Fix special chars escaping in container env

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

Author: pditommaso

modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy

@@ -100,6 +100,7 @@ import nextflow.script.params.ValueOutParam
 import nextflow.util.ArrayBag
 import nextflow.util.BlankSeparatedList
 import nextflow.util.CacheHelper
+import nextflow.util.Escape
 import nextflow.util.LockManager
 import nextflow.util.LoggerHelper
 import nextflow.util.TestOnly
@@ -1961,7 +1962,7 @@ class TaskProcessor {
             }
             else {
                 // escape both wrapping double quotes and the dollar var placeholder
-                script << /export $name="${value.replace('$','\\$')}"/
+                script << /export $name="${Escape.variable(value)}"/
             }
         }
         script << ''

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

@@ -986,8 +986,8 @@ class BashWrapperBuilderTest extends Specification {
                 nxf_container_env() {
                 cat << EOF
                 export FOO="hello"
-                export BAR="hello world"
-                export PATH="/some/path:\\$PATH"
+                export BAR="hello\\ world"
+                export PATH="/some/path\\:\\$PATH"
                 EOF
                 }
                 '''

modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy

@@ -779,9 +779,12 @@ class TaskProcessorTest extends Specification {
                 .stripIndent().leftTrim()
 
         when:
-        env = TaskProcessor.bashEnvironmentScript([PATH: 'foo:$PATH'], true)
+        env = TaskProcessor.bashEnvironmentScript([PATH: 'foo:$PATH', HOLA: 'one|two'], true)
         then:
-        env.trim() == 'export PATH="foo:\\$PATH"'
+        env == '''\
+            export PATH="foo\\:\\$PATH"
+            export HOLA="one\\|two"
+            '''.stripIndent()
         env.charAt(env.size()-1) == '\n' as char
 
         when:

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

@@ -32,6 +32,8 @@ class Escape {
 
     private static List<String> SPECIAL_CHARS = ["'", '"', ' ', '(', ')', '\\', '!', '&', '|', '<', '>', '`', ':']
 
+    private static List<String> SPECIAL_CHARS_DOLLAR = SPECIAL_CHARS + ['$']
+
     private static List<String> WILDCARDS = ["*", "?", "{", "}", "[", "]", "'", '"', ' ', '(', ')', '\\', '!', '&', '|', '<', '>', '`', ':']
 
     private static String replace(List<String> special, String str, boolean doNotEscapeComplement=false) {
@@ -104,4 +106,8 @@ class Escape {
                 .replaceAll('\f',/\\f/)
 
     }
+
+    static String variable(String val) {
+        replace(SPECIAL_CHARS_DOLLAR, val, false)
+    }
 }

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

@@ -95,4 +95,24 @@ class EscapeTest extends Specification {
         'foo\f'     | 'foo\\f'
         'foo\r'     | 'foo\\r'
     }
+
+    def 'should escape special char' () {
+        expect:
+        Escape.variable(STR) == EXPECT
+        where:
+        STR         | EXPECT
+        'foo'       | 'foo'
+        'foo[x]bar' | 'foo[x]bar'
+        and:
+        'foo '      | 'foo\\ '
+        '$foo'      | '\\$foo'
+        'foo|bar'   | 'foo\\|bar'
+        'foo`bar'   | 'foo\\`bar'
+        'foo&bar'   | 'foo\\&bar'
+        'foo:bar'   | 'foo\\:bar'
+        'foo!bar'   | 'foo\\!bar'
+        'foo[!x]bar'| 'foo[\\!x]bar'
+        'foo(x)bar' | 'foo\\(x\\)bar'
+        'foo<x>bar' | 'foo\\<x\\>bar'
+    }
 }