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 stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
84 stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
86 stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
87 stubs.api.jobs().create().execute.return_value = {
88 "uuid": stubs.expect_job_uuid,
92 stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
93 stubs.api.container_requests().create().execute.return_value = {
94 "uuid": stubs.expect_container_request_uuid,
95 "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
99 stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
100 stubs.api.pipeline_templates().create().execute.return_value = {
101 "uuid": stubs.expect_pipeline_template_uuid,
103 stubs.expect_job_spec = {
104 'runtime_constraints': {
105 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
106 'min_ram_mb_per_node': 1024
108 'script_parameters': {
110 'basename': 'blorp.txt',
111 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
115 'basename': '99999999999999999999999999999998+99',
116 'location': 'keep:99999999999999999999999999999998+99',
120 'basename': 'anonymous',
122 "basename": "renamed.txt",
124 "location": "keep:99999999999999999999999999999998+99/file1.txt"
128 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main'
130 'repository': 'arvados',
131 'script_version': 'master',
132 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
133 'script': 'cwl-runner'
135 stubs.pipeline_component = stubs.expect_job_spec.copy()
136 stubs.expect_pipeline_instance = {
137 'name': 'submit_wf.cwl',
138 'state': 'RunningOnServer',
142 'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
143 'script_parameters': {
144 'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
145 'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'}},
146 'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
148 {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
150 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
151 'arv:enable_reuse': True,
152 'arv:on_error': 'continue'
154 'repository': 'arvados',
155 'script_version': 'master',
156 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
157 'script': 'cwl-runner',
158 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
162 stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
163 stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
164 stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
165 stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
166 stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
167 "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
170 stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
171 stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
173 with open("tests/wf/submit_wf_packed.cwl") as f:
174 expect_packed_workflow = yaml.round_trip_load(f)
176 stubs.expect_container_spec = {
183 '/var/lib/cwl/workflow.json': {
184 'content': expect_packed_workflow,
188 'path': '/var/spool/cwl/cwl.output.json',
191 '/var/lib/cwl/cwl.input.json': {
194 'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'},
195 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'},
196 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
197 {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
203 'state': 'Committed',
205 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
206 '--enable-reuse', '--on-error=continue',
207 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
208 'name': 'submit_wf.cwl',
209 'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
210 'output_path': '/var/spool/cwl',
211 'cwd': '/var/spool/cwl',
212 'runtime_constraints': {
215 'ram': 1024*1024*1024
220 stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
221 stubs.api.workflows().create().execute.return_value = {
222 "uuid": stubs.expect_workflow_uuid,
224 def update_mock(**kwargs):
225 stubs.updated_uuid = kwargs.get('uuid')
227 stubs.api.workflows().update.side_effect = update_mock
228 stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
229 "uuid": stubs.updated_uuid,
232 return func(self, stubs, *args, **kwargs)
236 class TestSubmit(unittest.TestCase):
237 @mock.patch("arvados_cwl.runner.arv_docker_get_image")
238 @mock.patch("time.sleep")
240 def test_submit(self, stubs, tm, arvdock):
241 capture_stdout = cStringIO.StringIO()
242 exited = arvados_cwl.main(
243 ["--submit", "--no-wait", "--api=jobs", "--debug",
244 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
245 capture_stdout, sys.stderr, api_client=stubs.api)
246 self.assertEqual(exited, 0)
248 stubs.api.collections().create.assert_has_calls([
249 mock.call(body=JsonDiffMatcher({
251 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
252 'replication_desired': None,
253 'name': 'submit_tool.cwl dependencies',
254 }), ensure_unique_name=True),
255 mock.call(body=JsonDiffMatcher({
257 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
258 'replication_desired': None,
259 'name': 'submit_wf.cwl input',
260 }), ensure_unique_name=True),
261 mock.call(body=JsonDiffMatcher({
263 '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n',
264 'replication_desired': None,
265 'name': 'submit_wf.cwl',
266 }), ensure_unique_name=True) ])
268 arvdock.assert_has_calls([
269 mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
270 mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
273 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
274 stubs.api.pipeline_instances().create.assert_called_with(
275 body=JsonDiffMatcher(expect_pipeline))
276 self.assertEqual(capture_stdout.getvalue(),
277 stubs.expect_pipeline_uuid + '\n')
280 @mock.patch("time.sleep")
282 def test_submit_no_reuse(self, stubs, tm):
283 capture_stdout = cStringIO.StringIO()
284 exited = arvados_cwl.main(
285 ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
286 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
287 capture_stdout, sys.stderr, api_client=stubs.api)
288 self.assertEqual(exited, 0)
290 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
291 expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
293 stubs.api.pipeline_instances().create.assert_called_with(
294 body=JsonDiffMatcher(expect_pipeline))
295 self.assertEqual(capture_stdout.getvalue(),
296 stubs.expect_pipeline_uuid + '\n')
298 @mock.patch("time.sleep")
300 def test_submit_on_error(self, stubs, tm):
301 capture_stdout = cStringIO.StringIO()
302 exited = arvados_cwl.main(
303 ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
304 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
305 capture_stdout, sys.stderr, api_client=stubs.api)
306 self.assertEqual(exited, 0)
308 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
309 expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
311 stubs.api.pipeline_instances().create.assert_called_with(
312 body=JsonDiffMatcher(expect_pipeline))
313 self.assertEqual(capture_stdout.getvalue(),
314 stubs.expect_pipeline_uuid + '\n')
317 @mock.patch("time.sleep")
319 def test_submit_runner_ram(self, stubs, tm):
320 capture_stdout = cStringIO.StringIO()
321 exited = arvados_cwl.main(
322 ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
323 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
324 capture_stdout, sys.stderr, api_client=stubs.api)
325 self.assertEqual(exited, 0)
327 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
328 expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
330 stubs.api.pipeline_instances().create.assert_called_with(
331 body=JsonDiffMatcher(expect_pipeline))
332 self.assertEqual(capture_stdout.getvalue(),
333 stubs.expect_pipeline_uuid + '\n')
336 @mock.patch("time.sleep")
338 def test_submit_invalid_runner_ram(self, stubs, tm):
339 capture_stdout = cStringIO.StringIO()
340 exited = arvados_cwl.main(
341 ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
342 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
343 capture_stdout, sys.stderr, api_client=stubs.api)
344 self.assertEqual(exited, 1)
346 @mock.patch("time.sleep")
348 def test_submit_output_name(self, stubs, tm):
349 output_name = "test_output_name"
351 capture_stdout = cStringIO.StringIO()
352 exited = arvados_cwl.main(
353 ["--submit", "--no-wait", "--debug", "--output-name", output_name,
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"]["script_parameters"]["arv:output_name"] = output_name
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_pipeline_name(self, stubs, tm):
370 capture_stdout = cStringIO.StringIO()
371 exited = arvados_cwl.main(
372 ["--submit", "--no-wait", "--debug", "--name=hello job 123",
373 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
374 capture_stdout, sys.stderr, api_client=stubs.api)
375 self.assertEqual(exited, 0)
377 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
378 expect_pipeline["name"] = "hello job 123"
380 stubs.api.pipeline_instances().create.assert_called_with(
381 body=JsonDiffMatcher(expect_pipeline))
382 self.assertEqual(capture_stdout.getvalue(),
383 stubs.expect_pipeline_uuid + '\n')
385 @mock.patch("time.sleep")
387 def test_submit_output_tags(self, stubs, tm):
388 output_tags = "tag0,tag1,tag2"
390 capture_stdout = cStringIO.StringIO()
391 exited = arvados_cwl.main(
392 ["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
393 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
394 capture_stdout, sys.stderr, api_client=stubs.api)
395 self.assertEqual(exited, 0)
397 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
398 expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
400 stubs.api.pipeline_instances().create.assert_called_with(
401 body=JsonDiffMatcher(expect_pipeline))
402 self.assertEqual(capture_stdout.getvalue(),
403 stubs.expect_pipeline_uuid + '\n')
405 @mock.patch("time.sleep")
407 def test_submit_with_project_uuid(self, stubs, tm):
408 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
410 exited = arvados_cwl.main(
411 ["--submit", "--no-wait",
412 "--project-uuid", project_uuid,
413 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
414 sys.stdout, sys.stderr, api_client=stubs.api)
415 self.assertEqual(exited, 0)
417 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
418 expect_pipeline["owner_uuid"] = project_uuid
419 stubs.api.pipeline_instances().create.assert_called_with(
420 body=JsonDiffMatcher(expect_pipeline))
423 def test_submit_container(self, stubs):
424 capture_stdout = cStringIO.StringIO()
426 exited = arvados_cwl.main(
427 ["--submit", "--no-wait", "--api=containers", "--debug",
428 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
429 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
430 self.assertEqual(exited, 0)
432 logging.exception("")
434 stubs.api.collections().create.assert_has_calls([
435 mock.call(body=JsonDiffMatcher({
437 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
438 'replication_desired': None,
439 'name': 'submit_tool.cwl dependencies',
440 }), ensure_unique_name=True),
441 mock.call(body=JsonDiffMatcher({
443 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
444 'replication_desired': None,
445 'name': 'submit_wf.cwl input',
446 }), ensure_unique_name=True)])
448 expect_container = copy.deepcopy(stubs.expect_container_spec)
449 stubs.api.container_requests().create.assert_called_with(
450 body=JsonDiffMatcher(expect_container))
451 self.assertEqual(capture_stdout.getvalue(),
452 stubs.expect_container_request_uuid + '\n')
455 def test_submit_container_no_reuse(self, stubs):
456 capture_stdout = cStringIO.StringIO()
458 exited = arvados_cwl.main(
459 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
460 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
461 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
462 self.assertEqual(exited, 0)
464 logging.exception("")
466 expect_container = copy.deepcopy(stubs.expect_container_spec)
467 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
468 '--disable-reuse', '--on-error=continue',
469 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
471 stubs.api.container_requests().create.assert_called_with(
472 body=JsonDiffMatcher(expect_container))
473 self.assertEqual(capture_stdout.getvalue(),
474 stubs.expect_container_request_uuid + '\n')
478 def test_submit_container_on_error(self, stubs):
479 capture_stdout = cStringIO.StringIO()
481 exited = arvados_cwl.main(
482 ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
483 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
484 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
485 self.assertEqual(exited, 0)
487 logging.exception("")
489 expect_container = copy.deepcopy(stubs.expect_container_spec)
490 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
491 '--enable-reuse', '--on-error=stop',
492 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
494 stubs.api.container_requests().create.assert_called_with(
495 body=JsonDiffMatcher(expect_container))
496 self.assertEqual(capture_stdout.getvalue(),
497 stubs.expect_container_request_uuid + '\n')
500 def test_submit_container_output_name(self, stubs):
501 output_name = "test_output_name"
503 capture_stdout = cStringIO.StringIO()
505 exited = arvados_cwl.main(
506 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
507 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
508 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
509 self.assertEqual(exited, 0)
511 logging.exception("")
513 expect_container = copy.deepcopy(stubs.expect_container_spec)
514 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
515 "--output-name="+output_name, '--enable-reuse', '--on-error=continue',
516 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
517 expect_container["output_name"] = output_name
519 stubs.api.container_requests().create.assert_called_with(
520 body=JsonDiffMatcher(expect_container))
521 self.assertEqual(capture_stdout.getvalue(),
522 stubs.expect_container_request_uuid + '\n')
526 def test_submit_container_output_ttl(self, stubs):
527 capture_stdout = cStringIO.StringIO()
529 exited = arvados_cwl.main(
530 ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
531 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
532 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
533 self.assertEqual(exited, 0)
535 logging.exception("")
537 expect_container = copy.deepcopy(stubs.expect_container_spec)
538 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
539 '--enable-reuse', '--on-error=continue',
540 "--intermediate-output-ttl=3600",
541 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
543 stubs.api.container_requests().create.assert_called_with(
544 body=JsonDiffMatcher(expect_container))
545 self.assertEqual(capture_stdout.getvalue(),
546 stubs.expect_container_request_uuid + '\n')
549 def test_submit_container_trash_intermediate(self, stubs):
550 capture_stdout = cStringIO.StringIO()
552 exited = arvados_cwl.main(
553 ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
554 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
555 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
556 self.assertEqual(exited, 0)
558 logging.exception("")
560 expect_container = copy.deepcopy(stubs.expect_container_spec)
561 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
562 '--enable-reuse', '--on-error=continue',
563 "--trash-intermediate",
564 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
566 stubs.api.container_requests().create.assert_called_with(
567 body=JsonDiffMatcher(expect_container))
568 self.assertEqual(capture_stdout.getvalue(),
569 stubs.expect_container_request_uuid + '\n')
572 def test_submit_container_output_tags(self, stubs):
573 output_tags = "tag0,tag1,tag2"
575 capture_stdout = cStringIO.StringIO()
577 exited = arvados_cwl.main(
578 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
579 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
580 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
581 self.assertEqual(exited, 0)
583 logging.exception("")
585 expect_container = copy.deepcopy(stubs.expect_container_spec)
586 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
587 "--output-tags="+output_tags, '--enable-reuse', '--on-error=continue',
588 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
590 stubs.api.container_requests().create.assert_called_with(
591 body=JsonDiffMatcher(expect_container))
592 self.assertEqual(capture_stdout.getvalue(),
593 stubs.expect_container_request_uuid + '\n')
596 def test_submit_container_runner_ram(self, stubs):
597 capture_stdout = cStringIO.StringIO()
599 exited = arvados_cwl.main(
600 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
601 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
602 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
603 self.assertEqual(exited, 0)
605 logging.exception("")
607 expect_container = copy.deepcopy(stubs.expect_container_spec)
608 expect_container["runtime_constraints"]["ram"] = 2048*1024*1024
610 stubs.api.container_requests().create.assert_called_with(
611 body=JsonDiffMatcher(expect_container))
612 self.assertEqual(capture_stdout.getvalue(),
613 stubs.expect_container_request_uuid + '\n')
615 @mock.patch("arvados.collection.CollectionReader")
616 @mock.patch("time.sleep")
618 def test_submit_file_keepref(self, stubs, tm, collectionReader):
619 capture_stdout = cStringIO.StringIO()
620 exited = arvados_cwl.main(
621 ["--submit", "--no-wait", "--api=containers", "--debug",
622 "tests/wf/submit_keepref_wf.cwl"],
623 capture_stdout, sys.stderr, api_client=stubs.api)
624 self.assertEqual(exited, 0)
627 @mock.patch("arvados.collection.CollectionReader")
628 @mock.patch("time.sleep")
630 def test_submit_keepref(self, stubs, tm, reader):
631 capture_stdout = cStringIO.StringIO()
633 with open("tests/wf/expect_arvworkflow.cwl") as f:
634 reader().open().__enter__().read.return_value = f.read()
636 exited = arvados_cwl.main(
637 ["--submit", "--no-wait", "--api=containers", "--debug",
638 "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
639 capture_stdout, sys.stderr, api_client=stubs.api)
640 self.assertEqual(exited, 0)
650 'path': '/var/spool/cwl/cwl.output.json',
653 '/var/lib/cwl/workflow': {
654 'portable_data_hash': '99999999999999999999999999999994+99',
657 '/var/lib/cwl/cwl.input.json': {
663 }, 'state': 'Committed',
665 'output_path': '/var/spool/cwl',
666 'name': 'expect_arvworkflow.cwl#main',
667 'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
668 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
669 '--enable-reuse', '--on-error=continue',
670 '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
671 'cwd': '/var/spool/cwl',
672 'runtime_constraints': {
680 stubs.api.container_requests().create.assert_called_with(
681 body=JsonDiffMatcher(expect_container))
682 self.assertEqual(capture_stdout.getvalue(),
683 stubs.expect_container_request_uuid + '\n')
686 @mock.patch("arvados.collection.CollectionReader")
687 @mock.patch("time.sleep")
689 def test_submit_jobs_keepref(self, stubs, tm, reader):
690 capture_stdout = cStringIO.StringIO()
692 with open("tests/wf/expect_arvworkflow.cwl") as f:
693 reader().open().__enter__().read.return_value = f.read()
695 exited = arvados_cwl.main(
696 ["--submit", "--no-wait", "--api=jobs", "--debug",
697 "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
698 capture_stdout, sys.stderr, api_client=stubs.api)
699 self.assertEqual(exited, 0)
701 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
702 expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
703 del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
704 del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
705 expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
706 expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
707 stubs.api.pipeline_instances().create.assert_called_with(
708 body=JsonDiffMatcher(expect_pipeline))
710 @mock.patch("time.sleep")
712 def test_submit_arvworkflow(self, stubs, tm):
713 capture_stdout = cStringIO.StringIO()
715 with open("tests/wf/expect_arvworkflow.cwl") as f:
716 stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
718 exited = arvados_cwl.main(
719 ["--submit", "--no-wait", "--api=containers", "--debug",
720 "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
721 capture_stdout, sys.stderr, api_client=stubs.api)
722 self.assertEqual(exited, 0)
732 'path': '/var/spool/cwl/cwl.output.json',
735 '/var/lib/cwl/workflow.json': {
738 'cwlVersion': 'v1.0',
743 {'type': 'string', 'id': '#main/x'}
746 {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
747 'run': '#submit_tool.cwl',
757 'inputBinding': {'position': 1},
759 'id': '#submit_tool.cwl/x'}
762 {'dockerPull': 'debian:8', 'class': 'DockerRequirement'}
764 'id': '#submit_tool.cwl',
766 'baseCommand': 'cat',
767 'class': 'CommandLineTool'
772 '/var/lib/cwl/cwl.input.json': {
778 }, 'state': 'Committed',
780 'output_path': '/var/spool/cwl',
781 'name': 'a test workflow',
782 'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
783 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
784 '--enable-reuse', '--on-error=continue',
785 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
786 'cwd': '/var/spool/cwl',
787 'runtime_constraints': {
793 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
797 stubs.api.container_requests().create.assert_called_with(
798 body=JsonDiffMatcher(expect_container))
799 self.assertEqual(capture_stdout.getvalue(),
800 stubs.expect_container_request_uuid + '\n')
804 def test_submit_container_name(self, stubs):
805 capture_stdout = cStringIO.StringIO()
807 exited = arvados_cwl.main(
808 ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
809 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
810 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
811 self.assertEqual(exited, 0)
813 logging.exception("")
815 expect_container = copy.deepcopy(stubs.expect_container_spec)
816 expect_container["name"] = "hello container 123"
818 stubs.api.container_requests().create.assert_called_with(
819 body=JsonDiffMatcher(expect_container))
820 self.assertEqual(capture_stdout.getvalue(),
821 stubs.expect_container_request_uuid + '\n')
825 def test_submit_job_runner_image(self, stubs):
826 capture_stdout = cStringIO.StringIO()
828 exited = arvados_cwl.main(
829 ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
830 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
831 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
832 self.assertEqual(exited, 0)
834 logging.exception("")
836 stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123"
838 expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
839 stubs.api.pipeline_instances().create.assert_called_with(
840 body=JsonDiffMatcher(expect_pipeline))
841 self.assertEqual(capture_stdout.getvalue(),
842 stubs.expect_pipeline_uuid + '\n')
845 def test_submit_container_runner_image(self, stubs):
846 capture_stdout = cStringIO.StringIO()
848 exited = arvados_cwl.main(
849 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
850 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
851 capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
852 self.assertEqual(exited, 0)
854 logging.exception("")
856 stubs.expect_container_spec["container_image"] = "arvados/jobs:123"
858 expect_container = copy.deepcopy(stubs.expect_container_spec)
859 stubs.api.container_requests().create.assert_called_with(
860 body=JsonDiffMatcher(expect_container))
861 self.assertEqual(capture_stdout.getvalue(),
862 stubs.expect_container_request_uuid + '\n')
865 @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
866 @mock.patch("cwltool.docker.get_image")
867 @mock.patch("arvados.api")
868 def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
869 arvrunner = mock.MagicMock()
870 arvrunner.project_uuid = ""
871 api.return_value = mock.MagicMock()
872 arvrunner.api = api.return_value
873 arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
874 "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
875 "link_class": "docker_image_repo+tag",
876 "name": "arvados/jobs:"+arvados_cwl.__version__,
878 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
879 {"items": [{"created_at": "",
881 "link_class": "docker_image_hash",
884 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
886 find_one_image_hash.return_value = "123456"
888 arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
892 }], "items_available": 1, "offset": 0},)
893 arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
894 self.assertEqual("arvados/jobs:"+arvados_cwl.__version__,
895 arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
897 class TestCreateTemplate(unittest.TestCase):
898 existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
900 def _adjust_script_params(self, expect_component):
901 expect_component['script_parameters']['x'] = {
905 'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
907 expect_component['script_parameters']['y'] = {
908 'dataclass': 'Collection',
911 'value': '99999999999999999999999999999998+99',
913 expect_component['script_parameters']['z'] = {
914 'dataclass': 'Collection',
920 def test_create(self, stubs):
921 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
923 capture_stdout = cStringIO.StringIO()
925 exited = arvados_cwl.main(
926 ["--create-workflow", "--debug",
928 "--project-uuid", project_uuid,
929 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
930 capture_stdout, sys.stderr, api_client=stubs.api)
931 self.assertEqual(exited, 0)
933 stubs.api.pipeline_instances().create.refute_called()
934 stubs.api.jobs().create.refute_called()
936 expect_component = copy.deepcopy(stubs.expect_job_spec)
937 self._adjust_script_params(expect_component)
940 "submit_wf.cwl": expect_component,
942 "name": "submit_wf.cwl",
943 "owner_uuid": project_uuid,
945 stubs.api.pipeline_templates().create.assert_called_with(
946 body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
948 self.assertEqual(capture_stdout.getvalue(),
949 stubs.expect_pipeline_template_uuid + '\n')
953 def test_create_name(self, stubs):
954 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
956 capture_stdout = cStringIO.StringIO()
958 exited = arvados_cwl.main(
959 ["--create-workflow", "--debug",
960 "--project-uuid", project_uuid,
962 "--name", "testing 123",
963 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
964 capture_stdout, sys.stderr, api_client=stubs.api)
965 self.assertEqual(exited, 0)
967 stubs.api.pipeline_instances().create.refute_called()
968 stubs.api.jobs().create.refute_called()
970 expect_component = copy.deepcopy(stubs.expect_job_spec)
971 self._adjust_script_params(expect_component)
974 "testing 123": expect_component,
976 "name": "testing 123",
977 "owner_uuid": project_uuid,
979 stubs.api.pipeline_templates().create.assert_called_with(
980 body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
982 self.assertEqual(capture_stdout.getvalue(),
983 stubs.expect_pipeline_template_uuid + '\n')
987 def test_update_name(self, stubs):
988 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
990 capture_stdout = cStringIO.StringIO()
992 exited = arvados_cwl.main(
993 ["--update-workflow", self.existing_template_uuid,
995 "--project-uuid", project_uuid,
997 "--name", "testing 123",
998 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
999 capture_stdout, sys.stderr, api_client=stubs.api)
1000 self.assertEqual(exited, 0)
1002 stubs.api.pipeline_instances().create.refute_called()
1003 stubs.api.jobs().create.refute_called()
1005 expect_component = copy.deepcopy(stubs.expect_job_spec)
1006 self._adjust_script_params(expect_component)
1009 "testing 123": expect_component,
1011 "name": "testing 123",
1012 "owner_uuid": project_uuid,
1014 stubs.api.pipeline_templates().create.refute_called()
1015 stubs.api.pipeline_templates().update.assert_called_with(
1016 body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
1018 self.assertEqual(capture_stdout.getvalue(),
1019 self.existing_template_uuid + '\n')
1022 class TestCreateWorkflow(unittest.TestCase):
1023 existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
1024 expect_workflow = StripYAMLComments(
1025 open("tests/wf/expect_packed.cwl").read())
1028 def test_create(self, stubs):
1029 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1031 capture_stdout = cStringIO.StringIO()
1033 exited = arvados_cwl.main(
1034 ["--create-workflow", "--debug",
1036 "--project-uuid", project_uuid,
1037 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1038 capture_stdout, sys.stderr, api_client=stubs.api)
1039 self.assertEqual(exited, 0)
1041 stubs.api.pipeline_templates().create.refute_called()
1042 stubs.api.container_requests().create.refute_called()
1046 "owner_uuid": project_uuid,
1047 "name": "submit_wf.cwl",
1049 "definition": self.expect_workflow,
1052 stubs.api.workflows().create.assert_called_with(
1053 body=JsonDiffMatcher(body))
1055 self.assertEqual(capture_stdout.getvalue(),
1056 stubs.expect_workflow_uuid + '\n')
1060 def test_create_name(self, stubs):
1061 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1063 capture_stdout = cStringIO.StringIO()
1065 exited = arvados_cwl.main(
1066 ["--create-workflow", "--debug",
1068 "--project-uuid", project_uuid,
1069 "--name", "testing 123",
1070 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1071 capture_stdout, sys.stderr, api_client=stubs.api)
1072 self.assertEqual(exited, 0)
1074 stubs.api.pipeline_templates().create.refute_called()
1075 stubs.api.container_requests().create.refute_called()
1079 "owner_uuid": project_uuid,
1080 "name": "testing 123",
1082 "definition": self.expect_workflow,
1085 stubs.api.workflows().create.assert_called_with(
1086 body=JsonDiffMatcher(body))
1088 self.assertEqual(capture_stdout.getvalue(),
1089 stubs.expect_workflow_uuid + '\n')
1092 def test_incompatible_api(self, stubs):
1093 capture_stderr = cStringIO.StringIO()
1094 logging.getLogger('arvados.cwl-runner').addHandler(
1095 logging.StreamHandler(capture_stderr))
1097 exited = arvados_cwl.main(
1098 ["--update-workflow", self.existing_workflow_uuid,
1101 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1102 sys.stderr, sys.stderr, api_client=stubs.api)
1103 self.assertEqual(exited, 1)
1104 self.assertRegexpMatches(
1105 capture_stderr.getvalue(),
1106 "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
1109 def test_update(self, stubs):
1110 capture_stdout = cStringIO.StringIO()
1112 exited = arvados_cwl.main(
1113 ["--update-workflow", self.existing_workflow_uuid,
1115 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1116 capture_stdout, sys.stderr, api_client=stubs.api)
1117 self.assertEqual(exited, 0)
1121 "name": "submit_wf.cwl",
1123 "definition": self.expect_workflow,
1126 stubs.api.workflows().update.assert_called_with(
1127 uuid=self.existing_workflow_uuid,
1128 body=JsonDiffMatcher(body))
1129 self.assertEqual(capture_stdout.getvalue(),
1130 self.existing_workflow_uuid + '\n')
1134 def test_update_name(self, stubs):
1135 capture_stdout = cStringIO.StringIO()
1137 exited = arvados_cwl.main(
1138 ["--update-workflow", self.existing_workflow_uuid,
1139 "--debug", "--name", "testing 123",
1140 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1141 capture_stdout, sys.stderr, api_client=stubs.api)
1142 self.assertEqual(exited, 0)
1146 "name": "testing 123",
1148 "definition": self.expect_workflow,
1151 stubs.api.workflows().update.assert_called_with(
1152 uuid=self.existing_workflow_uuid,
1153 body=JsonDiffMatcher(body))
1154 self.assertEqual(capture_stdout.getvalue(),
1155 self.existing_workflow_uuid + '\n')
1159 def test_create_collection_per_tool(self, stubs):
1160 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1162 capture_stdout = cStringIO.StringIO()
1164 exited = arvados_cwl.main(
1165 ["--create-workflow", "--debug",
1167 "--project-uuid", project_uuid,
1168 "tests/collection_per_tool/collection_per_tool.cwl"],
1169 capture_stdout, sys.stderr, api_client=stubs.api)
1170 self.assertEqual(exited, 0)
1172 toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
1173 expect_workflow = StripYAMLComments(open(toolfile).read())
1177 "owner_uuid": project_uuid,
1178 "name": "collection_per_tool.cwl",
1180 "definition": expect_workflow,
1183 stubs.api.workflows().create.assert_called_with(
1184 body=JsonDiffMatcher(body))
1186 self.assertEqual(capture_stdout.getvalue(),
1187 stubs.expect_workflow_uuid + '\n')
1189 class TestTemplateInputs(unittest.TestCase):
1192 "inputs_test.cwl": {
1193 'runtime_constraints': {
1194 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
1195 'min_ram_mb_per_node': 1024
1197 'script_parameters': {
1199 '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main',
1200 'optionalFloatInput': None,
1203 'dataclass': 'File',
1205 'title': "It's a file; we expect to find some characters in it.",
1206 'description': 'If there were anything further to say, it would be said here,\nor here.'
1210 'dataclass': 'number',
1212 'title': 'Floats like a duck',
1216 'optionalFloatInput': {
1217 'type': ['null', 'float'],
1218 'dataclass': 'number',
1223 'dataclass': 'boolean',
1225 'title': 'True or false?',
1228 'repository': 'arvados',
1229 'script_version': 'master',
1230 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
1231 'script': 'cwl-runner',
1234 "name": "inputs_test.cwl",
1238 def test_inputs_empty(self, stubs):
1239 exited = arvados_cwl.main(
1240 ["--create-template",
1241 "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
1242 cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1243 self.assertEqual(exited, 0)
1245 stubs.api.pipeline_templates().create.assert_called_with(
1246 body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
1249 def test_inputs(self, stubs):
1250 exited = arvados_cwl.main(
1251 ["--create-template",
1252 "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
1253 cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
1254 self.assertEqual(exited, 0)
1256 expect_template = copy.deepcopy(self.expect_template)
1257 params = expect_template[
1258 "components"]["inputs_test.cwl"]["script_parameters"]
1259 params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
1260 params["cwl:tool"] = '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main'
1261 params["floatInput"]["value"] = 1.234
1262 params["boolInput"]["value"] = True
1264 stubs.api.pipeline_templates().create.assert_called_with(
1265 body=JsonDiffMatcher(expect_template), ensure_unique_name=True)