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