2 from arvados_cwl.arvdocker import arv_docker_clear_cache
9 from schema_salad.ref_resolver import Loader
11 from .matcher import JsonDiffMatcher
13 if not os.getenv('ARVADOS_DEBUG'):
14 logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
15 logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
18 class TestContainer(unittest.TestCase):
20 # The test passes no builder.resources
21 # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
22 @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
23 def test_run(self, keepdocker):
24 for enable_reuse in (True, False):
25 arv_docker_clear_cache()
27 runner = mock.MagicMock()
28 runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
29 runner.ignore_docker_for_reuse = False
31 keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
32 runner.api.collections().get().execute.return_value = {
33 "portable_data_hash": "99999999999999999999999999999993+99"}
35 document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
41 "arguments": [{"valueFrom": "$(runtime.outdir)"}]
43 make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
44 arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names,
45 basedir="", make_fs_access=make_fs_access, loader=Loader({}))
46 arvtool.formatgraph = None
47 for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run_"+str(enable_reuse),
48 make_fs_access=make_fs_access, tmpdir="/tmp"):
49 j.run(enable_reuse=enable_reuse)
50 runner.api.container_requests().create.assert_called_with(
51 body=JsonDiffMatcher({
53 'HOME': '/var/spool/cwl',
56 'name': 'test_run_'+str(enable_reuse),
57 'runtime_constraints': {
61 'use_existing': enable_reuse,
64 '/var/spool/cwl': {'kind': 'tmp'}
67 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
68 'output_path': '/var/spool/cwl',
69 'container_image': '99999999999999999999999999999993+99',
70 'command': ['ls', '/var/spool/cwl'],
71 'cwd': '/var/spool/cwl',
72 'scheduling_parameters': {},
76 # The test passes some fields in builder.resources
77 # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
78 @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
79 def test_resource_requirements(self, keepdocker):
80 arv_docker_clear_cache()
81 runner = mock.MagicMock()
82 runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
83 runner.ignore_docker_for_reuse = False
84 document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
86 keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
87 runner.api.collections().get().execute.return_value = {
88 "portable_data_hash": "99999999999999999999999999999993+99"}
94 "class": "ResourceRequirement",
99 "class": "http://arvados.org/cwl#RuntimeConstraints",
102 "class": "http://arvados.org/cwl#APIRequirement",
104 "class": "http://arvados.org/cwl#PartitionRequirement",
109 make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
110 arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers",
111 avsc_names=avsc_names, make_fs_access=make_fs_access,
113 arvtool.formatgraph = None
114 for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_resource_requirements",
115 make_fs_access=make_fs_access, tmpdir="/tmp"):
118 call_args, call_kwargs = runner.api.container_requests().create.call_args
120 call_body_expected = {
122 'HOME': '/var/spool/cwl',
125 'name': 'test_resource_requirements',
126 'runtime_constraints': {
129 'keep_cache_ram': 512,
132 'use_existing': True,
135 '/var/spool/cwl': {'kind': 'tmp'}
137 'state': 'Committed',
138 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
139 'output_path': '/var/spool/cwl',
140 'container_image': '99999999999999999999999999999993+99',
142 'cwd': '/var/spool/cwl',
143 'scheduling_parameters': {
144 'partitions': ['blurb']
149 call_body = call_kwargs.get('body', None)
150 self.assertNotEqual(None, call_body)
151 for key in call_body:
152 self.assertEqual(call_body_expected.get(key), call_body.get(key))
154 @mock.patch("arvados.collection.Collection")
155 def test_done(self, col):
156 api = mock.MagicMock()
158 runner = mock.MagicMock()
160 runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
161 runner.num_retries = 0
162 runner.ignore_docker_for_reuse = False
164 runner.api.containers().get().execute.return_value = {"state":"Complete",
168 col().open.return_value = []
170 arvjob = arvados_cwl.ArvadosContainer(runner)
171 arvjob.name = "testjob"
172 arvjob.builder = mock.MagicMock()
173 arvjob.output_callback = mock.MagicMock()
174 arvjob.collect_outputs = mock.MagicMock()
175 arvjob.successCodes = [0]
176 arvjob.outdir = "/var/spool/cwl"
178 arvjob.collect_outputs.return_value = {"out": "stuff"}
182 "log_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1",
183 "output_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
184 "uuid": "zzzzz-xvhdp-zzzzzzzzzzzzzzz",
185 "container_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
188 self.assertFalse(api.collections().create.called)
190 arvjob.collect_outputs.assert_called_with("keep:abc+123")
191 arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")