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 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 TestContainer(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     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  19     def test_run(self, keepdocker):
  20         runner = mock.MagicMock()
  21         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  22         runner.ignore_docker_for_reuse = False
  23
  24         keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  25         runner.api.collections().get().execute.return_value = {
  26             "portable_data_hash": "99999999999999999999999999999993+99"}
  27
  28         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  29
  30         tool = {
  31             "inputs": [],
  32             "outputs": [],
  33             "baseCommand": "ls",
  34             "arguments": [{"valueFrom": "$(runtime.outdir)"}]
  35         }
  36         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  37         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names,
  38                                                  basedir="", make_fs_access=make_fs_access)
  39         arvtool.formatgraph = None
  40         for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run",
  41                              make_fs_access=make_fs_access, tmpdir="/tmp"):
  42             j.run()
  43             runner.api.container_requests().create.assert_called_with(
  44                 body={
  45                     'environment': {
  46                         'HOME': '/var/spool/cwl',
  47                         'TMPDIR': '/tmp'
  48                     },
  49                     'name': 'test_run',
  50                     'runtime_constraints': {
  51                         'vcpus': 1,
  52                         'ram': 1073741824
  53                     }, 'priority': 1,
  54                     'mounts': {
  55                         '/var/spool/cwl': {'kind': 'tmp'}
  56                     },
  57                     'state': 'Committed',
  58                     'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
  59                     'output_path': '/var/spool/cwl',
  60                     'container_image': '99999999999999999999999999999993+99',
  61                     'command': ['ls', '/var/spool/cwl'],
  62                     'cwd': '/var/spool/cwl'
  63                 })
  64
  65     # The test passes some fields in builder.resources
  66     # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
  67     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
  68     def test_resource_requirements(self, keepdocker):
  69         runner = mock.MagicMock()
  70         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
  71         runner.ignore_docker_for_reuse = False
  72         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
  73
  74         keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
  75         runner.api.collections().get().execute.return_value = {
  76             "portable_data_hash": "99999999999999999999999999999993+99"}
  77
  78         tool = {
  79             "inputs": [],
  80             "outputs": [],
  81             "hints": [{
  82                 "class": "ResourceRequirement",
  83                 "coresMin": 3,
  84                 "ramMin": 3000,
  85                 "tmpdirMin": 4000
  86             }],
  87             "baseCommand": "ls"
  88         }
  89         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
  90         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers",
  91                                                  avsc_names=avsc_names, make_fs_access=make_fs_access)
  92         arvtool.formatgraph = None
  93         for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_resource_requirements",
  94                              make_fs_access=make_fs_access, tmpdir="/tmp"):
  95             j.run()
  96
  97         runner.api.container_requests().create.assert_called_with(
  98             body={
  99                 'environment': {
 100                     'HOME': '/var/spool/cwl',
 101                     'TMPDIR': '/tmp'
 102                 },
 103                 'name': 'test_resource_requirements',
 104                 'runtime_constraints': {
 105                     'vcpus': 3,
 106                     'ram': 3145728000
 107                 }, 'priority': 1,
 108                 'mounts': {
 109                     '/var/spool/cwl': {'kind': 'tmp'}
 110                 },
 111                 'state': 'Committed',
 112                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 113                 'output_path': '/var/spool/cwl',
 114                 'container_image': '99999999999999999999999999999993+99',
 115                 'command': ['ls'],
 116                 'cwd': '/var/spool/cwl'
 117             })
 118
 119     @mock.patch("arvados.collection.Collection")
 120     def test_done(self, col):
 121         api = mock.MagicMock()
 122
 123         runner = mock.MagicMock()
 124         runner.api = api
 125         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 126         runner.num_retries = 0
 127         runner.ignore_docker_for_reuse = False
 128
 129         col().open.return_value = []
 130         api.collections().list().execute.side_effect = ({"items": []},
 131                                                         {"items": [{"manifest_text": "XYZ"}]})
 132
 133         arvjob = arvados_cwl.ArvadosContainer(runner)
 134         arvjob.name = "testjob"
 135         arvjob.builder = mock.MagicMock()
 136         arvjob.output_callback = mock.MagicMock()
 137         arvjob.collect_outputs = mock.MagicMock()
 138         arvjob.successCodes = [0]
 139         arvjob.outdir = "/var/spool/cwl"
 140
 141         arvjob.done({
 142             "state": "Complete",
 143             "output": "99999999999999999999999999999993+99",
 144             "log": "99999999999999999999999999999994+99",
 145             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 146             "exit_code": 0
 147         })
 148
 149         api.collections().list.assert_has_calls([
 150             mock.call(),
 151             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 152                           ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 153                           ['name', '=', 'Output 9999999 of testjob']]),
 154             mock.call().execute(num_retries=0),
 155             mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
 156                  select=['manifest_text']),
 157             mock.call().execute(num_retries=0)])
 158
 159         api.collections().create.assert_called_with(
 160             ensure_unique_name=True,
 161             body={'portable_data_hash': '99999999999999999999999999999993+99',
 162                   'manifest_text': 'XYZ',
 163                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
 164                   'name': 'Output 9999999 of testjob'})
 165
 166     @mock.patch("arvados.collection.Collection")
 167     def test_done_use_existing_collection(self, col):
 168         api = mock.MagicMock()
 169
 170         runner = mock.MagicMock()
 171         runner.api = api
 172         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
 173         runner.num_retries = 0
 174
 175         col().open.return_value = []
 176         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 177
 178         arvjob = arvados_cwl.ArvadosContainer(runner)
 179         arvjob.name = "testjob"
 180         arvjob.builder = mock.MagicMock()
 181         arvjob.output_callback = mock.MagicMock()
 182         arvjob.collect_outputs = mock.MagicMock()
 183         arvjob.successCodes = [0]
 184         arvjob.outdir = "/var/spool/cwl"
 185
 186         arvjob.done({
 187             "state": "Complete",
 188             "output": "99999999999999999999999999999993+99",
 189             "log": "99999999999999999999999999999994+99",
 190             "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
 191             "exit_code": 0
 192         })
 193
 194         api.collections().list.assert_has_calls([
 195             mock.call(),
 196             mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
 197                                ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
 198                                ['name', '=', 'Output 9999999 of testjob']]),
 199             mock.call().execute(num_retries=0)])
 200
 201         self.assertFalse(api.collections().create.called)