From 56555817311d4cadf261cd3aa380361690e6fe65 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Fri, 3 May 2019 16:43:41 -0400 Subject: [PATCH] 15028: Fix timelimit, set_secondaryfiles Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- sdk/cwl/arvados_cwl/arvcontainer.py | 2 +- sdk/cwl/arvados_cwl/runner.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index 860bd954c6..0c7ad732d2 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -260,7 +260,7 @@ class ArvadosContainer(JobBase): if self.output_ttl < 0: raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"]) - if self.timelimit is not None: + if self.timelimit is not None and self.timelimit > 0: scheduling_parameters["max_run_time"] = self.timelimit extra_submit_params = {} diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py index 68b2fd827a..3a37840501 100644 --- a/sdk/cwl/arvados_cwl/runner.py +++ b/sdk/cwl/arvados_cwl/runner.py @@ -137,7 +137,8 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov # set secondaryFiles, may be inherited by compound types. secondaryspec = inputschema["secondaryFiles"] - if isinstance(inputschema["type"], (Mapping, Sequence)): + if (isinstance(inputschema["type"], (Mapping, Sequence)) and + not isinstance(inputschema["type"], basestring)): # compound type (union, array, record) set_secondary(fsaccess, builder, inputschema["type"], secondaryspec, primary, discovered) -- 2.39.5