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:buster-slim": [("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"
90 stubs.api._rootDesc["revision"] = "20210628"
92 stubs.api.users().current().execute.return_value = {
93 "uuid": stubs.fake_user_uuid,
95 stubs.api.collections().list().execute.return_value = {"items": []}
96 stubs.api.containers().current().execute.return_value = {
97 "uuid": stubs.fake_container_uuid,
99 stubs.api.config()["StorageClasses"].items.return_value = {
105 class CollectionExecute(object):
106 def __init__(self, exe):
108 def execute(self, num_retries=None):
111 def collection_createstub(created_collections, body, ensure_unique_name=None):
112 mt = body["manifest_text"].encode('utf-8')
113 uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%d" % len(created_collections)
114 pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
115 created_collections[uuid] = {
117 "portable_data_hash": pdh,
118 "manifest_text": mt.decode('utf-8')
120 return CollectionExecute(created_collections[uuid])
122 def collection_getstub(created_collections, uuid):
123 for v in viewvalues(created_collections):
124 if uuid in (v["uuid"], v["portable_data_hash"]):
125 return CollectionExecute(v)
127 created_collections = {
128 "99999999999999999999999999999998+99": {
130 "portable_data_hash": "99999999999999999999999999999998+99",
131 "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
133 "99999999999999999999999999999997+99": {
135 "portable_data_hash": "99999999999999999999999999999997+99",
136 "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt"
138 "99999999999999999999999999999994+99": {
140 "portable_data_hash": "99999999999999999999999999999994+99",
141 "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
143 "zzzzz-4zz18-zzzzzzzzzzzzzd3": {
144 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd3",
145 "portable_data_hash": "999999999999999999999999999999d3+99",
148 "zzzzz-4zz18-zzzzzzzzzzzzzd4": {
149 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd4",
150 "portable_data_hash": "999999999999999999999999999999d4+99",
153 "zzzzz-4zz18-zzzzzzzzzzzzzd5": {
154 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd5",
155 "portable_data_hash": "999999999999999999999999999999d5+99",
158 "zzzzz-4zz18-zzzzzzzzzzzzzd6": {
159 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd6",
160 "portable_data_hash": "999999999999999999999999999999d6+99",
164 stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
165 stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
167 stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
168 stubs.api.jobs().create().execute.return_value = {
169 "uuid": stubs.expect_job_uuid,
173 stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
174 stubs.api.container_requests().create().execute.return_value = {
175 "uuid": stubs.expect_container_request_uuid,
176 "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
180 stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
181 stubs.api.pipeline_templates().create().execute.return_value = {
182 "uuid": stubs.expect_pipeline_template_uuid,
184 stubs.expect_job_spec = {
185 'runtime_constraints': {
186 'docker_image': '999999999999999999999999999999d3+99',
187 'min_ram_mb_per_node': 1024
189 'script_parameters': {
191 'basename': 'blorp.txt',
192 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
196 'basename': '99999999999999999999999999999998+99',
197 'location': 'keep:99999999999999999999999999999998+99',
201 'basename': 'anonymous',
203 "basename": "renamed.txt",
205 "location": "keep:99999999999999999999999999999998+99/file1.txt",
210 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main'
212 'repository': 'arvados',
213 'script_version': 'master',
214 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
215 'script': 'cwl-runner'
217 stubs.pipeline_component = stubs.expect_job_spec.copy()
218 stubs.expect_pipeline_instance = {
219 'name': 'submit_wf.cwl',
220 'state': 'RunningOnServer',
224 'runtime_constraints': {'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024},
225 'script_parameters': {
226 'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
228 'basename': 'blorp.txt',
230 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
233 'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
236 'basename': 'renamed.txt',
237 'class': 'File', 'location':
238 'keep:99999999999999999999999999999998+99/file1.txt',
242 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main',
244 'arv:enable_reuse': True,
245 'arv:on_error': 'continue'
247 'repository': 'arvados',
248 'script_version': 'master',
249 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
250 'script': 'cwl-runner',
251 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
255 stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
256 stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
257 stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
258 stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
259 stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
260 "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
263 stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
264 stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
266 with open("tests/wf/submit_wf_packed.cwl") as f:
267 expect_packed_workflow = yaml.round_trip_load(f)
269 stubs.expect_container_spec = {
276 '/var/lib/cwl/workflow.json': {
277 'content': expect_packed_workflow,
281 'path': '/var/spool/cwl/cwl.output.json',
284 '/var/lib/cwl/cwl.input.json': {
288 'basename': '99999999999999999999999999999998+99',
289 'location': 'keep:99999999999999999999999999999998+99',
290 'class': 'Directory'},
292 'basename': u'blorp.txt',
294 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
297 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
298 {'basename': 'renamed.txt',
300 'location': 'keep:99999999999999999999999999999998+99/file1.txt',
309 'state': 'Committed',
310 'command': ['arvados-cwl-runner', '--local', '--api=containers',
311 '--no-log-timestamps', '--disable-validate', '--disable-color',
312 '--eval-timeout=20', '--thread-count=0',
313 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
314 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
315 'name': 'submit_wf.cwl',
316 'container_image': '999999999999999999999999999999d3+99',
317 'output_path': '/var/spool/cwl',
318 'cwd': '/var/spool/cwl',
319 'runtime_constraints': {
322 'ram': (1024+256)*1024*1024
324 'use_existing': False,
329 stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
330 stubs.api.workflows().create().execute.return_value = {
331 "uuid": stubs.expect_workflow_uuid,
333 def update_mock(**kwargs):
334 stubs.updated_uuid = kwargs.get('uuid')
336 stubs.api.workflows().update.side_effect = update_mock
337 stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
338 "uuid": stubs.updated_uuid,
341 return func(self, stubs, *args, **kwargs)
345 class TestSubmit(unittest.TestCase):
348 cwltool.process._names = set()
349 arvados_cwl.arvdocker.arv_docker_clear_cache()
352 @mock.patch("time.sleep")
354 def test_submit_invalid_runner_ram(self, stubs, tm):
355 exited = arvados_cwl.main(
356 ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
357 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
358 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
359 self.assertEqual(exited, 1)
363 def test_submit_container(self, stubs):
364 exited = arvados_cwl.main(
365 ["--submit", "--no-wait", "--api=containers", "--debug",
366 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
367 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
369 stubs.api.collections().create.assert_has_calls([
370 mock.call(body=JsonDiffMatcher({
372 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
373 'replication_desired': None,
374 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
375 }), ensure_unique_name=False),
376 mock.call(body=JsonDiffMatcher({
378 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
379 'replication_desired': None,
380 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
381 }), ensure_unique_name=False),
384 expect_container = copy.deepcopy(stubs.expect_container_spec)
385 stubs.api.container_requests().create.assert_called_with(
386 body=JsonDiffMatcher(expect_container))
387 self.assertEqual(stubs.capture_stdout.getvalue(),
388 stubs.expect_container_request_uuid + '\n')
389 self.assertEqual(exited, 0)
393 def test_submit_container_tool(self, stubs):
394 # test for issue #16139
395 exited = arvados_cwl.main(
396 ["--submit", "--no-wait", "--api=containers", "--debug",
397 "tests/tool/tool_with_sf.cwl", "tests/tool/tool_with_sf.yml"],
398 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
400 self.assertEqual(stubs.capture_stdout.getvalue(),
401 stubs.expect_container_request_uuid + '\n')
402 self.assertEqual(exited, 0)
405 def test_submit_container_no_reuse(self, stubs):
406 exited = arvados_cwl.main(
407 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
408 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
409 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
411 expect_container = copy.deepcopy(stubs.expect_container_spec)
412 expect_container["command"] = [
413 'arvados-cwl-runner', '--local', '--api=containers',
414 '--no-log-timestamps', '--disable-validate', '--disable-color',
415 '--eval-timeout=20', '--thread-count=0',
416 '--disable-reuse', "--collection-cache-size=256",
417 '--debug', '--on-error=continue',
418 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
419 expect_container["use_existing"] = False
421 stubs.api.container_requests().create.assert_called_with(
422 body=JsonDiffMatcher(expect_container))
423 self.assertEqual(stubs.capture_stdout.getvalue(),
424 stubs.expect_container_request_uuid + '\n')
425 self.assertEqual(exited, 0)
428 def test_submit_container_reuse_disabled_by_workflow(self, stubs):
429 exited = arvados_cwl.main(
430 ["--submit", "--no-wait", "--api=containers", "--debug",
431 "tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"],
432 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
433 self.assertEqual(exited, 0)
435 expect_container = copy.deepcopy(stubs.expect_container_spec)
436 expect_container["command"] = [
437 'arvados-cwl-runner', '--local', '--api=containers',
438 '--no-log-timestamps', '--disable-validate', '--disable-color',
439 '--eval-timeout=20', '--thread-count=0',
440 '--disable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
441 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
442 expect_container["use_existing"] = False
443 expect_container["name"] = "submit_wf_no_reuse.cwl"
444 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
446 "class": "http://arvados.org/cwl#ReuseRequirement",
447 "enableReuse": False,
450 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
451 "arv": "http://arvados.org/cwl#",
452 "cwltool": "http://commonwl.org/cwltool#"
455 stubs.api.container_requests().create.assert_called_with(
456 body=JsonDiffMatcher(expect_container))
457 self.assertEqual(stubs.capture_stdout.getvalue(),
458 stubs.expect_container_request_uuid + '\n')
462 def test_submit_container_on_error(self, stubs):
463 exited = arvados_cwl.main(
464 ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
465 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
466 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
468 expect_container = copy.deepcopy(stubs.expect_container_spec)
469 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
470 '--no-log-timestamps', '--disable-validate', '--disable-color',
471 '--eval-timeout=20', '--thread-count=0',
472 '--enable-reuse', "--collection-cache-size=256",
473 '--debug', '--on-error=stop',
474 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
476 stubs.api.container_requests().create.assert_called_with(
477 body=JsonDiffMatcher(expect_container))
478 self.assertEqual(stubs.capture_stdout.getvalue(),
479 stubs.expect_container_request_uuid + '\n')
480 self.assertEqual(exited, 0)
483 def test_submit_container_output_name(self, stubs):
484 output_name = "test_output_name"
486 exited = arvados_cwl.main(
487 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
488 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
489 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
491 expect_container = copy.deepcopy(stubs.expect_container_spec)
492 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
493 '--no-log-timestamps', '--disable-validate', '--disable-color',
494 '--eval-timeout=20', '--thread-count=0',
495 '--enable-reuse', "--collection-cache-size=256",
496 "--output-name="+output_name, '--debug', '--on-error=continue',
497 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
498 expect_container["output_name"] = output_name
500 stubs.api.container_requests().create.assert_called_with(
501 body=JsonDiffMatcher(expect_container))
502 self.assertEqual(stubs.capture_stdout.getvalue(),
503 stubs.expect_container_request_uuid + '\n')
504 self.assertEqual(exited, 0)
507 def test_submit_storage_classes(self, stubs):
508 exited = arvados_cwl.main(
509 ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
510 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
511 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
513 expect_container = copy.deepcopy(stubs.expect_container_spec)
514 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
515 '--no-log-timestamps', '--disable-validate', '--disable-color',
516 '--eval-timeout=20', '--thread-count=0',
517 '--enable-reuse', "--collection-cache-size=256", "--debug",
518 "--storage-classes=foo", '--on-error=continue',
519 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
521 stubs.api.container_requests().create.assert_called_with(
522 body=JsonDiffMatcher(expect_container))
523 self.assertEqual(stubs.capture_stdout.getvalue(),
524 stubs.expect_container_request_uuid + '\n')
525 self.assertEqual(exited, 0)
528 def test_submit_multiple_storage_classes(self, stubs):
529 exited = arvados_cwl.main(
530 ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
531 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
532 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
534 expect_container = copy.deepcopy(stubs.expect_container_spec)
535 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
536 '--no-log-timestamps', '--disable-validate', '--disable-color',
537 '--eval-timeout=20', '--thread-count=0',
538 '--enable-reuse', "--collection-cache-size=256", "--debug",
539 "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--on-error=continue',
540 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
542 stubs.api.container_requests().create.assert_called_with(
543 body=JsonDiffMatcher(expect_container))
544 self.assertEqual(stubs.capture_stdout.getvalue(),
545 stubs.expect_container_request_uuid + '\n')
546 self.assertEqual(exited, 0)
548 @mock.patch("cwltool.task_queue.TaskQueue")
549 @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
550 @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
552 def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
553 final_output_c = arvados.collection.Collection()
554 make_output.return_value = ({},final_output_c)
556 def set_final_output(job_order, output_callback, runtimeContext):
557 output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
559 job.side_effect = set_final_output
561 exited = arvados_cwl.main(
562 ["--debug", "--local", "--storage-classes=foo",
563 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
564 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
566 make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
567 self.assertEqual(exited, 0)
569 @mock.patch("cwltool.task_queue.TaskQueue")
570 @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
571 @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
573 def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
574 final_output_c = arvados.collection.Collection()
575 make_output.return_value = ({},final_output_c)
576 stubs.api.config().get.return_value = {"default": {"Default": True}}
578 def set_final_output(job_order, output_callback, runtimeContext):
579 output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
581 job.side_effect = set_final_output
583 exited = arvados_cwl.main(
584 ["--debug", "--local",
585 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
586 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
588 make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
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_class_hint_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("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
602 job.side_effect = set_final_output
604 exited = arvados_cwl.main(
605 ["--debug", "--local",
606 "tests/wf/submit_storage_class_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_storage_class_wf.cwl', ['foo', 'bar'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
610 self.assertEqual(exited, 0)
613 def test_submit_container_output_ttl(self, stubs):
614 exited = arvados_cwl.main(
615 ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
616 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
617 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
619 expect_container = copy.deepcopy(stubs.expect_container_spec)
620 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
621 '--no-log-timestamps', '--disable-validate', '--disable-color',
622 '--eval-timeout=20', '--thread-count=0',
623 '--enable-reuse', "--collection-cache-size=256", '--debug',
624 '--on-error=continue',
625 "--intermediate-output-ttl=3600",
626 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
628 stubs.api.container_requests().create.assert_called_with(
629 body=JsonDiffMatcher(expect_container))
630 self.assertEqual(stubs.capture_stdout.getvalue(),
631 stubs.expect_container_request_uuid + '\n')
632 self.assertEqual(exited, 0)
635 def test_submit_container_trash_intermediate(self, stubs):
636 exited = arvados_cwl.main(
637 ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
638 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
639 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
642 expect_container = copy.deepcopy(stubs.expect_container_spec)
643 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
644 '--no-log-timestamps', '--disable-validate', '--disable-color',
645 '--eval-timeout=20', '--thread-count=0',
646 '--enable-reuse', "--collection-cache-size=256",
647 '--debug', '--on-error=continue',
648 "--trash-intermediate",
649 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
651 stubs.api.container_requests().create.assert_called_with(
652 body=JsonDiffMatcher(expect_container))
653 self.assertEqual(stubs.capture_stdout.getvalue(),
654 stubs.expect_container_request_uuid + '\n')
655 self.assertEqual(exited, 0)
658 def test_submit_container_output_tags(self, stubs):
659 output_tags = "tag0,tag1,tag2"
661 exited = arvados_cwl.main(
662 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
663 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
664 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
666 expect_container = copy.deepcopy(stubs.expect_container_spec)
667 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
668 '--no-log-timestamps', '--disable-validate', '--disable-color',
669 '--eval-timeout=20', '--thread-count=0',
670 '--enable-reuse', "--collection-cache-size=256",
671 "--output-tags="+output_tags, '--debug', '--on-error=continue',
672 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
674 stubs.api.container_requests().create.assert_called_with(
675 body=JsonDiffMatcher(expect_container))
676 self.assertEqual(stubs.capture_stdout.getvalue(),
677 stubs.expect_container_request_uuid + '\n')
678 self.assertEqual(exited, 0)
681 def test_submit_container_runner_ram(self, stubs):
682 exited = arvados_cwl.main(
683 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
684 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
685 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
687 expect_container = copy.deepcopy(stubs.expect_container_spec)
688 expect_container["runtime_constraints"]["ram"] = (2048+256)*1024*1024
690 stubs.api.container_requests().create.assert_called_with(
691 body=JsonDiffMatcher(expect_container))
692 self.assertEqual(stubs.capture_stdout.getvalue(),
693 stubs.expect_container_request_uuid + '\n')
694 self.assertEqual(exited, 0)
696 @mock.patch("arvados.collection.CollectionReader")
697 @mock.patch("time.sleep")
699 def test_submit_file_keepref(self, stubs, tm, collectionReader):
700 collectionReader().exists.return_value = True
701 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
702 exited = arvados_cwl.main(
703 ["--submit", "--no-wait", "--api=containers", "--debug",
704 "tests/wf/submit_keepref_wf.cwl"],
705 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
706 self.assertEqual(exited, 0)
708 @mock.patch("arvados.collection.CollectionReader")
709 @mock.patch("time.sleep")
711 def test_submit_keepref(self, stubs, tm, reader):
712 with open("tests/wf/expect_arvworkflow.cwl") as f:
713 reader().open().__enter__().read.return_value = f.read()
715 exited = arvados_cwl.main(
716 ["--submit", "--no-wait", "--api=containers", "--debug",
717 "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
718 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
728 'path': '/var/spool/cwl/cwl.output.json',
731 '/var/lib/cwl/workflow': {
732 'portable_data_hash': '99999999999999999999999999999994+99',
735 '/var/lib/cwl/cwl.input.json': {
741 }, 'state': 'Committed',
742 'output_path': '/var/spool/cwl',
743 'name': 'expect_arvworkflow.cwl#main',
744 'container_image': '999999999999999999999999999999d3+99',
745 'command': ['arvados-cwl-runner', '--local', '--api=containers',
746 '--no-log-timestamps', '--disable-validate', '--disable-color',
747 '--eval-timeout=20', '--thread-count=0',
748 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
749 '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
750 'cwd': '/var/spool/cwl',
751 'runtime_constraints': {
756 'use_existing': False,
761 stubs.api.container_requests().create.assert_called_with(
762 body=JsonDiffMatcher(expect_container))
763 self.assertEqual(stubs.capture_stdout.getvalue(),
764 stubs.expect_container_request_uuid + '\n')
765 self.assertEqual(exited, 0)
767 @mock.patch("time.sleep")
769 def test_submit_arvworkflow(self, stubs, tm):
770 with open("tests/wf/expect_arvworkflow.cwl") as f:
771 stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
773 exited = arvados_cwl.main(
774 ["--submit", "--no-wait", "--api=containers", "--debug",
775 "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
776 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
786 'path': '/var/spool/cwl/cwl.output.json',
789 '/var/lib/cwl/workflow.json': {
792 'cwlVersion': 'v1.0',
797 {'type': 'string', 'id': '#main/x'}
800 {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
801 'run': '#submit_tool.cwl',
811 'inputBinding': {'position': 1},
813 'id': '#submit_tool.cwl/x'}
817 'dockerPull': 'debian:buster-slim',
818 'class': 'DockerRequirement',
819 "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
822 'id': '#submit_tool.cwl',
824 'baseCommand': 'cat',
825 'class': 'CommandLineTool'
830 '/var/lib/cwl/cwl.input.json': {
836 }, 'state': 'Committed',
837 'output_path': '/var/spool/cwl',
838 'name': 'a test workflow',
839 'container_image': "999999999999999999999999999999d3+99",
840 'command': ['arvados-cwl-runner', '--local', '--api=containers',
841 '--no-log-timestamps', '--disable-validate', '--disable-color',
842 '--eval-timeout=20', '--thread-count=0',
843 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
844 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
845 'cwd': '/var/spool/cwl',
846 'runtime_constraints': {
851 'use_existing': False,
853 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
858 stubs.api.container_requests().create.assert_called_with(
859 body=JsonDiffMatcher(expect_container))
860 self.assertEqual(stubs.capture_stdout.getvalue(),
861 stubs.expect_container_request_uuid + '\n')
862 self.assertEqual(exited, 0)
865 def test_submit_container_name(self, stubs):
866 exited = arvados_cwl.main(
867 ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
868 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
869 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
871 expect_container = copy.deepcopy(stubs.expect_container_spec)
872 expect_container["name"] = "hello container 123"
874 stubs.api.container_requests().create.assert_called_with(
875 body=JsonDiffMatcher(expect_container))
876 self.assertEqual(stubs.capture_stdout.getvalue(),
877 stubs.expect_container_request_uuid + '\n')
878 self.assertEqual(exited, 0)
881 def test_submit_missing_input(self, stubs):
882 exited = arvados_cwl.main(
883 ["--submit", "--no-wait", "--api=containers", "--debug",
884 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
885 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
886 self.assertEqual(exited, 0)
888 exited = arvados_cwl.main(
889 ["--submit", "--no-wait", "--api=containers", "--debug",
890 "tests/wf/submit_wf.cwl", "tests/submit_test_job_missing.json"],
891 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
892 self.assertEqual(exited, 1)
895 def test_submit_container_project(self, stubs):
896 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
897 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
898 exited = arvados_cwl.main(
899 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
900 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
901 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
903 expect_container = copy.deepcopy(stubs.expect_container_spec)
904 expect_container["owner_uuid"] = project_uuid
905 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
906 '--no-log-timestamps', '--disable-validate', '--disable-color',
907 "--eval-timeout=20", "--thread-count=0",
908 '--enable-reuse', "--collection-cache-size=256", '--debug',
909 '--on-error=continue',
910 '--project-uuid='+project_uuid,
911 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
913 stubs.api.container_requests().create.assert_called_with(
914 body=JsonDiffMatcher(expect_container))
915 self.assertEqual(stubs.capture_stdout.getvalue(),
916 stubs.expect_container_request_uuid + '\n')
917 self.assertEqual(exited, 0)
920 def test_submit_container_eval_timeout(self, stubs):
921 exited = arvados_cwl.main(
922 ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
923 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
924 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
926 expect_container = copy.deepcopy(stubs.expect_container_spec)
927 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
928 '--no-log-timestamps', '--disable-validate', '--disable-color',
929 '--eval-timeout=60.0', '--thread-count=0',
930 '--enable-reuse', "--collection-cache-size=256",
931 '--debug', '--on-error=continue',
932 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
934 stubs.api.container_requests().create.assert_called_with(
935 body=JsonDiffMatcher(expect_container))
936 self.assertEqual(stubs.capture_stdout.getvalue(),
937 stubs.expect_container_request_uuid + '\n')
938 self.assertEqual(exited, 0)
941 def test_submit_container_collection_cache(self, stubs):
942 exited = arvados_cwl.main(
943 ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
944 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
945 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
947 expect_container = copy.deepcopy(stubs.expect_container_spec)
948 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
949 '--no-log-timestamps', '--disable-validate', '--disable-color',
950 '--eval-timeout=20', '--thread-count=0',
951 '--enable-reuse', "--collection-cache-size=500",
952 '--debug', '--on-error=continue',
953 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
954 expect_container["runtime_constraints"]["ram"] = (1024+500)*1024*1024
956 stubs.api.container_requests().create.assert_called_with(
957 body=JsonDiffMatcher(expect_container))
958 self.assertEqual(stubs.capture_stdout.getvalue(),
959 stubs.expect_container_request_uuid + '\n')
960 self.assertEqual(exited, 0)
963 def test_submit_container_thread_count(self, stubs):
964 exited = arvados_cwl.main(
965 ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
966 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
967 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
969 expect_container = copy.deepcopy(stubs.expect_container_spec)
970 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
971 '--no-log-timestamps', '--disable-validate', '--disable-color',
972 '--eval-timeout=20', '--thread-count=20',
973 '--enable-reuse', "--collection-cache-size=256",
974 '--debug', '--on-error=continue',
975 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
977 stubs.api.container_requests().create.assert_called_with(
978 body=JsonDiffMatcher(expect_container))
979 self.assertEqual(stubs.capture_stdout.getvalue(),
980 stubs.expect_container_request_uuid + '\n')
981 self.assertEqual(exited, 0)
984 def test_submit_container_runner_image(self, stubs):
985 exited = arvados_cwl.main(
986 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
987 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
988 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
990 stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99"
992 expect_container = copy.deepcopy(stubs.expect_container_spec)
993 stubs.api.container_requests().create.assert_called_with(
994 body=JsonDiffMatcher(expect_container))
995 self.assertEqual(stubs.capture_stdout.getvalue(),
996 stubs.expect_container_request_uuid + '\n')
997 self.assertEqual(exited, 0)
1000 def test_submit_priority(self, stubs):
1001 exited = arvados_cwl.main(
1002 ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
1003 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1004 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1006 stubs.expect_container_spec["priority"] = 669
1008 expect_container = copy.deepcopy(stubs.expect_container_spec)
1009 stubs.api.container_requests().create.assert_called_with(
1010 body=JsonDiffMatcher(expect_container))
1011 self.assertEqual(stubs.capture_stdout.getvalue(),
1012 stubs.expect_container_request_uuid + '\n')
1013 self.assertEqual(exited, 0)
1016 def test_submit_wf_runner_resources(self, stubs):
1017 exited = arvados_cwl.main(
1018 ["--submit", "--no-wait", "--api=containers", "--debug",
1019 "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"],
1020 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1022 expect_container = copy.deepcopy(stubs.expect_container_spec)
1023 expect_container["runtime_constraints"] = {
1026 "ram": (2000+512) * 2**20
1028 expect_container["name"] = "submit_wf_runner_resources.cwl"
1029 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
1031 "class": "http://arvados.org/cwl#WorkflowRunnerResources",
1037 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
1038 "arv": "http://arvados.org/cwl#",
1040 expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
1041 '--no-log-timestamps', '--disable-validate', '--disable-color',
1042 '--eval-timeout=20', '--thread-count=0',
1043 '--enable-reuse', "--collection-cache-size=512", '--debug', '--on-error=continue',
1044 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1046 stubs.api.container_requests().create.assert_called_with(
1047 body=JsonDiffMatcher(expect_container))
1048 self.assertEqual(stubs.capture_stdout.getvalue(),
1049 stubs.expect_container_request_uuid + '\n')
1050 self.assertEqual(exited, 0)
1053 arvados_cwl.arvdocker.arv_docker_clear_cache()
1055 @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
1056 @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
1057 @mock.patch("arvados.api")
1058 def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
1059 arvados_cwl.arvdocker.arv_docker_clear_cache()
1061 arvrunner = mock.MagicMock()
1062 arvrunner.project_uuid = ""
1063 api.return_value = mock.MagicMock()
1064 arvrunner.api = api.return_value
1065 arvrunner.runtimeContext.match_local_docker = False
1066 arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
1067 "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1068 "link_class": "docker_image_repo+tag",
1069 "name": "arvados/jobs:"+arvados_cwl.__version__,
1071 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
1072 {"items": [{"created_at": "",
1074 "link_class": "docker_image_hash",
1077 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
1079 find_one_image_hash.return_value = "123456"
1081 arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1083 "manifest_text": "",
1085 }], "items_available": 1, "offset": 0},)
1086 arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
1087 arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1088 "portable_data_hash": "9999999999999999999999999999999b+99"}
1089 self.assertEqual("9999999999999999999999999999999b+99",
1090 arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
1094 def test_submit_secrets(self, stubs):
1095 exited = arvados_cwl.main(
1096 ["--submit", "--no-wait", "--api=containers", "--debug",
1097 "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
1098 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1100 expect_container = {
1102 "arvados-cwl-runner",
1105 "--no-log-timestamps",
1106 "--disable-validate",
1108 "--eval-timeout=20",
1111 "--collection-cache-size=256",
1113 "--on-error=continue",
1114 "/var/lib/cwl/workflow.json#main",
1115 "/var/lib/cwl/cwl.input.json"
1117 "container_image": "999999999999999999999999999999d3+99",
1118 "cwd": "/var/spool/cwl",
1120 "/var/lib/cwl/cwl.input.json": {
1123 "$include": "/secrets/s0"
1128 "/var/lib/cwl/workflow.json": {
1136 "class": "CommandLineTool",
1139 "class": "http://commonwl.org/cwltool#Secrets",
1141 "#secret_job.cwl/pw"
1145 "id": "#secret_job.cwl",
1148 "id": "#secret_job.cwl/pw",
1154 "id": "#secret_job.cwl/out",
1157 "glob": "hashed_example.txt"
1161 "stdout": "hashed_example.txt",
1164 "class": "InitialWorkDirRequirement",
1167 "entry": "username: user\npassword: $(inputs.pw)\n",
1168 "entryname": "example.conf"
1175 "class": "Workflow",
1178 "class": "DockerRequirement",
1179 "dockerPull": "debian:buster-slim",
1180 "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
1183 "class": "http://commonwl.org/cwltool#Secrets",
1199 "outputSource": "#main/step1/out",
1205 "id": "#main/step1",
1208 "id": "#main/step1/pw",
1209 "source": "#main/pw"
1215 "run": "#secret_job.cwl"
1221 "cwltool": "http://commonwl.org/cwltool#"
1223 "cwlVersion": "v1.0"
1228 "kind": "collection",
1233 "path": "/var/spool/cwl/cwl.output.json"
1236 "name": "secret_wf.cwl",
1237 "output_path": "/var/spool/cwl",
1240 "runtime_constraints": {
1251 "state": "Committed",
1252 "use_existing": False
1255 stubs.api.container_requests().create.assert_called_with(
1256 body=JsonDiffMatcher(expect_container))
1257 self.assertEqual(stubs.capture_stdout.getvalue(),
1258 stubs.expect_container_request_uuid + '\n')
1259 self.assertEqual(exited, 0)
1262 def test_submit_request_uuid(self, stubs):
1263 stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
1264 stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
1266 stubs.api.container_requests().update().execute.return_value = {
1267 "uuid": stubs.expect_container_request_uuid,
1268 "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
1272 exited = arvados_cwl.main(
1273 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
1274 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1275 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1277 stubs.api.container_requests().update.assert_called_with(
1278 uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec))
1279 self.assertEqual(stubs.capture_stdout.getvalue(),
1280 stubs.expect_container_request_uuid + '\n')
1281 self.assertEqual(exited, 0)
1284 def test_submit_container_cluster_id(self, stubs):
1285 stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
1287 exited = arvados_cwl.main(
1288 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb",
1289 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1290 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1292 expect_container = copy.deepcopy(stubs.expect_container_spec)
1294 stubs.api.container_requests().create.assert_called_with(
1295 body=JsonDiffMatcher(expect_container), cluster_id="zbbbb")
1296 self.assertEqual(stubs.capture_stdout.getvalue(),
1297 stubs.expect_container_request_uuid + '\n')
1298 self.assertEqual(exited, 0)
1301 def test_submit_validate_cluster_id(self, stubs):
1302 stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
1303 exited = arvados_cwl.main(
1304 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zcccc",
1305 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1306 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1307 self.assertEqual(exited, 1)
1310 def test_submit_validate_project_uuid(self, stubs):
1311 # Fails with bad cluster prefix
1312 exited = arvados_cwl.main(
1313 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzb-j7d0g-zzzzzzzzzzzzzzz",
1314 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1315 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1316 self.assertEqual(exited, 1)
1318 # Project lookup fails
1319 stubs.api.groups().get().execute.side_effect = Exception("Bad project")
1320 exited = arvados_cwl.main(
1321 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-j7d0g-zzzzzzzzzzzzzzx",
1322 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1323 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1324 self.assertEqual(exited, 1)
1326 # It should work this time because it is looking up a user (and only group is stubbed out to fail)
1327 exited = arvados_cwl.main(
1328 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-tpzed-zzzzzzzzzzzzzzx",
1329 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1330 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1331 self.assertEqual(exited, 0)
1334 @mock.patch("arvados.collection.CollectionReader")
1336 def test_submit_uuid_inputs(self, stubs, collectionReader):
1337 collectionReader().exists.return_value = True
1338 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
1339 def list_side_effect(**kwargs):
1340 m = mock.MagicMock()
1341 if "count" in kwargs:
1342 m.execute.return_value = {"items": [
1343 {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999998+99"}
1346 m.execute.return_value = {"items": []}
1348 stubs.api.collections().list.side_effect = list_side_effect
1350 exited = arvados_cwl.main(
1351 ["--submit", "--no-wait", "--api=containers", "--debug",
1352 "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
1353 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1355 expect_container = copy.deepcopy(stubs.expect_container_spec)
1356 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['basename'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1357 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1358 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1360 stubs.api.collections().list.assert_has_calls([
1361 mock.call(count='none',
1362 filters=[['uuid', 'in', ['zzzzz-4zz18-zzzzzzzzzzzzzzz']]],
1363 select=['uuid', 'portable_data_hash'])])
1364 stubs.api.container_requests().create.assert_called_with(
1365 body=JsonDiffMatcher(expect_container))
1366 self.assertEqual(stubs.capture_stdout.getvalue(),
1367 stubs.expect_container_request_uuid + '\n')
1368 self.assertEqual(exited, 0)
1371 def test_submit_mismatched_uuid_inputs(self, stubs):
1372 def list_side_effect(**kwargs):
1373 m = mock.MagicMock()
1374 if "count" in kwargs:
1375 m.execute.return_value = {"items": [
1376 {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999997+99"}
1379 m.execute.return_value = {"items": []}
1381 stubs.api.collections().list.side_effect = list_side_effect
1383 for infile in ("tests/submit_test_job_with_mismatched_uuids.json", "tests/submit_test_job_with_inconsistent_uuids.json"):
1384 capture_stderr = StringIO()
1385 cwltool_logger = logging.getLogger('cwltool')
1386 stderr_logger = logging.StreamHandler(capture_stderr)
1387 cwltool_logger.addHandler(stderr_logger)
1390 exited = arvados_cwl.main(
1391 ["--submit", "--no-wait", "--api=containers", "--debug",
1392 "tests/wf/submit_wf.cwl", infile],
1393 stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1395 self.assertEqual(exited, 1)
1397 re.sub(r'[ \n]+', ' ', capture_stderr.getvalue()),
1398 r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99")
1400 cwltool_logger.removeHandler(stderr_logger)
1402 @mock.patch("arvados.collection.CollectionReader")
1404 def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
1405 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
1406 capture_stderr = StringIO()
1408 cwltool_logger = logging.getLogger('cwltool')
1409 stderr_logger = logging.StreamHandler(capture_stderr)
1410 cwltool_logger.addHandler(stderr_logger)
1412 exited = arvados_cwl.main(
1413 ["--submit", "--no-wait", "--api=containers", "--debug",
1414 "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
1415 stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1418 self.assertEqual(exited, 1)
1420 capture_stderr.getvalue(),
1421 r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found")
1423 cwltool_logger.removeHandler(stderr_logger)
1426 def test_submit_set_process_properties(self, stubs):
1427 exited = arvados_cwl.main(
1428 ["--submit", "--no-wait", "--api=containers", "--debug",
1429 "tests/wf/submit_wf_process_properties.cwl", "tests/submit_test_job.json"],
1430 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1432 expect_container = copy.deepcopy(stubs.expect_container_spec)
1433 expect_container["name"] = "submit_wf_process_properties.cwl"
1434 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
1436 "class": "http://arvados.org/cwl#ProcessProperties",
1437 "processProperties": [
1438 {"propertyName": "baz",
1439 "propertyValue": "$(inputs.x.basename)"},
1440 {"propertyName": "foo",
1441 "propertyValue": "bar"},
1442 {"propertyName": "quux",
1451 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
1452 "arv": "http://arvados.org/cwl#"
1455 expect_container["properties"] = {
1464 stubs.api.container_requests().create.assert_called_with(
1465 body=JsonDiffMatcher(expect_container))
1466 self.assertEqual(stubs.capture_stdout.getvalue(),
1467 stubs.expect_container_request_uuid + '\n')
1468 self.assertEqual(exited, 0)
1472 def test_submit_enable_preemptible(self, stubs):
1473 exited = arvados_cwl.main(
1474 ["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
1475 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1476 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1478 expect_container = copy.deepcopy(stubs.expect_container_spec)
1479 expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
1480 '--no-log-timestamps', '--disable-validate', '--disable-color',
1481 '--eval-timeout=20', '--thread-count=0',
1482 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
1483 '--enable-preemptible',
1484 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1486 stubs.api.container_requests().create.assert_called_with(
1487 body=JsonDiffMatcher(expect_container))
1488 self.assertEqual(stubs.capture_stdout.getvalue(),
1489 stubs.expect_container_request_uuid + '\n')
1490 self.assertEqual(exited, 0)
1493 def test_submit_disable_preemptible(self, stubs):
1494 exited = arvados_cwl.main(
1495 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
1496 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1497 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1499 expect_container = copy.deepcopy(stubs.expect_container_spec)
1500 expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
1501 '--no-log-timestamps', '--disable-validate', '--disable-color',
1502 '--eval-timeout=20', '--thread-count=0',
1503 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
1504 '--disable-preemptible',
1505 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1507 stubs.api.container_requests().create.assert_called_with(
1508 body=JsonDiffMatcher(expect_container))
1509 self.assertEqual(stubs.capture_stdout.getvalue(),
1510 stubs.expect_container_request_uuid + '\n')
1511 self.assertEqual(exited, 0)
1514 class TestCreateWorkflow(unittest.TestCase):
1515 existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
1516 expect_workflow = StripYAMLComments(
1517 open("tests/wf/expect_upload_packed.cwl").read().rstrip())
1520 cwltool.process._names = set()
1521 arvados_cwl.arvdocker.arv_docker_clear_cache()
1524 def test_create(self, stubs):
1525 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1526 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1528 exited = arvados_cwl.main(
1529 ["--create-workflow", "--debug",
1531 "--project-uuid", project_uuid,
1532 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1533 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1535 stubs.api.pipeline_templates().create.refute_called()
1536 stubs.api.container_requests().create.refute_called()
1540 "owner_uuid": project_uuid,
1541 "name": "submit_wf.cwl",
1543 "definition": self.expect_workflow,
1546 stubs.api.workflows().create.assert_called_with(
1547 body=JsonDiffMatcher(body))
1549 self.assertEqual(stubs.capture_stdout.getvalue(),
1550 stubs.expect_workflow_uuid + '\n')
1551 self.assertEqual(exited, 0)
1554 def test_create_name(self, stubs):
1555 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1556 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1558 exited = arvados_cwl.main(
1559 ["--create-workflow", "--debug",
1561 "--project-uuid", project_uuid,
1562 "--name", "testing 123",
1563 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1564 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1566 stubs.api.pipeline_templates().create.refute_called()
1567 stubs.api.container_requests().create.refute_called()
1571 "owner_uuid": project_uuid,
1572 "name": "testing 123",
1574 "definition": self.expect_workflow,
1577 stubs.api.workflows().create.assert_called_with(
1578 body=JsonDiffMatcher(body))
1580 self.assertEqual(stubs.capture_stdout.getvalue(),
1581 stubs.expect_workflow_uuid + '\n')
1582 self.assertEqual(exited, 0)
1586 def test_update(self, stubs):
1587 exited = arvados_cwl.main(
1588 ["--update-workflow", self.existing_workflow_uuid,
1590 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1591 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1595 "name": "submit_wf.cwl",
1597 "definition": self.expect_workflow,
1600 stubs.api.workflows().update.assert_called_with(
1601 uuid=self.existing_workflow_uuid,
1602 body=JsonDiffMatcher(body))
1603 self.assertEqual(stubs.capture_stdout.getvalue(),
1604 self.existing_workflow_uuid + '\n')
1605 self.assertEqual(exited, 0)
1608 def test_update_name(self, stubs):
1609 exited = arvados_cwl.main(
1610 ["--update-workflow", self.existing_workflow_uuid,
1611 "--debug", "--name", "testing 123",
1612 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1613 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1617 "name": "testing 123",
1619 "definition": self.expect_workflow,
1622 stubs.api.workflows().update.assert_called_with(
1623 uuid=self.existing_workflow_uuid,
1624 body=JsonDiffMatcher(body))
1625 self.assertEqual(stubs.capture_stdout.getvalue(),
1626 self.existing_workflow_uuid + '\n')
1627 self.assertEqual(exited, 0)
1630 def test_create_collection_per_tool(self, stubs):
1631 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1632 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1634 exited = arvados_cwl.main(
1635 ["--create-workflow", "--debug",
1637 "--project-uuid", project_uuid,
1638 "tests/collection_per_tool/collection_per_tool.cwl"],
1639 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1641 toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
1642 expect_workflow = StripYAMLComments(open(toolfile).read().rstrip())
1646 "owner_uuid": project_uuid,
1647 "name": "collection_per_tool.cwl",
1649 "definition": expect_workflow,
1652 stubs.api.workflows().create.assert_called_with(
1653 body=JsonDiffMatcher(body))
1655 self.assertEqual(stubs.capture_stdout.getvalue(),
1656 stubs.expect_workflow_uuid + '\n')
1657 self.assertEqual(exited, 0)
1660 def test_create_with_imports(self, stubs):
1661 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1662 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1664 exited = arvados_cwl.main(
1665 ["--create-workflow", "--debug",
1667 "--project-uuid", project_uuid,
1668 "tests/wf/feddemo/feddemo.cwl"],
1669 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1671 stubs.api.pipeline_templates().create.refute_called()
1672 stubs.api.container_requests().create.refute_called()
1674 self.assertEqual(stubs.capture_stdout.getvalue(),
1675 stubs.expect_workflow_uuid + '\n')
1676 self.assertEqual(exited, 0)
1679 def test_create_with_no_input(self, stubs):
1680 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1681 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1683 exited = arvados_cwl.main(
1684 ["--create-workflow", "--debug",
1686 "--project-uuid", project_uuid,
1687 "tests/wf/revsort/revsort.cwl"],
1688 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1690 stubs.api.pipeline_templates().create.refute_called()
1691 stubs.api.container_requests().create.refute_called()
1693 self.assertEqual(stubs.capture_stdout.getvalue(),
1694 stubs.expect_workflow_uuid + '\n')
1695 self.assertEqual(exited, 0)