Merge pull request #9 from nextflow-io/8-update-plugin-to-nextflow-22.08.0-edge

feature: upgrade nextflow version to 22.08

Author: pditommaso

plugins/nf-sqldb/build.gradle

@@ -54,9 +54,12 @@ sourceSets {
     test.resources.srcDirs = []
 }
 
+ext{
+    nextflowVersion = '22.08.1-edge'
+}
 
 dependencies {
-    compileOnly 'io.nextflow:nextflow:22.04.0'
+    compileOnly "io.nextflow:nextflow:$nextflowVersion"
     compileOnly 'org.slf4j:slf4j-api:1.7.10'
     compileOnly 'org.pf4j:pf4j:3.4.1'
 
@@ -69,7 +72,7 @@ dependencies {
     api 'org.duckdb:duckdb_jdbc:0.3.0'
     api files('src/dist/lib/AthenaJDBC42_2.0.25.1001.jar')
 
-    testImplementation 'io.nextflow:nextflow:22.06.0-edge'
+    testImplementation "io.nextflow:nextflow:$nextflowVersion"
     testImplementation "org.codehaus.groovy:groovy:3.0.10"
     testImplementation "org.codehaus.groovy:groovy-nio:3.0.10"
     testImplementation ("org.codehaus.groovy:groovy-test:3.0.10") { exclude group: 'org.codehaus.groovy' }
@@ -78,6 +81,9 @@ dependencies {
     testImplementation ("org.spockframework:spock-core:2.1-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
     testImplementation ('org.spockframework:spock-junit4:2.1-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
     testImplementation ('com.google.jimfs:jimfs:1.1')
+
+    testImplementation(testFixtures("io.nextflow:nextflow:$nextflowVersion"))
+    testImplementation(testFixtures("io.nextflow:nf-commons:$nextflowVersion"))
 }
 
 test {

plugins/nf-sqldb/src/main/nextflow/sql/ChannelSqlExtension.groovy

@@ -27,9 +27,8 @@ import nextflow.Channel
 import nextflow.NF
 import nextflow.Session
 import nextflow.extension.CH
-import nextflow.extension.ChannelExtensionPoint
 import nextflow.extension.DataflowHelper
-import nextflow.plugin.Scoped
+import nextflow.plugin.extension.PluginExtensionPoint
 import nextflow.sql.config.SqlConfig
 import nextflow.sql.config.SqlDataSource
 import nextflow.util.CheckHelper
@@ -40,8 +39,7 @@ import nextflow.util.CheckHelper
  */
 @Slf4j
 @CompileStatic
-@Scoped('sql')
-class ChannelSqlExtension extends ChannelExtensionPoint {
+class ChannelSqlExtension extends PluginExtensionPoint {
 
     private static final Map QUERY_PARAMS = [
             db: CharSequence,

plugins/nf-sqldb/src/main/nextflow/sql/InsertHandler.groovy

@@ -208,7 +208,7 @@ class InsertHandler implements Closeable {
         final metaData  = conn.getMetaData()
         final resultSet = metaData.getColumns(null, null, tableName, null);
 
-        final result = []
+        final result = [] as List<String>
         while (resultSet.next()){
             result.add( resultSet.getString("COLUMN_NAME") )
         }

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: 0.4.1
-Plugin-Requires: >=21.08.0-edge
+Plugin-Requires: >=22.08.1-edge

plugins/nf-sqldb/src/test/nextflow/sql/SqlDslTest.groovy

@@ -19,28 +19,54 @@ package nextflow.sql
 
 import groovy.sql.Sql
 import nextflow.Channel
-import nextflow.extension.ChannelExtensionProvider
+import nextflow.plugin.Plugins
+import nextflow.plugin.TestPluginDescriptorFinder
+import nextflow.plugin.TestPluginManager
+import nextflow.plugin.extension.PluginExtensionProvider
+import org.pf4j.PluginDescriptorFinder
+import spock.lang.Shared
 import spock.lang.Timeout
-import test.BaseSpec
+import test.Dsl2Spec
 import test.MockScriptRunner
 
+import java.nio.file.Path
+
 /**
  *
  * @author Paolo Di Tommaso <[email protected]>
  */
 @Timeout(10)
-class SqlDslTest extends BaseSpec {
-
-    def setup () {
-        new ChannelExtensionProvider()
-                .install()
-                .loadPluginExtensionMethods(new ChannelSqlExtension(), ['fromQuery':'fromQuery', sqlInsert:'sqlInsert'])
+class SqlDslTest extends Dsl2Spec {
+
+    @Shared String pluginsMode
+
+    def setup() {
+        // reset previous instances
+        PluginExtensionProvider.reset()
+        // this need to be set *before* the plugin manager class is created
+        pluginsMode = System.getProperty('pf4j.mode')
+        System.setProperty('pf4j.mode', 'dev')
+        // the plugin root should
+        def root = Path.of('.').toAbsolutePath().normalize()
+        def manager = new TestPluginManager(root){
+            @Override
+            protected PluginDescriptorFinder createPluginDescriptorFinder() {
+                return new TestPluginDescriptorFinder(){
+                    @Override
+                    protected Path getManifestPath(Path pluginPath) {
+                        return pluginPath.resolve('build/resources/main/META-INF/MANIFEST.MF')
+                    }
+                }
+            }
+        }
+        Plugins.init(root, 'dev', manager)
     }
 
     def cleanup() {
-        ChannelExtensionProvider.reset()
+        Plugins.stop()
+        PluginExtensionProvider.reset()
+        pluginsMode ? System.setProperty('pf4j.mode',pluginsMode) : System.clearProperty('pf4j.mode')
     }
-
     def 'should perform a query and create a channel' () {
         given:
         def JDBC_URL = 'jdbc:h2:mem:test_' + Random.newInstance().nextInt(1_000_000)
@@ -55,6 +81,7 @@ class SqlDslTest extends BaseSpec {
 
         when:
         def SCRIPT = '''
+            include { fromQuery; sqlInsert } from 'plugin/nf-sqldb'
             def table = 'FOO'
             def sql = "select * from $table"
             channel.fromQuery(sql, db: "test") 
@@ -80,6 +107,7 @@ class SqlDslTest extends BaseSpec {
 
         when:
         def SCRIPT = '''
+            include { fromQuery; sqlInsert } from 'plugin/nf-sqldb'
             channel
               .of(100,200,300)
               .sqlInsert(into:"FOO", columns:'id', db:"ds1")
@@ -110,6 +138,7 @@ class SqlDslTest extends BaseSpec {
 
         when:
         def SCRIPT = '''
+            include { fromQuery; sqlInsert } from 'plugin/nf-sqldb'
             channel
               .of(100,200,300,400,500)
               .sqlInsert(into:'FOO', columns:'id', db:'ds1', batchSize: 2)
@@ -145,6 +174,7 @@ class SqlDslTest extends BaseSpec {
 
         when:
         def SCRIPT = '''
+            include { fromQuery; sqlInsert } from 'plugin/nf-sqldb'
             def table = 'FOO'
             def sql = "select * from $table"
             channel.fromQuery(sql, db: "test", emitColumns:true)