Tests for unstage strategy and fix for special characters

modules/nextflow/src/main/groovy/nextflow/executor/SimpleFileCopyStrategy.groovy

@@ -168,14 +168,17 @@ class SimpleFileCopyStrategy implements ScriptFileCopyStrategy {
 
         final escape = new ArrayList(outputFiles.size())
         for( String it : patterns )
-            escape.add( Escape.path(it) )
+            escape.add( Escape.path( it, true ) )
 
         final mode = stageoutMode ?: ( workDir==targetDir ? 'copy' : 'move' )
         return """\
             IFS=\$'\\n'
-            for name in \$(eval "ls -1d ${escape.join(' ')}" | sort | uniq); do
+            pathes=`ls -1d ${escape.join(' ')} | sort | uniq`
+            set -f
+            for name in \$pathes; do
                 ${stageOutCommand('$name', targetDir, mode)} || true
             done
+            set +f
             unset IFS""".stripIndent(true)
     }
 

modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy

@@ -408,9 +408,12 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.unstage_outputs == '''\
                 IFS=$'\\n'
-                for name in $(eval "ls -1d test.bam test.bai" | sort | uniq); do
+                pathes=`ls -1d test.bam test.bai | sort | uniq`
+                set -f
+                for name in $pathes; do
                     nxf_fs_copy "$name" /work/dir || true
                 done
+                set +f
                 unset IFS
                 '''.stripIndent().rightTrim()
 
@@ -425,9 +428,12 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.unstage_outputs == '''\
                 IFS=$'\\n'
-                for name in $(eval "ls -1d test.bam test.bai" | sort | uniq); do
+                pathes=`ls -1d test.bam test.bai | sort | uniq`
+                set -f
+                for name in $pathes; do
                     nxf_fs_move "$name" /another/dir || true
                 done
+                set +f
                 unset IFS
                 '''.stripIndent().rightTrim()
     }

modules/nf-commons/src/main/nextflow/util/Escape.groovy

@@ -55,7 +55,11 @@ class Escape {
         replace(WILDCARDS, str)
     }
 
-    static String path(String val) {
+    static String path(String val, boolean glob = false) {
+        List<String> SPECIAL_CHARS = Escape.SPECIAL_CHARS
+        if ( glob ){
+            SPECIAL_CHARS = SPECIAL_CHARS.findAll {it != '\\' }
+        }
         replace(SPECIAL_CHARS, val, true)
     }
 

modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy

@@ -70,6 +70,16 @@ class EscapeTest extends Specification {
         Escape.wildcards('file_[!a].txt') == 'file_\\[\\!a\\].txt'
     }
 
+    def 'should ignore globs in file names' () {
+
+        expect:
+        Escape.path('hell?.txt', true ) == "hell?.txt"
+        Escape.path('hell\\?.txt', true ) == "hell\\?.txt"
+        Escape.path('hell*.txt', true ) == "hell*.txt"
+        Escape.path('hell**.txt', true ) == "hell**.txt"
+
+    }
+
     def 'should escape cli' () {
         expect: 
         Escape.cli('nextflow','run','this') == 'nextflow run this'

plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy

@@ -58,9 +58,12 @@ class BashWrapperBuilderWithS3Test extends Specification {
         then:
         binding.unstage_outputs == '''\
                     IFS=$'\\n'
-                    for name in $(eval "ls -1d test.bam test.bai" | sort | uniq); do
+                    pathes=`ls -1d test.bam test.bai | sort | uniq`
+                    set -f
+                    for name in $pathes; do
                         nxf_s3_upload '$name' s3://some/bucket || true
                     done
+                    set +f
                     unset IFS
                     '''.stripIndent().rightTrim()
 

plugins/nf-azure/src/test/nextflow/executor/BashWrapperBuilderWithAzTest.groovy

@@ -46,9 +46,12 @@ class BashWrapperBuilderWithAzTest extends Specification {
         then:
         binding.unstage_outputs == """\
                     IFS=\$'\\n'
-                    for name in \$(eval "ls -1d test.bam test.bai" | sort | uniq); do
+                    pathes=`ls -1d test.bam test.bai | sort | uniq`
+                    set -f
+                    for name in \$pathes; do
                         nxf_az_upload '\$name' '${AzHelper.toHttpUrl(target)}' || true
                     done
+                    set +f
                     unset IFS
                     """.stripIndent().rightTrim()