sdk/cwl/tests/test_job.py

   1 import logging
   2 import mock
   3 import unittest
   4 import os
   5 import functools
   6 import json
   7
   8 import arvados_cwl
   9 import cwltool.process
  10 from schema_salad.ref_resolver import Loader
  11
  12 if not os.getenv('ARVADOS_DEBUG'):
  13     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
  14     logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
  15
  16
  17 class TestJob(unittest.TestCase):
  18
  19     # The test passes no builder.resources
  20     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  21     def test_run(self):
  22         runner = mock.MagicMock()
  23         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  24         runner.ignore_docker_for_reuse = False
  25         runner.num_retries = 0
  26         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  27
  28         tool = {
  29             "inputs": [],
  30             "outputs": [],
  31             "baseCommand": "ls",
  32             "arguments": [{"valueFrom": "$(runtime.outdir)"}]
  33         }
  34         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  35         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
  36                                                  basedir="", make_fs_access=make_fs_access, loader=Loader({}))
  37         arvtool.formatgraph = None
  38         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
  39             j.run()
  40             runner.api.jobs().create.assert_called_with(
  41                 body={
  42                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  43                     'runtime_constraints': {},
  44                     'script_parameters': {
  45                         'tasks': [{
  46                             'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
  47                             'command': ['ls', '$(task.outdir)']
  48                         }],
  49                     },
  50                     'script_version': 'master',
  51                     'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
  52                     'repository': 'arvados',
  53                     'script': 'crunchrunner',
  54                     'runtime_constraints': {
  55                         'docker_image': 'arvados/jobs',
  56                         'min_cores_per_node': 1,
  57                         'min_ram_mb_per_node': 1024,
  58                         'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
  59                     }
  60                 },
  61                 find_or_create=True,
  62                 filters=[['repository', '=', 'arvados'],
  63                          ['script', '=', 'crunchrunner'],
  64                          ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
  65                          ['docker_image_locator', 'in docker', 'arvados/jobs']]
  66             )
  67
  68     # The test passes some fields in builder.resources
  69     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  70     def test_resource_requirements(self):
  71         runner = mock.MagicMock()
  72         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  73         runner.ignore_docker_for_reuse = False
  74         runner.num_retries = 0
  75         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  76
  77         tool = {
  78             "inputs": [],
  79             "outputs": [],
  80             "hints": [{
  81                 "class": "ResourceRequirement",
  82                 "coresMin": 3,
  83                 "ramMin": 3000,
  84                 "tmpdirMin": 4000
  85             }, {
  86                 "class": "http://arvados.org/cwl#RuntimeConstraints",
  87                 "keep_cache": 512
  88             }, {
  89                 "class": "http://arvados.org/cwl#APIRequirement",
  90             }],
  91             "baseCommand": "ls"
  92         }
  93         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  94         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
  95                                                  make_fs_access=make_fs_access, loader=Loader({}))
  96         arvtool.formatgraph = None
  97         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
  98             j.run()
  99         runner.api.jobs().create.assert_called_with(
 100             body={
 101                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 102                 'runtime_constraints': {},
 103                 'script_parameters': {
 104                     'tasks': [{
 105                         'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
 106                         'command': ['ls']
 107                     }]
 108             },
 109             'script_version': 'master',
 110                 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
 111                 'repository': 'arvados',
 112                 'script': 'crunchrunner',
 113                 'runtime_constraints': {
 114                     'docker_image': 'arvados/jobs',
 115                     'min_cores_per_node': 3,
 116                     'min_ram_mb_per_node': 3000,
 117                     'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
 118                     'keep_cache_mb_per_task': 512
 119                 }
 120             },
 121             find_or_create=True,
 122             filters=[['repository', '=', 'arvados'],
 123                      ['script', '=', 'crunchrunner'],
 124                      ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
 125                      ['docker_image_locator', 'in docker', 'arvados/jobs']])
 126
 127     @mock.patch("arvados.collection.CollectionReader")
 128     def test_done(self, reader):
 129         api = mock.MagicMock()
 130
 131         runner = mock.MagicMock()
 132         runner.api = api
 133         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 134         runner.num_retries = 0
 135         runner.ignore_docker_for_reuse = False
 136
 137         reader().open.return_value = []
 138         api.collections().list().execute.side_effect = ({"items": []},
 139                                                         {"items": [{"manifest_text": "XYZ"}]})
 140
 141         arvjob = arvados_cwl.ArvadosJob(runner)
 142         arvjob.name = "testjob"
 143         arvjob.builder = mock.MagicMock()
 144         arvjob.output_callback = mock.MagicMock()
 145         arvjob.collect_outputs = mock.MagicMock()
 146
 147         arvjob.done({
 148             "state": "Complete",
 149             "output": "99999999999999999999999999999993+99",
 150             "log": "99999999999999999999999999999994+99",
 151             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 152         })
 153
 154         api.collections().list.assert_has_calls([
 155             mock.call(),
 156             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 157                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 158                           ['name', '=', 'Output 9999999 of testjob']]),
 159             mock.call().execute(num_retries=0),
 160             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 161                  select=['manifest_text']),
 162             mock.call().execute(num_retries=0)])
 163
 164         api.collections().create.assert_called_with(
 165             ensure_unique_name=True,
 166             body={'portable_data_hash': '99999999999999999999999999999993+99',
 167                   'manifest_text': 'XYZ',
 168                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 169                   'name': 'Output 9999999 of testjob'})
 170
 171     @mock.patch("arvados.collection.CollectionReader")
 172     def test_done_use_existing_collection(self, reader):
 173         api = mock.MagicMock()
 174
 175         runner = mock.MagicMock()
 176         runner.api = api
 177         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 178         runner.num_retries = 0
 179
 180         reader().open.return_value = []
 181         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 182
 183         arvjob = arvados_cwl.ArvadosJob(runner)
 184         arvjob.name = "testjob"
 185         arvjob.builder = mock.MagicMock()
 186         arvjob.output_callback = mock.MagicMock()
 187         arvjob.collect_outputs = mock.MagicMock()
 188
 189         arvjob.done({
 190             "state": "Complete",
 191             "output": "99999999999999999999999999999993+99",
 192             "log": "99999999999999999999999999999994+99",
 193             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 194         })
 195
 196         api.collections().list.assert_has_calls([
 197             mock.call(),
 198             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 199                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 200                                ['name', '=', 'Output 9999999 of testjob']]),
 201             mock.call().execute(num_retries=0)])
 202
 203         self.assertFalse(api.collections().create.called)
 204
 205
 206 class TestWorkflow(unittest.TestCase):
 207     # The test passes no builder.resources
 208     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 209     @mock.patch("arvados.collection.Collection")
 210     def test_run(self, mockcollection):
 211         try:
 212             arvados_cwl.add_arv_hints()
 213
 214             runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
 215             runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 216             runner.ignore_docker_for_reuse = False
 217             runner.num_retries = 0
 218             document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
 219
 220             tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
 221             metadata["cwlVersion"] = tool["cwlVersion"]
 222
 223             mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
 224
 225             make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
 226             arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
 227                                                   basedir="", make_fs_access=make_fs_access, loader=document_loader,
 228                                                   makeTool=runner.arv_make_tool, metadata=metadata)
 229             arvtool.formatgraph = None
 230             it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
 231             it.next().run()
 232             it.next().run()
 233
 234             with open("tests/wf/scatter2_subwf.cwl") as f:
 235                 subwf = f.read()
 236
 237             mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
 238             mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
 239
 240             runner.api.jobs().create.assert_called_with(
 241                 body={
 242                     'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
 243                     'repository': 'arvados',
 244                     'script_version': 'master',
 245                     'script': 'crunchrunner',
 246                     'script_parameters': {
 247                         'tasks': [{'task.env': {
 248                             'HOME': '$(task.outdir)',
 249                             'TMPDIR': '$(task.tmpdir)'},
 250                                    'task.vwd': {
 251                                        'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
 252                                        'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
 253                                    },
 254                         'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
 255                         'task.stdout': 'cwl.output.json'}]},
 256                     'runtime_constraints': {
 257                         'min_scratch_mb_per_node': 2048,
 258                         'min_cores_per_node': 1,
 259                         'docker_image': 'arvados/jobs',
 260                         'min_ram_mb_per_node': 1024
 261                     },
 262                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
 263                 filters=[['repository', '=', 'arvados'],
 264                          ['script', '=', 'crunchrunner'],
 265                          ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
 266                          ['docker_image_locator', 'in docker', 'arvados/jobs']],
 267                 find_or_create=True)
 268         except:
 269             logging.exception("")