From: Peter Amstutz Date: Mon, 16 May 2022 18:51:20 +0000 (-0400) Subject: Fix set_secondary recursion error X-Git-Tag: 2.5.0~173 X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/aa03bc3e2a1122e02bb305bda7fadb96c68706b1?ds=sidebyside 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 --- diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py index f232178c5d..644713bce2 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 d38414fc81..6268266ddd 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