sdk/cwl/tests/test_job.py

   1 import functools
   2 import json
   3 import logging
   4 import mock
   5 import os
   6 import unittest
   7 import copy
   8 import StringIO
   9
  10 import arvados
  11 import arvados_cwl
  12 import cwltool.process
  13 from arvados.errors import ApiError
  14 from schema_salad.ref_resolver import Loader
  15 from schema_salad.sourceline import cmap
  16 from .mock_discovery import get_rootDesc
  17 from .matcher import JsonDiffMatcher
  18
  19 if not os.getenv('ARVADOS_DEBUG'):
  20     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
  21     logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
  22
  23 class TestJob(unittest.TestCase):
  24
  25     # The test passes no builder.resources
  26     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  27     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
  28     def test_run(self, list_images_in_arv):
  29         for enable_reuse in (True, False):
  30             runner = mock.MagicMock()
  31             runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  32             runner.ignore_docker_for_reuse = False
  33             runner.num_retries = 0
  34             document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
  35
  36             list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
  37             runner.api.collections().get().execute.return_value = {"portable_data_hash": "99999999999999999999999999999993+99"}
  38             # Simulate reused job from another project so that we can check is a can_read
  39             # link is added.
  40             runner.api.jobs().create().execute.return_value = {
  41                 'state': 'Complete' if enable_reuse else 'Queued',
  42                 'owner_uuid': 'zzzzz-tpzed-yyyyyyyyyyyyyyy' if enable_reuse else 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  43                 'uuid': 'zzzzz-819sb-yyyyyyyyyyyyyyy',
  44                 'output': None,
  45             }
  46
  47             tool = cmap({
  48                 "inputs": [],
  49                 "outputs": [],
  50                 "baseCommand": "ls",
  51                 "arguments": [{"valueFrom": "$(runtime.outdir)"}]
  52             })
  53             make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
  54                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
  55             arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
  56                                                      basedir="", make_fs_access=make_fs_access, loader=Loader({}))
  57             arvtool.formatgraph = None
  58             for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
  59                 j.run(enable_reuse=enable_reuse)
  60                 runner.api.jobs().create.assert_called_with(
  61                     body=JsonDiffMatcher({
  62                         'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  63                         'runtime_constraints': {},
  64                         'script_parameters': {
  65                             'tasks': [{
  66                                 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
  67                                 'command': ['ls', '$(task.outdir)']
  68                             }],
  69                         },
  70                         'script_version': 'master',
  71                         'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
  72                         'repository': 'arvados',
  73                         'script': 'crunchrunner',
  74                         'runtime_constraints': {
  75                             'docker_image': 'arvados/jobs',
  76                             'min_cores_per_node': 1,
  77                             'min_ram_mb_per_node': 1024,
  78                             'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
  79                         }
  80                     }),
  81                     find_or_create=enable_reuse,
  82                     filters=[['repository', '=', 'arvados'],
  83                              ['script', '=', 'crunchrunner'],
  84                              ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
  85                              ['docker_image_locator', 'in docker', 'arvados/jobs']]
  86                 )
  87                 if enable_reuse:
  88                     runner.api.links().create.assert_called_with(
  89                         body=JsonDiffMatcher({
  90                             'link_class': 'permission',
  91                             'name': 'can_read',
  92                             "tail_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
  93                             "head_uuid": "zzzzz-819sb-yyyyyyyyyyyyyyy",
  94                         })
  95                     )
  96                     # Simulate an API excepction when trying to create a
  97                     # sharing link on the job
  98                     runner.api.links().create.side_effect = ApiError(
  99                         mock.MagicMock(return_value={'status': 403}),
 100                         'Permission denied')
 101                     j.run(enable_reuse=enable_reuse)
 102                     j.output_callback.assert_called_with({}, 'success')
 103                 else:
 104                     assert not runner.api.links().create.called
 105
 106     # The test passes some fields in builder.resources
 107     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 108     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
 109     def test_resource_requirements(self, list_images_in_arv):
 110         runner = mock.MagicMock()
 111         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 112         runner.ignore_docker_for_reuse = False
 113         runner.num_retries = 0
 114         arvados_cwl.add_arv_hints()
 115
 116         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
 117         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
 118
 119         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
 120
 121
 122         tool = {
 123             "inputs": [],
 124             "outputs": [],
 125             "hints": [{
 126                 "class": "ResourceRequirement",
 127                 "coresMin": 3,
 128                 "ramMin": 3000,
 129                 "tmpdirMin": 4000
 130             }, {
 131                 "class": "http://arvados.org/cwl#RuntimeConstraints",
 132                 "keep_cache": 512,
 133                 "outputDirType": "keep_output_dir"
 134             }, {
 135                 "class": "http://arvados.org/cwl#APIRequirement",
 136             },
 137             {
 138                 "class": "http://arvados.org/cwl#ReuseRequirement",
 139                 "enableReuse": False
 140             }],
 141             "baseCommand": "ls"
 142         }
 143         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
 144                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
 145         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
 146                                                  make_fs_access=make_fs_access, loader=Loader({}))
 147         arvtool.formatgraph = None
 148         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
 149             j.run(enable_reuse=True)
 150         runner.api.jobs().create.assert_called_with(
 151             body=JsonDiffMatcher({
 152                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 153                 'runtime_constraints': {},
 154                 'script_parameters': {
 155                     'tasks': [{
 156                         'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
 157                         'task.keepTmpOutput': True,
 158                         'command': ['ls']
 159                     }]
 160             },
 161             'script_version': 'master',
 162                 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
 163                 'repository': 'arvados',
 164                 'script': 'crunchrunner',
 165                 'runtime_constraints': {
 166                     'docker_image': 'arvados/jobs',
 167                     'min_cores_per_node': 3,
 168                     'min_ram_mb_per_node': 3512,     # ramMin + keep_cache
 169                     'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
 170                     'keep_cache_mb_per_task': 512
 171                 }
 172             }),
 173             find_or_create=False,
 174             filters=[['repository', '=', 'arvados'],
 175                      ['script', '=', 'crunchrunner'],
 176                      ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
 177                      ['docker_image_locator', 'in docker', 'arvados/jobs']])
 178
 179     @mock.patch("arvados.collection.CollectionReader")
 180     def test_done(self, reader):
 181         api = mock.MagicMock()
 182
 183         runner = mock.MagicMock()
 184         runner.api = api
 185         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 186         runner.num_retries = 0
 187         runner.ignore_docker_for_reuse = False
 188
 189         reader().open.return_value = StringIO.StringIO(
 190             """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
 191 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
 192 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
 193         """)
 194         api.collections().list().execute.side_effect = ({"items": []},
 195                                                         {"items": [{"manifest_text": "XYZ"}]},
 196                                                         {"items": []},
 197                                                         {"items": [{"manifest_text": "ABC"}]})
 198
 199         arvjob = arvados_cwl.ArvadosJob(runner)
 200         arvjob.name = "testjob"
 201         arvjob.builder = mock.MagicMock()
 202         arvjob.output_callback = mock.MagicMock()
 203         arvjob.collect_outputs = mock.MagicMock()
 204         arvjob.collect_outputs.return_value = {"out": "stuff"}
 205
 206         arvjob.done({
 207             "state": "Complete",
 208             "output": "99999999999999999999999999999993+99",
 209             "log": "99999999999999999999999999999994+99",
 210             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 211         })
 212
 213         api.collections().list.assert_has_calls([
 214             mock.call(),
 215             # Output collection check
 216             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 217                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 218                           ['name', '=', 'Output 9999999 of testjob']]),
 219             mock.call().execute(num_retries=0),
 220             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 221                  select=['manifest_text']),
 222             mock.call().execute(num_retries=0),
 223             # Log collection's turn
 224             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 225                           ['portable_data_hash', '=', '99999999999999999999999999999994+99'],
 226                           ['name', '=', 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz']]),
 227             mock.call().execute(num_retries=0),
 228             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999994+99']],
 229                  select=['manifest_text']),
 230             mock.call().execute(num_retries=0)])
 231
 232         api.collections().create.assert_has_calls([
 233             mock.call(ensure_unique_name=True,
 234                       body={'portable_data_hash': '99999999999999999999999999999993+99',
 235                             'manifest_text': 'XYZ',
 236                             'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 237                             'name': 'Output 9999999 of testjob'}),
 238             mock.call().execute(num_retries=0),
 239             mock.call(ensure_unique_name=True,
 240                       body={'portable_data_hash': '99999999999999999999999999999994+99',
 241                             'manifest_text': 'ABC',
 242                             'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 243                             'name': 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
 244             mock.call().execute(num_retries=0),
 245         ])
 246
 247         arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
 248
 249     @mock.patch("arvados.collection.CollectionReader")
 250     def test_done_use_existing_collection(self, reader):
 251         api = mock.MagicMock()
 252
 253         runner = mock.MagicMock()
 254         runner.api = api
 255         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 256         runner.num_retries = 0
 257
 258         reader().open.return_value = StringIO.StringIO(
 259             """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
 260 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
 261 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
 262         """)
 263
 264         api.collections().list().execute.side_effect = (
 265             {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},
 266             {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},
 267         )
 268
 269         arvjob = arvados_cwl.ArvadosJob(runner)
 270         arvjob.name = "testjob"
 271         arvjob.builder = mock.MagicMock()
 272         arvjob.output_callback = mock.MagicMock()
 273         arvjob.collect_outputs = mock.MagicMock()
 274         arvjob.collect_outputs.return_value = {"out": "stuff"}
 275
 276         arvjob.done({
 277             "state": "Complete",
 278             "output": "99999999999999999999999999999993+99",
 279             "log": "99999999999999999999999999999994+99",
 280             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 281         })
 282
 283         api.collections().list.assert_has_calls([
 284             mock.call(),
 285             # Output collection
 286             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 287                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 288                                ['name', '=', 'Output 9999999 of testjob']]),
 289             mock.call().execute(num_retries=0),
 290             # Log collection
 291             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 292                                ['portable_data_hash', '=', '99999999999999999999999999999994+99'],
 293                                ['name', '=', 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz']]),
 294             mock.call().execute(num_retries=0)
 295         ])
 296
 297         self.assertFalse(api.collections().create.called)
 298
 299         arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
 300
 301
 302 class TestWorkflow(unittest.TestCase):
 303     # The test passes no builder.resources
 304     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 305     @mock.patch("arvados.collection.Collection")
 306     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
 307     def test_run(self, list_images_in_arv, mockcollection):
 308         arvados_cwl.add_arv_hints()
 309
 310         api = mock.MagicMock()
 311         api._rootDesc = get_rootDesc()
 312
 313         runner = arvados_cwl.ArvCwlRunner(api)
 314         self.assertEqual(runner.work_api, 'jobs')
 315
 316         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
 317         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
 318
 319         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 320         runner.ignore_docker_for_reuse = False
 321         runner.num_retries = 0
 322         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
 323
 324         tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
 325         metadata["cwlVersion"] = tool["cwlVersion"]
 326
 327         mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
 328
 329         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
 330                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
 331         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
 332                                               basedir="", make_fs_access=make_fs_access, loader=document_loader,
 333                                               makeTool=runner.arv_make_tool, metadata=metadata)
 334         arvtool.formatgraph = None
 335         it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
 336         it.next().run()
 337         it.next().run()
 338
 339         with open("tests/wf/scatter2_subwf.cwl") as f:
 340             subwf = f.read()
 341
 342         runner.api.jobs().create.assert_called_with(
 343             body=JsonDiffMatcher({
 344                 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
 345                 'repository': 'arvados',
 346                 'script_version': 'master',
 347                 'script': 'crunchrunner',
 348                 'script_parameters': {
 349                     'tasks': [{'task.env': {
 350                         'HOME': '$(task.outdir)',
 351                         'TMPDIR': '$(task.tmpdir)'},
 352                                'task.vwd': {
 353                                    'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
 354                                    'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
 355                                },
 356                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
 357                     'task.stdout': 'cwl.output.json'}]},
 358                 'runtime_constraints': {
 359                     'min_scratch_mb_per_node': 2048,
 360                     'min_cores_per_node': 1,
 361                     'docker_image': 'arvados/jobs',
 362                     'min_ram_mb_per_node': 1024
 363                 },
 364                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
 365             filters=[['repository', '=', 'arvados'],
 366                      ['script', '=', 'crunchrunner'],
 367                      ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
 368                      ['docker_image_locator', 'in docker', 'arvados/jobs']],
 369             find_or_create=True)
 370
 371         mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
 372         mockcollection().open().__enter__().write.assert_has_calls([mock.call(
 373 '''{
 374   "sleeptime": 5
 375 }''')])
 376
 377     def test_default_work_api(self):
 378         arvados_cwl.add_arv_hints()
 379
 380         api = mock.MagicMock()
 381         api._rootDesc = copy.deepcopy(get_rootDesc())
 382         del api._rootDesc.get('resources')['jobs']['methods']['create']
 383         runner = arvados_cwl.ArvCwlRunner(api)
 384         self.assertEqual(runner.work_api, 'containers')