X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/3386dd9826cf143d078aa8985726516932fafa5b..6f1c0e1dd16f53ce4fb7e8785a130e5f588500e5:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 4e343b6265..6f056ab0c4 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -1,60 +1,335 @@ -import unittest -import mock -import arvados_cwl -import sys import arvados import arvados.keep import arvados.collection +import arvados_cwl +import copy +import cStringIO +import functools import hashlib +import mock +import sys +import unittest -class TestSubmit(unittest.TestCase): +from .matcher import JsonDiffMatcher + + +def stubs(func): + @functools.wraps(func) @mock.patch("arvados.commands.keepdocker.list_images_in_arv") @mock.patch("arvados.collection.KeepClient") @mock.patch("arvados.events.subscribe") - def test_submit(self, events, keep, keepdocker): - api = mock.MagicMock() + def wrapped(self, events, KeepClient, keepdocker, *args, **kwargs): + class Stubs: + pass + stubs = Stubs() + stubs.events = events + stubs.KeepClient = KeepClient + stubs.keepdocker = keepdocker + def putstub(p, **kwargs): return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p)) - keep().put.side_effect = putstub - keepdocker.return_value = True - api.users().current().execute.return_value = {"uuid": "zzzzz-tpzed-zzzzzzzzzzzzzzz"} - api.collections().list().execute.return_value = {"items": []} - api.collections().create().execute.side_effect = ({"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1", - "portable_data_hash": "99999999999999999999999999999991+99"}, - {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2", - "portable_data_hash": "99999999999999999999999999999992+99"}) - api.jobs().create().execute.return_value = {"uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", "state": "Queued"} - - arvados_cwl.main(["--debug", "--submit", "--no-wait", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - sys.stdout, sys.stderr, api_client=api) - - api.collections().create.assert_has_calls([ - mock.call(), - mock.call(body={'manifest_text': './tool 84ec4df683711de31b782505389a8843+429 0:16:blub.txt 16:413:submit_tool.cwl\n./wf 81d977a245a41b8e79859fbe00623fd0+344 0:344: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': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', - 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', - 'name': '#' - }, ensure_unique_name=True), - mock.call().execute()]) + stubs.KeepClient().put.side_effect = putstub - api.jobs().create.assert_called_with( - body={ - 'runtime_constraints': { - 'docker_image': 'arvados/jobs' - }, + stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] + stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz" + + stubs.api = mock.MagicMock() + stubs.api.users().current().execute.return_value = { + "uuid": stubs.fake_user_uuid, + } + stubs.api.collections().list().execute.return_value = {"items": []} + stubs.api.collections().create().execute.side_effect = ({ + "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1", + "portable_data_hash": "99999999999999999999999999999991+99", + }, { + "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2", + "portable_data_hash": "99999999999999999999999999999992+99", + }, + { + "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz4", + "portable_data_hash": "99999999999999999999999999999994+99", + "manifest_text": "" + }) + stubs.api.collections().get().execute.return_value = { + "portable_data_hash": "99999999999999999999999999999993+99"} + + stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" + stubs.api.jobs().create().execute.return_value = { + "uuid": stubs.expect_job_uuid, + "state": "Queued", + } + + stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz" + stubs.api.container_requests().create().execute.return_value = { + "uuid": stubs.expect_container_request_uuid, + "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz", + "state": "Queued" + } + + stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz" + stubs.api.pipeline_templates().create().execute.return_value = { + "uuid": stubs.expect_pipeline_template_uuid, + } + stubs.expect_job_spec = { + 'runtime_constraints': { + 'docker_image': 'arvados/jobs' + }, 'script_parameters': { 'x': { 'path': '99999999999999999999999999999992+99/blorp.txt', 'class': 'File' }, - 'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl' + 'cwl:tool': + '99999999999999999999999999999991+99/wf/submit_wf.cwl' }, 'repository': 'arvados', - 'script_version': 'master', - 'script': 'cwl-runner' + 'script_version': 'master', + 'script': 'cwl-runner' + } + + stubs.expect_container_spec = { + 'priority': 1, + 'mounts': { + '/var/spool/cwl': { + 'writable': True, + 'kind': 'collection' + }, + '/var/lib/cwl/workflow': { + 'portable_data_hash': '99999999999999999999999999999991+99', + 'kind': 'collection' + }, + 'stdout': { + 'path': '/var/spool/cwl/cwl.output.json', + 'kind': 'file' + }, + '/var/lib/cwl/job/cwl.input.json': { + 'portable_data_hash': '33be5c865fe12e1e4788d2f1bc627f7a+60/cwl.input.json', + 'kind': 'collection' + } }, + 'state': 'Committed', + 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', + 'command': ['arvados-cwl-runner', '--local', '--api=containers', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'], + 'name': 'submit_wf.cwl', + 'container_image': '99999999999999999999999999999993+99', + 'output_path': '/var/spool/cwl', + 'cwd': '/var/spool/cwl', + 'runtime_constraints': { + 'API': True, + 'vcpus': 1, + 'ram': 268435456 + } + } + return func(self, stubs, *args, **kwargs) + return wrapped + + +class TestSubmit(unittest.TestCase): + @stubs + def test_submit(self, stubs): + capture_stdout = cStringIO.StringIO() + exited = arvados_cwl.main( + ["--submit", "--no-wait", + "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={ + 'manifest_text': + './tool a3954c369b8924d40547ec8cf5f6a7f4+449 ' + '0:16:blub.txt 16:433:submit_tool.cwl\n./wf ' + 'e046cace0b1a0a6ee645f6ea8688f7e2+364 0:364: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': + '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', + 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', + 'name': '#', + }, ensure_unique_name=True), + mock.call().execute()]) + + expect_job = copy.deepcopy(stubs.expect_job_spec) + expect_job["owner_uuid"] = stubs.fake_user_uuid + stubs.api.jobs().create.assert_called_with( + body=expect_job, + find_or_create=True) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_job_uuid + '\n') + + @stubs + def test_submit_with_project_uuid(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + + exited = arvados_cwl.main( + ["--submit", "--no-wait", + "--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_body = copy.deepcopy(stubs.expect_job_spec) + expect_body["owner_uuid"] = project_uuid + stubs.api.jobs().create.assert_called_with( + body=expect_body, find_or_create=True) + + @stubs + def test_submit_container(self, stubs): + capture_stdout = cStringIO.StringIO() + 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) + self.assertEqual(exited, 0) + + stubs.api.collections().create.assert_has_calls([ + mock.call(), + mock.call(body={ + 'manifest_text': + './tool a3954c369b8924d40547ec8cf5f6a7f4+449 ' + '0:16:blub.txt 16:433:submit_tool.cwl\n./wf ' + 'e046cace0b1a0a6ee645f6ea8688f7e2+364 0:364: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': + '. 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", "--no-wait", + "--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': '99999999999999999999999999999992+99/blorp.txt', + } + 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 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"] = '99999999999999999999999999999992+99/blorp.txt' + params["floatInput"]["value"] = 1.234 + params["boolInput"]["value"] = True + + stubs.api.pipeline_templates().create.assert_called_with( + body=JsonDiffMatcher(expect_template), ensure_unique_name=True)