[ARVADOS] created: 73b52efcc4f3426fdebf379b3d8992f0b4d7163c
Git user
git at public.curoverse.com
Wed Sep 20 16:10:18 EDT 2017
at 73b52efcc4f3426fdebf379b3d8992f0b4d7163c (commit)
commit 73b52efcc4f3426fdebf379b3d8992f0b4d7163c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Sep 20 16:05:18 2017 -0400
12292: Find crunchrunner vars even when mixed into a partial line
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index e607951..fb2d425 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -32,7 +32,7 @@ from ._version import __version__
logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
-crunchrunner_re = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.(tmpdir|outdir|keep)\)=(.*)")
+crunchrunner_re = re.compile(r"^.*crunchrunner: \$\(task\.(tmpdir|outdir|keep)\)=(.*)$")
crunchrunner_git_commit = 'a3f2cb186e437bfce0031b024b2157b73ed2717d'
commit 1176895e0f35576e27739b5459517d5757705306
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Sep 20 15:24:34 2017 -0400
12292: Set defaults for tmpdir, outdir, keepdir
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index d104d56..e607951 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -222,10 +222,11 @@ class ArvadosJob(object):
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
log = logc.open(logc.keys()[0])
- dirs = {}
- tmpdir = None
- outdir = None
- keepdir = None
+ dirs = {
+ "tmpdir": "/tmpdir",
+ "outdir": "/outdir",
+ "keepdir": "/keep"
+ }
for l in log:
# Determine the tmpdir, outdir and keepdir paths from
# the job run. Unfortunately, we can't take the first
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