[ARVADOS] updated: b9df977af1ca8d7fe942cbe13956fa19ed88b91d

Git user git at public.curoverse.com
Fri Dec 30 14:12:32 EST 2016


Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py      | 27 ++++++++++++---
 sdk/cwl/arvados_cwl/arvcontainer.py  | 42 +++++++++++++++--------
 sdk/cwl/arvados_cwl/arvjob.py        | 14 +++++---
 sdk/cwl/arvados_cwl/arvworkflow.py   |  3 ++
 sdk/cwl/arvados_cwl/crunch_script.py |  5 ++-
 sdk/cwl/arvados_cwl/done.py          | 29 ++++++++++++++--
 sdk/cwl/arvados_cwl/runner.py        | 64 +++++++++++++++++++++---------------
 sdk/cwl/tests/test_submit.py         | 19 +++++++----
 8 files changed, 144 insertions(+), 59 deletions(-)

       via  b9df977af1ca8d7fe942cbe13956fa19ed88b91d (commit)
       via  1fa9990d33e5cde82d5986b382851b8ea0314553 (commit)
       via  e367f2eea8974cc137b2c74bfbfcf0e5d334f15f (commit)
       via  7f9a68fbef2de18f274437b6161cd7269d87f04e (commit)
       via  a4f7583ef9d76101415bace9b250df983ba7212d (commit)
       via  5af0f99a1dc3d6dbc9066c2649272abf27482ebf (commit)
       via  970835342e02cb7a97f228f67602b7f847ab6875 (commit)
       via  1f5fee78438f06ec9531939247321dfb30af2b1a (commit)
       via  25275859b01a1f8c8bff018878842d194d99c173 (commit)
       via  b9f7a8693579045f05d142dba8bffd2c5660dfce (commit)
      from  48d810686a66ac2d554d4f5696fda9a61904992c (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit b9df977af1ca8d7fe942cbe13956fa19ed88b91d
Merge: 1fa9990 e367f2e
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Fri Dec 30 14:12:27 2016 -0500

    Merge branch '10497-cwl-job-logs' closes #10497


commit 1fa9990d33e5cde82d5986b382851b8ea0314553
Merge: 48d8106 7f9a68f
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Fri Dec 30 14:12:16 2016 -0500

    Merge branch '10722-cwl-subworkflow' closes #10722


commit e367f2eea8974cc137b2c74bfbfcf0e5d334f15f
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Fri Dec 30 13:34:27 2016 -0500

    10497: Replace \d\d\d\d with \d{4}

diff --git a/sdk/cwl/arvados_cwl/done.py b/sdk/cwl/arvados_cwl/done.py
index 7abaedf..87908c2 100644
--- a/sdk/cwl/arvados_cwl/done.py
+++ b/sdk/cwl/arvados_cwl/done.py
@@ -44,8 +44,8 @@ def done_outputs(self, record, tmpdir, outdir, keepdir):
     self.builder.pathmapper.keepdir = keepdir
     return self.collect_outputs("keep:" + record["output"])
 
-crunchstat_re = re.compile(r"^\d\d\d\d-\d\d-\d\d_\d\d:\d\d:\d\d [a-z0-9]{5}-8i9sb-[a-z0-9]{15} \d+ \d+ stderr crunchstat:")
-timestamp_re = re.compile(r"^(\d\d\d\d-\d\d-\d\dT\d\d:\d\d:\d\d\.\d+Z) (.*)")
+crunchstat_re = re.compile(r"^\d{4}-\d\d-\d\d_\d\d:\d\d:\d\d [a-z0-9]{5}-8i9sb-[a-z0-9]{15} \d+ \d+ stderr crunchstat:")
+timestamp_re = re.compile(r"^(\d{4}-\d\d-\d\dT\d\d:\d\d:\d\d\.\d+Z) (.*)")
 
 def logtail(logcollection, logger, header, maxlen=25):
     logtail = deque([], maxlen*len(logcollection))

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