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Add name checking for config files
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
1 parent fdbd247 commit cd8f956

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14 files changed

+937
-472
lines changed

14 files changed

+937
-472
lines changed

‎modules/compiler/src/main/java/config/ast/ConfigAssignNode.java‎

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@@ -25,7 +25,7 @@
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*/
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public class ConfigAssignNode extends ConfigStatement {
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public final List<String> names;
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public final Expression value;
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public Expression value;
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public ConfigAssignNode(List<String> names, Expression value) {
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this.names = names;

‎modules/compiler/src/main/java/config/ast/ConfigIncludeNode.java‎

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@@ -22,7 +22,7 @@
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* @author Ben Sherman <bentshermann@gmail.com>
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*/
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public class ConfigIncludeNode extends ConfigStatement {
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public final Expression source;
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public Expression source;
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public ConfigIncludeNode(Expression source) {
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this.source = source;

‎modules/compiler/src/main/java/config/control/ConfigResolveVisitor.java‎

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/*
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* Copyright 2024-2025, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package nextflow.config.control;
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import java.util.Collections;
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import nextflow.config.ast.ConfigAssignNode;
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import nextflow.config.ast.ConfigIncludeNode;
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import nextflow.config.ast.ConfigNode;
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import nextflow.config.ast.ConfigVisitorSupport;
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import nextflow.script.control.ResolveVisitor;
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import org.codehaus.groovy.ast.DynamicVariable;
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import org.codehaus.groovy.ast.expr.Expression;
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import org.codehaus.groovy.ast.expr.VariableExpression;
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import org.codehaus.groovy.control.CompilationUnit;
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import org.codehaus.groovy.control.SourceUnit;
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/**
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*
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* @author Ben Sherman <bentshermann@gmail.com>
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*/
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public class ConfigResolveVisitor extends ConfigVisitorSupport {
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private SourceUnit sourceUnit;
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private ResolveVisitor resolver;
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public ConfigResolveVisitor(SourceUnit sourceUnit, CompilationUnit compilationUnit) {
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this.sourceUnit = sourceUnit;
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this.resolver = new ResolveVisitor(sourceUnit, compilationUnit, Collections.emptyList(), Collections.emptyList());
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}
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@Override
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protected SourceUnit getSourceUnit() {
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return sourceUnit;
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}
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public void visit() {
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var moduleNode = sourceUnit.getAST();
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if( moduleNode instanceof ConfigNode cn ) {
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// initialize variable scopes
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new VariableScopeVisitor(sourceUnit).visit();
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// resolve type names
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super.visit(cn);
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// report errors for any unresolved variable references
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new DynamicVariablesVisitor().visit(cn);
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}
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}
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@Override
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public void visitConfigAssign(ConfigAssignNode node) {
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node.value = resolver.transform(node.value);
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}
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@Override
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public void visitConfigInclude(ConfigIncludeNode node) {
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node.source = resolver.transform(node.source);
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}
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private class DynamicVariablesVisitor extends ConfigVisitorSupport {
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@Override
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protected SourceUnit getSourceUnit() {
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return sourceUnit;
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}
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@Override
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public void visitVariableExpression(VariableExpression node) {
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var variable = node.getAccessedVariable();
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if( variable instanceof DynamicVariable )
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resolver.addError("`" + node.getName() + "` is not defined", node);
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}
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}
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}

‎modules/compiler/src/main/java/config/control/VariableScopeVisitor.java‎

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/*
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* Copyright 2024-2025, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
11+
* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package nextflow.config.control;
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import java.util.ArrayList;
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import java.util.List;
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import nextflow.config.ast.ConfigAssignNode;
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import nextflow.config.ast.ConfigBlockNode;
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import nextflow.config.ast.ConfigIncludeNode;
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import nextflow.config.ast.ConfigNode;
25+
import nextflow.config.ast.ConfigVisitorSupport;
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import nextflow.config.dsl.ConfigDsl;
27+
import nextflow.script.control.VariableScopeChecker;
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import nextflow.script.dsl.ProcessDsl;
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import nextflow.script.dsl.ScriptDsl;
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import org.codehaus.groovy.ast.ClassNode;
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import org.codehaus.groovy.ast.DynamicVariable;
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import org.codehaus.groovy.ast.Variable;
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import org.codehaus.groovy.ast.VariableScope;
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import org.codehaus.groovy.ast.expr.BinaryExpression;
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import org.codehaus.groovy.ast.expr.ClosureExpression;
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import org.codehaus.groovy.ast.expr.ConstantExpression;
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import org.codehaus.groovy.ast.expr.DeclarationExpression;
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import org.codehaus.groovy.ast.expr.Expression;
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import org.codehaus.groovy.ast.expr.MethodCallExpression;
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import org.codehaus.groovy.ast.expr.TupleExpression;
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import org.codehaus.groovy.ast.expr.VariableExpression;
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import org.codehaus.groovy.ast.stmt.BlockStatement;
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import org.codehaus.groovy.ast.stmt.CatchStatement;
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import org.codehaus.groovy.ast.stmt.ExpressionStatement;
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import org.codehaus.groovy.control.SourceUnit;
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import org.codehaus.groovy.syntax.Types;
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/**
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* Initialize the variable scopes for an AST.
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*
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* See: org.codehaus.groovy.classgen.VariableScopeVisitor
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*
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* @author Ben Sherman <bentshermann@gmail.com>
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*/
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class VariableScopeVisitor extends ConfigVisitorSupport {
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private SourceUnit sourceUnit;
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private VariableScopeChecker vsc;
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private List<String> configScopes = new ArrayList<>();
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public VariableScopeVisitor(SourceUnit sourceUnit) {
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this.sourceUnit = sourceUnit;
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this.vsc = new VariableScopeChecker(sourceUnit, new ClassNode(ConfigDsl.class));
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}
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@Override
69+
protected SourceUnit getSourceUnit() {
70+
return sourceUnit;
71+
}
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public void visit() {
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var moduleNode = sourceUnit.getAST();
75+
if( moduleNode instanceof ConfigNode cn ) {
76+
super.visit(cn);
77+
vsc.checkUnusedVariables();
78+
}
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}
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@Override
82+
public void visitConfigBlock(ConfigBlockNode node) {
83+
var newScope = node.kind == null;
84+
if( newScope )
85+
configScopes.add(node.name);
86+
super.visitConfigBlock(node);
87+
if( newScope )
88+
configScopes.remove(configScopes.size() - 1);
89+
}
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@Override
92+
public void visitConfigInclude(ConfigIncludeNode node) {
93+
checkConfigInclude(node);
94+
visit(node.source);
95+
}
96+
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private void checkConfigInclude(ConfigIncludeNode node) {
98+
if( configScopes.isEmpty() )
99+
return;
100+
if( configScopes.size() == 2 && "profiles".equals(configScopes.get(0)) )
101+
return;
102+
vsc.addError("Config includes are only allowed at the top-level or in a profile.", node);
103+
}
104+
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// statements
106+
107+
@Override
108+
public void visitBlockStatement(BlockStatement node) {
109+
var newScope = node.getVariableScope() != null;
110+
if( newScope ) vsc.pushScope();
111+
node.setVariableScope(currentScope());
112+
super.visitBlockStatement(node);
113+
if( newScope ) vsc.popScope();
114+
}
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@Override
117+
public void visitCatchStatement(CatchStatement node) {
118+
vsc.pushScope();
119+
vsc.declare(node.getVariable(), node);
120+
super.visitCatchStatement(node);
121+
vsc.popScope();
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}
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@Override
125+
public void visitExpressionStatement(ExpressionStatement node) {
126+
var exp = node.getExpression();
127+
if( exp instanceof BinaryExpression be && Types.isAssignment(be.getOperation().getType()) ) {
128+
var source = be.getRightExpression();
129+
var target = be.getLeftExpression();
130+
visit(source);
131+
if( !checkImplicitDeclaration(target) ) {
132+
visit(target);
133+
}
134+
return;
135+
}
136+
super.visitExpressionStatement(node);
137+
}
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private boolean checkImplicitDeclaration(Expression node) {
140+
if( node instanceof TupleExpression te ) {
141+
var result = false;
142+
for( var el : te.getExpressions() )
143+
result |= declareAssignedVariable((VariableExpression) el);
144+
return result;
145+
}
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else if( node instanceof VariableExpression ve ) {
147+
return declareAssignedVariable(ve);
148+
}
149+
return false;
150+
}
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private boolean declareAssignedVariable(VariableExpression ve) {
153+
var variable = vsc.findVariableDeclaration(ve.getName(), ve);
154+
if( variable != null ) {
155+
ve.setAccessedVariable(variable);
156+
return false;
157+
}
158+
else {
159+
vsc.addError("`" + ve.getName() + "` was assigned but not declared", ve);
160+
return true;
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}
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}
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// expressions
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private static final List<String> KEYWORDS = List.of(
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"case",
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"for",
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"switch",
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"while"
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);
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@Override
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public void visitMethodCallExpression(MethodCallExpression node) {
175+
if( node.isImplicitThis() && node.getMethod() instanceof ConstantExpression ) {
176+
var name = node.getMethodAsString();
177+
var variable = vsc.findVariableDeclaration(name, node);
178+
if( variable == null ) {
179+
if( !KEYWORDS.contains(name) )
180+
vsc.addError("`" + name + "` is not defined", node.getMethod());
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}
182+
}
183+
super.visitMethodCallExpression(node);
184+
}
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@Override
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public void visitDeclarationExpression(DeclarationExpression node) {
188+
visit(node.getRightExpression());
189+
190+
if( node.isMultipleAssignmentDeclaration() ) {
191+
for( var el : node.getTupleExpression() )
192+
vsc.declare((VariableExpression) el);
193+
}
194+
else {
195+
vsc.declare(node.getVariableExpression());
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}
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}
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private boolean inClosure;
200+
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@Override
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public void visitClosureExpression(ClosureExpression node) {
203+
var ic = inClosure;
204+
inClosure = true;
205+
vsc.pushScope(ic ? null : ScriptDsl.class);
206+
var inProcess = "process".equals(configScopes.get(configScopes.size() - 1));
207+
if( !ic && inProcess )
208+
vsc.pushScope(ProcessDsl.class);
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node.setVariableScope(currentScope());
210+
if( node.getParameters() != null ) {
211+
for( var parameter : node.getParameters() ) {
212+
vsc.declare(parameter, parameter);
213+
if( parameter.hasInitialExpression() )
214+
visit(parameter.getInitialExpression());
215+
}
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}
217+
super.visitClosureExpression(node);
218+
for( var it = currentScope().getReferencedLocalVariablesIterator(); it.hasNext(); ) {
219+
var variable = it.next();
220+
variable.setClosureSharedVariable(true);
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}
222+
if( !ic && inProcess )
223+
vsc.popScope();
224+
vsc.popScope();
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inClosure = ic;
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}
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@Override
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public void visitVariableExpression(VariableExpression node) {
230+
var name = node.getName();
231+
Variable variable = vsc.findVariableDeclaration(name, node);
232+
if( variable == null ) {
233+
if( "it".equals(name) ) {
234+
vsc.addFutureWarning("Implicit closure parameter `it` will not be supported in a future version", node);
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}
236+
else {
237+
variable = new DynamicVariable(name, false);
238+
}
239+
}
240+
if( variable != null ) {
241+
node.setAccessedVariable(variable);
242+
}
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}
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// helpers
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private VariableScope currentScope() {
248+
return vsc.getCurrentScope();
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}
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}

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