Fix validation of plugin config options (#5952)

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

Author: bentsherman

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

@@ -24,6 +24,7 @@ import com.beust.jcommander.Parameters
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
+import nextflow.NF
 import nextflow.config.ConfigBuilder
 import nextflow.config.ConfigValidator
 import nextflow.exception.AbortOperationException
@@ -117,7 +118,10 @@ class CmdConfig extends CmdBase {
         final config = builder.buildConfigObject()
 
         // -- validate config options
-        new ConfigValidator().validate(config)
+        if( NF.getSyntaxParserVersion() == 'v2' ) {
+            Plugins.load(config)
+            new ConfigValidator().validate(config)
+        }
 
         // -- print config options
         if( printValue ) {

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

@@ -340,7 +340,8 @@ class CmdRun extends CmdBase implements HubOptions {
         Plugins.load(cfg)
 
         // -- validate config options
-        new ConfigValidator().validate(config)
+        if( NF.getSyntaxParserVersion() == 'v2' )
+            new ConfigValidator().validate(config)
 
         // -- create a new runner instance
         final runner = new ScriptRunner(config)

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

@@ -18,7 +18,6 @@ package nextflow.config
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import nextflow.NF
 import nextflow.config.schema.ConfigScope
 import nextflow.config.schema.SchemaNode
 import nextflow.config.schema.ScopeName
@@ -74,14 +73,10 @@ class ConfigValidator {
     }
 
     void validate(ConfigMap config) {
-        if( NF.getSyntaxParserVersion() != 'v2' )
-            return
         validate(config.toConfigObject())
     }
 
     void validate(ConfigObject config) {
-        if( NF.getSyntaxParserVersion() != 'v2' )
-            return
         final flatConfig = config.flatten()
         for( String key : flatConfig.keySet() ) {
             final names = key.tokenize('.')

modules/nextflow/src/test/groovy/nextflow/config/ConfigValidatorTest.groovy

@@ -16,7 +16,6 @@
 
 package nextflow.config
 
-import nextflow.SysEnv
 import org.junit.Rule
 import spock.lang.Specification
 import test.OutputCapture
@@ -29,14 +28,6 @@ class ConfigValidatorTest extends Specification {
     @Rule
     OutputCapture capture = new OutputCapture()
 
-    def setupSpec() {
-        SysEnv.push(NXF_SYNTAX_PARSER: 'v2')
-    }
-
-    def cleanupSpec() {
-        SysEnv.pop()
-    }
-
     def 'should warn about invalid config options' () {
         given:
         def config = new ConfigMap([