Replace output labels with label directive (#6035)

---------

Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
Co-authored-by: Ben Sherman <[email protected]>

Author: pditommaso

docs/workflow.md

@@ -635,17 +635,14 @@ The following directives are available for each output in the output block:
   `header`
   : When `true`, the keys of the first record are used as the column names (default: `false`). Can also be a list of column names. Only used for CSV files.
 
-  `labels`
-  : Specify labels to be applied to the index file as a list of strings.
-
   `path`
   : The name of the index file relative to the base output directory (required). Can be a CSV, JSON, or YAML file.
 
   `sep`
   : The character used to separate values (default: `','`). Only used for CSV files.
 
-`labels`
-: Specify labels to be applied to every published file. Can be a list of strings or a closure that returns a list.
+`label`
+: Specify a label to be applied to every published file. Can be specified multiple times.
 
 `path`
 : Specify the publish path relative to the output directory (default: `'.'`). Can be a path, a closure that defines a custom directory for each published value, or a closure that publishes individual files using the `>>` operator.

modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy

@@ -99,7 +99,6 @@ class PublishOp {
             overrides.saveAs = targetResolver
         else
             overrides.path = targetResolver
-        overrides.labels = getLabels(publishOpts.labels, value)
 
         final publisher = PublishDir.create(publishOpts + overrides)
 
@@ -188,30 +187,6 @@ class PublishOp {
         }
     }
 
-    /**
-     * Get or resolve the labels of a workflow output.
-     *
-     * @param labels List | Closure<List>
-     * @param value
-     */
-    protected static List<String> getLabels(labels, value) {
-        if( labels == null )
-            return []
-        if( labels instanceof List<String> )
-            return labels
-        if( labels instanceof Closure ) {
-            try {
-                final result = labels.call(value)
-                if( result instanceof List<String> )
-                    return result
-            } catch (Throwable e) {
-                log.warn("Exception while evaluating dynamic `labels` directive for value '$value' -- ${e.getMessage()}")
-                return []
-            }
-        }
-        throw new ScriptRuntimeException("Invalid output `labels` directive -- it should be either a List or a closure that returns a List")
-    }
-
     /**
      * Once all channel values have been published, publish the final
      * workflow output and index file (if enabled).
@@ -242,7 +217,7 @@ class PublishOp {
             else {
                 log.warn "Invalid extension '${ext}' for index file '${indexPath}' -- should be CSV, JSON, or YAML"
             }
-            session.notifyFilePublish(new FilePublishEvent(null, indexPath, indexOpts.labels))
+            session.notifyFilePublish(new FilePublishEvent(null, indexPath, publishOpts.labels as List))
         }
 
         log.trace "Publish operator complete"
@@ -369,16 +344,13 @@ class PublishOp {
     static class IndexOpts {
         Path path
         def /* boolean | List<String> */ header = false
-        List<String> labels
         String sep = ','
 
         IndexOpts(Path targetDir, Map opts) {
             this.path = targetDir.resolve(opts.path as String)
 
             if( opts.header != null )
                 this.header = opts.header
-            if( opts.labels )
-                this.labels = opts.labels as List<String>
             if( opts.sep )
                 this.sep = opts.sep as String
         }

modules/nextflow/src/main/groovy/nextflow/script/OutputDsl.groovy

@@ -16,17 +16,12 @@
 
 package nextflow.script
 
-import java.nio.file.Path
-
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import groovyx.gpars.dataflow.DataflowWriteChannel
 import nextflow.Session
 import nextflow.exception.ScriptRuntimeException
 import nextflow.extension.CH
-import nextflow.extension.MixOp
 import nextflow.extension.PublishOp
-import nextflow.file.FileHelper
 /**
  * Implements the DSL for publishing workflow outputs
  *
@@ -133,12 +128,13 @@ class OutputDsl {
             setOption('index', dsl.getOptions())
         }
 
-        void labels(List<String> value) {
-            setOption('labels', value)
-        }
-
-        void labels(Closure value) {
-            setOption('labels', value)
+        void label(CharSequence value) {
+            final opts = getOptions()
+            final current = opts.get('labels')
+            if( current instanceof List )
+                current.add(value)
+            else
+                opts.put('labels', [value])
         }
 
         void mode(String value) {
@@ -194,10 +190,6 @@ class OutputDsl {
             setOption('header', value)
         }
 
-        void labels(List<String> value) {
-            setOption('labels', value)
-        }
-
         void path(String value) {
             setOption('path', value)
         }

modules/nextflow/src/test/groovy/nextflow/script/OutputDslTest.groovy

@@ -71,6 +71,8 @@ class OutputDslTest extends Specification {
         }
         dsl.declare('bar') {
             path { v -> "${'barbar'}" }
+            label 'foo'
+            label 'bar'
             index {
                 path 'index.csv'
             }
@@ -84,11 +86,11 @@ class OutputDslTest extends Specification {
             "${outputDir}/barbar/file2.txt"
             """.stripIndent()
         and:
-        1 * session.notifyFilePublish(new FilePublishEvent(file1, outputDir.resolve('foo/file1.txt'), []))
-        1 * session.notifyFilePublish(new FilePublishEvent(file2, outputDir.resolve('barbar/file2.txt'), []))
+        1 * session.notifyFilePublish(new FilePublishEvent(file1, outputDir.resolve('foo/file1.txt'), null))
+        1 * session.notifyFilePublish(new FilePublishEvent(file2, outputDir.resolve('barbar/file2.txt'), ['foo', 'bar']))
         1 * session.notifyWorkflowOutput(new WorkflowOutputEvent('foo', [outputDir.resolve('foo/file1.txt')], null))
         1 * session.notifyWorkflowOutput(new WorkflowOutputEvent('bar', [outputDir.resolve('barbar/file2.txt')], outputDir.resolve('index.csv')))
-        1 * session.notifyFilePublish(new FilePublishEvent(null, outputDir.resolve('index.csv'), null))
+        1 * session.notifyFilePublish(new FilePublishEvent(null, outputDir.resolve('index.csv'), ['foo', 'bar']))
 
         cleanup:
         SysEnv.pop()
@@ -125,7 +127,7 @@ class OutputDslTest extends Specification {
         then:
         outputDir.resolve('file1.txt').text == 'Hello'
         and:
-        1 * session.notifyFilePublish(new FilePublishEvent(file1, outputDir.resolve('file1.txt'), []))
+        1 * session.notifyFilePublish(new FilePublishEvent(file1, outputDir.resolve('file1.txt'), null))
         1 * session.notifyWorkflowOutput(new WorkflowOutputEvent('foo', [outputDir.resolve('file1.txt')], null))
 
         cleanup:
@@ -149,7 +151,6 @@ class OutputDslTest extends Specification {
         dsl2.overwrite(true)
         dsl2.storageClass('someClass')
         dsl2.tags([foo:'1',bar:'2'])
-        dsl2.labels(['label'])
         then:
         dsl2.getOptions() == [
             contentType:'simple/text',
@@ -159,7 +160,6 @@ class OutputDslTest extends Specification {
             overwrite: true,
             storageClass: 'someClass',
             tags: [foo:'1',bar:'2'],
-            labels: ['label']
         ]
     }
 
@@ -175,13 +175,11 @@ class OutputDslTest extends Specification {
         dsl2.header(true)
         dsl2.path('path')
         dsl2.sep(',')
-        dsl2.labels(['label'])
         then:
         dsl2.getOptions() == [
             header: true,
             path: 'path',
             sep: ',',
-            labels: ['label']
         ]
     }