/lib/galaxy/model/migrate/check.py

  1import os.path, logging
  2
  3from galaxy import eggs
  4
  5import pkg_resources
  6pkg_resources.require( "sqlalchemy-migrate" )
  7
  8from migrate.versioning import repository, schema
  9from sqlalchemy import *
 10from sqlalchemy.exceptions import NoSuchTableError
 11
 12log = logging.getLogger( __name__ )
 13
 14# path relative to galaxy
 15migrate_repository_directory = os.path.dirname( __file__ ).replace( os.getcwd() + os.path.sep, '', 1 )
 16migrate_repository = repository.Repository( migrate_repository_directory )
 17dialect_to_egg = { 
 18    "sqlite" : "pysqlite>=2",
 19    "postgres" : "psycopg2",
 20    "mysql" : "MySQL_python"
 21}
 22
 23def create_or_verify_database( url, engine_options={} ):
 24    """
 25    Check that the database is use-able, possibly creating it if empty (this is
 26    the only time we automatically create tables, otherwise we force the
 27    user to do it using the management script so they can create backups).
 28    
 29    1) Empty database --> initialize with latest version and return
 30    2) Database older than migration support --> fail and require manual update
 31    3) Database at state where migrate support introduced --> add version control information but make no changes (might still require manual update)
 32    4) Database versioned but out of date --> fail with informative message, user must run "sh manage_db.sh upgrade"
 33    
 34    """
 35
 36    dialect = ( url.split( ':', 1 ) )[0]
 37    try:
 38        egg = dialect_to_egg[dialect]
 39        try:
 40            pkg_resources.require( egg )
 41            log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) )
 42        except:
 43            # If the module is in the path elsewhere (i.e. non-egg), it'll still load.
 44            log.warning( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) )
 45    except KeyError:
 46        # Let this go, it could possibly work with db's we don't support
 47        log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect )
 48
 49    # Create engine and metadata
 50    engine = create_engine( url, **engine_options )
 51    meta = MetaData( bind=engine )
 52    # Try to load dataset table
 53    try:
 54        dataset_table = Table( "dataset", meta, autoload=True )
 55    except NoSuchTableError:
 56        # No 'dataset' table means a completely uninitialized database, which
 57        # is fine, init the database in a versioned state
 58        log.info( "No database, initializing" )
 59        # Database might or might not be versioned
 60        try:
 61            # Declare the database to be under a repository's version control
 62            db_schema = schema.ControlledSchema.create( engine, migrate_repository )
 63        except:
 64            # The database is already under version control
 65            db_schema = schema.ControlledSchema( engine, migrate_repository )
 66        # Apply all scripts to get to current version
 67        migrate_to_current_version( engine, db_schema )
 68        return
 69    try:
 70        hda_table = Table( "history_dataset_association", meta, autoload=True )
 71    except NoSuchTableError:
 72        raise Exception( "Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually" )
 73    # There is a 'history_dataset_association' table, so we (hopefully) have
 74    # version 1 of the database, but without the migrate_version table. This
 75    # happens if the user has a build from right before migration was added.
 76    # Verify that this is true, if it is any older they'll have to update
 77    # manually
 78    if 'copied_from_history_dataset_association_id' not in hda_table.c:
 79        # The 'copied_from_history_dataset_association_id' column was added in
 80        # rev 1464:c7acaa1bb88f.  This is the oldest revision we currently do
 81        # automated versioning for, so stop here
 82        raise Exception( "Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually" )
 83    # At revision 1464:c7acaa1bb88f or greater (database version 1), make sure
 84    # that the db has version information. This is the trickiest case -- we
 85    # have a database but no version control, and are assuming it is a certain
 86    # version. If the user has postion version 1 changes this could cause
 87    # problems
 88    try:
 89        version_table = Table( "migrate_version", meta, autoload=True )
 90    except NoSuchTableError:
 91        # The database exists but is not yet under migrate version control, so init with version 1
 92        log.info( "Adding version control to existing database" )
 93        try:
 94            metadata_file_table = Table( "metadata_file", meta, autoload=True )
 95            schema.ControlledSchema.create( engine, migrate_repository, version=2 )
 96        except NoSuchTableError:
 97            schema.ControlledSchema.create( engine, migrate_repository, version=1 )
 98    # Verify that the code and the DB are in sync
 99    db_schema = schema.ControlledSchema( engine, migrate_repository )
100    if migrate_repository.versions.latest != db_schema.version:
101        raise Exception( "Your database has version '%d' but this code expects version '%d'.  Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'."
102                            % ( db_schema.version, migrate_repository.versions.latest ) )
103    else:
104        log.info( "At database version %d" % db_schema.version )
105        
106def migrate_to_current_version( engine, schema ):
107    # Changes to get to current version
108    changeset = schema.changeset( None )
109    for ver, change in changeset:
110        nextver = ver + changeset.step
111        log.info( 'Migrating %s -> %s... ' % ( ver, nextver ) )
112        schema.runchange( ver, change, changeset.step )