def pipe_chunk_to_command(command, chunk):
"""
Executes the given command, passing the chunk to its stdin via buf_size buffers.
"""
logger = logging.getLogger(__name__)
sys.stdout.buffer.write(f"Piping chunk | {command}\n".encode('utf8'))
sys.stdout.flush()
child = spawn(command)
child.logfile_read = sys.stdout.buffer
for buf in chunk:
child.send(buf)
child.sendeof()
child.expect(EOF)
retcode = child.wait()
logger.debug(f"Process returned {retcode}")
return retcode
def setup(self):
cmdls = [
key + "=\"" + self.session_vars[key] + "\""
for key in self.session_vars.keys()
]
if self.exec_profile["type"] == "bash":
init_pref = ""
elif self.exec_profile["type"] == "powershell":
init_pref = "$"
else:
raise AssertionError("Error unkown type \"" +
self.exec_profile["type"] + "\".")
cmdls = [(init_pref + c) for c in cmdls]
self.pexpect_process = spawn(self.exec_profile["type"], timeout=None)
self.send_commands(cmdls)
def prepare_shell():
var_cmdls = [
"JOB_ID=\"" + job_id + "\"", "RUN_ID=\"" + run_id + "\"",
"CWL=\"" + cwl + "\"", "RUN_YAML=\"" + yaml + "\"",
"OUTPUT_DIR=\"" + out_dir + "\"",
"GLOBAL_TEMP_DIR=\"" + global_temp_dir + "\"",
"LOG_FILE=\"" + log + "\"", "SUCCESS=\"True\"", "ERR_MESSAGE=\"None\"",
"FINISH_TAG=\"DONE\"", "PYTHON_PATH=\"" + python_interpreter + "\""
]
if exec_profile["shell"] == "bash":
init_pref = ""
elif exec_profile["shell"] == "powershell":
init_pref = "$"
else:
sys.exit("Error unkown shell \"" + exec_profile["shell"] + "\".")
var_cmdls = [(init_pref + c) for c in var_cmdls]
p = spawn(exec_profile["shell"], timeout=None)
[p.sendline(cmdl) for cmdl in var_cmdls]
return p