Remove deprecated workflow publish [DSL2]

Author: pditommaso

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

@@ -108,10 +108,10 @@ class NextflowDSLImpl implements ASTTransformation {
     static class DslCodeVisitor extends ClassCodeVisitorSupport {
 
         @Deprecated final static String WORKFLOW_GET = 'get'
+        @Deprecated final static String WORKFLOW_PUBLISH = 'publish'
         final static String WORKFLOW_TAKE = 'take'
         final static String WORKFLOW_EMIT = 'emit'
         final static String WORKFLOW_MAIN = 'main'
-        @Deprecated final static String WORKFLOW_PUBLISH = 'publish'
 
         final static Random RND = new Random()
 
@@ -415,10 +415,6 @@ class NextflowDSLImpl implements ASTTransformation {
                 return createAssignX(stat, body, type, uniqueNames)
             }
 
-            if( type == WORKFLOW_PUBLISH ) {
-                return createAssignX(stat, body, type, uniqueNames)
-            }
-
             syntaxError(stat, "Workflow malformed parameter definition")
             return stat
         }
@@ -509,9 +505,7 @@ class NextflowDSLImpl implements ASTTransformation {
                         syntaxError(stm, "Workflow 'get' is not supported anymore use 'take' instead")
 
                     case WORKFLOW_PUBLISH:
-                        if( !anonymous ) {
-                            syntaxError(stm, "Publish declaration is only allowed in main workflow definition")
-                        }
+                        syntaxError(stm, "Workflow 'publish' is not supported anymore use process 'publishDir' instead")
 
                     case WORKFLOW_TAKE:
                     case WORKFLOW_EMIT:

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

@@ -23,8 +23,6 @@ import groovyx.gpars.dataflow.DataflowWriteChannel
 import nextflow.exception.MissingValueException
 import nextflow.exception.ScriptRuntimeException
 import nextflow.extension.CH
-import nextflow.extension.PublishOp
-
 /**
  * Models a script workflow component
  *
@@ -42,8 +40,6 @@ class WorkflowDef extends BindableDef implements ChainableDef, ExecutionContext
 
     private List<String> declaredOutputs
 
-    private Map<String,Map> declaredPublish
-
     private Set<String> variableNames
 
     private BaseScript owner
@@ -67,7 +63,6 @@ class WorkflowDef extends BindableDef implements ChainableDef, ExecutionContext
         // now it can access the parameters
         this.declaredInputs = new ArrayList<>(resolver.getTakes().keySet())
         this.declaredOutputs = new ArrayList<>(resolver.getEmits().keySet())
-        this.declaredPublish = new LinkedHashMap<>(resolver.getPublish())
         this.variableNames = getVarNames0()
     }
 
@@ -164,29 +159,7 @@ class WorkflowDef extends BindableDef implements ChainableDef, ExecutionContext
         }
         return new ChannelOut(channels)
     }
-
-    protected publishOutputs(Map<String,Map> publishDefs) {
-        for( Map.Entry<String,Map> pub : publishDefs.entrySet() ) {
-            final name = pub.key
-            final opts = pub.value
-            if( !binding.hasVariable(name) )
-                throw new MissingValueException("Missing workflow publish parameter: $name")
-            final obj = binding.getVariable(name)
-
-            if( CH.isChannel(obj) ) {
-                new PublishOp(CH.getReadChannel(obj), opts).apply()
-            }
-
-            else if( obj instanceof ChannelOut ) {
-                for( DataflowWriteChannel ch : ((ChannelOut)obj) ) {
-                    new PublishOp(CH.getReadChannel(ch), opts).apply()
-                }
-            }
-
-            else throw new IllegalArgumentException("Illegal workflow publish parameter: $name value: $obj")
-        }
-    }
-
+    
 
     Object run(Object[] args) {
         binding = new WorkflowBinding(owner)
@@ -208,7 +181,6 @@ class WorkflowDef extends BindableDef implements ChainableDef, ExecutionContext
         closure.call()
         // collect the workflow outputs
         output = collectOutputs(declaredOutputs)
-        publishOutputs(declaredPublish)
         return output
     }
 
@@ -223,12 +195,10 @@ class WorkflowParamsResolver implements GroovyInterceptable {
 
     static final private String TAKE_PREFIX = '_take_'
     static final private String EMIT_PREFIX = '_emit_'
-    @Deprecated static final private String PUBLISH_PREFIX = '_publish_'
 
 
     Map<String,Object> takes = new LinkedHashMap<>(10)
     Map<String,Object> emits = new LinkedHashMap<>(10)
-    Map<String,Map> publish = new LinkedHashMap<>(10)
 
     @Override
     def invokeMethod(String name, Object args) {
@@ -238,14 +208,8 @@ class WorkflowParamsResolver implements GroovyInterceptable {
         else if( name.startsWith(EMIT_PREFIX) )
             emits.put(name.substring(EMIT_PREFIX.size()), args)
 
-        else if( name.startsWith(PUBLISH_PREFIX)) {
-            log.warn1 "Workflow `publish` is deprecated -- Use process directive `publishDir` instead"
-            publish.put(name.substring(PUBLISH_PREFIX.size()), argToPublishOpts(args))
-        }
-
         else
             throw new MissingMethodException(name, WorkflowDef, args)
-
     }
 
     private Map argsToMap(Object args) {

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

@@ -183,12 +183,8 @@ class WorkflowDefTest extends Dsl2Spec {
 
         when:
         def script = (TestScript)new GroovyShell(new ScriptBinding(), config).parse(SCRIPT).run()
-        def meta = ScriptMeta.get(script)
         then:
-        meta.definitions.size() == 1
-        meta.getWorkflow(null) .declaredInputs == []
-        meta.getWorkflow(null) .declaredVariables == ['baz.out', 'x', '$out0']
-        meta.getWorkflow(null) .getDeclaredPublish() == [foo: [:], bar: [to:'some/path'], '$out0': [to:'other/path']]
+        thrown(MultipleCompilationErrorsException)
     }
 
     def 'should not allow publish is sub-workflow' () {