Mercurial > repos > devteam > data_manager_build_kraken_database

annotate data_manager/make_json.py @ 5:0a9ff888a4e2 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 11:36:13 -0400 (2020-08-18)
parents 065d8a4d74f4
children 889a857303e0
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065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
1 import argparse
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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2 import json
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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3 import os
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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diff changeset
4 import shutil
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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5
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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7 def main(args):
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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8 data_manager_entry = {}
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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9 data_manager_entry['value'] = args.database.lower()
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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10 data_manager_entry['name'] = args.database
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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11 data_manager_entry['path'] = '.'
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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12 data_manager_json = dict(data_tables=dict(kraken_databases=data_manager_entry))
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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13 params = json.loads(open(args.output).read())
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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14 target_directory = params['output_data'][0]['extra_files_path']
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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15 os.mkdir(target_directory)
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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16 output_path = os.path.join(os.getcwd(), 'kraken-database')
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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17 for filename in os.listdir(output_path):
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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18 shutil.move(os.path.join(output_path, filename), target_directory)
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0a9ff888a4e2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d5f5241444bf471d3f89a6e0aeb4d9f4075811"
iuc
parents: 2
diff changeset
19 with open(args.output, 'w') as out:
0a9ff888a4e2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d5f5241444bf471d3f89a6e0aeb4d9f4075811"
iuc
parents: 2
diff changeset
20 out.write(json.dumps(data_manager_json, sort_keys=True))
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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065d8a4d74f4 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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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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23 if __name__ == '__main__':
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065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
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24 parser = argparse.ArgumentParser(description='Create data manager json.')
065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
25 parser.add_argument('--db', dest='database', action='store', help='Database name')
065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
26 parser.add_argument('--out', dest='output', action='store', help='JSON filename')
065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
27 args = parser.parse_args()
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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28 main(args)