From: Peter Amstutz Date: Mon, 17 Dec 2018 17:46:54 +0000 (-0500) Subject: Update cwltool refs #14510 X-Git-Tag: 1.4.0~185 X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/79379f5d68466922964d71f03d9bbe1b918f6252 Update cwltool refs #14510 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index 4f8c0338b3..6a91d6ff3c 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -133,7 +133,7 @@ class ArvadosContainer(JobBase): vwd = arvados.collection.Collection(api_client=self.arvrunner.api, keep_client=self.arvrunner.keep_client, num_retries=self.arvrunner.num_retries) - generatemapper = NoFollowPathMapper([self.generatefiles], "", "", + generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "", separateDirs=False) sorteditems = sorted(generatemapper.items(), None, key=lambda n: n[1].target) diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py index 2e4ef55015..87d6d1049a 100644 --- a/sdk/cwl/arvados_cwl/arvjob.py +++ b/sdk/cwl/arvados_cwl/arvjob.py @@ -67,7 +67,7 @@ class ArvadosJob(JobBase): keep_client=self.arvrunner.keep_client, num_retries=self.arvrunner.num_retries) script_parameters["task.vwd"] = {} - generatemapper = VwdPathMapper([self.generatefiles], "", "", + generatemapper = VwdPathMapper(self.generatefiles["listing"], "", "", separateDirs=False) with Perf(metrics, "createfiles %s" % self.name): diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py index f731db9555..3bd62532a8 100644 --- a/sdk/cwl/setup.py +++ b/sdk/cwl/setup.py @@ -33,7 +33,7 @@ setup(name='arvados-cwl-runner', # Note that arvados/build/run-build-packages.sh looks at this # file to determine what version of cwltool and schema-salad to build. install_requires=[ - 'cwltool==1.0.20181201184214', + 'cwltool==1.0.20181217162649', 'schema-salad==3.0.20181129082112', 'typing >= 3.6.4', 'ruamel.yaml >=0.15.54, <=0.15.77',