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