From 14db4dcdc2b0b7e5fbc81d62cf581dea5ccc07f4 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Tue, 28 May 2019 13:03:41 -0400 Subject: [PATCH] 15028: Bump cwltool to accept v1.1 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- sdk/cwl/arvados_cwl/__init__.py | 15 +++++++++------ sdk/cwl/arvados_cwl/executor.py | 2 +- sdk/cwl/setup.py | 2 +- 3 files changed, 11 insertions(+), 8 deletions(-) diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index f8069a3cb3..1f8edb70db 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -219,12 +219,15 @@ def arg_parser(): # type: () -> argparse.ArgumentParser def add_arv_hints(): cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*") cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE - res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.0.yml') - res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.1.yml') - customschema = res.read() - use_custom_schema("v1.0", "http://arvados.org/cwl", customschema) - use_custom_schema("v1.1.0-dev1", "http://arvados.org/cwl", customschema) - res.close() + res10 = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.0.yml') + res11 = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.1.yml') + customschema10 = res10.read() + customschema11 = res11.read() + use_custom_schema("v1.0", "http://arvados.org/cwl", customschema10) + use_custom_schema("v1.1.0-dev1", "http://arvados.org/cwl", customschema11) + use_custom_schema("v1.1", "http://arvados.org/cwl", customschema11) + res10.close() + res11.close() cwltool.process.supportedProcessRequirements.extend([ "http://arvados.org/cwl#RunInSingleContainer", "http://arvados.org/cwl#OutputDirType", diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py index 9ff06fa4aa..d2fd0088ca 100644 --- a/sdk/cwl/arvados_cwl/executor.py +++ b/sdk/cwl/arvados_cwl/executor.py @@ -534,7 +534,7 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods raise WorkflowException( "`cwl:requirements` in the input object is not part of CWL " "v1.0. You can adjust to use `cwltool:overrides` instead; or you " - "can set the cwlVersion to v1.1.0-dev1 or greater and re-run with " + "can set the cwlVersion to v1.1 or greater and re-run with " "--enable-dev.") job_reqs = job_order_object["https://w3id.org/cwl/cwl#requirements"] for req in job_reqs: diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py index def79ece40..31195fd372 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==1.0.20190503175737', + 'cwltool==1.0.20190525125941', 'schema-salad==4.1.20190305210046', 'typing >= 3.6.4', 'ruamel.yaml >=0.15.54, <=0.15.77', -- 2.30.2