#!/usr/bin/env python3 #optparse is deprecated in favor of argparse as of Python 2.7. However, # since 2.7 is not always present on many systems, at this writing, # it is safer to stick with optparse for now. It should be easy # to change later, since the syntax is very similar between argparse and optparse. from optparse import OptionParser import os import os.path import stat import subprocess import sys import re import shutil ''' BIRCHUserSettings.py - Set environment variables for BioLegato Helper Applications Synopsis: BIRCHUserSettings.py --setvar variable_name=value @modified: July 5, 2020 @author: Brian Fristensky @contact: frist@cc.umanitoba.ca ''' blib = os.environ.get("BIRCHPYLIB") HOMEDIR = os.environ.get("HOME") sys.path.append(blib) from birchlib import Birchmod PROGRAM = "BIRCHUserSettings.py : " USAGE = "\n\t\tBIRCHUserSettings.py --setvar variable_name=value" DEBUG = True if DEBUG : print('Debugging mode on') BM = Birchmod(PROGRAM, USAGE) BIRCHvariables = ["BIRCH_PROMPT","BL_EMAIL","NCBI_ENTREZ_KEY"] # - - - - - - - - - - - - - Utility classes - - - - - - - - - - - - - - - - - def chmod_rw(filename): if os.path.exists(filename): st = os.stat(filename) os.chmod(filename, stat.S_IRUSR | stat.S_IWUSR) def chmod_rwx(filename): if os.path.exists(filename): st = os.stat(filename) os.chmod(filename, stat.S_IRWXU) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - class Parameters: """ Wrapper class for command line parameters """ def __init__(self): """ Initializes arguments: SETVAR = False VSTRING = "" VNAME = "" VALUE = "" SFN= "" Then calls read_args() to fill in their values from command line """ self.SETVAR = False self.VSTRING = "" self.VNAME = "" self.VALUE = "" self.read_args() self.SFN = os.path.join(HOMEDIR , '.config' , 'BIRCH' , 'BIRCHsettings.source') if DEBUG : print('------------ Parameters from command line ------') print(' SETVAR: ' + str(self.SETVAR)) print(' VNAME: ' + self.VNAME) print(' VALUE: ' + self.VALUE) print(' Settings file: ' + self.SFN) print() def read_args(self): """ Read command line arguments into a Parameter object """ parser = OptionParser() parser.add_option("--setvar", dest="vstring", action="store", default="", help="set an environment variable to the specified value") (options, args) = parser.parse_args() self.VSTRING = options.vstring if self.VSTRING != "" : self.SETVAR = True tokens = self.VSTRING.split("=") self.VNAME = tokens[0] self.VALUE = tokens[1] # - - - - - - - - - - Make sure that the user's config directory exists - - - - - - def CheckConfigDir(): OKAY=True configpath=os.path.join(HOMEDIR,".config") configBIRCHpath=os.path.join(HOMEDIR,".config","BIRCH") #try : if not os.path.exists(configpath) : os.mkdir(configpath) chmod_rwx(configBIRCHpath) if not os.path.exists(configBIRCHpath) : os.mkdir(configBIRCHpath) chmod_rwx(configBIRCHpath) #except : # print("BIRCHUserSettings.py: Couldn't create " + configBIRCHpath) # OKAY = False return OKAY # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - class BIRCHUserSettings: """ Data and methods for the BIRCH Settings file. """ def __init__(self,P): """ Initializes arguments: dict = {} """ self.dict = {} for var in BIRCHvariables: self.dict[var] = "" if os.path.exists(P.SFN) : self.ReadBIRCHUserSettings(P.SFN) #else: # DFN = os.path.join(self.BIRCH , 'admin' , 'BIRCH.settings.default') # self.ReadBIRCHUserSettings(DFN) if DEBUG : print('- - - - - BIRCH Settings - - - - -') for k in self.dict : print(' ' + k + ',' + self.dict[k]) def ReadBIRCHUserSettings(self,FN): """ Read current values of BIRCHvariables from BIRCH.settings. """ if os.path.exists(FN) : Sfile = open(FN,'r') for line in Sfile : line = line.strip() # ignore blank lines and comment lines if (line != "" and line[0] != '#') : print(line) tokens = line.split("=") if tokens[0] in BIRCHvariables : self.dict[tokens[0]] = tokens[1] Sfile.close() def WriteBIRCHUserSettings(self,SFN): """ Write current values of BIRCHvariables to $HOME/.config/BIRCH/BIRCHsettings.source file. """ Sfile = open(SFN,'w') Sfile.write('#!/bin/bash\n') Sfile.write('# DO NOT EDIT THIS FILE!\n') Sfile.write('# This file is automatically generated by BIRCHUserSettings.py \n') # Write a bash statement setting each variable. Build an export line as we go # Because these parameters are designed to override system parametera, # we only write those variables that are non-blank. ExLine = "export " for k in self.dict : if not self.dict[k] == "" : Sfile.write(k + '=' + self.dict[k] + '\n') ExLine = ExLine + " " + k # Write a bash statement exporting each variable to the shell Sfile.write(ExLine) Sfile.write("\n") Sfile.close() os.chmod(SFN, 0o700) #======================== MAIN PROCEDURE ========================== def main(): """ Called when not in documentation mode. """ # Read parameters from command line P = Parameters() if CheckConfigDir() : Settings = BIRCHUserSettings(P) if P.SETVAR: print("Setvar") if P.VNAME in BIRCHvariables: Settings.dict[P.VNAME] = P.VALUE Settings.WriteBIRCHUserSettings(P.SFN) else: print(USAGE) BM.exit_success() if (BM.documentor() or "-test" in sys.argv): pass else: main()