self.work_api = work_api
self.stop_polling = threading.Event()
self.poll_api = None
+ self.pipeline = None
if self.work_api is None:
# todo: autodetect API to use.
_, cwlnames, _, _ = cwltool.process.get_schema("v1.0")
_, extnames, _, _ = schema_salad.schema.load_schema("https://w3id.org/cwl/arv-cwl-schema.yml", cache=cache)
for n in extnames.names:
- cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, ""))
+ if not cwlnames.has_name("http://arvados.org/cwl#"+n, ""):
+ cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, ""))
def main(args, stdout, stderr, api_client=None):
parser = arg_parser()
# The test passes no builder.resources
# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
def test_run(self):
+ arvados_cwl.add_arv_hints()
+
runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
basedir="", make_fs_access=make_fs_access, loader=document_loader,
makeTool=runner.arv_make_tool, metadata=metadata)
arvtool.formatgraph = None
- for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
- j.run()
+ it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
+ it.next().run()
+ it.next().run()
+
runner.api.jobs().create.assert_called_with(
body={
'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',