10 import cwltool.process
11 from schema_salad.ref_resolver import Loader
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 TestJob(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, list_images_in_arv):
24 runner = mock.MagicMock()
25 runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
26 runner.ignore_docker_for_reuse = False
27 runner.num_retries = 0
28 document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
30 list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
31 runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
37 "arguments": [{"valueFrom": "$(runtime.outdir)"}]
39 make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
40 arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
41 basedir="", make_fs_access=make_fs_access, loader=Loader({}))
42 arvtool.formatgraph = None
43 for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
45 runner.api.jobs().create.assert_called_with(
47 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
48 'runtime_constraints': {},
49 'script_parameters': {
51 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
52 'command': ['ls', '$(task.outdir)']
55 'script_version': 'master',
56 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
57 'repository': 'arvados',
58 'script': 'crunchrunner',
59 'runtime_constraints': {
60 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
61 'min_cores_per_node': 1,
62 'min_ram_mb_per_node': 1024,
63 'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
67 filters=[['repository', '=', 'arvados'],
68 ['script', '=', 'crunchrunner'],
69 ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
70 ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]]
73 # The test passes some fields in builder.resources
74 # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
75 @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
76 def test_resource_requirements(self, list_images_in_arv):
77 runner = mock.MagicMock()
78 runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
79 runner.ignore_docker_for_reuse = False
80 runner.num_retries = 0
81 arvados_cwl.add_arv_hints()
83 list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
84 runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
86 document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
93 "class": "ResourceRequirement",
98 "class": "http://arvados.org/cwl#RuntimeConstraints",
100 "outputDirType": "keep_output_dir"
102 "class": "http://arvados.org/cwl#APIRequirement",
106 make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
107 arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
108 make_fs_access=make_fs_access, loader=Loader({}))
109 arvtool.formatgraph = None
110 for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
112 runner.api.jobs().create.assert_called_with(
114 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
115 'runtime_constraints': {},
116 'script_parameters': {
118 'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
119 'task.keepTmpOutput': True,
123 'script_version': 'master',
124 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
125 'repository': 'arvados',
126 'script': 'crunchrunner',
127 'runtime_constraints': {
128 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
129 'min_cores_per_node': 3,
130 'min_ram_mb_per_node': 3000,
131 'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
132 'keep_cache_mb_per_task': 512
136 filters=[['repository', '=', 'arvados'],
137 ['script', '=', 'crunchrunner'],
138 ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
139 ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]])
141 @mock.patch("arvados.collection.CollectionReader")
142 def test_done(self, reader):
143 api = mock.MagicMock()
145 runner = mock.MagicMock()
147 runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
148 runner.num_retries = 0
149 runner.ignore_docker_for_reuse = False
151 reader().open.return_value = []
152 api.collections().list().execute.side_effect = ({"items": []},
153 {"items": [{"manifest_text": "XYZ"}]})
155 arvjob = arvados_cwl.ArvadosJob(runner)
156 arvjob.name = "testjob"
157 arvjob.builder = mock.MagicMock()
158 arvjob.output_callback = mock.MagicMock()
159 arvjob.collect_outputs = mock.MagicMock()
163 "output": "99999999999999999999999999999993+99",
164 "log": "99999999999999999999999999999994+99",
165 "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
168 api.collections().list.assert_has_calls([
170 mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
171 ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
172 ['name', '=', 'Output 9999999 of testjob']]),
173 mock.call().execute(num_retries=0),
174 mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
175 select=['manifest_text']),
176 mock.call().execute(num_retries=0)])
178 api.collections().create.assert_called_with(
179 ensure_unique_name=True,
180 body={'portable_data_hash': '99999999999999999999999999999993+99',
181 'manifest_text': 'XYZ',
182 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
183 'name': 'Output 9999999 of testjob'})
185 @mock.patch("arvados.collection.CollectionReader")
186 def test_done_use_existing_collection(self, reader):
187 api = mock.MagicMock()
189 runner = mock.MagicMock()
191 runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
192 runner.num_retries = 0
194 reader().open.return_value = []
195 api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
197 arvjob = arvados_cwl.ArvadosJob(runner)
198 arvjob.name = "testjob"
199 arvjob.builder = mock.MagicMock()
200 arvjob.output_callback = mock.MagicMock()
201 arvjob.collect_outputs = mock.MagicMock()
205 "output": "99999999999999999999999999999993+99",
206 "log": "99999999999999999999999999999994+99",
207 "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
210 api.collections().list.assert_has_calls([
212 mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
213 ['portable_data_hash', '=', '99999999999999999999999999999993+99'],
214 ['name', '=', 'Output 9999999 of testjob']]),
215 mock.call().execute(num_retries=0)])
217 self.assertFalse(api.collections().create.called)
220 class TestWorkflow(unittest.TestCase):
221 # The test passes no builder.resources
222 # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
223 @mock.patch("arvados.collection.Collection")
224 @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
225 def test_run(self, list_images_in_arv, mockcollection):
226 arvados_cwl.add_arv_hints()
228 api = mock.MagicMock()
229 api._rootDesc = arvados.api('v1')._rootDesc
230 runner = arvados_cwl.ArvCwlRunner(api)
231 self.assertEqual(runner.work_api, 'jobs')
233 list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
234 runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
236 runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
237 runner.ignore_docker_for_reuse = False
238 runner.num_retries = 0
239 document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
241 tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
242 metadata["cwlVersion"] = tool["cwlVersion"]
244 mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
246 make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
247 arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
248 basedir="", make_fs_access=make_fs_access, loader=document_loader,
249 makeTool=runner.arv_make_tool, metadata=metadata)
250 arvtool.formatgraph = None
251 it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
255 with open("tests/wf/scatter2_subwf.cwl") as f:
258 runner.api.jobs().create.assert_called_with(
260 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
261 'repository': 'arvados',
262 'script_version': 'master',
263 'script': 'crunchrunner',
264 'script_parameters': {
265 'tasks': [{'task.env': {
266 'HOME': '$(task.outdir)',
267 'TMPDIR': '$(task.tmpdir)'},
269 'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
270 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
272 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
273 'task.stdout': 'cwl.output.json'}]},
274 'runtime_constraints': {
275 'min_scratch_mb_per_node': 2048,
276 'min_cores_per_node': 1,
277 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
278 'min_ram_mb_per_node': 1024
280 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
281 filters=[['repository', '=', 'arvados'],
282 ['script', '=', 'crunchrunner'],
283 ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
284 ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]],
287 mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
288 mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
290 def test_default_work_api(self):
291 arvados_cwl.add_arv_hints()
293 api = mock.MagicMock()
294 api._rootDesc = arvados.api('v1')._rootDesc
295 del api._rootDesc.get('resources')['jobs']['methods']['create']
296 runner = arvados_cwl.ArvCwlRunner(api)
297 self.assertEqual(runner.work_api, 'containers')