def convert_local_to_cell_path(cls, path, cell=''):
if not path:
return ''
if cls.is_local_path(path) and EnvUtil.get_other_env_variable(
var='GALAXY_fs_cell'):
cell_name = cell if cell else EnvUtil.get_other_env_variable(
var='GALAXY_fs_cell')
path = path.replace('/LOCAL', '/galaxy/' + cell_name + '-d')
return path
def get_cell_path_local_path(cls, path, cell=''):
if cls.is_local_path(path) or '/galaxy/' not in path:
return path
try:
this_cell = cell if cell else EnvUtil.get_other_env_variable(
var='GALAXY_fs_cell')
with open(
EnvUtil.get_other_env_variable('GALAXY_fs_global_config'),
'r') as infile:
config = json.load(infile)
root = config[this_cell]['fs_root']
if root and root[-1] != '/':
root += '/'
return root + '/'.join(path.split('/')[3:])
except Exception as _:
return ''
def get_cell_from_path(cls, path):
if cls.is_local_path(path):
return EnvUtil.get_other_env_variable(var='GALAXY_fs_cell')
else:
return path.replace('/galaxy/', '').split('-')[0]
def get_container_snapshot(self, send_backend=True):
if not self._is_initialized:
self._logger.error(
"Warning: taking snapshot when the container [" +
self.get_container_name() + "] is not initialized.")
self._SYS_LOGGER.error(
"Warning: taking snapshot when the container [" +
self.get_container_name() + "] is not initialized.")
snapshot = ContainerSnapshot()
snapshot.container_name = self._container_name
snapshot.is_initialized = self._is_initialized
snapshot.status = self._status
snapshot.class_name = self.get_full_class_name()
snapshot.mode = self._mode
snapshot.data_model = self.DATA_MODEL
snapshot.log_file = FileUtil.convert_local_to_cell_path(
glogging.get_logger_file(self._logger))
snapshot.run_cell = EnvUtil.get_other_env_variable(
var='GALAXY_fs_cell', fallback_value='')
snapshot.snapshot_cell = FileUtil.get_cell_from_path(
FileUtil.convert_local_to_cell_path(self._snapshot_file_folder))
for key, val in self._counter.items():
snapshot.counters[key] = val
if self._start_time:
snapshot.start_time = str(self._start_time)
if self._end_time:
snapshot.end_time = str(self._end_time)
for op_name, op in self._node_name_to_node_dict.items():
if 'Dummy' in op.get_class_name():
continue
op_output_file = FileUtil.join_paths_to_file(
root_dir=FileUtil.join_paths_to_dir(
FileUtil.dir_name(self._snapshot_file_folder),
'operators'),
base_name=op_name + '_SNAPSHOT_' +
str(TimezoneUtil.cur_time_in_pst()) + '.pb')
snapshot.operator_snapshot_map[op_name].CopyFrom(
op.get_operator_snapshot(output_file=op_output_file))
self._SYS_LOGGER.info(
"Snapshot saved to folder [" +
FileUtil.convert_local_to_cell_path(self._snapshot_file_folder) +
'].')
self._logger.info(
"Snapshot saved to folder [" +
FileUtil.convert_local_to_cell_path(self._snapshot_file_folder) +
'].')
output_file_name = FileUtil.join_paths_to_file(
root_dir=FileUtil.join_paths_to_dir(
FileUtil.dir_name(self._snapshot_file_folder), 'containers'),
base_name=self._container_name + '_SNAPSHOT_' +
str(TimezoneUtil.cur_time_in_pst()) + '.pb')
FileUtil.write_proto_to_file(proto=snapshot,
file_name=output_file_name)
if self._backend and send_backend:
try:
self._backend.send_to_backend(snapshot=snapshot)
except Exception as err:
self._logger.error("Sending backend failed with error " +
str(err) + '.')
return snapshot
