Use only currently loaded plugins when resolving script includes

Author: bentsherman

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

@@ -27,6 +27,7 @@
 import nextflow.config.ast.ConfigVisitorSupport;
 import nextflow.config.spec.SpecNode;
 import nextflow.lsp.spec.ConfigSpecFactory;
+import nextflow.lsp.spec.PluginRef;
 import nextflow.lsp.spec.PluginSpecCache;
 import nextflow.script.control.PhaseAware;
 import nextflow.script.control.Phases;
@@ -94,8 +95,8 @@ private SpecNode.Scope getPluginScopes(ConfigNode cn) {
     }
 
     private Map<String, SpecNode> pluginConfigScopes(ConfigNode cn) {
-        var entries = cn.getConfigStatements().stream()
-            // get plugin refs from `plugins` block
+        // get plugin refs from `plugins` block
+        var refs = cn.getConfigStatements().stream()
             .map(stmt ->
                 stmt instanceof ConfigApplyBlockNode node && "plugins".equals(node.name) ? node : null
             )
@@ -106,18 +107,26 @@ private Map<String, SpecNode> pluginConfigScopes(ConfigNode cn) {
                 var firstArg = arguments.get(0);
                 return firstArg instanceof ConstantExpression ce ? ce.getText() : null;
             })
-            // fetch plugin specs from plugin registry
             .filter(ref -> ref != null)
             .map((ref) -> {
                 var tokens = ref.split("@");
                 var name = tokens[0];
                 var version = tokens.length == 2 ? tokens[1] : null;
-                return pluginSpecCache.get(name, version);
+                return new PluginRef(name, version);
             })
+            .toList();
+
+        // fetch plugin specs from plugin registry
+        var entries = refs.stream()
+            .map((ref) -> pluginSpecCache.get(ref.name(), ref.version()))
             .filter(spec -> spec != null)
             .map(spec -> spec.configScopes())
             .toList();
 
+        // set current versions in plugin spec cache
+        pluginSpecCache.setCurrentVersions(refs);
+
+        // collect config scopes from plugin specs
         var result = new HashMap<String, SpecNode>();
         for( var entry : entries )
             result.putAll(entry);

src/main/java/nextflow/lsp/services/script/ResolvePluginIncludeVisitor.java

@@ -62,7 +62,7 @@ public void visitInclude(IncludeNode node) {
         if( !source.startsWith("plugin/") )
             return;
         var pluginName = source.split("/")[1];
-        var spec = pluginSpecCache.get(pluginName, null);
+        var spec = pluginSpecCache.getCurrent(pluginName);
         if( spec == null ) {
             addError("Plugin '" + pluginName + "' does not exist or is not specified in the configuration file", node);
             return;

src/main/java/nextflow/lsp/spec/PluginRef.java

@@ -0,0 +1,21 @@
+/*
+ * Copyright 2024-2025, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package nextflow.lsp.spec;
+
+public record PluginRef(
+    String name,
+    String version
+) {}

src/main/java/nextflow/lsp/spec/PluginSpecCache.java

@@ -44,6 +44,8 @@ public class PluginSpecCache {
 
     private Map<PluginRef, PluginSpec> cache = new HashMap<>();
 
+    private List<PluginRef> currentVersions;
+
     public PluginSpecCache(String registryUrl) {
         this.registryUri = URI.create(registryUrl);
     }
@@ -138,10 +140,29 @@ private static PluginSpec pluginSpec(Map release) {
         );
     }
 
-}
+    /**
+     * Set the plugin versions currently specified by the config.
+     *
+     * @param currentVersions
+     */
+    public void setCurrentVersions(List<PluginRef> currentVersions) {
+        this.currentVersions = currentVersions;
+    }
 
+    /**
+     * Get the currently loaded spec for a plugin.
+     * 
+     * @param name
+     */
+    public PluginSpec getCurrent(String name) {
+        if( currentVersions == null )
+            return null;
+        var ref = currentVersions.stream()
+            .filter(r -> r.name().equals(name))
+            .findFirst().orElse(null);
+        if( ref == null )
+            return null;
+        return cache.get(ref);
+    }
 
-record PluginRef(
-    String name,
-    String version
-) {}
+}