Don't mark inputs (or outputs) executable for no reason (#4728)

* Be explicit about executable representation

* Add testing to make sure outputs aren't unexpecteldy executable

* Let js expressions in the scatters take a long time to start Node

---------

Co-authored-by: Lon Blauvelt <[email protected]>

src/toil/fileStores/__init__.py

@@ -40,7 +40,7 @@ def __init__(self, fileStoreID: str, size: int, executable: bool = False) -> Non
 
     def pack(self) -> str:
         """Pack the FileID into a string so it can be passed through external code."""
-        return f'{self.size}:{int(self.executable)}:{self}'
+        return f'{self.size}:{"1" if self.executable else "0"}:{self}'
 
     @classmethod
     def forPath(cls, fileStoreID: str, filePath: str) -> 'FileID':
@@ -54,7 +54,7 @@ def unpack(cls, packedFileStoreID: str) -> 'FileID':
         vals = packedFileStoreID.split(':', 2)
         # Break up the packed value
         size = int(vals[0])
-        executable = bool(vals[1])
+        executable = (vals[1] == "1")
         value = vals[2]
         # Create the FileID
         return cls(value, size, executable)

src/toil/test/cwl/cwlTest.py

@@ -17,6 +17,7 @@
 import os
 import re
 import shutil
+import stat
 import subprocess
 import sys
 import unittest
@@ -136,6 +137,8 @@ def run_conformance_tests(
             "--statusWait=10",
             "--retryCount=2",
             "--relax-path-checks",
+            # Defaults to 20s but we can't start hundreds of nodejs processes that fast on our CI potatoes
+            "--eval-timeout=600",
             f"--caching={caching}"
         ]
 
@@ -254,6 +257,13 @@ def _tester(self, cwlfile, jobfile, expect, main_args=[], out_name="output", out
         out.get(out_name, {}).pop("nameroot", None)
         self.assertEqual(out, expect)
 
+        for k, v in expect.items():
+            if isinstance(v, dict) and "class" in v and v["class"] == "File" and "path" in v:
+                # This is a top-level output file.
+                # None of our output files should be executable.
+                self.assertTrue(os.path.exists(v["path"]))
+                self.assertFalse(os.stat(v["path"]).st_mode & stat.S_IXUSR)
+
     def _debug_worker_tester(self, cwlfile, jobfile, expect):
         from toil.cwl import cwltoil