[ARVADOS] created: 48d9bbb8368fa34922ea0849ec8da1e5b3ded5dc

[Git user]

        at  48d9bbb8368fa34922ea0849ec8da1e5b3ded5dc (commit)


commit 48d9bbb8368fa34922ea0849ec8da1e5b3ded5dc
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 8ffed5c..7a0bb5e 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 10f7d7d9462830855bbaef848f5eeb5839916d53
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Sep 20 15:24:34 2017 -0400

    12292: Set defaults for tmpdir, outdir, keep
    
    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..8ffed5c 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",
+                            "keep": "/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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