Fix additional code issues in module system

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

Author: pditommaso

modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleInfo.groovy

@@ -119,7 +119,7 @@ class CmdModuleInfo extends CmdBase {
             throw new AbortOperationException("No release information available for ${reference}")
         }
         if( !release.metadata ) {
-            log.info("No metadata found for $reference ${release.version ? "($release.version)" : ''}")
+            throw new AbortOperationException("No metadata found for ${reference}${release.version ? " (${release.version})" : ''}")
         }
         def moduleUrl = buildModuleUrl(registryConfig.url, reference, release.version)
         if( !output || output == 'text' ) {

modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModulePublish.groovy

@@ -260,7 +260,7 @@ class CmdModulePublish extends CmdBase {
         final localStorage = new ModuleStorage(root ?: Paths.get('.').toAbsolutePath().normalize())
 
         if (!localStorage.isInstalled(ref)){
-            throw new AbortOperationException("No module diretory found for $module")
+            throw new AbortOperationException("No module directory found for $module")
         }
         useModuleReference = true
         return localStorage.getModuleDir(ref)

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

@@ -94,13 +94,13 @@ class ModuleInfo {
      * Load all properties from the .module-info file in the module directory
      *
      * @param moduleDir The module directory path
-     * @return The checksum, or null if file doesn't exist
+     * @return Map of properties, or null if file doesn't exist
      */
     static Map<String, String> load(Path moduleDir) {
         def moduleInfoFile = moduleDir.resolve(MODULE_INFO_FILE)
         if( !Files.exists(moduleInfoFile) ) {
             log.debug("Module file $moduleInfoFile not found")
-            return [:]
+            return null
         }
         def props = new Properties()
         moduleInfoFile.withInputStream { is -> props.load(is) }

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

@@ -31,9 +31,7 @@ import java.util.regex.Pattern
 @EqualsAndHashCode
 class ModuleReference {
 
-    // Pattern allows: scope with letters/digits/hyphens/dots/underscores, name segments separated by slashes (no trailing slash)
-    // Scope: starts with letter/digit, followed by letters/digits/dots/underscores/hyphens
-    // Name: one or more segments (each starting with letter, followed by letters/digits/underscores/hyphens), separated by slashes
+    // Must stay in sync with ModuleResolver.REMOTE_MODULE_PATTERN in nf-lang
     private static final Pattern MODULE_NAME_PATTERN = ~/^([a-z0-9][a-z0-9._\-]*)\/([a-z][a-z0-9._\-]*(?:\/[a-z][a-z0-9._\-]*)*)$/
 
     final String scope

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

@@ -276,7 +276,9 @@ class ModuleRegistryClient {
             }
 
             // Write response body to file
-            Files.copy(response.body(), targetPath)
+            try( def body = response.body() ) {
+                Files.copy(body, targetPath)
+            }
             log.debug "Downloaded module to: ${targetPath}"
 
             validateDownloadIntegrity(response, uri, targetPath, name, version)

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

@@ -228,7 +228,7 @@ class ModuleStorage {
     boolean removeModule(ModuleReference reference, boolean force) {
         final installed = getInstalledModule(reference)
         if( !installed )
-            return
+            return false
         final integrity = installed.integrity
         if( integrity == ModuleIntegrity.NO_REMOTE_MODULE && !force ) {
             throw new AbortOperationException(

modules/nextflow/src/test/groovy/nextflow/module/ModuleInfoTest.groovy

@@ -169,7 +169,7 @@ class ModuleInfoTest extends Specification {
         result['registryUrl'] == 'http://registry.com'
     }
 
-    def 'should return empty map when loading all from non-existent file'() {
+    def 'should return null when loading all from non-existent file'() {
         given:
         def moduleDir = tempDir.resolve('module')
         Files.createDirectories(moduleDir)
@@ -178,6 +178,6 @@ class ModuleInfoTest extends Specification {
         def result = ModuleInfo.load(moduleDir)
 
         then:
-        result == [:]
+        result == null
     }
 }

modules/nextflow/src/test/groovy/nextflow/module/ModuleStorageTest.groovy

@@ -507,19 +507,21 @@ class ModuleStorageTest extends Specification {
             new GZIPOutputStream(fos).withCloseable { gzos ->
                 new TarArchiveOutputStream(gzos).withCloseable { tos ->
                     // Add all files from tempModuleDir
-                    Files.walk(tempModuleDir).each { Path path ->
-                        if (Files.isRegularFile(path)) {
-                            // Get relative path
-                            def relativePath = tempModuleDir.relativize(path).toString()
+                    Files.walk(tempModuleDir).withCloseable { stream ->
+                        stream.each { Path path ->
+                            if (Files.isRegularFile(path)) {
+                                // Get relative path
+                                def relativePath = tempModuleDir.relativize(path).toString()
 
-                            // Create tar entry
-                            def entry = new TarArchiveEntry(path.toFile(), relativePath)
-                            tos.putArchiveEntry(entry)
+                                // Create tar entry
+                                def entry = new TarArchiveEntry(path.toFile(), relativePath)
+                                tos.putArchiveEntry(entry)
 
-                            // Write file content
-                            Files.copy(path, tos)
+                                // Write file content
+                                Files.copy(path, tos)
 
-                            tos.closeArchiveEntry()
+                                tos.closeArchiveEntry()
+                            }
                         }
                     }
                 }

modules/nf-commons/src/main/nextflow/config/RegistryConfig.groovy

@@ -55,9 +55,9 @@ class RegistryConfig implements ConfigScope {
     RegistryConfig(Map opts) {
         final urlObject = opts.url ?: [DEFAULT_REGISTRY_URL]
         if (urlObject instanceof Collection<String>)
-            this.url = urlObject as Collection<String>
+            this.url = (urlObject as Collection<String>).collect { it.replaceAll(/\/+$/, '') }
         else
-            this.url = [urlObject.toString()]
+            this.url = [urlObject.toString().replaceAll(/\/+$/, '')]
         this.apiKey = opts.apiKey as String
     }
 

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

@@ -97,11 +97,17 @@ private SourceUnit resolveInclude(IncludeNode node, SourceUnit sourceUnit, Funct
         return includeSource;
     }
 
+    /**
+     * Module name pattern matching the canonical format used by ModuleReference.
+     * Scope: lowercase alphanumeric with dots/underscores/hyphens.
+     * Name: one or more slash-separated segments, each lowercase alphanumeric with dots/underscores/hyphens.
+     */
+    static final String REMOTE_MODULE_PATTERN = "^[a-z0-9][a-z0-9._\\-]*/[a-z][a-z0-9._\\-]*(/[a-z][a-z0-9._\\-]*)*$";
+
     static boolean isRemoteModule(String source) {
         if( source.startsWith("/") || source.startsWith("./") || source.startsWith("../") )
             return false;
-        // Must match scope/name pattern: scope is lowercase alphanumeric with dots/underscores/hyphens
-        return source.matches("^[a-z0-9][a-z0-9._\\-]*/[a-z][a-z0-9._\\-]*(/[a-z][a-z0-9._\\-]*)*$");
+        return source.matches(REMOTE_MODULE_PATTERN);
     }
 
     private static URI getIncludeUri(Path parent, String source) {