root/galaxy-central/tools/filters/grep.py

# Filename: grep.py
# Author: Ian N. Schenck
# Version: 8/23/2005
#
# This script accepts regular expressions, as well as an "invert"
# option, and applies the regular expression using grep.  This wrapper
# provides security and pipeline.
#
# Grep is launched based on these inputs:
# -i            Input file
# -o            Output file
# -pattern      RegEx pattern
# -v            true or false (output NON-matching lines)

import sys
import os
import re
import string
import commands
from tempfile import NamedTemporaryFile

# This function is exceedingly useful, perhaps package for reuse?
def getopts(argv):
    opts = {}
    while argv:
        if argv[0][0] == '-':
            opts[argv[0]] = argv[1]
            argv = argv[2:]
        else:
            argv = argv[1:]
    return opts

def main():
    args = sys.argv[1:]

    try:
        opts = getopts(args)
    except IndexError:
        print "Usage:"
        print " -i              Input file"
        print " -o              Output file"
        print " -pattern        RegEx pattern"
        print " -v              true or false (Invert match)"
        return 0

    outputfile = opts.get("-o")
    if outputfile == None:
        print "No output file specified."
        return -1
    
    inputfile = opts.get("-i")
    if inputfile == None:
        print "No input file specified."
        return -2

    invert = opts.get("-v")
    if invert == None:
        print "Match style (Invert or normal) not specified."
        return -3

    pattern = opts.get("-pattern")
    if pattern == None:
        print "RegEx pattern not specified."
        return -4

    # All inputs have been specified at this point, now validate.

    # replace if input has been escaped, remove sq
    # characters that are allowed but need to be escaped
    mapped_chars = { '>' :'__gt__', 
                 '<' :'__lt__', 
                 '\'' :'__sq__',
                 '"' :'__dq__',
                 '[' :'__ob__',
                 ']' :'__cb__',
                 '{' :'__oc__',
                 '}' :'__cc__'
                 }
    
    #with new sanitizing we only need to replace for single quote, but this needs to remain for backwards compatibility
    for key, value in mapped_chars.items():
        pattern = pattern.replace(value, key)
    
    fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$") #why?
    invertRegEx = re.compile("(true)|(false)") #why?

    if not fileRegEx.match(outputfile):
        print "Illegal output filename."
        return -5
    if not fileRegEx.match(inputfile):
        print "Illegal input filename."
        return -6
    if not invertRegEx.match(invert):
        print "Illegal invert option."
        return -7

    # invert grep search?
    if invert == "true":
        invertflag = " -v"
        print "Not matching pattern: %s" % pattern
    else:
        invertflag = ""
        print "Matching pattern: %s" % pattern
    
    #Create temp file holding pattern
    #By using a file to hold the pattern, we don't have worry about sanitizing grep commandline and can include single quotes in pattern
    pattern_file_name = NamedTemporaryFile().name
    open( pattern_file_name, 'w' ).write( pattern )
    
    #generate grep command
    commandline = "grep -E %s -f %s %s > %s" % ( invertflag, pattern_file_name, inputfile, outputfile )
    
    #run grep
    errorcode, stdout = commands.getstatusoutput(commandline)
    
    #remove temp pattern file
    os.unlink( pattern_file_name )
    
    #return error code
    return errorcode

if __name__ == "__main__":
    main()