'99999999999999999999999999999991+99/wf/submit_wf.cwl'
},
'repository': 'arvados',
- 'script_version': arvados_cwl.__version__,
+ 'script_version': 'master',
+ 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
'script': 'cwl-runner'
}
stubs.pipeline_component = stubs.expect_job_spec.copy()
'arv:enable_reuse': True
},
'repository': 'arvados',
- 'script_version': arvados_cwl.__version__,
+ 'script_version': 'master',
+ 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
'script': 'cwl-runner',
'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
}
'path': '/var/spool/cwl/cwl.output.json',
'kind': 'file'
},
- '/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': 'd20d7cddd1984f105dd3702c7f125afb+60/cwl.input.json',
- 'kind': 'collection'
+ '/var/lib/cwl/cwl.input.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'},
+ 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
+ {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+ ]}
+ },
+ 'kind': 'json'
}
},
'state': 'Committed',
'owner_uuid': None,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'],
'name': 'submit_wf.cwl',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'output_path': '/var/spool/cwl',
'API': True,
'vcpus': 1,
'ram': 1024*1024*1024
- }
+ },
+ "properties": {}
}
stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
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')
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')
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')
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')
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["owner_uuid"] = project_uuid
stubs.api.pipeline_instances().create.assert_called_with(
- body=expect_pipeline)
+ body=JsonDiffMatcher(expect_pipeline))
@stubs
def test_submit_container(self, stubs):
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')
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/job/cwl.input.json']
+ stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
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')
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/job/cwl.input.json']
+ stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ "--output-name="+output_name, '--enable-reuse',
+ '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
+ stubs.expect_container_spec["output_name"] = output_name
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')
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/job/cwl.input.json']
+ stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ "--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)
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')
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')
+ @mock.patch("arvados.collection.CollectionReader")
+ @mock.patch("time.sleep")
+ @stubs
+ def test_submit_file_keepref(self, stubs, tm, collectionReader):
+ capture_stdout = cStringIO.StringIO()
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_keepref_wf.cwl"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+
+ @mock.patch("arvados.collection.CollectionReader")
+ @mock.patch("time.sleep")
+ @stubs
+ def test_submit_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=containers", "--debug",
+ "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ expect_container = {
+ 'priority': 1,
+ 'mounts': {
+ '/var/spool/cwl': {
+ 'writable': True,
+ 'kind': 'collection'
+ },
+ 'stdout': {
+ 'path': '/var/spool/cwl/cwl.output.json',
+ 'kind': 'file'
+ },
+ '/var/lib/cwl/workflow': {
+ 'portable_data_hash': '99999999999999999999999999999994+99',
+ 'kind': 'collection'
+ },
+ '/var/lib/cwl/cwl.input.json': {
+ 'content': {
+ 'x': 'XxX'
+ },
+ 'kind': 'json'
+ }
+ }, 'state': 'Committed',
+ 'owner_uuid': None,
+ 'output_path': '/var/spool/cwl',
+ 'name': 'expect_arvworkflow.cwl#main',
+ 'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
+ 'cwd': '/var/spool/cwl',
+ 'runtime_constraints': {
+ 'API': True,
+ 'vcpus': 1,
+ 'ram': 1073741824
+ },
+ "properties": {}
+ }
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+ @mock.patch("time.sleep")
+ @stubs
+ def test_submit_arvworkflow(self, stubs, tm):
+ capture_stdout = cStringIO.StringIO()
+
+ with open("tests/wf/expect_arvworkflow.cwl") as f:
+ stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
+
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ expect_container = {
+ 'priority': 1,
+ 'mounts': {
+ '/var/spool/cwl': {
+ 'writable': True,
+ 'kind': 'collection'
+ },
+ 'stdout': {
+ 'path': '/var/spool/cwl/cwl.output.json',
+ 'kind': 'file'
+ },
+ '/var/lib/cwl/workflow.json': {
+ 'kind': 'json',
+ 'json': {
+ 'cwlVersion': 'v1.0',
+ '$graph': [
+ {
+ 'inputs': [
+ {
+ 'inputBinding': {'position': 1},
+ 'type': 'string',
+ 'id': '#submit_tool.cwl/x'}
+ ],
+ 'requirements': [
+ {'dockerPull': 'debian:8', 'class': 'DockerRequirement'}
+ ],
+ 'id': '#submit_tool.cwl',
+ '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': []
+ }
+ ]
+ }
+ },
+ '/var/lib/cwl/cwl.input.json': {
+ 'content': {
+ 'x': 'XxX'
+ },
+ 'kind': 'json'
+ }
+ }, 'state': 'Committed',
+ 'owner_uuid': None,
+ 'output_path': '/var/spool/cwl',
+ 'name': 'a test workflow',
+ 'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--enable-reuse', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
+ 'cwd': '/var/spool/cwl',
+ 'runtime_constraints': {
+ 'API': True,
+ 'vcpus': 1,
+ 'ram': 1073741824
+ },
+ "properties": {
+ "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
+ }
+ }
+
+ 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_name(self, stubs):
capture_stdout = cStringIO.StringIO()
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+
@mock.patch("arvados.commands.keepdocker.find_one_image_hash")
@mock.patch("cwltool.docker.get_image")
@mock.patch("arvados.api")
},
},
'repository': 'arvados',
- 'script_version': arvados_cwl.__version__,
+ 'script_version': 'master',
+ 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
'script': 'cwl-runner',
},
},
projects / arvados.git / blobdiff