Source code for galaxy.model.orm.scripts

"""
Code to support database helper scripts (create_db.py, manage_db.py, etc...).
"""
import argparse
import logging
import os
import sys

from migrate.versioning.shell import main as migrate_main

from galaxy.util.path import get_ext
from galaxy.util.properties import find_config_file, get_data_dir, load_app_properties
from galaxy.util.script import populate_config_args


log = logging.getLogger(__name__)

DEFAULT_CONFIG_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'config', 'sample'))
DEFAULT_CONFIG_NAMES = ['galaxy', 'universe_wsgi']
DEFAULT_CONFIG_PREFIX = ''
DEFAULT_DATABASE = 'galaxy'

DATABASE = {
    "galaxy":
        {
            'repo': 'galaxy/model/migrate',
            'default_sqlite_file': 'universe.sqlite',
            'config_override': 'GALAXY_CONFIG_',
        },
    "tools":
        {
            'repo': 'galaxy/model/tool_shed_install/migrate',
            'default_sqlite_file': 'universe.sqlite',
            'config_override': 'GALAXY_CONFIG_',
        },
    "tool_shed":
        {
            'repo': 'tool_shed/webapp/model/migrate',
            'config_names': ['tool_shed', 'tool_shed_wsgi'],
            'default_sqlite_file': 'community.sqlite',
            'config_override': 'TOOL_SHED_CONFIG_',
            'config_section': 'tool_shed',
        },
    "install":
        {
            'repo': 'galaxy/model/tool_shed_install/migrate',
            'config_prefix': 'install_',
            'default_sqlite_file': 'install.sqlite',
            'config_override': 'GALAXY_INSTALL_CONFIG_',
        },
}


def _read_model_arguments(argv, use_argparse=False):
    if use_argparse:
        parser = argparse.ArgumentParser()
        parser.add_argument('database', metavar='DATABASE', type=str,
                            default="galaxy",
                            nargs='?',
                            help='database to target (galaxy, tool_shed, install)')
        populate_config_args(parser)
        args = parser.parse_args(argv[1:] if argv else [])
        return args.config_file, args.config_section, args.database
    else:
        config_file = None
        for arg in ["-c", "--config", "--config-file"]:
            if arg in argv:
                pos = argv.index(arg)
                argv.pop(pos)
                config_file = argv.pop(pos)
        config_section = None
        if "--config-section" in argv:
            pos = argv.index("--config-section")
            argv.pop(pos)
            config_section = argv.pop(pos)
        if argv and (argv[-1] in DATABASE):
            database = argv.pop()  # database name tool_shed, galaxy, or install.
        else:
            database = 'galaxy'
        return config_file, config_section, database


[docs]def get_config(argv, use_argparse=True, cwd=None): """ Read sys.argv and parse out repository of migrations and database url. >>> import os >>> from configparser import ConfigParser >>> from shutil import rmtree >>> from tempfile import mkdtemp >>> config_dir = mkdtemp() >>> os.makedirs(os.path.join(config_dir, 'config')) >>> def write_ini(path, property, value): ... p = ConfigParser() ... p.add_section('app:main') ... p.set('app:main', property, value) ... with open(os.path.join(config_dir, 'config', path), 'w') as f: p.write(f) >>> write_ini('tool_shed.ini', 'database_connection', 'sqlite:///pg/testdb1') >>> config = get_config(['manage_db.py', 'tool_shed'], cwd=config_dir) >>> config['repo'].endswith('tool_shed/webapp/model/migrate') True >>> config['db_url'] 'sqlite:///pg/testdb1' >>> write_ini('galaxy.ini', 'data_dir', '/moo') >>> config = get_config(['manage_db.py'], cwd=config_dir) >>> uri_with_env = os.getenv("GALAXY_TEST_DBURI", "sqlite:////moo/universe.sqlite?isolation_level=IMMEDIATE") >>> config['db_url'] == uri_with_env True >>> config['repo'].endswith('galaxy/model/migrate') True >>> rmtree(config_dir) """ config_file, config_section, database = _read_model_arguments(argv, use_argparse=use_argparse) database_defaults = DATABASE[database] if config_file is None: config_names = database_defaults.get('config_names', DEFAULT_CONFIG_NAMES) if cwd: cwd = [cwd, os.path.join(cwd, 'config')] else: cwd = [DEFAULT_CONFIG_DIR] config_file = find_config_file(config_names, dirs=cwd) repo = os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, database_defaults['repo']) config_prefix = database_defaults.get('config_prefix', DEFAULT_CONFIG_PREFIX) config_override = database_defaults.get('config_override', 'GALAXY_CONFIG_') default_sqlite_file = database_defaults['default_sqlite_file'] if config_section is None: if not config_file or get_ext(config_file, ignore='sample') == 'yaml': config_section = database_defaults.get('config_section', None) else: # Just use the default found by load_app_properties. config_section = None properties = load_app_properties(config_file=config_file, config_prefix=config_override, config_section=config_section) if ("%sdatabase_connection" % config_prefix) in properties: db_url = properties["%sdatabase_connection" % config_prefix] else: db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % os.path.join(get_data_dir(properties), default_sqlite_file) install_database_connection = properties.get('install_database_connection') return dict(db_url=db_url, repo=repo, config_file=config_file, database=database, install_database_connection=install_database_connection)
[docs]def manage_db(): # Migrate has its own args, so cannot use argparse config = get_config(sys.argv, use_argparse=False, cwd=os.getcwd()) migrate_main(repository=config['repo'], url=config['db_url'])