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
   9 if not os.getenv('ARVADOS_DEBUG'):
  10     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
  11     logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
  12
  13
  14 class TestJob(unittest.TestCase):
  15
  16     # The test passes no builder.resources
  17     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  18     def test_run(self):
  19         runner = mock.MagicMock()
  20         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  21         runner.ignore_docker_for_reuse = False
  22         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  23
  24         tool = {
  25             "inputs": [],
  26             "outputs": [],
  27             "baseCommand": "ls",
  28             "arguments": [{"valueFrom": "$(runtime.outdir)"}]
  29         }
  30         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  31         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="", make_fs_access=make_fs_access)
  32         arvtool.formatgraph = None
  33         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
  34             j.run()
  35             runner.api.jobs().create.assert_called_with(
  36                 body={
  37                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  38                     'runtime_constraints': {},
  39                     'script_parameters': {
  40                         'tasks': [{
  41                             'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
  42                             'command': ['ls', '$(task.outdir)']
  43                         }],
  44                     },
  45                     'script_version': 'master',
  46                     'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
  47                     'repository': 'arvados',
  48                     'script': 'crunchrunner',
  49                     'runtime_constraints': {
  50                         'docker_image': 'arvados/jobs',
  51                         'min_cores_per_node': 1,
  52                         'min_ram_mb_per_node': 1024,
  53                         'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
  54                     }
  55                 },
  56                 find_or_create=True,
  57                 filters=[['repository', '=', 'arvados'],
  58                          ['script', '=', 'crunchrunner'],
  59                          ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
  60                          ['docker_image_locator', 'in docker', 'arvados/jobs']]
  61             )
  62
  63     # The test passes some fields in builder.resources
  64     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  65     def test_resource_requirements(self):
  66         runner = mock.MagicMock()
  67         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  68         runner.ignore_docker_for_reuse = False
  69         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  70
  71         tool = {
  72             "inputs": [],
  73             "outputs": [],
  74             "hints": [{
  75                 "class": "ResourceRequirement",
  76                 "coresMin": 3,
  77                 "ramMin": 3000,
  78                 "tmpdirMin": 4000
  79             }],
  80             "baseCommand": "ls"
  81         }
  82         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  83         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, make_fs_access=make_fs_access)
  84         arvtool.formatgraph = None
  85         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
  86             j.run()
  87         runner.api.jobs().create.assert_called_with(
  88             body={
  89                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  90                 'runtime_constraints': {},
  91                 'script_parameters': {
  92                     'tasks': [{
  93                         'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
  94                         'command': ['ls']
  95                     }]
  96             },
  97             'script_version': 'master',
  98                 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
  99                 'repository': 'arvados',
 100                 'script': 'crunchrunner',
 101                 'runtime_constraints': {
 102                     'docker_image': 'arvados/jobs',
 103                     'min_cores_per_node': 3,
 104                     'min_ram_mb_per_node': 3000,
 105                     'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize
 106                 }
 107             },
 108             find_or_create=True,
 109             filters=[['repository', '=', 'arvados'],
 110                      ['script', '=', 'crunchrunner'],
 111                      ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
 112                      ['docker_image_locator', 'in docker', 'arvados/jobs']])
 113
 114     @mock.patch("arvados.collection.Collection")
 115     def test_done(self, col):
 116         api = mock.MagicMock()
 117
 118         runner = mock.MagicMock()
 119         runner.api = api
 120         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 121         runner.num_retries = 0
 122         runner.ignore_docker_for_reuse = False
 123
 124         col().open.return_value = []
 125         api.collections().list().execute.side_effect = ({"items": []},
 126                                                         {"items": [{"manifest_text": "XYZ"}]})
 127
 128         arvjob = arvados_cwl.ArvadosJob(runner)
 129         arvjob.name = "testjob"
 130         arvjob.builder = mock.MagicMock()
 131         arvjob.output_callback = mock.MagicMock()
 132         arvjob.collect_outputs = mock.MagicMock()
 133
 134         arvjob.done({
 135             "state": "Complete",
 136             "output": "99999999999999999999999999999993+99",
 137             "log": "99999999999999999999999999999994+99",
 138             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 139         })
 140
 141         api.collections().list.assert_has_calls([
 142             mock.call(),
 143             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 144                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 145                           ['name', '=', 'Output 9999999 of testjob']]),
 146             mock.call().execute(num_retries=0),
 147             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 148                  select=['manifest_text']),
 149             mock.call().execute(num_retries=0)])
 150
 151         api.collections().create.assert_called_with(
 152             ensure_unique_name=True,
 153             body={'portable_data_hash': '99999999999999999999999999999993+99',
 154                   'manifest_text': 'XYZ',
 155                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 156                   'name': 'Output 9999999 of testjob'})
 157
 158     @mock.patch("arvados.collection.Collection")
 159     def test_done_use_existing_collection(self, col):
 160         api = mock.MagicMock()
 161
 162         runner = mock.MagicMock()
 163         runner.api = api
 164         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 165         runner.num_retries = 0
 166
 167         col().open.return_value = []
 168         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 169
 170         arvjob = arvados_cwl.ArvadosJob(runner)
 171         arvjob.name = "testjob"
 172         arvjob.builder = mock.MagicMock()
 173         arvjob.output_callback = mock.MagicMock()
 174         arvjob.collect_outputs = mock.MagicMock()
 175
 176         arvjob.done({
 177             "state": "Complete",
 178             "output": "99999999999999999999999999999993+99",
 179             "log": "99999999999999999999999999999994+99",
 180             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 181         })
 182
 183         api.collections().list.assert_has_calls([
 184             mock.call(),
 185             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 186                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 187                                ['name', '=', 'Output 9999999 of testjob']]),
 188             mock.call().execute(num_retries=0)])
 189
 190         self.assertFalse(api.collections().create.called)