sdk/cwl/tests/test_job.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 import functools
   6 import json
   7 import logging
   8 import mock
   9 import os
  10 import unittest
  11 import copy
  12 import StringIO
  13 import datetime
  14
  15 import arvados
  16 import arvados_cwl
  17 import cwltool.process
  18 from arvados.errors import ApiError
  19 from schema_salad.ref_resolver import Loader
  20 from schema_salad.sourceline import cmap
  21 from .mock_discovery import get_rootDesc
  22 from .matcher import JsonDiffMatcher, StripYAMLComments
  23
  24 if not os.getenv('ARVADOS_DEBUG'):
  25     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
  26     logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
  27
  28 class MockDateTime(datetime.datetime):
  29     @classmethod
  30     def now(cls):
  31         return datetime.datetime(2018, 1, 1, 0, 0, 0, 0)
  32
  33 datetime.datetime = MockDateTime
  34
  35 class TestJob(unittest.TestCase):
  36
  37     def helper(self, runner, enable_reuse=True):
  38         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
  39
  40         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
  41                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
  42         loadingContext = arvados_cwl.context.ArvLoadingContext(
  43             {"avsc_names": avsc_names,
  44              "basedir": "",
  45              "make_fs_access": make_fs_access,
  46              "loader": Loader({}),
  47              "metadata": {"cwlVersion": "v1.0"},
  48              "makeTool": runner.arv_make_tool})
  49         runtimeContext = arvados_cwl.context.ArvRuntimeContext(
  50             {"work_api": "jobs",
  51              "basedir": "",
  52              "name": "test_run_job_"+str(enable_reuse),
  53              "make_fs_access": make_fs_access,
  54              "enable_reuse": enable_reuse,
  55              "priority": 500})
  56
  57         return loadingContext, runtimeContext
  58
  59     # The test passes no builder.resources
  60     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  61     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
  62     def test_run(self, list_images_in_arv):
  63         for enable_reuse in (True, False):
  64             runner = mock.MagicMock()
  65             runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  66             runner.ignore_docker_for_reuse = False
  67             runner.num_retries = 0
  68
  69             list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
  70             runner.api.collections().get().execute.return_value = {"portable_data_hash": "99999999999999999999999999999993+99"}
  71             # Simulate reused job from another project so that we can check is a can_read
  72             # link is added.
  73             runner.api.jobs().create().execute.return_value = {
  74                 'state': 'Complete' if enable_reuse else 'Queued',
  75                 'owner_uuid': 'zzzzz-tpzed-yyyyyyyyyyyyyyy' if enable_reuse else 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  76                 'uuid': 'zzzzz-819sb-yyyyyyyyyyyyyyy',
  77                 'output': None,
  78             }
  79
  80             tool = cmap({
  81                 "inputs": [],
  82                 "outputs": [],
  83                 "baseCommand": "ls",
  84                 "arguments": [{"valueFrom": "$(runtime.outdir)"}],
  85                 "id": "#",
  86                 "class": "CommandLineTool"
  87             })
  88
  89             loadingContext, runtimeContext = self.helper(runner, enable_reuse)
  90
  91             arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
  92             arvtool.formatgraph = None
  93             for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
  94                 j.run(runtimeContext)
  95                 runner.api.jobs().create.assert_called_with(
  96                     body=JsonDiffMatcher({
  97                         'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  98                         'runtime_constraints': {},
  99                         'script_parameters': {
 100                             'tasks': [{
 101                                 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
 102                                 'command': ['ls', '$(task.outdir)']
 103                             }],
 104                         },
 105                         'script_version': 'master',
 106                         'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
 107                         'repository': 'arvados',
 108                         'script': 'crunchrunner',
 109                         'runtime_constraints': {
 110                             'docker_image': 'arvados/jobs',
 111                             'min_cores_per_node': 1,
 112                             'min_ram_mb_per_node': 1024,
 113                             'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
 114                         }
 115                     }),
 116                     find_or_create=enable_reuse,
 117                     filters=[['repository', '=', 'arvados'],
 118                              ['script', '=', 'crunchrunner'],
 119                              ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
 120                              ['docker_image_locator', 'in docker', 'arvados/jobs']]
 121                 )
 122                 if enable_reuse:
 123                     runner.api.links().create.assert_called_with(
 124                         body=JsonDiffMatcher({
 125                             'link_class': 'permission',
 126                             'name': 'can_read',
 127                             "tail_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 128                             "head_uuid": "zzzzz-819sb-yyyyyyyyyyyyyyy",
 129                         })
 130                     )
 131                     # Simulate an API excepction when trying to create a
 132                     # sharing link on the job
 133                     runner.api.links().create.side_effect = ApiError(
 134                         mock.MagicMock(return_value={'status': 403}),
 135                         'Permission denied')
 136                     j.run(runtimeContext)
 137                 else:
 138                     assert not runner.api.links().create.called
 139
 140     # The test passes some fields in builder.resources
 141     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 142     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
 143     def test_resource_requirements(self, list_images_in_arv):
 144         runner = mock.MagicMock()
 145         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 146         runner.ignore_docker_for_reuse = False
 147         runner.num_retries = 0
 148         arvados_cwl.add_arv_hints()
 149
 150         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
 151         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
 152
 153         tool = {
 154             "inputs": [],
 155             "outputs": [],
 156             "hints": [{
 157                 "class": "ResourceRequirement",
 158                 "coresMin": 3,
 159                 "ramMin": 3000,
 160                 "tmpdirMin": 4000
 161             }, {
 162                 "class": "http://arvados.org/cwl#RuntimeConstraints",
 163                 "keep_cache": 512,
 164                 "outputDirType": "keep_output_dir"
 165             }, {
 166                 "class": "http://arvados.org/cwl#APIRequirement",
 167             },
 168             {
 169                 "class": "http://arvados.org/cwl#ReuseRequirement",
 170                 "enableReuse": False
 171             }],
 172             "baseCommand": "ls",
 173             "id": "#",
 174             "class": "CommandLineTool"
 175         }
 176
 177         loadingContext, runtimeContext = self.helper(runner)
 178
 179         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
 180         arvtool.formatgraph = None
 181         for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
 182             j.run(runtimeContext)
 183         runner.api.jobs().create.assert_called_with(
 184             body=JsonDiffMatcher({
 185                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 186                 'runtime_constraints': {},
 187                 'script_parameters': {
 188                     'tasks': [{
 189                         'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
 190                         'task.keepTmpOutput': True,
 191                         'command': ['ls']
 192                     }]
 193             },
 194             'script_version': 'master',
 195                 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
 196                 'repository': 'arvados',
 197                 'script': 'crunchrunner',
 198                 'runtime_constraints': {
 199                     'docker_image': 'arvados/jobs',
 200                     'min_cores_per_node': 3,
 201                     'min_ram_mb_per_node': 3512,     # ramMin + keep_cache
 202                     'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
 203                     'keep_cache_mb_per_task': 512
 204                 }
 205             }),
 206             find_or_create=False,
 207             filters=[['repository', '=', 'arvados'],
 208                      ['script', '=', 'crunchrunner'],
 209                      ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
 210                      ['docker_image_locator', 'in docker', 'arvados/jobs']])
 211
 212     @mock.patch("arvados.collection.CollectionReader")
 213     def test_done(self, reader):
 214         api = mock.MagicMock()
 215
 216         runner = mock.MagicMock()
 217         runner.api = api
 218         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 219         runner.num_retries = 0
 220         runner.ignore_docker_for_reuse = False
 221
 222         reader().open.return_value = StringIO.StringIO(
 223             """2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.tmpdir)=/tmp/crunch-job-task-work/compute3.1/tmpdir
 224 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.outdir)=/tmp/crunch-job-task-work/compute3.1/outdir
 225 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
 226         """)
 227         api.collections().list().execute.side_effect = ({"items": []},
 228                                                         {"items": [{"manifest_text": "XYZ"}]},
 229                                                         {"items": []},
 230                                                         {"items": [{"manifest_text": "ABC"}]})
 231
 232         arvjob = arvados_cwl.ArvadosJob(runner,
 233                                         mock.MagicMock(),
 234                                         {},
 235                                         None,
 236                                         [],
 237                                         [],
 238                                         "testjob")
 239         arvjob.output_callback = mock.MagicMock()
 240         arvjob.collect_outputs = mock.MagicMock()
 241         arvjob.collect_outputs.return_value = {"out": "stuff"}
 242
 243         arvjob.done({
 244             "state": "Complete",
 245             "output": "99999999999999999999999999999993+99",
 246             "log": "99999999999999999999999999999994+99",
 247             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 248         })
 249
 250         api.collections().list.assert_has_calls([
 251             mock.call(),
 252             # Output collection check
 253             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 254                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 255                           ['name', '=', 'Output 9999999 of testjob']]),
 256             mock.call().execute(num_retries=0),
 257             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 258                  select=['manifest_text']),
 259             mock.call().execute(num_retries=0),
 260             # Log collection's turn
 261             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 262                           ['portable_data_hash', '=', '99999999999999999999999999999994+99'],
 263                           ['name', '=', 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz']]),
 264             mock.call().execute(num_retries=0),
 265             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999994+99']],
 266                  select=['manifest_text']),
 267             mock.call().execute(num_retries=0)])
 268
 269         api.collections().create.assert_has_calls([
 270             mock.call(ensure_unique_name=True,
 271                       body={'portable_data_hash': '99999999999999999999999999999993+99',
 272                             'manifest_text': 'XYZ',
 273                             'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 274                             'name': 'Output 9999999 of testjob'}),
 275             mock.call().execute(num_retries=0),
 276             mock.call(ensure_unique_name=True,
 277                       body={'portable_data_hash': '99999999999999999999999999999994+99',
 278                             'manifest_text': 'ABC',
 279                             'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 280                             'name': 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
 281             mock.call().execute(num_retries=0),
 282         ])
 283
 284         arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
 285
 286     @mock.patch("arvados.collection.CollectionReader")
 287     def test_done_use_existing_collection(self, reader):
 288         api = mock.MagicMock()
 289
 290         runner = mock.MagicMock()
 291         runner.api = api
 292         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 293         runner.num_retries = 0
 294
 295         reader().open.return_value = StringIO.StringIO(
 296             """2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.tmpdir)=/tmp/crunch-job-task-work/compute3.1/tmpdir
 297 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.outdir)=/tmp/crunch-job-task-work/compute3.1/outdir
 298 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
 299         """)
 300
 301         api.collections().list().execute.side_effect = (
 302             {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},
 303             {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},
 304         )
 305
 306         arvjob = arvados_cwl.ArvadosJob(runner,
 307                                         mock.MagicMock(),
 308                                         {},
 309                                         None,
 310                                         [],
 311                                         [],
 312                                         "testjob")
 313         arvjob.output_callback = mock.MagicMock()
 314         arvjob.collect_outputs = mock.MagicMock()
 315         arvjob.collect_outputs.return_value = {"out": "stuff"}
 316
 317         arvjob.done({
 318             "state": "Complete",
 319             "output": "99999999999999999999999999999993+99",
 320             "log": "99999999999999999999999999999994+99",
 321             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 322         })
 323
 324         api.collections().list.assert_has_calls([
 325             mock.call(),
 326             # Output collection
 327             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 328                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 329                                ['name', '=', 'Output 9999999 of testjob']]),
 330             mock.call().execute(num_retries=0),
 331             # Log collection
 332             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 333                                ['portable_data_hash', '=', '99999999999999999999999999999994+99'],
 334                                ['name', '=', 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz']]),
 335             mock.call().execute(num_retries=0)
 336         ])
 337
 338         self.assertFalse(api.collections().create.called)
 339
 340         arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
 341
 342     def test_get_intermediate_collection_info(self):
 343         arvrunner = mock.MagicMock()
 344         arvrunner.intermediate_output_ttl = 60
 345         arvrunner.api.containers().current().execute.return_value = {"uuid" : "zzzzz-8i9sb-zzzzzzzzzzzzzzz"}
 346
 347         job = arvados_cwl.ArvadosJob(arvrunner)
 348
 349         info = job._get_intermediate_collection_info()
 350
 351         self.assertEqual(info["name"], "Intermediate collection")
 352         self.assertEqual(info["trash_at"], datetime.datetime(2018, 1, 1, 0, 1))
 353         self.assertEqual(info["properties"], {"type" : "Intermediate", "container" : "zzzzz-8i9sb-zzzzzzzzzzzzzzz"})
 354
 355
 356
 357 class TestWorkflow(unittest.TestCase):
 358     def helper(self, runner, enable_reuse=True):
 359         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
 360
 361         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
 362                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
 363
 364         document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=make_fs_access(""))
 365         document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session)
 366         document_loader.fetch_text = document_loader.fetcher.fetch_text
 367         document_loader.check_exists = document_loader.fetcher.check_exists
 368
 369         loadingContext = arvados_cwl.context.ArvLoadingContext(
 370             {"avsc_names": avsc_names,
 371              "basedir": "",
 372              "make_fs_access": make_fs_access,
 373              "loader": document_loader,
 374              "metadata": {"cwlVersion": "v1.0"},
 375              "construct_tool_object": runner.arv_make_tool})
 376         runtimeContext = arvados_cwl.context.ArvRuntimeContext(
 377             {"work_api": "jobs",
 378              "basedir": "",
 379              "name": "test_run_wf_"+str(enable_reuse),
 380              "make_fs_access": make_fs_access,
 381              "enable_reuse": enable_reuse,
 382              "priority": 500})
 383
 384         return loadingContext, runtimeContext
 385
 386     # The test passes no builder.resources
 387     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 388     @mock.patch("arvados.collection.CollectionReader")
 389     @mock.patch("arvados.collection.Collection")
 390     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
 391     def test_run(self, list_images_in_arv, mockcollection, mockcollectionreader):
 392         arvados_cwl.add_arv_hints()
 393
 394         api = mock.MagicMock()
 395         api._rootDesc = get_rootDesc()
 396
 397         runner = arvados_cwl.ArvCwlRunner(api)
 398         self.assertEqual(runner.work_api, 'jobs')
 399
 400         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
 401         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
 402         runner.api.collections().list().execute.return_vaulue = {"items": [{"portable_data_hash": "99999999999999999999999999999993+99"}]}
 403
 404         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 405         runner.ignore_docker_for_reuse = False
 406         runner.num_retries = 0
 407
 408         loadingContext, runtimeContext = self.helper(runner)
 409
 410         tool, metadata = loadingContext.loader.resolve_ref("tests/wf/scatter2.cwl")
 411         metadata["cwlVersion"] = tool["cwlVersion"]
 412
 413         mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
 414
 415         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
 416         arvtool.formatgraph = None
 417         it = arvtool.job({}, mock.MagicMock(), runtimeContext)
 418
 419         it.next().run(runtimeContext)
 420         it.next().run(runtimeContext)
 421
 422         with open("tests/wf/scatter2_subwf.cwl") as f:
 423             subwf = StripYAMLComments(f.read())
 424
 425         runner.api.jobs().create.assert_called_with(
 426             body=JsonDiffMatcher({
 427                 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
 428                 'repository': 'arvados',
 429                 'script_version': 'master',
 430                 'script': 'crunchrunner',
 431                 'script_parameters': {
 432                     'tasks': [{'task.env': {
 433                         'HOME': '$(task.outdir)',
 434                         'TMPDIR': '$(task.tmpdir)'},
 435                                'task.vwd': {
 436                                    'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
 437                                    'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
 438                                },
 439                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
 440                     'task.stdout': 'cwl.output.json'}]},
 441                 'runtime_constraints': {
 442                     'min_scratch_mb_per_node': 2048,
 443                     'min_cores_per_node': 1,
 444                     'docker_image': 'arvados/jobs',
 445                     'min_ram_mb_per_node': 1024
 446                 },
 447                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
 448             filters=[['repository', '=', 'arvados'],
 449                      ['script', '=', 'crunchrunner'],
 450                      ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
 451                      ['docker_image_locator', 'in docker', 'arvados/jobs']],
 452             find_or_create=True)
 453
 454         mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
 455         mockcollection().open().__enter__().write.assert_has_calls([mock.call(
 456 '''{
 457   "fileblub": {
 458     "basename": "token.txt",
 459     "class": "File",
 460     "location": "/keep/99999999999999999999999999999999+118/token.txt"
 461   },
 462   "sleeptime": 5
 463 }''')])
 464
 465     # The test passes no builder.resources
 466     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 467     @mock.patch("arvados.collection.CollectionReader")
 468     @mock.patch("arvados.collection.Collection")
 469     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
 470     def test_overall_resource_singlecontainer(self, list_images_in_arv, mockcollection, mockcollectionreader):
 471         arvados_cwl.add_arv_hints()
 472
 473         api = mock.MagicMock()
 474         api._rootDesc = get_rootDesc()
 475
 476         runner = arvados_cwl.ArvCwlRunner(api)
 477         self.assertEqual(runner.work_api, 'jobs')
 478
 479         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
 480         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
 481         runner.api.collections().list().execute.return_vaulue = {"items": [{"portable_data_hash": "99999999999999999999999999999993+99"}]}
 482
 483         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 484         runner.ignore_docker_for_reuse = False
 485         runner.num_retries = 0
 486
 487         loadingContext, runtimeContext = self.helper(runner)
 488
 489         tool, metadata = loadingContext.loader.resolve_ref("tests/wf/echo-wf.cwl")
 490         metadata["cwlVersion"] = tool["cwlVersion"]
 491
 492         mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
 493
 494         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
 495         arvtool.formatgraph = None
 496         it = arvtool.job({}, mock.MagicMock(), runtimeContext)
 497         it.next().run(runtimeContext)
 498         it.next().run(runtimeContext)
 499
 500         with open("tests/wf/echo-subwf.cwl") as f:
 501             subwf = StripYAMLComments(f.read())
 502
 503         runner.api.jobs().create.assert_called_with(
 504             body=JsonDiffMatcher({
 505                 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
 506                 'repository': 'arvados',
 507                 'script_version': 'master',
 508                 'script': 'crunchrunner',
 509                 'script_parameters': {
 510                     'tasks': [{'task.env': {
 511                         'HOME': '$(task.outdir)',
 512                         'TMPDIR': '$(task.tmpdir)'},
 513                                'task.vwd': {
 514                                    'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
 515                                    'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
 516                                },
 517                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
 518                     'task.stdout': 'cwl.output.json'}]},
 519                 'runtime_constraints': {
 520                     'min_scratch_mb_per_node': 4096,
 521                     'min_cores_per_node': 3,
 522                     'docker_image': 'arvados/jobs',
 523                     'min_ram_mb_per_node': 1024
 524                 },
 525                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
 526             filters=[['repository', '=', 'arvados'],
 527                      ['script', '=', 'crunchrunner'],
 528                      ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
 529                      ['docker_image_locator', 'in docker', 'arvados/jobs']],
 530             find_or_create=True)
 531
 532     def test_default_work_api(self):
 533         arvados_cwl.add_arv_hints()
 534
 535         api = mock.MagicMock()
 536         api._rootDesc = copy.deepcopy(get_rootDesc())
 537         del api._rootDesc.get('resources')['jobs']['methods']['create']
 538         runner = arvados_cwl.ArvCwlRunner(api)
 539         self.assertEqual(runner.work_api, 'containers')