Fix default fields in trace config (#6403)

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

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/trace/TraceFileObserver.groovy

@@ -30,7 +30,6 @@ import nextflow.processor.TaskHandler
 import nextflow.processor.TaskId
 import nextflow.trace.config.TraceConfig
 import nextflow.trace.event.TaskEvent
-import nextflow.util.TestOnly
 /**
  * Create a CSV file containing the processes execution information
  *
@@ -43,22 +42,7 @@ class TraceFileObserver implements TraceObserverV2 {
     /**
      * The list of fields included in the trace report
      */
-    List<String> fields = [
-            'task_id',
-            'hash',
-            'native_id',
-            'name',
-            'status',
-            'exit',
-            'submit',
-            'duration',
-            'realtime',
-            '%cpu',
-            'peak_rss',
-            'peak_vmem',
-            'rchar',
-            'wchar'
-    ]
+    List<String> fields
 
     List<String> formats
 
@@ -99,9 +83,6 @@ class TraceFileObserver implements TraceObserverV2 {
         setFieldsAndFormats(config.fields)
     }
 
-    @TestOnly
-    protected TraceFileObserver() {}
-
     void setFields( List<String> entries ) {
 
         final names = TraceRecord.FIELDS.keySet()
@@ -126,17 +107,7 @@ class TraceFileObserver implements TraceObserverV2 {
         this.fields = result
     }
 
-    TraceFileObserver setFieldsAndFormats( value ) {
-        List<String> entries
-        if( value instanceof String ) {
-            entries = value.tokenize(', ')
-        }
-        else if( value instanceof List ) {
-            entries = (List)value
-        }
-        else {
-            throw new IllegalArgumentException("Not a valid trace fields value: $value")
-        }
+    TraceFileObserver setFieldsAndFormats( List<String> entries ) {
 
         List<String> fields = new ArrayList<>(entries.size())
         List<String> formats = new ArrayList<>(entries.size())

modules/nextflow/src/main/groovy/nextflow/trace/config/TraceConfig.groovy

@@ -29,17 +29,34 @@ import nextflow.trace.TraceHelper
 @CompileStatic
 class TraceConfig implements ConfigScope {
 
+    private static final List<String> DEF_FIELDS = List.of(
+        'task_id',
+        'hash',
+        'native_id',
+        'name',
+        'status',
+        'exit',
+        'submit',
+        'duration',
+        'realtime',
+        '%cpu',
+        'peak_rss',
+        'peak_vmem',
+        'rchar',
+        'wchar'
+    )
+
     @ConfigOption
     @Description("""
         Create the execution trace file on workflow completion (default: `false`).
     """)
     final boolean enabled
 
-    @ConfigOption
+    @ConfigOption(types=[String])
     @Description("""
         Comma-separated list of [trace fields](https://nextflow.io/docs/latest/tracing.html#trace-report) to include in the report.
     """)
-    final String fields
+    final List<String> fields
 
     @ConfigOption
     @Description("""
@@ -70,13 +87,23 @@ class TraceConfig implements ConfigScope {
 
     TraceConfig(Map opts) {
         enabled = opts.enabled as boolean
-        fields = opts.fields ?: ''
+        fields = parseFields(opts.fields)
         file = opts.file ?: defaultFileName()
         overwrite = opts.overwrite as boolean
         raw = opts.raw as boolean
         sep = opts.sep ?: '\t'
     }
 
+    private List<String> parseFields(value) {
+        if( value == null )
+            return DEF_FIELDS
+        if( value instanceof CharSequence )
+            return value.tokenize(',').collect(it -> it.trim())
+        if( value instanceof List )
+            return value
+        throw new IllegalArgumentException("Not a valid trace fields value: $value")
+    }
+
     static final String defaultFileName() {
         return "trace-${TraceHelper.launchTimestampFmt()}.txt"
     }

modules/nextflow/src/test/groovy/nextflow/trace/TraceFileObserverTest.groovy

@@ -26,6 +26,7 @@ import nextflow.processor.TaskId
 import nextflow.processor.TaskProcessor
 import nextflow.processor.TaskRun
 import nextflow.processor.TaskStatus
+import nextflow.trace.config.TraceConfig
 import nextflow.trace.event.TaskEvent
 import nextflow.util.CacheHelper
 import nextflow.util.Duration
@@ -43,16 +44,21 @@ class TraceFileObserverTest extends Specification {
         TraceRecord.TIMEZONE = TimeZone.getTimeZone('UTC') // note: set the timezone to be sure the time string does not change on CI test servers
     }
 
+    def createObserver() {
+        def config = new TraceConfig([:])
+        return new TraceFileObserver(config)
+    }
+
     def 'test set fields'() {
 
         when:
-        def trace = [:] as TraceFileObserver
+        def trace = createObserver()
         trace.fields = ['task_id','name','status']
         then:
         trace.fields ==  ['task_id','name','status']
 
         when:
-        trace = [:] as TraceFileObserver
+        trace = createObserver()
         trace.fields = ['task_id','name','status','xxx']
         then:
         thrown(IllegalArgumentException)
@@ -63,7 +69,7 @@ class TraceFileObserverTest extends Specification {
     def 'test set formats'() {
 
         when:
-        def trace = [:] as TraceFileObserver
+        def trace = createObserver()
         trace.formats = ['str','num','date']
         then:
         trace.formats == ['str','num','date']
@@ -75,14 +81,14 @@ class TraceFileObserverTest extends Specification {
         def trace
 
         when:
-        trace = [:] as TraceFileObserver
+        trace = createObserver()
         trace.setFieldsAndFormats(['task_id:str','name:str','status:num', 'start', 'duration'])
         then:
         trace.fields ==  ['task_id','name','status', 'start', 'duration']
         trace.formats == ['str','str','num', 'date', 'time']
 
         when:
-        trace = [:] as TraceFileObserver
+        trace = createObserver()
         trace.useRawNumbers(true)
         trace.setFieldsAndFormats(['task_id:str','name:str','status:num', 'start:date', 'duration:time', 'realtime'])
         then:
@@ -109,7 +115,8 @@ class TraceFileObserverTest extends Specification {
         def now = System.currentTimeMillis()
 
         // the observer class under test
-        def observer = new TraceFileObserver(tracePath: file)
+        def config = new TraceConfig(file: file.toString())
+        def observer = new TraceFileObserver(config)
 
         when:
         observer.onFlowCreate(null)
@@ -190,7 +197,7 @@ class TraceFileObserverTest extends Specification {
         record.wchar = 10_000 * 1024
 
         when:
-        def trace = [:] as TraceFileObserver
+        def trace = createObserver()
         def result = trace.render(record).split('\t')
         then:
         result[0] == '30'                       // task id
@@ -221,8 +228,8 @@ class TraceFileObserverTest extends Specification {
         record.rss = 10 * MB
 
         when:
-        def trace = [:] as TraceFileObserver
-        trace.setFieldsAndFormats( 'task_id,syscr,syscw,rss,rss:num' )
+        def trace = createObserver()
+        trace.setFieldsAndFormats( ['task_id', 'syscr', 'syscw', 'rss', 'rss:num'] )
         def result = trace.render(record).split('\t')
         then:
         result[0] == '5'
@@ -261,8 +268,8 @@ class TraceFileObserverTest extends Specification {
         record.realtime = 9005022
         record.queue = 'bigjobs'
 
-        def trace = [:] as TraceFileObserver
-        trace.setFieldsAndFormats('task_id,hash,native_id,name,status,exit,submit,duration,realtime,%cpu,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,duration:num,realtime:num,rss:num,vmem:num,peak_rss:num,peak_vmem:num,rchar:num,wchar:num,queue')
+        def trace = createObserver()
+        trace.setFieldsAndFormats(['task_id', 'hash', 'native_id', 'name', 'status', 'exit', 'submit', 'duration', 'realtime', '%cpu', 'rss', 'vmem', 'peak_rss', 'peak_vmem', 'rchar', 'wchar', 'syscr', 'syscw', 'duration:num', 'realtime:num', 'rss:num', 'vmem:num', 'peak_rss:num', 'peak_vmem:num', 'rchar:num', 'wchar:num', 'queue'])
         def result = trace.render(record).split('\t')
 
         then: