8654: Passes in local testing.

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 8cbf4d876ed87c660c9c365c114844c294ec834f..59f681733695260a73210ee33d1ca976bb49051e 100755 (executable)
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -8,6 +8,7 @@ from cwltool.process import shortname
 import cwltool.main
 import logging
 import os
+import json
 from arvados.api import OrderedJsonModel
 
 api = arvados.api("v1")
@@ -28,8 +29,8 @@ try:
     outputObj = runner.arvExecutor(t, job_order_object, "", None)
 
     c = arvados.collection.Collection()
-    with c.open("cwl.output.json") as f:
-        json.dump(f, indent=4)
+    with c.open("cwl.output.json", "w") as f:
+        json.dump(outputObj, f, indent=4)
 
     api.job_tasks().update(uuid=arvados.current_task()['uuid'],
                                          body={

diff --git a/docker/jobs/Dockerfile b/docker/jobs/Dockerfile
index 836634909b215c2cc77dc8b7948d4f3446d986cc..bbe7844b7dd8f5accd7745c331bf802271a2682a 100644 (file)
--- a/docker/jobs/Dockerfile
+++ b/docker/jobs/Dockerfile
@@ -6,10 +6,8 @@ ENV DEBIAN_FRONTEND noninteractive
 
 ADD apt.arvados.org.list /etc/apt/sources.list.d/
 RUN apt-key adv --keyserver pool.sks-keyservers.net --recv 1078ECD7
-RUN apt-get update -q
 
-RUN apt-get install -qy git python-pip python-virtualenv python-arvados-python-client python-dev libcurl4-gnutls-dev nodejs
-RUN pip install arvados-cwl-runner
+RUN apt-get update -q && apt-get install -qy git python-pip python-virtualenv python-arvados-python-client python-dev libcurl4-gnutls-dev nodejs python-arvados-cwl-runner
 
 RUN gpg --keyserver pool.sks-keyservers.net --recv-keys D39DC0E3
 

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 885497171e8828852c27f0ece6c455cc75c4ee49..67a324ac850e692d4cb4b6a75ae5aba769debc01 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -362,7 +362,8 @@ class ArvCwlRunner(object):
         self.fs_access = CollectionFsAccess(input_basedir)
 
         kwargs["fs_access"] = self.fs_access
-        kwargs["enable_reuse"] = args.enable_reuse
+        if args:
+            kwargs["enable_reuse"] = args.enable_reuse
 
         kwargs["outdir"] = "$(task.outdir)"
         kwargs["tmpdir"] = "$(task.tmpdir)"