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Source code for galaxy.model.tool_shed_install.migrate.check

import logging
import os.path
import sys

from migrate.versioning import (
from sqlalchemy import (
from sqlalchemy.exc import NoSuchTableError

from galaxy.model.database_utils import create_database, database_exists
from galaxy.model.tool_shed_install 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, engine_options=None, app=None): """ """ # Create engine and metadata engine_options = engine_options or {} if not database_exists(url): message = "Creating database for URI [%s]" % url log.info(message) create_database(url) 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 app and getattr(app.config, 'database_auto_migrate', False): migrate() return # Try to load tool_shed_repository table try: Table("tool_shed_repository", meta, autoload=True) except NoSuchTableError: # No 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. log.info("Creating install database from scratch, skipping migrations") mapping.init(url=url, create_tables=True) current_version = migrate_repository.version().version schema.ControlledSchema.create(engine, migrate_repository, version=current_version) db_schema = schema.ControlledSchema(engine, migrate_repository) assert db_schema.version == current_version migrate() return 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: 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 install\n" 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(f'Migrating {ver} -> {nextver}... ') old_stdout = sys.stdout class FakeStdout: 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