from .matcher import JsonDiffMatcher
from .mock_discovery import get_rootDesc
+import ruamel.yaml as yaml
+
_rootDesc = None
def stubs(func):
'script_parameters': {
'x': {
'basename': 'blorp.txt',
- 'location': 'keep:99999999999999999999999999999994+99/blorp.txt',
+ 'location': 'keep:99999999999999999999999999999992+99/blorp.txt',
'class': 'File'
},
'y': {
'class': 'Directory'
},
'cwl:tool':
- '99999999999999999999999999999991+99/wf/submit_wf.cwl'
+ '99999999999999999999999999999994+99/workflow.cwl#main'
},
'repository': 'arvados',
'script_version': 'master',
'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
'script_parameters': {
'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
- 'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999994+99/blorp.txt'}},
+ 'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999992+99/blorp.txt'}},
'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
'listing': [
{'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
]}},
- 'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl',
- 'arv:enable_reuse': True
+ 'cwl:tool': '99999999999999999999999999999994+99/workflow.cwl#main',
+ 'arv:enable_reuse': True,
+ 'arv:on_error': 'continue'
},
'repository': 'arvados',
'script_version': 'master',
stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
+ with open("tests/wf/submit_wf_packed.cwl") as f:
+ expect_packed_workflow = yaml.round_trip_load(f)
+
stubs.expect_container_spec = {
'priority': 1,
'mounts': {
'writable': True,
'kind': 'collection'
},
- '/var/lib/cwl/workflow': {
- 'portable_data_hash': '99999999999999999999999999999991+99',
- 'kind': 'collection'
+ '/var/lib/cwl/workflow.json': {
+ 'content': expect_packed_workflow,
+ 'kind': 'json'
},
'stdout': {
'path': '/var/spool/cwl/cwl.output.json',
'kind': 'json',
'content': {
'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'},
- 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:99999999999999999999999999999994+99/blorp.txt'},
+ 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:99999999999999999999999999999992+99/blorp.txt'},
'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
{'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
]}
},
'state': 'Committed',
'owner_uuid': None,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'name': 'submit_wf.cwl',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'output_path': '/var/spool/cwl',
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", "--debug",
+ ["--submit", "--no-wait", "--api=jobs", "--debug",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.api.collections().create.assert_has_calls([
mock.call(),
- mock.call(body={
+ mock.call(body=JsonDiffMatcher({
'manifest_text':
- './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
- '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
- 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
- 'owner_uuid': None,
- 'name': 'submit_wf.cwl',
- }, ensure_unique_name=True),
- mock.call().execute(),
- mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
- '0:0:blub.txt 0:0:submit_tool.cwl\n',
- 'replication_desired': None,
- 'name': 'New collection'
- }, ensure_unique_name=True),
+ '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
+ 'replication_desired': None,
+ 'name': 'submit_tool.cwl dependencies',
+ }), ensure_unique_name=True),
mock.call().execute(num_retries=4),
- mock.call(body={
+ mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'owner_uuid': None,
- 'name': '#',
- }, ensure_unique_name=True),
- mock.call().execute()])
+ 'replication_desired': None,
+ 'name': 'submit_wf.cwl input',
+ }), ensure_unique_name=True),
+ 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(
- body=expect_pipeline)
+ body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
def test_submit_no_reuse(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug", "--disable-reuse",
+ ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
+ expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
+
+ stubs.api.pipeline_instances().create.assert_called_with(
+ body=JsonDiffMatcher(expect_pipeline))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_pipeline_uuid + '\n')
+
+ @mock.patch("time.sleep")
+ @stubs
+ def test_submit_on_error(self, stubs, tm):
+ capture_stdout = cStringIO.StringIO()
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
+
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
-
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
+
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
-
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
+
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- stubs.expect_pipeline_instance["name"] = "hello job 123"
-
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ 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')
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
-
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
+
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.api.collections().create.assert_has_calls([
mock.call(),
- mock.call(body={
+ mock.call(body=JsonDiffMatcher({
'manifest_text':
- './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
- '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
- 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
- 'owner_uuid': None,
- 'name': 'submit_wf.cwl',
- }, ensure_unique_name=True),
- mock.call().execute(),
- mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
- '0:0:blub.txt 0:0:submit_tool.cwl\n',
- 'name': 'New collection',
- 'replication_desired': None,
- }, ensure_unique_name=True),
+ '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
+ 'replication_desired': None,
+ 'name': 'submit_tool.cwl dependencies',
+ }), ensure_unique_name=True),
mock.call().execute(num_retries=4),
- mock.call(body={
+ mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'owner_uuid': None,
- 'name': '#',
- }, ensure_unique_name=True),
- mock.call().execute()])
+ 'replication_desired': None,
+ 'name': 'submit_wf.cwl input',
+ }), ensure_unique_name=True),
+ mock.call().execute(num_retries=4)])
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
except:
logging.exception("")
- stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--disable-reuse', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+
+ @stubs
+ def test_submit_container_on_error(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '--on-error=stop',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
except:
logging.exception("")
- stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-name="+output_name, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
-
expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ "--output-name="+output_name, '--enable-reuse', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+ expect_container["output_name"] = output_name
+
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
except:
logging.exception("")
- stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-tags="+output_tags, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
-
expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ "--output-tags="+output_tags, '--enable-reuse', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
except:
logging.exception("")
- stubs.expect_container_spec["runtime_constraints"]["ram"] = 2048*1024*1024
-
expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["runtime_constraints"]["ram"] = 2048*1024*1024
+
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
'output_path': '/var/spool/cwl',
'name': 'expect_arvworkflow.cwl#main',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '--on-error=continue',
+ '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+
+ @mock.patch("arvados.collection.CollectionReader")
+ @mock.patch("time.sleep")
+ @stubs
+ def test_submit_jobs_keepref(self, stubs, tm, reader):
+ capture_stdout = cStringIO.StringIO()
+
+ with open("tests/wf/expect_arvworkflow.cwl") as f:
+ reader().open().__enter__().read.return_value = f.read()
+
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=jobs", "--debug",
+ "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
+ del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
+ del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
+ expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
+ expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
+ stubs.api.pipeline_instances().create.assert_called_with(
+ body=JsonDiffMatcher(expect_pipeline))
+
@mock.patch("time.sleep")
@stubs
def test_submit_arvworkflow(self, stubs, tm):
},
'/var/lib/cwl/workflow.json': {
'kind': 'json',
- 'json': {
+ 'content': {
'cwlVersion': 'v1.0',
'$graph': [
+ {
+ 'id': '#main',
+ 'inputs': [
+ {'type': 'string', 'id': '#main/x'}
+ ],
+ 'steps': [
+ {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
+ 'run': '#submit_tool.cwl',
+ 'id': '#main/step1',
+ 'out': []}
+ ],
+ 'class': 'Workflow',
+ 'outputs': []
+ },
{
'inputs': [
{
'outputs': [],
'baseCommand': 'cat',
'class': 'CommandLineTool'
- }, {
- 'id': '#main',
- 'inputs': [
- {'type': 'string', 'id': '#main/x'}
- ],
- 'steps': [
- {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
- 'run': '#submit_tool.cwl',
- 'id': '#main/step1',
- 'out': []}
- ],
- 'class': 'Workflow',
- 'outputs': []
}
]
}
'output_path': '/var/spool/cwl',
'name': 'a test workflow',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
except:
logging.exception("")
- stubs.expect_container_spec["name"] = "hello container 123"
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["name"] = "hello container 123"
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+
+ @stubs
+ def test_submit_job_runner_image(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+ stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123"
+
+ expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
+ stubs.api.pipeline_instances().create.assert_called_with(
+ body=JsonDiffMatcher(expect_pipeline))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_pipeline_uuid + '\n')
+
+ @stubs
+ def test_submit_container_runner_image(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+ stubs.expect_container_spec["container_image"] = "arvados/jobs:123"
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
- body=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
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))
+ 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"
'dataclass': 'File',
'required': True,
'type': 'File',
- 'value': '99999999999999999999999999999994+99/blorp.txt',
+ 'value': '99999999999999999999999999999992+99/blorp.txt',
}
expect_component['script_parameters']['y'] = {
'dataclass': 'Collection',
},
'script_parameters': {
'cwl:tool':
- '99999999999999999999999999999991+99/'
- 'wf/inputs_test.cwl',
+ '99999999999999999999999999999992+99/workflow.cwl#main',
'optionalFloatInput': None,
'fileInput': {
'type': 'File',
expect_template = copy.deepcopy(self.expect_template)
params = expect_template[
"components"]["inputs_test.cwl"]["script_parameters"]
- params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
+ params["fileInput"]["value"] = '99999999999999999999999999999992+99/blorp.txt'
+ params["cwl:tool"] = '99999999999999999999999999999994+99/workflow.cwl#main'
params["floatInput"]["value"] = 1.234
params["boolInput"]["value"] = True