Add type checking utils (#6482)

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

docs/reference/process.md

@@ -649,7 +649,7 @@ The `disk` directive allows you to define how much local disk storage the proces
 
 ```nextflow
 process hello {
-    disk '2 GB'
+    disk 2.GB
 
     script:
     """
@@ -692,17 +692,17 @@ The `errorStrategy` directive allows you to define how the process manages an er
 
 The following error strategies are available:
 
-`terminate` (default)
+`'terminate'` (default)
 : When a task fails, terminate the pipeline immediately and report an error. Pending and running jobs are killed.
 
-`finish`
+`'finish'`
 : When a task fails, wait for submitted and running tasks to finish and then terminate the pipeline, reporting an error.
 
-`ignore`
+`'ignore'`
 : When a task fails, ignore it and continue the pipeline execution. If the `workflow.failOnIgnore` config option is set to `true`, the pipeline will report an error (i.e. return a non-zero exit code) upon completion. Otherwise, the pipeline will complete successfully.
 : See the {ref}`stdlib-namespaces-workflow` namespace for more information.
 
-`retry`
+`'retry'`
 : When a task fails, retry it.
 
 When setting the `errorStrategy` directive to `ignore` the process doesn't stop on an error condition, it just reports a message notifying you of the error event.
@@ -908,34 +908,6 @@ process hello {
 
 See also: [cpus](#cpus) and [memory](#memory).
 
-(process-maxsubmitawait)=
-
-### maxSubmitAwait
-
-The `maxSubmitAwait` directive allows you to specify how long a task can remain in submission queue without being executed.
-Elapsed this time the task execution will fail.
-
-When used along with `retry` error strategy, it can be useful to re-schedule the task to a difference queue or
-resource requirement. For example:
-
-```nextflow
-process hello {
-  errorStrategy 'retry'
-  maxSubmitAwait '10 mins'
-  maxRetries 3
-  queue "${task.submitAttempt==1 ? 'spot-compute' : 'on-demand-compute'}"
-
-  script:
-  """
-  your_command --here
-  """
-}
-```
-
-In the above example the task is submitted to the `spot-compute` on the first attempt (`task.submitAttempt==1`). If the
-task execution does not start in the 10 minutes, a failure is reported and a new submission is attempted using the
-queue named `on-demand-compute`.
-
 (process-maxerrors)=
 
 ### maxErrors
@@ -1003,6 +975,34 @@ There is a subtle but important difference between `maxRetries` and the `maxErro
 
 See also: [errorStrategy](#errorstrategy) and [maxErrors](#maxerrors).
 
+(process-maxsubmitawait)=
+
+### maxSubmitAwait
+
+The `maxSubmitAwait` directive allows you to specify how long a task can remain in submission queue without being executed.
+Elapsed this time the task execution will fail.
+
+When used along with `retry` error strategy, it can be useful to re-schedule the task to a difference queue or
+resource requirement. For example:
+
+```nextflow
+process hello {
+  errorStrategy 'retry'
+  maxSubmitAwait 10.m
+  maxRetries 3
+  queue "${task.submitAttempt==1 ? 'spot-compute' : 'on-demand-compute'}"
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+In the above example the task is submitted to the `spot-compute` on the first attempt (`task.submitAttempt==1`). If the
+task execution does not start in the 10 minutes, a failure is reported and a new submission is attempted using the
+queue named `on-demand-compute`.
+
 (process-memory)=
 
 ### memory
@@ -1011,7 +1011,7 @@ The `memory` directive allows you to define how much memory the process is allow
 
 ```nextflow
 process hello {
-    memory '2 GB'
+    memory 2.GB
 
     script:
     """
@@ -1746,7 +1746,7 @@ The `time` directive allows you to define how long a process is allowed to run.
 
 ```nextflow
 process hello {
-    time '1h'
+    time 1.h
 
     script:
     """
@@ -1757,15 +1757,13 @@ process hello {
 
 The following time unit suffixes can be used when specifying the duration value:
 
-| Unit                            | Description  |
-| ------------------------------- | ------------ |
-| `ms`, `milli`, `millis`         | Milliseconds |
-| `s`, `sec`, `second`, `seconds` | Seconds      |
-| `m`, `min`, `minute`, `minutes` | Minutes      |
-| `h`, `hour`, `hours`            | Hours        |
-| `d`, `day`, `days`              | Days         |
-
-Multiple units can be used in a single declaration, for example: `'1day 6hours 3minutes 30seconds'`
+| Unit | Description  |
+| ---- | ------------ |
+| `ms` | Milliseconds |
+| `s`  | Seconds      |
+| `m`  | Minutes      |
+| `h`  | Hours        |
+| `d`  | Days         |
 
 See {ref}`stdlib-types-duration` for more information.
 

modules/nextflow/src/main/groovy/nextflow/script/parser/v2/ScriptCompiler.java

@@ -42,6 +42,7 @@
 import nextflow.script.control.ResolveIncludeVisitor;
 import nextflow.script.control.ScriptResolveVisitor;
 import nextflow.script.control.ScriptToGroovyVisitor;
+import nextflow.script.control.StripTypesVisitor;
 import nextflow.script.control.TypeCheckingVisitor;
 import nextflow.script.parser.ScriptParserPluginFactory;
 import org.codehaus.groovy.ast.ASTNode;
@@ -290,6 +291,7 @@ private void analyze(SourceUnit source) {
 
             // convert to Groovy
             new ScriptToGroovyVisitor(source).visit();
+            new StripTypesVisitor(source).visitClass(cn);
             new PathCompareVisitor(source).visitClass(cn);
             new OpCriteriaVisitor(source).visitClass(cn);
             new GStringToStringVisitor(source).visitClass(cn);

modules/nextflow/src/test/groovy/nextflow/script/parser/v2/ScriptLoaderV2Test.groovy

@@ -232,4 +232,26 @@ class ScriptLoaderV2Test extends Dsl2Spec {
         noExceptionThrown()
     }
 
+    def 'should strip unsupported type annotations' () {
+
+        given:
+        def session = new Session()
+        def parser = new ScriptLoaderV2(session)
+
+        def TEXT = '''
+            // strip cast type
+            ['1', '1.fastq', '2.fastq'] as Tuple<String,String,String>
+
+            // strip type annotation in variable declaration
+            def ch: Channel = channel.empty()
+            '''
+
+        when:
+        parser.parse(TEXT)
+        parser.runScript()
+
+        then:
+        noExceptionThrown()
+    }
+
 }

modules/nf-lang/src/main/java/nextflow/config/control/VariableScopeVisitor.java

@@ -285,9 +285,11 @@ private void checkMethodCall(MethodCallExpression node) {
         if( !node.isImplicitThis() )
             return;
         var name = node.getMethodAsString();
-        var defNode = vsc.findDslFunction(name, node);
-        if( defNode != null )
-            node.putNodeMetaData(ASTNodeMarker.METHOD_TARGET, defNode);
+        var methods = vsc.findDslFunction(name, node);
+        if( methods.size() == 1 )
+            node.putNodeMetaData(ASTNodeMarker.METHOD_TARGET, methods.get(0));
+        else if( !methods.isEmpty() )
+            node.putNodeMetaData(ASTNodeMarker.METHOD_OVERLOADS, methods);
         else if( !KEYWORDS.contains(name) )
             vsc.addError("`" + name + "` is not defined", node.getMethod());
     }

modules/nf-lang/src/main/java/nextflow/script/ast/ASTNodeMarker.java

@@ -27,6 +27,9 @@ public enum ASTNodeMarker {
     // denotes that an assignment is an implicit declaration
     IMPLICIT_DECLARATION,
 
+    // the inferred return type of a closure expression
+    INFERRED_RETURN_TYPE,
+
     // the inferred type of an expression
     INFERRED_TYPE,
 
@@ -39,6 +42,9 @@ public enum ASTNodeMarker {
     // the verbatim text of a Groovy-style type annotation (ClassNode)
     LEGACY_TYPE,
 
+    // the list of candidate MethodNode's for a MethodCallExpression
+    METHOD_OVERLOADS,
+
     // the MethodNode targeted by a MethodCallExpression
     METHOD_TARGET,
 
@@ -48,6 +54,9 @@ public enum ASTNodeMarker {
     // denotes a nullable type annotation (ClassNode)
     NULLABLE,
 
+    // the FieldNode targeted by a PropertyExpression
+    PROPERTY_TARGET,
+
     // the starting quote sequence of a string literal or gstring expression
     QUOTE_CHAR,
 

modules/nf-lang/src/main/java/nextflow/script/ast/ASTUtils.java

@@ -18,10 +18,13 @@
 
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Optional;
 import java.util.stream.Stream;
 
+import groovy.transform.NamedParams;
 import org.codehaus.groovy.ast.ClassHelper;
 import org.codehaus.groovy.ast.ClassNode;
 import org.codehaus.groovy.ast.AnnotatedNode;
@@ -30,9 +33,12 @@
 import org.codehaus.groovy.ast.Parameter;
 import org.codehaus.groovy.ast.PropertyNode;
 import org.codehaus.groovy.ast.Variable;
+import org.codehaus.groovy.ast.expr.AnnotationConstantExpression;
+import org.codehaus.groovy.ast.expr.ClassExpression;
 import org.codehaus.groovy.ast.expr.ClosureExpression;
 import org.codehaus.groovy.ast.expr.ConstantExpression;
 import org.codehaus.groovy.ast.expr.Expression;
+import org.codehaus.groovy.ast.expr.ListExpression;
 import org.codehaus.groovy.ast.expr.MapExpression;
 import org.codehaus.groovy.ast.expr.MapEntryExpression;
 import org.codehaus.groovy.ast.expr.MethodCall;
@@ -145,6 +151,40 @@ public static List<MapEntryExpression> asNamedArgs(MethodCall call) {
             : Collections.emptyList();
     }
 
+    /**
+     * Given a parameter with a @NamedParams annotation,
+     * return the map of named params.
+     *
+     * @param parameter
+     */
+    public static Map<String, AnnotationNode> asNamedParams(Parameter parameter) {
+        var namedParams = new LinkedHashMap<String, AnnotationNode>();
+        parameter.getAnnotations().stream()
+            .filter(an -> an.getClassNode().getName().equals(NamedParams.class.getName()))
+            .flatMap(an -> {
+                var value = an.getMember("value");
+                return value instanceof ListExpression le
+                    ? le.getExpressions().stream()
+                    : Stream.empty();
+            })
+            .forEach((value) -> {
+                if( !(value instanceof AnnotationConstantExpression) )
+                    return;
+                var ace = (AnnotationConstantExpression) value;
+                var namedParam = (AnnotationNode) ace.getValue();
+                var name = namedParam.getMember("value").getText();
+                namedParams.put(name, namedParam);
+            });
+        return namedParams;
+    }
+
+    public static Parameter asNamedParam(AnnotationNode node) {
+        var name = node.getMember("value").getText();
+        var typeX = (ClassExpression) node.getMember("type");
+        var type = typeX != null ? typeX.getType() : ClassHelper.dynamicType();
+        return new Parameter(type, name);
+    }
+
     public static VariableExpression asVarX(Statement statement) {
         return statement instanceof ExpressionStatement es ? asVarX(es.getExpression()) : null;
     }

modules/nf-lang/src/main/java/nextflow/script/ast/OutputNode.java

@@ -15,23 +15,20 @@
  */
 package nextflow.script.ast;
 
-import org.codehaus.groovy.ast.ASTNode;
 import org.codehaus.groovy.ast.ClassNode;
+import org.codehaus.groovy.ast.Parameter;
 import org.codehaus.groovy.ast.stmt.Statement;
 
 /**
  * An output declaration.
  *
  * @author Ben Sherman <[email protected]>
  */
-public class OutputNode extends ASTNode {
-    public final String name;
-    public final ClassNode type;
+public class OutputNode extends Parameter {
     public final Statement body;
 
     public OutputNode(String name, ClassNode type, Statement body) {
-        this.name = name;
-        this.type = type;
+        super(type, name);
         this.body = body;
     }
 }

modules/nf-lang/src/main/java/nextflow/script/ast/ProcessNodeV2.java

@@ -69,30 +69,28 @@ private static ClassNode dummyReturnType(Statement block) {
         if( outputs.size() == 1 ) {
             var first = outputs.get(0);
             var output = ((ExpressionStatement) first).getExpression();
-            if( outputName(output) == null )
+            if( outputTarget(output) == null )
                 return output.getType();
         }
         var cn = new ClassNode(Record.class);
         outputs.stream()
             .map(stmt -> ((ExpressionStatement) stmt).getExpression())
-            .map(output -> outputName(output))
-            .filter(name -> name != null)
-            .forEach((name) -> {
-                var type = ClassHelper.dynamicType();
-                var fn = new FieldNode(name, Modifier.PUBLIC, type, cn, null);
+            .map(output -> outputTarget(output))
+            .filter(target -> target != null)
+            .forEach((target) -> {
+                var fn = new FieldNode(target.getName(), Modifier.PUBLIC, target.getType(), cn, null);
                 fn.setDeclaringClass(cn);
                 cn.addField(fn);
             });
         return cn;
     }
 
-    private static String outputName(Expression output) {
+    private static VariableExpression outputTarget(Expression output) {
         if( output instanceof VariableExpression ve ) {
-            return ve.getName();
+            return ve;
         }
-        else if( output instanceof AssignmentExpression ae ) {
-            var target = (VariableExpression)ae.getLeftExpression();
-            return target.getName();
+        if( output instanceof AssignmentExpression ae ) {
+            return (VariableExpression)ae.getLeftExpression();
         }
         return null;
     }