Update nf-sqldb plugin

Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

.gitignore

@@ -2,4 +2,5 @@
 .idea
 .nextflow
 build
-dist
+dist
+out

act.sh

@@ -0,0 +1,14 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Support convention plugins written in Groovy. Convention plugins are build scripts in 'src/main' that automatically become available as plugins in the main build.
+    id 'groovy-gradle-plugin'
+}
+
+repositories {
+    // Use the plugin portal to apply community plugins in convention plugins.
+    gradlePluginPortal()
+}
+

buildSrc/build.gradle

@@ -0,0 +1,11 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Apply the common convention plugin for shared build configuration between library and application projects.
+    id 'io.nextflow.groovy-common-conventions'
+
+    // Apply the application plugin to add support for building a CLI application in Java.
+    id 'application'
+}

buildSrc/src/main/groovy/io.nextflow.groovy-application-conventions.gradle

@@ -0,0 +1,48 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Apply the groovy Plugin to add support for Groovy.
+    id 'groovy'
+}
+
+repositories {
+    // Use Maven Central for resolving dependencies.
+    mavenCentral()
+}
+
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(19)
+    }
+}
+
+compileJava {
+    options.release.set(11)
+}
+
+tasks.withType(GroovyCompile) {
+    sourceCompatibility = '11'
+    targetCompatibility = '11'
+}
+
+tasks.withType(Test) {
+    jvmArgs ([
+            '--add-opens=java.base/java.lang=ALL-UNNAMED',
+            '--add-opens=java.base/java.io=ALL-UNNAMED',
+            '--add-opens=java.base/java.nio=ALL-UNNAMED',
+            '--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED',
+            '--add-opens=java.base/java.net=ALL-UNNAMED',
+            '--add-opens=java.base/java.util=ALL-UNNAMED',
+            '--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED',
+            '--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED',
+            '--add-opens=java.base/sun.nio.ch=ALL-UNNAMED',
+            '--add-opens=java.base/sun.nio.fs=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED',
+            '--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED',
+    ])
+}

buildSrc/src/main/groovy/io.nextflow.groovy-common-conventions.gradle

@@ -0,0 +1,11 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Apply the common convention plugin for shared build configuration between library and application projects.
+    id 'io.nextflow.groovy-common-conventions'
+    // Apply the java-library plugin for API and implementation separation.
+    id 'java-library'
+}
+

buildSrc/src/main/groovy/io.nextflow.groovy-library-conventions.gradle

@@ -1,5 +1,15 @@
 NF-SQLDB CHANGE-LOG
 ===================
+0.6.0 - 5 Nov 2024
+- Update build scripts
+- Remove nf-bigquery plugin
+- Bump Nextflow to version 24.04.0
+- Bump mysql-connector-java:8.0.33
+- Bump mariadb-java-client:2.7.0
+- Bump postgresql:42.7.4
+- Bump sqlite-jdbc:3.47.0.0
+- Bump duckdb_jdbc:0.10.2
+
 0.5.0 - 30 Aug 2022
 - Bump nextflow required version to 22.08.1-edge
 

changelog.txt

@@ -17,6 +17,6 @@
 
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradle/wrapper/gradle-wrapper.properties

@@ -17,7 +17,6 @@
 plugins {
     id "java"
     id "io.nextflow.nf-build-plugin" version "1.0.1"
-    id "idea"
 }
 
 ext.github_organization = 'nextflow-io'
@@ -37,6 +36,12 @@ String now() {
     "${java.time.OffsetDateTime.now().format(java.time.format.DateTimeFormatter.ISO_DATE_TIME)}"
 }
 
+List<String> allPlugins() {
+    def plugins = []
+    new File(rootProject.rootDir, 'plugins') .eachDir { if(it.name.startsWith('nf-')) plugins.add(it.name) }
+    return plugins
+}
+
 String metaFromManifest(String meta, File file) {
     def str = file.text
     def regex = ~/(?m)^$meta:\s*([\w-\.<>=]+)$/
@@ -91,6 +96,8 @@ subprojects {
                 "sha512sum": "${computeSha512(zip)}"
               }
             """.stripIndent()
+            // cleanup tmp dir
+            file("$buildDir/tmp/makeZip").deleteDir()
         }
         outputs.file("$buildDir/libs/${project.name}-${project.version}.zip")
     }
@@ -134,18 +141,36 @@ subprojects {
         skipExisting = true
     }
 
+    jar {
+        from sourceSets.main.allSource
+        doLast {
+            file("$buildDir/tmp/jar").deleteDir()
+        }
+    }
+
+    tasks.withType(GenerateModuleMetadata) {
+        enabled = false
+    }
+    
+    task upload(dependsOn: [uploadPlugin] ) { }
 }
 
+/*
+ * Upload all plugins to the corresponding GitHub repos
+ */
 task upload(dependsOn: [subprojects.uploadPlugin]) { }
 
+/*
+ * Copies the plugins required dependencies in the corresponding lib directory
+ */
 classes.dependsOn subprojects.copyPluginLibs
 
 /*
  * Merge and publish the plugins index file
  */
 task publishIndex( type: io.nextflow.gradle.tasks.GithubRepositoryPublisher ) {
     indexUrl = 'https://github.com/nextflow-io/plugins/main/plugins.json'
-    repos = ['nf-sqldb']
+    repos = allPlugins()
     owner = github_organization
     githubUser = github_username
     githubEmail = github_commit_email