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