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https://github.com/galaxyproject/galaxy.git
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Daniel Blankenberg
f92b25d2f5
Sanitization now occurs as part of the InputValueWrapper logic. Previously sanitization occurred as soon as parameter values were provided by the user via form submits, causing the sanitized values to be stored in the database. Now the original user specified values are stored in the database and sanitation happens when str is called on the InputValueWrapper, i.e. during command-line generation and when generating configfiles. Abstract out param name and value translations that are performed on data source tools. This changes some of the names of the tags used for these purposes (e.g. data_type_translation becomes value_translation) to reflect this generalization. The ToolConfigSyntax wiki page has been updated with these changes. Future Enhancement: Allow methods with arguments and keywords to be specified for sanitation and translation purposes.
124 lines
3.2 KiB
Python
124 lines
3.2 KiB
Python
# Filename: grep.py
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# Author: Ian N. Schenck
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# Version: 8/23/2005
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#
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# This script accepts regular expressions, as well as an "invert"
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# option, and applies the regular expression using grep. This wrapper
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# provides security and pipeline.
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#
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# Grep is launched based on these inputs:
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# -i Input file
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# -o Output file
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# -pattern RegEx pattern
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# -v true or false (output NON-matching lines)
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import sys
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import os
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import re
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import string
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import commands
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from tempfile import NamedTemporaryFile
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# This function is exceedingly useful, perhaps package for reuse?
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def getopts(argv):
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opts = {}
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while argv:
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if argv[0][0] == '-':
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opts[argv[0]] = argv[1]
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argv = argv[2:]
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else:
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argv = argv[1:]
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return opts
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def main():
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args = sys.argv[1:]
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try:
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opts = getopts(args)
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except IndexError:
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print "Usage:"
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print " -i Input file"
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print " -o Output file"
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print " -pattern RegEx pattern"
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print " -v true or false (Invert match)"
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return 0
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outputfile = opts.get("-o")
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if outputfile == None:
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print "No output file specified."
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return -1
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inputfile = opts.get("-i")
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if inputfile == None:
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print "No input file specified."
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return -2
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invert = opts.get("-v")
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if invert == None:
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print "Match style (Invert or normal) not specified."
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return -3
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pattern = opts.get("-pattern")
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if pattern == None:
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print "RegEx pattern not specified."
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return -4
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# All inputs have been specified at this point, now validate.
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# replace if input has been escaped, remove sq
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# characters that are allowed but need to be escaped
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mapped_chars = { '>' :'__gt__',
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'<' :'__lt__',
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'\'' :'__sq__',
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'"' :'__dq__',
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'[' :'__ob__',
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']' :'__cb__',
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'{' :'__oc__',
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'}' :'__cc__'
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}
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#with new sanitizing we only need to replace for single quote, but this needs to remain for backwards compatibility
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for key, value in mapped_chars.items():
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pattern = pattern.replace(value, key)
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fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$") #why?
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invertRegEx = re.compile("(true)|(false)") #why?
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if not fileRegEx.match(outputfile):
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print "Illegal output filename."
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return -5
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if not fileRegEx.match(inputfile):
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print "Illegal input filename."
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return -6
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if not invertRegEx.match(invert):
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print "Illegal invert option."
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return -7
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# invert grep search?
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if invert == "true":
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invertflag = " -v"
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print "Not matching pattern: %s" % pattern
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else:
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invertflag = ""
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print "Matching pattern: %s" % pattern
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#Create temp file holding pattern
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#By using a file to hold the pattern, we don't have worry about sanitizing grep commandline and can include single quotes in pattern
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pattern_file_name = NamedTemporaryFile().name
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open( pattern_file_name, 'w' ).write( pattern )
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#generate grep command
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commandline = "grep -E %s -f %s %s > %s" % ( invertflag, pattern_file_name, inputfile, outputfile )
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#run grep
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errorcode, stdout = commands.getstatusoutput(commandline)
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#remove temp pattern file
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os.unlink( pattern_file_name )
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#return error code
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return errorcode
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if __name__ == "__main__":
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main()
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