# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@mock.patch("arvados.collection.Collection")
def test_run(self, mockcollection):
- try:
- arvados_cwl.add_arv_hints()
+ arvados_cwl.add_arv_hints()
- runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
- 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")
+ runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
- tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
- metadata["cwlVersion"] = tool["cwlVersion"]
+ 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")
- mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+ tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
+ metadata["cwlVersion"] = tool["cwlVersion"]
- 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()
+ mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
- with open("tests/wf/scatter2_subwf.cwl") as f:
- subwf = f.read()
+ 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()
- mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
- mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
+ with open("tests/wf/scatter2_subwf.cwl") as f:
+ subwf = f.read()
- 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("")
+ 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)