Bump Groovy 4 (nextflow-io#4443) [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Signed-off-by: Jorge Aguilera <jorge.aguilera@seqera.io> Signed-off-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Jorge Aguilera <jorge.aguilera@seqera.io> Co-authored-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com> Signed-off-by: Niklas Schandry <niklas@bio.lmu.de>
nschan · Apr 3, 2024 · 813ea35 · 813ea35
1 parent 751408a
commit 813ea35
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Showing 37 changed files with 185 additions and 100 deletions.
diff --git a/build.gradle b/build.gradle
@@ -32,7 +32,7 @@ if (groovyVer) {
 
         configurations.all {
             resolutionStrategy.eachDependency { DependencyResolveDetails details ->
-                if (details.requested.group == 'org.codehaus.groovy') {
+                if (details.requested.group == 'org.apache.groovy') {
                     if( groovyVer.contains(':') )
                         details.useTarget(groovyVer)
                     else
@@ -95,8 +95,8 @@ allprojects {
 
     configurations {
         // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
-        all*.exclude group: 'org.codehaus.groovy', module: 'groovy-all'
-        all*.exclude group: 'org.codehaus.groovy', module: 'groovy-cli-picocli'
+        all*.exclude group: 'org.apache.groovy', module: 'groovy-all'
+        all*.exclude group: 'org.apache.groovy', module: 'groovy-cli-picocli'
         // groovydoc libs
         groovyDoc.extendsFrom runtime
     }
@@ -109,8 +109,8 @@ allprojects {
 
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:1.11'
-        groovyDoc "org.codehaus.groovy:groovy-groovydoc:3.0.19"
-        groovyDoc "org.codehaus.groovy:groovy-ant:3.0.19"
+        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.18"
+        groovyDoc "org.apache.groovy:groovy-ant:4.0.18"
     }
 
     test {

diff --git a/gradle.properties b/gradle.properties
@@ -1 +1,2 @@
 org.gradle.caching=true
+org.gradle.jvmargs=-Xmx4g
diff --git a/modules/nextflow/build.gradle b/modules/nextflow/build.gradle
@@ -17,12 +17,12 @@ compileGroovy {
 dependencies {
     api(project(':nf-commons'))
     api(project(':nf-httpfs'))
-    api "org.codehaus.groovy:groovy:3.0.19"
-    api "org.codehaus.groovy:groovy-nio:3.0.19"
-    api "org.codehaus.groovy:groovy-xml:3.0.19"
-    api "org.codehaus.groovy:groovy-json:3.0.19"
-    api "org.codehaus.groovy:groovy-templates:3.0.19"
-    api "org.codehaus.groovy:groovy-yaml:3.0.19"
+    api "org.apache.groovy:groovy:4.0.18"
+    api "org.apache.groovy:groovy-nio:4.0.18"
+    api "org.apache.groovy:groovy-xml:4.0.18"
+    api "org.apache.groovy:groovy-json:4.0.18"
+    api "org.apache.groovy:groovy-templates:4.0.18"
+    api "org.apache.groovy:groovy-yaml:4.0.18"
     api "org.slf4j:jcl-over-slf4j:2.0.7"
     api "org.slf4j:jul-to-slf4j:2.0.7"
     api "org.slf4j:log4j-over-slf4j:2.0.7"
@@ -48,19 +48,19 @@ dependencies {
     testImplementation 'org.subethamail:subethasmtp:3.1.7'
 
     // test configuration
-    testFixturesApi ("org.codehaus.groovy:groovy-test:3.0.19") { exclude group: 'org.codehaus.groovy' }
+    testFixturesApi ("org.apache.groovy:groovy-test:4.0.18") { exclude group: 'org.apache.groovy' }
     testFixturesApi ("cglib:cglib-nodep:3.3.0")
     testFixturesApi ("org.objenesis:objenesis:3.2")
-    testFixturesApi ("org.spockframework:spock-core:2.3-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
-    testFixturesApi ('org.spockframework:spock-junit4:2.3-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
+    testFixturesApi ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
+    testFixturesApi ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
     testFixturesApi 'com.google.jimfs:jimfs:1.2'
 
 }
 
 
 test {
     minHeapSize = "512m"
-    maxHeapSize = "2048m"
+    maxHeapSize = "4096m"
 }
 
 application {

diff --git a/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy b/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
@@ -60,7 +60,7 @@ class CondaCache {
 
     private String createOptions
 
-    private boolean useMamba 
+    private boolean useMamba
 
     private boolean useMicromamba 
 
@@ -98,23 +98,24 @@ class CondaCache {
     CondaCache(CondaConfig config) {
         this.config = config
 
-        if( config.createTimeout )
-            createTimeout = config.createTimeout as Duration
+        if( config.createTimeout() )
+            createTimeout = config.createTimeout()
 
-        if( config.createOptions )
-            createOptions = config.createOptions
+        if( config.createOptions() )
+            createOptions = config.createOptions()
 
-        if( config.cacheDir )
-            configCacheDir0 = (config.cacheDir as Path).toAbsolutePath()
+        if( config.cacheDir() )
+            configCacheDir0 = config.cacheDir().toAbsolutePath()
 
-        if( config.useMamba && config.useMicroMamba)
+        if( config.useMamba() && config.useMicromamba() )
             throw new IllegalArgumentException("Both conda.useMamba and conda.useMicromamba were enabled -- Please choose only one")
 
-        if( config.useMamba )
-            useMamba = config.useMamba as boolean
+        if( config.useMamba() ) {
+            useMamba = config.useMamba()
+        }
 
-        if( config.useMicromamba )
-            useMicromamba = config.useMicromamba as boolean
+        if( config.useMicromamba() )
+            useMicromamba = config.useMicromamba()
 
         if( config.getChannels() )
             channels = config.getChannels()

diff --git a/modules/nextflow/src/main/groovy/nextflow/conda/CondaConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/conda/CondaConfig.groovy
@@ -16,7 +16,10 @@
 
 package nextflow.conda
 
+import java.nio.file.Path
+
 import groovy.transform.CompileStatic
+import nextflow.util.Duration
 
 /**
  * Model Conda configuration
@@ -57,4 +60,24 @@ class CondaConfig extends LinkedHashMap {
 
         throw new IllegalArgumentException("Unexpected conda.channels value: $value")
     }
+
+    Duration createTimeout() {
+        get('createTimeout') as Duration
+    }
+
+    String createOptions() {
+        get('createOptions') as String
+    }
+
+    Path cacheDir() {
+        get('cacheDir') as Path
+    }
+
+    boolean useMamba() {
+        get('useMamba') as boolean
+    }
+
+    boolean useMicromamba() {
+        get('useMicromamba') as boolean
+    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/MoabExecutor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/MoabExecutor.groovy
@@ -16,6 +16,8 @@
 
 package nextflow.executor
 
+import groovy.xml.XmlSlurper
+
 import java.nio.file.Path
 
 import groovy.transform.CompileDynamic

diff --git a/modules/nextflow/src/main/groovy/nextflow/file/SlurperEx.groovy b/modules/nextflow/src/main/groovy/nextflow/file/SlurperEx.groovy
@@ -27,7 +27,7 @@ import org.yaml.snakeyaml.Yaml
 /**
  * Add helper methods to {@link groovy.json.JsonSlurper} class
  *
- * Check resource file: `META-INF/services/org.codehaus.groovy.runtime.ExtensionModule
+ * Check resource file: `META-INF/services/org.apache.groovy.runtime.ExtensionModule
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */

diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy
@@ -16,6 +16,8 @@
 
 package nextflow.k8s
 
+import groovy.transform.MapConstructor
+
 import java.lang.reflect.Field
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
@@ -48,6 +50,7 @@ import org.codehaus.groovy.runtime.MethodClosure
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @Slf4j
+@MapConstructor(includeFields = true)
 class K8sDriverLauncher {
 
     /**
@@ -60,12 +63,12 @@ class K8sDriverLauncher {
      */
     private String headImage
 
-    /** 
+    /**
      * Request CPUs to be used for the Nextflow driver pod
      */
     private int headCpus
 
-    /** 
+    /**
      * Request memory to be used for the Nextflow driver pod
      */
     private String headMemory
@@ -580,6 +583,26 @@ class K8sDriverLauncher {
         ProviderConfig.getScmConfigPath()
     }
 
+    String getPodImage() {
+        return podImage
+    }
+
+    int getHeadCpus() {
+        return headCpus
+    }
+
+    String getHeadMemory() {
+        return headMemory
+    }
+
+    String getRunName() {
+        return runName
+    }
+
+    CmdKubeRun getCmd() {
+        return cmd
+    }
+
     protected String getPipelineName() {
         return pipelineName
     }

diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
@@ -124,9 +124,9 @@ class K8sTaskHandler extends TaskHandler implements FusionAwareTask {
         }
 
         // get input files paths
-        final paths = DockerBuilder.inputFilesToPaths(builder.getInputFiles())
-        final binDirs = builder.binDirs
-        final workDir = builder.workDir
+        final List<Path> paths = DockerBuilder.inputFilesToPaths(builder.getInputFiles())
+        final List<Path> binDirs = builder.binDirs
+        final Path workDir = builder.workDir
         // add standard paths
         if( binDirs )
             paths.addAll(binDirs)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy
@@ -382,6 +382,10 @@ class TaskConfig extends LazyMap implements Cloneable {
         throw new IllegalArgumentException("Not a valid PublishDir collection [${dirs.getClass().getName()}] $dirs")
     }
 
+    String getClusterOptions() {
+        return get('clusterOptions')
+    }
+
     def getContainer() {
         return get('container')
     }

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskContext.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskContext.groovy
@@ -128,8 +128,7 @@ class TaskContext implements Map<String,Object>, Cloneable {
         "DelegateMap[process: $name; script: ${script?.class?.name}; holder: ${holder}]"
     }
 
-    @Override
-    Object get(Object property) {
+    private Object get0(Object property, boolean throwMissingProperty) {
         assert property
 
         if( holder.containsKey(property) ) {
@@ -140,7 +139,14 @@ class TaskContext implements Map<String,Object>, Cloneable {
             return script.getBinding().getVariable(property.toString())
         }
 
-        throw new MissingPropertyException("Unknown variable '$property' -- Make sure it is not misspelled or defined later in the script", property as String, null)
+        if( throwMissingProperty )
+            throw new MissingPropertyException("Unknown variable '$property' -- Make sure it is not misspelled or defined later in the script", property as String, null)
+        return null
+    }
+
+    @Override
+    Object get(Object property) {
+        return get0(property, false)
     }
 
     /**
@@ -162,7 +168,7 @@ class TaskContext implements Map<String,Object>, Cloneable {
 
     @Override
     def getProperty( String name ) {
-        get((String)name)
+        get0((String)name, true)
     }
 
     @Override
@@ -171,7 +177,7 @@ class TaskContext implements Map<String,Object>, Cloneable {
     }
 
     @Override
-    put(String property, Object newValue) {
+    Object put(String property, Object newValue) {
 
         if( property == 'task' && !(newValue instanceof TaskConfig ) && !overrideWarnShown.getAndSet(true) ) {
             log.warn "Process $name overrides reserved variable `task`"

diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
@@ -980,11 +980,11 @@ class AssetManager {
             return
 
         List<String> filter = []
-        if( modules instanceof List ) {
-            filter.addAll(modules as List)
+        if( modules instanceof List<String> ) {
+            filter.addAll(modules)
         }
         else if( modules instanceof String ) {
-            filter.addAll( (modules as String).tokenize(', ') )
+            filter.addAll( modules.tokenize(', ') )
         }
 
         final init = git.submoduleInit()

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy
@@ -72,8 +72,8 @@ class ScriptBinding extends WorkflowBinding {
         // create and populate args
         args = new ArrayList<>()
         if( vars.args ) {
-            if( !(vars.args instanceof List) ) throw new IllegalArgumentException("ScriptBinding 'args' must be a List value")
-            args.addAll((List)vars.args)
+            if( !(vars.args instanceof List<String>) ) throw new IllegalArgumentException("ScriptBinding 'args' must be a List value")
+            args.addAll((List<String>)vars.args)
         }
         vars.put('args', args)
 

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
@@ -16,6 +16,7 @@
 
 package nextflow.script
 
+import java.lang.reflect.Modifier
 import java.nio.file.Path
 import java.nio.file.Paths
 import java.time.OffsetDateTime
@@ -424,7 +425,7 @@ class WorkflowMetadata {
         final allProperties = this.metaClass.getProperties()
         final result = new LinkedHashMap(allProperties.size())
         for( MetaProperty property : allProperties ) {
-            if( property.name == 'class' )
+            if( property.name == 'class' || !Modifier.isPublic(property.modifiers) )
                 continue
             try {
                 result[property.name] = property.getProperty(this)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/bundle/ResourcesBundle.groovy b/modules/nextflow/src/main/groovy/nextflow/script/bundle/ResourcesBundle.groovy
@@ -205,7 +205,7 @@ class ResourcesBundle {
     final private static List<String> BIN_PATHS = ['bin','usr/bin','usr/local/bin']
 
     List<Path> getBinDirs() {
-        final result = new ArrayList(10)
+        final result = new ArrayList<Path>(10)
         for( Map.Entry<String,Path> it : content ) {
             if( it.key in BIN_PATHS && Files.isDirectory(it.value) && !result.contains(it.value) )
                 result.add(it.value)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/ValueOutParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/ValueOutParam.groovy
@@ -18,6 +18,7 @@ package nextflow.script.params
 
 import groovy.transform.InheritConstructors
 import nextflow.script.TokenVar
+import org.codehaus.groovy.runtime.InvokerHelper
 
 
 /**
@@ -57,7 +58,7 @@ class ValueOutParam extends BaseOutParam {
 
         switch( target ) {
             case TokenVar:
-                return context.get(target.name)
+                return InvokerHelper.getProperty(context,target.name)
 
             case Closure:
                 return target.cloneWith(context).call()