[ARVADOS] updated: fa57e1ba30bbf2ab2956d5a7ae3da14380da8669

[Git user]

Summary of changes:
 crunch_scripts/cwl-runner            |  23 ++++++--
 sdk/cwl/arvados_cwl/crunch_script.py | 102 +++++++++++++++++++++++++++++++++++
 sdk/cwl/arvados_cwl/runner.py        |   6 +--
 3 files changed, 124 insertions(+), 7 deletions(-)
 create mode 100644 sdk/cwl/arvados_cwl/crunch_script.py

       via  fa57e1ba30bbf2ab2956d5a7ae3da14380da8669 (commit)
       via  a85e7c7526d985f66f073320155ae5d70590be60 (commit)
       via  570509ab4d2ef93d870fd2b1f2eab178afb1bad9 (commit)
       via  5a0d9381edaa6c7eede45c9171ac089d1a4debf8 (commit)
      from  f156def25b0720dac1e102727f3a3821b98fb551 (commit)

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commit fa57e1ba30bbf2ab2956d5a7ae3da14380da8669
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Oct 17 15:27:25 2016 -0400

    10259: Move trim_listing out of upload_instance

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 054d353..6d38245 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -129,8 +129,6 @@ def upload_instance(arvrunner, name, tool, job_order):
                                         job_order.get("id", "#"),
                                         False)
 
-        adjustDirObjs(job_order, trim_listing)
-
         if "id" in job_order:
             del job_order["id"]
 
@@ -153,7 +151,9 @@ class Runner(object):
 
     def arvados_job_spec(self, *args, **kwargs):
         self.name = os.path.basename(self.tool.tool["id"])
-        return upload_instance(self.arvrunner, self.name, self.tool, self.job_order)
+        workflowmapper = upload_instance(self.arvrunner, self.name, self.tool, self.job_order)
+        adjustDirObjs(self.job_order, trim_listing)
+        return workflowmapper
 
     def done(self, record):
         if record["state"] == "Complete":

commit a85e7c7526d985f66f073320155ae5d70590be60
Merge: f156def 570509a
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Oct 17 15:07:09 2016 -0400

    Merge branch 'master' into 10259-cwl-pipeline-null


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