build directory
106-
* Reference: https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html
107-
*/
131+
// AWS Athena dependencies setup - migrated from the original build.gradle
132+
apply plugin: 'de.undercouch.download'
133+
108134
task downloadAthenDep(type: Download) {
109135
src 'https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC-2.0.25.1001/SimbaAthenaJDBC-2.0.25.1001.zip'
110136
dest new File(buildDir, 'downloads/SimbaAthenaJDBC-2.0.25.1001.zip')
@@ -122,11 +148,13 @@ task unzipAthenDep(dependsOn: verifyAthenDep, type: Copy) {
122148
into "${buildDir}/downloads/unzip/awsathena/"
123149
}
124150

125-
// Files under src/dist are included into the distribution zip
126-
// https://docs.gradle.org/current/userguide/application_plugin.html
127151
task copyAthenDep(dependsOn: unzipAthenDep, type: Copy) {
128152
from file(new File(buildDir, '/downloads/unzip/awsathena/SimbaAthenaJDBC-2.0.25.1001/AthenaJDBC42_2.0.25.1001.jar'))
129153
into "src/dist/lib"
130154
}
131-
project.copyPluginLibs.dependsOn('copyAthenDep')
132-
project.compileGroovy.dependsOn('copyAthenDep')
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// Make sure compileGroovy depends on copyAthenDep
157+
compileGroovy.dependsOn(copyAthenDep)
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// Hook into the assemble task to ensure Athena dependencies are properly set up
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assemble.dependsOn('copyAthenDep')

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