build: Use nextflow gradle plugin

Signed-off-by: Edmund Miller <[email protected]>

Author: edmundmiller

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

plugins/nf-sqldb/build.gradle renamed to 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:$nextflowVersion"
-    compileOnly 'org.slf4j:slf4j-api:2.0.16'
-    compileOnly 'org.pf4j:pf4j:3.12.0'
-    
+    // Latest database dependencies from master branch
     api("org.apache.groovy:groovy-sql:4.0.26") { transitive = false }
     api 'com.h2database:h2:1.4.200'
     api 'mysql:mysql-connector-java:8.0.33'
@@ -77,25 +49,29 @@ dependencies {
     // test configuration
     testImplementation "org.apache.groovy:groovy:4.0.26"
     testImplementation "org.apache.groovy:groovy-nio:4.0.26"
-    testImplementation "io.nextflow:nextflow:$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 +103,10 @@ 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')
+
+test {
+    useJUnitPlatform()
+}