Upgrade nextflow version to 22.08 (#6)

Signed-off-by: Jorge Aguilera <[email protected]>

plugins/nf-hello/build.gradle

@@ -54,24 +54,31 @@ sourceSets {
     test.resources.srcDirs = ['src/testResources']
 }
 
+ext{
+    nextflowVersion = '22.08.1-edge'
+}
+
 dependencies {
     // This dependency is exported to consumers, that is to say found on their compile classpath.
-    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'
     // add here plugins depepencies
 
     // test configuration
     testImplementation "org.codehaus.groovy:groovy:3.0.8"
     testImplementation "org.codehaus.groovy:groovy-nio:3.0.8"
-    testImplementation 'io.nextflow:nextflow:22.04.0'
+    testImplementation "io.nextflow:nextflow:$nextflowVersion"
     testImplementation ("org.codehaus.groovy:groovy-test:3.0.8") { exclude group: 'org.codehaus.groovy' }
     testImplementation ("cglib:cglib-nodep:3.3.0")
     testImplementation ("org.objenesis:objenesis:3.1")
     testImplementation ("org.spockframework:spock-core:2.0-M3-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
     testImplementation ('org.spockframework:spock-junit4:2.0-M3-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"))
+
     // 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") }

plugins/nf-hello/src/main/nextflow/hello/HelloExtension.groovy

@@ -3,15 +3,14 @@ package nextflow.hello
 import groovy.util.logging.Slf4j
 import groovyx.gpars.dataflow.DataflowReadChannel
 import groovyx.gpars.dataflow.DataflowWriteChannel
-import groovyx.gpars.dataflow.expression.DataflowExpression
 import nextflow.Channel
 import nextflow.Global
 import nextflow.Session
-import nextflow.extension.ChannelExtensionPoint
 import nextflow.extension.CH
 import nextflow.NF
 import nextflow.extension.DataflowHelper
-import nextflow.plugin.Scoped
+import nextflow.plugin.extension.Function
+import nextflow.plugin.extension.PluginExtensionPoint
 
 import java.util.concurrent.CompletableFuture
 
@@ -20,8 +19,7 @@ import java.util.concurrent.CompletableFuture
  *
  */
 @Slf4j
-@Scoped('hello')
-class HelloExtension extends ChannelExtensionPoint{
+class HelloExtension extends PluginExtensionPoint{
 
     /*
      * A session hold information about current execution of the script
@@ -107,6 +105,15 @@ class HelloExtension extends ChannelExtensionPoint{
         future.exceptionally(this.&handlerException)
     }
 
+    /*
+    * Generate a random string
+    * Using @Function annotation we allow this function can be imported into our script
+     */
+    @Function
+    String randomString(int length=9){
+        new Random().with {(1..length).collect {(('a'..'z')).join()[ nextInt((('a'..'z')).join().length())]}.join()}
+    }
+
     /*
     * an util class to trace exceptions
     */

plugins/nf-hello/src/test/nextflow/hello/ChannelExtensionHelloTest.groovy

@@ -3,7 +3,6 @@ package nextflow.hello
 import groovyx.gpars.dataflow.DataflowQueue
 import nextflow.Channel
 import nextflow.Session
-import nextflow.extension.ChannelExtensionDelegate
 import spock.lang.Specification
 
 

plugins/nf-hello/src/test/nextflow/hello/HelloDslTest.groovy

@@ -1,27 +1,60 @@
 package nextflow.hello
 
 import nextflow.Channel
-import nextflow.extension.ChannelExtensionDelegate
 import nextflow.plugin.Plugins
-import spock.lang.Specification
+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.Dsl2Spec
+
+import java.nio.file.Path
 
 
 /**
  * @author : jorge <[email protected]>
  *
  */
 @Timeout(10)
-class HelloDslTest extends Specification{
+class HelloDslTest 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 setup () {
-        ChannelExtensionDelegate.reloadExtensionPoints()
+    def cleanup() {
+        Plugins.stop()
+        PluginExtensionProvider.reset()
+        pluginsMode ? System.setProperty('pf4j.mode',pluginsMode) : System.clearProperty('pf4j.mode')
     }
 
     def 'should perform a hi and create a channel' () {
         when:
         def SCRIPT = '''
-            channel.hello.reverse('hi!') 
+            include {reverse} from 'plugin/nf-hello'
+            channel.reverse('hi!') 
             '''
         and:
         def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
@@ -33,6 +66,7 @@ class HelloDslTest extends Specification{
     def 'should store a goodbye' () {
         when:
         def SCRIPT = '''
+            include {goodbye} from 'plugin/nf-hello'
             channel
                 .of('Bye bye folks')
                 .goodbye() 
@@ -46,4 +80,19 @@ class HelloDslTest extends Specification{
         and:
         HelloExtension.goodbyeMessage == 'Bye bye folks'.toUpperCase()
     }
+
+    def 'can use an imported function' () {
+        when:
+        def SCRIPT = '''
+            include {randomString} from 'plugin/nf-hello'
+            channel
+                .of( randomString(20) )                
+            '''
+        and:
+        def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
+        then:
+        result.val.size() == 20
+        result.val == Channel.STOP
+    }
+
 }