split to #27

Author: maxulysse

src/main/groovy/nfcore/plugin/NfcorePipelineObserver.groovy

@@ -44,12 +44,12 @@ class NfcorePipelineObserver implements TraceObserver {
         }
         configValidator.checkConfigProvided(projectName, config)
         configValidator.checkProfileProvided(session.profile, session.commandLine, true)
-        log.trace "Pipeline is starting! 🚀"
+        println "Pipeline is starting! 🚀"
     }
 
     @Override
     void onFlowComplete() {
-        log.trace "Pipeline complete! 👋"
+        println "Pipeline complete! 👋"
         // TODO dumpParametersToJSON(session.params.outdir, session.params)
     }
 }

src/test/groovy/nfcore/plugin/NfcorePipelineObserverTest.groovy

@@ -1,11 +1,6 @@
 package nfcore.plugin
 
-import ch.qos.logback.classic.Level
-import ch.qos.logback.classic.Logger
-import ch.qos.logback.classic.spi.ILoggingEvent
-import ch.qos.logback.core.read.ListAppender
 import nfcore.plugin.nfcore.NfcoreConfigValidator
-import org.slf4j.LoggerFactory
 import spock.lang.PendingFeature
 import spock.lang.Specification
 
@@ -33,27 +28,7 @@ class NfcorePipelineObserverTest extends Specification {
         1 * validator.checkProfileProvided('standard', '--foo bar', true)
     }
 
-    @PendingFeature()
-    def 'onFlowCreate handles missing metadata gracefully'() {
-        given:
-        def validator = Spy(NfcoreConfigValidator)
-        def observer = new NfcorePipelineObserver(validator)
-        def session = Mock(nextflow.Session) {
-            workflowMetadata >> null
-            config >> [profile: 'standard', configFiles: []]
-            profile >> 'standard'
-            commandLine >> ''
-        }
-
-        when:
-        observer.onFlowCreate(session)
-
-        then:
-        1 * validator.checkConfigProvided(null, { it.profile == 'standard' && it.configFiles == [] })
-        1 * validator.checkProfileProvided('standard', '', true)
-    }
-
-    def 'onFlowCreate should log start message at TRACE level'() {
+    def 'onFlowCreate should print the start message'() {
         given:
         def observer = new NfcorePipelineObserver()
         def session = Mock(nextflow.Session) {
@@ -62,102 +37,56 @@ class NfcorePipelineObserverTest extends Specification {
             profile >> 'standard'
             commandLine >> ''
         }
-
-        // Set up logging capture
-        Logger logger = (Logger) LoggerFactory.getLogger(NfcorePipelineObserver)
-        ListAppender<ILoggingEvent> listAppender = new ListAppender<>()
-        listAppender.start()
-        logger.addAppender(listAppender)
-        def originalLevel = logger.level
-        logger.setLevel(Level.TRACE)
+        def out = new ByteArrayOutputStream()
+        def oldOut = System.out
+        System.out = new PrintStream(out)
 
         when:
         observer.onFlowCreate(session)
+        System.out.flush()
 
         then:
-        def logEvents = listAppender.list
-        logEvents.any { it.level == Level.TRACE && it.message.contains('Pipeline is starting! 🚀') }
+        out.toString().contains('Pipeline is starting! 🚀')
 
         cleanup:
-        logger.setLevel(originalLevel)
-        logger.detachAppender(listAppender)
+        System.out = oldOut
     }
 
-    def 'onFlowComplete should log complete message at TRACE level'() {
+    def 'onFlowComplete should print the complete message'() {
         given:
         def observer = new NfcorePipelineObserver()
-
-        // Set up logging capture
-        Logger logger = (Logger) LoggerFactory.getLogger(NfcorePipelineObserver)
-        ListAppender<ILoggingEvent> listAppender = new ListAppender<>()
-        listAppender.start()
-        logger.addAppender(listAppender)
-        def originalLevel = logger.level
-        logger.setLevel(Level.TRACE)
+        def out = new ByteArrayOutputStream()
+        def oldOut = System.out
+        System.out = new PrintStream(out)
 
         when:
         observer.onFlowComplete()
+        System.out.flush()
 
         then:
-        def logEvents = listAppender.list
-        logEvents.any { it.level == Level.TRACE && it.message.contains('Pipeline complete! 👋') }
+        out.toString().contains('Pipeline complete! 👋')
 
         cleanup:
-        logger.setLevel(originalLevel)
-        logger.detachAppender(listAppender)
+        System.out = oldOut
     }
 
-    def 'onFlowCreate should NOT log start message below TRACE level'() {
+    @PendingFeature()
+    def 'onFlowCreate handles missing metadata gracefully'() {
         given:
-        def observer = new NfcorePipelineObserver()
+        def validator = Spy(NfcoreConfigValidator)
+        def observer = new NfcorePipelineObserver(validator)
         def session = Mock(nextflow.Session) {
-            workflowMetadata >> [projectName: 'test-pipeline']
-            config >> [:]
+            workflowMetadata >> null
+            config >> [profile: 'standard', configFiles: []]
             profile >> 'standard'
             commandLine >> ''
         }
 
-        // Set up logging capture with DEBUG level
-        Logger logger = (Logger) LoggerFactory.getLogger(NfcorePipelineObserver)
-        ListAppender<ILoggingEvent> listAppender = new ListAppender<>()
-        listAppender.start()
-        logger.addAppender(listAppender)
-        def originalLevel = logger.level
-        logger.setLevel(Level.DEBUG)
-
         when:
         observer.onFlowCreate(session)
 
         then:
-        def logEvents = listAppender.list
-        !logEvents.any { it.message.contains('Pipeline is starting! 🚀') }
-
-        cleanup:
-        logger.setLevel(originalLevel)
-        logger.detachAppender(listAppender)
-    }
-
-    def 'onFlowComplete should NOT log complete message below TRACE level'() {
-        given:
-        def observer = new NfcorePipelineObserver()
-
-        // Set up logging capture with DEBUG level
-        Logger logger = (Logger) LoggerFactory.getLogger(NfcorePipelineObserver)
-        ListAppender<ILoggingEvent> listAppender = new ListAppender<>()
-        listAppender.start()
-        logger.addAppender(listAppender)
-        def originalLevel = logger.level
-        logger.setLevel(Level.DEBUG)
-
-        when:
-        observer.onFlowComplete()
-
-        then:
-        def logEvents = listAppender.list
-        !logEvents.any { it.message.contains('Pipeline complete! 👋') }
-
-        cleanup:
-        logger.setLevel(originalLevel)
-        logger.detachAppender(listAppender)
+        1 * validator.checkConfigProvided(null, { it.profile == 'standard' && it.configFiles == [] })
+        1 * validator.checkProfileProvided('standard', '', true)
     }
 }