Fix optional param in params block (#6657)

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/script/ParamsDsl.groovy

@@ -36,12 +36,8 @@ class ParamsDsl {
 
     private Map<String,Param> declarations = [:]
 
-    void declare(String name, Class type) {
-        declarations[name] = new Param(name, type, Optional.empty())
-    }
-
-    void declare(String name, Class type, Object defaultValue) {
-        declarations[name] = new Param(name, type, Optional.of(defaultValue))
+    void declare(String name, Class type, boolean optional, Object defaultValue = null) {
+        declarations[name] = new Param(name, type, optional, defaultValue)
     }
 
     void apply(Session session) {
@@ -56,17 +52,24 @@ class ParamsDsl {
         final params = new HashMap<String,?>()
         for( final name : declarations.keySet() ) {
             final decl = declarations[name]
-            if( cliParams.containsKey(name) )
+            if( cliParams.containsKey(name) ) {
                 params[name] = resolveFromCli(decl, cliParams[name])
-            else if( configParams.containsKey(name) )
+            }
+            else if( configParams.containsKey(name) ) {
                 params[name] = resolveFromCode(decl, configParams[name])
-            else if( decl.defaultValue.isPresent() )
-                params[name] = resolveFromCode(decl, decl.defaultValue.get())
-            else
+            }
+            else if( decl.defaultValue != null ) {
+                params[name] = resolveFromCode(decl, decl.defaultValue)
+            }
+            else if( decl.optional ) {
+                params[name] = null
+            }
+            else {
                 throw new ScriptRuntimeException("Parameter `$name` is required but was not specified on the command line, params file, or config")
+            }
 
-            final actualType = params[name].getClass()
-            if( !isAssignableFrom(decl.type, actualType) )
+            final actualType = params[name]?.getClass()
+            if( actualType != null && !isAssignableFrom(decl.type, actualType) )
                 throw new ScriptRuntimeException("Parameter `$name` with type ${Types.getName(decl.type)} cannot be assigned to ${params[name]} [${Types.getName(actualType)}]")
         }
 
@@ -130,7 +133,8 @@ class ParamsDsl {
     private static class Param {
         String name
         Class type
-        Optional<?> defaultValue
+        boolean optional
+        Object defaultValue
     }
 
 }

modules/nextflow/src/test/groovy/nextflow/script/ParamsDslTest.groovy

@@ -22,14 +22,27 @@ class ParamsDslTest extends Specification {
 
         when:
         def dsl = new ParamsDsl()
-        dsl.declare('input', Path)
-        dsl.declare('chunk_size', Integer, 1)
-        dsl.declare('save_intermeds', Boolean, false)
+        dsl.declare('input', Path, false)
+        dsl.declare('chunk_size', Integer, false, 1)
+        dsl.declare('save_intermeds', Boolean, false, false)
         dsl.apply(session)
         then:
         session.binding.getParams() == [input: FileHelper.asPath('./data'), chunk_size: 3, save_intermeds: false, outdir: 'results']
     }
 
+    def 'should allow optional param'() {
+        given:
+        def session = new Session()
+        session.init(null)
+
+        when:
+        def dsl = new ParamsDsl()
+        dsl.declare('input', Path, true)
+        dsl.apply(session)
+        then:
+        noExceptionThrown()
+    }
+
     def 'should report error for missing required param'() {
         given:
         def cliParams = [:]
@@ -39,8 +52,8 @@ class ParamsDslTest extends Specification {
 
         when:
         def dsl = new ParamsDsl()
-        dsl.declare('input', Path)
-        dsl.declare('save_intermeds', Boolean, false)
+        dsl.declare('input', Path, false)
+        dsl.declare('save_intermeds', Boolean, false, false)
         dsl.apply(session)
         then:
         def e = thrown(ScriptRuntimeException)
@@ -56,8 +69,8 @@ class ParamsDslTest extends Specification {
 
         when:
         def dsl = new ParamsDsl()
-        dsl.declare('input', Path)
-        dsl.declare('save_intermeds', Boolean, false)
+        dsl.declare('input', Path, false)
+        dsl.declare('save_intermeds', Boolean, false, false)
         dsl.apply(session)
         then:
         def e = thrown(ScriptRuntimeException)
@@ -73,8 +86,8 @@ class ParamsDslTest extends Specification {
 
         when:
         def dsl = new ParamsDsl()
-        dsl.declare('input', Path)
-        dsl.declare('save_intermeds', Boolean, false)
+        dsl.declare('input', Path, false)
+        dsl.declare('save_intermeds', Boolean, false, false)
         dsl.apply(session)
         then:
         def e = thrown(ScriptRuntimeException)
@@ -89,7 +102,7 @@ class ParamsDslTest extends Specification {
 
         when:
         def dsl = new ParamsDsl()
-        dsl.declare('factor', Float, DEF_VALUE)
+        dsl.declare('factor', Float, false, DEF_VALUE)
         dsl.apply(session)
         then:
         noExceptionThrown()
@@ -106,7 +119,7 @@ class ParamsDslTest extends Specification {
 
         when:
         def dsl = new ParamsDsl()
-        dsl.declare('factor', Integer, DEF_VALUE)
+        dsl.declare('factor', Integer, false, DEF_VALUE)
         dsl.apply(session)
         then:
         noExceptionThrown()

modules/nf-lang/src/main/java/nextflow/script/control/ScriptToGroovyVisitor.java

@@ -20,6 +20,7 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import nextflow.script.ast.ASTNodeMarker;
 import nextflow.script.ast.AssignmentExpression;
 import nextflow.script.ast.FeatureFlagNode;
 import nextflow.script.ast.FunctionNode;
@@ -122,9 +123,10 @@ public void visitParams(ParamBlockNode node) {
             .map((param) -> {
                 var name = constX(param.getName());
                 var type = classX(param.getType());
+                var optional = constX(type.getNodeMetaData(ASTNodeMarker.NULLABLE) != null);
                 var arguments = param.hasInitialExpression()
-                    ? args(name, type, param.getInitialExpression())
-                    : args(name, type);
+                    ? args(name, type, optional, param.getInitialExpression())
+                    : args(name, type, optional);
                 return stmt(callThisX("declare", arguments));
             })
             .toList();