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
   9 from schema_salad.ref_resolver import Loader
  10
  11 if not os.getenv('ARVADOS_DEBUG'):
  12     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
  13     logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
  14
  15
  16 class TestContainer(unittest.TestCase):
  17
  18     # The test passes no builder.resources
  19     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  20     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  21     def test_run(self, keepdocker):
  22         runner = mock.MagicMock()
  23         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  24         runner.ignore_docker_for_reuse = False
  25
  26         keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  27         runner.api.collections().get().execute.return_value = {
  28             "portable_data_hash": "99999999999999999999999999999993+99"}
  29
  30         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  31
  32         tool = {
  33             "inputs": [],
  34             "outputs": [],
  35             "baseCommand": "ls",
  36             "arguments": [{"valueFrom": "$(runtime.outdir)"}]
  37         }
  38         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  39         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names,
  40                                                  basedir="", make_fs_access=make_fs_access, loader=Loader({}))
  41         arvtool.formatgraph = None
  42         for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run",
  43                              make_fs_access=make_fs_access, tmpdir="/tmp"):
  44             j.run()
  45             runner.api.container_requests().create.assert_called_with(
  46                 body={
  47                     'environment': {
  48                         'HOME': '/var/spool/cwl',
  49                         'TMPDIR': '/tmp'
  50                     },
  51                     'name': 'test_run',
  52                     'runtime_constraints': {
  53                         'vcpus': 1,
  54                         'ram': 1073741824
  55                     }, 'priority': 1,
  56                     'mounts': {
  57                         '/var/spool/cwl': {'kind': 'tmp'}
  58                     },
  59                     'state': 'Committed',
  60                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  61                     'output_path': '/var/spool/cwl',
  62                     'container_image': '99999999999999999999999999999993+99',
  63                     'command': ['ls', '/var/spool/cwl'],
  64                     'cwd': '/var/spool/cwl'
  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     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  70     def test_resource_requirements(self, keepdocker):
  71         runner = mock.MagicMock()
  72         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  73         runner.ignore_docker_for_reuse = False
  74         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  75
  76         keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  77         runner.api.collections().get().execute.return_value = {
  78             "portable_data_hash": "99999999999999999999999999999993+99"}
  79
  80         tool = {
  81             "inputs": [],
  82             "outputs": [],
  83             "hints": [{
  84                 "class": "ResourceRequirement",
  85                 "coresMin": 3,
  86                 "ramMin": 3000,
  87                 "tmpdirMin": 4000
  88             }],
  89             "baseCommand": "ls"
  90         }
  91         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  92         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers",
  93                                                  avsc_names=avsc_names, make_fs_access=make_fs_access,
  94                                                  loader=Loader({}))
  95         arvtool.formatgraph = None
  96         for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_resource_requirements",
  97                              make_fs_access=make_fs_access, tmpdir="/tmp"):
  98             j.run()
  99
 100         runner.api.container_requests().create.assert_called_with(
 101             body={
 102                 'environment': {
 103                     'HOME': '/var/spool/cwl',
 104                     'TMPDIR': '/tmp'
 105                 },
 106                 'name': 'test_resource_requirements',
 107                 'runtime_constraints': {
 108                     'vcpus': 3,
 109                     'ram': 3145728000
 110                 }, 'priority': 1,
 111                 'mounts': {
 112                     '/var/spool/cwl': {'kind': 'tmp'}
 113                 },
 114                 'state': 'Committed',
 115                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 116                 'output_path': '/var/spool/cwl',
 117                 'container_image': '99999999999999999999999999999993+99',
 118                 'command': ['ls'],
 119                 'cwd': '/var/spool/cwl'
 120             })
 121
 122     @mock.patch("arvados.collection.Collection")
 123     def test_done(self, col):
 124         api = mock.MagicMock()
 125
 126         runner = mock.MagicMock()
 127         runner.api = api
 128         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 129         runner.num_retries = 0
 130         runner.ignore_docker_for_reuse = False
 131
 132         col().open.return_value = []
 133         api.collections().list().execute.side_effect = ({"items": []},
 134                                                         {"items": [{"manifest_text": "XYZ"}]})
 135
 136         arvjob = arvados_cwl.ArvadosContainer(runner)
 137         arvjob.name = "testjob"
 138         arvjob.builder = mock.MagicMock()
 139         arvjob.output_callback = mock.MagicMock()
 140         arvjob.collect_outputs = mock.MagicMock()
 141         arvjob.successCodes = [0]
 142         arvjob.outdir = "/var/spool/cwl"
 143
 144         arvjob.done({
 145             "state": "Complete",
 146             "output": "99999999999999999999999999999993+99",
 147             "log": "99999999999999999999999999999994+99",
 148             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 149             "exit_code": 0
 150         })
 151
 152         api.collections().list.assert_has_calls([
 153             mock.call(),
 154             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 155                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 156                           ['name', '=', 'Output 9999999 of testjob']]),
 157             mock.call().execute(num_retries=0),
 158             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 159                  select=['manifest_text']),
 160             mock.call().execute(num_retries=0)])
 161
 162         api.collections().create.assert_called_with(
 163             ensure_unique_name=True,
 164             body={'portable_data_hash': '99999999999999999999999999999993+99',
 165                   'manifest_text': 'XYZ',
 166                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 167                   'name': 'Output 9999999 of testjob'})
 168
 169     @mock.patch("arvados.collection.Collection")
 170     def test_done_use_existing_collection(self, col):
 171         api = mock.MagicMock()
 172
 173         runner = mock.MagicMock()
 174         runner.api = api
 175         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 176         runner.num_retries = 0
 177
 178         col().open.return_value = []
 179         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 180
 181         arvjob = arvados_cwl.ArvadosContainer(runner)
 182         arvjob.name = "testjob"
 183         arvjob.builder = mock.MagicMock()
 184         arvjob.output_callback = mock.MagicMock()
 185         arvjob.collect_outputs = mock.MagicMock()
 186         arvjob.successCodes = [0]
 187         arvjob.outdir = "/var/spool/cwl"
 188
 189         arvjob.done({
 190             "state": "Complete",
 191             "output": "99999999999999999999999999999993+99",
 192             "log": "99999999999999999999999999999994+99",
 193             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 194             "exit_code": 0
 195         })
 196
 197         api.collections().list.assert_has_calls([
 198             mock.call(),
 199             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 200                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 201                                ['name', '=', 'Output 9999999 of testjob']]),
 202             mock.call().execute(num_retries=0)])
 203
 204         self.assertFalse(api.collections().create.called)