sdk/cwl/tests/test_container.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 TestContainer(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     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  18     def test_run(self, keepdocker):
  19         runner = mock.MagicMock()
  20         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  21         runner.ignore_docker_for_reuse = False
  22
  23         keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  24         runner.api.collections().get().execute.return_value = {
  25             "portable_data_hash": "99999999999999999999999999999993+99"}
  26
  27         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  28
  29         tool = {
  30             "inputs": [],
  31             "outputs": [],
  32             "baseCommand": "ls"
  33         }
  34         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names, basedir="")
  35         arvtool.formatgraph = None
  36         for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run"):
  37             j.run()
  38             runner.api.container_requests().create.assert_called_with(
  39                 body={
  40                     'environment': {
  41                         'TMPDIR': '/tmp'
  42                     },
  43                     'name': 'test_run',
  44                     'runtime_constraints': {
  45                         'vcpus': 1,
  46                         'ram': 1073741824
  47                     }, 'priority': 1,
  48                     'mounts': {
  49                         '/var/spool/cwl': {'kind': 'tmp'}
  50                     },
  51                     'state': 'Committed',
  52                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  53                     'output_path': '/var/spool/cwl',
  54                     'container_image': '99999999999999999999999999999993+99',
  55                     'command': ['ls'],
  56                     'cwd': '/var/spool/cwl'
  57                 })
  58
  59     # The test passes some fields in builder.resources
  60     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  61     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  62     def test_resource_requirements(self, keepdocker):
  63         runner = mock.MagicMock()
  64         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  65         runner.ignore_docker_for_reuse = False
  66         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  67
  68         keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  69         runner.api.collections().get().execute.return_value = {
  70             "portable_data_hash": "99999999999999999999999999999993+99"}
  71
  72         tool = {
  73             "inputs": [],
  74             "outputs": [],
  75             "hints": [{
  76                 "class": "ResourceRequirement",
  77                 "coresMin": 3,
  78                 "ramMin": 3000,
  79                 "tmpdirMin": 4000
  80             }],
  81             "baseCommand": "ls"
  82         }
  83         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names)
  84         arvtool.formatgraph = None
  85         for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_resource_requirements"):
  86             j.run()
  87
  88         runner.api.container_requests().create.assert_called_with(
  89             body={
  90                 'environment': {
  91                     'TMPDIR': '/tmp'
  92                 },
  93                 'name': 'test_resource_requirements',
  94                 'runtime_constraints': {
  95                     'vcpus': 3,
  96                     'ram': 3145728000
  97                 }, 'priority': 1,
  98                 'mounts': {
  99                     '/var/spool/cwl': {'kind': 'tmp'}
 100                 },
 101                 'state': 'Committed',
 102                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 103                 'output_path': '/var/spool/cwl',
 104                 'container_image': '99999999999999999999999999999993+99',
 105                 'command': ['ls'],
 106                 'cwd': '/var/spool/cwl'
 107             })
 108
 109     @mock.patch("arvados.collection.Collection")
 110     def test_done(self, col):
 111         api = mock.MagicMock()
 112
 113         runner = mock.MagicMock()
 114         runner.api = api
 115         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 116         runner.num_retries = 0
 117         runner.ignore_docker_for_reuse = False
 118
 119         col().open.return_value = []
 120         api.collections().list().execute.side_effect = ({"items": []},
 121                                                         {"items": [{"manifest_text": "XYZ"}]})
 122
 123         arvjob = arvados_cwl.ArvadosContainer(runner)
 124         arvjob.name = "testjob"
 125         arvjob.builder = mock.MagicMock()
 126         arvjob.output_callback = mock.MagicMock()
 127         arvjob.collect_outputs = mock.MagicMock()
 128         arvjob.successCodes = [0]
 129
 130         arvjob.done({
 131             "state": "Complete",
 132             "output": "99999999999999999999999999999993+99",
 133             "log": "99999999999999999999999999999994+99",
 134             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 135             "exit_code": 0
 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.ArvadosContainer(runner)
 168         arvjob.name = "testjob"
 169         arvjob.builder = mock.MagicMock()
 170         arvjob.output_callback = mock.MagicMock()
 171         arvjob.collect_outputs = mock.MagicMock()
 172         arvjob.successCodes = [0]
 173
 174         arvjob.done({
 175             "state": "Complete",
 176             "output": "99999999999999999999999999999993+99",
 177             "log": "99999999999999999999999999999994+99",
 178             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 179             "exit_code": 0
 180         })
 181
 182         api.collections().list.assert_has_calls([
 183             mock.call(),
 184             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 185                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 186                                ['name', '=', 'Output 9999999 of testjob']]),
 187             mock.call().execute(num_retries=0)])
 188
 189         self.assertFalse(api.collections().create.called)