Deprecate isDsl2Final method

As DSL2 *preview* mode is not supported any more
the semantic for 'isDsl2' and 'isDsl2Final' is identical.

This commit remove the use of the latter and mark it as
deprecated since it's not needed anymore.

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

modules/nextflow/src/main/groovy/nextflow/NF.groovy

@@ -51,6 +51,7 @@ class NF {
         NextflowMeta.instance.isDsl2()
     }
 
+    @Deprecated
     static boolean isDsl2Final() {
         NextflowMeta.instance.isDsl2Final()
     }

modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy

@@ -108,10 +108,22 @@ class NextflowMeta {
         fmt.parse(str)
     }
 
+    /**
+     * Determine if the workflow script uses DSL2 mode
+     * 
+     * {@code true} when the workflow script uses DSL2 syntax, {@code false} otherwise.
+     */
     boolean isDsl2() {
         enable.dsl == 2
     }
 
+    /**
+     * As of the removal of DSL2 preview mode, the semantic of this method
+     * is identical to {@link #isDsl2()}.
+     * @return
+     *  {@code true} when the workflow script uses DSL2 syntax, {@code false} otherwise.
+     */
+    @Deprecated
     boolean isDsl2Final() {
         enable.dsl == 2
     }

modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy

@@ -917,7 +917,7 @@ class NextflowDSLImpl implements ASTTransformation {
                     }
                 }
             }
-            else if( (varX=isVariableX(stm.expression)) && (varX.name=='stdin' || varX.name=='stdout') && NF.isDsl2Final() ) {
+            else if( (varX=isVariableX(stm.expression)) && (varX.name=='stdin' || varX.name=='stdout') && NF.isDsl2() ) {
                 final name = varX.name=='stdin' ? '_in_stdin' : '_out_stdout'
                 final call = new MethodCallExpression( new VariableExpression('this'), name, new ArgumentListExpression()  )
                 // remove replace the old one with the new one

modules/nextflow/src/main/groovy/nextflow/extension/OpCall.groovy

@@ -323,20 +323,14 @@ class OpCall implements Callable {
     protected void checkDeprecation(Method method) {
         if( method.getAnnotation(Deprecated) ) {
             def messg = "Operator `$methodName` is deprecated -- it will be removed in a future release"
-            if( NF.dsl2Final )
+            if( NF.isDsl2() )
                 throw new DeprecationException(messg)
             log.warn messg
         }
         else if( method.getAnnotation(DeprecatedDsl2) && NF.isDsl2() ) {
             def annot = method.getAnnotation(DeprecatedDsl2)
-            def messg
-            if( NF.dsl2Final ) {
-                messg = annot.message() ?: "Operator `$methodName` is deprecated".toString()
-                throw new DeprecationException(messg)
-            } else {
-                messg = annot.message() ?: "Operator `$methodName` is deprecated -- it will be removed in a future release".toString()
-            }
-            log.warn messg
+            def messg = annot.message() ?: "Operator `$methodName` has been deprecated -- it's not available in DSL2 syntax".toString()
+            throw new DeprecationException(messg)
         }
     }
 

modules/nextflow/src/main/groovy/nextflow/processor/TaskContext.groovy

@@ -315,7 +315,7 @@ class TaskContext implements Map<String,Object>, Cloneable {
             return path
 
         // make from the module dir
-        def module = NF.isDsl2Final() ? ScriptMeta.get(this.script)?.getModuleDir() : null
+        def module = NF.isDsl2() ? ScriptMeta.get(this.script)?.getModuleDir() : null
         if( module ) {
             def target = module.resolve('templates').resolve(path)
             if (Files.exists(target))

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

@@ -66,7 +66,7 @@ abstract class BaseScript extends Script implements ExecutionContext {
      */
     protected Map getConfig() {
         final msg = "The access of `config` object is deprecated"
-        if( NF.dsl2Final )
+        if( NF.dsl2 )
             throw new DeprecationException(msg)
         log.warn(msg)
         session.getConfig()
@@ -84,7 +84,7 @@ abstract class BaseScript extends Script implements ExecutionContext {
      */
     protected void echo(boolean value = true) {
         final msg = "The use of `echo` method has been deprecated"
-        if( NF.dsl2Final )
+        if( NF.dsl2 )
             throw new DeprecationException(msg)
         log.warn(msg)
         session.getConfig().process.echo = value

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

@@ -54,7 +54,7 @@ class IncludeDef {
     @Deprecated
     IncludeDef( String module ) {
         final msg = "Anonymous module inclusion is deprecated -- Replace `include '${module}'` with `include { MODULE_NAME } from '${module}'`"
-        if( NF.isDsl2Final() )
+        if( NF.isDsl2() )
             throw new DeprecationException(msg)
         log.warn msg
         this.path = module
@@ -65,7 +65,7 @@ class IncludeDef {
     IncludeDef(TokenVar token, String alias=null) {
         def component = token.name; if(alias) component += " as $alias"
         def msg = "Unwrapped module inclusion is deprecated -- Replace `include $component from './MODULE/PATH'` with `include { $component } from './MODULE/PATH'`"
-        if( NF.isDsl2Final() )
+        if( NF.isDsl2() )
             throw new DeprecationException(msg)
         log.warn msg
 

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

@@ -534,8 +534,7 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
 
     InParam _in_set( Object... obj ) {
         final msg = "Input of type `set` is deprecated -- Use `tuple` instead"
-        if( NF.dsl2Final ) throw new DeprecationException(msg)
-        if( NF.isDsl2() ) log.warn1(msg)
+        if( NF.isDsl2() ) throw new DeprecationException(msg)
         new TupleInParam(this).bind(obj)
     }
 
@@ -605,8 +604,7 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
 
     OutParam _out_set( Object... obj ) {
         final msg = "Output of type `set` is deprecated -- Use `tuple` instead"
-        if( NF.dsl2Final ) throw new DeprecationException(msg)
-        if( NF.isDsl2() ) log.warn1(msg)
+        if( NF.isDsl2() ) throw new DeprecationException(msg)
         new TupleOutParam(this) .bind(obj)
     }
 

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

@@ -187,7 +187,7 @@ class ScriptBinding extends WorkflowBinding {
     void setVariable( String name, Object value ) {
         if( name == 'channel' ) {
             final msg = 'The use of the identifier `channel` as variable name is discouraged and will be deprecated in a future version'
-            if( NF.isDsl2Final() ) throw new DeprecationException(msg)
+            if( NF.isDsl2() ) throw new DeprecationException(msg)
             log.warn(msg)
         }
         if( name != 'args' && name != 'params' )

modules/nextflow/src/main/groovy/nextflow/script/params/BaseOutParam.groovy

@@ -197,10 +197,8 @@ abstract class BaseOutParam extends BaseParam implements OutParam {
 
     BaseOutParam mode( def mode ) {
         final msg = "Process output `mode` is not supported any more"
-        if( NF.isDsl2Final() )
+        if( NF.isDsl2() )
             throw new DeprecationException(msg)
-        else if( NF.isDsl2() )
-            log.warn(msg)
         this.mode = BasicMode.parseValue(mode)
         return this
     }

modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy

@@ -58,7 +58,7 @@ class FileInParam extends BaseInParam implements PathQualifier {
 
         // the ability to pass a closure as file name has been replaced by
         // lazy gstring -- this should be deprecated
-        if( obj instanceof Closure && !NF.dsl2Final ) {
+        if( obj instanceof Closure && !NF.dsl2 ) {
             filePattern = obj
             return this
         }

modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy

@@ -95,57 +95,57 @@ class FileOutParam extends BaseOutParam implements OutParam, OptionalParam, Path
 
     @Deprecated
     FileOutParam separatorChar( String value ) {
-        if( NF.dsl2Final ) throw new DeprecationException("Option `separatorChar is not supported any more")
+        if( NF.dsl2 ) throw new DeprecationException("Option `separatorChar is not supported any more")
         this.separatorChar = value
         return this
     }
 
     @Deprecated
     FileOutParam includeInputs( boolean flag ) {
-        if( NF.dsl2Final ) throw new DeprecationException("Deprecated syntax error - replace `includeInputs $flag` with `, includeInputs: $flag` ")
+        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `includeInputs $flag` with `, includeInputs: $flag` ")
         this.includeInputs = flag
         return this
     }
 
     @Deprecated
     FileOutParam includeHidden( boolean flag ) {
-        if( NF.dsl2Final ) throw new DeprecationException("Deprecated syntax error - replace `includeHidden $flag` with `, includeHidden: $flag`")
+        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `includeHidden $flag` with `, includeHidden: $flag`")
         this.hidden = flag
         return this
     }
 
     @Deprecated
     FileOutParam hidden( boolean flag ) {
-        if( NF.dsl2Final ) throw new DeprecationException("Deprecated syntax error - replace `hidden $flag` with use `, hidden: $flag`")
+        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `hidden $flag` with use `, hidden: $flag`")
         this.hidden = flag
         return this
     }
 
     @Deprecated
     FileOutParam type( String value ) {
-        if( NF.dsl2Final ) throw new DeprecationException("Deprecated syntax error - replace `type $value` with `, type: $value`")
+        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `type $value` with `, type: $value`")
         assert value in ['file','dir','any']
         type = value
         return this
     }
 
     @Deprecated
     FileOutParam maxDepth( int value ) {
-        if( NF.dsl2Final ) throw new DeprecationException("Deprecated syntax error - replace `maxDepth $value` with `, maxDepth: $value`")
+        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `maxDepth $value` with `, maxDepth: $value`")
         maxDepth = value
         return this
     }
 
     @Deprecated
     FileOutParam followLinks( boolean value ) {
-        if( NF.dsl2Final ) throw new DeprecationException("Deprecated syntax error - replace `followLinks $value` with `, followLinks: $value`")
+        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `followLinks $value` with `, followLinks: $value`")
         followLinks = value
         return this
     }
 
     @Deprecated
     FileOutParam glob( boolean value ) {
-        if( NF.dsl2Final ) throw new DeprecationException("Deprecated syntax error - replace `glob $value` with `, glob: $value` ")
+        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `glob $value` with `, glob: $value` ")
         glob = value
         return this
     }

modules/nextflow/src/main/groovy/nextflow/script/params/TupleInParam.groovy

@@ -55,7 +55,7 @@ class TupleInParam extends BaseInParam {
         for( def item : obj ) {
 
             if( item instanceof TokenVar ) {
-                if( NF.dsl2Final ) {
+                if( NF.dsl2 ) {
                     final msg = "Unqualified input value declaration has been deprecated - replace `tuple ${item.name},..` with `tuple val(${item.name}),..`"
                     throw new DeprecationException(msg)
                 }
@@ -71,7 +71,7 @@ class TupleInParam extends BaseInParam {
                         .bind( item.target )
             }
             else if( item instanceof Map ) {
-                if( NF.dsl2Final ) {
+                if( NF.dsl2 ) {
                     final msg = "Unqualified input file declaration has been deprecated - replace `tuple $item,..` with `tuple path(${item.key}, stageAs:'${item.value}'),..`"
                     throw new DeprecationException(msg)
                 }
@@ -87,15 +87,15 @@ class TupleInParam extends BaseInParam {
                 newItem(StdInParam)
             }
             else if( item instanceof GString ) {
-                if( NF.dsl2Final )
+                if( NF.dsl2 )
                     throw new DeprecationException("Unqualified input file declaration has been deprecated - replace `tuple \"$item\".. with `tuple path(\"$item\")..`")
                 newItem(FileInParam).bind(item)
             }
             else if( item == '-' ) {
                 newItem(StdInParam)
             }
             else if( item instanceof String ) {
-                if( NF.dsl2Final )
+                if( NF.dsl2 )
                     throw new DeprecationException("Unqualified input file declaration has been deprecated - replace `tuple '$item',..` with `tuple path('$item'),..`")
                 newItem(FileInParam).bind(item)
             }

modules/nextflow/src/main/groovy/nextflow/script/params/TupleOutParam.groovy

@@ -52,7 +52,7 @@ class TupleOutParam extends BaseOutParam implements OptionalParam {
 
         for( def item : obj ) {
             if( item instanceof TokenVar ) {
-                if( NF.dsl2Final )
+                if( NF.dsl2 )
                     throw new DeprecationException("Unqualified output value declaration has been deprecated - replace `tuple ${item.name},..` with `tuple val(${item.name}),..`")
                 create(ValueOutParam).bind(item)
             }
@@ -63,15 +63,15 @@ class TupleOutParam extends BaseOutParam implements OptionalParam {
                 create(EnvOutParam).bind(item.val)
             }
             else if( item instanceof GString ) {
-                if( NF.dsl2Final )
+                if( NF.dsl2 )
                     throw new DeprecationException("Unqualified output path declaration has been deprecated - replace `tuple \"$item\",..` with `tuple path(\"$item\"),..`")
                 create(FileOutParam).bind(item)
             }
             else if( item instanceof TokenStdoutCall || item == '-'  ) {
                 create(StdOutParam).bind('-')
             }
             else if( item instanceof String ) {
-                if( NF.dsl2Final )
+                if( NF.dsl2 )
                     throw new DeprecationException("Unqualified output path declaration has been deprecated - replace `tuple '$item',..` with `tuple path('$item'),..`")
                 create(FileOutParam).bind(item)
             }