import mock
import sys
import unittest
+import cwltool.process
from io import BytesIO
stubs.api = mock.MagicMock()
stubs.api._rootDesc = get_rootDesc()
+ stubs.api._rootDesc["uuidPrefix"] = "zzzzz"
stubs.api.users().current().execute.return_value = {
"uuid": stubs.fake_user_uuid,
'vcpus': 1,
'ram': (1024+256)*1024*1024
},
- 'use_existing': True,
+ 'use_existing': False,
'properties': {},
'secret_mounts': {}
}
class TestSubmit(unittest.TestCase):
- @mock.patch("arvados_cwl.arvdocker.arv_docker_get_image")
- @mock.patch("time.sleep")
- @stubs
- def test_submit(self, stubs, tm, arvdock):
- def get_image(api_client, dockerRequirement, pull_image, project_uuid):
- if dockerRequirement["dockerPull"] == 'arvados/jobs:'+arvados_cwl.__version__:
- return '999999999999999999999999999999d3+99'
- elif dockerRequirement["dockerPull"] == "debian:8":
- return '999999999999999999999999999999d4+99'
- arvdock.side_effect = get_image
-
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
- stubs.api.collections().create.assert_has_calls([
- mock.call(body=JsonDiffMatcher({
- 'manifest_text':
- '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
- 'replication_desired': None,
- 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
- }), ensure_unique_name=False),
- mock.call(body=JsonDiffMatcher({
- 'manifest_text':
- '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'replication_desired': None,
- 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
- }), ensure_unique_name=False),
- mock.call(body=JsonDiffMatcher({
- 'manifest_text':
- ". 68089141fbf7e020ac90a9d6a575bc8f+1312 0:1312:workflow.cwl\n",
- 'replication_desired': None,
- 'name': 'submit_wf.cwl',
- }), ensure_unique_name=True) ])
-
- arvdock.assert_has_calls([
- mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
- mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8", 'http://arvados.org/cwl#dockerCollectionPDH': '999999999999999999999999999999d4+99'}, 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))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
-
- @mock.patch("time.sleep")
- @stubs
- def test_submit_no_reuse(self, stubs, tm):
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
- expect_pipeline["properties"] = {"run_options": {"enable_job_reuse": False}}
-
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
+ def setUp(self):
+ cwltool.process._names = set()
@stubs
def test_error_when_multiple_storage_classes_specified(self, stubs):
sys.stdin, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 1)
- @mock.patch("time.sleep")
- @stubs
- def test_submit_on_error(self, stubs, tm):
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- 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(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
-
- @mock.patch("time.sleep")
- @stubs
- def test_submit_runner_ram(self, stubs, tm):
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- 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(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
-
@mock.patch("time.sleep")
@stubs
def test_submit_invalid_runner_ram(self, stubs, tm):
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 1)
- @mock.patch("time.sleep")
- @stubs
- def test_submit_output_name(self, stubs, tm):
- output_name = "test_output_name"
-
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug", "--output-name", output_name,
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- 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(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
-
- @mock.patch("time.sleep")
- @stubs
- def test_submit_pipeline_name(self, stubs, tm):
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug", "--name=hello job 123",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["name"] = "hello job 123"
-
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
-
- @mock.patch("time.sleep")
- @stubs
- def test_submit_output_tags(self, stubs, tm):
- output_tags = "tag0,tag1,tag2"
-
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.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:output_tags"] = output_tags
-
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
-
- @mock.patch("time.sleep")
- @stubs
- def test_submit_with_project_uuid(self, stubs, tm):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
-
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug",
- "--project-uuid", project_uuid,
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["owner_uuid"] = project_uuid
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
@stubs
def test_submit_container(self, stubs):
stubs.api.collections().create.assert_has_calls([
mock.call(body=JsonDiffMatcher({
'manifest_text':
- '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
+ '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
'replication_desired': None,
- 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
+ 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
}), ensure_unique_name=False),
mock.call(body=JsonDiffMatcher({
'manifest_text':
- '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
+ '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
'replication_desired': None,
- 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
- }), ensure_unique_name=False)])
+ 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
+ }), ensure_unique_name=False),
+ ])
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
+
+ @stubs
+ def test_submit_container_tool(self, stubs):
+ # test for issue #16139
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/tool/tool_with_sf.cwl", "tests/tool/tool_with_sf.yml"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
@stubs
def test_submit_container_no_reuse(self, stubs):
exited = arvados_cwl.main(
'vcpus': 1,
'ram': 1342177280
},
- 'use_existing': True,
+ 'use_existing': False,
'properties': {},
'secret_mounts': {}
}
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @mock.patch("arvados.collection.CollectionReader")
- @mock.patch("time.sleep")
- @stubs
- def test_submit_jobs_keepref(self, stubs, tm, reader):
- 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"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- 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))
- self.assertEqual(exited, 0)
-
@mock.patch("time.sleep")
@stubs
def test_submit_arvworkflow(self, stubs, tm):
'vcpus': 1,
'ram': 1342177280
},
- 'use_existing': True,
+ 'use_existing': False,
'properties': {
"template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
},
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
- def test_submit_job_runner_image(self, stubs):
- 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"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
-
- stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "999999999999999999999999999999d5+99"
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
-
@stubs
def test_submit_container_runner_image(self, stubs):
exited = arvados_cwl.main(
}
},
"state": "Committed",
- "use_existing": True
+ "use_existing": False
}
stubs.api.container_requests().create.assert_called_with(
@stubs
def test_submit_request_uuid(self, stubs):
+ stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
stubs.api.container_requests().update().execute.return_value = {
cwltool_logger.removeHandler(stderr_logger)
-class TestCreateTemplate(unittest.TestCase):
- existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
-
- def _adjust_script_params(self, expect_component):
- expect_component['script_parameters']['x'] = {
- 'dataclass': 'File',
- 'required': True,
- 'type': 'File',
- 'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
- }
- expect_component['script_parameters']['y'] = {
- 'dataclass': 'Collection',
- 'required': True,
- 'type': 'Directory',
- 'value': '99999999999999999999999999999998+99',
- }
- expect_component['script_parameters']['z'] = {
- 'dataclass': 'Collection',
- 'required': True,
- 'type': 'Directory',
- }
-
- @stubs
- def test_create(self, stubs):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
-
- exited = arvados_cwl.main(
- ["--create-workflow", "--debug",
- "--api=jobs",
- "--project-uuid", project_uuid,
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- stubs.api.pipeline_instances().create.refute_called()
- stubs.api.jobs().create.refute_called()
-
- expect_component = copy.deepcopy(stubs.expect_job_spec)
- self._adjust_script_params(expect_component)
- expect_template = {
- "components": {
- "submit_wf.cwl": expect_component,
- },
- "name": "submit_wf.cwl",
- "owner_uuid": project_uuid,
- }
- stubs.api.pipeline_templates().create.assert_called_with(
- body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
-
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_template_uuid + '\n')
- self.assertEqual(exited, 0)
-
- @stubs
- def test_create_name(self, stubs):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
-
- exited = arvados_cwl.main(
- ["--create-workflow", "--debug",
- "--project-uuid", project_uuid,
- "--api=jobs",
- "--name", "testing 123",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- stubs.api.pipeline_instances().create.refute_called()
- stubs.api.jobs().create.refute_called()
-
- expect_component = copy.deepcopy(stubs.expect_job_spec)
- self._adjust_script_params(expect_component)
- expect_template = {
- "components": {
- "testing 123": expect_component,
- },
- "name": "testing 123",
- "owner_uuid": project_uuid,
- }
- stubs.api.pipeline_templates().create.assert_called_with(
- body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
-
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_template_uuid + '\n')
- self.assertEqual(exited, 0)
-
- @stubs
- def test_update_name(self, stubs):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
-
- exited = arvados_cwl.main(
- ["--update-workflow", self.existing_template_uuid,
- "--debug",
- "--project-uuid", project_uuid,
- "--api=jobs",
- "--name", "testing 123",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- stubs.api.pipeline_instances().create.refute_called()
- stubs.api.jobs().create.refute_called()
-
- expect_component = copy.deepcopy(stubs.expect_job_spec)
- self._adjust_script_params(expect_component)
- expect_template = {
- "components": {
- "testing 123": expect_component,
- },
- "name": "testing 123",
- "owner_uuid": project_uuid,
- }
- stubs.api.pipeline_templates().create.refute_called()
- stubs.api.pipeline_templates().update.assert_called_with(
- body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
-
- self.assertEqual(stubs.capture_stdout.getvalue(),
- self.existing_template_uuid + '\n')
- self.assertEqual(exited, 0)
-
-
class TestCreateWorkflow(unittest.TestCase):
existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
expect_workflow = StripYAMLComments(
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
- def test_incompatible_api(self, stubs):
- capture_stderr = StringIO()
- acr_logger = logging.getLogger('arvados.cwl-runner')
- stderr_logger = logging.StreamHandler(capture_stderr)
- acr_logger.addHandler(stderr_logger)
-
- try:
- exited = arvados_cwl.main(
- ["--update-workflow", self.existing_workflow_uuid,
- "--api=jobs",
- "--debug",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stderr, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 1)
- self.assertRegexpMatches(
- capture_stderr.getvalue(),
- "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
- finally:
- acr_logger.removeHandler(stderr_logger)
@stubs
def test_update(self, stubs):
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
-class TestTemplateInputs(unittest.TestCase):
- expect_template = {
- "components": {
- "inputs_test.cwl": {
- 'runtime_constraints': {
- 'docker_image': '999999999999999999999999999999d3+99',
- 'min_ram_mb_per_node': 1024
- },
- 'script_parameters': {
- 'cwl:tool':
- 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main',
- 'optionalFloatInput': None,
- 'fileInput': {
- 'type': 'File',
- 'dataclass': 'File',
- 'required': True,
- 'title': "It's a file; we expect to find some characters in it.",
- 'description': 'If there were anything further to say, it would be said here,\nor here.'
- },
- 'floatInput': {
- 'type': 'float',
- 'dataclass': 'number',
- 'required': True,
- 'title': 'Floats like a duck',
- 'default': 0.1,
- 'value': 0.1,
- },
- 'optionalFloatInput': {
- 'type': ['null', 'float'],
- 'dataclass': 'number',
- 'required': False,
- },
- 'boolInput': {
- 'type': 'boolean',
- 'dataclass': 'boolean',
- 'required': True,
- 'title': 'True or false?',
- },
- },
- 'repository': 'arvados',
- 'script_version': 'master',
- 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
- 'script': 'cwl-runner',
- },
- },
- "name": "inputs_test.cwl",
- }
-
@stubs
- def test_inputs_empty(self, stubs):
+ def test_create_with_imports(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
exited = arvados_cwl.main(
- ["--create-template",
- "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
+ ["--create-workflow", "--debug",
+ "--api=containers",
+ "--project-uuid", project_uuid,
+ "tests/wf/feddemo/feddemo.cwl"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
- stubs.api.pipeline_templates().create.assert_called_with(
- body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
+ stubs.api.pipeline_templates().create.refute_called()
+ stubs.api.container_requests().create.refute_called()
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
@stubs
- def test_inputs(self, stubs):
+ def test_create_with_no_input(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
exited = arvados_cwl.main(
- ["--create-template",
- "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
+ ["--create-workflow", "--debug",
+ "--api=containers",
+ "--project-uuid", project_uuid,
+ "tests/wf/revsort/revsort.cwl"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
- expect_template = copy.deepcopy(self.expect_template)
- params = expect_template[
- "components"]["inputs_test.cwl"]["script_parameters"]
- params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
- params["cwl:tool"] = 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main'
- params["floatInput"]["value"] = 1.234
- params["boolInput"]["value"] = True
+ stubs.api.pipeline_templates().create.refute_called()
+ stubs.api.container_requests().create.refute_called()
- stubs.api.pipeline_templates().create.assert_called_with(
- body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
projects / arvados.git / blobdiff