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 .mock_discovery import get_rootDesc
  15
  16 if not os.getenv('ARVADOS_DEBUG'):
  17     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
  18     logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
  19
  20 class TestJob(unittest.TestCase):
  21
  22     # The test passes no builder.resources
  23     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  24     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
  25     def test_run(self, list_images_in_arv):
  26         for enable_reuse in (True, False):
  27             runner = mock.MagicMock()
  28             runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  29             runner.ignore_docker_for_reuse = False
  30             runner.num_retries = 0
  31             document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
  32
  33             list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
  34             runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
  35
  36             tool = {
  37                 "inputs": [],
  38                 "outputs": [],
  39                 "baseCommand": "ls",
  40                 "arguments": [{"valueFrom": "$(runtime.outdir)"}]
  41             }
  42             make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  43             arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
  44                                                      basedir="", make_fs_access=make_fs_access, loader=Loader({}))
  45             arvtool.formatgraph = None
  46             for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
  47                 j.run(enable_reuse=enable_reuse)
  48                 runner.api.jobs().create.assert_called_with(
  49                     body={
  50                         'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  51                         'runtime_constraints': {},
  52                         'script_parameters': {
  53                             'tasks': [{
  54                                 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
  55                                 'command': ['ls', '$(task.outdir)']
  56                             }],
  57                         },
  58                         'script_version': 'master',
  59                         'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
  60                         'repository': 'arvados',
  61                         'script': 'crunchrunner',
  62                         'runtime_constraints': {
  63                             'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
  64                             'min_cores_per_node': 1,
  65                             'min_ram_mb_per_node': 1024,
  66                             'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
  67                         }
  68                     },
  69                     find_or_create=enable_reuse,
  70                     filters=[['repository', '=', 'arvados'],
  71                              ['script', '=', 'crunchrunner'],
  72                              ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
  73                              ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]]
  74                 )
  75
  76     # The test passes some fields in builder.resources
  77     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  78     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
  79     def test_resource_requirements(self, list_images_in_arv):
  80         runner = mock.MagicMock()
  81         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  82         runner.ignore_docker_for_reuse = False
  83         runner.num_retries = 0
  84         arvados_cwl.add_arv_hints()
  85
  86         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
  87         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
  88
  89         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
  90
  91
  92         tool = {
  93             "inputs": [],
  94             "outputs": [],
  95             "hints": [{
  96                 "class": "ResourceRequirement",
  97                 "coresMin": 3,
  98                 "ramMin": 3000,
  99                 "tmpdirMin": 4000
 100             }, {
 101                 "class": "http://arvados.org/cwl#RuntimeConstraints",
 102                 "keep_cache": 512,
 103                 "outputDirType": "keep_output_dir"
 104             }, {
 105                 "class": "http://arvados.org/cwl#APIRequirement",
 106             }],
 107             "baseCommand": "ls"
 108         }
 109         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
 110         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
 111                                                  make_fs_access=make_fs_access, loader=Loader({}))
 112         arvtool.formatgraph = None
 113         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
 114             j.run()
 115         runner.api.jobs().create.assert_called_with(
 116             body={
 117                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 118                 'runtime_constraints': {},
 119                 'script_parameters': {
 120                     'tasks': [{
 121                         'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
 122                         'task.keepTmpOutput': True,
 123                         'command': ['ls']
 124                     }]
 125             },
 126             'script_version': 'master',
 127                 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
 128                 'repository': 'arvados',
 129                 'script': 'crunchrunner',
 130                 'runtime_constraints': {
 131                     'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
 132                     'min_cores_per_node': 3,
 133                     'min_ram_mb_per_node': 3000,
 134                     'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
 135                     'keep_cache_mb_per_task': 512
 136                 }
 137             },
 138             find_or_create=True,
 139             filters=[['repository', '=', 'arvados'],
 140                      ['script', '=', 'crunchrunner'],
 141                      ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
 142                      ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]])
 143
 144     @mock.patch("arvados.collection.CollectionReader")
 145     def test_done(self, reader):
 146         api = mock.MagicMock()
 147
 148         runner = mock.MagicMock()
 149         runner.api = api
 150         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 151         runner.num_retries = 0
 152         runner.ignore_docker_for_reuse = False
 153
 154         reader().open.return_value = StringIO.StringIO(
 155             """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
 156 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
 157 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
 158         """)
 159         api.collections().list().execute.side_effect = ({"items": []},
 160                                                         {"items": [{"manifest_text": "XYZ"}]})
 161
 162         arvjob = arvados_cwl.ArvadosJob(runner)
 163         arvjob.name = "testjob"
 164         arvjob.builder = mock.MagicMock()
 165         arvjob.output_callback = mock.MagicMock()
 166         arvjob.collect_outputs = mock.MagicMock()
 167
 168         arvjob.done({
 169             "state": "Complete",
 170             "output": "99999999999999999999999999999993+99",
 171             "log": "99999999999999999999999999999994+99",
 172             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 173         })
 174
 175         api.collections().list.assert_has_calls([
 176             mock.call(),
 177             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 178                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 179                           ['name', '=', 'Output 9999999 of testjob']]),
 180             mock.call().execute(num_retries=0),
 181             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 182                  select=['manifest_text']),
 183             mock.call().execute(num_retries=0)])
 184
 185         api.collections().create.assert_called_with(
 186             ensure_unique_name=True,
 187             body={'portable_data_hash': '99999999999999999999999999999993+99',
 188                   'manifest_text': 'XYZ',
 189                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 190                   'name': 'Output 9999999 of testjob'})
 191
 192     @mock.patch("arvados.collection.CollectionReader")
 193     def test_done_use_existing_collection(self, reader):
 194         api = mock.MagicMock()
 195
 196         runner = mock.MagicMock()
 197         runner.api = api
 198         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 199         runner.num_retries = 0
 200
 201         reader().open.return_value = StringIO.StringIO(
 202             """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
 203 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
 204 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
 205         """)
 206
 207         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 208
 209         arvjob = arvados_cwl.ArvadosJob(runner)
 210         arvjob.name = "testjob"
 211         arvjob.builder = mock.MagicMock()
 212         arvjob.output_callback = mock.MagicMock()
 213         arvjob.collect_outputs = mock.MagicMock()
 214
 215         arvjob.done({
 216             "state": "Complete",
 217             "output": "99999999999999999999999999999993+99",
 218             "log": "99999999999999999999999999999994+99",
 219             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 220         })
 221
 222         api.collections().list.assert_has_calls([
 223             mock.call(),
 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
 229         self.assertFalse(api.collections().create.called)
 230
 231
 232 class TestWorkflow(unittest.TestCase):
 233     # The test passes no builder.resources
 234     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 235     @mock.patch("arvados.collection.Collection")
 236     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
 237     def test_run(self, list_images_in_arv, mockcollection):
 238         arvados_cwl.add_arv_hints()
 239
 240         api = mock.MagicMock()
 241         api._rootDesc = get_rootDesc()
 242
 243         runner = arvados_cwl.ArvCwlRunner(api)
 244         self.assertEqual(runner.work_api, 'jobs')
 245
 246         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
 247         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
 248
 249         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 250         runner.ignore_docker_for_reuse = False
 251         runner.num_retries = 0
 252         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
 253
 254         tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
 255         metadata["cwlVersion"] = tool["cwlVersion"]
 256
 257         mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
 258
 259         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
 260         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
 261                                               basedir="", make_fs_access=make_fs_access, loader=document_loader,
 262                                               makeTool=runner.arv_make_tool, metadata=metadata)
 263         arvtool.formatgraph = None
 264         it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
 265         it.next().run()
 266         it.next().run()
 267
 268         with open("tests/wf/scatter2_subwf.cwl") as f:
 269             subwf = f.read()
 270
 271         runner.api.jobs().create.assert_called_with(
 272             body={
 273                 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
 274                 'repository': 'arvados',
 275                 'script_version': 'master',
 276                 'script': 'crunchrunner',
 277                 'script_parameters': {
 278                     'tasks': [{'task.env': {
 279                         'HOME': '$(task.outdir)',
 280                         'TMPDIR': '$(task.tmpdir)'},
 281                                'task.vwd': {
 282                                    'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
 283                                    'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
 284                                },
 285                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
 286                     'task.stdout': 'cwl.output.json'}]},
 287                 'runtime_constraints': {
 288                     'min_scratch_mb_per_node': 2048,
 289                     'min_cores_per_node': 1,
 290                     'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
 291                     'min_ram_mb_per_node': 1024
 292                 },
 293                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
 294             filters=[['repository', '=', 'arvados'],
 295                      ['script', '=', 'crunchrunner'],
 296                      ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
 297                      ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]],
 298             find_or_create=True)
 299
 300         mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
 301         mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
 302
 303     def test_default_work_api(self):
 304         arvados_cwl.add_arv_hints()
 305
 306         api = mock.MagicMock()
 307         api._rootDesc = copy.deepcopy(get_rootDesc())
 308         del api._rootDesc.get('resources')['jobs']['methods']['create']
 309         runner = arvados_cwl.ArvCwlRunner(api)
 310         self.assertEqual(runner.work_api, 'containers')