1 # Copyright (C) The Arvados Authors. All rights reserved.
3 # SPDX-License-Identifier: Apache-2.0
5 from future import standard_library
6 standard_library.install_aliases()
7 from builtins import object
8 from builtins import str
9 from future.utils import viewvalues
20 import cwltool.process
23 from io import BytesIO
25 # StringIO.StringIO and io.StringIO have different behavior write() is
26 # called with both python2 (byte) strings and unicode strings
27 # (specifically there's some logging in cwltool that causes trouble).
28 # This isn't a problem on python3 because all string are unicode.
29 if sys.version_info[0] < 3:
30 from StringIO import StringIO
32 from io import StringIO
35 import arvados.collection
37 import arvados_cwl.executor
38 import arvados_cwl.runner
41 from .matcher import JsonDiffMatcher, StripYAMLComments
42 from .mock_discovery import get_rootDesc
44 import ruamel.yaml as yaml
49 @functools.wraps(func)
50 @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
51 @mock.patch("arvados.collection.KeepClient")
52 @mock.patch("arvados.keep.KeepClient")
53 @mock.patch("arvados.events.subscribe")
54 def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs):
59 stubs.keepdocker = keepdocker
61 def putstub(p, **kwargs):
62 return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
63 keep_client1().put.side_effect = putstub
64 keep_client1.put.side_effect = putstub
65 keep_client2().put.side_effect = putstub
66 keep_client2.put.side_effect = putstub
68 stubs.keep_client = keep_client2
69 stubs.docker_images = {
70 "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", "")],
71 "debian:8": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", "")],
72 "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", "")],
73 "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", "")],
75 def kd(a, b, image_name=None, image_tag=None):
76 return stubs.docker_images.get("%s:%s" % (image_name, image_tag), [])
77 stubs.keepdocker.side_effect = kd
79 stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
80 stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz"
82 if sys.version_info[0] < 3:
83 stubs.capture_stdout = BytesIO()
85 stubs.capture_stdout = StringIO()
87 stubs.api = mock.MagicMock()
88 stubs.api._rootDesc = get_rootDesc()
89 stubs.api._rootDesc["uuidPrefix"] = "zzzzz"
91 stubs.api.users().current().execute.return_value = {
92 "uuid": stubs.fake_user_uuid,
94 stubs.api.collections().list().execute.return_value = {"items": []}
95 stubs.api.containers().current().execute.return_value = {
96 "uuid": stubs.fake_container_uuid,
99 class CollectionExecute(object):
100 def __init__(self, exe):
102 def execute(self, num_retries=None):
105 def collection_createstub(created_collections, body, ensure_unique_name=None):
106 mt = body["manifest_text"].encode('utf-8')
107 uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%d" % len(created_collections)
108 pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
109 created_collections[uuid] = {
111 "portable_data_hash": pdh,
112 "manifest_text": mt.decode('utf-8')
114 return CollectionExecute(created_collections[uuid])
116 def collection_getstub(created_collections, uuid):
117 for v in viewvalues(created_collections):
118 if uuid in (v["uuid"], v["portable_data_hash"]):
119 return CollectionExecute(v)
121 created_collections = {
122 "99999999999999999999999999999998+99": {
124 "portable_data_hash": "99999999999999999999999999999998+99",
125 "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
127 "99999999999999999999999999999997+99": {
129 "portable_data_hash": "99999999999999999999999999999997+99",
130 "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt"
132 "99999999999999999999999999999994+99": {
134 "portable_data_hash": "99999999999999999999999999999994+99",
135 "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
137 "zzzzz-4zz18-zzzzzzzzzzzzzd3": {
138 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd3",
139 "portable_data_hash": "999999999999999999999999999999d3+99",
142 "zzzzz-4zz18-zzzzzzzzzzzzzd4": {
143 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd4",
144 "portable_data_hash": "999999999999999999999999999999d4+99",
147 "zzzzz-4zz18-zzzzzzzzzzzzzd5": {
148 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd5",
149 "portable_data_hash": "999999999999999999999999999999d5+99",
152 "zzzzz-4zz18-zzzzzzzzzzzzzd6": {
153 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd6",
154 "portable_data_hash": "999999999999999999999999999999d6+99",
158 stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
159 stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
161 stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
162 stubs.api.jobs().create().execute.return_value = {
163 "uuid": stubs.expect_job_uuid,
167 stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
168 stubs.api.container_requests().create().execute.return_value = {
169 "uuid": stubs.expect_container_request_uuid,
170 "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
174 stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
175 stubs.api.pipeline_templates().create().execute.return_value = {
176 "uuid": stubs.expect_pipeline_template_uuid,
178 stubs.expect_job_spec = {
179 'runtime_constraints': {
180 'docker_image': '999999999999999999999999999999d3+99',
181 'min_ram_mb_per_node': 1024
183 'script_parameters': {
185 'basename': 'blorp.txt',
186 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
190 'basename': '99999999999999999999999999999998+99',
191 'location': 'keep:99999999999999999999999999999998+99',
195 'basename': 'anonymous',
197 "basename": "renamed.txt",
199 "location": "keep:99999999999999999999999999999998+99/file1.txt",
204 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main'
206 'repository': 'arvados',
207 'script_version': 'master',
208 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
209 'script': 'cwl-runner'
211 stubs.pipeline_component = stubs.expect_job_spec.copy()
212 stubs.expect_pipeline_instance = {
213 'name': 'submit_wf.cwl',
214 'state': 'RunningOnServer',
218 'runtime_constraints': {'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024},
219 'script_parameters': {
220 'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
222 'basename': 'blorp.txt',
224 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
227 'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
230 'basename': 'renamed.txt',
231 'class': 'File', 'location':
232 'keep:99999999999999999999999999999998+99/file1.txt',
236 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main',
238 'arv:enable_reuse': True,
239 'arv:on_error': 'continue'
241 'repository': 'arvados',
242 'script_version': 'master',
243 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
244 'script': 'cwl-runner',
245 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
249 stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
250 stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
251 stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
252 stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
253 stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
254 "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
257 stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
258 stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
260 with open("tests/wf/submit_wf_packed.cwl") as f:
261 expect_packed_workflow = yaml.round_trip_load(f)
263 stubs.expect_container_spec = {
270 '/var/lib/cwl/workflow.json': {
271 'content': expect_packed_workflow,
275 'path': '/var/spool/cwl/cwl.output.json',
278 '/var/lib/cwl/cwl.input.json': {
282 'basename': '99999999999999999999999999999998+99',
283 'location': 'keep:99999999999999999999999999999998+99',
284 'class': 'Directory'},
286 'basename': u'blorp.txt',
288 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
291 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
292 {'basename': 'renamed.txt',
294 'location': 'keep:99999999999999999999999999999998+99/file1.txt',
303 'state': 'Committed',
304 'command': ['arvados-cwl-runner', '--local', '--api=containers',
305 '--no-log-timestamps', '--disable-validate',
306 '--eval-timeout=20', '--thread-count=1',
307 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
308 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
309 'name': 'submit_wf.cwl',
310 'container_image': '999999999999999999999999999999d3+99',
311 'output_path': '/var/spool/cwl',
312 'cwd': '/var/spool/cwl',
313 'runtime_constraints': {
316 'ram': (1024+256)*1024*1024
318 'use_existing': False,
323 stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
324 stubs.api.workflows().create().execute.return_value = {
325 "uuid": stubs.expect_workflow_uuid,
327 def update_mock(**kwargs):
328 stubs.updated_uuid = kwargs.get('uuid')
330 stubs.api.workflows().update.side_effect = update_mock
331 stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
332 "uuid": stubs.updated_uuid,
335 return func(self, stubs, *args, **kwargs)
339 class TestSubmit(unittest.TestCase):
342 cwltool.process._names = set()
345 def test_error_when_multiple_storage_classes_specified(self, stubs):
346 storage_classes = "foo,bar"
347 exited = arvados_cwl.main(
348 ["--debug", "--storage-classes", storage_classes,
349 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
350 sys.stdin, sys.stderr, api_client=stubs.api)
351 self.assertEqual(exited, 1)
353 @mock.patch("time.sleep")
355 def test_submit_invalid_runner_ram(self, stubs, tm):
356 exited = arvados_cwl.main(
357 ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
358 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
359 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
360 self.assertEqual(exited, 1)
364 def test_submit_container(self, stubs):
365 exited = arvados_cwl.main(
366 ["--submit", "--no-wait", "--api=containers", "--debug",
367 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
368 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
370 stubs.api.collections().create.assert_has_calls([
371 mock.call(body=JsonDiffMatcher({
373 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
374 'replication_desired': None,
375 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
376 }), ensure_unique_name=False),
377 mock.call(body=JsonDiffMatcher({
379 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
380 'replication_desired': None,
381 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
382 }), ensure_unique_name=False),
385 expect_container = copy.deepcopy(stubs.expect_container_spec)
386 stubs.api.container_requests().create.assert_called_with(
387 body=JsonDiffMatcher(expect_container))
388 self.assertEqual(stubs.capture_stdout.getvalue(),
389 stubs.expect_container_request_uuid + '\n')
390 self.assertEqual(exited, 0)
394 def test_submit_container_tool(self, stubs):
395 # test for issue #16139
396 exited = arvados_cwl.main(
397 ["--submit", "--no-wait", "--api=containers", "--debug",
398 "tests/tool/tool_with_sf.cwl", "tests/tool/tool_with_sf.yml"],
399 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
401 self.assertEqual(stubs.capture_stdout.getvalue(),
402 stubs.expect_container_request_uuid + '\n')
403 self.assertEqual(exited, 0)
406 def test_submit_container_no_reuse(self, stubs):
407 exited = arvados_cwl.main(
408 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
409 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
410 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
412 expect_container = copy.deepcopy(stubs.expect_container_spec)
413 expect_container["command"] = [
414 'arvados-cwl-runner', '--local', '--api=containers',
415 '--no-log-timestamps', '--disable-validate',
416 '--eval-timeout=20', '--thread-count=1',
417 '--disable-reuse', "--collection-cache-size=256",
418 '--debug', '--on-error=continue',
419 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
420 expect_container["use_existing"] = False
422 stubs.api.container_requests().create.assert_called_with(
423 body=JsonDiffMatcher(expect_container))
424 self.assertEqual(stubs.capture_stdout.getvalue(),
425 stubs.expect_container_request_uuid + '\n')
426 self.assertEqual(exited, 0)
429 def test_submit_container_reuse_disabled_by_workflow(self, stubs):
430 exited = arvados_cwl.main(
431 ["--submit", "--no-wait", "--api=containers", "--debug",
432 "tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"],
433 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
434 self.assertEqual(exited, 0)
436 expect_container = copy.deepcopy(stubs.expect_container_spec)
437 expect_container["command"] = [
438 'arvados-cwl-runner', '--local', '--api=containers',
439 '--no-log-timestamps', '--disable-validate',
440 '--eval-timeout=20', '--thread-count=1',
441 '--disable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
442 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
443 expect_container["use_existing"] = False
444 expect_container["name"] = "submit_wf_no_reuse.cwl"
445 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
447 "class": "http://arvados.org/cwl#ReuseRequirement",
448 "enableReuse": False,
451 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
452 "arv": "http://arvados.org/cwl#",
453 "cwltool": "http://commonwl.org/cwltool#"
456 stubs.api.container_requests().create.assert_called_with(
457 body=JsonDiffMatcher(expect_container))
458 self.assertEqual(stubs.capture_stdout.getvalue(),
459 stubs.expect_container_request_uuid + '\n')
463 def test_submit_container_on_error(self, stubs):
464 exited = arvados_cwl.main(
465 ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
466 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
467 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
469 expect_container = copy.deepcopy(stubs.expect_container_spec)
470 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
471 '--no-log-timestamps', '--disable-validate',
472 '--eval-timeout=20', '--thread-count=1',
473 '--enable-reuse', "--collection-cache-size=256",
474 '--debug', '--on-error=stop',
475 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
477 stubs.api.container_requests().create.assert_called_with(
478 body=JsonDiffMatcher(expect_container))
479 self.assertEqual(stubs.capture_stdout.getvalue(),
480 stubs.expect_container_request_uuid + '\n')
481 self.assertEqual(exited, 0)
484 def test_submit_container_output_name(self, stubs):
485 output_name = "test_output_name"
487 exited = arvados_cwl.main(
488 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
489 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
490 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
492 expect_container = copy.deepcopy(stubs.expect_container_spec)
493 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
494 '--no-log-timestamps', '--disable-validate',
495 '--eval-timeout=20', '--thread-count=1',
496 '--enable-reuse', "--collection-cache-size=256",
497 "--output-name="+output_name, '--debug', '--on-error=continue',
498 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
499 expect_container["output_name"] = output_name
501 stubs.api.container_requests().create.assert_called_with(
502 body=JsonDiffMatcher(expect_container))
503 self.assertEqual(stubs.capture_stdout.getvalue(),
504 stubs.expect_container_request_uuid + '\n')
505 self.assertEqual(exited, 0)
508 def test_submit_storage_classes(self, stubs):
509 exited = arvados_cwl.main(
510 ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
511 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
512 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
514 expect_container = copy.deepcopy(stubs.expect_container_spec)
515 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
516 '--no-log-timestamps', '--disable-validate',
517 '--eval-timeout=20', '--thread-count=1',
518 '--enable-reuse', "--collection-cache-size=256", "--debug",
519 "--storage-classes=foo", '--on-error=continue',
520 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
522 stubs.api.container_requests().create.assert_called_with(
523 body=JsonDiffMatcher(expect_container))
524 self.assertEqual(stubs.capture_stdout.getvalue(),
525 stubs.expect_container_request_uuid + '\n')
526 self.assertEqual(exited, 0)
528 @mock.patch("arvados_cwl.task_queue.TaskQueue")
529 @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
530 @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
532 def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
533 def set_final_output(job_order, output_callback, runtimeContext):
534 output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
536 job.side_effect = set_final_output
538 exited = arvados_cwl.main(
539 ["--debug", "--local", "--storage-classes=foo",
540 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
541 sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
543 make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
544 self.assertEqual(exited, 0)
546 @mock.patch("arvados_cwl.task_queue.TaskQueue")
547 @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
548 @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
550 def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
551 def set_final_output(job_order, output_callback, runtimeContext):
552 output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
554 job.side_effect = set_final_output
556 exited = arvados_cwl.main(
557 ["--debug", "--local",
558 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
559 sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
561 make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
562 self.assertEqual(exited, 0)
565 def test_submit_container_output_ttl(self, stubs):
566 exited = arvados_cwl.main(
567 ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
568 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
569 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
571 expect_container = copy.deepcopy(stubs.expect_container_spec)
572 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
573 '--no-log-timestamps', '--disable-validate',
574 '--eval-timeout=20', '--thread-count=1',
575 '--enable-reuse', "--collection-cache-size=256", '--debug',
576 '--on-error=continue',
577 "--intermediate-output-ttl=3600",
578 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
580 stubs.api.container_requests().create.assert_called_with(
581 body=JsonDiffMatcher(expect_container))
582 self.assertEqual(stubs.capture_stdout.getvalue(),
583 stubs.expect_container_request_uuid + '\n')
584 self.assertEqual(exited, 0)
587 def test_submit_container_trash_intermediate(self, stubs):
588 exited = arvados_cwl.main(
589 ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
590 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
591 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
594 expect_container = copy.deepcopy(stubs.expect_container_spec)
595 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
596 '--no-log-timestamps', '--disable-validate',
597 '--eval-timeout=20', '--thread-count=1',
598 '--enable-reuse', "--collection-cache-size=256",
599 '--debug', '--on-error=continue',
600 "--trash-intermediate",
601 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
603 stubs.api.container_requests().create.assert_called_with(
604 body=JsonDiffMatcher(expect_container))
605 self.assertEqual(stubs.capture_stdout.getvalue(),
606 stubs.expect_container_request_uuid + '\n')
607 self.assertEqual(exited, 0)
610 def test_submit_container_output_tags(self, stubs):
611 output_tags = "tag0,tag1,tag2"
613 exited = arvados_cwl.main(
614 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
615 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
616 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
618 expect_container = copy.deepcopy(stubs.expect_container_spec)
619 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
620 '--no-log-timestamps', '--disable-validate',
621 '--eval-timeout=20', '--thread-count=1',
622 '--enable-reuse', "--collection-cache-size=256",
623 "--output-tags="+output_tags, '--debug', '--on-error=continue',
624 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
626 stubs.api.container_requests().create.assert_called_with(
627 body=JsonDiffMatcher(expect_container))
628 self.assertEqual(stubs.capture_stdout.getvalue(),
629 stubs.expect_container_request_uuid + '\n')
630 self.assertEqual(exited, 0)
633 def test_submit_container_runner_ram(self, stubs):
634 exited = arvados_cwl.main(
635 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
636 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
637 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
639 expect_container = copy.deepcopy(stubs.expect_container_spec)
640 expect_container["runtime_constraints"]["ram"] = (2048+256)*1024*1024
642 stubs.api.container_requests().create.assert_called_with(
643 body=JsonDiffMatcher(expect_container))
644 self.assertEqual(stubs.capture_stdout.getvalue(),
645 stubs.expect_container_request_uuid + '\n')
646 self.assertEqual(exited, 0)
648 @mock.patch("arvados.collection.CollectionReader")
649 @mock.patch("time.sleep")
651 def test_submit_file_keepref(self, stubs, tm, collectionReader):
652 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
653 exited = arvados_cwl.main(
654 ["--submit", "--no-wait", "--api=containers", "--debug",
655 "tests/wf/submit_keepref_wf.cwl"],
656 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
657 self.assertEqual(exited, 0)
659 @mock.patch("arvados.collection.CollectionReader")
660 @mock.patch("time.sleep")
662 def test_submit_keepref(self, stubs, tm, reader):
663 with open("tests/wf/expect_arvworkflow.cwl") as f:
664 reader().open().__enter__().read.return_value = f.read()
666 exited = arvados_cwl.main(
667 ["--submit", "--no-wait", "--api=containers", "--debug",
668 "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
669 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
679 'path': '/var/spool/cwl/cwl.output.json',
682 '/var/lib/cwl/workflow': {
683 'portable_data_hash': '99999999999999999999999999999994+99',
686 '/var/lib/cwl/cwl.input.json': {
692 }, 'state': 'Committed',
693 'output_path': '/var/spool/cwl',
694 'name': 'expect_arvworkflow.cwl#main',
695 'container_image': '999999999999999999999999999999d3+99',
696 'command': ['arvados-cwl-runner', '--local', '--api=containers',
697 '--no-log-timestamps', '--disable-validate',
698 '--eval-timeout=20', '--thread-count=1',
699 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
700 '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
701 'cwd': '/var/spool/cwl',
702 'runtime_constraints': {
707 'use_existing': False,
712 stubs.api.container_requests().create.assert_called_with(
713 body=JsonDiffMatcher(expect_container))
714 self.assertEqual(stubs.capture_stdout.getvalue(),
715 stubs.expect_container_request_uuid + '\n')
716 self.assertEqual(exited, 0)
718 @mock.patch("time.sleep")
720 def test_submit_arvworkflow(self, stubs, tm):
721 with open("tests/wf/expect_arvworkflow.cwl") as f:
722 stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
724 exited = arvados_cwl.main(
725 ["--submit", "--no-wait", "--api=containers", "--debug",
726 "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
727 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
737 'path': '/var/spool/cwl/cwl.output.json',
740 '/var/lib/cwl/workflow.json': {
743 'cwlVersion': 'v1.0',
748 {'type': 'string', 'id': '#main/x'}
751 {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
752 'run': '#submit_tool.cwl',
762 'inputBinding': {'position': 1},
764 'id': '#submit_tool.cwl/x'}
768 'dockerPull': 'debian:8',
769 'class': 'DockerRequirement',
770 "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
773 'id': '#submit_tool.cwl',
775 'baseCommand': 'cat',
776 'class': 'CommandLineTool'
781 '/var/lib/cwl/cwl.input.json': {
787 }, 'state': 'Committed',
788 'output_path': '/var/spool/cwl',
789 'name': 'a test workflow',
790 'container_image': "999999999999999999999999999999d3+99",
791 'command': ['arvados-cwl-runner', '--local', '--api=containers',
792 '--no-log-timestamps', '--disable-validate',
793 '--eval-timeout=20', '--thread-count=1',
794 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
795 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
796 'cwd': '/var/spool/cwl',
797 'runtime_constraints': {
802 'use_existing': False,
804 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
809 stubs.api.container_requests().create.assert_called_with(
810 body=JsonDiffMatcher(expect_container))
811 self.assertEqual(stubs.capture_stdout.getvalue(),
812 stubs.expect_container_request_uuid + '\n')
813 self.assertEqual(exited, 0)
816 def test_submit_container_name(self, stubs):
817 exited = arvados_cwl.main(
818 ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
819 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
820 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
822 expect_container = copy.deepcopy(stubs.expect_container_spec)
823 expect_container["name"] = "hello container 123"
825 stubs.api.container_requests().create.assert_called_with(
826 body=JsonDiffMatcher(expect_container))
827 self.assertEqual(stubs.capture_stdout.getvalue(),
828 stubs.expect_container_request_uuid + '\n')
829 self.assertEqual(exited, 0)
832 def test_submit_missing_input(self, stubs):
833 exited = arvados_cwl.main(
834 ["--submit", "--no-wait", "--api=containers", "--debug",
835 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
836 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
837 self.assertEqual(exited, 0)
839 exited = arvados_cwl.main(
840 ["--submit", "--no-wait", "--api=containers", "--debug",
841 "tests/wf/submit_wf.cwl", "tests/submit_test_job_missing.json"],
842 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
843 self.assertEqual(exited, 1)
846 def test_submit_container_project(self, stubs):
847 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
848 exited = arvados_cwl.main(
849 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
850 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
851 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
853 expect_container = copy.deepcopy(stubs.expect_container_spec)
854 expect_container["owner_uuid"] = project_uuid
855 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
856 '--no-log-timestamps', '--disable-validate',
857 "--eval-timeout=20", "--thread-count=1",
858 '--enable-reuse', "--collection-cache-size=256", '--debug',
859 '--on-error=continue',
860 '--project-uuid='+project_uuid,
861 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
863 stubs.api.container_requests().create.assert_called_with(
864 body=JsonDiffMatcher(expect_container))
865 self.assertEqual(stubs.capture_stdout.getvalue(),
866 stubs.expect_container_request_uuid + '\n')
867 self.assertEqual(exited, 0)
870 def test_submit_container_eval_timeout(self, stubs):
871 exited = arvados_cwl.main(
872 ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
873 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
874 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
876 expect_container = copy.deepcopy(stubs.expect_container_spec)
877 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
878 '--no-log-timestamps', '--disable-validate',
879 '--eval-timeout=60.0', '--thread-count=1',
880 '--enable-reuse', "--collection-cache-size=256",
881 '--debug', '--on-error=continue',
882 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
884 stubs.api.container_requests().create.assert_called_with(
885 body=JsonDiffMatcher(expect_container))
886 self.assertEqual(stubs.capture_stdout.getvalue(),
887 stubs.expect_container_request_uuid + '\n')
888 self.assertEqual(exited, 0)
891 def test_submit_container_collection_cache(self, stubs):
892 exited = arvados_cwl.main(
893 ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
894 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
895 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
897 expect_container = copy.deepcopy(stubs.expect_container_spec)
898 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
899 '--no-log-timestamps', '--disable-validate',
900 '--eval-timeout=20', '--thread-count=1',
901 '--enable-reuse', "--collection-cache-size=500",
902 '--debug', '--on-error=continue',
903 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
904 expect_container["runtime_constraints"]["ram"] = (1024+500)*1024*1024
906 stubs.api.container_requests().create.assert_called_with(
907 body=JsonDiffMatcher(expect_container))
908 self.assertEqual(stubs.capture_stdout.getvalue(),
909 stubs.expect_container_request_uuid + '\n')
910 self.assertEqual(exited, 0)
913 def test_submit_container_thread_count(self, stubs):
914 exited = arvados_cwl.main(
915 ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
916 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
917 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
919 expect_container = copy.deepcopy(stubs.expect_container_spec)
920 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
921 '--no-log-timestamps', '--disable-validate',
922 '--eval-timeout=20', '--thread-count=20',
923 '--enable-reuse', "--collection-cache-size=256",
924 '--debug', '--on-error=continue',
925 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
927 stubs.api.container_requests().create.assert_called_with(
928 body=JsonDiffMatcher(expect_container))
929 self.assertEqual(stubs.capture_stdout.getvalue(),
930 stubs.expect_container_request_uuid + '\n')
931 self.assertEqual(exited, 0)
934 def test_submit_container_runner_image(self, stubs):
935 exited = arvados_cwl.main(
936 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
937 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
938 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
940 stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99"
942 expect_container = copy.deepcopy(stubs.expect_container_spec)
943 stubs.api.container_requests().create.assert_called_with(
944 body=JsonDiffMatcher(expect_container))
945 self.assertEqual(stubs.capture_stdout.getvalue(),
946 stubs.expect_container_request_uuid + '\n')
947 self.assertEqual(exited, 0)
950 def test_submit_priority(self, stubs):
951 exited = arvados_cwl.main(
952 ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
953 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
954 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
956 stubs.expect_container_spec["priority"] = 669
958 expect_container = copy.deepcopy(stubs.expect_container_spec)
959 stubs.api.container_requests().create.assert_called_with(
960 body=JsonDiffMatcher(expect_container))
961 self.assertEqual(stubs.capture_stdout.getvalue(),
962 stubs.expect_container_request_uuid + '\n')
963 self.assertEqual(exited, 0)
966 def test_submit_wf_runner_resources(self, stubs):
967 exited = arvados_cwl.main(
968 ["--submit", "--no-wait", "--api=containers", "--debug",
969 "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"],
970 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
972 expect_container = copy.deepcopy(stubs.expect_container_spec)
973 expect_container["runtime_constraints"] = {
976 "ram": (2000+512) * 2**20
978 expect_container["name"] = "submit_wf_runner_resources.cwl"
979 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
981 "class": "http://arvados.org/cwl#WorkflowRunnerResources",
987 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
988 "arv": "http://arvados.org/cwl#",
990 expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
991 '--no-log-timestamps', '--disable-validate',
992 '--eval-timeout=20', '--thread-count=1',
993 '--enable-reuse', "--collection-cache-size=512", '--debug', '--on-error=continue',
994 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
996 stubs.api.container_requests().create.assert_called_with(
997 body=JsonDiffMatcher(expect_container))
998 self.assertEqual(stubs.capture_stdout.getvalue(),
999 stubs.expect_container_request_uuid + '\n')
1000 self.assertEqual(exited, 0)
1003 arvados_cwl.arvdocker.arv_docker_clear_cache()
1005 @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
1006 @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
1007 @mock.patch("arvados.api")
1008 def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
1009 arvados_cwl.arvdocker.arv_docker_clear_cache()
1011 arvrunner = mock.MagicMock()
1012 arvrunner.project_uuid = ""
1013 api.return_value = mock.MagicMock()
1014 arvrunner.api = api.return_value
1015 arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
1016 "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1017 "link_class": "docker_image_repo+tag",
1018 "name": "arvados/jobs:"+arvados_cwl.__version__,
1020 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
1021 {"items": [{"created_at": "",
1023 "link_class": "docker_image_hash",
1026 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
1028 find_one_image_hash.return_value = "123456"
1030 arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1032 "manifest_text": "",
1034 }], "items_available": 1, "offset": 0},)
1035 arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
1036 arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1037 "portable_data_hash": "9999999999999999999999999999999b+99"}
1038 self.assertEqual("9999999999999999999999999999999b+99",
1039 arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
1043 def test_submit_secrets(self, stubs):
1044 exited = arvados_cwl.main(
1045 ["--submit", "--no-wait", "--api=containers", "--debug",
1046 "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
1047 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1049 expect_container = {
1051 "arvados-cwl-runner",
1054 "--no-log-timestamps",
1055 "--disable-validate",
1056 "--eval-timeout=20",
1059 "--collection-cache-size=256",
1061 "--on-error=continue",
1062 "/var/lib/cwl/workflow.json#main",
1063 "/var/lib/cwl/cwl.input.json"
1065 "container_image": "999999999999999999999999999999d3+99",
1066 "cwd": "/var/spool/cwl",
1068 "/var/lib/cwl/cwl.input.json": {
1071 "$include": "/secrets/s0"
1076 "/var/lib/cwl/workflow.json": {
1081 "cwltool": "http://commonwl.org/cwltool#"
1087 "class": "CommandLineTool",
1090 "class": "http://commonwl.org/cwltool#Secrets",
1092 "#secret_job.cwl/pw"
1096 "id": "#secret_job.cwl",
1099 "id": "#secret_job.cwl/pw",
1105 "id": "#secret_job.cwl/out",
1109 "stdout": "hashed_example.txt",
1112 "class": "InitialWorkDirRequirement",
1115 "entry": "username: user\npassword: $(inputs.pw)\n",
1116 "entryname": "example.conf"
1123 "class": "Workflow",
1126 "class": "DockerRequirement",
1127 "dockerPull": "debian:8",
1128 "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
1131 "class": "http://commonwl.org/cwltool#Secrets",
1147 "outputSource": "#main/step1/out",
1153 "id": "#main/step1",
1156 "id": "#main/step1/pw",
1157 "source": "#main/pw"
1163 "run": "#secret_job.cwl"
1168 "cwlVersion": "v1.0"
1173 "kind": "collection",
1178 "path": "/var/spool/cwl/cwl.output.json"
1181 "name": "secret_wf.cwl",
1182 "output_path": "/var/spool/cwl",
1185 "runtime_constraints": {
1196 "state": "Committed",
1197 "use_existing": False
1200 stubs.api.container_requests().create.assert_called_with(
1201 body=JsonDiffMatcher(expect_container))
1202 self.assertEqual(stubs.capture_stdout.getvalue(),
1203 stubs.expect_container_request_uuid + '\n')
1204 self.assertEqual(exited, 0)
1207 def test_submit_request_uuid(self, stubs):
1208 stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
1209 stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
1211 stubs.api.container_requests().update().execute.return_value = {
1212 "uuid": stubs.expect_container_request_uuid,
1213 "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
1217 exited = arvados_cwl.main(
1218 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
1219 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1220 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1222 stubs.api.container_requests().update.assert_called_with(
1223 uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec))
1224 self.assertEqual(stubs.capture_stdout.getvalue(),
1225 stubs.expect_container_request_uuid + '\n')
1226 self.assertEqual(exited, 0)
1229 def test_submit_container_cluster_id(self, stubs):
1230 stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
1232 exited = arvados_cwl.main(
1233 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb",
1234 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1235 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1237 expect_container = copy.deepcopy(stubs.expect_container_spec)
1239 stubs.api.container_requests().create.assert_called_with(
1240 body=JsonDiffMatcher(expect_container), cluster_id="zbbbb")
1241 self.assertEqual(stubs.capture_stdout.getvalue(),
1242 stubs.expect_container_request_uuid + '\n')
1243 self.assertEqual(exited, 0)
1246 def test_submit_validate_cluster_id(self, stubs):
1247 stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
1248 exited = arvados_cwl.main(
1249 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zcccc",
1250 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1251 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1252 self.assertEqual(exited, 1)
1254 @mock.patch("arvados.collection.CollectionReader")
1256 def test_submit_uuid_inputs(self, stubs, collectionReader):
1257 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
1258 def list_side_effect(**kwargs):
1259 m = mock.MagicMock()
1260 if "count" in kwargs:
1261 m.execute.return_value = {"items": [
1262 {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999998+99"}
1265 m.execute.return_value = {"items": []}
1267 stubs.api.collections().list.side_effect = list_side_effect
1269 exited = arvados_cwl.main(
1270 ["--submit", "--no-wait", "--api=containers", "--debug",
1271 "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
1272 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1274 expect_container = copy.deepcopy(stubs.expect_container_spec)
1275 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['basename'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1276 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1277 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1279 stubs.api.collections().list.assert_has_calls([
1280 mock.call(count='none',
1281 filters=[['uuid', 'in', ['zzzzz-4zz18-zzzzzzzzzzzzzzz']]],
1282 select=['uuid', 'portable_data_hash'])])
1283 stubs.api.container_requests().create.assert_called_with(
1284 body=JsonDiffMatcher(expect_container))
1285 self.assertEqual(stubs.capture_stdout.getvalue(),
1286 stubs.expect_container_request_uuid + '\n')
1287 self.assertEqual(exited, 0)
1290 def test_submit_mismatched_uuid_inputs(self, stubs):
1291 def list_side_effect(**kwargs):
1292 m = mock.MagicMock()
1293 if "count" in kwargs:
1294 m.execute.return_value = {"items": [
1295 {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999997+99"}
1298 m.execute.return_value = {"items": []}
1300 stubs.api.collections().list.side_effect = list_side_effect
1302 for infile in ("tests/submit_test_job_with_mismatched_uuids.json", "tests/submit_test_job_with_inconsistent_uuids.json"):
1303 capture_stderr = StringIO()
1304 cwltool_logger = logging.getLogger('cwltool')
1305 stderr_logger = logging.StreamHandler(capture_stderr)
1306 cwltool_logger.addHandler(stderr_logger)
1309 exited = arvados_cwl.main(
1310 ["--submit", "--no-wait", "--api=containers", "--debug",
1311 "tests/wf/submit_wf.cwl", infile],
1312 stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1314 self.assertEqual(exited, 1)
1315 self.assertRegexpMatches(
1316 re.sub(r'[ \n]+', ' ', capture_stderr.getvalue()),
1317 r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99")
1319 cwltool_logger.removeHandler(stderr_logger)
1321 @mock.patch("arvados.collection.CollectionReader")
1323 def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
1324 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
1325 capture_stderr = StringIO()
1327 cwltool_logger = logging.getLogger('cwltool')
1328 stderr_logger = logging.StreamHandler(capture_stderr)
1329 cwltool_logger.addHandler(stderr_logger)
1331 exited = arvados_cwl.main(
1332 ["--submit", "--no-wait", "--api=containers", "--debug",
1333 "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
1334 stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1337 self.assertEqual(exited, 1)
1338 self.assertRegexpMatches(
1339 capture_stderr.getvalue(),
1340 r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found")
1342 cwltool_logger.removeHandler(stderr_logger)
1345 class TestCreateWorkflow(unittest.TestCase):
1346 existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
1347 expect_workflow = StripYAMLComments(
1348 open("tests/wf/expect_packed.cwl").read())
1351 def test_create(self, stubs):
1352 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1354 exited = arvados_cwl.main(
1355 ["--create-workflow", "--debug",
1357 "--project-uuid", project_uuid,
1358 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1359 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1361 stubs.api.pipeline_templates().create.refute_called()
1362 stubs.api.container_requests().create.refute_called()
1366 "owner_uuid": project_uuid,
1367 "name": "submit_wf.cwl",
1369 "definition": self.expect_workflow,
1372 stubs.api.workflows().create.assert_called_with(
1373 body=JsonDiffMatcher(body))
1375 self.assertEqual(stubs.capture_stdout.getvalue(),
1376 stubs.expect_workflow_uuid + '\n')
1377 self.assertEqual(exited, 0)
1380 def test_create_name(self, stubs):
1381 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1383 exited = arvados_cwl.main(
1384 ["--create-workflow", "--debug",
1386 "--project-uuid", project_uuid,
1387 "--name", "testing 123",
1388 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1389 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1391 stubs.api.pipeline_templates().create.refute_called()
1392 stubs.api.container_requests().create.refute_called()
1396 "owner_uuid": project_uuid,
1397 "name": "testing 123",
1399 "definition": self.expect_workflow,
1402 stubs.api.workflows().create.assert_called_with(
1403 body=JsonDiffMatcher(body))
1405 self.assertEqual(stubs.capture_stdout.getvalue(),
1406 stubs.expect_workflow_uuid + '\n')
1407 self.assertEqual(exited, 0)
1411 def test_update(self, stubs):
1412 exited = arvados_cwl.main(
1413 ["--update-workflow", self.existing_workflow_uuid,
1415 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1416 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1420 "name": "submit_wf.cwl",
1422 "definition": self.expect_workflow,
1425 stubs.api.workflows().update.assert_called_with(
1426 uuid=self.existing_workflow_uuid,
1427 body=JsonDiffMatcher(body))
1428 self.assertEqual(stubs.capture_stdout.getvalue(),
1429 self.existing_workflow_uuid + '\n')
1430 self.assertEqual(exited, 0)
1433 def test_update_name(self, stubs):
1434 exited = arvados_cwl.main(
1435 ["--update-workflow", self.existing_workflow_uuid,
1436 "--debug", "--name", "testing 123",
1437 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1438 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1442 "name": "testing 123",
1444 "definition": self.expect_workflow,
1447 stubs.api.workflows().update.assert_called_with(
1448 uuid=self.existing_workflow_uuid,
1449 body=JsonDiffMatcher(body))
1450 self.assertEqual(stubs.capture_stdout.getvalue(),
1451 self.existing_workflow_uuid + '\n')
1452 self.assertEqual(exited, 0)
1455 def test_create_collection_per_tool(self, stubs):
1456 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1458 exited = arvados_cwl.main(
1459 ["--create-workflow", "--debug",
1461 "--project-uuid", project_uuid,
1462 "tests/collection_per_tool/collection_per_tool.cwl"],
1463 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1465 toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
1466 expect_workflow = StripYAMLComments(open(toolfile).read())
1470 "owner_uuid": project_uuid,
1471 "name": "collection_per_tool.cwl",
1473 "definition": expect_workflow,
1476 stubs.api.workflows().create.assert_called_with(
1477 body=JsonDiffMatcher(body))
1479 self.assertEqual(stubs.capture_stdout.getvalue(),
1480 stubs.expect_workflow_uuid + '\n')
1481 self.assertEqual(exited, 0)
1484 def test_create_with_imports(self, stubs):
1485 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1487 exited = arvados_cwl.main(
1488 ["--create-workflow", "--debug",
1490 "--project-uuid", project_uuid,
1491 "tests/wf/feddemo/feddemo.cwl"],
1492 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1494 stubs.api.pipeline_templates().create.refute_called()
1495 stubs.api.container_requests().create.refute_called()
1497 self.assertEqual(stubs.capture_stdout.getvalue(),
1498 stubs.expect_workflow_uuid + '\n')
1499 self.assertEqual(exited, 0)
1502 def test_create_with_no_input(self, stubs):
1503 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1505 exited = arvados_cwl.main(
1506 ["--create-workflow", "--debug",
1508 "--project-uuid", project_uuid,
1509 "tests/wf/revsort/revsort.cwl"],
1510 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1512 stubs.api.pipeline_templates().create.refute_called()
1513 stubs.api.container_requests().create.refute_called()
1515 self.assertEqual(stubs.capture_stdout.getvalue(),
1516 stubs.expect_workflow_uuid + '\n')
1517 self.assertEqual(exited, 0)