65 lines
2.4 KiB
Python
65 lines
2.4 KiB
Python
'''
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Created on 23 sept. 2010
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@author: coissac
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'''
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import psycopg2
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from obitools.ecobarcode.taxonomy import EcoTaxonomyDB
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def addEcoBarcodeDBOption(optionManager):
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optionManager.add_option('--dbname',
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action="store", dest="ecobarcodedb",
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type='str',
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default=None,
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help="Specify the name of the ecobarcode database")
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optionManager.add_option('--server',
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action="store", dest="dbserver",
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type='str',
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default="localhost",
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help="Specify the adress of the ecobarcode database server")
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optionManager.add_option('--user',
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action="store", dest="dbuser",
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type='str',
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default='postgres',
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help="Specify the user of the ecobarcode database")
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optionManager.add_option('--port',
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action="store", dest="dbport",
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type='str',
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default=5432,
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help="Specify the port of the ecobarcode database")
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optionManager.add_option('--passwd',
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action="store", dest="dbpasswd",
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type='str',
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default='',
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help="Specify the passwd of the ecobarcode database")
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optionManager.add_option('--primer',
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action="store", dest="primer",
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type='str',
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default=None,
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help="Specify the primer used for amplification")
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def ecobarcodeDatabaseConnection(options):
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if options.ecobarcodedb is not None:
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connection = psycopg2.connect(database=options.ecobarcodedb,
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user=options.dbuser,
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password=options.dbpasswd,
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host=options.dbserver,
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port=options.dbport)
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options.dbname=options.ecobarcodedb
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else:
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connection=None
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if connection is not None:
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options.ecobarcodedb=connection
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taxonomy = EcoTaxonomyDB(connection)
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else:
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taxonomy=None
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return taxonomy
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