Mercurial > repos > devteam > data_manager_build_kraken_database

annotate data_manager/make_json.py @ 2:065d8a4d74f4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:06:46 -0400
parents c3276afba416
children 0a9ff888a4e2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
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
0
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
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
parents:
diff changeset
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
parents:
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
parents:
diff changeset
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
parents:
diff changeset
6
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
18 shutil.move(os.path.join(output_path, filename), 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
parents:
diff changeset
19 file(args.output, 'w').write(json.dumps(data_manager_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
parents:
diff changeset
20
2
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
21
0
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
22 if __name__ == '__main__':
2
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
23 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
24 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
25 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
26 args = parser.parse_args()
0
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
27 main(args)