Add warning on publish with a null var

nextflow-io · Apr 10, 2019 · 7d58bfb · 7d58bfb
1 parent b2cfb66
commit 7d58bfb
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diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
@@ -88,11 +88,14 @@ class PublishDir {
 
     private String stageInMode
 
+    private boolean nullPathWarn
+
     void setPath( Closure obj ) {
         setPath( obj.call() as Path )
     }
 
     void setPath( String str ) {
+        nullPathWarn = checkNull(str)
         setPath(str as Path)
     }
 
@@ -108,6 +111,10 @@ class PublishDir {
         this.mode = mode
     }
 
+    @PackageScope boolean checkNull(String str) {
+        ( str =~ /\bnull\b/  ).find()
+    }
+
     /**
      * Object factory method
      *
@@ -154,6 +161,9 @@ class PublishDir {
         if( !path )
             throw new IllegalStateException("Target path for directive publishDir cannot be null")
 
+        if( nullPathWarn )
+            log.warn "Process `$task.processor.name` publishDir path contains a variable with a null value"
+
         this.processor = task.processor
         this.sourceDir = task.targetDir
         this.sourceFileSystem = sourceDir.fileSystem

diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/PublishDirTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/PublishDirTest.groovy
@@ -279,4 +279,15 @@ class PublishDirTest extends Specification {
         then:
         publisher.mode == PublishDir.Mode.COPY
     }
+
+    def 'should check null path' () {
+        given:
+        def pub = new PublishDir()
+
+        expect:
+        !pub.checkNull('ciao')
+        pub.checkNull('null')
+        pub.checkNull('null-x')
+        pub.checkNull(' null')
+    }
 }