[ARVADOS] updated: c9b5db991553e3a6eb6ec1f268e94f4a7b2a64d0

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvcontainer.py |  1 +
 sdk/cwl/arvados_cwl/arvdocker.py    |  1 +
 sdk/cwl/arvados_cwl/arvjob.py       |  1 +
 sdk/cwl/test_with_arvbox.sh         | 29 ++++++++++++++++++++++++-----
 4 files changed, 27 insertions(+), 5 deletions(-)

       via  c9b5db991553e3a6eb6ec1f268e94f4a7b2a64d0 (commit)
      from  7cd03709ba594237b9cf88afac76d39f28011b35 (commit)

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commit c9b5db991553e3a6eb6ec1f268e94f4a7b2a64d0
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jun 21 11:55:43 2016 -0400

    8442: Bugfixes from end-to-end testing.

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 384b03b..2fb2c33 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -19,6 +19,7 @@ class ArvadosContainer(object):
     def __init__(self, runner):
         self.arvrunner = runner
         self.running = False
+        self.uuid = None
 
     def update_pipeline_component(self, r):
         pass
diff --git a/sdk/cwl/arvados_cwl/arvdocker.py b/sdk/cwl/arvados_cwl/arvdocker.py
index 253df99..3cc1a42 100644
--- a/sdk/cwl/arvados_cwl/arvdocker.py
+++ b/sdk/cwl/arvados_cwl/arvdocker.py
@@ -1,6 +1,7 @@
 import logging
 import cwltool.docker
 import arvados.commands.keepdocker
+import sys
 
 logger = logging.getLogger('arvados.cwl-runner')
 
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 693bbeb..f129dfa 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -26,6 +26,7 @@ class ArvadosJob(object):
     def __init__(self, runner):
         self.arvrunner = runner
         self.running = False
+        self.uuid = None
 
     def run(self, dry_run=False, pull_image=True, **kwargs):
         script_parameters = {
diff --git a/sdk/cwl/test_with_arvbox.sh b/sdk/cwl/test_with_arvbox.sh
index bee1938..5501e29 100755
--- a/sdk/cwl/test_with_arvbox.sh
+++ b/sdk/cwl/test_with_arvbox.sh
@@ -7,6 +7,7 @@ fi
 reset_container=1
 leave_running=0
 config=dev
+docker_pull=1
 
 while test -n "$1" ; do
     arg="$1"
@@ -23,11 +24,15 @@ while test -n "$1" ; do
             config=$2
             shift ; shift
             ;;
+        --no-docker-pull)
+            docker_pull=0
+            shift
+            ;;
         -h|--help)
-            echo "$0 [--no-reset-container] [--leave-running] [--config dev|localdemo]"
+            echo "$0 [--no-reset-container] [--leave-running] [--no-docker-pull] [--config dev|localdemo]"
             exit
             ;;
-        -*)
+        *)
             break
             ;;
     esac
@@ -50,7 +55,7 @@ set -eu -o pipefail
 
 cd /usr/src/arvados/sdk/cwl
 python setup.py sdist
-pip_install \$(ls dist/arvados-cwl-runner-*.tar.gz | tail -n1)
+pip_install \$(ls -r dist/arvados-cwl-runner-*.tar.gz | head -n1)
 
 mkdir -p /tmp/cwltest
 cd /tmp/cwltest
@@ -63,10 +68,24 @@ export ARVADOS_API_HOST=localhost:8000
 export ARVADOS_API_HOST_INSECURE=1
 export ARVADOS_API_TOKEN=\$(cat /var/lib/arvados/superuser_token)
 
-arv-keepdocker --pull arvados/jobs
+if test $docker_pull = 1 ; then
+  arv-keepdocker --pull arvados/jobs
+fi
+
+cat >/tmp/cwltest/arv-cwl-jobs <<EOF2
+#!/bin/sh
+exec arvados-cwl-runner --api=jobs \\\$@
+EOF2
+chmod +x /tmp/cwltest/arv-cwl-jobs
+
+cat >/tmp/cwltest/arv-cwl-containers <<EOF2
+#!/bin/sh
+exec arvados-cwl-runner --api=containers \\\$@
+EOF2
+chmod +x /tmp/cwltest/arv-cwl-containers
 
 env
-exec ./run_test.sh "$@"
+exec ./run_test.sh $@
 EOF
 
 CODE=$?

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