Improve resolution of plugin includes

Author: bentsherman

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

@@ -131,8 +131,9 @@ private Map<String, SpecNode> pluginConfigScopes(ConfigNode cn) {
             .map(spec -> spec.configScopes())
             .toList();
 
-        // set current versions in plugin spec cache
-        pluginSpecCache.setCurrentVersions(refs);
+        // save current versions to plugin cache
+        var uri = sourceUnit.getSource().getURI();
+        pluginSpecCache.setCurrentVersions(uri, refs);
 
         // collect config scopes from plugin specs
         var result = new HashMap<String, SpecNode>();

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

@@ -58,11 +58,12 @@ public void visit() {
 
     @Override
     public void visitInclude(IncludeNode node) {
+        var uri = sourceUnit.getSource().getURI();
         var source = node.source.getText();
         if( !source.startsWith("plugin/") )
             return;
         var pluginName = source.split("/")[1];
-        var spec = pluginSpecCache.getCurrent(pluginName);
+        var spec = pluginSpecCache.getCurrent(uri, 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/PluginSpecCache.java

@@ -19,6 +19,7 @@
 import java.net.URI;
 import java.net.http.HttpClient;
 import java.net.http.HttpRequest;
+import java.nio.file.Path;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
@@ -43,7 +44,7 @@ public class PluginSpecCache {
 
     private Map<PluginRef, PluginSpec> cache = new HashMap<>();
 
-    private List<PluginRef> currentVersions;
+    private Map<Path, List<PluginRef>> pluginsMap = new HashMap<>();
 
     public PluginSpecCache(String registryUrl) {
         this.registryUri = URI.create(registryUrl);
@@ -136,23 +137,39 @@ private static List<Map> pluginDefinitions(Map release) {
     }
 
     /**
-     * Set the plugin versions currently specified by the config.
+     * Set the plugin versions currently specified for a given config file.
      *
-     * @param currentVersions
+     * Only "main" config files, i.e. files named `nextflow.config`, are recorded.
+     *
+     * @param uri
+     * @param refs
      */
-    public void setCurrentVersions(List<PluginRef> currentVersions) {
-        this.currentVersions = currentVersions;
+    public void setCurrentVersions(URI uri, List<PluginRef> refs) {
+        if( uri.getPath() == null || !uri.getPath().endsWith("nextflow.config") )
+            return;
+        var parent = Path.of(uri).getParent();
+        this.pluginsMap.put(parent, refs);
     }
 
     /**
      * Get the currently loaded spec for a plugin.
-     * 
+     *
+     * Given the URI of the including file, "./nextflow.config" is
+     * used if present, otherwise "../nextflow.config" is used if
+     * present, and so on.
+     *
+     * @param uri
      * @param name
      */
-    public PluginSpec getCurrent(String name) {
-        if( currentVersions == null )
+    public PluginSpec getCurrent(URI uri, String name) {
+        var parent = Path.of(uri).getParent();
+        var key = pluginsMap.keySet().stream()
+            .filter(p -> parent.startsWith(p))
+            .sorted((a, b) -> b.compareTo(a))
+            .findFirst().orElse(null);
+        if( key == null )
             return null;
-        var ref = currentVersions.stream()
+        var ref = pluginsMap.get(key).stream()
             .filter(r -> r.name().equals(name))
             .findFirst().orElse(null);
         if( ref == null )

src/test/groovy/nextflow/lsp/spec/PluginSpecCacheTest.groovy

@@ -26,12 +26,76 @@ class PluginSpecCacheTest extends Specification {
 
     def 'should fetch a plugin spec' () {
         given:
-        def pluginSpecCache = new PluginSpecCache('https://registry.nextflow.io/api/')
+        def psc = pluginSpecCache()
 
         when:
-        def spec = pluginSpecCache.get('nf-prov', '1.6.0')
+        def spec = psc.get('nf-prov', '1.6.0')
         then:
         spec.configScopes().containsKey('prov')
     }
 
+    def 'should only track plugin versions for main config files' () {
+        given:
+        def psc = pluginSpecCache()
+        def refs = [new PluginRef('nf-hello', '0.9.0')]
+
+        when:
+        psc.setCurrentVersions(uri('/project/other.config'), refs)
+        then:
+        psc.getCurrent(uri('/project/main.nf'), 'nf-hello') == null
+    }
+
+    def 'should return current plugin versions for a given script file' () {
+        given:
+        def ref1 = new PluginRef('nf-hello', '0.9.0')
+        def ref2 = new PluginRef('nf-hello', '1.0.0')
+        def spec1 = new PluginSpec([:], [], [], [])
+        def spec2 = new PluginSpec([:], [], [], [])
+        def psc = pluginSpecCache([(ref1): spec1, (ref2): spec2])
+
+        // return nothing when no config files are registered
+        expect:
+        psc.getCurrent(uri('/project/main.nf'), 'nf-hello') == null
+
+        // return nothing when script has no parent config file
+        when:
+        psc.setCurrentVersions(uri('/project/nextflow.config'), [new PluginRef('nf-hello', '0.9.0')])
+        then:
+        psc.getCurrent(uri('/other-project/main.nf'), 'nf-hello') == null
+
+        // return nothing when requested plugin is not enabled
+        when:
+        psc.setCurrentVersions(uri('/project/nextflow.config'), [new PluginRef('nf-other', '1.0.0')])
+        then:
+        psc.getCurrent(uri('/project/main.nf'), 'nf-hello') == null
+
+        // return plugin spec from nearest parent config
+        when:
+        psc.setCurrentVersions(uri('/project/nextflow.config'), [ref1])
+        then:
+        psc.getCurrent(uri('/project/main.nf'), 'nf-hello') == spec2
+        psc.getCurrent(uri('/project/subdir/module.nf'), 'nf-hello') == spec2
+
+        when:
+        psc.setCurrentVersions(uri('/project/nextflow.config'), [ref1])
+        psc.setCurrentVersions(uri('/project/subdir/nextflow.config'), [ref2])
+        then:
+        psc.getCurrent(uri('/project/main.nf'), 'nf-hello') == spec1
+        psc.getCurrent(uri('/project/subdir/module.nf'), 'nf-hello') == spec2
+    }
+
+    def pluginSpecCache(Map entries = null) {
+        def result = new PluginSpecCache('https://registry.nextflow.io/api/')
+        if( entries ) {
+            def field = PluginSpecCache.getDeclaredField('cache')
+            field.setAccessible(true)
+            field.set(result, entries)
+        }
+        return result
+    }
+
+    def uri(String path) {
+        return URI.create('file://' + path)
+    }
+
 }