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     def test_run(self):
  23         runner = mock.MagicMock()
  24         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  25         runner.ignore_docker_for_reuse = False
  26         runner.num_retries = 0
  27         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
  28
  29         tool = {
  30             "inputs": [],
  31             "outputs": [],
  32             "baseCommand": "ls",
  33             "arguments": [{"valueFrom": "$(runtime.outdir)"}]
  34         }
  35         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  36         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
  37                                                  basedir="", make_fs_access=make_fs_access, loader=Loader({}))
  38         arvtool.formatgraph = None
  39         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
  40             j.run()
  41             runner.api.jobs().create.assert_called_with(
  42                 body={
  43                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  44                     'runtime_constraints': {},
  45                     'script_parameters': {
  46                         'tasks': [{
  47                             'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
  48                             'command': ['ls', '$(task.outdir)']
  49                         }],
  50                     },
  51                     'script_version': 'master',
  52                     'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
  53                     'repository': 'arvados',
  54                     'script': 'crunchrunner',
  55                     'runtime_constraints': {
  56                         'docker_image': 'arvados/jobs',
  57                         'min_cores_per_node': 1,
  58                         'min_ram_mb_per_node': 1024,
  59                         'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
  60                     }
  61                 },
  62                 find_or_create=True,
  63                 filters=[['repository', '=', 'arvados'],
  64                          ['script', '=', 'crunchrunner'],
  65                          ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
  66                          ['docker_image_locator', 'in docker', 'arvados/jobs']]
  67             )
  68
  69     # The test passes some fields in builder.resources
  70     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  71     def test_resource_requirements(self):
  72         runner = mock.MagicMock()
  73         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  74         runner.ignore_docker_for_reuse = False
  75         runner.num_retries = 0
  76         arvados_cwl.add_arv_hints()
  77
  78         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
  79
  80
  81         tool = {
  82             "inputs": [],
  83             "outputs": [],
  84             "hints": [{
  85                 "class": "ResourceRequirement",
  86                 "coresMin": 3,
  87                 "ramMin": 3000,
  88                 "tmpdirMin": 4000
  89             }, {
  90                 "class": "http://arvados.org/cwl#RuntimeConstraints",
  91                 "keep_cache": 512,
  92                 "outputDirType": "keep_output_dir"
  93             }, {
  94                 "class": "http://arvados.org/cwl#APIRequirement",
  95             }],
  96             "baseCommand": "ls"
  97         }
  98         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  99         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
 100                                                  make_fs_access=make_fs_access, loader=Loader({}))
 101         arvtool.formatgraph = None
 102         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
 103             j.run()
 104         runner.api.jobs().create.assert_called_with(
 105             body={
 106                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 107                 'runtime_constraints': {},
 108                 'script_parameters': {
 109                     'tasks': [{
 110                         'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
 111                         'task.keepTmpOutput': True,
 112                         'command': ['ls']
 113                     }]
 114             },
 115             'script_version': 'master',
 116                 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
 117                 'repository': 'arvados',
 118                 'script': 'crunchrunner',
 119                 'runtime_constraints': {
 120                     'docker_image': 'arvados/jobs',
 121                     'min_cores_per_node': 3,
 122                     'min_ram_mb_per_node': 3000,
 123                     'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
 124                     'keep_cache_mb_per_task': 512
 125                 }
 126             },
 127             find_or_create=True,
 128             filters=[['repository', '=', 'arvados'],
 129                      ['script', '=', 'crunchrunner'],
 130                      ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
 131                      ['docker_image_locator', 'in docker', 'arvados/jobs']])
 132
 133     @mock.patch("arvados.collection.CollectionReader")
 134     def test_done(self, reader):
 135         api = mock.MagicMock()
 136
 137         runner = mock.MagicMock()
 138         runner.api = api
 139         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 140         runner.num_retries = 0
 141         runner.ignore_docker_for_reuse = False
 142
 143         reader().open.return_value = []
 144         api.collections().list().execute.side_effect = ({"items": []},
 145                                                         {"items": [{"manifest_text": "XYZ"}]})
 146
 147         arvjob = arvados_cwl.ArvadosJob(runner)
 148         arvjob.name = "testjob"
 149         arvjob.builder = mock.MagicMock()
 150         arvjob.output_callback = mock.MagicMock()
 151         arvjob.collect_outputs = mock.MagicMock()
 152
 153         arvjob.done({
 154             "state": "Complete",
 155             "output": "99999999999999999999999999999993+99",
 156             "log": "99999999999999999999999999999994+99",
 157             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 158         })
 159
 160         api.collections().list.assert_has_calls([
 161             mock.call(),
 162             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 163                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 164                           ['name', '=', 'Output 9999999 of testjob']]),
 165             mock.call().execute(num_retries=0),
 166             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 167                  select=['manifest_text']),
 168             mock.call().execute(num_retries=0)])
 169
 170         api.collections().create.assert_called_with(
 171             ensure_unique_name=True,
 172             body={'portable_data_hash': '99999999999999999999999999999993+99',
 173                   'manifest_text': 'XYZ',
 174                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 175                   'name': 'Output 9999999 of testjob'})
 176
 177     @mock.patch("arvados.collection.CollectionReader")
 178     def test_done_use_existing_collection(self, reader):
 179         api = mock.MagicMock()
 180
 181         runner = mock.MagicMock()
 182         runner.api = api
 183         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 184         runner.num_retries = 0
 185
 186         reader().open.return_value = []
 187         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 188
 189         arvjob = arvados_cwl.ArvadosJob(runner)
 190         arvjob.name = "testjob"
 191         arvjob.builder = mock.MagicMock()
 192         arvjob.output_callback = mock.MagicMock()
 193         arvjob.collect_outputs = mock.MagicMock()
 194
 195         arvjob.done({
 196             "state": "Complete",
 197             "output": "99999999999999999999999999999993+99",
 198             "log": "99999999999999999999999999999994+99",
 199             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 200         })
 201
 202         api.collections().list.assert_has_calls([
 203             mock.call(),
 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
 209         self.assertFalse(api.collections().create.called)
 210
 211
 212 class TestWorkflow(unittest.TestCase):
 213     # The test passes no builder.resources
 214     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 215     @mock.patch("arvados.collection.Collection")
 216     def test_run(self, mockcollection):
 217         arvados_cwl.add_arv_hints()
 218
 219         api = mock.MagicMock()
 220         api._rootDesc = arvados.api('v1')._rootDesc
 221         runner = arvados_cwl.ArvCwlRunner(api)
 222         self.assertEqual(runner.work_api, 'jobs')
 223
 224         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 225         runner.ignore_docker_for_reuse = False
 226         runner.num_retries = 0
 227         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
 228
 229         tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
 230         metadata["cwlVersion"] = tool["cwlVersion"]
 231
 232         mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
 233
 234         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
 235         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
 236                                               basedir="", make_fs_access=make_fs_access, loader=document_loader,
 237                                               makeTool=runner.arv_make_tool, metadata=metadata)
 238         arvtool.formatgraph = None
 239         it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
 240         it.next().run()
 241         it.next().run()
 242
 243         with open("tests/wf/scatter2_subwf.cwl") as f:
 244             subwf = f.read()
 245
 246         mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
 247         mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
 248
 249         runner.api.jobs().create.assert_called_with(
 250             body={
 251                 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
 252                 'repository': 'arvados',
 253                 'script_version': 'master',
 254                 'script': 'crunchrunner',
 255                 'script_parameters': {
 256                     'tasks': [{'task.env': {
 257                         'HOME': '$(task.outdir)',
 258                         'TMPDIR': '$(task.tmpdir)'},
 259                                'task.vwd': {
 260                                    'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
 261                                    'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
 262                                },
 263                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
 264                     'task.stdout': 'cwl.output.json'}]},
 265                 'runtime_constraints': {
 266                     'min_scratch_mb_per_node': 2048,
 267                     'min_cores_per_node': 1,
 268                     'docker_image': 'arvados/jobs',
 269                     'min_ram_mb_per_node': 1024
 270                 },
 271                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
 272             filters=[['repository', '=', 'arvados'],
 273                      ['script', '=', 'crunchrunner'],
 274                      ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
 275                      ['docker_image_locator', 'in docker', 'arvados/jobs']],
 276             find_or_create=True)
 277
 278     def test_default_work_api(self):
 279         arvados_cwl.add_arv_hints()
 280
 281         api = mock.MagicMock()
 282         api._rootDesc = arvados.api('v1')._rootDesc
 283         del api._rootDesc.get('resources')['jobs']['methods']['create']
 284         runner = arvados_cwl.ArvCwlRunner(api)
 285         self.assertEqual(runner.work_api, 'containers')