Source code for galaxy.model.orm.scripts

"""
Code to support database helper scripts (create_toolshed_db.py, migrate_toolshed_db.py, etc...).
"""

import argparse
import logging
import os
import sys

import alembic.config

from galaxy.model.migrations import (
    GXY,
    TSI,
)
from galaxy.model.migrations.scripts import get_configuration
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": {
        "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": {
        "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
    >>> 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 = database_defaults.get("repo")
    if repo:
        repo = os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 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 (f"{config_prefix}database_connection") in properties:
        db_url = properties[f"{config_prefix}database_connection"]
    else:
        db_url = f"sqlite:///{os.path.join(get_data_dir(properties), default_sqlite_file)}?isolation_level=IMMEDIATE"
    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():
    # This is a duplicate implementation of scripts/migrate_db.py.
    # See run_alembic.sh for usage.
    def _insert_x_argument(key, value):
        sys.argv.insert(1, f"{key}={value}")
        sys.argv.insert(1, "-x")

    gxy_config, tsi_config, _ = get_configuration(sys.argv, os.getcwd())
    _insert_x_argument("tsi_url", tsi_config.url)
    _insert_x_argument("gxy_url", gxy_config.url)

    if "heads" in sys.argv and "upgrade" in sys.argv:
        i = sys.argv.index("heads")
        sys.argv[i] = f"{GXY}@head"
        alembic.config.main()
        sys.argv[i] = f"{TSI}@head"
        alembic.config.main()
    else:
        alembic.config.main()