build: Use nextflow gradle plugin

Makefile

@@ -1,82 +1,21 @@
-config ?= compileClasspath
-version ?= $(shell grep 'Plugin-Version' plugins/nf-sqldb/src/resources/META-INF/MANIFEST.MF | awk '{ print $$2 }')
-
-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
-
-
-upload-plugins:
-	./gradlew plugins:upload
-
-publish-index:
-	./gradlew plugins:publishIndex
+	./gradlew test
 
 # Install the plugin into local nextflow plugins dir
 install:
-	./gradlew copyPluginZip
-	rm -rf ${HOME}/.nextflow/plugins/nf-sqldb-${version}
-	cp -r build/plugins/nf-sqldb-${version} ${HOME}/.nextflow/plugins/nf-sqldb-${version}
-
+	./gradlew install
 
-publish-jar:
-	./gradlew plugins:nf-sqldb:publishMavenPublicationToMavenRepository
+# Publish the plugin
+release:
+	./gradlew releasePlugin

README.md

@@ -241,3 +241,4 @@ The `CSVREAD` function provided by the H2 database engine allows you to query an
 Like all dataflow operators in Nextflow, the operators provided by this plugin are executed asynchronously.
 
 In particular, data inserted using the `sqlInsert` operator is _not_ guaranteed to be available to any subsequent queries using the `fromQuery` operator, as it is not possible to make a channel factory operation dependent on some upstream operation.
+

plugins/nf-sqldb/build.gradle → build.gradle

@@ -15,19 +15,12 @@
  */
 
 plugins {
-    // Apply the groovy plugin to add support for Groovy
-    id 'io.nextflow.groovy-library-conventions'
-    id 'idea'
+    id 'io.nextflow.nextflow-plugin' version '1.0.0-beta.6'
     id 'de.undercouch.download' version '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
-
-idea {
-    module.inheritOutputDirs = true
-}
+// Plugin version (from latest MANIFEST.MF)
+version = '0.7.1'
 
 repositories {
     mavenCentral()
@@ -36,29 +29,8 @@ 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 = '25.04.0'
-}
-
 dependencies {
-    compileOnly "io.nextflow:nextflow:$nextflowVersion"
-    compileOnly 'org.slf4j:slf4j-api:2.0.16'
-    compileOnly 'org.pf4j:pf4j:3.12.0'
-
+    // Database dependencies
     api("org.apache.groovy:groovy-sql:4.0.26") { transitive = false }
     api 'com.h2database:h2:1.4.200'
     api 'mysql:mysql-connector-java:8.0.33'
@@ -73,29 +45,18 @@ dependencies {
 
     //NOTE: Had to remove the slf4j jar due to a conflict
     implementation fileTree(dir: 'src/dist/lib/libs', include: '*.jar')
-
-    // test configuration
-    testImplementation "org.apache.groovy:groovy:4.0.26"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.26"
-    testImplementation "io.nextflow:nextflow:$nextflowVersion"
-    testImplementation ("org.apache.groovy:groovy-test:4.0.26") { exclude group: 'org.apache.groovy' }
-    testImplementation ("cglib:cglib-nodep:3.3.0")
-    testImplementation ("org.objenesis:objenesis:3.1")
-    testImplementation ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation ('com.google.jimfs:jimfs:1.1')
-
-    testImplementation(testFixtures("io.nextflow:nextflow:$nextflowVersion"))
-    testImplementation(testFixtures("io.nextflow:nf-commons:$nextflowVersion"))
-
-    // 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") }
-    }
 }
 
-test {
-    useJUnitPlatform()
+nextflowPlugin {
+    // Minimum Nextflow version
+    nextflowVersion = '25.04.0'
+
+    // Plugin metadata
+    provider = 'Seqera Labs'
+    className = 'nextflow.sql.SqlPlugin'
+    extensionPoints = [
+        'nextflow.sql.ChannelSqlExtension'
+    ]
 }
 
 /**
@@ -127,5 +88,11 @@ 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')
+
+// Hook into the new plugin's build process
+compileGroovy.dependsOn('copyAthenDep')
+
+// Configure the packagePlugin task to handle duplicates
+tasks.named('packagePlugin') {
+    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
+}