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Fix validation of plugin config options #5952

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Merged
merged 2 commits into from
Apr 9, 2025
Merged

Fix validation of plugin config options #5952

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2fd67f2
Fix validation of plugin config options
bentsherman Apr 7, 2025
a271c22
Don't load plugins in `config` command if schema checking is disabled
bentsherman Apr 7, 2025
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6 changes: 5 additions & 1 deletion modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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 ) {
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3 changes: 2 additions & 1 deletion modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
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Expand Up @@ -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)
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5 changes: 0 additions & 5 deletions modules/nextflow/src/main/groovy/nextflow/config/ConfigValidator.groovy
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Expand Up @@ -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
Expand Down Expand Up @@ -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('.')
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9 changes: 0 additions & 9 deletions modules/nextflow/src/test/groovy/nextflow/config/ConfigValidatorTest.groovy
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Expand Up @@ -16,7 +16,6 @@

package nextflow.config

import nextflow.SysEnv
import org.junit.Rule
import spock.lang.Specification
import test.OutputCapture
Expand All @@ -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([
Expand Down