[ARVADOS] created: 28d004144ec33c44784b1c62ce2f67a64b4555f7

[Git user]

        at  28d004144ec33c44784b1c62ce2f67a64b4555f7 (commit)


commit 28d004144ec33c44784b1c62ce2f67a64b4555f7
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 18538fb..794c994 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 3656c8294d2cbf9ee1b706d89a9326ada285be50
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..18538fb 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -222,12 +222,13 @@ 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
+                            # Determine the tmpdir, outdir and keep paths from
                             # the job run.  Unfortunately, we can't take the first
                             # values we find (which are expected to be near the
                             # top) and stop scanning because if the node fails and

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