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bashCoat.py
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Mon, May 6, 03:47

bashCoat.py
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#!/usr/bin/env python
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
# from BlackDynamite import *
import os
import stat
import subprocess
admissible_params = {"stdout": bool,
"stop_on_error": bool}
default_params = {"stop_on_error": False}
help = {"stdout": "Specify if you want the standard output instead of a file",
"stop_on_error":
"Specify if should raise an error in case "
"of an error in the bash script"}
def launch(run, params):
_exec = run.getExecFile()
head = \
"""#!/bin/bash
export BLACKDYNAMITE_HOST=__BLACKDYNAMITE__dbhost__
export BLACKDYNAMITE_STUDY=__BLACKDYNAMITE__study__
export BLACKDYNAMITE_SCHEMA=__BLACKDYNAMITE__study__
export BLACKDYNAMITE_RUN_ID=__BLACKDYNAMITE__run_id__
export BLACKDYNAMITE_USER={0}
""".format(params["user"])
_exec["file"] = run.replaceBlackDynamiteVariables(head) + _exec["file"]
f = open(_exec["filename"], 'w')
f.write(_exec["file"])
f.close()
os.chmod(_exec["filename"], stat.S_IRWXU)
print("execute ./" + _exec["filename"])
if params["truerun"] is True:
run["state"] = "launched"
run.update()
run.commit()
filename = run["run_name"] + ".o" + str(run.id)
filename_err = run["run_name"] + ".e" + str(run.id)
if params["stdout"] is True:
ret = subprocess.call("./" + _exec["filename"])
else:
with open(filename, "w") as outfile:
with open(filename_err, "w") as errfile:
ret = subprocess.call(
"./" + _exec["filename"],
stdout=outfile,
stderr=errfile)
if ret == 0:
run["state"] = "FINISHED"
else:
run["state"] = "BASH error"
run.update()
run.commit()
if params["stop_on_error"] is True and not ret == 0:
raise Exception(
"The underlying bash script returned "
"with the error code {0}.".format(ret))

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