'class': 'Directory'
},
'cwl:tool':
- 'f57578d5cfda7f70fef00cbc4b621e6b+58/workflow.cwl'
+ '4db32e8a15aa48ea084b2f38108f406d+60/workflow.cwl#main'
},
'repository': 'arvados',
'script_version': 'master',
'listing': [
{'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
]}},
- 'cwl:tool': 'f57578d5cfda7f70fef00cbc4b621e6b+58/workflow.cwl',
+ 'cwl:tool': '4db32e8a15aa48ea084b2f38108f406d+60/workflow.cwl#main',
'arv:enable_reuse': True,
'arv:on_error': 'continue'
},
'kind': 'collection'
},
'/var/lib/cwl/workflow.json': {
- 'json': expect_packed_workflow,
+ 'content': expect_packed_workflow,
'kind': 'json'
},
'stdout': {
class TestSubmit(unittest.TestCase):
+ @mock.patch("arvados_cwl.runner.arv_docker_get_image")
@mock.patch("time.sleep")
@stubs
- def test_submit(self, stubs, tm):
+ def test_submit(self, stubs, tm, arvdock):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=jobs", "--debug",
}), ensure_unique_name=True),
mock.call().execute()])
+ arvdock.assert_has_calls([
+ mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
+ mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
+ ])
+
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
},
'/var/lib/cwl/workflow.json': {
'kind': 'json',
- 'json': {
+ 'content': {
'cwlVersion': 'v1.0',
'$graph': [
{
},
'script_parameters': {
'cwl:tool':
- '5800682d508698dc9ce6d2fc618f21d8+58/workflow.cwl',
+ '00e281847a33e1c0df93161d70a6fc5d+60/workflow.cwl#main',
'optionalFloatInput': None,
'fileInput': {
'type': 'File',