[ARVADOS] updated: 1.3.0-2544-g5c222ee2f

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Summary of changes:
 sdk/cwl/arvados_cwl/runner.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

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       via  b316dddaba6d8aca00df7d368705088aac1171f5 (commit)
      from  e3958bed53ae018ae2bb826e429d45c8046fecdb (commit)

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commit 5c222ee2fb1f54f41d6e34561f37a2898e1fac0f
Merge: e3958bed5 b316dddab
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Mon May 11 11:08:47 2020 -0400

    Merge branch '16339-cwl-schema-refs' refs #16339
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>


commit b316dddaba6d8aca00df7d368705088aac1171f5
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Mon May 11 11:08:01 2020 -0400

    16339: Fix $schemas rewriting bug
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index f0be83032..7bb66a158 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -42,6 +42,7 @@ import schema_salad.validate as validate
 import arvados.collection
 from .util import collectionUUID
 import ruamel.yaml as yaml
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 import arvados_cwl.arvdocker
 from .pathmapper import ArvPathMapper, trim_listing, collection_pdh_pattern, collection_uuid_pattern
@@ -392,7 +393,7 @@ def upload_dependencies(arvrunner, name, document_loader,
             discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d]
 
     if "$schemas" in workflowobj:
-        sch = []
+        sch = CommentedSeq()
         for s in workflowobj["$schemas"]:
             sch.append(mapper.mapper(s).resolved)
         workflowobj["$schemas"] = sch

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