Mercurial > repos > devteam > data_manager_build_kraken_database

annotate data_manager/make_json.py @ 10:1e701a731d48 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:41:47 +0000
parents 1d616842e1db
children
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6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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1 import argparse
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2 import json
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3 import os
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4 import shutil
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7 def main(args):
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8 data_manager_entry = {}
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9 data_manager_entry['value'] = args.database.lower()
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10 data_manager_entry['name'] = args.database
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11 data_manager_entry['path'] = '.'
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12 data_manager_json = dict(data_tables=dict(kraken_databases=data_manager_entry))
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1e701a731d48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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13 with open(args.output) as fh:
1e701a731d48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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14 params = json.load(fh)
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15 target_directory = params['output_data'][0]['extra_files_path']
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16 os.mkdir(target_directory)
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17 output_path = os.path.join(os.getcwd(), 'kraken-database')
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18 for filename in os.listdir(output_path):
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19 shutil.move(os.path.join(output_path, filename), target_directory)
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1e701a731d48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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20 with open(args.output, 'w') as fh:
1e701a731d48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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21 json.dump(data_manager_json, fh, sort_keys=True)
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6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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23
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24 if __name__ == '__main__':
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6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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25 parser = argparse.ArgumentParser(description='Create data manager json.')
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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26 parser.add_argument('--db', dest='database', action='store', help='Database name')
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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27 parser.add_argument('--out', dest='output', action='store', help='JSON filename')
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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28 args = parser.parse_args()
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29 main(args)