sdk/cwl/tests/test_job.py

   1 import arvados_cwl
   2 import logging
   3 import mock
   4 import unittest
   5 import os
   6 import cwltool.process
   7
   8 if not os.getenv('ARVADOS_DEBUG'):
   9     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
  10     logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
  11
  12
  13 class TestJob(unittest.TestCase):
  14
  15     # The test passes no builder.resources
  16     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  17     def test_run(self):
  18         runner = mock.MagicMock()
  19         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  20         runner.ignore_docker_for_reuse = False
  21         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  22
  23         tool = {
  24             "inputs": [],
  25             "outputs": [],
  26             "baseCommand": "ls",
  27             "arguments": [{"valueFrom": "$(runtime.outdir)"}]
  28         }
  29         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="")
  30         arvtool.formatgraph = None
  31         for j in arvtool.job({}, mock.MagicMock(), basedir=""):
  32             j.run()
  33             runner.api.jobs().create.assert_called_with(
  34                 body={
  35                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  36                     'runtime_constraints': {},
  37                     'script_parameters': {
  38                         'tasks': [{
  39                             'task.env': {'TMPDIR': '$(task.tmpdir)'},
  40                             'command': ['ls', '$(task.outdir)']
  41                         }],
  42                     },
  43                     'script_version': 'master',
  44                     'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
  45                     'repository': 'arvados',
  46                     'script': 'crunchrunner',
  47                     'runtime_constraints': {
  48                         'docker_image': 'arvados/jobs',
  49                         'min_cores_per_node': 1,
  50                         'min_ram_mb_per_node': 1024,
  51                         'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
  52                     }
  53                 },
  54                 find_or_create=True,
  55                 filters=[['repository', '=', 'arvados'],
  56                          ['script', '=', 'crunchrunner'],
  57                          ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
  58                          ['docker_image_locator', 'in docker', 'arvados/jobs']]
  59             )
  60
  61     # The test passes some fields in builder.resources
  62     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  63     def test_resource_requirements(self):
  64         runner = mock.MagicMock()
  65         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  66         runner.ignore_docker_for_reuse = False
  67         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  68
  69         tool = {
  70             "inputs": [],
  71             "outputs": [],
  72             "hints": [{
  73                 "class": "ResourceRequirement",
  74                 "coresMin": 3,
  75                 "ramMin": 3000,
  76                 "tmpdirMin": 4000
  77             }],
  78             "baseCommand": "ls"
  79         }
  80         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names)
  81         arvtool.formatgraph = None
  82         for j in arvtool.job({}, mock.MagicMock(), basedir=""):
  83             j.run()
  84         runner.api.jobs().create.assert_called_with(
  85             body={
  86                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  87                 'runtime_constraints': {},
  88                 'script_parameters': {
  89                     'tasks': [{
  90                         'task.env': {'TMPDIR': '$(task.tmpdir)'},
  91                         'command': ['ls']
  92                     }]
  93             },
  94             'script_version': 'master',
  95                 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
  96                 'repository': 'arvados',
  97                 'script': 'crunchrunner',
  98                 'runtime_constraints': {
  99                     'docker_image': 'arvados/jobs',
 100                     'min_cores_per_node': 3,
 101                     'min_ram_mb_per_node': 3000,
 102                     'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize
 103                 }
 104             },
 105             find_or_create=True,
 106             filters=[['repository', '=', 'arvados'],
 107                      ['script', '=', 'crunchrunner'],
 108                      ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
 109                      ['docker_image_locator', 'in docker', 'arvados/jobs']])
 110
 111     @mock.patch("arvados.collection.Collection")
 112     def test_done(self, col):
 113         api = mock.MagicMock()
 114
 115         runner = mock.MagicMock()
 116         runner.api = api
 117         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 118         runner.num_retries = 0
 119         runner.ignore_docker_for_reuse = False
 120
 121         col().open.return_value = []
 122         api.collections().list().execute.side_effect = ({"items": []},
 123                                                         {"items": [{"manifest_text": "XYZ"}]})
 124
 125         arvjob = arvados_cwl.ArvadosJob(runner)
 126         arvjob.name = "testjob"
 127         arvjob.builder = mock.MagicMock()
 128         arvjob.output_callback = mock.MagicMock()
 129         arvjob.collect_outputs = mock.MagicMock()
 130
 131         arvjob.done({
 132             "state": "Complete",
 133             "output": "99999999999999999999999999999993+99",
 134             "log": "99999999999999999999999999999994+99",
 135             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 136         })
 137
 138         api.collections().list.assert_has_calls([
 139             mock.call(),
 140             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 141                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 142                           ['name', '=', 'Output 9999999 of testjob']]),
 143             mock.call().execute(num_retries=0),
 144             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 145                  select=['manifest_text']),
 146             mock.call().execute(num_retries=0)])
 147
 148         api.collections().create.assert_called_with(
 149             ensure_unique_name=True,
 150             body={'portable_data_hash': '99999999999999999999999999999993+99',
 151                   'manifest_text': 'XYZ',
 152                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 153                   'name': 'Output 9999999 of testjob'})
 154
 155     @mock.patch("arvados.collection.Collection")
 156     def test_done_use_existing_collection(self, col):
 157         api = mock.MagicMock()
 158
 159         runner = mock.MagicMock()
 160         runner.api = api
 161         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 162         runner.num_retries = 0
 163
 164         col().open.return_value = []
 165         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 166
 167         arvjob = arvados_cwl.ArvadosJob(runner)
 168         arvjob.name = "testjob"
 169         arvjob.builder = mock.MagicMock()
 170         arvjob.output_callback = mock.MagicMock()
 171         arvjob.collect_outputs = mock.MagicMock()
 172
 173         arvjob.done({
 174             "state": "Complete",
 175             "output": "99999999999999999999999999999993+99",
 176             "log": "99999999999999999999999999999994+99",
 177             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 178         })
 179
 180         api.collections().list.assert_has_calls([
 181             mock.call(),
 182             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 183                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 184                                ['name', '=', 'Output 9999999 of testjob']]),
 185             mock.call().execute(num_retries=0)])
 186
 187         self.assertFalse(api.collections().create.called)