Fix glob resolution for remove files

Signed-off-by: Paolo Di Tommaso <[email protected]>
nextflow-io · Jul 31, 2023 · 19a72c4 · 19a72c4
1 parent f2a2ea3
commit 19a72c4
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Showing 3 changed files with 16 additions and 2 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy b/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy
@@ -18,6 +18,7 @@ package nextflow
 
 import static nextflow.file.FileHelper.*
 
+import java.nio.file.FileSystem
 import java.nio.file.Files
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
@@ -60,7 +61,8 @@ class Nextflow {
     static private fileNamePattern( FilePatternSplitter splitter, Map opts ) {
 
         final scheme = splitter.scheme
-        final folder = toCanonicalPath(splitter.parent)
+        final target = scheme ? "$scheme://$splitter.parent" : splitter.parent
+        final folder = toCanonicalPath(target)
         final pattern = splitter.fileName
 
         if( opts == null ) opts = [:]

diff --git a/modules/nf-commons/src/test/nextflow/file/FilePatternSplitterTest.groovy b/modules/nf-commons/src/test/nextflow/file/FilePatternSplitterTest.groovy
@@ -112,7 +112,8 @@ class FilePatternSplitterTest extends Specification {
         'test/data/file[a-b]'                   | 'test/data/'      | 'file[a-b]'           | null
         'test/data[a-b]/file'                   | 'test/'           | 'data[a-b]/file'      | null
         '/some/path\\[a-b\\]/data{a,b}/file\\?' | '/some/path[a-b]/'| 'data{a,b}/file\\?'   | null
-
+        's3://foo/bar/*'                        | 'foo/bar/'        | '*'                   | 's3'
+        's3://foo/bar/file.txt'                 | 'foo/bar/'        | 'file.txt'            | 's3'
     }
 
     def 'should strip glob escape chars' () {

diff --git a/plugins/nf-amazon/src/test/nextflow/S3NextflowTest.groovy b/plugins/nf-amazon/src/test/nextflow/S3NextflowTest.groovy
@@ -19,6 +19,8 @@ package nextflow
 
 import java.nio.file.Paths
 
+import spock.lang.IgnoreIf
+import spock.lang.Requires
 import spock.lang.Specification
 /**
  *
@@ -46,4 +48,13 @@ class S3NextflowTest extends Specification {
         SysEnv.pop()
     }
 
+    @IgnoreIf({System.getenv('NXF_SMOKE')})
+    @Requires({System.getenv('AWS_S3FS_ACCESS_KEY') && System.getenv('AWS_S3FS_SECRET_KEY')})
+    def 'should resolve list of files' () {
+        when:
+        def result = Nextflow.files('s3://ngi-igenomes/*')
+        then:
+        result.size() == 3
+    }
+
 }