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 from future import standard_library
   6 standard_library.install_aliases()
   7 from builtins import str
   8 from builtins import next
   9
  10 import functools
  11 import json
  12 import logging
  13 import mock
  14 import os
  15 import unittest
  16 import copy
  17 import io
  18
  19 import arvados
  20 import arvados_cwl
  21 import arvados_cwl.executor
  22 import cwltool.process
  23 from arvados.errors import ApiError
  24 from schema_salad.ref_resolver import Loader
  25 from schema_salad.sourceline import cmap
  26 from .mock_discovery import get_rootDesc
  27 from .matcher import JsonDiffMatcher, StripYAMLComments
  28 from .test_container import CollectionMock
  29
  30 if not os.getenv('ARVADOS_DEBUG'):
  31     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
  32     logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
  33
  34 class TestJob(unittest.TestCase):
  35
  36     def helper(self, runner, enable_reuse=True):
  37         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1.0-dev1")
  38
  39         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
  40                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
  41         loadingContext = arvados_cwl.context.ArvLoadingContext(
  42             {"avsc_names": avsc_names,
  43              "basedir": "",
  44              "make_fs_access": make_fs_access,
  45              "loader": Loader({}),
  46              "metadata": {"cwlVersion": "v1.1.0-dev1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"},
  47              "makeTool": runner.arv_make_tool})
  48         runtimeContext = arvados_cwl.context.ArvRuntimeContext(
  49             {"work_api": "jobs",
  50              "basedir": "",
  51              "name": "test_run_job_"+str(enable_reuse),
  52              "make_fs_access": make_fs_access,
  53              "enable_reuse": enable_reuse,
  54              "priority": 500})
  55
  56         return loadingContext, runtimeContext
  57
  58     # The test passes no builder.resources
  59     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  60     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
  61     def test_run(self, list_images_in_arv):
  62         for enable_reuse in (True, False):
  63             runner = mock.MagicMock()
  64             runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  65             runner.ignore_docker_for_reuse = False
  66             runner.num_retries = 0
  67
  68             list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
  69             runner.api.collections().get().execute.return_value = {"portable_data_hash": "99999999999999999999999999999993+99"}
  70             # Simulate reused job from another project so that we can check is a can_read
  71             # link is added.
  72             runner.api.jobs().create().execute.return_value = {
  73                 'state': 'Complete' if enable_reuse else 'Queued',
  74                 'owner_uuid': 'zzzzz-tpzed-yyyyyyyyyyyyyyy' if enable_reuse else 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  75                 'uuid': 'zzzzz-819sb-yyyyyyyyyyyyyyy',
  76                 'output': None,
  77             }
  78
  79             tool = cmap({
  80                 "inputs": [],
  81                 "outputs": [],
  82                 "baseCommand": "ls",
  83                 "arguments": [{"valueFrom": "$(runtime.outdir)"}],
  84                 "id": "#",
  85                 "class": "CommandLineTool"
  86             })
  87
  88             loadingContext, runtimeContext = self.helper(runner, enable_reuse)
  89
  90             arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
  91             arvtool.formatgraph = None
  92             for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
  93                 j.run(runtimeContext)
  94                 runner.api.jobs().create.assert_called_with(
  95                     body=JsonDiffMatcher({
  96                         'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  97                         'runtime_constraints': {},
  98                         'script_parameters': {
  99                             'tasks': [{
 100                                 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
 101                                 'command': ['ls', '$(task.outdir)']
 102                             }],
 103                         },
 104                         'script_version': 'master',
 105                         'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
 106                         'repository': 'arvados',
 107                         'script': 'crunchrunner',
 108                         'runtime_constraints': {
 109                             'docker_image': 'arvados/jobs',
 110                             'min_cores_per_node': 1,
 111                             'min_ram_mb_per_node': 1024,
 112                             'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
 113                         }
 114                     }),
 115                     find_or_create=enable_reuse,
 116                     filters=[['repository', '=', 'arvados'],
 117                              ['script', '=', 'crunchrunner'],
 118                              ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
 119                              ['docker_image_locator', 'in docker', 'arvados/jobs']]
 120                 )
 121                 if enable_reuse:
 122                     runner.api.links().create.assert_called_with(
 123                         body=JsonDiffMatcher({
 124                             'link_class': 'permission',
 125                             'name': 'can_read',
 126                             "tail_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 127                             "head_uuid": "zzzzz-819sb-yyyyyyyyyyyyyyy",
 128                         })
 129                     )
 130                     # Simulate an API excepction when trying to create a
 131                     # sharing link on the job
 132                     runner.api.links().create.side_effect = ApiError(
 133                         mock.MagicMock(return_value={'status': 403}),
 134                         bytes(b'Permission denied'))
 135                     j.run(runtimeContext)
 136                 else:
 137                     assert not runner.api.links().create.called
 138
 139     # The test passes some fields in builder.resources
 140     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 141     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
 142     def test_resource_requirements(self, list_images_in_arv):
 143         runner = mock.MagicMock()
 144         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 145         runner.ignore_docker_for_reuse = False
 146         runner.num_retries = 0
 147         arvados_cwl.add_arv_hints()
 148
 149         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
 150         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
 151
 152         tool = {
 153             "inputs": [],
 154             "outputs": [],
 155             "hints": [{
 156                 "class": "ResourceRequirement",
 157                 "coresMin": 3,
 158                 "ramMin": 3000,
 159                 "tmpdirMin": 4000
 160             }, {
 161                 "class": "http://arvados.org/cwl#RuntimeConstraints",
 162                 "keep_cache": 512,
 163                 "outputDirType": "keep_output_dir"
 164             }, {
 165                 "class": "http://arvados.org/cwl#APIRequirement",
 166             },
 167             {
 168                 "class": "http://arvados.org/cwl#ReuseRequirement",
 169                 "enableReuse": False
 170             }],
 171             "baseCommand": "ls",
 172             "id": "#",
 173             "class": "CommandLineTool"
 174         }
 175
 176         loadingContext, runtimeContext = self.helper(runner)
 177
 178         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
 179         arvtool.formatgraph = None
 180         for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
 181             j.run(runtimeContext)
 182         runner.api.jobs().create.assert_called_with(
 183             body=JsonDiffMatcher({
 184                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 185                 'runtime_constraints': {},
 186                 'script_parameters': {
 187                     'tasks': [{
 188                         'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
 189                         'task.keepTmpOutput': True,
 190                         'command': ['ls']
 191                     }]
 192             },
 193             'script_version': 'master',
 194                 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
 195                 'repository': 'arvados',
 196                 'script': 'crunchrunner',
 197                 'runtime_constraints': {
 198                     'docker_image': 'arvados/jobs',
 199                     'min_cores_per_node': 3,
 200                     'min_ram_mb_per_node': 3512,     # ramMin + keep_cache
 201                     'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
 202                     'keep_cache_mb_per_task': 512
 203                 }
 204             }),
 205             find_or_create=False,
 206             filters=[['repository', '=', 'arvados'],
 207                      ['script', '=', 'crunchrunner'],
 208                      ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
 209                      ['docker_image_locator', 'in docker', 'arvados/jobs']])
 210
 211     @mock.patch("arvados.collection.CollectionReader")
 212     def test_done(self, reader):
 213         api = mock.MagicMock()
 214
 215         runner = mock.MagicMock()
 216         runner.api = api
 217         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 218         runner.num_retries = 0
 219         runner.ignore_docker_for_reuse = False
 220
 221         reader().keys.return_value = "log.txt"
 222         reader().open.return_value = io.StringIO(
 223             str(u"""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().keys.return_value = "log.txt"
 296         reader().open.return_value = io.StringIO(
 297             str(u"""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
 298 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
 299 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
 300         """))
 301
 302         api.collections().list().execute.side_effect = (
 303             {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},
 304             {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},
 305         )
 306
 307         arvjob = arvados_cwl.ArvadosJob(runner,
 308                                         mock.MagicMock(),
 309                                         {},
 310                                         None,
 311                                         [],
 312                                         [],
 313                                         "testjob")
 314         arvjob.output_callback = mock.MagicMock()
 315         arvjob.collect_outputs = mock.MagicMock()
 316         arvjob.collect_outputs.return_value = {"out": "stuff"}
 317
 318         arvjob.done({
 319             "state": "Complete",
 320             "output": "99999999999999999999999999999993+99",
 321             "log": "99999999999999999999999999999994+99",
 322             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 323         })
 324
 325         api.collections().list.assert_has_calls([
 326             mock.call(),
 327             # Output collection
 328             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 329                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 330                                ['name', '=', 'Output 9999999 of testjob']]),
 331             mock.call().execute(num_retries=0),
 332             # Log collection
 333             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 334                                ['portable_data_hash', '=', '99999999999999999999999999999994+99'],
 335                                ['name', '=', 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz']]),
 336             mock.call().execute(num_retries=0)
 337         ])
 338
 339         self.assertFalse(api.collections().create.called)
 340
 341         arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
 342
 343
 344 class TestWorkflow(unittest.TestCase):
 345     def helper(self, runner, enable_reuse=True):
 346         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1.0-dev1")
 347
 348         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
 349                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
 350
 351         document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=make_fs_access(""))
 352         document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session)
 353         document_loader.fetch_text = document_loader.fetcher.fetch_text
 354         document_loader.check_exists = document_loader.fetcher.check_exists
 355
 356         loadingContext = arvados_cwl.context.ArvLoadingContext(
 357             {"avsc_names": avsc_names,
 358              "basedir": "",
 359              "make_fs_access": make_fs_access,
 360              "loader": document_loader,
 361              "metadata": {"cwlVersion": "v1.1.0-dev1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"},
 362              "construct_tool_object": runner.arv_make_tool})
 363         runtimeContext = arvados_cwl.context.ArvRuntimeContext(
 364             {"work_api": "jobs",
 365              "basedir": "",
 366              "name": "test_run_wf_"+str(enable_reuse),
 367              "make_fs_access": make_fs_access,
 368              "enable_reuse": enable_reuse,
 369              "priority": 500})
 370
 371         return loadingContext, runtimeContext
 372
 373     # The test passes no builder.resources
 374     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 375     @mock.patch("arvados.collection.CollectionReader")
 376     @mock.patch("arvados.collection.Collection")
 377     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
 378     def test_run(self, list_images_in_arv, mockcollection, mockcollectionreader):
 379         arvados_cwl.add_arv_hints()
 380
 381         api = mock.MagicMock()
 382         api._rootDesc = get_rootDesc()
 383
 384         runner = arvados_cwl.executor.ArvCwlExecutor(api)
 385         self.assertEqual(runner.work_api, 'jobs')
 386
 387         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
 388         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
 389         runner.api.collections().list().execute.return_vaulue = {"items": [{"portable_data_hash": "99999999999999999999999999999993+99"}]}
 390
 391         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 392         runner.ignore_docker_for_reuse = False
 393         runner.num_retries = 0
 394
 395         loadingContext, runtimeContext = self.helper(runner)
 396
 397         tool, metadata = loadingContext.loader.resolve_ref("tests/wf/scatter2.cwl")
 398         metadata["cwlVersion"] = tool["cwlVersion"]
 399
 400         mockc = mock.MagicMock()
 401         mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mockc, *args, **kwargs)
 402         mockcollectionreader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "token.txt")
 403
 404         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
 405         arvtool.formatgraph = None
 406         it = arvtool.job({}, mock.MagicMock(), runtimeContext)
 407
 408         next(it).run(runtimeContext)
 409         next(it).run(runtimeContext)
 410
 411         with open("tests/wf/scatter2_subwf.cwl") as f:
 412             subwf = StripYAMLComments(f.read())
 413
 414         runner.api.jobs().create.assert_called_with(
 415             body=JsonDiffMatcher({
 416                 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
 417                 'repository': 'arvados',
 418                 'script_version': 'master',
 419                 'script': 'crunchrunner',
 420                 'script_parameters': {
 421                     'tasks': [{'task.env': {
 422                         'HOME': '$(task.outdir)',
 423                         'TMPDIR': '$(task.tmpdir)'},
 424                                'task.vwd': {
 425                                    'workflow.cwl': '$(task.keep)/99999999999999999999999999999996+99/workflow.cwl',
 426                                    'cwl.input.yml': '$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml'
 427                                },
 428                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
 429                     'task.stdout': 'cwl.output.json'}]},
 430                 'runtime_constraints': {
 431                     'min_scratch_mb_per_node': 2048,
 432                     'min_cores_per_node': 1,
 433                     'docker_image': 'arvados/jobs',
 434                     'min_ram_mb_per_node': 1024
 435                 },
 436                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
 437             filters=[['repository', '=', 'arvados'],
 438                      ['script', '=', 'crunchrunner'],
 439                      ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
 440                      ['docker_image_locator', 'in docker', 'arvados/jobs']],
 441             find_or_create=True)
 442
 443         mockc.open().__enter__().write.assert_has_calls([mock.call(subwf)])
 444         mockc.open().__enter__().write.assert_has_calls([mock.call(
 445 bytes(b'''{
 446   "fileblub": {
 447     "basename": "token.txt",
 448     "class": "File",
 449     "location": "/keep/99999999999999999999999999999999+118/token.txt",
 450     "size": 0
 451   },
 452   "sleeptime": 5
 453 }'''))])
 454
 455     # The test passes no builder.resources
 456     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 457     @mock.patch("arvados.collection.CollectionReader")
 458     @mock.patch("arvados.collection.Collection")
 459     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
 460     def test_overall_resource_singlecontainer(self, list_images_in_arv, mockcollection, mockcollectionreader):
 461         # TODO copy this over to test_container
 462         arvados_cwl.add_arv_hints()
 463
 464         api = mock.MagicMock()
 465         api._rootDesc = get_rootDesc()
 466
 467         runner = arvados_cwl.executor.ArvCwlExecutor(api)
 468         self.assertEqual(runner.work_api, 'jobs')
 469
 470         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
 471         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
 472         runner.api.collections().list().execute.return_vaulue = {"items": [{"portable_data_hash": "99999999999999999999999999999993+99"}]}
 473
 474         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 475         runner.ignore_docker_for_reuse = False
 476         runner.num_retries = 0
 477
 478         loadingContext, runtimeContext = self.helper(runner)
 479         loadingContext.do_update = True
 480         tool, metadata = loadingContext.loader.resolve_ref("tests/wf/echo-wf.cwl")
 481
 482         mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mock.MagicMock(), *args, **kwargs)
 483
 484         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
 485         arvtool.formatgraph = None
 486         it = arvtool.job({}, mock.MagicMock(), runtimeContext)
 487
 488         next(it).run(runtimeContext)
 489         next(it).run(runtimeContext)
 490
 491         with open("tests/wf/echo-subwf.cwl") as f:
 492             subwf = StripYAMLComments(f.read())
 493
 494         runner.api.jobs().create.assert_called_with(
 495             body=JsonDiffMatcher({
 496                 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
 497                 'repository': 'arvados',
 498                 'script_version': 'master',
 499                 'script': 'crunchrunner',
 500                 'script_parameters': {
 501                     'tasks': [{'task.env': {
 502                         'HOME': '$(task.outdir)',
 503                         'TMPDIR': '$(task.tmpdir)'},
 504                                'task.vwd': {
 505                                    'workflow.cwl': '$(task.keep)/99999999999999999999999999999996+99/workflow.cwl',
 506                                    'cwl.input.yml': '$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml'
 507                                },
 508                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
 509                     'task.stdout': 'cwl.output.json'}]},
 510                 'runtime_constraints': {
 511                     'min_scratch_mb_per_node': 4096,
 512                     'min_cores_per_node': 3,
 513                     'docker_image': 'arvados/jobs',
 514                     'min_ram_mb_per_node': 1024
 515                 },
 516                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
 517             filters=[['repository', '=', 'arvados'],
 518                      ['script', '=', 'crunchrunner'],
 519                      ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
 520                      ['docker_image_locator', 'in docker', 'arvados/jobs']],
 521             find_or_create=True)
 522
 523     def test_default_work_api(self):
 524         arvados_cwl.add_arv_hints()
 525
 526         api = mock.MagicMock()
 527         api._rootDesc = copy.deepcopy(get_rootDesc())
 528         del api._rootDesc.get('resources')['jobs']['methods']['create']
 529         runner = arvados_cwl.executor.ArvCwlExecutor(api)
 530         self.assertEqual(runner.work_api, 'containers')