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
24 from io import BytesIO
26 # StringIO.StringIO and io.StringIO have different behavior write() is
27 # called with both python2 (byte) strings and unicode strings
28 # (specifically there's some logging in cwltool that causes trouble).
29 # This isn't a problem on python3 because all string are unicode.
30 if sys.version_info[0] < 3:
31 from StringIO import StringIO
33 from io import StringIO
36 import arvados.collection
38 import arvados_cwl.executor
39 import arvados_cwl.runner
42 from .matcher import JsonDiffMatcher, StripYAMLComments
43 from .mock_discovery import get_rootDesc
45 import ruamel.yaml as yaml
49 def stubs(wfdetails=('submit_wf.cwl', None)):
50 def outer_wrapper(func, *rest):
51 @functools.wraps(func)
52 @mock.patch("arvados_cwl.arvdocker.determine_image_id")
53 @mock.patch("uuid.uuid4")
54 @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
55 @mock.patch("arvados.collection.KeepClient")
56 @mock.patch("arvados.keep.KeepClient")
57 @mock.patch("arvados.events.subscribe")
58 def wrapped(self, events, keep_client1, keep_client2, keepdocker,
59 uuid4, determine_image_id, *args, **kwargs):
68 stubs.keepdocker = keepdocker
70 uuid4.side_effect = ["df80736f-f14d-4b10-b2e3-03aa27f034bb", "df80736f-f14d-4b10-b2e3-03aa27f034b1",
71 "df80736f-f14d-4b10-b2e3-03aa27f034b2", "df80736f-f14d-4b10-b2e3-03aa27f034b3",
72 "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5"]
74 determine_image_id.return_value = None
76 def putstub(p, **kwargs):
77 return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
78 keep_client1().put.side_effect = putstub
79 keep_client1.put.side_effect = putstub
80 keep_client2().put.side_effect = putstub
81 keep_client2.put.side_effect = putstub
83 stubs.keep_client = keep_client2
84 stubs.docker_images = {
85 "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", {})],
86 "debian:buster-slim": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", {})],
87 "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", {})],
88 "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", {})],
90 def kd(a, b, image_name=None, image_tag=None, project_uuid=None):
91 return stubs.docker_images.get("%s:%s" % (image_name, image_tag), [])
92 stubs.keepdocker.side_effect = kd
94 stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
95 stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz"
97 if sys.version_info[0] < 3:
98 stubs.capture_stdout = BytesIO()
100 stubs.capture_stdout = StringIO()
102 stubs.api = mock.MagicMock()
103 stubs.api._rootDesc = get_rootDesc()
104 stubs.api._rootDesc["uuidPrefix"] = "zzzzz"
105 stubs.api._rootDesc["revision"] = "20210628"
107 stubs.api.users().current().execute.return_value = {
108 "uuid": stubs.fake_user_uuid,
110 stubs.api.collections().list().execute.return_value = {"items": []}
111 stubs.api.containers().current().execute.return_value = {
112 "uuid": stubs.fake_container_uuid,
114 stubs.api.config()["StorageClasses"].items.return_value = {
120 class CollectionExecute(object):
121 def __init__(self, exe):
123 def execute(self, num_retries=None):
126 def collection_createstub(created_collections, body, ensure_unique_name=None):
127 mt = body["manifest_text"].encode('utf-8')
128 uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%d" % len(created_collections)
129 pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
130 created_collections[uuid] = {
132 "portable_data_hash": pdh,
133 "manifest_text": mt.decode('utf-8')
135 return CollectionExecute(created_collections[uuid])
137 def collection_getstub(created_collections, uuid):
138 for v in viewvalues(created_collections):
139 if uuid in (v["uuid"], v["portable_data_hash"]):
140 return CollectionExecute(v)
142 created_collections = {
143 "99999999999999999999999999999998+99": {
145 "portable_data_hash": "99999999999999999999999999999998+99",
146 "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
148 "99999999999999999999999999999997+99": {
150 "portable_data_hash": "99999999999999999999999999999997+99",
151 "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt"
153 "99999999999999999999999999999994+99": {
155 "portable_data_hash": "99999999999999999999999999999994+99",
156 "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
158 "zzzzz-4zz18-zzzzzzzzzzzzzd3": {
159 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd3",
160 "portable_data_hash": "999999999999999999999999999999d3+99",
163 "zzzzz-4zz18-zzzzzzzzzzzzzd4": {
164 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd4",
165 "portable_data_hash": "999999999999999999999999999999d4+99",
168 "zzzzz-4zz18-zzzzzzzzzzzzzd5": {
169 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd5",
170 "portable_data_hash": "999999999999999999999999999999d5+99",
173 "zzzzz-4zz18-zzzzzzzzzzzzzd6": {
174 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd6",
175 "portable_data_hash": "999999999999999999999999999999d6+99",
179 stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
180 stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
182 stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
183 stubs.api.jobs().create().execute.return_value = {
184 "uuid": stubs.expect_job_uuid,
188 stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
189 stubs.api.container_requests().create().execute.return_value = {
190 "uuid": stubs.expect_container_request_uuid,
191 "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
195 stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
196 stubs.api.pipeline_templates().create().execute.return_value = {
197 "uuid": stubs.expect_pipeline_template_uuid,
199 stubs.expect_job_spec = {
200 'runtime_constraints': {
201 'docker_image': '999999999999999999999999999999d3+99',
202 'min_ram_mb_per_node': 1024
204 'script_parameters': {
206 'basename': 'blorp.txt',
207 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
211 'basename': '99999999999999999999999999999998+99',
212 'location': 'keep:99999999999999999999999999999998+99',
216 'basename': 'anonymous',
218 "basename": "renamed.txt",
220 "location": "keep:99999999999999999999999999999998+99/file1.txt",
225 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main'
227 'repository': 'arvados',
228 'script_version': 'master',
229 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
230 'script': 'cwl-runner'
232 stubs.pipeline_component = stubs.expect_job_spec.copy()
233 stubs.expect_pipeline_instance = {
234 'name': 'submit_wf.cwl',
235 'state': 'RunningOnServer',
239 'runtime_constraints': {'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024},
240 'script_parameters': {
241 'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
243 'basename': 'blorp.txt',
245 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
248 'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
251 'basename': 'renamed.txt',
252 'class': 'File', 'location':
253 'keep:99999999999999999999999999999998+99/file1.txt',
257 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main',
259 'arv:enable_reuse': True,
260 'arv:on_error': 'continue'
262 'repository': 'arvados',
263 'script_version': 'master',
264 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
265 'script': 'cwl-runner',
266 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
270 stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
271 stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
272 stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
273 stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
274 stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
275 "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
278 stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
279 stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
282 filepath = os.path.join(cwd, "tests/wf/submit_wf_packed.cwl")
283 with open(filepath) as f:
284 expect_packed_workflow = yaml.round_trip_load(f)
289 gitinfo_workflow = copy.deepcopy(expect_packed_workflow)
290 gitinfo_workflow["$graph"][0]["id"] = "file://%s/tests/wf/%s" % (cwd, wfpath)
291 mocktool = mock.NonCallableMock(tool=gitinfo_workflow["$graph"][0], metadata=gitinfo_workflow)
293 git_info = arvados_cwl.executor.ArvCwlExecutor.get_git_info(mocktool)
294 expect_packed_workflow.update(git_info)
296 git_props = {"arv:"+k.split("#", 1)[1]: v for k,v in git_info.items()}
299 container_name = "%s (%s)" % (wfpath, git_props["arv:gitDescribe"])
301 container_name = wfname
303 stubs.expect_container_spec = {
310 '/var/lib/cwl/workflow.json': {
311 'content': expect_packed_workflow,
315 'path': '/var/spool/cwl/cwl.output.json',
318 '/var/lib/cwl/cwl.input.json': {
322 'basename': '99999999999999999999999999999998+99',
323 'location': 'keep:99999999999999999999999999999998+99',
324 'class': 'Directory'},
326 'basename': u'blorp.txt',
328 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
331 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
332 {'basename': 'renamed.txt',
334 'location': 'keep:99999999999999999999999999999998+99/file1.txt',
343 'state': 'Committed',
344 'command': ['arvados-cwl-runner', '--local', '--api=containers',
345 '--no-log-timestamps', '--disable-validate', '--disable-color',
346 '--eval-timeout=20', '--thread-count=0',
347 '--enable-reuse', "--collection-cache-size=256",
348 '--output-name=Output from workflow '+container_name,
349 '--debug', '--on-error=continue',
350 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
351 'name': container_name,
352 'container_image': '999999999999999999999999999999d3+99',
353 'output_name': 'Output from workflow %s' % (container_name),
354 'output_path': '/var/spool/cwl',
355 'cwd': '/var/spool/cwl',
356 'runtime_constraints': {
359 'ram': (1024+256)*1024*1024
361 'use_existing': False,
362 'properties': git_props,
366 stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
367 stubs.api.workflows().create().execute.return_value = {
368 "uuid": stubs.expect_workflow_uuid,
370 def update_mock(**kwargs):
371 stubs.updated_uuid = kwargs.get('uuid')
373 stubs.api.workflows().update.side_effect = update_mock
374 stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
375 "uuid": stubs.updated_uuid,
378 return func(self, stubs, *args, **kwargs)
382 class TestSubmit(unittest.TestCase):
385 cwltool.process._names = set()
386 arvados_cwl.arvdocker.arv_docker_clear_cache()
389 root_logger = logging.getLogger('')
391 # Remove existing RuntimeStatusLoggingHandlers if they exist
392 handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)]
393 root_logger.handlers = handlers
395 @mock.patch("time.sleep")
397 def test_submit_invalid_runner_ram(self, stubs, tm):
398 exited = arvados_cwl.main(
399 ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
400 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
401 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
402 self.assertEqual(exited, 1)
406 def test_submit_container(self, stubs):
407 exited = arvados_cwl.main(
408 ["--submit", "--no-wait", "--api=containers", "--debug",
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 stubs.api.collections().create.assert_has_calls([
413 mock.call(body=JsonDiffMatcher({
415 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
416 'replication_desired': None,
417 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
418 }), ensure_unique_name=False),
419 mock.call(body=JsonDiffMatcher({
421 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
422 'replication_desired': None,
423 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
424 }), ensure_unique_name=False),
427 expect_container = copy.deepcopy(stubs.expect_container_spec)
428 stubs.api.container_requests().create.assert_called_with(
429 body=JsonDiffMatcher(expect_container))
430 self.assertEqual(stubs.capture_stdout.getvalue(),
431 stubs.expect_container_request_uuid + '\n')
432 self.assertEqual(exited, 0)
436 def test_submit_container_tool(self, stubs):
437 # test for issue #16139
438 exited = arvados_cwl.main(
439 ["--submit", "--no-wait", "--api=containers", "--debug",
440 "tests/tool/tool_with_sf.cwl", "tests/tool/tool_with_sf.yml"],
441 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
443 self.assertEqual(stubs.capture_stdout.getvalue(),
444 stubs.expect_container_request_uuid + '\n')
445 self.assertEqual(exited, 0)
448 def test_submit_container_no_reuse(self, stubs):
449 exited = arvados_cwl.main(
450 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
451 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
452 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
454 expect_container = copy.deepcopy(stubs.expect_container_spec)
455 expect_container["command"] = [
456 'arvados-cwl-runner', '--local', '--api=containers',
457 '--no-log-timestamps', '--disable-validate', '--disable-color',
458 '--eval-timeout=20', '--thread-count=0',
459 '--disable-reuse', "--collection-cache-size=256",
460 "--output-name=Output from workflow submit_wf.cwl",
461 '--debug', '--on-error=continue',
462 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
463 expect_container["use_existing"] = False
465 stubs.api.container_requests().create.assert_called_with(
466 body=JsonDiffMatcher(expect_container))
467 self.assertEqual(stubs.capture_stdout.getvalue(),
468 stubs.expect_container_request_uuid + '\n')
469 self.assertEqual(exited, 0)
471 @stubs(('submit_wf_no_reuse.cwl', None))
472 def test_submit_container_reuse_disabled_by_workflow(self, stubs):
473 exited = arvados_cwl.main(
474 ["--submit", "--no-wait", "--api=containers", "--debug",
475 "tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"],
476 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
477 self.assertEqual(exited, 0)
479 expect_container = copy.deepcopy(stubs.expect_container_spec)
480 expect_container["command"] = ["--disable-reuse" if v == "--enable-reuse" else v for v in expect_container["command"]]
481 expect_container["use_existing"] = False
482 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
484 "class": "http://arvados.org/cwl#ReuseRequirement",
485 "enableReuse": False,
488 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
489 "arv": "http://arvados.org/cwl#",
490 "cwltool": "http://commonwl.org/cwltool#"
493 stubs.api.container_requests().create.assert_called_with(
494 body=JsonDiffMatcher(expect_container))
495 self.assertEqual(stubs.capture_stdout.getvalue(),
496 stubs.expect_container_request_uuid + '\n')
500 def test_submit_container_on_error(self, stubs):
501 exited = arvados_cwl.main(
502 ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
503 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
504 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
506 expect_container = copy.deepcopy(stubs.expect_container_spec)
507 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
508 '--no-log-timestamps', '--disable-validate', '--disable-color',
509 '--eval-timeout=20', '--thread-count=0',
510 '--enable-reuse', "--collection-cache-size=256",
511 "--output-name=Output from workflow submit_wf.cwl",
512 '--debug', '--on-error=stop',
513 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
515 stubs.api.container_requests().create.assert_called_with(
516 body=JsonDiffMatcher(expect_container))
517 self.assertEqual(stubs.capture_stdout.getvalue(),
518 stubs.expect_container_request_uuid + '\n')
519 self.assertEqual(exited, 0)
522 def test_submit_container_output_name(self, stubs):
523 output_name = "test_output_name"
525 exited = arvados_cwl.main(
526 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
527 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
528 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
530 expect_container = copy.deepcopy(stubs.expect_container_spec)
531 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
532 '--no-log-timestamps', '--disable-validate', '--disable-color',
533 '--eval-timeout=20', '--thread-count=0',
534 '--enable-reuse', "--collection-cache-size=256",
535 "--output-name="+output_name, '--debug', '--on-error=continue',
536 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
537 expect_container["output_name"] = output_name
539 stubs.api.container_requests().create.assert_called_with(
540 body=JsonDiffMatcher(expect_container))
541 self.assertEqual(stubs.capture_stdout.getvalue(),
542 stubs.expect_container_request_uuid + '\n')
543 self.assertEqual(exited, 0)
546 def test_submit_storage_classes(self, stubs):
547 exited = arvados_cwl.main(
548 ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
549 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
550 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
552 expect_container = copy.deepcopy(stubs.expect_container_spec)
553 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
554 '--no-log-timestamps', '--disable-validate', '--disable-color',
555 '--eval-timeout=20', '--thread-count=0',
556 '--enable-reuse', "--collection-cache-size=256",
557 '--output-name=Output from workflow submit_wf.cwl',
559 "--storage-classes=foo", '--on-error=continue',
560 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
562 stubs.api.container_requests().create.assert_called_with(
563 body=JsonDiffMatcher(expect_container))
564 self.assertEqual(stubs.capture_stdout.getvalue(),
565 stubs.expect_container_request_uuid + '\n')
566 self.assertEqual(exited, 0)
569 def test_submit_multiple_storage_classes(self, stubs):
570 exited = arvados_cwl.main(
571 ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
572 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
573 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
575 expect_container = copy.deepcopy(stubs.expect_container_spec)
576 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
577 '--no-log-timestamps', '--disable-validate', '--disable-color',
578 '--eval-timeout=20', '--thread-count=0',
579 '--enable-reuse', "--collection-cache-size=256",
580 "--output-name=Output from workflow submit_wf.cwl",
582 "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--on-error=continue',
583 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
585 stubs.api.container_requests().create.assert_called_with(
586 body=JsonDiffMatcher(expect_container))
587 self.assertEqual(stubs.capture_stdout.getvalue(),
588 stubs.expect_container_request_uuid + '\n')
589 self.assertEqual(exited, 0)
591 @mock.patch("cwltool.task_queue.TaskQueue")
592 @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
593 @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
595 def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
596 final_output_c = arvados.collection.Collection()
597 make_output.return_value = ({},final_output_c)
599 def set_final_output(job_order, output_callback, runtimeContext):
600 output_callback({"out": "zzzzz"}, "success")
602 job.side_effect = set_final_output
604 exited = arvados_cwl.main(
605 ["--debug", "--local", "--storage-classes=foo",
606 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
607 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
609 make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
610 self.assertEqual(exited, 0)
612 @mock.patch("cwltool.task_queue.TaskQueue")
613 @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
614 @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
616 def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
617 final_output_c = arvados.collection.Collection()
618 make_output.return_value = ({},final_output_c)
619 stubs.api.config().get.return_value = {"default": {"Default": True}}
621 def set_final_output(job_order, output_callback, runtimeContext):
622 output_callback({"out": "zzzzz"}, "success")
624 job.side_effect = set_final_output
626 exited = arvados_cwl.main(
627 ["--debug", "--local",
628 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
629 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
631 make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"})
632 self.assertEqual(exited, 0)
634 @mock.patch("cwltool.task_queue.TaskQueue")
635 @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
636 @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
638 def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq):
639 final_output_c = arvados.collection.Collection()
640 make_output.return_value = ({},final_output_c)
642 def set_final_output(job_order, output_callback, runtimeContext):
643 output_callback({"out": "zzzzz"}, "success")
645 job.side_effect = set_final_output
647 exited = arvados_cwl.main(
648 ["--debug", "--local",
649 "tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"],
650 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
652 make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
653 self.assertEqual(exited, 0)
656 def test_submit_container_output_ttl(self, stubs):
657 exited = arvados_cwl.main(
658 ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
659 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
660 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
662 expect_container = copy.deepcopy(stubs.expect_container_spec)
663 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
664 '--no-log-timestamps', '--disable-validate', '--disable-color',
665 '--eval-timeout=20', '--thread-count=0',
666 '--enable-reuse', "--collection-cache-size=256",
667 "--output-name=Output from workflow submit_wf.cwl", '--debug',
668 '--on-error=continue',
669 "--intermediate-output-ttl=3600",
670 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
672 stubs.api.container_requests().create.assert_called_with(
673 body=JsonDiffMatcher(expect_container))
674 self.assertEqual(stubs.capture_stdout.getvalue(),
675 stubs.expect_container_request_uuid + '\n')
676 self.assertEqual(exited, 0)
679 def test_submit_container_trash_intermediate(self, stubs):
680 exited = arvados_cwl.main(
681 ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
682 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
683 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
686 expect_container = copy.deepcopy(stubs.expect_container_spec)
687 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
688 '--no-log-timestamps', '--disable-validate', '--disable-color',
689 '--eval-timeout=20', '--thread-count=0',
690 '--enable-reuse', "--collection-cache-size=256",
691 '--debug', '--on-error=continue',
692 "--trash-intermediate",
693 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
695 stubs.api.container_requests().create.assert_called_with(
696 body=JsonDiffMatcher(expect_container))
697 self.assertEqual(stubs.capture_stdout.getvalue(),
698 stubs.expect_container_request_uuid + '\n')
699 self.assertEqual(exited, 0)
702 def test_submit_container_output_tags(self, stubs):
703 output_tags = "tag0,tag1,tag2"
705 exited = arvados_cwl.main(
706 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
707 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
708 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
710 expect_container = copy.deepcopy(stubs.expect_container_spec)
711 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
712 '--no-log-timestamps', '--disable-validate', '--disable-color',
713 '--eval-timeout=20', '--thread-count=0',
714 '--enable-reuse', "--collection-cache-size=256",
715 "--output-name=Output from workflow submit_wf.cwl",
716 "--output-tags="+output_tags, '--debug', '--on-error=continue',
717 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
719 stubs.api.container_requests().create.assert_called_with(
720 body=JsonDiffMatcher(expect_container))
721 self.assertEqual(stubs.capture_stdout.getvalue(),
722 stubs.expect_container_request_uuid + '\n')
723 self.assertEqual(exited, 0)
726 def test_submit_container_runner_ram(self, stubs):
727 exited = arvados_cwl.main(
728 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
729 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
730 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
732 expect_container = copy.deepcopy(stubs.expect_container_spec)
733 expect_container["runtime_constraints"]["ram"] = (2048+256)*1024*1024
735 stubs.api.container_requests().create.assert_called_with(
736 body=JsonDiffMatcher(expect_container))
737 self.assertEqual(stubs.capture_stdout.getvalue(),
738 stubs.expect_container_request_uuid + '\n')
739 self.assertEqual(exited, 0)
741 @mock.patch("arvados.collection.CollectionReader")
742 @mock.patch("time.sleep")
744 def test_submit_file_keepref(self, stubs, tm, collectionReader):
745 collectionReader().exists.return_value = True
746 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
747 exited = arvados_cwl.main(
748 ["--submit", "--no-wait", "--api=containers", "--debug",
749 "tests/wf/submit_keepref_wf.cwl"],
750 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
751 self.assertEqual(exited, 0)
753 @mock.patch("arvados.collection.CollectionReader")
754 @mock.patch("time.sleep")
756 def test_submit_keepref(self, stubs, tm, reader):
757 with open("tests/wf/expect_arvworkflow.cwl") as f:
758 reader().open().__enter__().read.return_value = f.read()
760 exited = arvados_cwl.main(
761 ["--submit", "--no-wait", "--api=containers", "--debug",
762 "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
763 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
773 'path': '/var/spool/cwl/cwl.output.json',
776 '/var/lib/cwl/workflow': {
777 'portable_data_hash': '99999999999999999999999999999994+99',
780 '/var/lib/cwl/cwl.input.json': {
786 }, 'state': 'Committed',
787 'output_path': '/var/spool/cwl',
788 'name': 'expect_arvworkflow.cwl#main',
789 'output_name': 'Output from workflow expect_arvworkflow.cwl#main',
790 'container_image': '999999999999999999999999999999d3+99',
791 'command': ['arvados-cwl-runner', '--local', '--api=containers',
792 '--no-log-timestamps', '--disable-validate', '--disable-color',
793 '--eval-timeout=20', '--thread-count=0',
794 '--enable-reuse', "--collection-cache-size=256",
795 '--output-name=Output from workflow expect_arvworkflow.cwl#main',
796 '--debug', '--on-error=continue',
797 '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
798 'cwd': '/var/spool/cwl',
799 'runtime_constraints': {
804 'use_existing': False,
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)
815 @mock.patch("time.sleep")
817 def test_submit_arvworkflow(self, stubs, tm):
818 with open("tests/wf/expect_arvworkflow.cwl") as f:
819 stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
821 exited = arvados_cwl.main(
822 ["--submit", "--no-wait", "--api=containers", "--debug",
823 "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
824 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
834 'path': '/var/spool/cwl/cwl.output.json',
837 '/var/lib/cwl/workflow.json': {
840 'cwlVersion': 'v1.0',
845 {'type': 'string', 'id': '#main/x'}
848 {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
849 'run': '#submit_tool.cwl',
859 'inputBinding': {'position': 1},
861 'id': '#submit_tool.cwl/x'}
865 'dockerPull': 'debian:buster-slim',
866 'class': 'DockerRequirement',
867 "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
870 'id': '#submit_tool.cwl',
872 'baseCommand': 'cat',
873 'class': 'CommandLineTool'
878 '/var/lib/cwl/cwl.input.json': {
884 }, 'state': 'Committed',
885 'output_path': '/var/spool/cwl',
886 'name': 'a test workflow',
887 'container_image': "999999999999999999999999999999d3+99",
888 'command': ['arvados-cwl-runner', '--local', '--api=containers',
889 '--no-log-timestamps', '--disable-validate', '--disable-color',
890 '--eval-timeout=20', '--thread-count=0',
891 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
892 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
893 'cwd': '/var/spool/cwl',
894 'runtime_constraints': {
899 'use_existing': False,
901 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
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)
912 @stubs(('hello container 123', 'submit_wf.cwl'))
913 def test_submit_container_name(self, stubs):
914 exited = arvados_cwl.main(
915 ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
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)
921 stubs.api.container_requests().create.assert_called_with(
922 body=JsonDiffMatcher(expect_container))
923 self.assertEqual(stubs.capture_stdout.getvalue(),
924 stubs.expect_container_request_uuid + '\n')
925 self.assertEqual(exited, 0)
928 def test_submit_missing_input(self, stubs):
929 exited = arvados_cwl.main(
930 ["--submit", "--no-wait", "--api=containers", "--debug",
931 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
932 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
933 self.assertEqual(exited, 0)
935 exited = arvados_cwl.main(
936 ["--submit", "--no-wait", "--api=containers", "--debug",
937 "tests/wf/submit_wf.cwl", "tests/submit_test_job_missing.json"],
938 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
939 self.assertEqual(exited, 1)
942 def test_submit_container_project(self, stubs):
943 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
944 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
945 exited = arvados_cwl.main(
946 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
947 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
948 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
950 expect_container = copy.deepcopy(stubs.expect_container_spec)
951 expect_container["owner_uuid"] = project_uuid
952 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
953 '--no-log-timestamps', '--disable-validate', '--disable-color',
954 "--eval-timeout=20", "--thread-count=0",
955 '--enable-reuse', "--collection-cache-size=256",
956 "--output-name=Output from workflow submit_wf.cwl", '--debug',
957 '--on-error=continue',
958 '--project-uuid='+project_uuid,
959 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
961 stubs.api.container_requests().create.assert_called_with(
962 body=JsonDiffMatcher(expect_container))
963 self.assertEqual(stubs.capture_stdout.getvalue(),
964 stubs.expect_container_request_uuid + '\n')
965 self.assertEqual(exited, 0)
968 def test_submit_container_eval_timeout(self, stubs):
969 exited = arvados_cwl.main(
970 ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
971 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
972 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
974 expect_container = copy.deepcopy(stubs.expect_container_spec)
975 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
976 '--no-log-timestamps', '--disable-validate', '--disable-color',
977 '--eval-timeout=60.0', '--thread-count=0',
978 '--enable-reuse', "--collection-cache-size=256",
979 '--debug', '--on-error=continue',
980 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
982 stubs.api.container_requests().create.assert_called_with(
983 body=JsonDiffMatcher(expect_container))
984 self.assertEqual(stubs.capture_stdout.getvalue(),
985 stubs.expect_container_request_uuid + '\n')
986 self.assertEqual(exited, 0)
989 def test_submit_container_collection_cache(self, stubs):
990 exited = arvados_cwl.main(
991 ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
992 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
993 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
995 expect_container = copy.deepcopy(stubs.expect_container_spec)
996 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
997 '--no-log-timestamps', '--disable-validate', '--disable-color',
998 '--eval-timeout=20', '--thread-count=0',
999 '--enable-reuse', "--collection-cache-size=500",
1000 '--debug', '--on-error=continue',
1001 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1002 expect_container["runtime_constraints"]["ram"] = (1024+500)*1024*1024
1004 stubs.api.container_requests().create.assert_called_with(
1005 body=JsonDiffMatcher(expect_container))
1006 self.assertEqual(stubs.capture_stdout.getvalue(),
1007 stubs.expect_container_request_uuid + '\n')
1008 self.assertEqual(exited, 0)
1011 def test_submit_container_thread_count(self, stubs):
1012 exited = arvados_cwl.main(
1013 ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
1014 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1015 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1017 expect_container = copy.deepcopy(stubs.expect_container_spec)
1018 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
1019 '--no-log-timestamps', '--disable-validate', '--disable-color',
1020 '--eval-timeout=20', '--thread-count=20',
1021 '--enable-reuse', "--collection-cache-size=256",
1022 '--debug', '--on-error=continue',
1023 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1025 stubs.api.container_requests().create.assert_called_with(
1026 body=JsonDiffMatcher(expect_container))
1027 self.assertEqual(stubs.capture_stdout.getvalue(),
1028 stubs.expect_container_request_uuid + '\n')
1029 self.assertEqual(exited, 0)
1032 def test_submit_container_runner_image(self, stubs):
1033 exited = arvados_cwl.main(
1034 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
1035 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1036 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1038 stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99"
1040 expect_container = copy.deepcopy(stubs.expect_container_spec)
1041 stubs.api.container_requests().create.assert_called_with(
1042 body=JsonDiffMatcher(expect_container))
1043 self.assertEqual(stubs.capture_stdout.getvalue(),
1044 stubs.expect_container_request_uuid + '\n')
1045 self.assertEqual(exited, 0)
1048 def test_submit_priority(self, stubs):
1049 exited = arvados_cwl.main(
1050 ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
1051 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1052 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1054 stubs.expect_container_spec["priority"] = 669
1056 expect_container = copy.deepcopy(stubs.expect_container_spec)
1057 stubs.api.container_requests().create.assert_called_with(
1058 body=JsonDiffMatcher(expect_container))
1059 self.assertEqual(stubs.capture_stdout.getvalue(),
1060 stubs.expect_container_request_uuid + '\n')
1061 self.assertEqual(exited, 0)
1063 @stubs(('submit_wf_runner_resources.cwl', None))
1064 def test_submit_wf_runner_resources(self, stubs):
1065 exited = arvados_cwl.main(
1066 ["--submit", "--no-wait", "--api=containers", "--debug",
1067 "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"],
1068 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1070 expect_container = copy.deepcopy(stubs.expect_container_spec)
1071 expect_container["runtime_constraints"] = {
1074 "ram": (2000+512) * 2**20
1076 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
1078 "class": "http://arvados.org/cwl#WorkflowRunnerResources",
1084 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
1085 "arv": "http://arvados.org/cwl#",
1087 expect_container["command"] = ["--collection-cache-size=512" if v == "--collection-cache-size=256" else v for v in expect_container["command"]]
1089 stubs.api.container_requests().create.assert_called_with(
1090 body=JsonDiffMatcher(expect_container))
1091 self.assertEqual(stubs.capture_stdout.getvalue(),
1092 stubs.expect_container_request_uuid + '\n')
1093 self.assertEqual(exited, 0)
1095 @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
1096 @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
1097 @mock.patch("arvados.api")
1098 def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
1099 arvados_cwl.arvdocker.arv_docker_clear_cache()
1101 arvrunner = mock.MagicMock()
1102 arvrunner.project_uuid = ""
1103 api.return_value = mock.MagicMock()
1104 arvrunner.api = api.return_value
1105 arvrunner.runtimeContext.match_local_docker = False
1106 arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
1107 "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1108 "link_class": "docker_image_repo+tag",
1109 "name": "arvados/jobs:"+arvados_cwl.__version__,
1111 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
1112 {"items": [{"created_at": "",
1114 "link_class": "docker_image_hash",
1117 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
1118 {"items": [{"created_at": "",
1119 "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1120 "link_class": "docker_image_repo+tag",
1121 "name": "arvados/jobs:"+arvados_cwl.__version__,
1123 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
1124 {"items": [{"created_at": "",
1126 "link_class": "docker_image_hash",
1129 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
1131 find_one_image_hash.return_value = "123456"
1133 arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1135 "manifest_text": "",
1137 }], "items_available": 1, "offset": 0},
1138 {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1140 "manifest_text": "",
1142 }], "items_available": 1, "offset": 0})
1143 arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
1144 arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1145 "portable_data_hash": "9999999999999999999999999999999b+99"}
1147 self.assertEqual("9999999999999999999999999999999b+99",
1148 arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__, arvrunner.runtimeContext))
1152 def test_submit_secrets(self, stubs):
1153 exited = arvados_cwl.main(
1154 ["--submit", "--no-wait", "--api=containers", "--debug",
1155 "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
1156 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1158 expect_container = {
1160 "arvados-cwl-runner",
1163 "--no-log-timestamps",
1164 "--disable-validate",
1166 "--eval-timeout=20",
1169 "--collection-cache-size=256",
1170 '--output-name=Output from workflow secret_wf.cwl'
1172 "--on-error=continue",
1173 "/var/lib/cwl/workflow.json#main",
1174 "/var/lib/cwl/cwl.input.json"
1176 "container_image": "999999999999999999999999999999d3+99",
1177 "cwd": "/var/spool/cwl",
1179 "/var/lib/cwl/cwl.input.json": {
1182 "$include": "/secrets/s0"
1187 "/var/lib/cwl/workflow.json": {
1195 "class": "CommandLineTool",
1198 "class": "http://commonwl.org/cwltool#Secrets",
1200 "#secret_job.cwl/pw"
1204 "id": "#secret_job.cwl",
1207 "id": "#secret_job.cwl/pw",
1213 "id": "#secret_job.cwl/out",
1216 "glob": "hashed_example.txt"
1220 "stdout": "hashed_example.txt",
1223 "class": "InitialWorkDirRequirement",
1226 "entry": "username: user\npassword: $(inputs.pw)\n",
1227 "entryname": "example.conf"
1234 "class": "Workflow",
1237 "class": "DockerRequirement",
1238 "dockerPull": "debian:buster-slim",
1239 "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
1242 "class": "http://commonwl.org/cwltool#Secrets",
1258 "outputSource": "#main/step1/out",
1264 "id": "#main/step1",
1267 "id": "#main/step1/pw",
1268 "source": "#main/pw"
1274 "run": "#secret_job.cwl"
1280 "cwltool": "http://commonwl.org/cwltool#"
1282 "cwlVersion": "v1.0"
1287 "kind": "collection",
1292 "path": "/var/spool/cwl/cwl.output.json"
1295 "name": "secret_wf.cwl",
1296 "output_name": "Output from workflow secret_wf.cwl",
1297 "output_path": "/var/spool/cwl",
1300 "runtime_constraints": {
1311 "state": "Committed",
1312 "use_existing": False
1315 stubs.api.container_requests().create.assert_called_with(
1316 body=JsonDiffMatcher(expect_container))
1317 self.assertEqual(stubs.capture_stdout.getvalue(),
1318 stubs.expect_container_request_uuid + '\n')
1319 self.assertEqual(exited, 0)
1322 def test_submit_request_uuid(self, stubs):
1323 stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
1324 stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
1326 stubs.api.container_requests().update().execute.return_value = {
1327 "uuid": stubs.expect_container_request_uuid,
1328 "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
1332 exited = arvados_cwl.main(
1333 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
1334 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1335 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1337 stubs.api.container_requests().update.assert_called_with(
1338 uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec))
1339 self.assertEqual(stubs.capture_stdout.getvalue(),
1340 stubs.expect_container_request_uuid + '\n')
1341 self.assertEqual(exited, 0)
1344 def test_submit_container_cluster_id(self, stubs):
1345 stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
1347 exited = arvados_cwl.main(
1348 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb",
1349 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1350 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1352 expect_container = copy.deepcopy(stubs.expect_container_spec)
1354 stubs.api.container_requests().create.assert_called_with(
1355 body=JsonDiffMatcher(expect_container), cluster_id="zbbbb")
1356 self.assertEqual(stubs.capture_stdout.getvalue(),
1357 stubs.expect_container_request_uuid + '\n')
1358 self.assertEqual(exited, 0)
1361 def test_submit_validate_cluster_id(self, stubs):
1362 stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
1363 exited = arvados_cwl.main(
1364 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zcccc",
1365 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1366 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1367 self.assertEqual(exited, 1)
1370 def test_submit_validate_project_uuid(self, stubs):
1371 # Fails with bad cluster prefix
1372 exited = arvados_cwl.main(
1373 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzb-j7d0g-zzzzzzzzzzzzzzz",
1374 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1375 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1376 self.assertEqual(exited, 1)
1378 # Project lookup fails
1379 stubs.api.groups().get().execute.side_effect = Exception("Bad project")
1380 exited = arvados_cwl.main(
1381 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-j7d0g-zzzzzzzzzzzzzzx",
1382 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1383 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1384 self.assertEqual(exited, 1)
1386 # It should work this time because it is looking up a user (and only group is stubbed out to fail)
1387 exited = arvados_cwl.main(
1388 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-tpzed-zzzzzzzzzzzzzzx",
1389 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1390 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1391 self.assertEqual(exited, 0)
1394 @mock.patch("arvados.collection.CollectionReader")
1396 def test_submit_uuid_inputs(self, stubs, collectionReader):
1397 collectionReader().exists.return_value = True
1398 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
1399 def list_side_effect(**kwargs):
1400 m = mock.MagicMock()
1401 if "count" in kwargs:
1402 m.execute.return_value = {"items": [
1403 {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999998+99"}
1406 m.execute.return_value = {"items": []}
1408 stubs.api.collections().list.side_effect = list_side_effect
1410 exited = arvados_cwl.main(
1411 ["--submit", "--no-wait", "--api=containers", "--debug",
1412 "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
1413 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1415 expect_container = copy.deepcopy(stubs.expect_container_spec)
1416 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['basename'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1417 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1418 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1420 stubs.api.collections().list.assert_has_calls([
1421 mock.call(count='none',
1422 filters=[['uuid', 'in', ['zzzzz-4zz18-zzzzzzzzzzzzzzz']]],
1423 select=['uuid', 'portable_data_hash'])])
1424 stubs.api.container_requests().create.assert_called_with(
1425 body=JsonDiffMatcher(expect_container))
1426 self.assertEqual(stubs.capture_stdout.getvalue(),
1427 stubs.expect_container_request_uuid + '\n')
1428 self.assertEqual(exited, 0)
1431 def test_submit_mismatched_uuid_inputs(self, stubs):
1432 def list_side_effect(**kwargs):
1433 m = mock.MagicMock()
1434 if "count" in kwargs:
1435 m.execute.return_value = {"items": [
1436 {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999997+99"}
1439 m.execute.return_value = {"items": []}
1441 stubs.api.collections().list.side_effect = list_side_effect
1443 for infile in ("tests/submit_test_job_with_mismatched_uuids.json", "tests/submit_test_job_with_inconsistent_uuids.json"):
1444 capture_stderr = StringIO()
1445 cwltool_logger = logging.getLogger('cwltool')
1446 stderr_logger = logging.StreamHandler(capture_stderr)
1447 cwltool_logger.addHandler(stderr_logger)
1450 exited = arvados_cwl.main(
1451 ["--submit", "--no-wait", "--api=containers", "--debug",
1452 "tests/wf/submit_wf.cwl", infile],
1453 stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1455 self.assertEqual(exited, 1)
1457 re.sub(r'[ \n]+', ' ', capture_stderr.getvalue()),
1458 r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99")
1460 cwltool_logger.removeHandler(stderr_logger)
1462 @mock.patch("arvados.collection.CollectionReader")
1464 def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
1465 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
1466 capture_stderr = StringIO()
1468 cwltool_logger = logging.getLogger('cwltool')
1469 stderr_logger = logging.StreamHandler(capture_stderr)
1470 cwltool_logger.addHandler(stderr_logger)
1472 exited = arvados_cwl.main(
1473 ["--submit", "--no-wait", "--api=containers", "--debug",
1474 "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
1475 stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1478 self.assertEqual(exited, 1)
1480 capture_stderr.getvalue(),
1481 r"Collection\s*uuid\s*zzzzz-4zz18-zzzzzzzzzzzzzzz\s*not\s*found")
1483 cwltool_logger.removeHandler(stderr_logger)
1485 @stubs(('submit_wf_process_properties.cwl', None))
1486 def test_submit_set_process_properties(self, stubs):
1487 exited = arvados_cwl.main(
1488 ["--submit", "--no-wait", "--api=containers", "--debug",
1489 "tests/wf/submit_wf_process_properties.cwl", "tests/submit_test_job.json"],
1490 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1492 expect_container = copy.deepcopy(stubs.expect_container_spec)
1494 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
1496 "class": "http://arvados.org/cwl#ProcessProperties",
1497 "processProperties": [
1498 {"propertyName": "baz",
1499 "propertyValue": "$(inputs.x.basename)"},
1500 {"propertyName": "foo",
1501 "propertyValue": "bar"},
1502 {"propertyName": "quux",
1511 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
1512 "arv": "http://arvados.org/cwl#"
1515 expect_container["properties"].update({
1524 stubs.api.container_requests().create.assert_called_with(
1525 body=JsonDiffMatcher(expect_container))
1526 self.assertEqual(stubs.capture_stdout.getvalue(),
1527 stubs.expect_container_request_uuid + '\n')
1528 self.assertEqual(exited, 0)
1532 def test_submit_enable_preemptible(self, stubs):
1533 exited = arvados_cwl.main(
1534 ["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
1535 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1536 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1538 expect_container = copy.deepcopy(stubs.expect_container_spec)
1539 expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
1540 '--no-log-timestamps', '--disable-validate', '--disable-color',
1541 '--eval-timeout=20', '--thread-count=0',
1542 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
1543 '--enable-preemptible',
1544 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1546 stubs.api.container_requests().create.assert_called_with(
1547 body=JsonDiffMatcher(expect_container))
1548 self.assertEqual(stubs.capture_stdout.getvalue(),
1549 stubs.expect_container_request_uuid + '\n')
1550 self.assertEqual(exited, 0)
1553 def test_submit_disable_preemptible(self, stubs):
1554 exited = arvados_cwl.main(
1555 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
1556 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1557 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1559 expect_container = copy.deepcopy(stubs.expect_container_spec)
1560 expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
1561 '--no-log-timestamps', '--disable-validate', '--disable-color',
1562 '--eval-timeout=20', '--thread-count=0',
1563 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
1564 '--disable-preemptible',
1565 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1567 stubs.api.container_requests().create.assert_called_with(
1568 body=JsonDiffMatcher(expect_container))
1569 self.assertEqual(stubs.capture_stdout.getvalue(),
1570 stubs.expect_container_request_uuid + '\n')
1571 self.assertEqual(exited, 0)
1574 class TestCreateWorkflow(unittest.TestCase):
1575 existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
1576 expect_workflow = StripYAMLComments(
1577 open("tests/wf/expect_upload_packed.cwl").read().rstrip())
1580 cwltool.process._names = set()
1581 arvados_cwl.arvdocker.arv_docker_clear_cache()
1584 root_logger = logging.getLogger('')
1586 # Remove existing RuntimeStatusLoggingHandlers if they exist
1587 handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)]
1588 root_logger.handlers = handlers
1591 def test_create(self, stubs):
1592 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1593 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1595 exited = arvados_cwl.main(
1596 ["--create-workflow", "--debug",
1598 "--project-uuid", project_uuid,
1599 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1600 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1602 stubs.api.pipeline_templates().create.refute_called()
1603 stubs.api.container_requests().create.refute_called()
1607 "owner_uuid": project_uuid,
1608 "name": "submit_wf.cwl",
1610 "definition": self.expect_workflow,
1613 stubs.api.workflows().create.assert_called_with(
1614 body=JsonDiffMatcher(body))
1616 self.assertEqual(stubs.capture_stdout.getvalue(),
1617 stubs.expect_workflow_uuid + '\n')
1618 self.assertEqual(exited, 0)
1621 def test_create_name(self, stubs):
1622 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1623 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1625 exited = arvados_cwl.main(
1626 ["--create-workflow", "--debug",
1628 "--project-uuid", project_uuid,
1629 "--name", "testing 123",
1630 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1631 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1633 stubs.api.pipeline_templates().create.refute_called()
1634 stubs.api.container_requests().create.refute_called()
1638 "owner_uuid": project_uuid,
1639 "name": "testing 123",
1641 "definition": self.expect_workflow,
1644 stubs.api.workflows().create.assert_called_with(
1645 body=JsonDiffMatcher(body))
1647 self.assertEqual(stubs.capture_stdout.getvalue(),
1648 stubs.expect_workflow_uuid + '\n')
1649 self.assertEqual(exited, 0)
1653 def test_update(self, stubs):
1654 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1655 stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
1657 exited = arvados_cwl.main(
1658 ["--update-workflow", self.existing_workflow_uuid,
1660 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1661 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1665 "name": "submit_wf.cwl",
1667 "definition": self.expect_workflow,
1668 "owner_uuid": project_uuid
1671 stubs.api.workflows().update.assert_called_with(
1672 uuid=self.existing_workflow_uuid,
1673 body=JsonDiffMatcher(body))
1674 self.assertEqual(stubs.capture_stdout.getvalue(),
1675 self.existing_workflow_uuid + '\n')
1676 self.assertEqual(exited, 0)
1680 def test_update_name(self, stubs):
1681 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1682 stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
1684 exited = arvados_cwl.main(
1685 ["--update-workflow", self.existing_workflow_uuid,
1686 "--debug", "--name", "testing 123",
1687 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1688 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1692 "name": "testing 123",
1694 "definition": self.expect_workflow,
1695 "owner_uuid": project_uuid
1698 stubs.api.workflows().update.assert_called_with(
1699 uuid=self.existing_workflow_uuid,
1700 body=JsonDiffMatcher(body))
1701 self.assertEqual(stubs.capture_stdout.getvalue(),
1702 self.existing_workflow_uuid + '\n')
1703 self.assertEqual(exited, 0)
1706 def test_create_collection_per_tool(self, stubs):
1707 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1708 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1710 exited = arvados_cwl.main(
1711 ["--create-workflow", "--debug",
1713 "--project-uuid", project_uuid,
1714 "tests/collection_per_tool/collection_per_tool.cwl"],
1715 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1717 toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
1718 expect_workflow = StripYAMLComments(open(toolfile).read().rstrip())
1722 "owner_uuid": project_uuid,
1723 "name": "collection_per_tool.cwl",
1725 "definition": expect_workflow,
1728 stubs.api.workflows().create.assert_called_with(
1729 body=JsonDiffMatcher(body))
1731 self.assertEqual(stubs.capture_stdout.getvalue(),
1732 stubs.expect_workflow_uuid + '\n')
1733 self.assertEqual(exited, 0)
1736 def test_create_with_imports(self, stubs):
1737 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1738 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1740 exited = arvados_cwl.main(
1741 ["--create-workflow", "--debug",
1743 "--project-uuid", project_uuid,
1744 "tests/wf/feddemo/feddemo.cwl"],
1745 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1747 stubs.api.pipeline_templates().create.refute_called()
1748 stubs.api.container_requests().create.refute_called()
1750 self.assertEqual(stubs.capture_stdout.getvalue(),
1751 stubs.expect_workflow_uuid + '\n')
1752 self.assertEqual(exited, 0)
1755 def test_create_with_no_input(self, stubs):
1756 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1757 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1759 exited = arvados_cwl.main(
1760 ["--create-workflow", "--debug",
1762 "--project-uuid", project_uuid,
1763 "tests/wf/revsort/revsort.cwl"],
1764 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1766 stubs.api.pipeline_templates().create.refute_called()
1767 stubs.api.container_requests().create.refute_called()
1769 self.assertEqual(stubs.capture_stdout.getvalue(),
1770 stubs.expect_workflow_uuid + '\n')
1771 self.assertEqual(exited, 0)