import sys
import os.path
import logging
from galaxy import eggs
eggs.require( "SQLAlchemy" )
eggs.require( "six" ) # Required by sqlalchemy-migrate
eggs.require( "sqlparse" ) # Required by sqlalchemy-migrate
eggs.require( "decorator" ) # Required by sqlalchemy-migrate
eggs.require( "Tempita " ) # Required by sqlalchemy-migrate
eggs.require( "sqlalchemy-migrate" )
from sqlalchemy import *
from sqlalchemy.exc import NoSuchTableError
from migrate.versioning import repository, schema
from galaxy.model.orm import dialect_to_egg
log = logging.getLogger( __name__ )
# path relative to galaxy
migrate_repository_directory = os.path.abspath(os.path.dirname( __file__ )).replace( os.getcwd() + os.path.sep, '', 1 )
migrate_repository = repository.Repository( migrate_repository_directory )
[docs]def create_or_verify_database( url, galaxy_config_file, engine_options={}, app=None ):
"""
Check that the database is use-able, possibly creating it if empty (this is
the only time we automatically create tables, otherwise we force the
user to do it using the management script so they can create backups).
1) Empty database --> initialize with latest version and return
2) Database older than migration support --> fail and require manual update
3) Database at state where migrate support introduced --> add version control information but make no changes (might still require manual update)
4) Database versioned but out of date --> fail with informative message, user must run "sh manage_db.sh upgrade"
"""
dialect = ( url.split( ':', 1 ) )[0]
try:
egg = dialect_to_egg[dialect]
try:
eggs.require( egg )
log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) )
except:
# If the module is in the path elsewhere (i.e. non-egg), it'll still load.
log.warning( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) )
except KeyError:
# Let this go, it could possibly work with db's we don't support
log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect )
# Create engine and metadata
engine = create_engine( url, **engine_options )
def migrate():
try:
# Declare the database to be under a repository's version control
db_schema = schema.ControlledSchema.create( engine, migrate_repository )
except:
# The database is already under version control
db_schema = schema.ControlledSchema( engine, migrate_repository )
# Apply all scripts to get to current version
migrate_to_current_version( engine, db_schema )
meta = MetaData( bind=engine )
if app and getattr( app.config, 'database_auto_migrate', False ):
migrate()
return
# Try to load dataset table
try:
dataset_table = Table( "dataset", meta, autoload=True )
except NoSuchTableError:
# No 'dataset' table means a completely uninitialized database. If we have an app, we'll
# set its new_installation setting to True so the tool migration process will be skipped.
if app:
app.new_installation = True
log.info( "No database, initializing" )
migrate()
return
try:
hda_table = Table( "history_dataset_association", meta, autoload=True )
except NoSuchTableError:
raise Exception( "Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually" )
# There is a 'history_dataset_association' table, so we (hopefully) have
# version 1 of the database, but without the migrate_version table. This
# happens if the user has a build from right before migration was added.
# Verify that this is true, if it is any older they'll have to update
# manually
if 'copied_from_history_dataset_association_id' not in hda_table.c:
# The 'copied_from_history_dataset_association_id' column was added in
# rev 1464:c7acaa1bb88f. This is the oldest revision we currently do
# automated versioning for, so stop here
raise Exception( "Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually" )
# At revision 1464:c7acaa1bb88f or greater (database version 1), make sure
# that the db has version information. This is the trickiest case -- we
# have a database but no version control, and are assuming it is a certain
# version. If the user has postion version 1 changes this could cause
# problems
try:
version_table = Table( "migrate_version", meta, autoload=True )
except NoSuchTableError:
# The database exists but is not yet under migrate version control, so init with version 1
log.info( "Adding version control to existing database" )
try:
metadata_file_table = Table( "metadata_file", meta, autoload=True )
schema.ControlledSchema.create( engine, migrate_repository, version=2 )
except NoSuchTableError:
schema.ControlledSchema.create( engine, migrate_repository, version=1 )
# Verify that the code and the DB are in sync
db_schema = schema.ControlledSchema( engine, migrate_repository )
if migrate_repository.versions.latest != db_schema.version:
config_arg = ''
if os.path.abspath( os.path.join( os.getcwd(), 'config', 'galaxy.ini' ) ) != galaxy_config_file:
config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' )
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%s upgrade'."
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
else:
log.info( "At database version %d" % db_schema.version )
[docs]def migrate_to_current_version( engine, schema ):
# Changes to get to current version
changeset = schema.changeset( None )
for ver, change in changeset:
nextver = ver + changeset.step
log.info( 'Migrating %s -> %s... ' % ( ver, nextver ) )
old_stdout = sys.stdout
class FakeStdout( object ):
def __init__( self ):
self.buffer = []
def write( self, s ):
self.buffer.append( s )
def flush( self ):
pass
sys.stdout = FakeStdout()
try:
schema.runchange( ver, change, changeset.step )
finally:
for message in "".join( sys.stdout.buffer ).split( "\n" ):
log.info( message )
sys.stdout = old_stdout