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("uuid.uuid4")
51 @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
52 @mock.patch("arvados.collection.KeepClient")
53 @mock.patch("arvados.keep.KeepClient")
54 @mock.patch("arvados.events.subscribe")
55 def wrapped(self, events, keep_client1, keep_client2, keepdocker, uuid4, *args, **kwargs):
60 stubs.keepdocker = keepdocker
62 uuid4.side_effect = ["df80736f-f14d-4b10-b2e3-03aa27f034bb", "df80736f-f14d-4b10-b2e3-03aa27f034b1",
63 "df80736f-f14d-4b10-b2e3-03aa27f034b2", "df80736f-f14d-4b10-b2e3-03aa27f034b3",
64 "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5"]
66 def putstub(p, **kwargs):
67 return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
68 keep_client1().put.side_effect = putstub
69 keep_client1.put.side_effect = putstub
70 keep_client2().put.side_effect = putstub
71 keep_client2.put.side_effect = putstub
73 stubs.keep_client = keep_client2
74 stubs.docker_images = {
75 "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", {})],
76 "debian:buster-slim": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", {})],
77 "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", {})],
78 "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", {})],
80 def kd(a, b, image_name=None, image_tag=None):
81 return stubs.docker_images.get("%s:%s" % (image_name, image_tag), [])
82 stubs.keepdocker.side_effect = kd
84 stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
85 stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz"
87 if sys.version_info[0] < 3:
88 stubs.capture_stdout = BytesIO()
90 stubs.capture_stdout = StringIO()
92 stubs.api = mock.MagicMock()
93 stubs.api._rootDesc = get_rootDesc()
94 stubs.api._rootDesc["uuidPrefix"] = "zzzzz"
95 stubs.api._rootDesc["revision"] = "20210628"
97 stubs.api.users().current().execute.return_value = {
98 "uuid": stubs.fake_user_uuid,
100 stubs.api.collections().list().execute.return_value = {"items": []}
101 stubs.api.containers().current().execute.return_value = {
102 "uuid": stubs.fake_container_uuid,
104 stubs.api.config()["StorageClasses"].items.return_value = {
110 class CollectionExecute(object):
111 def __init__(self, exe):
113 def execute(self, num_retries=None):
116 def collection_createstub(created_collections, body, ensure_unique_name=None):
117 mt = body["manifest_text"].encode('utf-8')
118 uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%d" % len(created_collections)
119 pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
120 created_collections[uuid] = {
122 "portable_data_hash": pdh,
123 "manifest_text": mt.decode('utf-8')
125 return CollectionExecute(created_collections[uuid])
127 def collection_getstub(created_collections, uuid):
128 for v in viewvalues(created_collections):
129 if uuid in (v["uuid"], v["portable_data_hash"]):
130 return CollectionExecute(v)
132 created_collections = {
133 "99999999999999999999999999999998+99": {
135 "portable_data_hash": "99999999999999999999999999999998+99",
136 "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
138 "99999999999999999999999999999997+99": {
140 "portable_data_hash": "99999999999999999999999999999997+99",
141 "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt"
143 "99999999999999999999999999999994+99": {
145 "portable_data_hash": "99999999999999999999999999999994+99",
146 "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
148 "zzzzz-4zz18-zzzzzzzzzzzzzd3": {
149 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd3",
150 "portable_data_hash": "999999999999999999999999999999d3+99",
153 "zzzzz-4zz18-zzzzzzzzzzzzzd4": {
154 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd4",
155 "portable_data_hash": "999999999999999999999999999999d4+99",
158 "zzzzz-4zz18-zzzzzzzzzzzzzd5": {
159 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd5",
160 "portable_data_hash": "999999999999999999999999999999d5+99",
163 "zzzzz-4zz18-zzzzzzzzzzzzzd6": {
164 "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd6",
165 "portable_data_hash": "999999999999999999999999999999d6+99",
169 stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
170 stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
172 stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
173 stubs.api.jobs().create().execute.return_value = {
174 "uuid": stubs.expect_job_uuid,
178 stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
179 stubs.api.container_requests().create().execute.return_value = {
180 "uuid": stubs.expect_container_request_uuid,
181 "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
185 stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
186 stubs.api.pipeline_templates().create().execute.return_value = {
187 "uuid": stubs.expect_pipeline_template_uuid,
189 stubs.expect_job_spec = {
190 'runtime_constraints': {
191 'docker_image': '999999999999999999999999999999d3+99',
192 'min_ram_mb_per_node': 1024
194 'script_parameters': {
196 'basename': 'blorp.txt',
197 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
201 'basename': '99999999999999999999999999999998+99',
202 'location': 'keep:99999999999999999999999999999998+99',
206 'basename': 'anonymous',
208 "basename": "renamed.txt",
210 "location": "keep:99999999999999999999999999999998+99/file1.txt",
215 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main'
217 'repository': 'arvados',
218 'script_version': 'master',
219 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
220 'script': 'cwl-runner'
222 stubs.pipeline_component = stubs.expect_job_spec.copy()
223 stubs.expect_pipeline_instance = {
224 'name': 'submit_wf.cwl',
225 'state': 'RunningOnServer',
229 'runtime_constraints': {'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024},
230 'script_parameters': {
231 'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
233 'basename': 'blorp.txt',
235 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
238 'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
241 'basename': 'renamed.txt',
242 'class': 'File', 'location':
243 'keep:99999999999999999999999999999998+99/file1.txt',
247 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main',
249 'arv:enable_reuse': True,
250 'arv:on_error': 'continue'
252 'repository': 'arvados',
253 'script_version': 'master',
254 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
255 'script': 'cwl-runner',
256 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
260 stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
261 stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
262 stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
263 stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
264 stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
265 "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
268 stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
269 stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
271 with open("tests/wf/submit_wf_packed.cwl") as f:
272 expect_packed_workflow = yaml.round_trip_load(f)
274 stubs.expect_container_spec = {
281 '/var/lib/cwl/workflow.json': {
282 'content': expect_packed_workflow,
286 'path': '/var/spool/cwl/cwl.output.json',
289 '/var/lib/cwl/cwl.input.json': {
293 'basename': '99999999999999999999999999999998+99',
294 'location': 'keep:99999999999999999999999999999998+99',
295 'class': 'Directory'},
297 'basename': u'blorp.txt',
299 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
302 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
303 {'basename': 'renamed.txt',
305 'location': 'keep:99999999999999999999999999999998+99/file1.txt',
314 'state': 'Committed',
315 'command': ['arvados-cwl-runner', '--local', '--api=containers',
316 '--no-log-timestamps', '--disable-validate', '--disable-color',
317 '--eval-timeout=20', '--thread-count=0',
318 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
319 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
320 'name': 'submit_wf.cwl',
321 'container_image': '999999999999999999999999999999d3+99',
322 'output_path': '/var/spool/cwl',
323 'cwd': '/var/spool/cwl',
324 'runtime_constraints': {
327 'ram': (1024+256)*1024*1024
329 'use_existing': False,
334 stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
335 stubs.api.workflows().create().execute.return_value = {
336 "uuid": stubs.expect_workflow_uuid,
338 def update_mock(**kwargs):
339 stubs.updated_uuid = kwargs.get('uuid')
341 stubs.api.workflows().update.side_effect = update_mock
342 stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
343 "uuid": stubs.updated_uuid,
346 return func(self, stubs, *args, **kwargs)
350 class TestSubmit(unittest.TestCase):
353 cwltool.process._names = set()
354 arvados_cwl.arvdocker.arv_docker_clear_cache()
357 @mock.patch("time.sleep")
359 def test_submit_invalid_runner_ram(self, stubs, tm):
360 exited = arvados_cwl.main(
361 ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
362 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
363 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
364 self.assertEqual(exited, 1)
368 def test_submit_container(self, stubs):
369 exited = arvados_cwl.main(
370 ["--submit", "--no-wait", "--api=containers", "--debug",
371 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
372 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
374 stubs.api.collections().create.assert_has_calls([
375 mock.call(body=JsonDiffMatcher({
377 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
378 'replication_desired': None,
379 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
380 }), ensure_unique_name=False),
381 mock.call(body=JsonDiffMatcher({
383 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
384 'replication_desired': None,
385 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
386 }), ensure_unique_name=False),
389 expect_container = copy.deepcopy(stubs.expect_container_spec)
390 stubs.api.container_requests().create.assert_called_with(
391 body=JsonDiffMatcher(expect_container))
392 self.assertEqual(stubs.capture_stdout.getvalue(),
393 stubs.expect_container_request_uuid + '\n')
394 self.assertEqual(exited, 0)
398 def test_submit_container_tool(self, stubs):
399 # test for issue #16139
400 exited = arvados_cwl.main(
401 ["--submit", "--no-wait", "--api=containers", "--debug",
402 "tests/tool/tool_with_sf.cwl", "tests/tool/tool_with_sf.yml"],
403 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
405 self.assertEqual(stubs.capture_stdout.getvalue(),
406 stubs.expect_container_request_uuid + '\n')
407 self.assertEqual(exited, 0)
410 def test_submit_container_no_reuse(self, stubs):
411 exited = arvados_cwl.main(
412 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
413 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
414 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
416 expect_container = copy.deepcopy(stubs.expect_container_spec)
417 expect_container["command"] = [
418 'arvados-cwl-runner', '--local', '--api=containers',
419 '--no-log-timestamps', '--disable-validate', '--disable-color',
420 '--eval-timeout=20', '--thread-count=0',
421 '--disable-reuse', "--collection-cache-size=256",
422 '--debug', '--on-error=continue',
423 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
424 expect_container["use_existing"] = False
426 stubs.api.container_requests().create.assert_called_with(
427 body=JsonDiffMatcher(expect_container))
428 self.assertEqual(stubs.capture_stdout.getvalue(),
429 stubs.expect_container_request_uuid + '\n')
430 self.assertEqual(exited, 0)
433 def test_submit_container_reuse_disabled_by_workflow(self, stubs):
434 exited = arvados_cwl.main(
435 ["--submit", "--no-wait", "--api=containers", "--debug",
436 "tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"],
437 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
438 self.assertEqual(exited, 0)
440 expect_container = copy.deepcopy(stubs.expect_container_spec)
441 expect_container["command"] = [
442 'arvados-cwl-runner', '--local', '--api=containers',
443 '--no-log-timestamps', '--disable-validate', '--disable-color',
444 '--eval-timeout=20', '--thread-count=0',
445 '--disable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
446 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
447 expect_container["use_existing"] = False
448 expect_container["name"] = "submit_wf_no_reuse.cwl"
449 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
451 "class": "http://arvados.org/cwl#ReuseRequirement",
452 "enableReuse": False,
455 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
456 "arv": "http://arvados.org/cwl#",
457 "cwltool": "http://commonwl.org/cwltool#"
460 stubs.api.container_requests().create.assert_called_with(
461 body=JsonDiffMatcher(expect_container))
462 self.assertEqual(stubs.capture_stdout.getvalue(),
463 stubs.expect_container_request_uuid + '\n')
467 def test_submit_container_on_error(self, stubs):
468 exited = arvados_cwl.main(
469 ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
470 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
471 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
473 expect_container = copy.deepcopy(stubs.expect_container_spec)
474 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
475 '--no-log-timestamps', '--disable-validate', '--disable-color',
476 '--eval-timeout=20', '--thread-count=0',
477 '--enable-reuse', "--collection-cache-size=256",
478 '--debug', '--on-error=stop',
479 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
481 stubs.api.container_requests().create.assert_called_with(
482 body=JsonDiffMatcher(expect_container))
483 self.assertEqual(stubs.capture_stdout.getvalue(),
484 stubs.expect_container_request_uuid + '\n')
485 self.assertEqual(exited, 0)
488 def test_submit_container_output_name(self, stubs):
489 output_name = "test_output_name"
491 exited = arvados_cwl.main(
492 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
493 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
494 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
496 expect_container = copy.deepcopy(stubs.expect_container_spec)
497 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
498 '--no-log-timestamps', '--disable-validate', '--disable-color',
499 '--eval-timeout=20', '--thread-count=0',
500 '--enable-reuse', "--collection-cache-size=256",
501 "--output-name="+output_name, '--debug', '--on-error=continue',
502 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
503 expect_container["output_name"] = output_name
505 stubs.api.container_requests().create.assert_called_with(
506 body=JsonDiffMatcher(expect_container))
507 self.assertEqual(stubs.capture_stdout.getvalue(),
508 stubs.expect_container_request_uuid + '\n')
509 self.assertEqual(exited, 0)
512 def test_submit_storage_classes(self, stubs):
513 exited = arvados_cwl.main(
514 ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
515 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
516 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
518 expect_container = copy.deepcopy(stubs.expect_container_spec)
519 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
520 '--no-log-timestamps', '--disable-validate', '--disable-color',
521 '--eval-timeout=20', '--thread-count=0',
522 '--enable-reuse', "--collection-cache-size=256", "--debug",
523 "--storage-classes=foo", '--on-error=continue',
524 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
526 stubs.api.container_requests().create.assert_called_with(
527 body=JsonDiffMatcher(expect_container))
528 self.assertEqual(stubs.capture_stdout.getvalue(),
529 stubs.expect_container_request_uuid + '\n')
530 self.assertEqual(exited, 0)
533 def test_submit_multiple_storage_classes(self, stubs):
534 exited = arvados_cwl.main(
535 ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
536 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
537 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
539 expect_container = copy.deepcopy(stubs.expect_container_spec)
540 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
541 '--no-log-timestamps', '--disable-validate', '--disable-color',
542 '--eval-timeout=20', '--thread-count=0',
543 '--enable-reuse', "--collection-cache-size=256", "--debug",
544 "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--on-error=continue',
545 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
547 stubs.api.container_requests().create.assert_called_with(
548 body=JsonDiffMatcher(expect_container))
549 self.assertEqual(stubs.capture_stdout.getvalue(),
550 stubs.expect_container_request_uuid + '\n')
551 self.assertEqual(exited, 0)
553 @mock.patch("cwltool.task_queue.TaskQueue")
554 @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
555 @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
557 def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
558 final_output_c = arvados.collection.Collection()
559 make_output.return_value = ({},final_output_c)
561 def set_final_output(job_order, output_callback, runtimeContext):
562 output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
564 job.side_effect = set_final_output
566 exited = arvados_cwl.main(
567 ["--debug", "--local", "--storage-classes=foo",
568 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
569 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
571 make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
572 self.assertEqual(exited, 0)
574 @mock.patch("cwltool.task_queue.TaskQueue")
575 @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
576 @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
578 def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
579 final_output_c = arvados.collection.Collection()
580 make_output.return_value = ({},final_output_c)
581 stubs.api.config().get.return_value = {"default": {"Default": True}}
583 def set_final_output(job_order, output_callback, runtimeContext):
584 output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
586 job.side_effect = set_final_output
588 exited = arvados_cwl.main(
589 ["--debug", "--local",
590 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
591 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
593 make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
594 self.assertEqual(exited, 0)
596 @mock.patch("cwltool.task_queue.TaskQueue")
597 @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
598 @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
600 def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq):
601 final_output_c = arvados.collection.Collection()
602 make_output.return_value = ({},final_output_c)
604 def set_final_output(job_order, output_callback, runtimeContext):
605 output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
607 job.side_effect = set_final_output
609 exited = arvados_cwl.main(
610 ["--debug", "--local",
611 "tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"],
612 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
614 make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
615 self.assertEqual(exited, 0)
618 def test_submit_container_output_ttl(self, stubs):
619 exited = arvados_cwl.main(
620 ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
621 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
622 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
624 expect_container = copy.deepcopy(stubs.expect_container_spec)
625 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
626 '--no-log-timestamps', '--disable-validate', '--disable-color',
627 '--eval-timeout=20', '--thread-count=0',
628 '--enable-reuse', "--collection-cache-size=256", '--debug',
629 '--on-error=continue',
630 "--intermediate-output-ttl=3600",
631 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
633 stubs.api.container_requests().create.assert_called_with(
634 body=JsonDiffMatcher(expect_container))
635 self.assertEqual(stubs.capture_stdout.getvalue(),
636 stubs.expect_container_request_uuid + '\n')
637 self.assertEqual(exited, 0)
640 def test_submit_container_trash_intermediate(self, stubs):
641 exited = arvados_cwl.main(
642 ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
643 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
644 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
647 expect_container = copy.deepcopy(stubs.expect_container_spec)
648 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
649 '--no-log-timestamps', '--disable-validate', '--disable-color',
650 '--eval-timeout=20', '--thread-count=0',
651 '--enable-reuse', "--collection-cache-size=256",
652 '--debug', '--on-error=continue',
653 "--trash-intermediate",
654 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
656 stubs.api.container_requests().create.assert_called_with(
657 body=JsonDiffMatcher(expect_container))
658 self.assertEqual(stubs.capture_stdout.getvalue(),
659 stubs.expect_container_request_uuid + '\n')
660 self.assertEqual(exited, 0)
663 def test_submit_container_output_tags(self, stubs):
664 output_tags = "tag0,tag1,tag2"
666 exited = arvados_cwl.main(
667 ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
668 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
669 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
671 expect_container = copy.deepcopy(stubs.expect_container_spec)
672 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
673 '--no-log-timestamps', '--disable-validate', '--disable-color',
674 '--eval-timeout=20', '--thread-count=0',
675 '--enable-reuse', "--collection-cache-size=256",
676 "--output-tags="+output_tags, '--debug', '--on-error=continue',
677 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
679 stubs.api.container_requests().create.assert_called_with(
680 body=JsonDiffMatcher(expect_container))
681 self.assertEqual(stubs.capture_stdout.getvalue(),
682 stubs.expect_container_request_uuid + '\n')
683 self.assertEqual(exited, 0)
686 def test_submit_container_runner_ram(self, stubs):
687 exited = arvados_cwl.main(
688 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
689 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
690 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
692 expect_container = copy.deepcopy(stubs.expect_container_spec)
693 expect_container["runtime_constraints"]["ram"] = (2048+256)*1024*1024
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)
701 @mock.patch("arvados.collection.CollectionReader")
702 @mock.patch("time.sleep")
704 def test_submit_file_keepref(self, stubs, tm, collectionReader):
705 collectionReader().exists.return_value = True
706 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
707 exited = arvados_cwl.main(
708 ["--submit", "--no-wait", "--api=containers", "--debug",
709 "tests/wf/submit_keepref_wf.cwl"],
710 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
711 self.assertEqual(exited, 0)
713 @mock.patch("arvados.collection.CollectionReader")
714 @mock.patch("time.sleep")
716 def test_submit_keepref(self, stubs, tm, reader):
717 with open("tests/wf/expect_arvworkflow.cwl") as f:
718 reader().open().__enter__().read.return_value = f.read()
720 exited = arvados_cwl.main(
721 ["--submit", "--no-wait", "--api=containers", "--debug",
722 "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
723 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
733 'path': '/var/spool/cwl/cwl.output.json',
736 '/var/lib/cwl/workflow': {
737 'portable_data_hash': '99999999999999999999999999999994+99',
740 '/var/lib/cwl/cwl.input.json': {
746 }, 'state': 'Committed',
747 'output_path': '/var/spool/cwl',
748 'name': 'expect_arvworkflow.cwl#main',
749 'container_image': '999999999999999999999999999999d3+99',
750 'command': ['arvados-cwl-runner', '--local', '--api=containers',
751 '--no-log-timestamps', '--disable-validate', '--disable-color',
752 '--eval-timeout=20', '--thread-count=0',
753 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
754 '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
755 'cwd': '/var/spool/cwl',
756 'runtime_constraints': {
761 'use_existing': False,
766 stubs.api.container_requests().create.assert_called_with(
767 body=JsonDiffMatcher(expect_container))
768 self.assertEqual(stubs.capture_stdout.getvalue(),
769 stubs.expect_container_request_uuid + '\n')
770 self.assertEqual(exited, 0)
772 @mock.patch("time.sleep")
774 def test_submit_arvworkflow(self, stubs, tm):
775 with open("tests/wf/expect_arvworkflow.cwl") as f:
776 stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
778 exited = arvados_cwl.main(
779 ["--submit", "--no-wait", "--api=containers", "--debug",
780 "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
781 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
791 'path': '/var/spool/cwl/cwl.output.json',
794 '/var/lib/cwl/workflow.json': {
797 'cwlVersion': 'v1.0',
802 {'type': 'string', 'id': '#main/x'}
805 {'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
806 'run': '#submit_tool.cwl',
816 'inputBinding': {'position': 1},
818 'id': '#submit_tool.cwl/x'}
822 'dockerPull': 'debian:buster-slim',
823 'class': 'DockerRequirement',
824 "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
827 'id': '#submit_tool.cwl',
829 'baseCommand': 'cat',
830 'class': 'CommandLineTool'
835 '/var/lib/cwl/cwl.input.json': {
841 }, 'state': 'Committed',
842 'output_path': '/var/spool/cwl',
843 'name': 'a test workflow',
844 'container_image': "999999999999999999999999999999d3+99",
845 'command': ['arvados-cwl-runner', '--local', '--api=containers',
846 '--no-log-timestamps', '--disable-validate', '--disable-color',
847 '--eval-timeout=20', '--thread-count=0',
848 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
849 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
850 'cwd': '/var/spool/cwl',
851 'runtime_constraints': {
856 'use_existing': False,
858 "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
863 stubs.api.container_requests().create.assert_called_with(
864 body=JsonDiffMatcher(expect_container))
865 self.assertEqual(stubs.capture_stdout.getvalue(),
866 stubs.expect_container_request_uuid + '\n')
867 self.assertEqual(exited, 0)
870 def test_submit_container_name(self, stubs):
871 exited = arvados_cwl.main(
872 ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
873 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
874 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
876 expect_container = copy.deepcopy(stubs.expect_container_spec)
877 expect_container["name"] = "hello container 123"
879 stubs.api.container_requests().create.assert_called_with(
880 body=JsonDiffMatcher(expect_container))
881 self.assertEqual(stubs.capture_stdout.getvalue(),
882 stubs.expect_container_request_uuid + '\n')
883 self.assertEqual(exited, 0)
886 def test_submit_missing_input(self, stubs):
887 exited = arvados_cwl.main(
888 ["--submit", "--no-wait", "--api=containers", "--debug",
889 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
890 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
891 self.assertEqual(exited, 0)
893 exited = arvados_cwl.main(
894 ["--submit", "--no-wait", "--api=containers", "--debug",
895 "tests/wf/submit_wf.cwl", "tests/submit_test_job_missing.json"],
896 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
897 self.assertEqual(exited, 1)
900 def test_submit_container_project(self, stubs):
901 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
902 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
903 exited = arvados_cwl.main(
904 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
905 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
906 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
908 expect_container = copy.deepcopy(stubs.expect_container_spec)
909 expect_container["owner_uuid"] = project_uuid
910 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
911 '--no-log-timestamps', '--disable-validate', '--disable-color',
912 "--eval-timeout=20", "--thread-count=0",
913 '--enable-reuse', "--collection-cache-size=256", '--debug',
914 '--on-error=continue',
915 '--project-uuid='+project_uuid,
916 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
918 stubs.api.container_requests().create.assert_called_with(
919 body=JsonDiffMatcher(expect_container))
920 self.assertEqual(stubs.capture_stdout.getvalue(),
921 stubs.expect_container_request_uuid + '\n')
922 self.assertEqual(exited, 0)
925 def test_submit_container_eval_timeout(self, stubs):
926 exited = arvados_cwl.main(
927 ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
928 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
929 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
931 expect_container = copy.deepcopy(stubs.expect_container_spec)
932 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
933 '--no-log-timestamps', '--disable-validate', '--disable-color',
934 '--eval-timeout=60.0', '--thread-count=0',
935 '--enable-reuse', "--collection-cache-size=256",
936 '--debug', '--on-error=continue',
937 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
939 stubs.api.container_requests().create.assert_called_with(
940 body=JsonDiffMatcher(expect_container))
941 self.assertEqual(stubs.capture_stdout.getvalue(),
942 stubs.expect_container_request_uuid + '\n')
943 self.assertEqual(exited, 0)
946 def test_submit_container_collection_cache(self, stubs):
947 exited = arvados_cwl.main(
948 ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
949 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
950 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
952 expect_container = copy.deepcopy(stubs.expect_container_spec)
953 expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
954 '--no-log-timestamps', '--disable-validate', '--disable-color',
955 '--eval-timeout=20', '--thread-count=0',
956 '--enable-reuse', "--collection-cache-size=500",
957 '--debug', '--on-error=continue',
958 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
959 expect_container["runtime_constraints"]["ram"] = (1024+500)*1024*1024
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_thread_count(self, stubs):
969 exited = arvados_cwl.main(
970 ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
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=20', '--thread-count=20',
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_runner_image(self, stubs):
990 exited = arvados_cwl.main(
991 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
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 stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99"
997 expect_container = copy.deepcopy(stubs.expect_container_spec)
998 stubs.api.container_requests().create.assert_called_with(
999 body=JsonDiffMatcher(expect_container))
1000 self.assertEqual(stubs.capture_stdout.getvalue(),
1001 stubs.expect_container_request_uuid + '\n')
1002 self.assertEqual(exited, 0)
1005 def test_submit_priority(self, stubs):
1006 exited = arvados_cwl.main(
1007 ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
1008 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1009 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1011 stubs.expect_container_spec["priority"] = 669
1013 expect_container = copy.deepcopy(stubs.expect_container_spec)
1014 stubs.api.container_requests().create.assert_called_with(
1015 body=JsonDiffMatcher(expect_container))
1016 self.assertEqual(stubs.capture_stdout.getvalue(),
1017 stubs.expect_container_request_uuid + '\n')
1018 self.assertEqual(exited, 0)
1021 def test_submit_wf_runner_resources(self, stubs):
1022 exited = arvados_cwl.main(
1023 ["--submit", "--no-wait", "--api=containers", "--debug",
1024 "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"],
1025 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1027 expect_container = copy.deepcopy(stubs.expect_container_spec)
1028 expect_container["runtime_constraints"] = {
1031 "ram": (2000+512) * 2**20
1033 expect_container["name"] = "submit_wf_runner_resources.cwl"
1034 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
1036 "class": "http://arvados.org/cwl#WorkflowRunnerResources",
1042 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
1043 "arv": "http://arvados.org/cwl#",
1045 expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
1046 '--no-log-timestamps', '--disable-validate', '--disable-color',
1047 '--eval-timeout=20', '--thread-count=0',
1048 '--enable-reuse', "--collection-cache-size=512", '--debug', '--on-error=continue',
1049 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1051 stubs.api.container_requests().create.assert_called_with(
1052 body=JsonDiffMatcher(expect_container))
1053 self.assertEqual(stubs.capture_stdout.getvalue(),
1054 stubs.expect_container_request_uuid + '\n')
1055 self.assertEqual(exited, 0)
1058 arvados_cwl.arvdocker.arv_docker_clear_cache()
1060 @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
1061 @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
1062 @mock.patch("arvados.api")
1063 def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
1064 arvados_cwl.arvdocker.arv_docker_clear_cache()
1066 arvrunner = mock.MagicMock()
1067 arvrunner.project_uuid = ""
1068 api.return_value = mock.MagicMock()
1069 arvrunner.api = api.return_value
1070 arvrunner.runtimeContext.match_local_docker = False
1071 arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
1072 "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1073 "link_class": "docker_image_repo+tag",
1074 "name": "arvados/jobs:"+arvados_cwl.__version__,
1076 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
1077 {"items": [{"created_at": "",
1079 "link_class": "docker_image_hash",
1082 "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
1084 find_one_image_hash.return_value = "123456"
1086 arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1088 "manifest_text": "",
1090 }], "items_available": 1, "offset": 0},)
1091 arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
1092 arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
1093 "portable_data_hash": "9999999999999999999999999999999b+99"}
1094 self.assertEqual("9999999999999999999999999999999b+99",
1095 arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
1099 def test_submit_secrets(self, stubs):
1100 exited = arvados_cwl.main(
1101 ["--submit", "--no-wait", "--api=containers", "--debug",
1102 "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
1103 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1105 expect_container = {
1107 "arvados-cwl-runner",
1110 "--no-log-timestamps",
1111 "--disable-validate",
1113 "--eval-timeout=20",
1116 "--collection-cache-size=256",
1118 "--on-error=continue",
1119 "/var/lib/cwl/workflow.json#main",
1120 "/var/lib/cwl/cwl.input.json"
1122 "container_image": "999999999999999999999999999999d3+99",
1123 "cwd": "/var/spool/cwl",
1125 "/var/lib/cwl/cwl.input.json": {
1128 "$include": "/secrets/s0"
1133 "/var/lib/cwl/workflow.json": {
1141 "class": "CommandLineTool",
1144 "class": "http://commonwl.org/cwltool#Secrets",
1146 "#secret_job.cwl/pw"
1150 "id": "#secret_job.cwl",
1153 "id": "#secret_job.cwl/pw",
1159 "id": "#secret_job.cwl/out",
1162 "glob": "hashed_example.txt"
1166 "stdout": "hashed_example.txt",
1169 "class": "InitialWorkDirRequirement",
1172 "entry": "username: user\npassword: $(inputs.pw)\n",
1173 "entryname": "example.conf"
1180 "class": "Workflow",
1183 "class": "DockerRequirement",
1184 "dockerPull": "debian:buster-slim",
1185 "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
1188 "class": "http://commonwl.org/cwltool#Secrets",
1204 "outputSource": "#main/step1/out",
1210 "id": "#main/step1",
1213 "id": "#main/step1/pw",
1214 "source": "#main/pw"
1220 "run": "#secret_job.cwl"
1226 "cwltool": "http://commonwl.org/cwltool#"
1228 "cwlVersion": "v1.0"
1233 "kind": "collection",
1238 "path": "/var/spool/cwl/cwl.output.json"
1241 "name": "secret_wf.cwl",
1242 "output_path": "/var/spool/cwl",
1245 "runtime_constraints": {
1256 "state": "Committed",
1257 "use_existing": False
1260 stubs.api.container_requests().create.assert_called_with(
1261 body=JsonDiffMatcher(expect_container))
1262 self.assertEqual(stubs.capture_stdout.getvalue(),
1263 stubs.expect_container_request_uuid + '\n')
1264 self.assertEqual(exited, 0)
1267 def test_submit_request_uuid(self, stubs):
1268 stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
1269 stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
1271 stubs.api.container_requests().update().execute.return_value = {
1272 "uuid": stubs.expect_container_request_uuid,
1273 "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
1277 exited = arvados_cwl.main(
1278 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
1279 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1280 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1282 stubs.api.container_requests().update.assert_called_with(
1283 uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec))
1284 self.assertEqual(stubs.capture_stdout.getvalue(),
1285 stubs.expect_container_request_uuid + '\n')
1286 self.assertEqual(exited, 0)
1289 def test_submit_container_cluster_id(self, stubs):
1290 stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
1292 exited = arvados_cwl.main(
1293 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb",
1294 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1295 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1297 expect_container = copy.deepcopy(stubs.expect_container_spec)
1299 stubs.api.container_requests().create.assert_called_with(
1300 body=JsonDiffMatcher(expect_container), cluster_id="zbbbb")
1301 self.assertEqual(stubs.capture_stdout.getvalue(),
1302 stubs.expect_container_request_uuid + '\n')
1303 self.assertEqual(exited, 0)
1306 def test_submit_validate_cluster_id(self, stubs):
1307 stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
1308 exited = arvados_cwl.main(
1309 ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zcccc",
1310 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1311 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1312 self.assertEqual(exited, 1)
1315 def test_submit_validate_project_uuid(self, stubs):
1316 # Fails with bad cluster prefix
1317 exited = arvados_cwl.main(
1318 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzb-j7d0g-zzzzzzzzzzzzzzz",
1319 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1320 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1321 self.assertEqual(exited, 1)
1323 # Project lookup fails
1324 stubs.api.groups().get().execute.side_effect = Exception("Bad project")
1325 exited = arvados_cwl.main(
1326 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-j7d0g-zzzzzzzzzzzzzzx",
1327 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1328 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1329 self.assertEqual(exited, 1)
1331 # It should work this time because it is looking up a user (and only group is stubbed out to fail)
1332 exited = arvados_cwl.main(
1333 ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-tpzed-zzzzzzzzzzzzzzx",
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)
1336 self.assertEqual(exited, 0)
1339 @mock.patch("arvados.collection.CollectionReader")
1341 def test_submit_uuid_inputs(self, stubs, collectionReader):
1342 collectionReader().exists.return_value = True
1343 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
1344 def list_side_effect(**kwargs):
1345 m = mock.MagicMock()
1346 if "count" in kwargs:
1347 m.execute.return_value = {"items": [
1348 {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999998+99"}
1351 m.execute.return_value = {"items": []}
1353 stubs.api.collections().list.side_effect = list_side_effect
1355 exited = arvados_cwl.main(
1356 ["--submit", "--no-wait", "--api=containers", "--debug",
1357 "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
1358 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1360 expect_container = copy.deepcopy(stubs.expect_container_spec)
1361 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['basename'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1362 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1363 expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
1365 stubs.api.collections().list.assert_has_calls([
1366 mock.call(count='none',
1367 filters=[['uuid', 'in', ['zzzzz-4zz18-zzzzzzzzzzzzzzz']]],
1368 select=['uuid', 'portable_data_hash'])])
1369 stubs.api.container_requests().create.assert_called_with(
1370 body=JsonDiffMatcher(expect_container))
1371 self.assertEqual(stubs.capture_stdout.getvalue(),
1372 stubs.expect_container_request_uuid + '\n')
1373 self.assertEqual(exited, 0)
1376 def test_submit_mismatched_uuid_inputs(self, stubs):
1377 def list_side_effect(**kwargs):
1378 m = mock.MagicMock()
1379 if "count" in kwargs:
1380 m.execute.return_value = {"items": [
1381 {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999997+99"}
1384 m.execute.return_value = {"items": []}
1386 stubs.api.collections().list.side_effect = list_side_effect
1388 for infile in ("tests/submit_test_job_with_mismatched_uuids.json", "tests/submit_test_job_with_inconsistent_uuids.json"):
1389 capture_stderr = StringIO()
1390 cwltool_logger = logging.getLogger('cwltool')
1391 stderr_logger = logging.StreamHandler(capture_stderr)
1392 cwltool_logger.addHandler(stderr_logger)
1395 exited = arvados_cwl.main(
1396 ["--submit", "--no-wait", "--api=containers", "--debug",
1397 "tests/wf/submit_wf.cwl", infile],
1398 stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1400 self.assertEqual(exited, 1)
1402 re.sub(r'[ \n]+', ' ', capture_stderr.getvalue()),
1403 r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99")
1405 cwltool_logger.removeHandler(stderr_logger)
1407 @mock.patch("arvados.collection.CollectionReader")
1409 def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
1410 collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
1411 capture_stderr = StringIO()
1413 cwltool_logger = logging.getLogger('cwltool')
1414 stderr_logger = logging.StreamHandler(capture_stderr)
1415 cwltool_logger.addHandler(stderr_logger)
1417 exited = arvados_cwl.main(
1418 ["--submit", "--no-wait", "--api=containers", "--debug",
1419 "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
1420 stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1423 self.assertEqual(exited, 1)
1425 capture_stderr.getvalue(),
1426 r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found")
1428 cwltool_logger.removeHandler(stderr_logger)
1431 def test_submit_set_process_properties(self, stubs):
1432 exited = arvados_cwl.main(
1433 ["--submit", "--no-wait", "--api=containers", "--debug",
1434 "tests/wf/submit_wf_process_properties.cwl", "tests/submit_test_job.json"],
1435 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1437 expect_container = copy.deepcopy(stubs.expect_container_spec)
1438 expect_container["name"] = "submit_wf_process_properties.cwl"
1439 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
1441 "class": "http://arvados.org/cwl#ProcessProperties",
1442 "processProperties": [
1443 {"propertyName": "baz",
1444 "propertyValue": "$(inputs.x.basename)"},
1445 {"propertyName": "foo",
1446 "propertyValue": "bar"},
1447 {"propertyName": "quux",
1456 expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
1457 "arv": "http://arvados.org/cwl#"
1460 expect_container["properties"] = {
1469 stubs.api.container_requests().create.assert_called_with(
1470 body=JsonDiffMatcher(expect_container))
1471 self.assertEqual(stubs.capture_stdout.getvalue(),
1472 stubs.expect_container_request_uuid + '\n')
1473 self.assertEqual(exited, 0)
1477 def test_submit_enable_preemptible(self, stubs):
1478 exited = arvados_cwl.main(
1479 ["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
1480 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1481 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1483 expect_container = copy.deepcopy(stubs.expect_container_spec)
1484 expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
1485 '--no-log-timestamps', '--disable-validate', '--disable-color',
1486 '--eval-timeout=20', '--thread-count=0',
1487 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
1488 '--enable-preemptible',
1489 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1491 stubs.api.container_requests().create.assert_called_with(
1492 body=JsonDiffMatcher(expect_container))
1493 self.assertEqual(stubs.capture_stdout.getvalue(),
1494 stubs.expect_container_request_uuid + '\n')
1495 self.assertEqual(exited, 0)
1498 def test_submit_disable_preemptible(self, stubs):
1499 exited = arvados_cwl.main(
1500 ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
1501 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1502 stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
1504 expect_container = copy.deepcopy(stubs.expect_container_spec)
1505 expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
1506 '--no-log-timestamps', '--disable-validate', '--disable-color',
1507 '--eval-timeout=20', '--thread-count=0',
1508 '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
1509 '--disable-preemptible',
1510 '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
1512 stubs.api.container_requests().create.assert_called_with(
1513 body=JsonDiffMatcher(expect_container))
1514 self.assertEqual(stubs.capture_stdout.getvalue(),
1515 stubs.expect_container_request_uuid + '\n')
1516 self.assertEqual(exited, 0)
1519 class TestCreateWorkflow(unittest.TestCase):
1520 existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
1521 expect_workflow = StripYAMLComments(
1522 open("tests/wf/expect_upload_packed.cwl").read().rstrip())
1525 cwltool.process._names = set()
1526 arvados_cwl.arvdocker.arv_docker_clear_cache()
1529 def test_create(self, stubs):
1530 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1531 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1533 exited = arvados_cwl.main(
1534 ["--create-workflow", "--debug",
1536 "--project-uuid", project_uuid,
1537 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1538 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1540 stubs.api.pipeline_templates().create.refute_called()
1541 stubs.api.container_requests().create.refute_called()
1545 "owner_uuid": project_uuid,
1546 "name": "submit_wf.cwl",
1548 "definition": self.expect_workflow,
1551 stubs.api.workflows().create.assert_called_with(
1552 body=JsonDiffMatcher(body))
1554 self.assertEqual(stubs.capture_stdout.getvalue(),
1555 stubs.expect_workflow_uuid + '\n')
1556 self.assertEqual(exited, 0)
1559 def test_create_name(self, stubs):
1560 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1561 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1563 exited = arvados_cwl.main(
1564 ["--create-workflow", "--debug",
1566 "--project-uuid", project_uuid,
1567 "--name", "testing 123",
1568 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1569 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1571 stubs.api.pipeline_templates().create.refute_called()
1572 stubs.api.container_requests().create.refute_called()
1576 "owner_uuid": project_uuid,
1577 "name": "testing 123",
1579 "definition": self.expect_workflow,
1582 stubs.api.workflows().create.assert_called_with(
1583 body=JsonDiffMatcher(body))
1585 self.assertEqual(stubs.capture_stdout.getvalue(),
1586 stubs.expect_workflow_uuid + '\n')
1587 self.assertEqual(exited, 0)
1591 def test_update(self, stubs):
1592 exited = arvados_cwl.main(
1593 ["--update-workflow", self.existing_workflow_uuid,
1595 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1596 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1600 "name": "submit_wf.cwl",
1602 "definition": self.expect_workflow,
1605 stubs.api.workflows().update.assert_called_with(
1606 uuid=self.existing_workflow_uuid,
1607 body=JsonDiffMatcher(body))
1608 self.assertEqual(stubs.capture_stdout.getvalue(),
1609 self.existing_workflow_uuid + '\n')
1610 self.assertEqual(exited, 0)
1614 def test_update_name(self, stubs):
1615 exited = arvados_cwl.main(
1616 ["--update-workflow", self.existing_workflow_uuid,
1617 "--debug", "--name", "testing 123",
1618 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
1619 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1623 "name": "testing 123",
1625 "definition": self.expect_workflow,
1628 stubs.api.workflows().update.assert_called_with(
1629 uuid=self.existing_workflow_uuid,
1630 body=JsonDiffMatcher(body))
1631 self.assertEqual(stubs.capture_stdout.getvalue(),
1632 self.existing_workflow_uuid + '\n')
1633 self.assertEqual(exited, 0)
1636 def test_create_collection_per_tool(self, stubs):
1637 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1638 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1640 exited = arvados_cwl.main(
1641 ["--create-workflow", "--debug",
1643 "--project-uuid", project_uuid,
1644 "tests/collection_per_tool/collection_per_tool.cwl"],
1645 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1647 toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
1648 expect_workflow = StripYAMLComments(open(toolfile).read().rstrip())
1652 "owner_uuid": project_uuid,
1653 "name": "collection_per_tool.cwl",
1655 "definition": expect_workflow,
1658 stubs.api.workflows().create.assert_called_with(
1659 body=JsonDiffMatcher(body))
1661 self.assertEqual(stubs.capture_stdout.getvalue(),
1662 stubs.expect_workflow_uuid + '\n')
1663 self.assertEqual(exited, 0)
1666 def test_create_with_imports(self, stubs):
1667 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1668 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1670 exited = arvados_cwl.main(
1671 ["--create-workflow", "--debug",
1673 "--project-uuid", project_uuid,
1674 "tests/wf/feddemo/feddemo.cwl"],
1675 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1677 stubs.api.pipeline_templates().create.refute_called()
1678 stubs.api.container_requests().create.refute_called()
1680 self.assertEqual(stubs.capture_stdout.getvalue(),
1681 stubs.expect_workflow_uuid + '\n')
1682 self.assertEqual(exited, 0)
1685 def test_create_with_no_input(self, stubs):
1686 project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
1687 stubs.api.groups().get().execute.return_value = {"group_class": "project"}
1689 exited = arvados_cwl.main(
1690 ["--create-workflow", "--debug",
1692 "--project-uuid", project_uuid,
1693 "tests/wf/revsort/revsort.cwl"],
1694 stubs.capture_stdout, sys.stderr, api_client=stubs.api)
1696 stubs.api.pipeline_templates().create.refute_called()
1697 stubs.api.container_requests().create.refute_called()
1699 self.assertEqual(stubs.capture_stdout.getvalue(),
1700 stubs.expect_workflow_uuid + '\n')
1701 self.assertEqual(exited, 0)