Improve paths validation

nextflow-io · Dec 6, 2021 · 0849d58 · 0849d58
1 parent 4daf8d0
commit 0849d58
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Showing 4 changed files with 46 additions and 2 deletions.
diff --git a/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy b/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
@@ -249,6 +249,10 @@ class FileHelper {
     static Path asPath( String str ) {
         if( !str )
             throw new IllegalArgumentException("Path string cannot be empty")
+        if( str != Bolts.leftTrim(str) )
+            throw new IllegalArgumentException("Path string cannot start with blank or a special characters -- Offending path: '${Escape.blanks(str)}'")
+        if( str != Bolts.rightTrim(str) )
+            throw new IllegalArgumentException("Path string cannot ends with blank or a special characters -- Offending path: '${Escape.blanks(str)}'")
 
         if( !str.contains(':/') ) {
             return Paths.get(str)
@@ -267,7 +271,7 @@ class FileHelper {
                 return result
         }
 
-        asPath(toPathURI(str))
+        return asPath(toPathURI(str))
     }
 
     static private Map<String,String> PLUGINS_MAP = [s3:'nf-amazon', gs:'nf-google', az:'nf-azure']

diff --git a/modules/nf-commons/src/main/nextflow/util/Escape.groovy b/modules/nf-commons/src/main/nextflow/util/Escape.groovy
@@ -95,4 +95,13 @@ class Escape {
             loc = loc.substring(0,loc.length()-1)
         return prefix + path(loc)
     }
+
+    static String blanks(String str) {
+        str
+                .replaceAll('\n',/\\n/)
+                .replaceAll('\t',/\\t/)
+                .replaceAll('\r',/\\r/)
+                .replaceAll('\f',/\\f/)
+
+    }
 }
diff --git a/modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy b/modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy
@@ -61,8 +61,26 @@ class FileHelperTest extends Specification {
         when:
         FileHelper.asPath('file://some/file.txt')
         then:
-        thrown(IllegalArgumentException)
+        def e = thrown(IllegalArgumentException)
+        e.message == 'Malformed file URI: file://some/file.txt -- It must start either with a `file:/` or `file:///` prefix'
 
+        when:
+        FileHelper.asPath('')
+        then:
+        e = thrown(IllegalArgumentException)
+        e.message == 'Path string cannot be empty'
+
+        when:
+        FileHelper.asPath('\n/some/file.txt')
+        then:
+        e = thrown(IllegalArgumentException)
+        e.message == "Path string cannot start with blank or a special characters -- Offending path: '\\n/some/file.txt'"
+
+        when:
+        FileHelper.asPath('/some/file.txt\n')
+        then:
+        e = thrown(IllegalArgumentException)
+        e.message == "Path string cannot ends with blank or a special characters -- Offending path: '/some/file.txt\\n'"
     }
 
     def 'should strip query params from http files' () {

diff --git a/modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy b/modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy
@@ -20,6 +20,7 @@ package nextflow.util
 import java.nio.file.Paths
 
 import spock.lang.Specification
+import spock.lang.Unroll
 
 /**
  *
@@ -82,4 +83,16 @@ class EscapeTest extends Specification {
         Escape.cli('nextflow','--foo','a[!b-c]') == "nextflow --foo 'a[!b-c]'"
     }
 
+    @Unroll
+    def 'should escape blanks' () {
+        expect:
+        Escape.blanks(STR) == EXPECT
+        where:
+        STR         | EXPECT
+        'foo '      | 'foo '
+        'foo\n'     | 'foo\\n'
+        'foo\t'     | 'foo\\t'
+        'foo\f'     | 'foo\\f'
+        'foo\r'     | 'foo\\r'
+    }
 }