sdk/cwl/tests/test_job.py

   1 import arvados_cwl
   2 import logging
   3 import mock
   4 import unittest
   5 import os
   6 import functools
   7 import cwltool.process
   8 from schema_salad.ref_resolver import Loader
   9
  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         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  26
  27         tool = {
  28             "inputs": [],
  29             "outputs": [],
  30             "baseCommand": "ls",
  31             "arguments": [{"valueFrom": "$(runtime.outdir)"}]
  32         }
  33         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  34         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
  35                                                  basedir="", make_fs_access=make_fs_access, loader=Loader({}))
  36         arvtool.formatgraph = None
  37         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
  38             j.run()
  39             runner.api.jobs().create.assert_called_with(
  40                 body={
  41                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  42                     'runtime_constraints': {},
  43                     'script_parameters': {
  44                         'tasks': [{
  45                             'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
  46                             'command': ['ls', '$(task.outdir)']
  47                         }],
  48                     },
  49                     'script_version': 'master',
  50                     'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
  51                     'repository': 'arvados',
  52                     'script': 'crunchrunner',
  53                     'runtime_constraints': {
  54                         'docker_image': 'arvados/jobs',
  55                         'min_cores_per_node': 1,
  56                         'min_ram_mb_per_node': 1024,
  57                         'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
  58                     }
  59                 },
  60                 find_or_create=True,
  61                 filters=[['repository', '=', 'arvados'],
  62                          ['script', '=', 'crunchrunner'],
  63                          ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
  64                          ['docker_image_locator', 'in docker', 'arvados/jobs']]
  65             )
  66
  67     # The test passes some fields in builder.resources
  68     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  69     def test_resource_requirements(self):
  70         runner = mock.MagicMock()
  71         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  72         runner.ignore_docker_for_reuse = False
  73         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  74
  75         tool = {
  76             "inputs": [],
  77             "outputs": [],
  78             "hints": [{
  79                 "class": "ResourceRequirement",
  80                 "coresMin": 3,
  81                 "ramMin": 3000,
  82                 "tmpdirMin": 4000
  83             }],
  84             "baseCommand": "ls"
  85         }
  86         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  87         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
  88                                                  make_fs_access=make_fs_access, loader=Loader({}))
  89         arvtool.formatgraph = None
  90         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
  91             j.run()
  92         runner.api.jobs().create.assert_called_with(
  93             body={
  94                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  95                 'runtime_constraints': {},
  96                 'script_parameters': {
  97                     'tasks': [{
  98                         'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
  99                         'command': ['ls']
 100                     }]
 101             },
 102             'script_version': 'master',
 103                 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
 104                 'repository': 'arvados',
 105                 'script': 'crunchrunner',
 106                 'runtime_constraints': {
 107                     'docker_image': 'arvados/jobs',
 108                     'min_cores_per_node': 3,
 109                     'min_ram_mb_per_node': 3000,
 110                     'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize
 111                 }
 112             },
 113             find_or_create=True,
 114             filters=[['repository', '=', 'arvados'],
 115                      ['script', '=', 'crunchrunner'],
 116                      ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
 117                      ['docker_image_locator', 'in docker', 'arvados/jobs']])
 118
 119     @mock.patch("arvados.collection.Collection")
 120     def test_done(self, col):
 121         api = mock.MagicMock()
 122
 123         runner = mock.MagicMock()
 124         runner.api = api
 125         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 126         runner.num_retries = 0
 127         runner.ignore_docker_for_reuse = False
 128
 129         col().open.return_value = []
 130         api.collections().list().execute.side_effect = ({"items": []},
 131                                                         {"items": [{"manifest_text": "XYZ"}]})
 132
 133         arvjob = arvados_cwl.ArvadosJob(runner)
 134         arvjob.name = "testjob"
 135         arvjob.builder = mock.MagicMock()
 136         arvjob.output_callback = mock.MagicMock()
 137         arvjob.collect_outputs = mock.MagicMock()
 138
 139         arvjob.done({
 140             "state": "Complete",
 141             "output": "99999999999999999999999999999993+99",
 142             "log": "99999999999999999999999999999994+99",
 143             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 144         })
 145
 146         api.collections().list.assert_has_calls([
 147             mock.call(),
 148             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 149                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 150                           ['name', '=', 'Output 9999999 of testjob']]),
 151             mock.call().execute(num_retries=0),
 152             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 153                  select=['manifest_text']),
 154             mock.call().execute(num_retries=0)])
 155
 156         api.collections().create.assert_called_with(
 157             ensure_unique_name=True,
 158             body={'portable_data_hash': '99999999999999999999999999999993+99',
 159                   'manifest_text': 'XYZ',
 160                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 161                   'name': 'Output 9999999 of testjob'})
 162
 163     @mock.patch("arvados.collection.Collection")
 164     def test_done_use_existing_collection(self, col):
 165         api = mock.MagicMock()
 166
 167         runner = mock.MagicMock()
 168         runner.api = api
 169         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 170         runner.num_retries = 0
 171
 172         col().open.return_value = []
 173         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 174
 175         arvjob = arvados_cwl.ArvadosJob(runner)
 176         arvjob.name = "testjob"
 177         arvjob.builder = mock.MagicMock()
 178         arvjob.output_callback = mock.MagicMock()
 179         arvjob.collect_outputs = mock.MagicMock()
 180
 181         arvjob.done({
 182             "state": "Complete",
 183             "output": "99999999999999999999999999999993+99",
 184             "log": "99999999999999999999999999999994+99",
 185             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 186         })
 187
 188         api.collections().list.assert_has_calls([
 189             mock.call(),
 190             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 191                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 192                                ['name', '=', 'Output 9999999 of testjob']]),
 193             mock.call().execute(num_retries=0)])
 194
 195         self.assertFalse(api.collections().create.called)