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#!/usr/bin/env python
import argparse
import shutil
import json
import sys
replacements = {
'tree_file': 'tree',
'phylo_model_file': 'phylo_model',
}
def main(args):
parser = argparse.ArgumentParser()
parser.add_argument('infile', metavar='CONTENTS.json',
type=argparse.FileType('rb+'))
args = parser.parse_args(args)
shutil.copyfile(args.infile.name, args.infile.name + '.bak')
contents = json.load(args.infile)
for key in ['files', 'md5']:
records = contents[key]
for repl_in, repl_out in replacements.iteritems():
if repl_in not in records:
continue
records[repl_out] = records.pop(repl_in)
contents.setdefault('metadata', {})['format_version'] = '1.1'
args.infile.seek(0)
args.infile.truncate()
json.dump(contents, args.infile, indent=2)
if __name__ == '__main__':
main(sys.argv[1:])
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