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