mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Nicola Soranzo
a353b2e88f
using: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 . ```
64 lines
2.5 KiB
Python
64 lines
2.5 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 os
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import sys
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from ConfigParser import ConfigParser
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from optparse import OptionParser
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sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, 'lib'))
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from galaxy.model import mapping
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from galaxy.web import security
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default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'config/galaxy.ini'))
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parser = OptionParser()
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parser.add_option('-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default=default_config)
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parser.add_option('-e', '--encode-id', dest='encode_id', help='Encode an ID')
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parser.add_option('-d', '--decode-id', dest='decode_id', help='Decode an ID')
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parser.add_option('--hda', dest='hda_id', help='Display HistoryDatasetAssociation info')
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parser.add_option('--ldda', dest='ldda_id', help='Display LibraryDatasetDatasetAssociation info')
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(options, args) = parser.parse_args()
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try:
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assert options.encode_id or options.decode_id or options.hda_id or options.ldda_id
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except:
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parser.print_help()
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sys.exit(1)
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options.config = os.path.abspath(options.config)
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config = ConfigParser(dict(file_path='database/files',
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id_secret='USING THE DEFAULT IS NOT SECURE!',
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database_connection='sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE'))
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config.read(options.config)
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helper = security.SecurityHelper(id_secret=config.get('app:main', 'id_secret'))
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model = mapping.init(config.get('app:main', 'file_path'), config.get('app:main', 'database_connection'), create_tables=False)
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if options.encode_id:
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print 'Encoded "%s": %s' % (options.encode_id, helper.encode_id(options.encode_id))
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if options.decode_id:
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print 'Decoded "%s": %s' % (options.decode_id, helper.decode_id(options.decode_id))
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if options.hda_id:
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try:
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hda_id = int(options.hda_id)
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except:
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hda_id = int(helper.decode_id(options.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 options.ldda_id:
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try:
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ldda_id = int(options.ldda_id)
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except:
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ldda_id = int(helper.decode_id(options.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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