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53 lines
2.0 KiB
Python
53 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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from __future__ import print_function
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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.util.script import app_properties_from_args, populate_config_args
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from galaxy.web import security
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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 = security.SecurityHelper(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 "%s": %s' % (args.encode_id, helper.encode_id(args.encode_id)))
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if args.decode_id:
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print('Decoded "%s": %s' % (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('HDA "%s" is Dataset "%s" at: %s' % (hda.id, hda.dataset.id, 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('LDDA "%s" is Dataset "%s" at: %s' % (ldda.id, ldda.dataset.id, ldda.file_name))
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