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