R3127/python/BlackDynamite/bashCoat.py
6562c0ce3860features/zeo

bashCoat.py
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			#!/usr/bin/env python

			import run
			import os,stat
			import subprocess
			import re
			import socket


			admissible_params = {"stdout":None}
			#default_params = {}
			help = {"stdout":"Specify if you want the standard output instead of a file"}


			def launch(run, params):

			_exec = run.getExecFile()
			head = \
			"""#!/bin/bash
			export BLACKDYNAMITE_HOST=__BLACKDYNAMITE__dbhost__
			export BLACKDYNAMITE_SCHEMA=__BLACKDYNAMITE__study__
			export BLACKDYNAMITE_RUN_ID=__BLACKDYNAMITE__run_id__
			export BLACKDYNAMITE_USER=$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"]):
			run["state"] = "launched"
			run.update()
			run.commit()
			filename = run["run_name"] + ".o" + str(run.id)
			filename_err = run["run_name"] + ".e" + str(run.id)
			with open(filename, "w") as outfile:
			with open(filename_err, "w") as errfile:
			ret = subprocess.call("./" + _exec["filename"], stdout=outfile, stderr=errfile)