Mercurial > repos > thanhlv > data_manager_build_ariba_database

annotate data_manager/ariba_database_builder.py @ 0:a8bb47cc7625 draft

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planemo upload for repository tbd commit 0af229dbbda0496819ca95938c2e0628db689134
author thanhlv
date Tue, 08 Jan 2019 11:04:25 -0500
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children b13f7ba85697
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a8bb47cc7625 planemo upload for repository tbd commit 0af229dbbda0496819ca95938c2e0628db689134
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1 # Thanh Le Viet
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2 # 7-Jan-2019
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3
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4 import argparse
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5 import json
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6 import os
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7 import shutil
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8
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10 def main(args):
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11 output_path = os.getcwd()
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12 db_folder = [d for d in os.listdir(output_path) if os.path.isdir(d)]
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13 params = json.loads(open(args.output).read())
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14 target_directory = params['output_data'][0]['extra_files_path']
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15 os.mkdir(target_directory)
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16 data_manager_entry = []
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17 for db in db_folder:
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18 # print("Current: ".format(os.path.join(output_path, d)))
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19 # print("Target: {}".format(target_directory))
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20 shutil.move(os.path.join(output_path, d), os.path.join(target_directory, d))
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21 data_manager_entry.append(dict(value=db.lower(),
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22 name=db,
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23 path=target_directory)
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24 )
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25 data_manager_json = dict(data_tables=dict(ariba_databases=data_manager_entry))
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26 file(args.output, 'w').write(json.dumps(data_manager_json))
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29 if __name__ == '__main__':
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30 parser = argparse.ArgumentParser(description='Create data manager json.')
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31 parser.add_argument('--out', dest='output', action='store', help='JSON filename')
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32 args = parser.parse_args()
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33 main(args)