import logging
import os.path
import sys
from galaxy import eggs
eggs.require( "SQLAlchemy" )
eggs.require( "decorator" )
eggs.require( "six" ) # Required by sqlalchemy-migrate
eggs.require( "sqlparse" ) # Required by sqlalchemy-migrate
eggs.require( "sqlalchemy-migrate" )
eggs.require( "Tempita" )
from migrate.versioning import repository, schema
from sqlalchemy import *
from sqlalchemy.exc import NoSuchTableError
from galaxy.model.orm import dialect_to_egg
log = logging.getLogger( __name__ )
# path relative to galaxy
migrate_repository_directory = 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, engine_options={} ):
"""
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4) Database versioned but out of date --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 )
meta = MetaData( bind=engine )
# Try to load dataset table
try:
galaxy_user_table = Table( "galaxy_user", meta, autoload=True )
except NoSuchTableError:
# No 'galaxy_user' table means a completely uninitialized database, which
# is fine, init the database in a versioned state
log.info( "No database, initializing" )
# Database might or might not be versioned
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 )
return
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:
exception_msg = "Your database has version '%d' but this code expects version '%d'. " % ( db_schema.version, migrate_repository.versions.latest )
exception_msg += "Back up your database and then migrate the schema by running the following from your Galaxy installation directory:"
exception_msg += "\n\nsh manage_db.sh upgrade tool_shed\n"
raise Exception( exception_msg )
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