From 6e0abcdabb14bcd21695420d3cfab0d57362a2be Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curoverse.com>
Date: Thu, 11 Aug 2016 14:19:37 -0400
Subject: [PATCH] 9751: Fix unit tests.  Rename dir6.cwl to
 keep-dir-test-input.cwl

---
 sdk/cwl/arvados_cwl/__init__.py                     | 4 ++--
 sdk/cwl/setup.py                                    | 2 +-
 sdk/cwl/tests/arvados-tests.yml                     | 2 +-
 sdk/cwl/tests/{dir6.cwl => keep-dir-test-input.cwl} | 0
 sdk/cwl/tests/test_job.py                           | 4 +++-
 5 files changed, 7 insertions(+), 5 deletions(-)
 rename sdk/cwl/tests/{dir6.cwl => keep-dir-test-input.cwl} (100%)

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index fd9e74f857..f7792cd35d 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -114,6 +114,8 @@ class ArvCwlRunner(object):
         useruuid = self.api.users().current().execute()["uuid"]
         self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid
         self.pipeline = None
+        make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api)
+        self.fs_access = make_fs_access(kwargs["basedir"])
 
         if kwargs.get("create_template"):
             tmpl = RunnerTemplate(self, tool, job_order, kwargs.get("enable_reuse"))
@@ -124,8 +126,6 @@ class ArvCwlRunner(object):
         self.debug = kwargs.get("debug")
         self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
 
-        make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api)
-        self.fs_access = make_fs_access(kwargs["basedir"])
         kwargs["make_fs_access"] = make_fs_access
         kwargs["enable_reuse"] = kwargs.get("enable_reuse")
         kwargs["use_container"] = True
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 99237e134f..35408b7b5f 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
       # Make sure to update arvados/build/run-build-packages.sh as well
       # when updating the cwltool version pin.
       install_requires=[
-          'cwltool==1.0.20160811124408',
+          'cwltool==1.0.20160811170313',
           'arvados-python-client>=0.1.20160714204738',
       ],
       data_files=[
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index 2526258641..1187962a8e 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -6,5 +6,5 @@
         "class": "File",
         "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
     }
-  tool: dir6.cwl
+  tool: keep-dir-test-input.cwl
   doc: Test directory in keep
diff --git a/sdk/cwl/tests/dir6.cwl b/sdk/cwl/tests/keep-dir-test-input.cwl
similarity index 100%
rename from sdk/cwl/tests/dir6.cwl
rename to sdk/cwl/tests/keep-dir-test-input.cwl
diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index 0d3a494f00..46d20485ad 100644
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -3,6 +3,7 @@ import logging
 import mock
 import unittest
 import os
+import functools
 import cwltool.process
 
 if not os.getenv('ARVADOS_DEBUG'):
@@ -28,7 +29,8 @@ class TestJob(unittest.TestCase):
         }
         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="")
         arvtool.formatgraph = None
-        for j in arvtool.job({}, mock.MagicMock(), basedir=""):
+        for j in arvtool.job({}, mock.MagicMock(), basedir="",
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)):
             j.run()
             runner.api.jobs().create.assert_called_with(
                 body={
-- 
2.39.5