#!/usr/env/bin python3

import sys, re, os, os.path, stat, getpass, shutil

def replaceAll(file, searchExp, replaceExp):
    shutil.move( file, file + "~" )
    destination = open( file, "w" )
    source= open( file + "~", "r" )
    for line in source:
            if searchExp in line:
                line = line.replace(searchExp,replaceExp)
            destination.write( line )
    source.close()
    destination.close()

def chmod_ar(filename):
    if os.path.exists(filename):
            st = os.stat(filename)
            os.chmod(filename, st.st_mode | stat.S_IREAD \
                | stat.S_IRGRP | stat.S_IROTH)
        
def chmod_arx(filename):
    if os.path.exists(filename):
            st = os.stat(filename)
            os.chmod(filename, st.st_mode | stat.S_IEXEC | stat.S_IREAD \
                | stat.S_IXGRP | stat.S_IRGRP | stat.S_IXOTH \
                | stat.S_IROTH)

def grep(pattern, filename):
    results = list()
    
    if os.path.exists(filename):
            file = open(filename, "r")
            for line in file:
                if re.search(pattern, line):
                    results.append(line)
    return results
    
def findbirch(BASE_DIR = '..'):
    grep_res = grep("BirchProps.homedir", os.path.join(BASE_DIR, 'local', 'admin', 'BIRCH.properties'))
    if len(grep_res) > 0:
            BIRCH = grep_res[0].split("=")[1].rstrip("\n\r ")
    else: # Deprecated
            birchdir = open(os.path.join(BASE_DIR, 'local', 'admin', 'birchdir.param'))
            BIRCH = birchdir.readline().rstrip("\n\r ")
            birchdir.close()
    return BIRCH

def birchhome(BIRCH):
    # Make sure that this script doesn't run in BIRCHDEV, which 
    # would clobber the master copy of BIRCH.
    if "BIRCHDEV" in BIRCH:
            print('>>> birchhome.py cannot be run in BIRCHDEV')
            print('>>> Doing so would clobber the master copy of BIRCH')
            sys.exit(1)
    else:
            if os.path.isdir(BIRCH):
                grep_res = grep("BirchProps.minibirch", os.path.join('..', 'local', 'admin', 'BIRCH.properties'))
                
                if len(grep_res) > 0 and grep_res[0].split("=")[1].lower() == "true":
                	FILELIST = [
                		os.path.join(BIRCH, 'admin', "cshrc.source"),
                		os.path.join(BIRCH, 'admin', "profile.source"),
                		os.path.join(BIRCH, 'admin', "add_to_cshrc"),
                		os.path.join(BIRCH, 'admin', "add_to_login"),
                		os.path.join(BIRCH, 'admin', "add_to_profile"),
                		os.path.join(BIRCH, 'admin', "newuser.py"),
                		os.path.join(BIRCH, 'admin', "newuser"),
                		os.path.join(BIRCH, 'dat', 'fasta', 'fastgbs'),
                		os.path.join(BIRCH, 'install-scripts', 'htmldir.param'),
                		os.path.join(BIRCH, 'install-scripts', 'newuser.py'),
                		os.path.join(BIRCH, 'dat', 'fasta', 'fastgbs'), 
                		os.path.join(BIRCH, 'dat', 'XLandscape', 'XLand'),
                		os.path.join(BIRCH, 'admin', 'launchers', 'birch.desktop'),
                		os.path.join(BIRCH, 'admin.uninstall', 'cshrc.source'),
                		os.path.join(BIRCH, 'admin.uninstall', 'profile.source')]
                else:	  
                	FILELIST = [
                		os.path.join(BIRCH, 'admin', 'cshrc.source'),
                		os.path.join(BIRCH, 'admin', 'profile.source'),
                		os.path.join(BIRCH, 'admin', 'add_to_cshrc'),
                		os.path.join(BIRCH, 'admin', 'add_to_login'),
                		os.path.join(BIRCH, 'admin', 'add_to_profile'),
                		os.path.join(BIRCH, 'admin', 'newuser.py'),
                		os.path.join(BIRCH, 'admin', 'newuser'),
                		os.path.join(BIRCH, 'dat', 'fasta', 'fastgbs'),
                		os.path.join(BIRCH, 'install-scripts', 'htmldir.param'),
                		os.path.join(BIRCH, 'install-scripts', 'newuser.py'),
                		os.path.join(BIRCH, 'dat', 'fasta', 'fastgbs'),
                		os.path.join(BIRCH, 'dat', 'XLandscape', 'XLand'),
                		os.path.join(BIRCH, 'admin', 'launchers', 'birch.desktop'),
                		os.path.join(BIRCH, 'admin.uninstall', 'cshrc.source'),
                		os.path.join(BIRCH, 'admin.uninstall', 'profile.source'),
                		os.path.join(BIRCH, 'java', 'ArrayNorm', 'ArrayNorm.lax'),
                	        os.path.join(BIRCH, 'java', 'Jalview', 'Jalview.lax'),
                	        os.path.join(BIRCH, 'java', 'genographer', 'genograph.cfg'),
                	        os.path.join(BIRCH, 'pkg', 'NCBI', '.ncbirc')
                                        ]
                         
                # For reasons I can't fathom, the last element in FILELIST prints the Setting lcoation message 30 times
                # to the output log. I don't know if this is executing 30 times, of if the line is getting echoed
                # 30 times. In any case, the script seems to work. The problem could be in getbirch.jar.                
                for filename in FILELIST:
                    if os.path.isfile(filename):
                        print("Setting location of BIRCH home directory as " + BIRCH + " in " + filename)

                        #replaceAll(os.path.join(BIRCH, filename), '/home/psgendb/BIRCHDEV', BIRCH)
                        #chmod_ar(os.path.join(BIRCH, filename))
                        replaceAll(filename, '/home/psgendb/BIRCHDEV', BIRCH)
                        chmod_ar(filename)

                # special cases - where execute permissions are required
                chmod_arx(os.path.join(BIRCH, 'admin', 'newuser'))
                chmod_arx(os.path.join(BIRCH, 'admin', 'newuser.py'))
                chmod_arx(os.path.join(BIRCH, 'install-birch', 'makelinks.sh'))
                chmod_arx(os.path.join(BIRCH, 'admin', 'launchers', 'birch.desktop'))

                # Make sure that all directories in $BIRCH are world
                # readable and world executable
                chmod_arx(BIRCH)
                for birchdir in ['admin','dat','doc','GenBank','install-scripts','java','labace','local','manl','pkg','python','public_html','script','tutorials']:
                    bdir = os.path.join(BIRCH,birchdir)
                    if (not os.path.islink(bdir)) and os.path.isdir(bdir) :
                        if os.access(bdir,os.W_OK) :
                            chmod_arx(bdir)
                
                # Set the userid of the birchdb database administrator
                stdwrm = os.path.join(BIRCH, 'public_html', 'birchdb', 'wspec', 'passwd.wrm')
                if os.path.exists(stdwrm):
                	replaceAll(stdwrm, 'psgendb', getpass.getuser())
                	chmod_ar(stdwrm)
                
                # Set the userid of the local birchdb database administrator
                lworm = os.path.join(BIRCH, 'public_html', 'local', 'birchdb', 'wspec', 'passwd.wrm')
                if os.path.exists(lworm):
                	replaceAll(lworm, 'psgendb', getpass.getuser())
                	chmod_ar(lworm)
            else:
                print("No such directory: " + BIRCH + ". Exiting")
                sys.exit(1)

if __name__=="__main__":
    birchhome(findbirch())