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67 lines
2.7 KiB
Python
67 lines
2.7 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, sys
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from ConfigParser import ConfigParser
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from optparse import OptionParser
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default_config = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', 'universe_wsgi.ini') )
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parser = OptionParser()
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parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.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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os.chdir( os.path.dirname( options.config ) )
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sys.path.append( 'lib' )
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from galaxy import eggs
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import pkg_resources
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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( os.path.basename( options.config ) )
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from galaxy.web import security
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from galaxy.model import mapping
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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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