Fix unqualified usage of stdin and stdout declarations

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

@@ -22,6 +22,7 @@ import static org.codehaus.groovy.ast.tools.GeneralUtils.*
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import nextflow.NF
 import nextflow.script.BaseScript
 import nextflow.script.BodyDef
 import nextflow.script.IncludeDef
@@ -821,6 +822,7 @@ class NextflowDSLImpl implements ASTTransformation {
             // transform the following syntax:
             //      `stdin from x`  --> stdin() from (x)
             //      `stdout into x` --> `stdout() into (x)`
+            VariableExpression varX
             if( stm.expression instanceof PropertyExpression ) {
                 def expr = (PropertyExpression)stm.expression
                 def obj = expr.objectExpression
@@ -862,6 +864,12 @@ class NextflowDSLImpl implements ASTTransformation {
                     }
                 }
             }
+            else if( (varX=isVariableX(stm.expression)) && (varX.name=='stdin' || varX.name=='stdout') && NF.isDsl2Final() ) {
+                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
+                stm.setExpression(call)
+            }
         }
 
         /*

modules/nextflow/src/test/groovy/nextflow/script/params/ParamsDsl2Test.groovy

@@ -0,0 +1,200 @@
+package nextflow.script.params
+
+import nextflow.Session
+import nextflow.ast.NextflowDSL
+import nextflow.script.BaseScript
+import nextflow.script.ScriptBinding
+import nextflow.script.ScriptMeta
+import org.codehaus.groovy.control.CompilerConfiguration
+import org.codehaus.groovy.control.customizers.ASTTransformationCustomizer
+import spock.lang.Timeout
+import test.Dsl2Spec
+import test.MockScriptRunner
+/**
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@Timeout(5)
+class ParamsDsl2Test extends Dsl2Spec {
+
+    def 'should not allow unqualified input file' () {
+        given:
+        def SCRIPT = '''
+         
+        process foo {
+          input: 
+          tuple 'x'
+          /touch x/
+        }
+       
+        workflow {
+            foo()
+        }
+        '''
+
+        when:
+        new MockScriptRunner() .setScript(SCRIPT).execute()
+        then:
+        def e = thrown(DeprecationException)
+        e.message == "Unqualified input file declaration has been deprecated - replace `tuple 'x',..` with `tuple path('x'),..`"
+    }
+
+    def 'should not allow unqualified input val' () {
+        given:
+        def SCRIPT = '''
+         
+        process foo {
+          input: 
+          tuple X
+          /echo $X/
+        }
+       
+        workflow {
+            foo()
+        }
+        '''
+
+        when:
+        new MockScriptRunner() .setScript(SCRIPT).execute()
+        then:
+        def e = thrown(DeprecationException)
+        e.message == "Unqualified input value declaration has been deprecated - replace `tuple X,..` with `tuple val(X),..`"
+    }
+
+
+    def 'should not allow unqualified output file' () {
+        given:
+        def SCRIPT = '''
+         
+        process foo {
+          output: 
+          tuple 'x'
+          /touch x/
+        }
+       
+        workflow {
+            foo()
+        }
+        '''
+
+        when:
+        new MockScriptRunner() .setScript(SCRIPT).execute()
+        then:
+        def e = thrown(DeprecationException)
+        e.message == "Unqualified output path declaration has been deprecated - replace `tuple 'x',..` with `tuple path('x'),..`"
+    }
+
+    def 'should not allow unqualified output value' () {
+        given:
+        def SCRIPT = '''
+         
+        process foo {
+          output: 
+          tuple X
+          /echo hello/
+        }
+       
+        workflow {
+            foo()
+        }
+        '''
+
+        when:
+        new MockScriptRunner() .setScript(SCRIPT).execute()
+        then:
+        def e = thrown(DeprecationException)
+        e.message == "Unqualified output value declaration has been deprecated - replace `tuple X,..` with `tuple val(X),..`"
+    }
+
+
+    def 'should allow unqualified stdin and stdout' () {
+
+        given:
+        new Session()
+        and:
+        def config = new CompilerConfiguration()
+        config.setScriptBaseClass(BaseScript.class.name)
+        config.addCompilationCustomizers( new ASTTransformationCustomizer(NextflowDSL))
+
+        def SCRIPT = '''
+                    
+         process alpha {
+              input:
+              stdin
+              output:
+              stdout 
+
+              /echo foo/
+          }
+
+         workflow { true } 
+        '''
+
+        when:
+        def binding = new ScriptBinding().setSession(Mock(Session))
+        def script = (BaseScript)new GroovyShell(binding,config).parse(SCRIPT); script.run()
+        and:
+        def process = ScriptMeta.get(script).getProcess('alpha'); process.initialize()
+
+        then:
+        def inputs = process.processConfig.getInputs()
+        def outputs = process.processConfig.getOutputs()
+        and:
+        inputs.size() == 1
+        inputs[0] instanceof StdInParam
+        and:
+        outputs.size() == 1
+        outputs[0] instanceof StdOutParam
+
+    }
+
+    def 'should allow unqualified tuple stdin and stdout' () {
+
+        given:
+        new Session()
+        and:
+        def config = new CompilerConfiguration()
+        config.setScriptBaseClass(BaseScript.class.name)
+        config.addCompilationCustomizers( new ASTTransformationCustomizer(NextflowDSL))
+
+        def SCRIPT = '''
+                    
+         process beta {
+              input:
+              tuple stdin, val(x)
+              output:
+              tuple stdout, path('z')
+
+              /echo foo/
+          }
+       
+         workflow { true } 
+        '''
+
+        when:
+        def binding = new ScriptBinding().setSession(Mock(Session))
+        def script = (BaseScript)new GroovyShell(binding,config).parse(SCRIPT); script.run()
+        and:
+        def process = ScriptMeta.get(script).getProcess('beta'); process.initialize()
+
+        then:
+        def inputs = process.processConfig.getInputs()
+        def outputs = process.processConfig.getOutputs()
+        and:
+        inputs.size() == 1
+        and:
+        def in_tuple = (TupleInParam) inputs.get(0)
+        and:
+        in_tuple.inner.size() == 2
+        in_tuple.inner[0] instanceof StdInParam
+        in_tuple.inner[1] instanceof ValueInParam
+
+        and:
+        def out_tuple = (TupleOutParam) outputs.get(0)
+        and:
+        out_tuple.inner.size() == 2
+        out_tuple.inner[0] instanceof StdOutParam
+        out_tuple.inner[1] instanceof FileOutParam
+
+    }
+}