Fix default imports in included configs (#6096)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/config/parser/v1/ConfigBase.groovy

@@ -25,8 +25,11 @@ import nextflow.SysEnv
 import nextflow.config.StripSecretsXform
 import nextflow.exception.IllegalConfigException
 import nextflow.file.FileHelper
+import nextflow.util.Duration
+import nextflow.util.MemoryUnit
 import org.codehaus.groovy.control.CompilerConfiguration
 import org.codehaus.groovy.control.customizers.ASTTransformationCustomizer
+import org.codehaus.groovy.control.customizers.ImportCustomizer
 import org.slf4j.Logger
 import org.slf4j.LoggerFactory
 /**
@@ -119,6 +122,11 @@ abstract class ConfigBase extends Script {
         if( renderClosureAsString )
             params.put('renderClosureAsString', true)
         config.addCompilationCustomizers(new ASTTransformationCustomizer(params, ConfigTransform))
+        //  -- add implicit types
+        def importCustomizer = new ImportCustomizer()
+        importCustomizer.addImports( Duration.name )
+        importCustomizer.addImports( MemoryUnit.name )
+        config.addCompilationCustomizers(importCustomizer)
 
         // -- setup the grengine instance
         def engine = new Grengine(this.class.classLoader,config)

modules/nextflow/src/test/groovy/nextflow/config/parser/v1/ConfigParserV1Test.groovy

@@ -510,29 +510,40 @@ class ConfigParserV1Test extends Specification {
     }
 
     def 'should handle extend mem and duration units' () {
-        ConfigObject result
-        def CONFIG = '''
+        given:
+        def folder = File.createTempDir()
+        def configFile = new File(folder,'nextflow.config')
+
+        new File(folder,'extra.config').text = """
+            mem4 = '8GB' as MemoryUnit
+            time4 = '24h' as Duration
+            """
+
+        configFile.text = '''
             mem1 = 1.GB
             mem2 = 1_000_000.toMemory()
             mem3 = MemoryUnit.of(2_000)
             time1 = 2.hours
             time2 = 60_000.toDuration()
             time3 = Duration.of(120_000)
             flag = 10000 < 1.GB
-           '''
+
+            includeConfig 'extra.config'
+            '''
 
         when:
-        result = new ConfigParserV1()
-                .parse(CONFIG)
+        def result = new ConfigParserV1().parse(configFile)
         then:
         result.mem1 instanceof MemoryUnit
         result.mem1 == MemoryUnit.of('1 GB')
         result.mem2 == MemoryUnit.of(1_000_000)
         result.mem3 == MemoryUnit.of(2_000)
+        result.mem4 == MemoryUnit.of('8 GB')
         result.time1 instanceof Duration
         result.time1 == Duration.of('2 hours')
         result.time2 == Duration.of(60_000)
         result.time3 == Duration.of(120_000)
+        result.time4 == Duration.of('24h')
         result.flag == true
     }
 

modules/nextflow/src/test/groovy/nextflow/config/parser/v2/ConfigParserV2Test.groovy

@@ -456,29 +456,40 @@ class ConfigParserV2Test extends Specification {
     }
 
     def 'should handle extend mem and duration units' () {
-        ConfigObject result
-        def CONFIG = '''
+        given:
+        def folder = File.createTempDir()
+        def configFile = new File(folder,'nextflow.config')
+
+        new File(folder,'extra.config').text = """
+            mem4 = '8GB' as MemoryUnit
+            time4 = '24h' as Duration
+            """
+
+        configFile.text = '''
             mem1 = 1.GB
             mem2 = 1_000_000.toMemory()
             mem3 = MemoryUnit.of(2_000)
             time1 = 2.hours
             time2 = 60_000.toDuration()
             time3 = Duration.of(120_000)
             flag = 10000 < 1.GB
+
+            includeConfig 'extra.config'
             '''
 
         when:
-        result = new ConfigParserV2()
-                .parse(CONFIG)
+        def result = new ConfigParserV2().parse(configFile)
         then:
         result.mem1 instanceof MemoryUnit
         result.mem1 == MemoryUnit.of('1 GB')
         result.mem2 == MemoryUnit.of(1_000_000)
         result.mem3 == MemoryUnit.of(2_000)
+        result.mem4 == MemoryUnit.of('8 GB')
         result.time1 instanceof Duration
         result.time1 == Duration.of('2 hours')
         result.time2 == Duration.of(60_000)
         result.time3 == Duration.of(120_000)
+        result.time4 == Duration.of('24h')
         result.flag == true
     }