annotate numerics/check.py @ 164:c16940bd2cee

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author Jeff Hammel <k0scist@gmail.com>
date Fri, 15 May 2015 16:59:09 -0700
parents a929d14c0701
children
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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3
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4 """
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5 data integrity checking
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6 """
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8 # imports
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9 import argparse
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10 import os
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11 import subprocess
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12 import sys
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14 # module globals
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15 __all__ = ['main', 'CheckParser']
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16 string = (str, unicode)
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18 class NumberOfColumnsException(Exception):
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19 """wrong number of columns"""
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21 def check_column_lengths(*rows):
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22 """ensure all column lengths are the same and return number"""
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23 lengths = set([len(row) for row in rows])
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24 if len(lengths) > 1:
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25 raise NumberOfColumnsException("Multiple numbers of columns: {}".format(', '.join(lengths)))
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26 return lengths.pop()
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29 class CheckParser(argparse.ArgumentParser):
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30 """CLI option parser"""
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31 def __init__(self, **kwargs):
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32 kwargs.setdefault('description', __doc__)
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33 argparse.ArgumentParser.__init__(self, **kwargs)
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34 self.options = None
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35
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36 def parse_args(self, *args, **kw):
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37 options = argparse.ArgumentParser.parse_args(self, *args, **kw)
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38 self.validate(options)
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39 self.options = options
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40 return options
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42 def validate(self, options):
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43 """validate options"""
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44
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45 def main(args=sys.argv[1:]):
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46 """CLI"""
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47
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48 # parse command line options
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49 parser = Parser()
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50 options = parser.parse_args(args)
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51
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52 if __name__ == '__main__':
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53 main()
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