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https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
John Chilton
79c8f59341
Shared across Tool Shed and Galaxy to reduce code duplication. Previously this was just a bunch, making it a real class allows placing some shared logic in there. This refactoring also eliminates some global variables galaxy.model.mapping.Session, galaxy.model.mapping.context, and same for tool shed. This may break things, but these are things that should probably be fixed anyway. In particular small changes to db_shell.py and a unit test that depended on these global variables have been updated. The functional test frameworks likewise needed to be updated to not depend on these - these changes were more substantial. To fix these functional tests, I essentially replace old references to global variables in Galaxy with references to global variables just defined in the test framework in test/functional/database_contexts.py (a slight improvement).
39 lines
1.1 KiB
Python
39 lines
1.1 KiB
Python
# This script allows easy access to Galaxy's database layer via the
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# Galaxy models. For example:
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# % python -i scripts/db_shell.py
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# >>> new_user = User("admin@gmail.com")
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# >>> new_user.set_password
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# >>> sa_session.add(new_user)
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# >>> sa_session.commit()
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# >>> sa_session.query(User).all()
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#
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# You can also use this script as a library, for instance see https://gist.github.com/1979583
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# TODO: This script overlaps a lot with manage_db.py and create_db.py,
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# these should maybe be refactored to remove duplication.
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import sys
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import os.path
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db_shell_path = __file__
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new_path = [ os.path.join( os.path.dirname( db_shell_path ), os.path.pardir, "lib" ) ]
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new_path.extend( sys.path[1:] ) # remove scripts/ from the path
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sys.path = new_path
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from galaxy.model.orm.scripts import get_config
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from galaxy import eggs
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eggs.require( "decorator" )
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eggs.require( "Tempita" )
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eggs.require( "SQLAlchemy" )
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db_url = get_config( sys.argv )['db_url']
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# Setup DB scripting environment
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from sqlalchemy import *
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from sqlalchemy.orm import *
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from sqlalchemy.exc import *
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from galaxy.model.mapping import init
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sa_session = init( '/tmp/', db_url ).context
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from galaxy.model import *
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