sdk/cwl/tests/test_container.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 TestContainer(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     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  22     def test_run(self, keepdocker):
  23         runner = mock.MagicMock()
  24         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  25         runner.ignore_docker_for_reuse = False
  26
  27         keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  28         runner.api.collections().get().execute.return_value = {
  29             "portable_data_hash": "99999999999999999999999999999993+99"}
  30
  31         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
  32
  33         tool = {
  34             "inputs": [],
  35             "outputs": [],
  36             "baseCommand": "ls",
  37             "arguments": [{"valueFrom": "$(runtime.outdir)"}]
  38         }
  39         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  40         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names,
  41                                                  basedir="", make_fs_access=make_fs_access, loader=Loader({}))
  42         arvtool.formatgraph = None
  43         for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run",
  44                              make_fs_access=make_fs_access, tmpdir="/tmp"):
  45             j.run()
  46             runner.api.container_requests().create.assert_called_with(
  47                 body={
  48                     'environment': {
  49                         'HOME': '/var/spool/cwl',
  50                         'TMPDIR': '/tmp'
  51                     },
  52                     'name': 'test_run',
  53                     'runtime_constraints': {
  54                         'vcpus': 1,
  55                         'ram': 1073741824
  56                     }, 'priority': 1,
  57                     'mounts': {
  58                         '/var/spool/cwl': {'kind': 'tmp'}
  59                     },
  60                     'state': 'Committed',
  61                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  62                     'output_path': '/var/spool/cwl',
  63                     'container_image': '99999999999999999999999999999993+99',
  64                     'command': ['ls', '/var/spool/cwl'],
  65                     'cwd': '/var/spool/cwl'
  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     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  71     def test_resource_requirements(self, keepdocker):
  72         runner = mock.MagicMock()
  73         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  74         runner.ignore_docker_for_reuse = False
  75         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
  76
  77         keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  78         runner.api.collections().get().execute.return_value = {
  79             "portable_data_hash": "99999999999999999999999999999993+99"}
  80
  81         tool = {
  82             "inputs": [],
  83             "outputs": [],
  84             "hints": [{
  85                 "class": "ResourceRequirement",
  86                 "coresMin": 3,
  87                 "ramMin": 3000,
  88                 "tmpdirMin": 4000
  89             }, {
  90                 "class": "http://arvados.org/cwl#RuntimeConstraints",
  91                 "keep_cache": 512
  92             }, {
  93                 "class": "http://arvados.org/cwl#APIRequirement",
  94             }, {
  95                 "class": "http://arvados.org/cwl#PartitionRequirement",
  96                 "partition": "blurb"
  97             }],
  98             "baseCommand": "ls"
  99         }
 100         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
 101         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers",
 102                                                  avsc_names=avsc_names, make_fs_access=make_fs_access,
 103                                                  loader=Loader({}))
 104         arvtool.formatgraph = None
 105         for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_resource_requirements",
 106                              make_fs_access=make_fs_access, tmpdir="/tmp"):
 107             j.run()
 108
 109         runner.api.container_requests().create.assert_called_with(
 110             body={
 111                 'environment': {
 112                     'HOME': '/var/spool/cwl',
 113                     'TMPDIR': '/tmp'
 114                 },
 115                 'name': 'test_resource_requirements',
 116                 'runtime_constraints': {
 117                     'vcpus': 3,
 118                     'ram': 3145728000,
 119                     'API': True,
 120                     'partition': ['blurb']
 121                 }, 'priority': 1,
 122                 'mounts': {
 123                     '/var/spool/cwl': {'kind': 'tmp'}
 124                 },
 125                 'state': 'Committed',
 126                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 127                 'output_path': '/var/spool/cwl',
 128                 'container_image': '99999999999999999999999999999993+99',
 129                 'command': ['ls'],
 130                 'cwd': '/var/spool/cwl'
 131             })
 132
 133     @mock.patch("arvados.collection.Collection")
 134     def test_done(self, col):
 135         api = mock.MagicMock()
 136
 137         runner = mock.MagicMock()
 138         runner.api = api
 139         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 140         runner.num_retries = 0
 141         runner.ignore_docker_for_reuse = False
 142
 143         col().open.return_value = []
 144         api.collections().list().execute.side_effect = ({"items": []},
 145                                                         {"items": [{"manifest_text": "XYZ"}]})
 146
 147         arvjob = arvados_cwl.ArvadosContainer(runner)
 148         arvjob.name = "testjob"
 149         arvjob.builder = mock.MagicMock()
 150         arvjob.output_callback = mock.MagicMock()
 151         arvjob.collect_outputs = mock.MagicMock()
 152         arvjob.successCodes = [0]
 153         arvjob.outdir = "/var/spool/cwl"
 154
 155         arvjob.done({
 156             "state": "Complete",
 157             "output": "99999999999999999999999999999993+99",
 158             "log": "99999999999999999999999999999994+99",
 159             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 160             "exit_code": 0
 161         })
 162
 163         api.collections().list.assert_has_calls([
 164             mock.call(),
 165             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 166                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 167                           ['name', '=', 'Output 9999999 of testjob']]),
 168             mock.call().execute(num_retries=0),
 169             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 170                  select=['manifest_text']),
 171             mock.call().execute(num_retries=0)])
 172
 173         api.collections().create.assert_called_with(
 174             ensure_unique_name=True,
 175             body={'portable_data_hash': '99999999999999999999999999999993+99',
 176                   'manifest_text': 'XYZ',
 177                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 178                   'name': 'Output 9999999 of testjob'})
 179
 180     @mock.patch("arvados.collection.Collection")
 181     def test_done_use_existing_collection(self, col):
 182         api = mock.MagicMock()
 183
 184         runner = mock.MagicMock()
 185         runner.api = api
 186         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 187         runner.num_retries = 0
 188
 189         col().open.return_value = []
 190         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 191
 192         arvjob = arvados_cwl.ArvadosContainer(runner)
 193         arvjob.name = "testjob"
 194         arvjob.builder = mock.MagicMock()
 195         arvjob.output_callback = mock.MagicMock()
 196         arvjob.collect_outputs = mock.MagicMock()
 197         arvjob.successCodes = [0]
 198         arvjob.outdir = "/var/spool/cwl"
 199
 200         arvjob.done({
 201             "state": "Complete",
 202             "output": "99999999999999999999999999999993+99",
 203             "log": "99999999999999999999999999999994+99",
 204             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 205             "exit_code": 0
 206         })
 207
 208         api.collections().list.assert_has_calls([
 209             mock.call(),
 210             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 211                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 212                                ['name', '=', 'Output 9999999 of testjob']]),
 213             mock.call().execute(num_retries=0)])
 214
 215         self.assertFalse(api.collections().create.called)