From f423aff73c1927a74e39c738e08bd6f1100a94c5 Mon Sep 17 00:00:00 2001 From: Ward Vandewege Date: Wed, 3 Jun 2020 15:42:03 -0400 Subject: [PATCH] 16482: bump a-c-r's cwltool dependency to version 3.0.20200530110633 so that CWL v1.2.0-dev3 tests are supported. This also requires an update to the schema-salad dependency, and some adjustment to account for code that moved around in cwltool. Also, a fix to make sure the output from resource_stream gets turned into a string, not a binary object. Arvados-DCO-1.1-Signed-off-by: Ward Vandewege --- sdk/cwl/arvados_cwl/__init__.py | 6 +++--- sdk/cwl/arvados_cwl/executor.py | 2 +- sdk/cwl/setup.py | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 3dd04040ab..adbce90d8d 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -23,7 +23,7 @@ import cwltool.workflow import cwltool.process import cwltool.argparser from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema -from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing +from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing import arvados import arvados.config @@ -220,8 +220,8 @@ def add_arv_hints(): cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE 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() + customschema10 = res10.read().decode('utf-8') + customschema11 = res11.read().decode('utf-8') 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) diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py index 99d4c4e9a1..ec91eea6aa 100644 --- a/sdk/cwl/arvados_cwl/executor.py +++ b/sdk/cwl/arvados_cwl/executor.py @@ -42,7 +42,7 @@ from .context import ArvLoadingContext, ArvRuntimeContext from ._version import __version__ from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema -from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing, visit_class +from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing, visit_class from cwltool.command_line_tool import compute_checksums from cwltool.load_tool import load_tool diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py index 72969de94c..40ee679857 100644 --- a/sdk/cwl/setup.py +++ b/sdk/cwl/setup.py @@ -39,8 +39,8 @@ setup(name='arvados-cwl-runner', # file to determine what version of cwltool and schema-salad to # build. install_requires=[ - 'cwltool==3.0.20200324120055', - 'schema-salad==5.0.20200302192450', + 'cwltool==3.0.20200530110633', + 'schema-salad==6.0.20200601095207', 'arvados-python-client{}'.format(pysdk_dep), 'setuptools', 'ciso8601 >= 2.0.0' -- 2.30.2