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
   8 import arvados
   9 import arvados_cwl
  10 import cwltool.process
  11 from schema_salad.ref_resolver import Loader
  12
  13 if not os.getenv('ARVADOS_DEBUG'):
  14     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
  15     logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
  16
  17
  18 class TestJob(unittest.TestCase):
  19
  20     # The test passes no builder.resources
  21     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  22     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
  23     def test_run(self, list_images_in_arv):
  24         runner = mock.MagicMock()
  25         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  26         runner.ignore_docker_for_reuse = False
  27         runner.num_retries = 0
  28         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
  29
  30         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
  31         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
  32
  33         tool = {
  34             "inputs": [],
  35             "outputs": [],
  36             "baseCommand": "ls",
  37             "arguments": [{"valueFrom": "$(runtime.outdir)"}]
  38         }
  39         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  40         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
  41                                                  basedir="", make_fs_access=make_fs_access, loader=Loader({}))
  42         arvtool.formatgraph = None
  43         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
  44             j.run()
  45             runner.api.jobs().create.assert_called_with(
  46                 body={
  47                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  48                     'runtime_constraints': {},
  49                     'script_parameters': {
  50                         'tasks': [{
  51                             'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
  52                             'command': ['ls', '$(task.outdir)']
  53                         }],
  54                     },
  55                     'script_version': 'master',
  56                     'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
  57                     'repository': 'arvados',
  58                     'script': 'crunchrunner',
  59                     'runtime_constraints': {
  60                         'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
  61                         'min_cores_per_node': 1,
  62                         'min_ram_mb_per_node': 1024,
  63                         'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
  64                     }
  65                 },
  66                 find_or_create=True,
  67                 filters=[['repository', '=', 'arvados'],
  68                          ['script', '=', 'crunchrunner'],
  69                          ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
  70                          ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]]
  71             )
  72
  73     # The test passes some fields in builder.resources
  74     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  75     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
  76     def test_resource_requirements(self, list_images_in_arv):
  77         runner = mock.MagicMock()
  78         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  79         runner.ignore_docker_for_reuse = False
  80         runner.num_retries = 0
  81         arvados_cwl.add_arv_hints()
  82
  83         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
  84         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
  85
  86         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
  87
  88
  89         tool = {
  90             "inputs": [],
  91             "outputs": [],
  92             "hints": [{
  93                 "class": "ResourceRequirement",
  94                 "coresMin": 3,
  95                 "ramMin": 3000,
  96                 "tmpdirMin": 4000
  97             }, {
  98                 "class": "http://arvados.org/cwl#RuntimeConstraints",
  99                 "keep_cache": 512,
 100                 "outputDirType": "keep_output_dir"
 101             }, {
 102                 "class": "http://arvados.org/cwl#APIRequirement",
 103             }],
 104             "baseCommand": "ls"
 105         }
 106         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
 107         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
 108                                                  make_fs_access=make_fs_access, loader=Loader({}))
 109         arvtool.formatgraph = None
 110         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
 111             j.run()
 112         runner.api.jobs().create.assert_called_with(
 113             body={
 114                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 115                 'runtime_constraints': {},
 116                 'script_parameters': {
 117                     'tasks': [{
 118                         'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
 119                         'task.keepTmpOutput': True,
 120                         'command': ['ls']
 121                     }]
 122             },
 123             'script_version': 'master',
 124                 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
 125                 'repository': 'arvados',
 126                 'script': 'crunchrunner',
 127                 'runtime_constraints': {
 128                     'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
 129                     'min_cores_per_node': 3,
 130                     'min_ram_mb_per_node': 3000,
 131                     'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
 132                     'keep_cache_mb_per_task': 512
 133                 }
 134             },
 135             find_or_create=True,
 136             filters=[['repository', '=', 'arvados'],
 137                      ['script', '=', 'crunchrunner'],
 138                      ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
 139                      ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]])
 140
 141     @mock.patch("arvados.collection.CollectionReader")
 142     def test_done(self, reader):
 143         api = mock.MagicMock()
 144
 145         runner = mock.MagicMock()
 146         runner.api = api
 147         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 148         runner.num_retries = 0
 149         runner.ignore_docker_for_reuse = False
 150
 151         reader().open.return_value = []
 152         api.collections().list().execute.side_effect = ({"items": []},
 153                                                         {"items": [{"manifest_text": "XYZ"}]})
 154
 155         arvjob = arvados_cwl.ArvadosJob(runner)
 156         arvjob.name = "testjob"
 157         arvjob.builder = mock.MagicMock()
 158         arvjob.output_callback = mock.MagicMock()
 159         arvjob.collect_outputs = mock.MagicMock()
 160
 161         arvjob.done({
 162             "state": "Complete",
 163             "output": "99999999999999999999999999999993+99",
 164             "log": "99999999999999999999999999999994+99",
 165             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 166         })
 167
 168         api.collections().list.assert_has_calls([
 169             mock.call(),
 170             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 171                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 172                           ['name', '=', 'Output 9999999 of testjob']]),
 173             mock.call().execute(num_retries=0),
 174             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 175                  select=['manifest_text']),
 176             mock.call().execute(num_retries=0)])
 177
 178         api.collections().create.assert_called_with(
 179             ensure_unique_name=True,
 180             body={'portable_data_hash': '99999999999999999999999999999993+99',
 181                   'manifest_text': 'XYZ',
 182                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 183                   'name': 'Output 9999999 of testjob'})
 184
 185     @mock.patch("arvados.collection.CollectionReader")
 186     def test_done_use_existing_collection(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
 194         reader().open.return_value = []
 195         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 196
 197         arvjob = arvados_cwl.ArvadosJob(runner)
 198         arvjob.name = "testjob"
 199         arvjob.builder = mock.MagicMock()
 200         arvjob.output_callback = mock.MagicMock()
 201         arvjob.collect_outputs = mock.MagicMock()
 202
 203         arvjob.done({
 204             "state": "Complete",
 205             "output": "99999999999999999999999999999993+99",
 206             "log": "99999999999999999999999999999994+99",
 207             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 208         })
 209
 210         api.collections().list.assert_has_calls([
 211             mock.call(),
 212             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 213                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 214                                ['name', '=', 'Output 9999999 of testjob']]),
 215             mock.call().execute(num_retries=0)])
 216
 217         self.assertFalse(api.collections().create.called)
 218
 219
 220 class TestWorkflow(unittest.TestCase):
 221     # The test passes no builder.resources
 222     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 223     @mock.patch("arvados.collection.Collection")
 224     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
 225     def test_run(self, list_images_in_arv, mockcollection):
 226         arvados_cwl.add_arv_hints()
 227
 228         api = mock.MagicMock()
 229         api._rootDesc = arvados.api('v1')._rootDesc
 230         runner = arvados_cwl.ArvCwlRunner(api)
 231         self.assertEqual(runner.work_api, 'jobs')
 232
 233         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
 234         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
 235
 236         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 237         runner.ignore_docker_for_reuse = False
 238         runner.num_retries = 0
 239         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
 240
 241         tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
 242         metadata["cwlVersion"] = tool["cwlVersion"]
 243
 244         mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
 245
 246         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
 247         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
 248                                               basedir="", make_fs_access=make_fs_access, loader=document_loader,
 249                                               makeTool=runner.arv_make_tool, metadata=metadata)
 250         arvtool.formatgraph = None
 251         it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
 252         it.next().run()
 253         it.next().run()
 254
 255         with open("tests/wf/scatter2_subwf.cwl") as f:
 256             subwf = f.read()
 257
 258         runner.api.jobs().create.assert_called_with(
 259             body={
 260                 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
 261                 'repository': 'arvados',
 262                 'script_version': 'master',
 263                 'script': 'crunchrunner',
 264                 'script_parameters': {
 265                     'tasks': [{'task.env': {
 266                         'HOME': '$(task.outdir)',
 267                         'TMPDIR': '$(task.tmpdir)'},
 268                                'task.vwd': {
 269                                    'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
 270                                    'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
 271                                },
 272                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
 273                     'task.stdout': 'cwl.output.json'}]},
 274                 'runtime_constraints': {
 275                     'min_scratch_mb_per_node': 2048,
 276                     'min_cores_per_node': 1,
 277                     'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
 278                     'min_ram_mb_per_node': 1024
 279                 },
 280                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
 281             filters=[['repository', '=', 'arvados'],
 282                      ['script', '=', 'crunchrunner'],
 283                      ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
 284                      ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]],
 285             find_or_create=True)
 286
 287         mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
 288         mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
 289
 290     def test_default_work_api(self):
 291         arvados_cwl.add_arv_hints()
 292
 293         api = mock.MagicMock()
 294         api._rootDesc = arvados.api('v1')._rootDesc
 295         del api._rootDesc.get('resources')['jobs']['methods']['create']
 296         runner = arvados_cwl.ArvCwlRunner(api)
 297         self.assertEqual(runner.work_api, 'containers')