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Fix runtime type reflection in nf-lang #7077

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Merged
bentsherman merged 1 commit into from
Apr 27, 2026
Merged

Fix runtime type reflection in nf-lang #7077

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21 changes: 11 additions & 10 deletions modules/nextflow/src/main/groovy/nextflow/plugin/spec/ConfigSpec.groovy
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Expand Up @@ -15,10 +15,12 @@
*/
package nextflow.plugin.spec

import java.lang.reflect.ParameterizedType
import java.lang.reflect.Type

import groovy.transform.CompileStatic
import nextflow.config.spec.SpecNode
import nextflow.script.types.Types
import org.codehaus.groovy.ast.ClassNode
import nextflow.script.dsl.Types

/**
* Generate specs for config scopes.
Expand All @@ -44,7 +46,7 @@ class ConfigSpec {

private static Map<String,?> fromOption(SpecNode.Option node, String name) {
final description = node.description().stripIndent(true).trim()
final types = node.types().collect { t -> fromType(new ClassNode(t)) }
final types = node.types().collect { t -> fromType(t) }

return [
type: 'ConfigOption',
Expand Down Expand Up @@ -89,14 +91,13 @@ class ConfigSpec {
]
}

private static Object fromType(ClassNode cn) {
final name = Types.getName(cn.getTypeClass())
if( !cn.isGenericsPlaceHolder() && cn.getGenericsTypes() != null ) {
final typeArguments = cn.getGenericsTypes().collect { gt -> fromType(gt.getType()) }
private static Object fromType(Type type) {
if( type instanceof ParameterizedType ) {
final name = Types.getName(type.getRawType())
final typeArguments = type.getActualTypeArguments().collect { t -> fromType(t) }
return [ name: name, typeArguments: typeArguments ]
}
else {
return name
}

return Types.getName(type)
}
}
24 changes: 10 additions & 14 deletions modules/nextflow/src/main/groovy/nextflow/plugin/spec/FunctionSpec.groovy
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Expand Up @@ -16,11 +16,12 @@
package nextflow.plugin.spec

import java.lang.reflect.Method
import java.lang.reflect.ParameterizedType
import java.lang.reflect.Type

import groovy.transform.CompileStatic
import nextflow.script.dsl.Description
import nextflow.script.types.Types
import org.codehaus.groovy.ast.ClassNode
import nextflow.script.dsl.Types

/**
* Generate specs for functions, channel factories, and operators.
Expand All @@ -37,7 +38,7 @@ class FunctionSpec {
final parameters = method.getParameters().collect { param ->
[
name: param.getName(),
type: fromType(param.getType())
type: fromType(param.getParameterizedType())
]
}

Expand All @@ -52,18 +53,13 @@ class FunctionSpec {
]
}

private static Object fromType(Class c) {
return fromType(new ClassNode(c))
}

private static Object fromType(ClassNode cn) {
final name = Types.getName(cn.getTypeClass())
if( !cn.isGenericsPlaceHolder() && cn.getGenericsTypes() != null ) {
final typeArguments = cn.getGenericsTypes().collect { gt -> fromType(gt.getType()) }
private static Object fromType(Type type) {
if( type instanceof ParameterizedType ) {
final name = Types.getName(type.getRawType())
final typeArguments = type.getActualTypeArguments().collect { t -> fromType(t) }
return [ name: name, typeArguments: typeArguments ]
}
else {
return name
}

return Types.getName(type)
}
}
2 changes: 1 addition & 1 deletion modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
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Expand Up @@ -75,6 +75,7 @@ import nextflow.script.ProcessConfigV2
import nextflow.script.ScriptMeta
import nextflow.script.ScriptType
import nextflow.script.bundle.ResourcesBundle
import nextflow.script.dsl.Types
import nextflow.script.params.BaseOutParam
import nextflow.script.params.CmdEvalParam
import nextflow.script.params.DefaultOutParam
Expand All @@ -97,7 +98,6 @@ import nextflow.script.params.v2.ProcessInput
import nextflow.script.params.v2.ProcessTupleInput
import nextflow.script.types.Record
import nextflow.script.types.Tuple
import nextflow.script.types.Types
import nextflow.trace.TraceRecord
import nextflow.util.Escape
import nextflow.util.HashBuilder
Expand Down
2 changes: 1 addition & 1 deletion modules/nextflow/src/main/groovy/nextflow/script/ParamsDsl.groovy
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Expand Up @@ -26,8 +26,8 @@ import groovy.util.logging.Slf4j
import nextflow.Session
import nextflow.file.FileHelper
import nextflow.exception.ScriptRuntimeException
import nextflow.script.dsl.Types
import nextflow.script.types.Bag
import nextflow.script.types.Types
import nextflow.splitter.CsvSplitter
import nextflow.util.ArrayBag
import nextflow.util.Duration
Expand Down
2 changes: 2 additions & 0 deletions modules/nextflow/src/main/groovy/nextflow/script/TypeDef.groovy
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Expand Up @@ -39,6 +39,8 @@ class TypeDef extends ComponentDef {
this.alias = alias
}

Class getTarget() { target }

@Override
String getType() { 'type' }

Expand Down
102 changes: 58 additions & 44 deletions modules/nextflow/src/test/groovy/nextflow/plugin/spec/PluginSpecTest.groovy
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Expand Up @@ -47,57 +47,65 @@ class PluginSpecTest extends Specification {
expect:
definitions.size() == 4
and:
definitions[0] == [
type: 'ConfigScope',
spec: [
name: 'hello',
description: 'The `hello` scope controls the behavior of the `nf-hello` plugin.',
children: [
[
type: 'ConfigOption',
spec: [
name: 'message',
description: 'Message to print to standard output when the plugin is enabled.',
type: 'String',
additionalTypes: []
]
]
definitions[0].type == 'ConfigScope'
definitions[0].spec.name == 'hello'
definitions[0].spec.description == 'The `hello` scope controls the behavior of the `nf-hello` plugin.'
definitions[0].spec.children.sort { it.spec.name } == [
[
type: 'ConfigOption',
spec: [
name: 'message',
description: 'Message to print to standard output when the plugin is enabled.',
type: 'String',
additionalTypes: []
]
],
[
type: 'ConfigOption',
spec: [
name: 'names',
description: 'Names to address when the plugin is enabled.',
type: [
name: 'List',
typeArguments: [ 'String' ]
],
additionalTypes: []
]
]
]
definitions[1] == [
type: 'Factory',
spec: [
name: 'helloFactory',
description: null,
returnType: 'DataflowWriteChannel',
parameters: []
]
and:
definitions[1].type == 'Factory'
definitions[1].spec == [
name: 'helloFactory',
description: null,
returnType: 'DataflowWriteChannel',
parameters: []
]
definitions[2] == [
type: 'Operator',
spec: [
name: 'helloOperator',
description: null,
returnType: 'DataflowWriteChannel',
parameters: [
[
name: 'arg0',
type: 'DataflowReadChannel'
]
and:
definitions[2].type == 'Operator'
definitions[2].spec == [
name: 'helloOperator',
description: null,
returnType: 'DataflowWriteChannel',
parameters: [
[
name: 'arg0',
type: 'DataflowReadChannel'
]
]
]
definitions[3] == [
type: 'Function',
spec: [
name: 'sayHello',
description: 'Say hello to the given targets',
returnType: 'void',
parameters: [
[
name: 'arg0',
type: 'List'
and:
definitions[3].type == 'Function'
definitions[3].spec == [
name: 'sayHello',
description: 'Say hello to the given targets',
returnType: 'void',
parameters: [
[
name: 'arg0',
type: [
name: 'List',
typeArguments: [ 'String' ]
]
]
]
Expand All @@ -115,6 +123,12 @@ class TestConfig implements ConfigScope {
Message to print to standard output when the plugin is enabled.
''')
String message

@ConfigOption
@Description('''
Names to address when the plugin is enabled.
''')
List<String> names
}


Expand Down
47 changes: 47 additions & 0 deletions modules/nextflow/src/test/groovy/nextflow/script/ScriptTypesTest.groovy
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Expand Up @@ -16,7 +16,9 @@

package nextflow.script

import java.lang.reflect.ParameterizedType
import java.nio.file.Files
import java.nio.file.Path

import nextflow.exception.ScriptCompilationException
import test.Dsl2Spec
Expand Down Expand Up @@ -195,4 +197,49 @@ class ScriptTypesTest extends Dsl2Spec {
cleanup:
folder?.deleteDir()
}

def 'should expose type annotations via reflection'() {
when:
def script = loadScript(
'''\
record Sample {
id: String
reads: List<Path>
}
''',
module: true
)
def meta = ScriptMeta.get(script)
def typeDef = meta.getComponent('Sample') as TypeDef
def type = typeDef.getTarget()
then:
type.getField('id').getType() == String
type.getField('id').getGenericType() instanceof Class
type.getField('id').getGenericType() == String
type.getField('reads').getType() == List
type.getField('reads').getGenericType() instanceof ParameterizedType
type.getField('reads').getGenericType().getRawType() == List
type.getField('reads').getGenericType().getActualTypeArguments()[0] instanceof Class
type.getField('reads').getGenericType().getActualTypeArguments()[0] == Path

when:
script = loadScript(
'''\
def greet(message: String, names: List<String>) {
}
''',
module: true
)
def method = script.getClass().getDeclaredMethods().find { m -> m.name == 'greet' }
def params = method.getParameters()
then:
params[0].getType() == String
params[0].getParameterizedType() instanceof Class
params[0].getParameterizedType() == String
params[1].getType() == List
params[1].getParameterizedType() instanceof ParameterizedType
params[1].getParameterizedType().getRawType() == List
params[1].getParameterizedType().getActualTypeArguments()[0] instanceof Class
params[1].getParameterizedType().getActualTypeArguments()[0] == String
}
}
2 changes: 1 addition & 1 deletion modules/nf-lang/src/main/java/nextflow/config/control/ConfigParser.java
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Expand Up @@ -21,7 +21,7 @@
import nextflow.config.parser.ConfigParserPluginFactory;
import nextflow.script.control.Compiler;
import nextflow.script.control.LazyErrorCollector;
import nextflow.script.types.Types;
import nextflow.script.dsl.Types;
import org.codehaus.groovy.control.CompilerConfiguration;
import org.codehaus.groovy.control.SourceUnit;
import org.codehaus.groovy.control.messages.WarningMessage;
Expand Down
33 changes: 21 additions & 12 deletions modules/nf-lang/src/main/java/nextflow/config/spec/SpecNode.java
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Expand Up @@ -19,6 +19,7 @@
import java.lang.reflect.Field;
import java.lang.reflect.Method;
import java.lang.reflect.ParameterizedType;
import java.lang.reflect.Type;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
Expand Down Expand Up @@ -109,10 +110,10 @@ private static String annotatedDescription(AnnotatedElement el, String defaultVa
return annot != null ? annot.value() : defaultValue;
}

private static List<Class> optionTypes(Field field) {
var result = new ArrayList<Class>();
private static List<Type> optionTypes(Field field) {
var result = new ArrayList<Type>();
// use the field type
result.add(field.getType());
result.add(field.getGenericType());
// append types from ConfigOption annotation if specified
var annot = field.getAnnotation(ConfigOption.class);
if( annot != null ) {
Expand All @@ -122,6 +123,14 @@ private static List<Class> optionTypes(Field field) {
return result;
}

private static Class rawType(Type type) {
if( type instanceof Class c )
return c;
if( type instanceof ParameterizedType pt )
return (Class) pt.getRawType();
throw new IllegalStateException();
}

/**
* Models a config option that is defined through a DSL
* instead of an assignment (i.e. `plugins`).
Expand All @@ -136,7 +145,7 @@ public static record DslOption(
*/
public static record Option(
String description,
List<Class> types
List<Type> types
) implements SpecNode {}

/**
Expand Down Expand Up @@ -212,23 +221,23 @@ public static Scope of(Class<? extends ConfigScope> scope, String description) {
var children = new HashMap<String, SpecNode>();
for( var field : scope.getDeclaredFields() ) {
var name = field.getName();
var type = field.getType();
var type = field.getGenericType();
var rawType = rawType(type);
var desc = annotatedDescription(field, description);
var placeholderName = field.getAnnotation(PlaceholderName.class);
// fields annotated with @ConfigOption are config options
if( field.getAnnotation(ConfigOption.class) != null ) {
if( DslScope.class.isAssignableFrom(type) )
children.put(name, new DslOption(desc, type));
if( DslScope.class.isAssignableFrom(rawType) )
children.put(name, new DslOption(desc, rawType));
else
children.put(name, new Option(desc, optionTypes(field)));
}
// fields of type ConfigScope are nested config scopes
else if( ConfigScope.class.isAssignableFrom(type) ) {
children.put(name, Scope.of((Class<? extends ConfigScope>) type, desc));
// fields of rawType ConfigScope are nested config scopes
else if( ConfigScope.class.isAssignableFrom(rawType) ) {
children.put(name, Scope.of((Class<? extends ConfigScope>) rawType, desc));
}
// fields of type Map<String, ConfigScope> are placeholder scopes
else if( Map.class.isAssignableFrom(type) && placeholderName != null ) {
var pt = (ParameterizedType)field.getGenericType();
else if( Map.class.isAssignableFrom(rawType) && type instanceof ParameterizedType pt && placeholderName != null ) {
var valueType = (Class<? extends ConfigScope>)pt.getActualTypeArguments()[1];
children.put(name, new Placeholder(desc, placeholderName.value(), Scope.of(valueType, desc)));
}
Expand Down
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