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