Fix matching symlink files

This commit fixes that matches of symlink files when the output
followLinks option is set to false.

Prior this fix symlinks where discarded when glob pattern was
matching the name of the link file.

However the correct behavior is that the file should be included
in the result set as file the represents the symlink.

Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

modules/nextflow/src/test/groovy/nextflow/NextflowTest.groovy

@@ -204,7 +204,7 @@ class NextflowTest extends Specification {
         when:
         result = Nextflow.files("$folder/**.fa", relative: true, followLinks: false)
         then:
-        result.collect { it.toString() } .sort() == ['dir1/dir2/file4.fa', 'file2.fa']
+        result.collect { it.toString() } .sort() == ['dir1/dir2/file4.fa', 'file2.fa', 'file_link.fa']
 
         when:
         result = Nextflow.files("$folder/**.fa", relative: true, maxDepth: 1)
@@ -227,8 +227,10 @@ class NextflowTest extends Specification {
         then:
         result.collect { it.toString() } .sort() == ['dir1/dir2/file4.fa',
                                                      'dir1/file3.txt',
+                                                     'dir_link',
                                                      'file1.txt',
-                                                     'file2.fa']
+                                                     'file2.fa',
+                                                     'file_link.fa']
 
         when:
         result = Nextflow.files("$folder/**", relative: true, type:'dir')
@@ -252,8 +254,10 @@ class NextflowTest extends Specification {
                                                      'dir1/dir2',
                                                      'dir1/dir2/file4.fa',
                                                      'dir1/file3.txt',
+                                                     'dir_link',
                                                      'file1.txt',
-                                                     'file2.fa']
+                                                     'file2.fa',
+                                                     'file_link.fa']
 
         cleanup:
         folder?.deleteDir()

modules/nf-commons/src/main/nextflow/file/FileHelper.groovy

@@ -795,14 +795,15 @@ class FileHelper {
         assert filePattern
         assert action
 
-        final type = options?.type ?: 'any'
-        final walkOptions = options?.followLinks == false ? EnumSet.noneOf(FileVisitOption.class) : EnumSet.of(FileVisitOption.FOLLOW_LINKS)
-        final int maxDepth = getMaxDepth(options?.maxDepth, filePattern)
-        final includeHidden = options?.hidden as Boolean ?: filePattern.startsWith('.')
+        if( options==null ) options = Map.of()
+        final type = options.type ?: 'any'
+        final walkOptions = options.followLinks == false ? EnumSet.noneOf(FileVisitOption.class) : EnumSet.of(FileVisitOption.FOLLOW_LINKS)
+        final int maxDepth = getMaxDepth(options.maxDepth, filePattern)
+        final includeHidden = options.hidden as Boolean ?: filePattern.startsWith('.')
         final includeDir = type in ['dir','any']
         final includeFile = type in ['file','any']
-        final syntax = options?.syntax ?: 'glob'
-        final relative = options?.relative == true
+        final syntax = options.syntax ?: 'glob'
+        final relative = options.relative == true
 
         final matcher = getPathMatcherFor("$syntax:${filePattern}", folder.fileSystem)
         final singleParam = action.getMaximumNumberOfParameters() == 1
@@ -828,7 +829,7 @@ class FileHelper {
                 final path = folder.relativize(fullPath)
                 log.trace "visitFiles > file=$path; includeFile=$includeFile; matches=${matcher.matches(path)}; isRegularFile=${attrs.isRegularFile()}"
 
-                if (includeFile && matcher.matches(path) && attrs.isRegularFile() && (includeHidden || !isHidden(fullPath))) {
+                if (includeFile && matcher.matches(path) && (attrs.isRegularFile() || (options.followLinks == false && attrs.isSymbolicLink())) && (includeHidden || !isHidden(fullPath))) {
                     def result = relative ? path : fullPath
                     singleParam ? action.call(result) : action.call(result,attrs)
                 }

modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy

@@ -463,18 +463,26 @@ class FileHelperTest extends Specification {
         Files.createSymbolicLink(
                 folder.resolve('file4.fa'),
                 folder.resolve('file3.bam'))
+        and:
+        folder.resolve('subdir_real').mkdirs()
+        folder.resolve('subdir_real/file5.fa').text = 'file 5'
+        and:
+        Files.createSymbolicLink(
+                folder.resolve('subdir_link'),
+                folder.resolve('subdir_real'))
 
         when:
         def result = []
-        FileHelper.visitFiles(folder, '*.fa', relative: true) { result << it.toString() }
+        FileHelper.visitFiles(folder, '**.fa', relative: true) { result << it.toString() }
         then:
-        result.sort() == ['file2.fa','file4.fa']
+        result.sort() == ['file2.fa','file4.fa','subdir_link/file5.fa', 'subdir_real/file5.fa']
 
         when:
         result = []
-        FileHelper.visitFiles(folder, '*.fa', relative: true, followLinks: false) { result << it.toString() }
+        FileHelper.visitFiles(folder, '**.fa', relative: true, followLinks: false) { result << it.toString() }
         then:
-        result.sort() == ['file2.fa']
+        // note: "file4.fa" is included in the result because it matches the name of the symlink file
+        result.sort() == ['file2.fa','file4.fa','subdir_real/file5.fa']
 
         cleanup:
         folder?.deleteDir()