[ARVADOS] updated: 8408c834128282437ad1741b17e5221f0eef7da4

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py     | 29 ++++++++++++++++++++++++++---
 sdk/cwl/setup.py                    |  2 +-
 sdk/go/crunchrunner/crunchrunner.go |  4 ++++
 3 files changed, 31 insertions(+), 4 deletions(-)

       via  8408c834128282437ad1741b17e5221f0eef7da4 (commit)
      from  affe4f1084284a14a8f60501029bb3ea83af95d4 (commit)

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commit 8408c834128282437ad1741b17e5221f0eef7da4
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Mar 1 20:50:48 2016 -0500

    8488: Determine actual output dir from reading logs.  Need to set
    $(runtime.outdir) correctly for arvados-cwl-runner.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 86619d5..105d754 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -25,10 +25,15 @@ from arvados.api import OrderedJsonModel
 logger = logging.getLogger('arvados.cwl-runner')
 logger.setLevel(logging.INFO)
 
-crunchrunner_pdh = "721abe848fd8e6e6d1c99b920e6b7a2c+140"
+crunchrunner_pdh = "83db29f08544e1c319572a6bd971088a+140"
 crunchrunner_download = "https://cloud.curoverse.com/collections/download/qr1hi-4zz18-n3m1yxd0vx78jic/1i1u2qtq66k1atziv4ocfgsg5nu5tj11n4r6e0bhvjg03rix4m/crunchrunner"
 certs_download = "https://cloud.curoverse.com/collections/download/qr1hi-4zz18-n3m1yxd0vx78jic/1i1u2qtq66k1atziv4ocfgsg5nu5tj11n4r6e0bhvjg03rix4m/ca-certificates.crt"
 
+tmpdirre = re.compile(r"\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.tmpdir\)=(.*)")
+outdirre = re.compile(r"\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.outdir\)=(.*)")
+keepre = re.compile(r"\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.keep\)=(.*)")
+
+
 def arv_docker_get_image(api_client, dockerRequirement, pull_image):
     if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
         dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]
@@ -194,8 +199,26 @@ class ArvadosJob(object):
             try:
                 outputs = {}
                 if record["output"]:
-                    self.builder.outdir = "keep:" + record["output"]
-                    outputs = self.collect_outputs(self.builder.outdir)
+                    logc = arvados.collection.Collection(record["log"])
+                    log = logc.open(logc.keys()[0])
+                    tmpdir = None
+                    outdir = None
+                    keepdir = None
+                    for l in log.readlines():
+                        g = tmpdirre.match(l)
+                        if g:
+                            tmpdir = g.group(1)
+                        g = outdirre.match(l)
+                        if g:
+                            outdir = g.group(1)
+                        g = keepre.match(l)
+                        if g:
+                            keepdir = g.group(1)
+                        if tmpdir and outdir and keepdir:
+                            break
+
+                    self.builder.outdir = outdir
+                    outputs = self.collect_outputs("keep:" + record["output"])
             except Exception as e:
                 logger.exception("Got exception while collecting job outputs:")
                 processStatus = "permanentFail"
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 4e127cc..3fe4e16 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -31,7 +31,7 @@ setup(name='arvados-cwl-runner',
       ],
       install_requires=[
           'cwltool>=1.0.20160225202307',
-          'arvados-python-client>=0.1.20160122132348'
+          'arvados-python-client>=0.1.20160219154918'
       ],
       zip_safe=True,
       cmdclass={'egg_info': tagger},
diff --git a/sdk/go/crunchrunner/crunchrunner.go b/sdk/go/crunchrunner/crunchrunner.go
index 081ba50..226cf91 100644
--- a/sdk/go/crunchrunner/crunchrunner.go
+++ b/sdk/go/crunchrunner/crunchrunner.go
@@ -213,6 +213,10 @@ func runner(api IArvadosClient,
 		"$(task.outdir)": outdir,
 		"$(task.keep)":   keepmount}
 
+	log.Printf("crunchrunner: $(task.tmpdir)=%v", tmpdir)
+	log.Printf("crunchrunner: $(task.outdir)=%v", outdir)
+	log.Printf("crunchrunner: $(task.keep)=%v", keepmount)
+
 	// Set up subprocess
 	for k, v := range taskp.Command {
 		taskp.Command[k] = substitute(v, replacements)

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