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R3127/BlackDynamite/coating/bashCoat.py
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bashCoat.py
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#!/usr/bin/env python
#from BlackDynamite import *
import os,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"] == 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"] == 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"] == True and not ret == 0):
raise Exception("The underlying bash script returned with the error code {0}.".format(ret))
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