mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Nicola Soranzo
9d74bba7fb
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
52 lines
1.9 KiB
Python
52 lines
1.9 KiB
Python
#!/usr/bin/env python
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"""
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A command line helper for common operations performed by Galaxy maintainers.
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Encodes and decodes IDs, returns Dataset IDs if provided an HDA or LDDA id,
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returns the disk path of a dataset.
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"""
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import argparse
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import os
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import sys
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sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, 'lib'))
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import galaxy.config
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from galaxy.security import idencoding
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from galaxy.util.script import app_properties_from_args, populate_config_args
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parser = argparse.ArgumentParser()
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populate_config_args(parser)
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parser.add_argument('-e', '--encode-id', dest='encode_id', help='Encode an ID')
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parser.add_argument('-d', '--decode-id', dest='decode_id', help='Decode an ID')
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parser.add_argument('--hda', dest='hda_id', help='Display HistoryDatasetAssociation info')
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parser.add_argument('--ldda', dest='ldda_id', help='Display LibraryDatasetDatasetAssociation info')
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args = parser.parse_args()
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app_properties = app_properties_from_args(args)
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config = galaxy.config.Configuration(**app_properties)
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helper = idencoding.IdEncodingHelper(id_secret=app_properties.get('id_secret'))
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model = galaxy.config.init_models_from_config(config)
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if args.encode_id:
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print('Encoded "{}": {}'.format(args.encode_id, helper.encode_id(args.encode_id)))
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if args.decode_id:
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print('Decoded "{}": {}'.format(args.decode_id, helper.decode_id(args.decode_id)))
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if args.hda_id:
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try:
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hda_id = int(args.hda_id)
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except Exception:
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hda_id = int(helper.decode_id(args.hda_id))
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hda = model.context.current.query(model.HistoryDatasetAssociation).get(hda_id)
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print(f'HDA "{hda.id}" is Dataset "{hda.dataset.id}" at: {hda.file_name}')
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if args.ldda_id:
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try:
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ldda_id = int(args.ldda_id)
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except Exception:
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ldda_id = int(helper.decode_id(args.ldda_id))
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ldda = model.context.current.query(model.HistoryDatasetAssociation).get(ldda_id)
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print(f'LDDA "{ldda.id}" is Dataset "{ldda.dataset.id}" at: {ldda.file_name}')
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