Resolve plugin definitions from registry (#141)

Author: bentsherman

build.gradle

@@ -30,7 +30,6 @@ test {
 
 configurations {
   nextflowRuntime
-  specImplementation.extendsFrom(nextflowRuntime)
 }
 
 dependencies {
@@ -57,6 +56,7 @@ dependencies {
   testImplementation ('org.objenesis:objenesis:3.4')
   testImplementation ('net.bytebuddy:byte-buddy:1.14.17')
   testImplementation ('org.spockframework:spock-core:2.3-groovy-4.0') { exclude group: 'org.apache.groovy' }
+  testRuntimeOnly 'org.junit.platform:junit-platform-launcher'
 }
 
 sourceSets {
@@ -67,6 +67,10 @@ sourceSets {
   }
 }
 
+configurations {
+  specImplementation.extendsFrom(nextflowRuntime)
+}
+
 task buildSpec(type: JavaExec) {
   description = 'Build spec file of core definitions'
   group = 'build'

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.12.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.1.0-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

src/main/java/nextflow/lsp/NextflowLanguageServer.java

@@ -121,8 +121,8 @@ public static void main(String[] args) {
     private LanguageClient client = null;
 
     private Map<String, String> workspaceRoots = new HashMap<>();
-    private Map<String, LanguageService> scriptServices = new HashMap<>();
-    private Map<String, LanguageService> configServices = new HashMap<>();
+    private Map<String, ConfigService> configServices = new HashMap<>();
+    private Map<String, ScriptService> scriptServices = new HashMap<>();
 
     private LanguageServerConfiguration configuration = LanguageServerConfiguration.defaults();
 
@@ -461,6 +461,7 @@ public void didChangeConfiguration(DidChangeConfigurationParams params) {
             withDefault(JsonUtils.getBoolean(settings, "nextflow.formatting.harshilAlignment"), configuration.harshilAlignment()),
             withDefault(JsonUtils.getBoolean(settings, "nextflow.formatting.maheshForm"), configuration.maheshForm()),
             withDefault(JsonUtils.getInteger(settings, "nextflow.completion.maxItems"), configuration.maxCompletionItems()),
+            withDefault(JsonUtils.getString(settings, "nextflow.pluginRegistryUrl"), configuration.pluginRegistryUrl()),
             withDefault(JsonUtils.getBoolean(settings, "nextflow.formatting.sortDeclarations"), configuration.sortDeclarations()),
             withDefault(JsonUtils.getBoolean(settings, "nextflow.typeChecking"), configuration.typeChecking())
         );
@@ -483,6 +484,7 @@ private <T> T withDefault(T value, T defaultValue) {
     private boolean shouldInitialize(LanguageServerConfiguration previous, LanguageServerConfiguration current) {
         return previous.errorReportingMode() != current.errorReportingMode()
             || !DefaultGroovyMethods.equals(previous.excludePatterns(), current.excludePatterns())
+            || previous.pluginRegistryUrl() != current.pluginRegistryUrl()
             || previous.typeChecking() != current.typeChecking();
     }
 
@@ -500,8 +502,8 @@ private void initializeWorkspaces() {
             progress.update(progressMessage, count * 100 / total);
             count++;
 
-            scriptServices.get(name).initialize(configuration);
             configServices.get(name).initialize(configuration);
+            scriptServices.get(name).initialize(configuration, configServices.get(name).getPluginSpecCache());
         }
 
         progress.end();
@@ -519,16 +521,16 @@ public void didChangeWorkspaceFolders(DidChangeWorkspaceFoldersParams params) {
             var name = workspaceFolder.getName();
             log.debug("workspace/didChangeWorkspaceFolders remove " + name);
             workspaceRoots.remove(name);
-            scriptServices.remove(name).clearDiagnostics();
             configServices.remove(name).clearDiagnostics();
+            scriptServices.remove(name).clearDiagnostics();
         }
         for( var workspaceFolder : event.getAdded() ) {
             var name = workspaceFolder.getName();
             var uri = workspaceFolder.getUri();
             log.debug("workspace/didChangeWorkspaceFolders add " + name + " " + uri);
             addWorkspaceFolder(name, uri);
-            scriptServices.get(name).initialize(configuration);
             configServices.get(name).initialize(configuration);
+            scriptServices.get(name).initialize(configuration, configServices.get(name).getPluginSpecCache());
         }
     }
 
@@ -620,13 +622,13 @@ public CompletableFuture<Either<List<? extends SymbolInformation>, List<? extend
     private void addWorkspaceFolder(String name, String uri) {
         workspaceRoots.put(name, uri);
 
-        var scriptService = new ScriptService(uri);
-        scriptService.connect(client);
-        scriptServices.put(name, scriptService);
-
         var configService = new ConfigService(uri);
         configService.connect(client);
         configServices.put(name, configService);
+
+        var scriptService = new ScriptService(uri);
+        scriptService.connect(client);
+        scriptServices.put(name, scriptService);
     }
 
     private String relativePath(String uri) {
@@ -654,12 +656,12 @@ private LanguageService getLanguageService(String uri) {
         return service;
     }
 
-    private LanguageService getLanguageService0(String uri, Map<String, LanguageService> services) {
+    private LanguageService getLanguageService0(String uri, Map<String, ? extends LanguageService> services) {
         var service = workspaceRoots.entrySet().stream()
             .filter((entry) -> entry.getValue() != null && uri.startsWith(entry.getValue()))
             .findFirst()
-            .map((entry) -> services.get(entry.getKey()))
-            .orElse(services.get(DEFAULT_WORKSPACE_FOLDER_NAME));
+            .map((entry) -> (LanguageService) services.get(entry.getKey()))
+            .orElse((LanguageService) services.get(DEFAULT_WORKSPACE_FOLDER_NAME));
         if( service == null || !service.matchesFile(uri) )
             return null;
         return service;

src/main/java/nextflow/lsp/services/LanguageServerConfiguration.java

@@ -27,6 +27,7 @@ public record LanguageServerConfiguration(
     boolean harshilAlignment,
     boolean maheshForm,
     int maxCompletionItems,
+    String pluginRegistryUrl,
     boolean sortDeclarations,
     boolean typeChecking
 ) {
@@ -41,6 +42,7 @@ public static LanguageServerConfiguration defaults() {
             false,
             false,
             100,
+            "https://registry.nextflow.io/api/",
             false,
             false
         );

src/main/java/nextflow/lsp/services/config/ConfigAstCache.java

@@ -21,6 +21,7 @@
 import java.util.Set;
 
 import groovy.lang.GroovyClassLoader;
+import nextflow.config.ast.ConfigNode;
 import nextflow.config.control.ConfigResolveVisitor;
 import nextflow.config.control.ResolveIncludeVisitor;
 import nextflow.config.parser.ConfigParserPluginFactory;
@@ -30,6 +31,7 @@
 import nextflow.lsp.compiler.LanguageServerErrorCollector;
 import nextflow.lsp.file.FileCache;
 import nextflow.lsp.services.LanguageServerConfiguration;
+import nextflow.lsp.spec.PluginSpecCache;
 import nextflow.script.control.PhaseAware;
 import nextflow.script.control.Phases;
 import nextflow.script.types.Types;
@@ -46,7 +48,7 @@ public class ConfigAstCache extends ASTNodeCache {
 
     private LanguageServerConfiguration configuration;
 
-    private Map<String,SpecNode> spec = ConfigSpecFactory.defaultScopes();
+    private PluginSpecCache pluginSpecCache;
 
     public ConfigAstCache() {
         super(createCompiler());
@@ -65,8 +67,9 @@ private static CompilerConfiguration createConfiguration() {
         return config;
     }
 
-    public void initialize(LanguageServerConfiguration configuration) {
+    public void initialize(LanguageServerConfiguration configuration, PluginSpecCache pluginSpecCache) {
         this.configuration = configuration;
+        this.pluginSpecCache = pluginSpecCache;
     }
 
     @Override
@@ -92,7 +95,7 @@ protected Set<URI> analyze(Set<URI> uris, FileCache fileCache) {
                 continue;
             // phase 3: name checking
             new ConfigResolveVisitor(sourceUnit, compiler().compilationUnit(), Types.DEFAULT_CONFIG_IMPORTS).visit();
-            new ConfigSpecVisitor(sourceUnit, spec, configuration.typeChecking()).visit();
+            new ConfigSpecVisitor(sourceUnit, pluginSpecCache, configuration.typeChecking()).visit();
             if( sourceUnit.getErrorCollector().hasErrors() )
                 continue;
             // phase 4: type checking
@@ -121,4 +124,8 @@ public boolean hasSyntaxErrors(URI uri) {
             .isPresent();
     }
 
+    public ConfigNode getConfigNode(URI uri) {
+        return (ConfigNode) getSourceUnit(uri).getAST();
+    }
+
 }

src/main/java/nextflow/lsp/services/config/ConfigCompletionProvider.java

@@ -25,7 +25,6 @@
 import nextflow.config.ast.ConfigIncompleteNode;
 import nextflow.config.dsl.ConfigDsl;
 import nextflow.config.spec.SpecNode;
-import nextflow.lsp.ast.ASTNodeCache;
 import nextflow.lsp.ast.CompletionHelper;
 import nextflow.lsp.services.CompletionProvider;
 import nextflow.lsp.util.Logger;
@@ -62,14 +61,12 @@
  */
 public class ConfigCompletionProvider implements CompletionProvider {
 
-    private static final List<CompletionItem> TOPLEVEL_ITEMS = topLevelItems();
-
     private static Logger log = Logger.getInstance();
 
-    private ASTNodeCache ast;
+    private ConfigAstCache ast;
     private CompletionHelper ch;
 
-    public ConfigCompletionProvider(ASTNodeCache ast, int maxItems) {
+    public ConfigCompletionProvider(ConfigAstCache ast, int maxItems) {
         this.ast = ast;
         this.ch = new CompletionHelper(maxItems);
     }
@@ -86,17 +83,18 @@ public Either<List<CompletionItem>, CompletionList> completion(TextDocumentIdent
             return Either.forLeft(Collections.emptyList());
 
         var nodeStack = ast.getNodesAtPosition(uri, position);
+        var spec = ast.getConfigNode(uri).getSpec();
         if( nodeStack.isEmpty() )
-            return Either.forLeft(TOPLEVEL_ITEMS);
+            return Either.forLeft(topLevelItems(spec));
 
         if( isConfigExpression(nodeStack) ) {
             addCompletionItems(nodeStack);
         }
         else {
             var names = currentConfigScope(nodeStack);
             if( names.isEmpty() )
-                return Either.forLeft(TOPLEVEL_ITEMS);
-            addConfigOptions(names);
+                return Either.forLeft(topLevelItems(spec));
+            addConfigOptions(names, spec);
         }
 
         return ch.isIncomplete()
@@ -179,8 +177,8 @@ private static List<String> currentConfigScope(List<ASTNode> nodeStack) {
         return names;
     }
 
-    private void addConfigOptions(List<String> names) {
-        var scope = SpecNode.ROOT.getScope(names);
+    private void addConfigOptions(List<String> names, SpecNode.Scope spec) {
+        var scope = spec.getScope(names);
         if( scope == null )
             return;
         scope.children().forEach((name, child) -> {
@@ -191,9 +189,9 @@ private void addConfigOptions(List<String> names) {
         });
     }
 
-    private static List<CompletionItem> topLevelItems() {
+    private static List<CompletionItem> topLevelItems(SpecNode.Scope spec) {
         var result = new ArrayList<CompletionItem>();
-        SpecNode.ROOT.children().forEach((name, child) -> {
+        spec.children().forEach((name, child) -> {
             if( child instanceof SpecNode.Option option ) {
                 result.add(configOption(name, option.description(), option.type()));
             }

src/main/java/nextflow/lsp/services/config/ConfigHoverProvider.java

@@ -23,7 +23,6 @@
 import nextflow.config.ast.ConfigAssignNode;
 import nextflow.config.ast.ConfigBlockNode;
 import nextflow.config.spec.SpecNode;
-import nextflow.lsp.ast.ASTNodeCache;
 import nextflow.lsp.ast.ASTNodeStringUtils;
 import nextflow.lsp.ast.LanguageServerASTUtils;
 import nextflow.lsp.services.HoverProvider;
@@ -49,9 +48,9 @@ public class ConfigHoverProvider implements HoverProvider {
 
     private static Logger log = Logger.getInstance();
 
-    private ASTNodeCache ast;
+    private ConfigAstCache ast;
 
-    public ConfigHoverProvider(ASTNodeCache ast) {
+    public ConfigHoverProvider(ConfigAstCache ast) {
         this.ast = ast;
     }
 
@@ -69,7 +68,7 @@ public Hover hover(TextDocumentIdentifier textDocument, Position position) {
 
         var builder = new StringBuilder();
 
-        var content = getHoverContent(nodeStack);
+        var content = getHoverContent(nodeStack, ast.getConfigNode(uri).getSpec());
         if( content != null ) {
             builder.append(content);
             builder.append('\n');
@@ -94,14 +93,14 @@ public Hover hover(TextDocumentIdentifier textDocument, Position position) {
         return new Hover(new MarkupContent(MarkupKind.MARKDOWN, value));
     }
 
-    protected String getHoverContent(List<ASTNode> nodeStack) {
+    protected String getHoverContent(List<ASTNode> nodeStack, SpecNode.Scope spec) {
         var offsetNode = nodeStack.get(0);
         if( offsetNode instanceof ConfigAssignNode assign ) {
             var names = getCurrentScope(nodeStack);
             names.addAll(assign.names);
 
             var fqName = String.join(".", names);
-            var option = SpecNode.ROOT.getOption(names);
+            var option = spec.getOption(names);
             if( option != null ) {
                 var description = StringGroovyMethods.stripIndent(option.description(), true).trim();
                 var builder = new StringBuilder();
@@ -120,7 +119,7 @@ else if( Logger.isDebugEnabled() ) {
             if( names.isEmpty() )
                 return null;
 
-            var scope = SpecNode.ROOT.getChild(names);
+            var scope = spec.getChild(names);
             if( scope != null ) {
                 return StringGroovyMethods.stripIndent(scope.description(), true).trim();
             }

src/main/java/nextflow/lsp/services/config/ConfigService.java

@@ -23,6 +23,7 @@
 import nextflow.lsp.services.LanguageService;
 import nextflow.lsp.services.LinkProvider;
 import nextflow.lsp.services.SemanticTokensProvider;
+import nextflow.lsp.spec.PluginSpecCache;
 
 /**
  * Implementation of language services for Nextflow config files.
@@ -31,6 +32,8 @@
  */
 public class ConfigService extends LanguageService {
 
+    private PluginSpecCache pluginSpecCache;
+
     private ConfigAstCache astCache;
 
     public ConfigService(String rootUri) {
@@ -45,12 +48,21 @@ public boolean matchesFile(String uri) {
 
     @Override
     public void initialize(LanguageServerConfiguration configuration) {
+        initialize(configuration, new PluginSpecCache(configuration.pluginRegistryUrl()));
+    }
+
+    public void initialize(LanguageServerConfiguration configuration, PluginSpecCache pluginSpecCache) {
         synchronized (this) {
-            astCache.initialize(configuration);
+            this.pluginSpecCache = pluginSpecCache;
+            astCache.initialize(configuration, pluginSpecCache);
         }
         super.initialize(configuration);
     }
 
+    public PluginSpecCache getPluginSpecCache() {
+        return pluginSpecCache;
+    }
+
     @Override
     protected ASTNodeCache getAstCache() {
         return astCache;