Validate config schema

Signed-off-by: Ben Sherman <[email protected]>

docs/developer/plugins.md

@@ -98,7 +98,7 @@ class MyObserver implements TraceObserver {
 
     @Override
     void onFlowCreate(Session session) {
-        final message = session.config.navigate('myplugin.create.message')
+        final message = session.config.navigate('myplugin.createMessage')
         println message
     }
 }
@@ -108,16 +108,49 @@ You can then set this option in your config file:
 
 ```groovy
 // dot syntax
-myplugin.create.message = "I'm alive!"
+myplugin.createMessage = "I'm alive!"
 
-// closure syntax
+// block syntax
 myplugin {
-    create {
-        message = "I'm alive!"
+    createMessage = "I'm alive!"
+}
+```
+
+:::{versionadded} 25.02.0-edge
+:::
+
+Plugins can declare their config options by implementing the `ConfigScope` interface and declaring each config option as a field with the `@ConfigOption` annotation:
+
+```groovy
+class MyPluginConfig implements ConfigScope {
+
+    MyPluginConfig() {}
+
+    MyPluginConfig(Map opts) {
+        this.createMessage = opts.createMessage
     }
+
+    @Override
+    String name() {
+        return 'myplugin'
+    }
+
+    @Override
+    String description() {
+        return '''
+            The `myplugin` scope...
+            '''
+    }
+
+    @ConfigOption('''
+        Message to print to standard output when a run is initialized.
+        ''')
+    String createMessage
 }
 ```
 
+While this approach is not required to support plugin config options, it is used by Nextflow to recognize plugin definitions when validating the config.
+
 ### Executors
 
 Plugins can define custom executors that can then be used with the `executor` process directive.

modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy

@@ -25,6 +25,7 @@ import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.config.ConfigBuilder
+import nextflow.config.ConfigValidator
 import nextflow.exception.AbortOperationException
 import nextflow.plugin.Plugins
 import nextflow.scm.AssetManager
@@ -81,6 +82,7 @@ class CmdConfig extends CmdBase {
         if( args ) base = getBaseDir(args[0])
         if( !base ) base = Paths.get('.')
 
+        // -- validate command line options
         if( profile && showAllProfiles ) {
             throw new AbortOperationException("Option `-profile` conflicts with option `-show-profiles`")
         }
@@ -103,6 +105,7 @@ class CmdConfig extends CmdBase {
         if( printProperties )
             outputFormat = 'properties'
 
+        // -- build the config
         final builder = new ConfigBuilder()
                 .setShowClosures(true)
                 .setStripSecrets(true)
@@ -113,6 +116,10 @@ class CmdConfig extends CmdBase {
 
         final config = builder.buildConfigObject()
 
+        // -- validate config options
+        new ConfigValidator().validate(config)
+
+        // -- print config options
         if( printValue ) {
             printValue0(config, printValue, stdout)
         }

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -37,6 +37,7 @@ import nextflow.NextflowMeta
 import nextflow.SysEnv
 import nextflow.config.ConfigBuilder
 import nextflow.config.ConfigMap
+import nextflow.config.ConfigValidator
 import nextflow.exception.AbortOperationException
 import nextflow.file.FileHelper
 import nextflow.plugin.Plugins
@@ -334,13 +335,13 @@ class CmdRun extends CmdBase implements HubOptions {
         // check DSL syntax in the config
         launchInfo(config, scriptFile)
 
-        // check if NXF_ variables are set in nextflow.config
-        checkConfigEnv(config)
-
         // -- load plugins
         final cfg = plugins ? [plugins: plugins.tokenize(',')] : config
         Plugins.load(cfg)
 
+        // -- validate config options
+        new ConfigValidator().validate(config)
+
         // -- create a new runner instance
         final runner = new ScriptRunner(config)
         runner.setScript(scriptFile)
@@ -407,17 +408,6 @@ class CmdRun extends CmdBase implements HubOptions {
         }
     }
 
-    protected checkConfigEnv(ConfigMap config) {
-        // Warn about setting NXF_ environment variables within env config scope
-        final env = config.env as Map<String, String>
-        for( String name : env.keySet() ) {
-            if( name.startsWith('NXF_') && name!='NXF_DEBUG' ) {
-                final msg = "Nextflow variables must be defined in the launching environment - The following variable set in the config file is going to be ignored: '$name'"
-                log.warn(msg)
-            }
-        }
-    }
-
     protected void launchInfo(ConfigMap config, ScriptFile scriptFile) {
         // -- determine strict mode
         detectStrictFeature(config, sysEnv)

modules/nextflow/src/main/groovy/nextflow/config/ConfigValidator.groovy

@@ -0,0 +1,92 @@
+/*
+ * Copyright 2013-2024, 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.config
+
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.config.dsl.ConfigSchema
+import nextflow.config.dsl.ConfigScope
+import nextflow.plugin.Plugins
+/**
+ * Validate the Nextflow configuration
+ *
+ * @author Ben Sherman <[email protected]>
+ */
+@Slf4j
+@CompileStatic
+class ConfigValidator {
+
+    void validate(ConfigMap config) {
+        validate(config.toConfigObject())
+    }
+
+    void validate(ConfigObject config) {
+        final schema = getSchema()
+        final flatConfig = config.flatten()
+        for( String key : flatConfig.keySet() ) {
+            final names = key.tokenize('.')
+            if( names.first() == 'profiles' ) {
+                if( !names.isEmpty() ) names.remove(0)
+                if( !names.isEmpty() ) names.remove(0)
+            }
+            final scope = names.first()
+            if( scope == 'env' ) {
+                checkEnv(names.last())
+                continue
+            }
+            if( scope == 'params' )
+                continue
+            final fqName = names.join('.')
+            if( fqName.startsWith('process.ext.') )
+                return
+            if( fqName !in schema ) {
+                log.warn "Unrecognized config option '${fqName}'"
+                continue
+            }
+        }
+    }
+
+    protected Set<String> getSchema() {
+        final schema = new HashSet<String>()
+        schema.addAll(ConfigSchema.OPTIONS.keySet())
+        for( final scope : Plugins.getExtensions(ConfigScope) )
+            schema.addAll(ConfigSchema.getConfigOptions(scope).keySet())
+        // hidden options added by ConfigBuilder
+        schema.addAll(List.of(
+            'bucketDir',
+            'cacheable',
+            'dumpChannels',
+            'libDir',
+            'poolSize',
+            'plugins',
+            'preview',
+            'runName',
+            'stubRun',
+        ))
+        return schema
+    }
+
+    /**
+     * Warn about setting `NXF_*` environment variables in the config.
+     *
+     * @param name
+     */
+    protected void checkEnv(String name) {
+        if( name.startsWith('NXF_') && name!='NXF_DEBUG' )
+            log.warn "Nextflow environment variables must be defined in the launch environment -- the following environment variable in the config will be ignored: `$name`"
+    }
+}