From 4161dfe7f8f4ea790d286cd1745893e0a250a02f Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 14 Nov 2018 13:22:16 -0500 Subject: [PATCH] 14198: Update cwltool and schema-salad Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- sdk/cwl/arvados_cwl/arvworkflow.py | 13 ++----------- sdk/cwl/setup.py | 4 ++-- 2 files changed, 4 insertions(+), 13 deletions(-) diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py index 72ef8fd4f4..e80c06f00d 100644 --- a/sdk/cwl/arvados_cwl/arvworkflow.py +++ b/sdk/cwl/arvados_cwl/arvworkflow.py @@ -132,7 +132,8 @@ class ArvadosWorkflow(Workflow): def job(self, joborder, output_callback, runtimeContext): - check_cluster_target(self, self._init_job(joborder, runtimeContext), runtimeContext) + builder = self._init_job(joborder, runtimeContext) + check_cluster_target(self, builder, runtimeContext) req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer") if not req: @@ -161,11 +162,6 @@ class ArvadosWorkflow(Workflow): packed = pack(document_loader, workflowobj, uri, self.metadata) - builder = Builder(joborder, - requirements=workflowobj["requirements"], - hints=workflowobj["hints"], - resources={}) - def visit(item): for t in ("hints", "requirements"): if t not in item: @@ -205,11 +201,6 @@ class ArvadosWorkflow(Workflow): if self.dynamic_resource_req: - builder = Builder(joborder, - requirements=self.requirements, - hints=self.hints, - resources={}) - # Evaluate dynamic resource requirements using current builder rs = copy.copy(self.static_resource_req) for dyn_rs in self.dynamic_resource_req: diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py index 2b7b31b9f3..91a03ed865 100644 --- a/sdk/cwl/setup.py +++ b/sdk/cwl/setup.py @@ -33,8 +33,8 @@ 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==1.0.20180806194258', - 'schema-salad==2.7.20180719125426', + 'cwltool==1.0.20181114114354', + 'schema-salad==2.7.20181017120439', 'typing >= 3.6.4', # Need to limit ruamel.yaml version to 0.15.26 because of bug # https://bitbucket.org/ruamel/yaml/issues/227/regression-parsing-flow-mapping -- 2.30.2