gitinfo_workflow["$graph"][0]["id"] = "file://%s/tests/wf/%s" % (cwd, wfpath)
mocktool = mock.NonCallableMock(tool=gitinfo_workflow["$graph"][0], metadata=gitinfo_workflow)
- git_info = arvados_cwl.executor.ArvCwlExecutor.get_git_info(mocktool)
- expect_packed_workflow.update(git_info)
+ stubs.git_info = arvados_cwl.executor.ArvCwlExecutor.get_git_info(mocktool)
+ expect_packed_workflow.update(stubs.git_info)
- git_props = {"arv:"+k.split("#", 1)[1]: v for k,v in git_info.items()}
+ stubs.git_props = {"arv:"+k.split("#", 1)[1]: v for k,v in stubs.git_info.items()}
if wfname == wfpath:
- container_name = "%s (%s)" % (wfpath, git_props["arv:gitDescribe"])
+ container_name = "%s (%s)" % (wfpath, stubs.git_props["arv:gitDescribe"])
else:
container_name = wfname
'ram': (1024+256)*1024*1024
},
'use_existing': False,
- 'properties': git_props,
+ 'properties': stubs.git_props,
'secret_mounts': {}
}
root_logger.handlers = handlers
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_invalid_runner_ram(self, stubs, tm):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
self.assertEqual(exited, 1)
- @stubs
+ @stubs()
def test_submit_container(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
'replication_desired': None,
- 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
+ 'name': 'submit_wf.cwl ('+ stubs.git_props["arv:gitDescribe"] +') input (169f39d466a5438ac4a90e779bf750c7+53)',
}), ensure_unique_name=False),
mock.call(body=JsonDiffMatcher({
'manifest_text':
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_tool(self, stubs):
# test for issue #16139
exited = arvados_cwl.main(
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_no_reuse(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--disable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["use_existing"] = False
stubs.expect_container_request_uuid + '\n')
- @stubs
+ @stubs()
def test_submit_container_on_error(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=stop',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_output_name(self, stubs):
output_name = "test_output_name"
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_storage_classes(self, stubs):
exited = arvados_cwl.main(
["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
- '--output-name=Output from workflow submit_wf.cwl',
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
"--debug",
"--storage-classes=foo", '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_multiple_storage_classes(self, stubs):
exited = arvados_cwl.main(
["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
"--debug",
"--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
@mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
- @stubs
+ @stubs()
def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
final_output_c = arvados.collection.Collection()
make_output.return_value = ({},final_output_c)
job.side_effect = set_final_output
exited = arvados_cwl.main(
- ["--debug", "--local", "--storage-classes=foo",
+ ["--debug", "--local", "--storage-classes=foo", "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
+ make_output.assert_called_with(u'Output from workflow submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
@mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
@mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
- @stubs
+ @stubs()
def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
final_output_c = arvados.collection.Collection()
make_output.return_value = ({},final_output_c)
job.side_effect = set_final_output
exited = arvados_cwl.main(
- ["--debug", "--local",
+ ["--debug", "--local", "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"})
+ make_output.assert_called_with(u'Output from workflow submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
@mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
@mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
- @stubs
+ @stubs()
def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq):
final_output_c = arvados.collection.Collection()
make_output.return_value = ({},final_output_c)
job.side_effect = set_final_output
exited = arvados_cwl.main(
- ["--debug", "--local",
+ ["--debug", "--local", "--disable-git",
"tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
+ make_output.assert_called_with(u'Output from workflow submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_output_ttl(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl", '--debug',
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug',
'--on-error=continue',
"--intermediate-output-ttl=3600",
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_trash_intermediate(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=continue',
"--trash-intermediate",
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_output_tags(self, stubs):
output_tags = "tag0,tag1,tag2"
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
"--output-tags="+output_tags, '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_runner_ram(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
@mock.patch("arvados.collection.CollectionReader")
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_file_keepref(self, stubs, tm, collectionReader):
collectionReader().exists.return_value = True
collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
@mock.patch("arvados.collection.CollectionReader")
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_keepref(self, stubs, tm, reader):
with open("tests/wf/expect_arvworkflow.cwl") as f:
reader().open().__enter__().read.return_value = f.read()
self.assertEqual(exited, 0)
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_arvworkflow(self, stubs, tm):
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",
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-git",
"962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
'requirements': [
{
'dockerPull': 'debian:buster-slim',
- 'class': 'DockerRequirement',
- "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
+ 'class': 'DockerRequirement'
}
],
'id': '#submit_tool.cwl',
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--enable-reuse', "--collection-cache-size=256",
+ "--output-name=Output from workflow a test workflow",
+ '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
+ 'output_name': 'Output from workflow a test workflow',
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_missing_input(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 1)
- @stubs
+ @stubs()
def test_submit_container_project(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
'--no-log-timestamps', '--disable-validate', '--disable-color',
"--eval-timeout=20", "--thread-count=0",
'--enable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl", '--debug',
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug',
'--on-error=continue',
'--project-uuid='+project_uuid,
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_eval_timeout(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=60.0', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_collection_cache(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=500",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["runtime_constraints"]["ram"] = (1024+500)*1024*1024
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_thread_count(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=20',
'--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_runner_image(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_priority(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__, arvrunner.runtimeContext))
- @stubs
+ @stubs()
def test_submit_secrets(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ stubs.git_props["arv:gitPath"] = "sdk/cwl/tests/wf/secret_wf.cwl"
+ stubs.git_info["http://arvados.org/cwl#gitPath"] = "sdk/cwl/tests/wf/secret_wf.cwl"
+
expect_container = {
"command": [
"arvados-cwl-runner",
'--thread-count=0',
"--enable-reuse",
"--collection-cache-size=256",
- '--output-name=Output from workflow secret_wf.cwl'
- '--debug',
+ '--output-name=Output from workflow secret_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ "--debug",
"--on-error=continue",
"/var/lib/cwl/workflow.json#main",
"/var/lib/cwl/cwl.input.json"
"path": "/var/spool/cwl/cwl.output.json"
}
},
- "name": "secret_wf.cwl",
- "output_name": "Output from workflow secret_wf.cwl",
+ "name": "secret_wf.cwl (%s)" % stubs.git_props["arv:gitDescribe"],
+ "output_name": "Output from workflow secret_wf.cwl (%s)" % stubs.git_props["arv:gitDescribe"],
"output_path": "/var/spool/cwl",
"priority": 500,
- "properties": {},
+ "properties": stubs.git_props,
"runtime_constraints": {
"API": True,
"ram": 1342177280,
"use_existing": False
}
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"].update(stubs.git_info)
+
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_request_uuid(self, stubs):
stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_cluster_id(self, stubs):
stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_validate_cluster_id(self, stubs):
stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
exited = arvados_cwl.main(
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 1)
- @stubs
+ @stubs()
def test_submit_validate_project_uuid(self, stubs):
# Fails with bad cluster prefix
exited = arvados_cwl.main(
@mock.patch("arvados.collection.CollectionReader")
- @stubs
+ @stubs()
def test_submit_uuid_inputs(self, stubs, collectionReader):
collectionReader().exists.return_value = True
collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_mismatched_uuid_inputs(self, stubs):
def list_side_effect(**kwargs):
m = mock.MagicMock()
cwltool_logger.removeHandler(stderr_logger)
@mock.patch("arvados.collection.CollectionReader")
- @stubs
+ @stubs()
def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
capture_stderr = StringIO()
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_enable_preemptible(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug', '--on-error=continue',
'--enable-preemptible',
- '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_disable_preemptible(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug', '--on-error=continue',
'--disable-preemptible',
- '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+ '/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(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+ @stubs()
+ def test_submit_container_prefer_cached_downloads(self, stubs):
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--prefer-cached-downloads",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug', "--on-error=continue", '--prefer-cached-downloads',
+ '/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(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+ @stubs()
+ def test_submit_container_varying_url_params(self, stubs):
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--varying-url-params", "KeyId,Signature",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug', "--on-error=continue", "--varying-url-params=KeyId,Signature",
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
class TestCreateWorkflow(unittest.TestCase):
existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
expect_workflow = StripYAMLComments(
- open("tests/wf/expect_upload_packed.cwl").read().rstrip())
+ open("tests/wf/expect_upload_wrapper.cwl").read().rstrip())
+ expect_workflow_altname = StripYAMLComments(
+ open("tests/wf/expect_upload_wrapper_altname.cwl").read().rstrip())
def setUp(self):
cwltool.process._names = set()
handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)]
root_logger.handlers = handlers
- @stubs
+ @stubs()
def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
["--create-workflow", "--debug",
"--api=containers",
"--project-uuid", project_uuid,
+ "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
"--api=containers",
"--project-uuid", project_uuid,
"--name", "testing 123",
+ "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
"owner_uuid": project_uuid,
"name": "testing 123",
"description": "",
- "definition": self.expect_workflow,
+ "definition": self.expect_workflow_altname,
}
}
stubs.api.workflows().create.assert_called_with(
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_update(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--debug",
+ "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_update_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--debug", "--name", "testing 123",
+ "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
"workflow": {
"name": "testing 123",
"description": "",
- "definition": self.expect_workflow,
+ "definition": self.expect_workflow_altname,
"owner_uuid": project_uuid
}
}
self.existing_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_collection_per_tool(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
["--create-workflow", "--debug",
"--api=containers",
"--project-uuid", project_uuid,
+ "--disable-git",
"tests/collection_per_tool/collection_per_tool.cwl"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
- toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
+ toolfile = "tests/collection_per_tool/collection_per_tool_wrapper.cwl"
expect_workflow = StripYAMLComments(open(toolfile).read().rstrip())
body = {
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_with_imports(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_with_no_input(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
projects / arvados.git / blobdiff