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Yakubov, Sergey
56 lines
2.0 KiB
Python
56 lines
2.0 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.model.mapping import init_models_from_config
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from galaxy.security import idencoding
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from galaxy.util.script import (
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app_properties_from_args,
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populate_config_args,
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)
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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 = init_models_from_config(config)
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if args.encode_id:
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print(f'Encoded "{args.encode_id}": {helper.encode_id(args.encode_id)}')
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if args.decode_id:
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print(f'Decoded "{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.session.get(model.HistoryDatasetAssociation, hda_id)
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print(f'HDA "{hda.id}" is Dataset "{hda.dataset.id}" at: {hda.get_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.session.get(model.LibraryDatasetDatasetAssociation, ldda_id)
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print(f'LDDA "{ldda.id}" is Dataset "{ldda.dataset.id}" at: {ldda.get_file_name()}')
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