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@curii.com>

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index f232178c5d5400ab90aad300d2f1d2d70909b98d..644713bce25385938df289dbdcb4cf68b77f3ca5 100644 (file)
--- 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"]
         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):
         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 d38414fc811d433acb5751613c9974f1bbc0b0c5..6268266ddd9344a80dbe501509b822bb31cb18c0 100755 (executable)
--- 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
    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
 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
 
 fi
 EOF