+ 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=expect_pipeline)
+
+ @stubs
+ def test_submit_container(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "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.api.collections().create.assert_has_calls([
+ mock.call(),
+ mock.call(body={
+ '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': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ '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',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'name': 'New collection',
+ 'replication_desired': None,
+ }, ensure_unique_name=True),
+ mock.call().execute(num_retries=4),
+ mock.call(body={
+ 'manifest_text':
+ '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'name': '#',
+ }, ensure_unique_name=True),
+ mock.call().execute()])
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["owner_uuid"] = stubs.fake_user_uuid
+ stubs.api.container_requests().create.assert_called_with(
+ body=expect_container)
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+
+class TestCreateTemplate(unittest.TestCase):
+ @stubs
+ def test_create(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--create-template", "--debug",
+ "--project-uuid", project_uuid,
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ stubs.api.pipeline_instances().create.refute_called()
+ stubs.api.jobs().create.refute_called()
+
+ expect_component = copy.deepcopy(stubs.expect_job_spec)
+ expect_component['script_parameters']['x'] = {
+ 'dataclass': 'File',
+ 'required': True,
+ 'type': 'File',
+ 'value': '99999999999999999999999999999994+99/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',
+ }
+ 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(capture_stdout.getvalue(),
+ stubs.expect_pipeline_template_uuid + '\n')
+
+
+class TestCreateWorkflow(unittest.TestCase):
+ @stubs
+ def test_create(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--create-workflow", "--debug",
+ "--project-uuid", project_uuid,
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ stubs.api.pipeline_templates().create.refute_called()
+ stubs.api.container_requests().create.refute_called()
+
+ with open("tests/wf/expect_packed.cwl") as f:
+ expect_workflow = f.read()
+
+ body = {
+ "workflow": {
+ "owner_uuid": project_uuid,
+ "name": "submit_wf.cwl",
+ "description": "",
+ "definition": expect_workflow
+ }
+ }
+ stubs.api.workflows().create.assert_called_with(
+ body=JsonDiffMatcher(body))
+
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_workflow_uuid + '\n')
+
+
+class TestTemplateInputs(unittest.TestCase):
+ expect_template = {
+ "components": {
+ "inputs_test.cwl": {
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs',
+ },
+ 'script_parameters': {
+ 'cwl:tool':
+ '99999999999999999999999999999991+99/'
+ 'wf/inputs_test.cwl',
+ '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',
+ 'script': 'cwl-runner',
+ },
+ },
+ "name": "inputs_test.cwl",
+ }
+
+ @stubs
+ def test_inputs_empty(self, stubs):
+ exited = arvados_cwl.main(
+ ["--create-template", "--no-wait",
+ "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
+ cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ expect_template = copy.deepcopy(self.expect_template)
+ expect_template["owner_uuid"] = stubs.fake_user_uuid
+
+ stubs.api.pipeline_templates().create.assert_called_with(
+ body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+
+ @stubs
+ def test_inputs(self, stubs):
+ exited = arvados_cwl.main(
+ ["--create-template", "--no-wait",
+ "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
+ cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ self.expect_template["owner_uuid"] = stubs.fake_user_uuid
+
+ expect_template = copy.deepcopy(self.expect_template)
+ expect_template["owner_uuid"] = stubs.fake_user_uuid
+ params = expect_template[
+ "components"]["inputs_test.cwl"]["script_parameters"]
+ params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
+ params["floatInput"]["value"] = 1.234
+ params["boolInput"]["value"] = True