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)
13 class TestContainer(unittest.TestCase):
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
23 keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
24 runner.api.collections().get().execute.return_value = {
25 "portable_data_hash": "99999999999999999999999999999993+99"}
27 document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
33 "arguments": [{"valueFrom": "$(runtime.outdir)"}]
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"):
39 runner.api.container_requests().create.assert_called_with(
45 'runtime_constraints': {
50 '/var/spool/cwl': {'kind': 'tmp'}
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'
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")
69 keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
70 runner.api.collections().get().execute.return_value = {
71 "portable_data_hash": "99999999999999999999999999999993+99"}
77 "class": "ResourceRequirement",
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"):
89 runner.api.container_requests().create.assert_called_with(
94 'name': 'test_resource_requirements',
95 'runtime_constraints': {
100 '/var/spool/cwl': {'kind': 'tmp'}
102 'state': 'Committed',
103 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
104 'output_path': '/var/spool/cwl',
105 'container_image': '99999999999999999999999999999993+99',
107 'cwd': '/var/spool/cwl'
110 @mock.patch("arvados.collection.Collection")
111 def test_done(self, col):
112 api = mock.MagicMock()
114 runner = mock.MagicMock()
116 runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
117 runner.num_retries = 0
118 runner.ignore_docker_for_reuse = False
120 col().open.return_value = []
121 api.collections().list().execute.side_effect = ({"items": []},
122 {"items": [{"manifest_text": "XYZ"}]})
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"
134 "output": "99999999999999999999999999999993+99",
135 "log": "99999999999999999999999999999994+99",
136 "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
140 api.collections().list.assert_has_calls([
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)])
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'})
157 @mock.patch("arvados.collection.Collection")
158 def test_done_use_existing_collection(self, col):
159 api = mock.MagicMock()
161 runner = mock.MagicMock()
163 runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
164 runner.num_retries = 0
166 col().open.return_value = []
167 api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
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"
179 "output": "99999999999999999999999999999993+99",
180 "log": "99999999999999999999999999999994+99",
181 "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
185 api.collections().list.assert_has_calls([
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)])
192 self.assertFalse(api.collections().create.called)