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annotate lemuriformes/issubset.py @ 18:56596902e9ae default tip

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add some setup + tests
author Jeff Hammel <k0scist@gmail.com>
date Sun, 10 Dec 2017 17:57:03 -0800
parents 0d1b8bb1d97b
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 determine if one CSV column is a subsset of another.
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6 If it is a subset, output nothing and exit 0.
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7 If it is not a subset, output all elements that are
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8 in the asserted subset but not the total set
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9 and exits 1.
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10 Exits 2 on error.
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11 """
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12
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13 import os
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14 import sys
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15 from collections import OrderedDict
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16 from .cli import ConfigurationParser
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17 from .uniques import uniques
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18
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19 def main(args=sys.argv[1:]):
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20 """CLI"""
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21
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22 sets = OrderedDict([('subset', "the `PATH` to the CSV and `COLUMN` of the asserted subset"),
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23 ('total', "the `PATH` to the CSV and `COLUMN` of the total set")])
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24
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25 # parse command line
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26 parser = ConfigurationParser(description=__doc__)
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27 for key, description in sets.items():
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28 parser.add_argument(key, nargs=2,
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29 help=description)
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30 options = parser.parse_args(args)
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31
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32 # sanity
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33 filenames = set()
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34 for key in sets.keys():
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35 # - ensure the values are listw
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36 setattr(options, key, list(getattr(options, key)))
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37 value = getattr(options, key)
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38 # - make files absolute
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39 value[0] = os.path.realpath(value[0])
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40 # - ensure files exist
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41 filename = value[0]
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42 if not os.path.isfile(filename):
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43 parser.error("Not a file: {}".format(filename))
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44 filenames.add(filename)
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45
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46 # read the files
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47 columns = {filename: uniques(filename)
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48 for filename in filenames}
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49
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50 # assert that the columns are in the files they have been ascribed to
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51 for key in sets.keys():
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52 filename, column = getattr(options, key)
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53 if column not in columns[filename]:
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54 parser.error("Column '{}' not found in file '{}'".format(column, filename))
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55
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56 # calculate the difference
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57 difference = columns[options.subset[0]][options.subset[1]].difference(
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58 columns[options.total[0]][options.total[1]])
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59 if not difference:
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60 return
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61 print ("\n".join([str(i) for i in sorted(difference)]))
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62 sys.exit(1)
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63
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64
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65 if __name__ == '__main__':
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66 main()