[ARVADOS] updated: 22a6d5ae6a942759ae893e69a47627173d60bdc2
Git user
git at public.curoverse.com
Tue Mar 28 10:07:38 EDT 2017
Summary of changes:
sdk/cwl/arvados_cwl/crunch_script.py | 3 +--
sdk/cwl/setup.py | 1 +
2 files changed, 2 insertions(+), 2 deletions(-)
via 22a6d5ae6a942759ae893e69a47627173d60bdc2 (commit)
via 86fec403b8b00442210e8a265071672e3dd2d053 (commit)
from 262dfdbc9e795d258e8b2b0951784da2efcde080 (commit)
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commit 22a6d5ae6a942759ae893e69a47627173d60bdc2
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Mar 28 09:57:12 2017 -0400
10401: Update crunch script, no longer expands directories by default.
diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index f336193..8073620 100644
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -19,7 +19,7 @@ import re
import functools
from arvados.api import OrderedJsonModel
-from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, getListing, normalizeFilesDirs
+from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, normalizeFilesDirs
from cwltool.load_tool import load_tool
from cwltool.errors import WorkflowException
@@ -64,7 +64,6 @@ def run():
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
normalizeFilesDirs(job_order_object)
- adjustDirObjs(job_order_object, functools.partial(getListing, arvados_cwl.fsaccess.CollectionFsAccess("", api_client=api)))
output_name = None
output_tags = None
commit 86fec403b8b00442210e8a265071672e3dd2d053
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Mar 28 09:56:40 2017 -0400
10401: Pin 'typing' dependency to resolve dependency conflict.
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index ac331fa..c065917 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -51,6 +51,7 @@ setup(name='arvados-cwl-runner',
'cwltool==1.0.20170327143622',
'schema-salad==2.5.20170327140858',
'ruamel.yaml==0.13.7',
+ 'typing==3.5.3',
'arvados-python-client>=0.1.20170327195441',
'setuptools'
],
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