Mercurial > repos > devteam > data_manager_build_kraken_database

annotate data_manager/make_json.py @ 9:c668a45d8a55 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 02d5f5241444bf471d3f89a6e0aeb4d9f4075811"
author iuc
date Tue, 18 Aug 2020 15:35:38 +0000
parents 1d616842e1db
children 1e701a731d48
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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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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 output_path = os.path.join(os.getcwd(), 'kraken-database')
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17 for filename in os.listdir(output_path):
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18 shutil.move(os.path.join(output_path, filename), target_directory)
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1d616842e1db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8b77954efb8d46dfb3bec5421819076f3757ad06"
iuc
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19 with open(args.output, 'w') as out:
1d616842e1db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8b77954efb8d46dfb3bec5421819076f3757ad06"
iuc
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20 out.write(json.dumps(data_manager_json, 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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22
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23 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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24 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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25 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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26 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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27 args = parser.parse_args()
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28 main(args)