- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
- arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
- basedir="", make_fs_access=make_fs_access, loader=document_loader,
- makeTool=runner.arv_make_tool, metadata=metadata)
- arvtool.formatgraph = None
- it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
- it.next().run()
- it.next().run()
-
- with open("tests/wf/scatter2_subwf.cwl") as f:
- subwf = f.read()
-
- mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
- mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
-
- runner.api.jobs().create.assert_called_with(
- body={
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
- 'repository': 'arvados',
- 'script_version': 'master',
- 'script': 'crunchrunner',
- 'script_parameters': {
- 'tasks': [{'task.env': {
- 'HOME': '$(task.outdir)',
- 'TMPDIR': '$(task.tmpdir)'},
- 'task.vwd': {
- 'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
- 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
- },
- 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
- 'task.stdout': 'cwl.output.json'}]},
- 'runtime_constraints': {
- 'min_scratch_mb_per_node': 2048,
- 'min_cores_per_node': 1,
- 'docker_image': 'arvados/jobs',
- 'min_ram_mb_per_node': 1024
- },
- 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
- filters=[['repository', '=', 'arvados'],
- ['script', '=', 'crunchrunner'],
- ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
- ['docker_image_locator', 'in docker', 'arvados/jobs']],
- find_or_create=True)
- except:
- logging.exception("")
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+ runner.num_retries = 0
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
+
+ tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
+ metadata["cwlVersion"] = tool["cwlVersion"]
+
+ mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
+ arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
+ basedir="", make_fs_access=make_fs_access, loader=document_loader,
+ makeTool=runner.arv_make_tool, metadata=metadata)
+ arvtool.formatgraph = None
+ it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
+ it.next().run()
+ it.next().run()
+
+ with open("tests/wf/scatter2_subwf.cwl") as f:
+ subwf = StripYAMLComments(f.read())
+
+ runner.api.jobs().create.assert_called_with(
+ body=JsonDiffMatcher({
+ 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'script': 'crunchrunner',
+ 'script_parameters': {
+ 'tasks': [{'task.env': {
+ 'HOME': '$(task.outdir)',
+ 'TMPDIR': '$(task.tmpdir)'},
+ 'task.vwd': {
+ 'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
+ 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
+ },
+ 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
+ 'task.stdout': 'cwl.output.json'}]},
+ 'runtime_constraints': {
+ 'min_scratch_mb_per_node': 2048,
+ 'min_cores_per_node': 1,
+ 'docker_image': 'arvados/jobs',
+ 'min_ram_mb_per_node': 1024
+ },
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
+ filters=[['repository', '=', 'arvados'],
+ ['script', '=', 'crunchrunner'],
+ ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']],
+ find_or_create=True)
+
+ mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
+ mockcollection().open().__enter__().write.assert_has_calls([mock.call(
+'''{
+ "sleeptime": 5
+}''')])
+
+ def test_default_work_api(self):
+ arvados_cwl.add_arv_hints()
+
+ api = mock.MagicMock()
+ api._rootDesc = copy.deepcopy(get_rootDesc())
+ del api._rootDesc.get('resources')['jobs']['methods']['create']
+ runner = arvados_cwl.ArvCwlRunner(api)
+ self.assertEqual(runner.work_api, 'containers')