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build: Use nextflow gradle plugin #26

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72 changes: 11 additions & 61 deletions Makefile
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Original file line number Diff line number Diff line change
@@ -1,71 +1,21 @@
config ?= compileClasspath

ifdef module
mm = :${module}:
else
mm =
endif
# Build the plugin
assemble:
./gradlew assemble

clean:
rm -rf .nextflow*
rm -rf work
rm -rf build
rm -rf plugins/*/build
./gradlew clean

compile:
./gradlew compileGroovy
@echo "DONE `date`"


check:
./gradlew check


#
# Show dependencies try `make deps config=runtime`, `make deps config=google`
#
deps:
./gradlew -q ${mm}dependencies --configuration ${config}

deps-all:
./gradlew -q dependencyInsight --configuration ${config} --dependency ${module}

#
# Refresh SNAPSHOTs dependencies
#
refresh:
./gradlew --refresh-dependencies

#
# Run all tests or selected ones
#
# Run plugin unit tests
test:
ifndef class
./gradlew ${mm}test
else
./gradlew ${mm}test --tests ${class}
endif

assemble:
./gradlew assemble

#
# generate build zips under build/plugins
# you can install the plugin copying manually these files to $HOME/.nextflow/plugins
#
buildPlugins:
./gradlew copyPluginZip

#
# Upload JAR artifacts to Maven Central
#
upload:
./gradlew upload

./gradlew test

upload-plugins:
./gradlew plugins:upload
# Install the plugin into local nextflow plugins dir
install:
./gradlew install

publish-index:
./gradlew plugins:publishIndex
# Publish the plugin
release:
./gradlew releasePlugin
140 changes: 84 additions & 56 deletions plugins/nf-sqldb/build.gradle → build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -14,19 +14,34 @@
* limitations under the License.
*/

plugins {
// Apply the groovy plugin to add support for Groovy
id 'io.nextflow.groovy-library-conventions'
id 'idea'
id 'de.undercouch.download' version '4.1.2'
// Add the download plugin
buildscript {
repositories {
mavenCentral()
}
dependencies {
classpath 'de.undercouch:gradle-download-task:4.1.2'
}
}

group = 'io.nextflow'
// DO NOT SET THE VERSION HERE
// THE VERSION FOR PLUGINS IS DEFINED IN THE `/resources/META-INF/MANIFEST.NF` file
plugins {
id 'io.nextflow.nextflow-plugin' version '0.0.1-alpha'
}

idea {
module.inheritOutputDirs = true
sourceSets {
main {
groovy {
srcDirs = ['src/main/groovy']
}
resources {
srcDirs = ['src/main/resources']
}
}
test {
groovy {
srcDirs = ['src/test/groovy']
}
}
}
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I think this can be removed


repositories {
Expand All @@ -36,75 +51,86 @@ repositories {
maven { url = 'https://s3-eu-west-1.amazonaws.com/maven.seqera.io/snapshots' }
}

configurations {
// see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
}

sourceSets {
main.java.srcDirs = []
main.groovy.srcDirs = ['src/main']
main.resources.srcDirs = ['src/resources']
test.groovy.srcDirs = ['src/test']
test.java.srcDirs = []
test.resources.srcDirs = []
}

ext{
nextflowVersion = '24.04.0'
}

dependencies {
compileOnly "io.nextflow:nextflow:$nextflowVersion"
compileOnly 'org.slf4j:slf4j-api:2.0.7'
compileOnly 'org.pf4j:pf4j:3.12.0'

// API dependencies from the original build.gradle
api("org.apache.groovy:groovy-sql:4.0.23") { transitive = false }
api 'com.h2database:h2:1.4.200'
api 'mysql:mysql-connector-java:8.0.33'
api 'org.mariadb.jdbc:mariadb-java-client:2.7.0'
api 'org.postgresql:postgresql:42.7.4'
api 'org.xerial:sqlite-jdbc:3.47.0.0'
api 'org.duckdb:duckdb_jdbc:0.10.2'


// JDBC driver setup for AWS Athena - the 3rd party JAR are being downloaded and setup as gradle tasks below.
// Reference https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html

// Replace commons-logging with jcl-over-slf4j
implementation 'org.slf4j:jcl-over-slf4j:2.0.7'
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I think this can be removed


// JDBC driver for AWS Athena
api files('src/dist/lib/AthenaJDBC42_2.0.25.1001.jar')

//NOTE: Had to remove the slf4j jar due to a conflict
implementation fileTree(dir: 'src/dist/lib/libs', include: '*.jar')

// test configuration
// Test dependencies
testImplementation "org.apache.groovy:groovy:4.0.23"
testImplementation "org.apache.groovy:groovy-nio:4.0.23"
testImplementation "io.nextflow:nextflow:$nextflowVersion"
testImplementation ("org.apache.groovy:groovy-test:4.0.23") { exclude group: 'org.apache.groovy' }
testImplementation ("cglib:cglib-nodep:3.3.0")
testImplementation ("org.objenesis:objenesis:3.1")
testImplementation ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
testImplementation ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
testImplementation ('com.google.jimfs:jimfs:1.1')

testImplementation(testFixtures("io.nextflow:nextflow:$nextflowVersion"))
testImplementation(testFixtures("io.nextflow:nf-commons:$nextflowVersion"))
// Add back Nextflow test dependencies
testImplementation "io.nextflow:nextflow:${nextflowPlugin.nextflowVersion}"
testImplementation(testFixtures("io.nextflow:nextflow:${nextflowPlugin.nextflowVersion}"))
testImplementation(testFixtures("io.nextflow:nf-commons:${nextflowPlugin.nextflowVersion}"))
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I think all of this can be removed

}

configurations {
// see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
}
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I think this can be removed


// see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
modules {
module("commons-logging:commons-logging") { replacedBy("org.slf4j:jcl-over-slf4j") }
// Use the version from the MANIFEST.MF
version = '0.6.0'

nextflowPlugin {
// From the MANIFEST.MF
nextflowVersion = '24.04.0'

provider = 'Seqera Labs'
className = 'nextflow.sql.SqlPlugin'
extensionPoints = [
'nextflow.sql.ChannelSqlExtension'
]

publishing {
github {
repository = 'seqera/nf-sqldb'
userName = project.findProperty('github_username')
authToken = project.findProperty('github_access_token')
email = project.findProperty('github_commit_email')

// You may need to adjust this URL if the central plugin index is different
indexUrl = 'https://github.com/nextflow-io/plugins/main/plugins.json'
}
}
}

// Configure the packagePlugin task to handle duplicates
tasks.named('packagePlugin') {
duplicatesStrategy = DuplicatesStrategy.EXCLUDE
}

// Add test configuration for Java modules
test {
useJUnitPlatform()
jvmArgs = ['--add-opens=java.base/java.lang=ALL-UNNAMED',
'--add-opens=java.base/java.util=ALL-UNNAMED',
'--add-opens=java.base/java.lang.reflect=ALL-UNNAMED']
}

/**
* AWS Athena
* The following tasks download and confirm the MD5 checksum of the ZIP archive
* for Simba Athena JDBC driver and extract its contents to the build directory
* Reference: https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html
*/
// AWS Athena dependencies setup - migrated from the original build.gradle
apply plugin: 'de.undercouch.download'
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This can be moved to the plugins block at the top


task downloadAthenDep(type: Download) {
src 'https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC-2.0.25.1001/SimbaAthenaJDBC-2.0.25.1001.zip'
dest new File(buildDir, 'downloads/SimbaAthenaJDBC-2.0.25.1001.zip')
Expand All @@ -122,11 +148,13 @@ task unzipAthenDep(dependsOn: verifyAthenDep, type: Copy) {
into "${buildDir}/downloads/unzip/awsathena/"
}

// Files under src/dist are included into the distribution zip
// https://docs.gradle.org/current/userguide/application_plugin.html
task copyAthenDep(dependsOn: unzipAthenDep, type: Copy) {
from file(new File(buildDir, '/downloads/unzip/awsathena/SimbaAthenaJDBC-2.0.25.1001/AthenaJDBC42_2.0.25.1001.jar'))
into "src/dist/lib"
}
project.copyPluginLibs.dependsOn('copyAthenDep')
project.compileGroovy.dependsOn('copyAthenDep')

// Make sure compileGroovy depends on copyAthenDep
compileGroovy.dependsOn(copyAthenDep)

// Hook into the assemble task to ensure Athena dependencies are properly set up
assemble.dependsOn('copyAthenDep')
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