1 # Copyright (C) The Arvados Authors. All rights reserved.
3 # SPDX-License-Identifier: Apache-2.0
16 import arvados.collection
18 import arvados_cwl.runner
21 from .matcher import JsonDiffMatcher, StripYAMLComments
22 from .mock_discovery import get_rootDesc
24 import ruamel.yaml as yaml
29 @functools.wraps(func)
30 @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
31 @mock.patch("arvados.collection.KeepClient")
32 @mock.patch("arvados.keep.KeepClient")
33 @mock.patch("arvados.events.subscribe")
34 def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs):
39 stubs.keepdocker = keepdocker
41 def putstub(p, **kwargs):
42 return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
43 keep_client1().put.side_effect = putstub
44 keep_client1.put.side_effect = putstub
45 keep_client2().put.side_effect = putstub
46 keep_client2.put.side_effect = putstub
48 stubs.keep_client = keep_client2
49 stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
50 stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
52 stubs.api = mock.MagicMock()
53 stubs.api._rootDesc = get_rootDesc()
55 stubs.api.users().current().execute.return_value = {
56 "uuid": stubs.fake_user_uuid,
58 stubs.api.collections().list().execute.return_value = {"items": []}
60 class CollectionExecute(object):
61 def __init__(self, exe):
63 def execute(self, num_retries=None):
66 def collection_createstub(created_collections, body, ensure_unique_name=None):
67 mt = body["manifest_text"]
68 uuid = "zzzzz-4zz18-zzzzzzzzzzzzzz%d" % len(created_collections)
69 pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
70 created_collections[uuid] = {
72 "portable_data_hash": pdh,
75 return CollectionExecute(created_collections[uuid])
77 def collection_getstub(created_collections, uuid):
78 for v in created_collections.itervalues():
79 if uuid in (v["uuid"], v["portable_data_hash"]):
80 return CollectionExecute(v)
82 created_collections = {
83 "99999999999999999999999999999998+99": {
85 "portable_data_hash": "99999999999999999999999999999998+99",
86 "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
88 "99999999999999999999999999999994+99": {
90 "portable_data_hash": "99999999999999999999999999999994+99",
91 "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
94 stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
95 stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
97 stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
98 stubs.api.jobs().create().execute.return_value = {
99 "uuid": stubs.expect_job_uuid,
103 stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
104 stubs.api.container_requests().create().execute.return_value = {
105 "uuid": stubs.expect_container_request_uuid,
106 "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
110 stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
111 stubs.api.pipeline_templates().create().execute.return_value = {
112 "uuid": stubs.expect_pipeline_template_uuid,
114 stubs.expect_job_spec = {
115 'runtime_constraints': {
116 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
117 'min_ram_mb_per_node': 1024
119 'script_parameters': {
121 'basename': 'blorp.txt',
122 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
126 'basename': '99999999999999999999999999999998+99',
127 'location': 'keep:99999999999999999999999999999998+99',
131 'basename': 'anonymous',
133 "basename": "renamed.txt",
135 "location": "keep:99999999999999999999999999999998+99/file1.txt"
139 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main'
141 'repository': 'arvados',
142 'script_version': 'master',
143 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
144 'script': 'cwl-runner'
146 stubs.pipeline_component = stubs.expect_job_spec.copy()
147 stubs.expect_pipeline_instance = {
148 'name': 'submit_wf.cwl',
149 'state': 'RunningOnServer',
153 'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
154 'script_parameters': {
155 'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
157 'basename': 'blorp.txt',
159 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
162 'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
165 'basename': 'renamed.txt',
166 'class': 'File', 'location':
167 'keep:99999999999999999999999999999998+99/file1.txt'
170 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
171 'arv:enable_reuse': True,
172 'arv:on_error': 'continue'
174 'repository': 'arvados',
175 'script_version': 'master',
176 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
177 'script': 'cwl-runner',
178 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
182 stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
183 stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
184 stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
185 stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
186 stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
187 "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
190 stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
191 stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
193 with open("tests/wf/submit_wf_packed.cwl") as f:
194 expect_packed_workflow = yaml.round_trip_load(f)
196 stubs.expect_container_spec = {
203 '/var/lib/cwl/workflow.json': {
204 'content': expect_packed_workflow,
208 'path': '/var/spool/cwl/cwl.output.json',
211 '/var/lib/cwl/cwl.input.json': {
215 'basename': '99999999999999999999999999999998+99',
216 'location': 'keep:99999999999999999999999999999998+99',
217 'class': 'Directory'},
219 'basename': u'blorp.txt',
221 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
224 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
225 {'basename': 'renamed.txt',
227 'location': 'keep:99999999999999999999999999999998+99/file1.txt'
234 'state': 'Committed',
236 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
237 '--enable-reuse', '--on-error=continue',
238 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
239 'name': 'submit_wf.cwl',
240 'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
241 'output_path': '/var/spool/cwl',
242 'cwd': '/var/spool/cwl',
243 'runtime_constraints': {
246 'ram': 1024*1024*1024
251 stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
252 stubs.api.workflows().create().execute.return_value = {
253 "uuid": stubs.expect_workflow_uuid,
255 def update_mock(**kwargs):
256 stubs.updated_uuid = kwargs.get('uuid')
258 stubs.api.workflows().update.side_effect = update_mock
259 stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
260 "uuid": stubs.updated_uuid,
263 return func(self, stubs, *args, **kwargs)
267 class TestSubmit(unittest.TestCase):
268 @mock.patch("arvados_cwl.runner.arv_docker_get_image")
269 @mock.patch("time.sleep")
271 def test_submit(self, stubs, tm, arvdock):
272 capture_stdout = cStringIO.StringIO()
273 exited = arvados_cwl.main(
274 ["--submit", "--no-wait", "--api=jobs", "--debug",
275 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
276 capture_stdout, sys.stderr, api_client=stubs.api)
277 self.assertEqual(exited, 0)
279 stubs.api.collections().create.assert_has_calls([
280 mock.call(body=JsonDiffMatcher({
282 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
283 'replication_desired': None,
284 'name': 'submit_tool.cwl dependencies',
285 }), ensure_unique_name=True),
286 mock.call(body=JsonDiffMatcher({
288 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
289 'replication_desired': None,
290 'name': 'submit_wf.cwl input',
291 }), ensure_unique_name=True),
292 mock.call(body=JsonDiffMatcher({
294 '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n',
295 'replication_desired': None,
296 'name': 'submit_wf.cwl',
297 }), ensure_unique_name=True) ])
299 arvdock.assert_has_calls([
300 mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
301 mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
304 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
305 stubs.api.pipeline_instances().create.assert_called_with(
306 body=JsonDiffMatcher(expect_pipeline))
307 self.assertEqual(capture_stdout.getvalue(),
308 stubs.expect_pipeline_uuid + '\n')
311 @mock.patch("time.sleep")
313 def test_submit_no_reuse(self, stubs, tm):
314 capture_stdout = cStringIO.StringIO()
315 exited = arvados_cwl.main(
316 ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
317 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
318 capture_stdout, sys.stderr, api_client=stubs.api)
319 self.assertEqual(exited, 0)
321 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
322 expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
324 stubs.api.pipeline_instances().create.assert_called_with(
325 body=JsonDiffMatcher(expect_pipeline))
326 self.assertEqual(capture_stdout.getvalue(),
327 stubs.expect_pipeline_uuid + '\n')
329 @mock.patch("time.sleep")
331 def test_submit_on_error(self, stubs, tm):
332 capture_stdout = cStringIO.StringIO()
333 exited = arvados_cwl.main(
334 ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
335 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
336 capture_stdout, sys.stderr, api_client=stubs.api)
337 self.assertEqual(exited, 0)
339 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
340 expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
342 stubs.api.pipeline_instances().create.assert_called_with(
343 body=JsonDiffMatcher(expect_pipeline))
344 self.assertEqual(capture_stdout.getvalue(),
345 stubs.expect_pipeline_uuid + '\n')
348 @mock.patch("time.sleep")
350 def test_submit_runner_ram(self, stubs, tm):
351 capture_stdout = cStringIO.StringIO()
352 exited = arvados_cwl.main(
353 ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
354 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
355 capture_stdout, sys.stderr, api_client=stubs.api)
356 self.assertEqual(exited, 0)
358 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
359 expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
361 stubs.api.pipeline_instances().create.assert_called_with(
362 body=JsonDiffMatcher(expect_pipeline))
363 self.assertEqual(capture_stdout.getvalue(),
364 stubs.expect_pipeline_uuid + '\n')
367 @mock.patch("time.sleep")
369 def test_submit_invalid_runner_ram(self, stubs, tm):
370 capture_stdout = cStringIO.StringIO()
371 exited = arvados_cwl.main(
372 ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
373 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
374 capture_stdout, sys.stderr, api_client=stubs.api)
375 self.assertEqual(exited, 1)
377 @mock.patch("time.sleep")
379 def test_submit_output_name(self, stubs, tm):
380 output_name = "test_output_name"
382 capture_stdout = cStringIO.StringIO()
383 exited = arvados_cwl.main(
384 ["--submit", "--no-wait", "--debug", "--output-name", output_name,
385 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
386 capture_stdout, sys.stderr, api_client=stubs.api)
387 self.assertEqual(exited, 0)
389 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
390 expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
392 stubs.api.pipeline_instances().create.assert_called_with(
393 body=JsonDiffMatcher(expect_pipeline))
394 self.assertEqual(capture_stdout.getvalue(),
395 stubs.expect_pipeline_uuid + '\n')
398 @mock.patch("time.sleep")
400 def test_submit_pipeline_name(self, stubs, tm):
401 capture_stdout = cStringIO.StringIO()
402 exited = arvados_cwl.main(
403 ["--submit", "--no-wait", "--debug", "--name=hello job 123",
404 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
405 capture_stdout, sys.stderr, api_client=stubs.api)
406 self.assertEqual(exited, 0)
408 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
409 expect_pipeline["name"] = "hello job 123"
411 stubs.api.pipeline_instances().create.assert_called_with(
412 body=JsonDiffMatcher(expect_pipeline))
413 self.assertEqual(capture_stdout.getvalue(),
414 stubs.expect_pipeline_uuid + '\n')
416 @mock.patch("time.sleep")
418 def test_submit_output_tags(self, stubs, tm):
419 output_tags = "tag0,tag1,tag2"
421 capture_stdout = cStringIO.StringIO()
422 exited = arvados_cwl.main(
423 ["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
424 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
425 capture_stdout, sys.stderr, api_client=stubs.api)
426 self.assertEqual(exited, 0)
428 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
429 expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
431 stubs.api.pipeline_instances().create.assert_called_with(
432 body=JsonDiffMatcher(expect_pipeline))
433 self.assertEqual(capture_stdout.getvalue(),
434 stubs.expect_pipeline_uuid + '\n')
436 @mock.patch("time.sleep")
438 def test_submit_with_project_uuid(self, stubs, tm):
439 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
441 exited = arvados_cwl.main(
442 ["--submit", "--no-wait",
443 "--project-uuid", project_uuid,
444 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
445 sys.stdout, sys.stderr, api_client=stubs.api)
446 self.assertEqual(exited, 0)
448 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
449 expect_pipeline["owner_uuid"] = project_uuid
450 stubs.api.pipeline_instances().create.assert_called_with(
451 body=JsonDiffMatcher(expect_pipeline))
454 def test_submit_container(self, stubs):
455 capture_stdout = cStringIO.StringIO()
457 exited = arvados_cwl.main(
458 ["--submit", "--no-wait", "--api=containers", "--debug",
459 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
460 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
461 self.assertEqual(exited, 0)
463 logging.exception("")
465 stubs.api.collections().create.assert_has_calls([
466 mock.call(body=JsonDiffMatcher({
468 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
469 'replication_desired': None,
470 'name': 'submit_tool.cwl dependencies',
471 }), ensure_unique_name=True),
472 mock.call(body=JsonDiffMatcher({
474 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
475 'replication_desired': None,
476 'name': 'submit_wf.cwl input',
477 }), ensure_unique_name=True)])
479 expect_container = copy.deepcopy(stubs.expect_container_spec)
480 stubs.api.container_requests().create.assert_called_with(
481 body=JsonDiffMatcher(expect_container))
482 self.assertEqual(capture_stdout.getvalue(),
483 stubs.expect_container_request_uuid + '\n')
486 def test_submit_container_no_reuse(self, stubs):
487 capture_stdout = cStringIO.StringIO()
489 exited = arvados_cwl.main(
490 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
491 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
492 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
493 self.assertEqual(exited, 0)
495 logging.exception("")
497 expect_container = copy.deepcopy(stubs.expect_container_spec)
498 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
499 '--disable-reuse', '--on-error=continue',
500 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
502 stubs.api.container_requests().create.assert_called_with(
503 body=JsonDiffMatcher(expect_container))
504 self.assertEqual(capture_stdout.getvalue(),
505 stubs.expect_container_request_uuid + '\n')
509 def test_submit_container_on_error(self, stubs):
510 capture_stdout = cStringIO.StringIO()
512 exited = arvados_cwl.main(
513 ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
514 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
515 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
516 self.assertEqual(exited, 0)
518 logging.exception("")
520 expect_container = copy.deepcopy(stubs.expect_container_spec)
521 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
522 '--enable-reuse', '--on-error=stop',
523 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
525 stubs.api.container_requests().create.assert_called_with(
526 body=JsonDiffMatcher(expect_container))
527 self.assertEqual(capture_stdout.getvalue(),
528 stubs.expect_container_request_uuid + '\n')
531 def test_submit_container_output_name(self, stubs):
532 output_name = "test_output_name"
534 capture_stdout = cStringIO.StringIO()
536 exited = arvados_cwl.main(
537 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
538 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
539 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
540 self.assertEqual(exited, 0)
542 logging.exception("")
544 expect_container = copy.deepcopy(stubs.expect_container_spec)
545 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
546 "--output-name="+output_name, '--enable-reuse', '--on-error=continue',
547 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
548 expect_container["output_name"] = output_name
550 stubs.api.container_requests().create.assert_called_with(
551 body=JsonDiffMatcher(expect_container))
552 self.assertEqual(capture_stdout.getvalue(),
553 stubs.expect_container_request_uuid + '\n')
557 def test_submit_container_output_ttl(self, stubs):
558 capture_stdout = cStringIO.StringIO()
560 exited = arvados_cwl.main(
561 ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
562 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
563 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
564 self.assertEqual(exited, 0)
566 logging.exception("")
568 expect_container = copy.deepcopy(stubs.expect_container_spec)
569 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
570 '--enable-reuse', '--on-error=continue',
571 "--intermediate-output-ttl=3600",
572 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
574 stubs.api.container_requests().create.assert_called_with(
575 body=JsonDiffMatcher(expect_container))
576 self.assertEqual(capture_stdout.getvalue(),
577 stubs.expect_container_request_uuid + '\n')
580 def test_submit_container_trash_intermediate(self, stubs):
581 capture_stdout = cStringIO.StringIO()
583 exited = arvados_cwl.main(
584 ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
585 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
586 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
587 self.assertEqual(exited, 0)
589 logging.exception("")
591 expect_container = copy.deepcopy(stubs.expect_container_spec)
592 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
593 '--enable-reuse', '--on-error=continue',
594 "--trash-intermediate",
595 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
597 stubs.api.container_requests().create.assert_called_with(
598 body=JsonDiffMatcher(expect_container))
599 self.assertEqual(capture_stdout.getvalue(),
600 stubs.expect_container_request_uuid + '\n')
603 def test_submit_container_output_tags(self, stubs):
604 output_tags = "tag0,tag1,tag2"
606 capture_stdout = cStringIO.StringIO()
608 exited = arvados_cwl.main(
609 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
610 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
611 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
612 self.assertEqual(exited, 0)
614 logging.exception("")
616 expect_container = copy.deepcopy(stubs.expect_container_spec)
617 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
618 "--output-tags="+output_tags, '--enable-reuse', '--on-error=continue',
619 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
621 stubs.api.container_requests().create.assert_called_with(
622 body=JsonDiffMatcher(expect_container))
623 self.assertEqual(capture_stdout.getvalue(),
624 stubs.expect_container_request_uuid + '\n')
627 def test_submit_container_runner_ram(self, stubs):
628 capture_stdout = cStringIO.StringIO()
630 exited = arvados_cwl.main(
631 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
632 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
633 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
634 self.assertEqual(exited, 0)
636 logging.exception("")
638 expect_container = copy.deepcopy(stubs.expect_container_spec)
639 expect_container["runtime_constraints"]["ram"] = 2048*1024*1024
641 stubs.api.container_requests().create.assert_called_with(
642 body=JsonDiffMatcher(expect_container))
643 self.assertEqual(capture_stdout.getvalue(),
644 stubs.expect_container_request_uuid + '\n')
646 @mock.patch("arvados.collection.CollectionReader")
647 @mock.patch("time.sleep")
649 def test_submit_file_keepref(self, stubs, tm, collectionReader):
650 capture_stdout = cStringIO.StringIO()
651 exited = arvados_cwl.main(
652 ["--submit", "--no-wait", "--api=containers", "--debug",
653 "tests/wf/submit_keepref_wf.cwl"],
654 capture_stdout, sys.stderr, api_client=stubs.api)
655 self.assertEqual(exited, 0)
658 @mock.patch("arvados.collection.CollectionReader")
659 @mock.patch("time.sleep")
661 def test_submit_keepref(self, stubs, tm, reader):
662 capture_stdout = cStringIO.StringIO()
664 with open("tests/wf/expect_arvworkflow.cwl") as f:
665 reader().open().__enter__().read.return_value = f.read()
667 exited = arvados_cwl.main(
668 ["--submit", "--no-wait", "--api=containers", "--debug",
669 "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
670 capture_stdout, sys.stderr, api_client=stubs.api)
671 self.assertEqual(exited, 0)
681 'path': '/var/spool/cwl/cwl.output.json',
684 '/var/lib/cwl/workflow': {
685 'portable_data_hash': '99999999999999999999999999999994+99',
688 '/var/lib/cwl/cwl.input.json': {
694 }, 'state': 'Committed',
696 'output_path': '/var/spool/cwl',
697 'name': 'expect_arvworkflow.cwl#main',
698 'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
699 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
700 '--enable-reuse', '--on-error=continue',
701 '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
702 'cwd': '/var/spool/cwl',
703 'runtime_constraints': {
711 stubs.api.container_requests().create.assert_called_with(
712 body=JsonDiffMatcher(expect_container))
713 self.assertEqual(capture_stdout.getvalue(),
714 stubs.expect_container_request_uuid + '\n')
717 @mock.patch("arvados.collection.CollectionReader")
718 @mock.patch("time.sleep")
720 def test_submit_jobs_keepref(self, stubs, tm, reader):
721 capture_stdout = cStringIO.StringIO()
723 with open("tests/wf/expect_arvworkflow.cwl") as f:
724 reader().open().__enter__().read.return_value = f.read()
726 exited = arvados_cwl.main(
727 ["--submit", "--no-wait", "--api=jobs", "--debug",
728 "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
729 capture_stdout, sys.stderr, api_client=stubs.api)
730 self.assertEqual(exited, 0)
732 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
733 expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
734 del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
735 del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
736 expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
737 expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
738 stubs.api.pipeline_instances().create.assert_called_with(
739 body=JsonDiffMatcher(expect_pipeline))
741 @mock.patch("time.sleep")
743 def test_submit_arvworkflow(self, stubs, tm):
744 capture_stdout = cStringIO.StringIO()
746 with open("tests/wf/expect_arvworkflow.cwl") as f:
747 stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
749 exited = arvados_cwl.main(
750 ["--submit", "--no-wait", "--api=containers", "--debug",
751 "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
752 capture_stdout, sys.stderr, api_client=stubs.api)
753 self.assertEqual(exited, 0)
763 'path': '/var/spool/cwl/cwl.output.json',
766 '/var/lib/cwl/workflow.json': {
769 'cwlVersion': 'v1.0',
774 {'type': 'string', 'id': '#main/x'}
777 {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
778 'run': '#submit_tool.cwl',
788 'inputBinding': {'position': 1},
790 'id': '#submit_tool.cwl/x'}
793 {'dockerPull': 'debian:8', 'class': 'DockerRequirement'}
795 'id': '#submit_tool.cwl',
797 'baseCommand': 'cat',
798 'class': 'CommandLineTool'
803 '/var/lib/cwl/cwl.input.json': {
809 }, 'state': 'Committed',
811 'output_path': '/var/spool/cwl',
812 'name': 'a test workflow',
813 'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
814 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
815 '--enable-reuse', '--on-error=continue',
816 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
817 'cwd': '/var/spool/cwl',
818 'runtime_constraints': {
824 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
828 stubs.api.container_requests().create.assert_called_with(
829 body=JsonDiffMatcher(expect_container))
830 self.assertEqual(capture_stdout.getvalue(),
831 stubs.expect_container_request_uuid + '\n')
835 def test_submit_container_name(self, stubs):
836 capture_stdout = cStringIO.StringIO()
838 exited = arvados_cwl.main(
839 ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
840 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
841 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
842 self.assertEqual(exited, 0)
844 logging.exception("")
846 expect_container = copy.deepcopy(stubs.expect_container_spec)
847 expect_container["name"] = "hello container 123"
849 stubs.api.container_requests().create.assert_called_with(
850 body=JsonDiffMatcher(expect_container))
851 self.assertEqual(capture_stdout.getvalue(),
852 stubs.expect_container_request_uuid + '\n')
856 def test_submit_container_project(self, stubs):
857 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
858 capture_stdout = cStringIO.StringIO()
860 exited = arvados_cwl.main(
861 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
862 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
863 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
864 self.assertEqual(exited, 0)
866 logging.exception("")
868 expect_container = copy.deepcopy(stubs.expect_container_spec)
869 expect_container["owner_uuid"] = project_uuid
870 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
871 '--enable-reuse', '--on-error=continue', '--project-uuid='+project_uuid,
872 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
874 stubs.api.container_requests().create.assert_called_with(
875 body=JsonDiffMatcher(expect_container))
876 self.assertEqual(capture_stdout.getvalue(),
877 stubs.expect_container_request_uuid + '\n')
881 def test_submit_job_runner_image(self, stubs):
882 capture_stdout = cStringIO.StringIO()
884 exited = arvados_cwl.main(
885 ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
886 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
887 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
888 self.assertEqual(exited, 0)
890 logging.exception("")
892 stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123"
894 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
895 stubs.api.pipeline_instances().create.assert_called_with(
896 body=JsonDiffMatcher(expect_pipeline))
897 self.assertEqual(capture_stdout.getvalue(),
898 stubs.expect_pipeline_uuid + '\n')
901 def test_submit_container_runner_image(self, stubs):
902 capture_stdout = cStringIO.StringIO()
904 exited = arvados_cwl.main(
905 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
906 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
907 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
908 self.assertEqual(exited, 0)
910 logging.exception("")
912 stubs.expect_container_spec["container_image"] = "arvados/jobs:123"
914 expect_container = copy.deepcopy(stubs.expect_container_spec)
915 stubs.api.container_requests().create.assert_called_with(
916 body=JsonDiffMatcher(expect_container))
917 self.assertEqual(capture_stdout.getvalue(),
918 stubs.expect_container_request_uuid + '\n')
921 @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
922 @mock.patch("cwltool.docker.get_image")
923 @mock.patch("arvados.api")
924 def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
925 arvrunner = mock.MagicMock()
926 arvrunner.project_uuid = ""
927 api.return_value = mock.MagicMock()
928 arvrunner.api = api.return_value
929 arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
930 "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
931 "link_class": "docker_image_repo+tag",
932 "name": "arvados/jobs:"+arvados_cwl.__version__,
934 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
935 {"items": [{"created_at": "",
937 "link_class": "docker_image_hash",
940 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
942 find_one_image_hash.return_value = "123456"
944 arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
948 }], "items_available": 1, "offset": 0},)
949 arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
950 self.assertEqual("arvados/jobs:"+arvados_cwl.__version__,
951 arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
953 class TestCreateTemplate(unittest.TestCase):
954 existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
956 def _adjust_script_params(self, expect_component):
957 expect_component['script_parameters']['x'] = {
961 'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
963 expect_component['script_parameters']['y'] = {
964 'dataclass': 'Collection',
967 'value': '99999999999999999999999999999998+99',
969 expect_component['script_parameters']['z'] = {
970 'dataclass': 'Collection',
976 def test_create(self, stubs):
977 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
979 capture_stdout = cStringIO.StringIO()
981 exited = arvados_cwl.main(
982 ["--create-workflow", "--debug",
984 "--project-uuid", project_uuid,
985 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
986 capture_stdout, sys.stderr, api_client=stubs.api)
987 self.assertEqual(exited, 0)
989 stubs.api.pipeline_instances().create.refute_called()
990 stubs.api.jobs().create.refute_called()
992 expect_component = copy.deepcopy(stubs.expect_job_spec)
993 self._adjust_script_params(expect_component)
996 "submit_wf.cwl": expect_component,
998 "name": "submit_wf.cwl",
999 "owner_uuid": project_uuid,
1001 stubs.api.pipeline_templates().create.assert_called_with(
1002 body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
1004 self.assertEqual(capture_stdout.getvalue(),
1005 stubs.expect_pipeline_template_uuid + '\n')
1009 def test_create_name(self, stubs):
1010 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1012 capture_stdout = cStringIO.StringIO()
1014 exited = arvados_cwl.main(
1015 ["--create-workflow", "--debug",
1016 "--project-uuid", project_uuid,
1018 "--name", "testing 123",
1019 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1020 capture_stdout, sys.stderr, api_client=stubs.api)
1021 self.assertEqual(exited, 0)
1023 stubs.api.pipeline_instances().create.refute_called()
1024 stubs.api.jobs().create.refute_called()
1026 expect_component = copy.deepcopy(stubs.expect_job_spec)
1027 self._adjust_script_params(expect_component)
1030 "testing 123": expect_component,
1032 "name": "testing 123",
1033 "owner_uuid": project_uuid,
1035 stubs.api.pipeline_templates().create.assert_called_with(
1036 body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
1038 self.assertEqual(capture_stdout.getvalue(),
1039 stubs.expect_pipeline_template_uuid + '\n')
1043 def test_update_name(self, stubs):
1044 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1046 capture_stdout = cStringIO.StringIO()
1048 exited = arvados_cwl.main(
1049 ["--update-workflow", self.existing_template_uuid,
1051 "--project-uuid", project_uuid,
1053 "--name", "testing 123",
1054 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1055 capture_stdout, sys.stderr, api_client=stubs.api)
1056 self.assertEqual(exited, 0)
1058 stubs.api.pipeline_instances().create.refute_called()
1059 stubs.api.jobs().create.refute_called()
1061 expect_component = copy.deepcopy(stubs.expect_job_spec)
1062 self._adjust_script_params(expect_component)
1065 "testing 123": expect_component,
1067 "name": "testing 123",
1068 "owner_uuid": project_uuid,
1070 stubs.api.pipeline_templates().create.refute_called()
1071 stubs.api.pipeline_templates().update.assert_called_with(
1072 body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
1074 self.assertEqual(capture_stdout.getvalue(),
1075 self.existing_template_uuid + '\n')
1078 class TestCreateWorkflow(unittest.TestCase):
1079 existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
1080 expect_workflow = StripYAMLComments(
1081 open("tests/wf/expect_packed.cwl").read())
1084 def test_create(self, stubs):
1085 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1087 capture_stdout = cStringIO.StringIO()
1089 exited = arvados_cwl.main(
1090 ["--create-workflow", "--debug",
1092 "--project-uuid", project_uuid,
1093 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1094 capture_stdout, sys.stderr, api_client=stubs.api)
1095 self.assertEqual(exited, 0)
1097 stubs.api.pipeline_templates().create.refute_called()
1098 stubs.api.container_requests().create.refute_called()
1102 "owner_uuid": project_uuid,
1103 "name": "submit_wf.cwl",
1105 "definition": self.expect_workflow,
1108 stubs.api.workflows().create.assert_called_with(
1109 body=JsonDiffMatcher(body))
1111 self.assertEqual(capture_stdout.getvalue(),
1112 stubs.expect_workflow_uuid + '\n')
1116 def test_create_name(self, stubs):
1117 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1119 capture_stdout = cStringIO.StringIO()
1121 exited = arvados_cwl.main(
1122 ["--create-workflow", "--debug",
1124 "--project-uuid", project_uuid,
1125 "--name", "testing 123",
1126 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1127 capture_stdout, sys.stderr, api_client=stubs.api)
1128 self.assertEqual(exited, 0)
1130 stubs.api.pipeline_templates().create.refute_called()
1131 stubs.api.container_requests().create.refute_called()
1135 "owner_uuid": project_uuid,
1136 "name": "testing 123",
1138 "definition": self.expect_workflow,
1141 stubs.api.workflows().create.assert_called_with(
1142 body=JsonDiffMatcher(body))
1144 self.assertEqual(capture_stdout.getvalue(),
1145 stubs.expect_workflow_uuid + '\n')
1148 def test_incompatible_api(self, stubs):
1149 capture_stderr = cStringIO.StringIO()
1150 logging.getLogger('arvados.cwl-runner').addHandler(
1151 logging.StreamHandler(capture_stderr))
1153 exited = arvados_cwl.main(
1154 ["--update-workflow", self.existing_workflow_uuid,
1157 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1158 sys.stderr, sys.stderr, api_client=stubs.api)
1159 self.assertEqual(exited, 1)
1160 self.assertRegexpMatches(
1161 capture_stderr.getvalue(),
1162 "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
1165 def test_update(self, stubs):
1166 capture_stdout = cStringIO.StringIO()
1168 exited = arvados_cwl.main(
1169 ["--update-workflow", self.existing_workflow_uuid,
1171 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1172 capture_stdout, sys.stderr, api_client=stubs.api)
1173 self.assertEqual(exited, 0)
1177 "name": "submit_wf.cwl",
1179 "definition": self.expect_workflow,
1182 stubs.api.workflows().update.assert_called_with(
1183 uuid=self.existing_workflow_uuid,
1184 body=JsonDiffMatcher(body))
1185 self.assertEqual(capture_stdout.getvalue(),
1186 self.existing_workflow_uuid + '\n')
1190 def test_update_name(self, stubs):
1191 capture_stdout = cStringIO.StringIO()
1193 exited = arvados_cwl.main(
1194 ["--update-workflow", self.existing_workflow_uuid,
1195 "--debug", "--name", "testing 123",
1196 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1197 capture_stdout, sys.stderr, api_client=stubs.api)
1198 self.assertEqual(exited, 0)
1202 "name": "testing 123",
1204 "definition": self.expect_workflow,
1207 stubs.api.workflows().update.assert_called_with(
1208 uuid=self.existing_workflow_uuid,
1209 body=JsonDiffMatcher(body))
1210 self.assertEqual(capture_stdout.getvalue(),
1211 self.existing_workflow_uuid + '\n')
1215 def test_create_collection_per_tool(self, stubs):
1216 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1218 capture_stdout = cStringIO.StringIO()
1220 exited = arvados_cwl.main(
1221 ["--create-workflow", "--debug",
1223 "--project-uuid", project_uuid,
1224 "tests/collection_per_tool/collection_per_tool.cwl"],
1225 capture_stdout, sys.stderr, api_client=stubs.api)
1226 self.assertEqual(exited, 0)
1228 toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
1229 expect_workflow = StripYAMLComments(open(toolfile).read())
1233 "owner_uuid": project_uuid,
1234 "name": "collection_per_tool.cwl",
1236 "definition": expect_workflow,
1239 stubs.api.workflows().create.assert_called_with(
1240 body=JsonDiffMatcher(body))
1242 self.assertEqual(capture_stdout.getvalue(),
1243 stubs.expect_workflow_uuid + '\n')
1245 class TestTemplateInputs(unittest.TestCase):
1248 "inputs_test.cwl": {
1249 'runtime_constraints': {
1250 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
1251 'min_ram_mb_per_node': 1024
1253 'script_parameters': {
1255 '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main',
1256 'optionalFloatInput': None,
1259 'dataclass': 'File',
1261 'title': "It's a file; we expect to find some characters in it.",
1262 'description': 'If there were anything further to say, it would be said here,\nor here.'
1266 'dataclass': 'number',
1268 'title': 'Floats like a duck',
1272 'optionalFloatInput': {
1273 'type': ['null', 'float'],
1274 'dataclass': 'number',
1279 'dataclass': 'boolean',
1281 'title': 'True or false?',
1284 'repository': 'arvados',
1285 'script_version': 'master',
1286 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
1287 'script': 'cwl-runner',
1290 "name": "inputs_test.cwl",
1294 def test_inputs_empty(self, stubs):
1295 exited = arvados_cwl.main(
1296 ["--create-template",
1297 "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
1298 cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1299 self.assertEqual(exited, 0)
1301 stubs.api.pipeline_templates().create.assert_called_with(
1302 body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
1305 def test_inputs(self, stubs):
1306 exited = arvados_cwl.main(
1307 ["--create-template",
1308 "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
1309 cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1310 self.assertEqual(exited, 0)
1312 expect_template = copy.deepcopy(self.expect_template)
1313 params = expect_template[
1314 "components"]["inputs_test.cwl"]["script_parameters"]
1315 params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
1316 params["cwl:tool"] = '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main'
1317 params["floatInput"]["value"] = 1.234
1318 params["boolInput"]["value"] = True
1320 stubs.api.pipeline_templates().create.assert_called_with(
1321 body=JsonDiffMatcher(expect_template), ensure_unique_name=True)