11549: Fix container requests so it doesn't mount each file individually,

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

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 1d2fa291ec1eee8953337f4ca1b97343ed7bcae2..3c7de77ebf7825a8ec3334f8b756460c3d0f73c9 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -247,10 +247,13 @@ class ArvCwlRunner(object):
                 raise Exception("Output source is not in keep or a literal")
             sp = k.split("/")
             srccollection = sp[0][5:]
-            reader = self.collection_cache.get(srccollection)
             try:
+                reader = self.collection_cache.get(srccollection)
                 srcpath = "/".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)
+                raise
             except IOError as e:
                 logger.warn("While preparing output collection: %s", e)
 
@@ -615,6 +618,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
 def add_arv_hints():
     cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
+    cwltool.draft2tool.ACCEPTLIST_RE = cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE
     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
     use_custom_schema("v1.0", "http://arvados.org/cwl", res.read())
     res.close()