18994: Fix for colon characters in filenames

[arvados.git] / sdk / cwl / arvados_cwl / executor.py

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index aa19633d8c7e86067a02d823d0c638abb318ad4d..5f24d2407d1ad727a9aa534382973399f89b0090 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -18,6 +18,7 @@ import json
 import re
 from functools import partial
 import time
+import urllib
 
 from cwltool.errors import WorkflowException
 import cwltool.workflow
@@ -450,7 +451,7 @@ The 'jobs' API is no longer supported.
             srccollection = sp[0][5:]
             try:
                 reader = self.collection_cache.get(srccollection)
-                srcpath = "/".join(sp[1:]) if len(sp) > 1 else "."
+                srcpath = urllib.parse.unquote("/".join(sp[1:]) if len(sp) > 1 else ".")
                 final.copy(srcpath, v.target, source_collection=reader, overwrite=False)
             except arvados.errors.ArgumentError as e:
                 logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
@@ -577,8 +578,8 @@ The 'jobs' API is no longer supported.
 
         loadingContext = self.loadingContext.copy()
         loadingContext.do_validate = False
-        loadingContext.do_update = False
         if submitting:
+            loadingContext.do_update = False
             # Document may have been auto-updated. Reload the original
             # document with updating disabled because we want to
             # submit the document with its original CWL version, not