Preserve error messages for user-friendliness

Signed-off-by: Ben Sherman <[email protected]>
nextflow-io · Sep 18, 2023 · 8a2db9a · 8a2db9a
1 parent 7f2fa29
commit 8a2db9a
Show file tree

Hide file tree

Showing 8 changed files with 64 additions and 18 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy b/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
@@ -203,7 +203,7 @@ class NextflowDSLImpl implements ASTTransformation {
             if( call.methodAsString=='include' && call.arguments instanceof ArgumentListExpression ) {
                 final allArgs = (ArgumentListExpression)call.arguments
                 if( allArgs.size() != 1 || allArgs[0] !instanceof ClosureExpression ) {
-                    syntaxError(call, "Invalid include statement -- the correct syntax is `include { ... } from '...'`")
+                    syntaxError(call, "Not a valid include statement -- the correct syntax is `include { ... } from '...'`")
                     return
                 }
 
@@ -230,13 +230,13 @@ class NextflowDSLImpl implements ASTTransformation {
                         }
                         // otherwise return an error
                         else {
-                            syntaxError(call, "Invalid include module name")
+                            syntaxError(call, "Not a valid include module name")
                             return
                         }
                         modulesList.addExpression(moduleX)
                     }
                     else {
-                        syntaxError(call, "Invalid include module name")
+                        syntaxError(call, "Not a valid include module name")
                         return
                     }
                 }
@@ -815,7 +815,7 @@ class NextflowDSLImpl implements ASTTransformation {
                 def nested = methodCall.objectExpression instanceof MethodCallExpression
                 log.trace "convert > input method: $methodName"
 
-                if( methodName in ['val','env','file','each','stdin','path','tuple'] ) {
+                if( methodName in ['val','env','file','each','set','stdin','path','tuple'] ) {
                     //this methods require a special prefix
                     if( !nested )
                         methodCall.setMethod( new ConstantExpression('_in_' + methodName) )
@@ -895,7 +895,7 @@ class NextflowDSLImpl implements ASTTransformation {
             def nested = methodCall.objectExpression instanceof MethodCallExpression
             log.trace "convert > output method: $methodName"
 
-            if( methodName in ['val','env','file','stdout','path','tuple'] && !nested ) {
+            if( methodName in ['val','env','file','set','stdout','path','tuple'] && !nested ) {
                 // prefix the method name with the string '_out_'
                 methodCall.setMethod( new ConstantExpression('_out_' + methodName) )
                 fixMethodCall(methodCall)
@@ -929,7 +929,7 @@ class NextflowDSLImpl implements ASTTransformation {
         protected void fixMethodCall( MethodCallExpression methodCall ) {
             final name = methodCall.methodAsString
 
-            withinTupleMethod = name == '_in_tuple' || name == '_out_tuple'
+            withinTupleMethod = name == '_in_set' || name == '_out_set' || name == '_in_tuple' || name == '_out_tuple'
             withinEachMethod = name == '_in_each'
 
             try {

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy b/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
@@ -91,7 +91,6 @@ abstract class BaseScript extends Script implements ExecutionContext {
     }
 
     protected process( String name, Closure<BodyDef> body ) {
-        log.info "BaseScript.process ${name}"
         def process = new ProcessDef(this,body,name)
         meta.addDefinition(process)
     }

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy b/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy
@@ -57,6 +57,17 @@ class IncludeDef {
     @PackageScope Map addedParams
     private Session session
 
+    @Deprecated
+    IncludeDef( String module ) {
+        throw new DeprecationException("Anonymous module inclusion is deprecated -- Replace `include '${module}'` with `include { MODULE_NAME } from '${module}'`")
+    }
+
+    @Deprecated
+    IncludeDef(TokenVar token, String alias=null) {
+        def component = token.name; if(alias) component += " as $alias"
+        throw new DeprecationException("Unwrapped module inclusion is deprecated -- Replace `include $component from './MODULE/PATH'` with `include { $component } from './MODULE/PATH'`")
+    }
+
     protected IncludeDef(List<Module> modules) {
         this.modules = new ArrayList<>(modules)
     }

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
@@ -49,20 +49,22 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
             'afterScript',
             'beforeScript',
             'cache',
-            'cleanup',
-            'clusterOptions',
             'conda',
+            'cpus',
             'container',
             'containerOptions',
-            'cpus',
+            'cleanup',
+            'clusterOptions',
             'debug',
             'disk',
+            'echo', // deprecated
             'errorStrategy',
             'executor',
             'ext',
             'fair',
-            'label',
             'machineType',
+            'queue',
+            'label',
             'maxErrors',
             'maxForks',
             'maxRetries',
@@ -71,24 +73,24 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
             'penv',
             'pod',
             'publishDir',
-            'queue',
-            'resourceLabels',
             'scratch',
-            'secret',
             'shell',
             'spack',
-            'stageInMode',
-            'stageOutMode',
             'storeDir',
             'tag',
             'time',
             // input-output qualifiers
             'file',
+            'set',
             'val',
             'each',
             'env',
+            'secret',
             'stdin',
-            'stdout'
+            'stdout',
+            'stageInMode',
+            'stageOutMode',
+            'resourceLabels'
     ]
 
     /**
@@ -533,6 +535,10 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
         new EachInParam(this).bind(obj)
     }
 
+    InParam _in_set( Object... obj ) {
+        throw new DeprecationException("Input of type `set` is deprecated -- Use `tuple` instead")
+    }
+
     InParam _in_tuple( Object... obj ) {
         new TupleInParam(this).bind(obj)
     }
@@ -597,6 +603,10 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
         }
     }
 
+    OutParam _out_set( Object... obj ) {
+        throw new DeprecationException("Output of type `set` is deprecated -- Use `tuple` instead")
+    }
+
     OutParam _out_tuple( Object... obj ) {
         new TupleOutParam(this) .bind(obj)
     }

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy
@@ -156,6 +156,10 @@ abstract class BaseInParam extends BaseParam implements InParam {
         throw new IllegalArgumentException(message)
     }
 
+    BaseInParam from( def obj ) {
+        throw new ScriptRuntimeException("Process clause `from` is no longer supported in DSL2")
+    }
+
     void setFrom( obj ) {
         checkFromNotNull(obj)
         fromObject = obj
@@ -169,6 +173,10 @@ abstract class BaseInParam extends BaseParam implements InParam {
         throw new IllegalStateException("Missing input channel")
     }
 
+    BaseInParam from( Object... obj ) {
+        throw new ScriptRuntimeException("Process clause `from` is no longer supported in DSL2")
+    }
+
     def decodeInputs( List inputs ) {
         final UNDEF = -1 as short
         def value = inputs[index]

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseOutParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseOutParam.groovy
@@ -150,6 +150,14 @@ abstract class BaseOutParam extends BaseParam implements OutParam {
         return this
     }
 
+    BaseOutParam into( def value ) {
+        throw new ScriptRuntimeException("Process clause `into` is no longer supported in DSL2")
+    }
+
+    BaseOutParam into( TokenVar... vars ) {
+        throw new ScriptRuntimeException("Process clause `into` is no longer supported in DSL2")
+    }
+
     void setInto( Object obj ) {
         intoObj = obj
     }
@@ -159,6 +167,12 @@ abstract class BaseOutParam extends BaseParam implements OutParam {
         return outChannels ? outChannels.get(0) : null
     }
 
+    @Deprecated
+    List<DataflowWriteChannel> getOutChannels() {
+        init()
+        return outChannels
+    }
+
     String getName() {
         if( nameObj != null )
             return nameObj.toString()

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/InParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/InParam.groovy
@@ -32,6 +32,10 @@ interface InParam extends Cloneable {
 
     Object getRawChannel()
 
+    InParam from( Object value )
+
+    InParam from( Object... values )
+
     short index
 
     short mapIndex

diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ScriptIncludesTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ScriptIncludesTest.groovy
@@ -1158,7 +1158,7 @@ class ScriptIncludesTest extends Dsl2Spec {
         def result = runner.setScript(SCRIPT).execute()
         then:
         def e = thrown(ScriptCompilationException)
-        e.message.contains "Invalid include statement -- the correct syntax is `include { ... } from '...'`"
+        e.message.contains "Not a valid include statement -- the correct syntax is `include { ... } from '...'`"
 
     }