[ARVADOS] updated: 7f13479614f773f4d25735fd440b4494fa2e85f8

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/crunch_script.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

       via  7f13479614f773f4d25735fd440b4494fa2e85f8 (commit)
      from  e049b1e74727680ebbf6efcf340377af9e6fb6ba (commit)

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commit 7f13479614f773f4d25735fd440b4494fa2e85f8
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Dec 27 17:06:17 2016 -0500

    10497: Pop cwl:tool parameter from job order

diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index 6f84d68..9804572 100644
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -48,8 +48,6 @@ def run():
         def keeppathObj(v):
             v["location"] = keeppath(v["location"])
 
-        job_order_object["cwl:tool"] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object["cwl:tool"])
-
         for k,v in job_order_object.items():
             if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
                 job_order_object[k] = {
@@ -80,7 +78,8 @@ def run():
         runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
                                           output_name=output_name, output_tags=output_tags)
 
-        t = load_tool(job_order_object, runner.arv_make_tool)
+        toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool"))
+        t = load_tool(toolpath, runner.arv_make_tool)
 
         args = argparse.Namespace()
         args.project_uuid = arvados.current_job()["owner_uuid"]

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