mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 00:12:08 +08:00
138 lines
3.8 KiB
Python
138 lines
3.8 KiB
Python
# 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)
|
|
from __future__ import print_function
|
|
|
|
import os
|
|
import re
|
|
import subprocess
|
|
import sys
|
|
from subprocess import PIPE, Popen
|
|
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 is None:
|
|
print("No output file specified.")
|
|
return -1
|
|
|
|
inputfile = opts.get("-i")
|
|
if inputfile is None:
|
|
print("No input file specified.")
|
|
return -2
|
|
|
|
invert = opts.get("-v")
|
|
if invert is None:
|
|
print("Match style (Invert or normal) not specified.")
|
|
return -3
|
|
|
|
pattern = opts.get("-pattern")
|
|
if pattern is 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)
|
|
|
|
# match filename and invert flag
|
|
fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$")
|
|
invertRegEx = re.compile("(true)|(false)")
|
|
|
|
# verify that filename and inversion flag are in the correct format
|
|
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)
|
|
|
|
# set version flag
|
|
versionflag = "-P"
|
|
|
|
# MacOS 10.8.2 does not support -P option for perl-regex anymore
|
|
versionmatch = Popen("grep -V | grep 'BSD'", shell=True, stdout=PIPE).communicate()[0]
|
|
if versionmatch:
|
|
versionflag = "-E"
|
|
|
|
# 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 %s %s -f %s %s > %s" % ( versionflag, invertflag, pattern_file_name, inputfile, outputfile )
|
|
|
|
# run grep
|
|
errorcode = subprocess.call(commandline, shell=True)
|
|
|
|
# remove temp pattern file
|
|
os.unlink( pattern_file_name )
|
|
|
|
# return error code
|
|
return errorcode
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|