'class': 'Directory'
},
'cwl:tool':
- 'f57578d5cfda7f70fef00cbc4b621e6b+58/workflow.cwl#main'
+ '99999999999999999999999999999994+99/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#main',
+ 'cwl:tool': '99999999999999999999999999999994+99/workflow.cwl#main',
'arv:enable_reuse': True,
'arv:on_error': 'continue'
},
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",
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
- 'owner_uuid': None,
+ 'replication_desired': None,
'name': 'submit_tool.cwl dependencies',
}), ensure_unique_name=True),
- mock.call().execute(),
+ mock.call().execute(num_retries=4),
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'owner_uuid': None,
+ 'replication_desired': None,
'name': 'submit_wf.cwl input',
}), ensure_unique_name=True),
- mock.call().execute()])
+ mock.call().execute(num_retries=4)])
+
+ 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(
expect_pipeline["name"] = "hello job 123"
stubs.api.pipeline_instances().create.assert_called_with(
- body=expect_pipeline)
+ body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
- 'owner_uuid': None,
+ 'replication_desired': None,
'name': 'submit_tool.cwl dependencies',
}), ensure_unique_name=True),
- mock.call().execute(),
+ mock.call().execute(num_retries=4),
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'owner_uuid': None,
+ 'replication_desired': None,
'name': 'submit_wf.cwl input',
}), ensure_unique_name=True),
- mock.call().execute()])
+ mock.call().execute(num_retries=4)])
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
arvrunner.project_uuid = ""
api.return_value = mock.MagicMock()
arvrunner.api = api.return_value
- arvrunner.api.links().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0},
- {"items": [], "items_available": 0, "offset": 0},
- {"items": [], "items_available": 0, "offset": 0},
- {"items": [{"created_at": "",
- "head_uuid": "",
- "link_class": "docker_image_hash",
- "name": "123456",
- "owner_uuid": "",
- "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
- {"items": [], "items_available": 0, "offset": 0},
- {"items": [{"created_at": "",
- "head_uuid": "",
+ arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
+ "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
"link_class": "docker_image_repo+tag",
"name": "arvados/jobs:"+arvados_cwl.__version__,
"owner_uuid": "",
"link_class": "docker_image_hash",
"name": "123456",
"owner_uuid": "",
- "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0} ,
+ "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
)
find_one_image_hash.return_value = "123456"
- arvrunner.api.collections().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0},
- {"items": [{"uuid": "",
+ arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
"owner_uuid": "",
"manifest_text": "",
"properties": ""
- }], "items_available": 1, "offset": 0},
- {"items": [{"uuid": ""}], "items_available": 1, "offset": 0})
+ }], "items_available": 1, "offset": 0},)
arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
- self.assertEqual("arvados/jobs:"+arvados_cwl.__version__, arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
+ self.assertEqual("arvados/jobs:"+arvados_cwl.__version__,
+ arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
class TestCreateTemplate(unittest.TestCase):
existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
},
'script_parameters': {
'cwl:tool':
- '5800682d508698dc9ce6d2fc618f21d8+58/workflow.cwl#main',
+ '99999999999999999999999999999992+99/workflow.cwl#main',
'optionalFloatInput': None,
'fileInput': {
'type': 'File',
params = expect_template[
"components"]["inputs_test.cwl"]["script_parameters"]
params["fileInput"]["value"] = '99999999999999999999999999999992+99/blorp.txt'
+ params["cwl:tool"] = '99999999999999999999999999999994+99/workflow.cwl#main'
params["floatInput"]["value"] = 1.234
params["boolInput"]["value"] = True