import arvados_cwl
import cwltool.process
from schema_salad.ref_resolver import Loader
+from schema_salad.sourceline import cmap
from .mock_discovery import get_rootDesc
+from .matcher import JsonDiffMatcher
if not os.getenv('ARVADOS_DEBUG'):
logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
- tool = {
+ tool = cmap({
"inputs": [],
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}]
- }
+ })
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
basedir="", make_fs_access=make_fs_access, loader=Loader({}))
for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
j.run(enable_reuse=enable_reuse)
runner.api.jobs().create.assert_called_with(
- body={
+ body=JsonDiffMatcher({
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'runtime_constraints': {},
'script_parameters': {
}],
},
'script_version': 'master',
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script': 'crunchrunner',
'runtime_constraints': {
- 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'docker_image': 'arvados/jobs',
'min_cores_per_node': 1,
'min_ram_mb_per_node': 1024,
'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
}
- },
+ }),
find_or_create=enable_reuse,
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
- ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
- ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]]
+ ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']]
)
# The test passes some fields in builder.resources
for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
j.run()
runner.api.jobs().create.assert_called_with(
- body={
+ body=JsonDiffMatcher({
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'runtime_constraints': {},
'script_parameters': {
}]
},
'script_version': 'master',
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script': 'crunchrunner',
'runtime_constraints': {
- 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'docker_image': 'arvados/jobs',
'min_cores_per_node': 3,
'min_ram_mb_per_node': 3000,
'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
'keep_cache_mb_per_task': 512
}
- },
+ }),
find_or_create=True,
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
- ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
- ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]])
+ ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']])
@mock.patch("arvados.collection.CollectionReader")
def test_done(self, reader):
arvjob.builder = mock.MagicMock()
arvjob.output_callback = mock.MagicMock()
arvjob.collect_outputs = mock.MagicMock()
+ arvjob.collect_outputs.return_value = {"out": "stuff"}
arvjob.done({
"state": "Complete",
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'name': 'Output 9999999 of testjob'})
+ arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
+
@mock.patch("arvados.collection.CollectionReader")
def test_done_use_existing_collection(self, reader):
api = mock.MagicMock()
arvjob.builder = mock.MagicMock()
arvjob.output_callback = mock.MagicMock()
arvjob.collect_outputs = mock.MagicMock()
+ arvjob.collect_outputs.return_value = {"out": "stuff"}
arvjob.done({
"state": "Complete",
self.assertFalse(api.collections().create.called)
+ arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
+
class TestWorkflow(unittest.TestCase):
# The test passes no builder.resources
subwf = f.read()
runner.api.jobs().create.assert_called_with(
- body={
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ body=JsonDiffMatcher({
+ 'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script_version': 'master',
'script': 'crunchrunner',
'runtime_constraints': {
'min_scratch_mb_per_node': 2048,
'min_cores_per_node': 1,
- 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'docker_image': 'arvados/jobs',
'min_ram_mb_per_node': 1024
},
- 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
- ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
- ['docker_image_locator', 'in docker', 'arvados/jobs:'+arvados_cwl.__version__]],
+ ['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}')])
+ mockcollection().open().__enter__().write.assert_has_calls([mock.call(
+'''{
+ "sleeptime": 5
+}''')])
def test_default_work_api(self):
arvados_cwl.add_arv_hints()