add projectDir in ModuleResolver and ResolveIncludeVisitor

Signed-off-by: jorgee <jorge.ejarque@seqera.io>

Author: jorgee

modules/nextflow/src/main/groovy/nextflow/module/DefaultRemoteModuleResolver.groovy

@@ -45,8 +45,8 @@ import java.nio.file.Path
 class DefaultRemoteModuleResolver implements RemoteModuleResolver {
 
     @Override
-    Path resolve(String moduleName) {
-        def baseDir = Global.session?.baseDir ?: Path.of('.').toAbsolutePath()
+    Path resolve(String moduleName, Path projectDir) {
+        final baseDir = projectDir ?: Path.of('.').toAbsolutePath()
         final config = Global.config ?: new ConfigBuilder().setBaseDir(baseDir).build()
         final registryConfig = config.navigate('registry') as RegistryConfig
 

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

@@ -181,7 +181,7 @@ class IncludeDef {
     Path resolveRemoteModulePath(String moduleName) {
         // Use SPI to get the remote module resolver implementation
         def resolver = RemoteModuleResolverProvider.getInstance()
-        return resolver.resolve(moduleName)
+        return resolver.resolve(moduleName, session.baseDir)
     }
 
     @PackageScope

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

@@ -32,6 +32,7 @@
 import groovy.lang.GroovyClassLoader;
 import groovy.lang.GroovyCodeSource;
 import com.google.common.hash.Hashing;
+import nextflow.Global;
 import nextflow.script.ast.RecordNode;
 import nextflow.script.ast.WorkflowNode;
 import nextflow.script.control.CallSiteCollector;
@@ -268,8 +269,9 @@ public void addPhaseOperation(IPrimaryClassNodeOperation op, int phase) {
 
         private void analyze(SourceUnit source) {
             // on first pass, recursively add included modules to queue
+            Path baseDir = Global.getSession() != null ? Global.getSession().getBaseDir() : null;
             if( entry == null ) {
-                modules = new ModuleResolver(compiler).resolve(source, uri -> createSourceUnit(uri));
+                modules = new ModuleResolver(compiler, baseDir).resolve(source, uri -> createSourceUnit(uri));
                 for( var su : modules )
                     addSource(su);
                 entry = source;
@@ -283,7 +285,7 @@ private void analyze(SourceUnit source) {
             var cn = source.getAST().getClasses().get(0);
 
             // perform strict syntax checking
-            var includeResolver = new ResolveIncludeVisitor(source, compiler);
+            var includeResolver = new ResolveIncludeVisitor(source, compiler, baseDir);
             includeResolver.visit();
             for( var error : includeResolver.getErrors() )
                 source.getErrorCollector().addErrorAndContinue(error);

modules/nf-lang/src/main/java/nextflow/module/spi/FallbackRemoteModuleResolver.java

@@ -31,14 +31,11 @@
 public class FallbackRemoteModuleResolver implements RemoteModuleResolver {
 
     @Override
-    public Path resolve(String moduleName) {
-        // Use CWD-relative "modules" directory as a best-effort fallback when no
-        // RemoteModuleResolver SPI implementation is available (e.g. running outside
-        // a full Nextflow session).
-        final Path baseDir = Path.of("modules").toAbsolutePath();
-        final var resolved = baseDir.resolve(moduleName).normalize();
+    public Path resolve(String moduleName, Path projectDir) {
+        final Path modulesDir = (projectDir == null) ? projectDir.resolve("modules") : Path.of("modules").toAbsolutePath();
+        final var resolved = modulesDir.resolve(moduleName).normalize();
         // Prevent path traversal outside the base directory
-        if (!resolved.startsWith(baseDir.normalize())) {
+        if (!resolved.startsWith(modulesDir.normalize())) {
             throw new IllegalStateException("Invalid module name '" + moduleName + "' - path escapes the modules directory");
         }
         if (!Files.exists(resolved)) {

modules/nf-lang/src/main/java/nextflow/module/spi/RemoteModuleResolver.java

@@ -47,10 +47,11 @@ public interface RemoteModuleResolver {
      * </ol>
      *
      * @param moduleName The module reference string (e.g., '@scope/name' or '@scope/name@version')
+     * @param projectDir The base directory for the project (used to locate the modules directory)
      * @return Path to the resolved module's main.nf file
      * @throws IllegalArgumentException if the module reference is invalid or resolution fails
      */
-    Path resolve(String moduleName);
+    Path resolve(String moduleName, Path projectDir);
 
     /**
      * Get the priority of this resolver. Higher priority resolvers are tried first.

modules/nf-lang/src/main/java/nextflow/script/control/ModuleResolver.java

@@ -37,9 +37,15 @@
 public class ModuleResolver {
 
     private Compiler compiler;
+    private Path projectDir;
 
-    public ModuleResolver(Compiler compiler) {
+    public ModuleResolver(Compiler compiler, Path projectDir) {
         this.compiler = compiler;
+        this.projectDir = projectDir;
+    }
+
+    public ModuleResolver(Compiler compiler) {
+        this(compiler, null);
     }
 
     /**
@@ -75,7 +81,7 @@ private SourceUnit resolveInclude(IncludeNode node, SourceUnit sourceUnit, Funct
             return null;
 
         var includeUri = isRemoteModule(source) ?
-            RemoteModuleResolverProvider.getInstance().resolve(source).normalize().toUri() :
+            RemoteModuleResolverProvider.getInstance().resolve(source, projectDir).normalize().toUri() :
             getIncludeUri(Path.of(sourceUnit.getSource().getURI()).getParent(), source);
         if( compiler.getSource(includeUri) != null )
             return null;

modules/nf-lang/src/main/java/nextflow/script/control/ResolveIncludeVisitor.java

@@ -57,15 +57,22 @@ public class ResolveIncludeVisitor extends ScriptVisitorSupport {
 
     private boolean changed;
 
-    public ResolveIncludeVisitor(SourceUnit sourceUnit, Compiler compiler, Set<URI> changedUris) {
+    private Path projectDir;
+
+    public ResolveIncludeVisitor(SourceUnit sourceUnit, Compiler compiler, Set<URI> changedUris, Path projectDir) {
         this.sourceUnit = sourceUnit;
         this.uri = sourceUnit.getSource().getURI();
         this.compiler = compiler;
         this.changedUris = changedUris;
+        this.projectDir = projectDir;
+    }
+
+    public ResolveIncludeVisitor(SourceUnit sourceUnit, Compiler compiler, Path projectDir) {
+        this(sourceUnit, compiler, null, projectDir);
     }
 
     public ResolveIncludeVisitor(SourceUnit sourceUnit, Compiler compiler) {
-        this(sourceUnit, compiler, null);
+        this(sourceUnit, compiler, null, null);
     }
 
     @Override
@@ -90,7 +97,7 @@ public void visitInclude(IncludeNode node) {
         URI includeUri;
         if( ModuleResolver.isRemoteModule(source) ) {
             try {
-                includeUri = RemoteModuleResolverProvider.getInstance().resolve(source).normalize().toUri();
+                includeUri = RemoteModuleResolverProvider.getInstance().resolve(source, projectDir).normalize().toUri();
             }
             catch( IllegalStateException e ) {
                 addError(e.getMessage(), node);

modules/nf-lang/src/main/java/nextflow/script/control/ScriptParser.java

@@ -16,6 +16,7 @@
 package nextflow.script.control;
 
 import java.io.File;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Collections;
 
@@ -34,11 +35,17 @@
 public class ScriptParser {
 
     private Compiler compiler;
+    private Path projectDir;
 
     public ScriptParser() {
+        this(null);
+    }
+
+    public ScriptParser(Path projectDir) {
         var config = getConfig();
         var classLoader = new GroovyClassLoader();
-        compiler = new Compiler(config, classLoader);
+        this.compiler = new Compiler(config, classLoader);
+        this.projectDir = projectDir;
     }
 
     public Compiler compiler() {
@@ -68,11 +75,11 @@ private void parse0(SourceUnit source) {
     public void analyze() {
         var sources = new ArrayList<>(compiler.getSources().values());
         for( var source : sources ) {
-            new ModuleResolver(compiler()).resolve(source, (uri) -> compiler.createSourceUnit(new File(uri)));
+            new ModuleResolver(compiler(), projectDir).resolve(source, (uri) -> compiler.createSourceUnit(new File(uri)));
         }
 
         for( var source : compiler.getSources().values() ) {
-            var includeResolver = new ResolveIncludeVisitor(source, compiler);
+            var includeResolver = new ResolveIncludeVisitor(source, compiler, projectDir);
             includeResolver.visit();
             for( var error : includeResolver.getErrors() )
                 source.getErrorCollector().addErrorAndContinue(error);