add flag to allow for spaces in file names

Author: mr-c

cwltool/draft2tool.py

@@ -25,7 +25,9 @@
 from .job import CommandLineJob
 from .stdfsaccess import StdFsAccess
 
-ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
+ACCEPTLIST_EN_STRICT_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
+ACCEPTLIST_EN_RELAXED_RE = re.compile(r"^[ a-zA-Z0-9._+-]+$")  # with spaces
+ACCEPTLIST_RE = ACCEPTLIST_EN_STRICT_RE
 
 from .flatten import flatten
 

cwltool/main.py

@@ -178,6 +178,9 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="Do not compute checksum of contents while collecting outputs",
                         dest="compute_checksum")
 
+    parser.add_argument("--relax-path-checks", action="store_true",
+            default=False, help="Relax requirements on path names. Currently "
+            "allows spaces.", dest="relax_path_checks")
     parser.add_argument("workflow", type=Text, nargs="?", default=None)
     parser.add_argument("job_order", nargs=argparse.REMAINDER)
 
@@ -616,6 +619,8 @@ def main(argsl=None,
                 _logger.error("")
                 _logger.error("CWL document required, try --help for details")
                 return 1
+        if args.relax_path_checks:
+            draft2tool.ACCEPTLIST_RE = draft2tool.ACCEPTLIST_EN_RELAXED_RE
 
         try:
             document_loader, workflowobj, uri = fetch_document(args.workflow, resolver=tool_resolver)

tests/test_relax_path_checks.py

@@ -0,0 +1,39 @@
+import unittest
+from tempfile import NamedTemporaryFile
+from cwltool.main import main
+
+
+class ToolArgparse(unittest.TestCase):
+
+
+    script='''
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+  - id: input
+    type: File
+    inputBinding:
+      position: 0
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: test.txt
+stdout: test.txt
+baseCommand: [cat]
+'''
+
+    def test_spaces_in_input_files(self):
+        with NamedTemporaryFile() as f:
+            f.write(self.script)
+            f.flush()
+            with NamedTemporaryFile(prefix="test with spaces") as spaces:
+                self.assertEquals(
+                    main(["--debug", f.name, '--input', spaces.name]), 1)
+                self.assertEquals(
+                    main(["--debug", "--relax-path-checks", f.name, '--input',
+                        spaces.name]), 0)
+
+if __name__ == '__main__':
+    unittest.main()