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Source code for galaxy.model.migrate.check
import logging
import os.path
import sys
from migrate.versioning import repository, schema
from sqlalchemy import (
create_engine,
MetaData,
Table
)
from sqlalchemy.exc import NoSuchTableError
from sqlalchemy_utils import create_database, database_exists
from galaxy.model import mapping
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, map_install_models=False):
"""
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4) Database versioned but out of date --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"
"""
# Create the base database if it doesn't yet exist.
new_database = not database_exists(url)
if new_database:
template = app and getattr(app.config, "database_template", None)
encoding = app and getattr(app.config, "database_encoding", None)
create_kwds = {}
message = "Creating database for URI [%s]" % url
if template:
message += " from template [%s]" % template
create_kwds["template"] = template
if encoding:
message += " with encoding [%s]" % encoding
create_kwds["encoding"] = encoding
log.info(message)
create_database(url, **create_kwds)
# 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 Exception:
# 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 new_database:
log.info("Creating new database from scratch, skipping migrations")
current_version = migrate_repository.version().version
mapping.init(file_path='/tmp', url=url, map_install_models=map_install_models, create_tables=True)
schema.ControlledSchema.create(engine, migrate_repository, version=current_version)
db_schema = schema.ControlledSchema(engine, migrate_repository)
assert db_schema.version == current_version
migrate()
return
elif app and getattr(app.config, 'database_auto_migrate', False):
migrate()
return
# Try to load dataset table
try:
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:
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:
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 galaxy_config_file and 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()), '.')
expect_msg = "Your database has version '%d' but this code expects version '%d'" % (db_schema.version, migrate_repository.versions.latest)
instructions = ""
if db_schema.version > migrate_repository.versions.latest:
instructions = "To downgrade the database schema you have to checkout the Galaxy version that you were running previously. "
cmd_msg = "sh manage_db.sh%s downgrade %d" % (config_arg, migrate_repository.versions.latest)
else:
cmd_msg = "sh manage_db.sh%s upgrade" % config_arg
backup_msg = "Please backup your database and then migrate the database schema by running '%s'." % cmd_msg
raise Exception("%s. %s%s" % (expect_msg, instructions, backup_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
try:
changeset = schema.changeset(None)
except Exception as e:
log.error("Problem determining migration changeset for engine [%s]" % engine)
raise e
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