Merge branch 'master' into databricks

Author: pditommaso

.github/workflows/build.yml

@@ -17,16 +17,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 17]
+        java_version: [17, 21]
 
     steps:
       - name: Environment
         run: env | sort
 
       - name: Checkout
-        uses: actions/checkout@v1
+        uses: actions/checkout@v4
         with:
-          fetch-depth: 1
           submodules: true
 
       - name: Setup Java ${{ matrix.java_version }}

README.md

@@ -239,3 +239,13 @@ 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.
+
+## Developtment 
+
+#### Publish artifacts to Maven repo 
+
+Use the following command: 
+
+```
+./gradlew plugins:nf-sqldb:publishMavenPublicationToMavenRepository
+```

changelog.txt

@@ -1,9 +1,9 @@
 NF-SQLDB CHANGE-LOG
 ===================
-0.6.0 - 5 Nov 2024
+0.6.0 - 23 May 2025
 - Update build scripts
 - Remove nf-bigquery plugin
-- Bump Nextflow to version 24.04.0
+- Bump Nextflow to version 25.04.0
 - Bump mysql-connector-java:8.0.33
 - Bump mariadb-java-client:2.7.0
 - Bump postgresql:42.7.4

plugins/build.gradle

@@ -60,6 +60,7 @@ subprojects {
     apply plugin: 'java'
     apply plugin: 'groovy'
     apply plugin: 'io.nextflow.nf-build-plugin'
+    apply plugin: 'maven-publish'
 
     repositories {
         mavenLocal()
@@ -153,6 +154,33 @@ subprojects {
     }
 
     task upload(dependsOn: [uploadPlugin] ) { }
+
+    /*
+     * publish jars maven repo on S3
+     */
+    ext.aws_access_key_id = project.findProperty('aws_access_key_id') ?: System.getenv('AWS_ACCESS_KEY_ID')
+    ext.aws_secret_access_key = project.findProperty('aws_secret_access_key') ?: System.getenv('AWS_SECRET_ACCESS_KEY')
+    ext.publishRepoUrl = project.findProperty('publish_repo_url') ?: System.getenv('PUBLISH_REPO_URL') ?: ( version.endsWith('-SNAPSHOT') ? "s3://maven.seqera.io/snapshots" : "s3://maven.seqera.io/releases" )
+
+    publishing {
+        publications {
+            maven(MavenPublication) {
+                from components.java
+                suppressPomMetadataWarningsFor('testFixturesApiElements')
+                suppressPomMetadataWarningsFor('testFixturesRuntimeElements')
+            }
+        }
+        repositories {
+            maven {
+                url = publishRepoUrl
+                credentials(AwsCredentials) {
+                    // keys are defined in the `gradle.properties` file
+                    accessKey aws_access_key_id
+                    secretKey aws_secret_access_key
+                }
+            }
+        }
+    }
 }
 
 /*

plugins/nf-sqldb/build.gradle

@@ -52,21 +52,21 @@ sourceSets {
 }
 
 ext{
-    nextflowVersion = '24.04.0'
+    nextflowVersion = '25.04.0'
 }
 
 dependencies {
     compileOnly "io.nextflow:nextflow:$nextflowVersion"
-    compileOnly 'org.slf4j:slf4j-api:2.0.7'
+    compileOnly 'org.slf4j:slf4j-api:2.0.16'
     compileOnly 'org.pf4j:pf4j:3.12.0'
 
-    api("org.apache.groovy:groovy-sql:4.0.23") { transitive = false }
+    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'
     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'
+    api 'org.postgresql:postgresql:42.7.5'
+    api 'org.xerial:sqlite-jdbc:3.49.1.0'
+    api 'org.duckdb:duckdb_jdbc:1.3.0.0'
 
     // 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
@@ -76,10 +76,10 @@ dependencies {
     implementation fileTree(dir: 'src/dist/lib/libs', include: '*.jar')
 
     // test configuration
-    testImplementation "org.apache.groovy:groovy:4.0.23"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    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:4.0.23") { exclude group: 'org.apache.groovy' }
+    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' }

plugins/nf-sqldb/src/main/nextflow/sql/config/DriverRegistry.groovy

@@ -11,7 +11,7 @@ class DriverRegistry {
 
     Map<String, String> drivers = [:]
 
-    static DriverRegistry DEFAULT = new DriverRegistry()
+    static public DriverRegistry DEFAULT = new DriverRegistry()
 
     DriverRegistry(){
         initDefaultDrivers()

plugins/nf-sqldb/src/resources/META-INF/MANIFEST.MF

@@ -3,4 +3,4 @@ Plugin-Class: nextflow.sql.SqlPlugin
 Plugin-Id: nf-sqldb
 Plugin-Provider: Seqera Labs
 Plugin-Version: 0.6.0
-Plugin-Requires: >=24.04.0
+Plugin-Requires: >=25.04.0