[ARVADOS] updated: 2.1.0-1041-g41e1b7ee5

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/runner.py            | 11 ++++++-----
 sdk/cwl/tests/17858-pack-visit-crash.cwl | 17 +++++++++++++++++
 sdk/cwl/tests/arvados-tests.yml          |  6 ++++++
 3 files changed, 29 insertions(+), 5 deletions(-)
 create mode 100644 sdk/cwl/tests/17858-pack-visit-crash.cwl

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commit 41e1b7ee572291733750cbe38d5bd562db126c43
Merge: a9b9c6ff0 5eb3dab23
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Wed Jul 7 16:18:58 2021 -0400

    Merge branch '17858-cwl-exprtool-defaults' into main refs #17858
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>


commit 5eb3dab2364f34d7f75f3d91fd5ad8cce6d31233
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Wed Jul 7 16:11:54 2021 -0400

    17858: Tweak logic to avoid KeyError
    
    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 9dc73f52f..66dff809e 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -479,10 +479,11 @@ def packed_workflow(arvrunner, tool, merged_map):
             if "path" in v and "location" not in v:
                 v["location"] = v["path"]
                 del v["path"]
-            if "location" in v and not v["location"].startswith("keep:"):
-                v["location"] = merged_map[cur_id].resolved[v["location"]]
-            if "location" in v and v["location"] in merged_map[cur_id].secondaryFiles:
-                v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[v["location"]]
+            if "location" in v and cur_id in merged_map:
+                if v["location"] in merged_map[cur_id].resolved:
+                    v["location"] = merged_map[cur_id].resolved[v["location"]]
+                if v["location"] in merged_map[cur_id].secondaryFiles:
+                    v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[v["location"]]
             if v.get("class") == "DockerRequirement":
                 v["http://arvados.org/cwl#dockerCollectionPDH"] = arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, v, True,
                                                                                                              arvrunner.project_uuid,

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