Mercurial > repos > wolma > packaged_annotation_loader

annotate retrieve_meta.py @ 0:36e37b29c1b0 draft default tip

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"planemo upload commit 3dc5291eccd1fb516be67694c18a27bda5f69f91-dirty"
author wolma
date Mon, 20 Dec 2021 10:15:18 +0000
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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import json
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5 import os
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6
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7 import yaml
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8
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9 if __name__ == "__main__":
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10 parser = argparse.ArgumentParser()
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11
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12 parser.add_argument('galaxy_json')
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13 parser.add_argument(
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14 '-o', '--ofile',
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15 required=True
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16 )
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17 parser.add_argument(
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18 '--format', choices=['yaml', 'tab'], default='yaml'
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19 )
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20 args = parser.parse_args()
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21
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22 galaxy_collection_info = json.load(open(args.galaxy_json))
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23 annotation_info = next(iter(galaxy_collection_info.values()))['elements']
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24 selected_ids = {i['name'] for i in annotation_info}
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25 package_meta_file = os.path.join(
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26 os.path.dirname(annotation_info[0]['filename']),
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27 'meta.yml'
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28 )
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29 meta = yaml.safe_load(open(package_meta_file))
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30 meta['records'] = [
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31 rec for rec in meta['records'] if rec['id'] in selected_ids
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32 ]
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33
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34 with open(args.ofile, 'w') as fo:
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35 if args.format == 'yaml':
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36 yaml.dump(
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37 meta, fo, allow_unicode=False, default_flow_style=False
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38 )
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39 else:
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40 print('Annotation\tVersion', file=fo)
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41 for record in meta['records']:
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42 print(record['name'], record['version'], sep='\t', file=fo)