[ARVADOS] updated: 2.1.0-2490-gaa03bc3e2

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/runner.py | 2 +-
 sdk/cwl/test_with_arvbox.sh   | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

       via  aa03bc3e2a1122e02bb305bda7fadb96c68706b1 (commit)
      from  ead34cd306205a1f477a3d72df3293f48d5da3eb (commit)

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commit aa03bc3e2a1122e02bb305bda7fadb96c68706b1
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Mon May 16 14:51:20 2022 -0400

    Fix set_secondary recursion error
    
    skip some problematic conformance tests in test_with_arvbox
    
    refs #19109
    
    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 f232178c5..644713bce 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -249,7 +249,7 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
         primary["secondaryFiles"] = cmap(found)
         if discovered is not None:
             discovered[primary["location"]] = primary["secondaryFiles"]
-    elif inputschema["type"] not in primitive_types_set:
+    elif inputschema["type"] not in primitive_types_set and inputschema["type"] not in ("File", "Directory"):
         set_secondary(fsaccess, builder, inputschema["type"], secondaryspec, primary, discovered)
 
 def discover_secondary_files(fsaccess, builder, inputs, job_order, discovered=None):
diff --git a/sdk/cwl/test_with_arvbox.sh b/sdk/cwl/test_with_arvbox.sh
index d38414fc8..6268266dd 100755
--- a/sdk/cwl/test_with_arvbox.sh
+++ b/sdk/cwl/test_with_arvbox.sh
@@ -166,9 +166,9 @@ if [[ "$suite" = "integration" ]] ; then
    cd /usr/src/arvados/sdk/cwl/tests
    exec ./arvados-tests.sh $@
 elif [[ "$suite" = "conformance-v1.2" ]] ; then
-   exec cwltest --tool arvados-cwl-runner --test conformance_tests.yaml -N307 $@ -- \$EXTRA
+   exec cwltest --tool arvados-cwl-runner --test conformance_tests.yaml -Sdocker_entrypoint,timelimit_invalid_wf -N307 $@ -- \$EXTRA
 else
-   exec ./run_test.sh RUNNER=arvados-cwl-runner EXTRA="\$EXTRA" $@
+   exec cwltest --tool arvados-cwl-runner --test conformance_tests.yaml -Sdocker_entrypoint,timelimit_invalid_wf $@ -- \$EXTRA
 fi
 EOF
 

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