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Source code for galaxy.config

Universe configuration builder.

# absolute_import needed for tool_shed package.

import configparser
import json
import locale
import logging
import logging.config
import os
import re
import socket
import string
import sys
import tempfile
import threading
from datetime import timedelta
from typing import (
from urllib.parse import urlparse

import yaml

from galaxy.carbon_emissions import get_carbon_intensity_entry
from galaxy.config.schema import AppSchema
from galaxy.exceptions import ConfigurationError
from galaxy.util import (
from galaxy.util.config_parsers import parse_allowlist_ips
from galaxy.util.custom_logging import LOGLV_TRACE
from galaxy.util.dynamic import HasDynamicProperties
from galaxy.util.facts import get_facts
from galaxy.util.properties import (
from galaxy.util.resources import (
from galaxy.util.themes import flatten_theme
from ..version import (

    from galaxy.model import User

log = logging.getLogger(__name__)

DEFAULT_LOCALE_FORMAT = "%a %b %e %H:%M:%S %Y"

GALAXY_APP_NAME = "galaxy"
GALAXY_SCHEMAS_PATH = resource_path(__package__, "schemas")
TOOL_SHED_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "tool_shed_config_schema.yml"
    "disable_existing_loggers": False,
    "version": 1,
    "root": {
        "handlers": ["console"],
        "level": "DEBUG",
    "loggers": {
        "paste.httpserver.ThreadPool": {
            "level": "WARN",
            "qualname": "paste.httpserver.ThreadPool",
        "sqlalchemy_json.track": {
            "level": "WARN",
            "qualname": "sqlalchemy_json.track",
        "urllib3.connectionpool": {
            "level": "WARN",
            "qualname": "urllib3.connectionpool",
        "routes.middleware": {
            "level": "WARN",
            "qualname": "routes.middleware",
        "amqp": {
            "level": "INFO",
            "qualname": "amqp",
        "botocore": {
            "level": "INFO",
            "qualname": "botocore",
        "gunicorn.access": {
            "level": "INFO",
            "qualname": "gunicorn.access",
            "propagate": False,
            "handlers": ["console"],
        "watchdog.observers.inotify_buffer": {
            "level": "INFO",
            "qualname": "watchdog.observers.inotify_buffer",
    "filters": {
        "stack": {
            "()": "galaxy.web_stack.application_stack_log_filter",
    "handlers": {
        "console": {
            "class": "logging.StreamHandler",
            "formatter": "stack",
            "level": "DEBUG",
            "stream": "ext://sys.stderr",
            "filters": ["stack"],
    "formatters": {
        "stack": {
            "()": "galaxy.web_stack.application_stack_log_formatter",
"""Default value for logging configuration, passed to :func:`logging.config.dictConfig`"""

    "mulled_resolution_cache_url": "database_connection",
    "citation_cache_url": "database_connection",
    "biotools_service_cache_url": "database_connection",
"""Config parameters whose default is the value of another config parameter
This should be moved to a .yml config file.

VERSION_JSON_FILE = "version.json"
DISABLED_FLAG = "disabled"  # Used to mark a config option as disabled

[docs]def configure_logging(config, facts=None): """Allow some basic logging configuration to be read from ini file. This should be able to consume either a galaxy.config.Configuration object or a simple dictionary of configuration variables. """ facts = facts or get_facts(config=config) # Get root logger logging.addLevelName(LOGLV_TRACE, "TRACE") # PasteScript will have already configured the logger if the # 'loggers' section was found in the config file, otherwise we do # some simple setup using the 'log_*' values from the config. parser = getattr(config, "global_conf_parser", None) if parser: paste_configures_logging = config.global_conf_parser.has_section("loggers") else: paste_configures_logging = False auto_configure_logging = not paste_configures_logging and string_as_bool( config.get("auto_configure_logging", "True") ) if auto_configure_logging: logging_conf = config.get("logging", None) if logging_conf is None: # if using the default logging config, honor the log_level setting logging_conf = LOGGING_CONFIG_DEFAULT if config.get("log_level", "DEBUG") != "DEBUG": logging_conf["handlers"]["console"]["level"] = config.get("log_level", "DEBUG") # configure logging with logging dict in config, template *FileHandler handler filenames with the `filename_template` option for name, conf in logging_conf.get("handlers", {}).items(): if ( conf["class"].startswith("logging.") and conf["class"].endswith("FileHandler") and "filename_template" in conf ): conf["filename"] = conf.pop("filename_template").format(**facts) logging_conf["handlers"][name] = conf logging.config.dictConfig(logging_conf)
[docs]def find_root(kwargs) -> str: return os.path.abspath(kwargs.get("root_dir", "."))
[docs]def expand_pretty_datetime_format(value): """ >>> expand_pretty_datetime_format("%H:%M:%S %Z") '%H:%M:%S %Z' >>> locale_format = expand_pretty_datetime_format("$locale (UTC)") >>> import locale >>> expected_format = '%s (UTC)' % locale.nl_langinfo(locale.D_T_FMT) >>> locale_format == expected_format True >>> expand_pretty_datetime_format("$iso8601") '%Y-%m-%d %H:%M:%S' """ locale_format = None try: locale_format = locale.nl_langinfo(locale.D_T_FMT) except AttributeError: # nl_langinfo not available pass if not locale_format: locale_format = DEFAULT_LOCALE_FORMAT stock_formats = dict( locale=locale_format, iso8601=ISO_DATETIME_FORMAT, ) return string.Template(value).safe_substitute(**stock_formats)
OptStr = TypeVar("OptStr", None, str)
[docs]class BaseAppConfiguration(HasDynamicProperties): # Override in subclasses (optional): {KEY: config option, VALUE: deprecated directory name} # If VALUE == first directory in a user-supplied path that resolves to KEY, it will be stripped from that path renamed_options: Optional[Dict[str, str]] = None deprecated_dirs: Dict[str, str] = {} paths_to_check_against_root: Set[str] = ( set() ) # backward compatibility: if resolved path doesn't exist, try resolving w.r.t root add_sample_file_to_defaults: Set[str] = set() # for these options, add sample config files to their defaults listify_options: Set[str] = set() # values for these options are processed as lists of values object_store_store_by: str shed_tools_dir: str
[docs] def __init__(self, **kwargs): self._preprocess_kwargs(kwargs) self._kwargs = kwargs # Save these as a record of explicitly set options self.config_dict = kwargs self.root = find_root(kwargs) self._set_config_base(kwargs) self.schema = self._load_schema() # Load schema from schema definition file self._raw_config = self.schema.defaults.copy() # Save schema defaults as initial config values (raw_config) self._update_raw_config_from_kwargs(kwargs) # Overwrite raw_config with values passed in kwargs self._create_attributes_from_raw_config() # Create attributes based on raw_config self._preprocess_paths_to_resolve() # Any preprocessing steps that need to happen before paths are resolved self._resolve_paths() # Overwrite attribute values with resolved paths self._postprocess_paths_to_resolve() # Any steps that need to happen after paths are resolved
def _preprocess_kwargs(self, kwargs): self._process_renamed_options(kwargs) self._fix_postgresql_dburl(kwargs) def _process_renamed_options(self, kwargs): """Update kwargs to set any unset renamed options to values of old-named options, if set. Does not remove the old options from kwargs so that deprecated option usage can be logged. """ if self.renamed_options is not None: for old, new in self.renamed_options.items(): if old in kwargs and new not in kwargs: kwargs[new] = kwargs[old] def _fix_postgresql_dburl(self, kwargs): """ Fix deprecated database URLs (postgres... >> postgresql...) https://docs.sqlalchemy.org/en/14/changelog/changelog_14.html#change-3687655465c25a39b968b4f5f6e9170b """ old_dialect, new_dialect = "postgres", "postgresql" old_prefixes = (f"{old_dialect}:", f"{old_dialect}+") # check for postgres://foo and postgres+driver//foo offset = len(old_dialect) keys = ("database_connection", "install_database_connection") for key in keys: if key in kwargs: value = kwargs[key] for prefix in old_prefixes: if value.startswith(prefix): value = f"{new_dialect}{value[offset:]}" kwargs[key] = value log.warning( 'PostgreSQL database URLs of the form "postgres://" have been ' 'deprecated. Please use "postgresql://".' )
[docs] def is_set(self, key): """Check if a configuration option has been explicitly set.""" # NOTE: This will check all supplied keyword arguments, including those not in the schema. # To check only schema options, change the line below to `if property not in self._raw_config:` if key not in self._raw_config: log.warning(f"Configuration option does not exist: '{key}'") return key in self._kwargs
[docs] def resolve_path(self, path): """Resolve a path relative to Galaxy's root.""" return self._in_root_dir(path)
def _set_config_base(self, config_kwargs): def _set_global_conf(): self.config_file = config_kwargs.get("__file__", None) self.global_conf = config_kwargs.get("global_conf") self.global_conf_parser = configparser.ConfigParser() if not self.config_file and self.global_conf and "__file__" in self.global_conf: self.config_file = os.path.join(self.root, self.global_conf["__file__"]) if self.config_file is None: log.warning("No Galaxy config file found, running from current working directory: %s", os.getcwd()) else: try: self.global_conf_parser.read(self.config_file) except OSError: raise except Exception: pass # Not an INI file def _set_config_directories(): # Set config_dir to value from kwargs OR dirname of config_file OR None _config_dir = os.path.dirname(self.config_file) if self.config_file else None self.config_dir = config_kwargs.get("config_dir", _config_dir) # Make path absolute before using it as base for other paths if self.config_dir: self.config_dir = os.path.abspath(self.config_dir) self.data_dir = config_kwargs.get("data_dir") if self.data_dir: self.data_dir = os.path.abspath(self.data_dir) self.sample_config_dir = os.path.join(os.path.dirname(__file__), "sample") if self.sample_config_dir: self.sample_config_dir = os.path.abspath(self.sample_config_dir) self.managed_config_dir = config_kwargs.get("managed_config_dir") if self.managed_config_dir: self.managed_config_dir = os.path.abspath(self.managed_config_dir) if running_from_source: if not self.config_dir: self.config_dir = os.path.join(self.root, "config") if not self.data_dir: self.data_dir = os.path.join(self.root, "database") if not self.managed_config_dir: self.managed_config_dir = self.config_dir else: if not self.config_dir: self.config_dir = os.getcwd() if not self.data_dir: self.data_dir = self._in_config_dir("data") if not self.managed_config_dir: self.managed_config_dir = self._in_data_dir("config") # TODO: do we still need to support ../shed_tools when running_from_source? self.shed_tools_dir = self._in_data_dir("shed_tools") log.debug("Configuration directory is %s", self.config_dir) log.debug("Data directory is %s", self.data_dir) log.debug("Managed config directory is %s", self.managed_config_dir) _set_global_conf() _set_config_directories() def _load_schema(self): # Override in subclasses raise Exception("Not implemented") def _preprocess_paths_to_resolve(self): # For these options, if option is not set, listify its defaults and add a sample config file. if self.add_sample_file_to_defaults: for key in self.add_sample_file_to_defaults: if not self.is_set(key): defaults = listify(getattr(self, key), do_strip=True) sample = f"{defaults[-1]}.sample" # if there are multiple defaults, use last as template sample = self._in_sample_dir(sample) # resolve w.r.t sample_dir defaults.append(sample) setattr(self, key, defaults) def _postprocess_paths_to_resolve(self): def select_one_path_from_list(): # To consider: options with a sample file added to defaults except options that can have multiple values. # If value is not set, check each path in list; set to first path that exists; if none exist, set to last path in list. keys = ( self.add_sample_file_to_defaults - self.listify_options if self.listify_options else self.add_sample_file_to_defaults ) for key in keys: if not self.is_set(key): paths = getattr(self, key) for path in paths: if self._path_exists(path): setattr(self, key, path) break else: setattr( self, key, paths[-1] ) # TODO: we assume it exists; but we've already checked in the loop! Raise error instead? def select_one_or_all_paths_from_list(): # Values for these options are lists of paths. If value is not set, use defaults if all paths in list exist; # otherwise, set to last path in list. for key in self.listify_options: if not self.is_set(key): paths = getattr(self, key) for path in paths: if not self._path_exists(path): setattr(self, key, [paths[-1]]) # value is a list break if ( self.add_sample_file_to_defaults ): # Currently, this is the ONLY case when we need to pick one file from a list select_one_path_from_list() if self.listify_options: select_one_or_all_paths_from_list() def _path_exists(self, path): # factored out so we can mock it in tests return os.path.exists(path) def _set_alt_paths(self, option, *alt_paths): # If `option` is not set, check *alt_paths. Set `option` to first path that exists and return it. if not self.is_set(option): for path in alt_paths: if self._path_exists(path): setattr(self, option, path) return path def _update_raw_config_from_kwargs(self, kwargs): type_converters: Dict[str, Callable[[Any], Union[bool, int, float, str]]] = { "bool": string_as_bool, "int": int, "float": float, "str": str, } def convert_datatype(key, value): datatype = self.schema.app_schema[key].get("type") # check for `not None` explicitly (value can be falsy) if value is not None and datatype in type_converters: # convert value or each item in value to type `datatype` f = type_converters[datatype] if isinstance(value, list): return [f(item) for item in value] else: return f(value) return value def strip_deprecated_dir(key, value): resolves_to = self.schema.paths_to_resolve.get(key) if resolves_to: # value contains paths that will be resolved paths = listify(value, do_strip=True) for i, path in enumerate(paths): first_dir = path.split(os.sep)[0] # get first directory component if first_dir == self.deprecated_dirs.get(resolves_to): # first_dir is deprecated for this option ignore = first_dir + os.sep log.warning( "Paths for the '%s' option are now relative to '%s', remove the leading '%s' " "to suppress this warning: %s", key, resolves_to, ignore, path, ) paths[i] = path[len(ignore) :] # return list or string, depending on type of `value` if isinstance(value, list): return paths return ",".join(paths) return value for key, value in kwargs.items(): if key in self.schema._deprecated_aliases: new_key = self.schema._deprecated_aliases[key] log.warning(f"Option {key} has been deprecated in favor of {new_key}") key = new_key if key in self.schema.app_schema: value = convert_datatype(key, value) if value and self.deprecated_dirs: value = strip_deprecated_dir(key, value) self._raw_config[key] = value def _create_attributes_from_raw_config(self): # `base_configs` are a special case: these attributes have been created and will be ignored # by the code below. Trying to overwrite any other existing attributes will raise an error. base_configs = {"config_dir", "data_dir", "managed_config_dir"} for key, value in self._raw_config.items(): if not hasattr(self, key): setattr(self, key, value) elif key not in base_configs: raise ConfigurationError(f"Attempting to override existing attribute '{key}'") def _resolve_paths(self): def resolve(key): if key in _cache: # resolve each path only once return _cache[key] path = getattr(self, key) # path prior to being resolved parent = self.schema.paths_to_resolve.get(key) if not parent: # base case: nothing else needs resolving return path parent_path = resolve(parent) # recursively resolve parent path if path is not None: path = os.path.join(parent_path, path) # resolve path else: path = parent_path # or use parent path setattr(self, key, path) # update property _cache[key] = path # cache it! return path _cache = {} for key in self.schema.paths_to_resolve: value = getattr(self, key) # Check if value is a list or should be listified; if so, listify and resolve each item separately. if isinstance(value, list) or (self.listify_options and key in self.listify_options): saved_values = listify(getattr(self, key), do_strip=True) # listify and save original value setattr(self, key, "_") # replace value with temporary placeholder resolve(key) # resolve temporary value (`_` becomes `parent-path/_`) resolved_base = getattr(self, key)[:-1] # get rid of placeholder in resolved path # apply resolved base to saved values resolved_paths = [os.path.join(resolved_base, value) for value in saved_values] setattr(self, key, resolved_paths) # set config.key to a list of resolved paths else: resolve(key) # Check options that have been set and may need to be resolved w.r.t. root if self.is_set(key) and self.paths_to_check_against_root and key in self.paths_to_check_against_root: self._check_against_root(key) def _check_against_root(self, key): def get_path(current_path, initial_path): # if path does not exist and was set as relative: if not self._path_exists(current_path) and not os.path.isabs(initial_path): new_path = self._in_root_dir(initial_path) if self._path_exists(new_path): # That's a bingo! resolves_to = self.schema.paths_to_resolve.get(key) log.warning( "Paths for the '%s' option should be relative to '%s'. To suppress this warning, " "move '%s' into '%s', or set its value to an absolute path.", key, resolves_to, key, resolves_to, ) return new_path return current_path current_value = getattr(self, key) # resolved path or list of resolved paths if isinstance(current_value, list): initial_paths = listify(self._raw_config[key], do_strip=True) # initial unresolved paths updated_paths = [] # check and, if needed, update each path in the list for current_path, initial_path in zip(current_value, initial_paths): path = get_path(current_path, initial_path) updated_paths.append(path) # add to new list regardless of whether path has changed or not setattr(self, key, updated_paths) # update: one or more paths may have changed else: initial_path = self._raw_config[key] # initial unresolved path path = get_path(current_value, initial_path) if path != current_value: setattr(self, key, path) # update if path has changed def _in_root_dir(self, path: OptStr) -> OptStr: return self._in_dir(self.root, path) def _in_managed_config_dir(self, path: OptStr) -> OptStr: return self._in_dir(self.managed_config_dir, path) def _in_config_dir(self, path: OptStr) -> OptStr: return self._in_dir(self.config_dir, path) def _in_sample_dir(self, path: OptStr) -> OptStr: return self._in_dir(self.sample_config_dir, path) def _in_data_dir(self, path: OptStr) -> OptStr: return self._in_dir(self.data_dir, path) def _in_dir(self, _dir: str, path: OptStr) -> OptStr: if path is not None: return os.path.join(_dir, path) return None
[docs]class CommonConfigurationMixin: """Shared configuration settings code for Galaxy and ToolShed.""" sentry_dsn: str config_dict: Dict[str, str] @property def admin_users(self): return self._admin_users @admin_users.setter def admin_users(self, value): self._admin_users = value self.admin_users_list = listify(value)
[docs] def is_admin_user(self, user: Optional["User"]) -> bool: """Determine if the provided user is listed in `admin_users`.""" return user is not None and (user.email in self.admin_users_list or user.bootstrap_admin_user)
@property def sentry_dsn_public(self): """ Sentry URL with private key removed for use in client side scripts, sentry server will need to be configured to accept events """ if self.sentry_dsn: return re.sub(r"^([^:/?#]+:)?//(\w+):(\w+)", r"\1//\2", self.sentry_dsn)
[docs] def get_bool(self, key, default): # Warning: the value of self.config_dict['foo'] may be different from self.foo if key in self.config_dict: return string_as_bool(self.config_dict[key]) else: return default
[docs] def get(self, key, default=None): # Warning: the value of self.config_dict['foo'] may be different from self.foo return self.config_dict.get(key, default)
def _ensure_directory(self, path): if path not in [None, False] and not os.path.isdir(path): try: os.makedirs(path) except Exception as e: raise ConfigurationError(f"Unable to create missing directory: {path}\n{unicodify(e)}")
[docs]class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin): renamed_options = { "blacklist_file": "email_domain_blocklist_file", "whitelist_file": "email_domain_allowlist_file", "sanitize_whitelist_file": "sanitize_allowlist_file", "user_library_import_symlink_whitelist": "user_library_import_symlink_allowlist", "fetch_url_whitelist": "fetch_url_allowlist", "containers_resolvers_config_file": "container_resolvers_config_file", "activation_email": "email_from", "ga4gh_service_organization_name": "organization_name", "ga4gh_service_organization_url": "organization_url", } deprecated_options = list(renamed_options.keys()) + [ "database_file", "track_jobs_in_database", ] default_config_file_name = "galaxy.yml" deprecated_dirs = {"config_dir": "config", "data_dir": "database"} paths_to_check_against_root = { "auth_config_file", "build_sites_config_file", "data_manager_config_file", "datatypes_config_file", "dependency_resolvers_config_file", "error_report_file", "job_config_file", "job_metrics_config_file", "job_resource_params_file", "local_conda_mapping_file", "migrated_tools_config", "modules_mapping_files", "object_store_config_file", "oidc_backends_config_file", "oidc_config_file", "shed_data_manager_config_file", "shed_tool_config_file", "shed_tool_data_table_config", "tool_destinations_config_file", "tool_sheds_config_file", "user_preferences_extra_conf_path", "workflow_resource_params_file", "workflow_schedulers_config_file", "markdown_export_css", "markdown_export_css_pages", "markdown_export_css_invocation_reports", "file_path", "tool_data_table_config_path", "tool_config_file", "themes_config_file", } add_sample_file_to_defaults = { "build_sites_config_file", "datatypes_config_file", "tool_data_table_config_path", "tool_config_file", } listify_options = { "tool_data_table_config_path", "tool_config_file", } allowed_origin_hostnames: List[str] builds_file_path: str carbon_intensity: float container_resolvers_config_file: str database_connection: str drmaa_external_runjob_script: str email_from: Optional[str] enable_tool_shed_check: bool galaxy_data_manager_data_path: str galaxy_infrastructure_url: str geographical_server_location_name: str hours_between_check: int integrated_tool_panel_config: str involucro_path: str len_file_path: str manage_dependency_relationships: bool monitor_thread_join_timeout: int mulled_channels: List[str] new_file_path: str nginx_upload_store: str password_expiration_period: timedelta preserve_python_environment: str pretty_datetime_format: str sanitize_allowlist_file: str shed_tool_data_path: str themes: Dict[str, Dict[str, str]] themes_by_host: Dict[str, Dict[str, Dict[str, str]]] tool_data_path: str tool_dependency_dir: Optional[str] tool_filters: List[str] tool_label_filters: List[str] tool_path: str tool_section_filters: List[str] toolbox_filter_base_modules: List[str] track_jobs_in_database: bool trust_jupyter_notebook_conversion: bool tus_upload_store: str use_remote_user: bool user_library_import_dir_auto_creation: bool user_library_import_symlink_allowlist: List[str] user_tool_filters: List[str] user_tool_label_filters: List[str] user_tool_section_filters: List[str] visualization_plugins_directory: str workflow_resource_params_mapper: str
[docs] def __init__(self, **kwargs): super().__init__(**kwargs) self._override_tempdir(kwargs) self._process_config(kwargs) self._set_dependent_defaults()
def _set_dependent_defaults(self): """Set values of unset parameters which take their default values from other parameters""" for dependent_config_param, config_param in DEPENDENT_CONFIG_DEFAULTS.items(): try: if getattr(self, dependent_config_param) is None: setattr(self, dependent_config_param, getattr(self, config_param)) except AttributeError: raise Exception( "One or more invalid config parameter names specified in " "DEPENDENT_CONFIG_DEFAULTS, " f"{dependent_config_param}, {config_param}" ) def _load_schema(self): return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME) def _override_tempdir(self, kwargs): if string_as_bool(kwargs.get("override_tempdir", "True")): tempfile.tempdir = self.new_file_path
[docs] def config_value_for_host(self, config_option, host): val = getattr(self, config_option) if config_option in self.schema.per_host_options: per_host_option = f"{config_option}_by_host" per_host: Dict[str, Any] = {} if per_host_option in self.config_dict: per_host = self.config_dict[per_host_option] or {} else: per_host = getattr(self, per_host_option, {}) for host_key, host_val in per_host.items(): if host_key in host: val = host_val break return val
def _process_config(self, kwargs: Dict[str, Any]) -> None: self._check_database_connection_strings() # Backwards compatibility for names used in too many places to fix self.datatypes_config = self.datatypes_config_file self.tool_configs = self.tool_config_file # Collect the umask and primary gid from the environment self.umask = os.umask(0o77) # get the current umask os.umask(self.umask) # can't get w/o set, so set it back self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster self.version_major = VERSION_MAJOR self.version_minor = VERSION_MINOR # Try loading extra version info self.version_extra = None json_file = os.environ.get( "GALAXY_VERSION_JSON_FILE", self._in_root_dir(VERSION_JSON_FILE) ) # TODO: add this to schema try: with open(json_file) as f: extra_info = json.load(f) except FileNotFoundError: log.debug("No extra version JSON file detected at %s", json_file) except ValueError: log.error("Error loading Galaxy extra version JSON file %s - details not loaded.", json_file) else: self.version_extra = extra_info # Carbon emissions configuration carbon_intensity_entry = get_carbon_intensity_entry(kwargs.get("geographical_server_location_code", "")) self.carbon_intensity = carbon_intensity_entry["carbon_intensity"] self.geographical_server_location_name = carbon_intensity_entry["location_name"] # Database related configuration self.check_migrate_databases = string_as_bool(kwargs.get("check_migrate_databases", True)) if not self.database_connection: # Provide default if not supplied by user db_path = self._in_data_dir("universe.sqlite") self.database_connection = f"sqlite:///{db_path}?isolation_level=IMMEDIATE" self.database_engine_options = get_database_engine_options(kwargs) self.database_encoding = kwargs.get("database_encoding") # Create new databases with this encoding self.thread_local_log = None if self.enable_per_request_sql_debugging: self.thread_local_log = threading.local() # Install database related configuration (if different) self.install_database_engine_options = get_database_engine_options(kwargs, model_prefix="install_") self.shared_home_dir = kwargs.get("shared_home_dir") self.cookie_path = kwargs.get("cookie_path") if not running_from_source and kwargs.get("tool_path") is None: try: with as_file(resource_path("galaxy.tools", "bundled")) as path: self.tool_path = os.fspath(path) except ModuleNotFoundError: # Might not be a full galaxy installation self.tool_path = self._in_root_dir(self.tool_path) else: self.tool_path = self._in_root_dir(self.tool_path) self.tool_data_path = self._in_root_dir(self.tool_data_path) if not running_from_source and kwargs.get("tool_data_path") is None: self.tool_data_path = self._in_data_dir(self.schema.defaults["tool_data_path"]) self.builds_file_path = os.path.join(self.tool_data_path, self.builds_file_path) self.len_file_path = os.path.join(self.tool_data_path, self.len_file_path) self.oidc: Dict[str, Dict] = {} self.fixed_delegated_auth: bool = False self.integrated_tool_panel_config = self._in_managed_config_dir(self.integrated_tool_panel_config) integrated_tool_panel_tracking_directory = kwargs.get("integrated_tool_panel_tracking_directory") if integrated_tool_panel_tracking_directory: self.integrated_tool_panel_tracking_directory = self._in_root_dir(integrated_tool_panel_tracking_directory) else: self.integrated_tool_panel_tracking_directory = None self.toolbox_filter_base_modules = listify(self.toolbox_filter_base_modules) self.tool_filters = listify(self.tool_filters, do_strip=True) self.tool_label_filters = listify(self.tool_label_filters, do_strip=True) self.tool_section_filters = listify(self.tool_section_filters, do_strip=True) self.user_tool_filters = listify(self.user_tool_filters, do_strip=True) self.user_tool_label_filters = listify(self.user_tool_label_filters, do_strip=True) self.user_tool_section_filters = listify(self.user_tool_section_filters, do_strip=True) self.has_user_tool_filters = bool( self.user_tool_filters or self.user_tool_label_filters or self.user_tool_section_filters ) self.password_expiration_period = timedelta(days=int(cast(SupportsInt, self.password_expiration_period))) if self.shed_tool_data_path: self.shed_tool_data_path = self._in_root_dir(self.shed_tool_data_path) else: self.shed_tool_data_path = self.tool_data_path self.running_functional_tests = string_as_bool(kwargs.get("running_functional_tests", False)) if isinstance(self.hours_between_check, str): self.hours_between_check = float(self.hours_between_check) try: if isinstance(self.hours_between_check, int): if self.hours_between_check < 1 or self.hours_between_check > 24: self.hours_between_check = 12 elif isinstance(self.hours_between_check, float): # If we're running functional tests, the minimum hours between check should be reduced to 0.001, or 3.6 seconds. if self.running_functional_tests: if self.hours_between_check < 0.001 or self.hours_between_check > 24.0: self.hours_between_check = 12.0 else: if self.hours_between_check < 1.0 or self.hours_between_check > 24.0: self.hours_between_check = 12.0 else: self.hours_between_check = 12 except Exception: self.hours_between_check = 12 self.update_integrated_tool_panel = kwargs.get("update_integrated_tool_panel", True) self.galaxy_data_manager_data_path = self.galaxy_data_manager_data_path or self.tool_data_path self.tool_secret = kwargs.get("tool_secret", "") self.metadata_strategy = kwargs.get("metadata_strategy", "directory") self.use_remote_user = self.use_remote_user or self.single_user self.fetch_url_allowlist_ips = parse_allowlist_ips(listify(kwargs.get("fetch_url_allowlist"))) self.job_queue_cleanup_interval = int(kwargs.get("job_queue_cleanup_interval", "5")) # Fall back to legacy job_working_directory config variable if set. self.jobs_directory = self._in_data_dir(kwargs.get("jobs_directory", self.job_working_directory)) if self.preserve_python_environment not in ["legacy_only", "legacy_and_local", "always"]: log.warning("preserve_python_environment set to unknown value [%s], defaulting to legacy_only") self.preserve_python_environment = "legacy_only" self.nodejs_path = kwargs.get("nodejs_path") self.container_image_cache_path = self._in_data_dir(kwargs.get("container_image_cache_path", "container_cache")) self.output_size_limit = int(kwargs.get("output_size_limit", 0)) self.email_domain_blocklist_content = ( self._load_list_from_file(self._in_config_dir(self.email_domain_blocklist_file)) if self.email_domain_blocklist_file else None ) self.email_domain_allowlist_content = ( self._load_list_from_file(self._in_config_dir(self.email_domain_allowlist_file)) if self.email_domain_allowlist_file else None ) # These are not even beta - just experiments - don't use them unless # you want yours tools to be broken in the future. self.enable_beta_tool_formats = string_as_bool(kwargs.get("enable_beta_tool_formats", "False")) if self.workflow_resource_params_mapper and ":" not in self.workflow_resource_params_mapper: # Assume it is not a Python function, so a file; else: a Python function self.workflow_resource_params_mapper = self._in_root_dir(self.workflow_resource_params_mapper) self.pbs_application_server = kwargs.get("pbs_application_server", "") self.pbs_dataset_server = kwargs.get("pbs_dataset_server", "") self.pbs_dataset_path = kwargs.get("pbs_dataset_path", "") self.pbs_stage_path = kwargs.get("pbs_stage_path", "") _sanitize_allowlist_path = self._in_managed_config_dir(self.sanitize_allowlist_file) if not os.path.isfile(_sanitize_allowlist_path): # then check old default location for deprecated in ( self._in_managed_config_dir("sanitize_whitelist.txt"), self._in_root_dir("config/sanitize_whitelist.txt"), ): if os.path.isfile(deprecated): log.warning( "The path '%s' for the 'sanitize_allowlist_file' config option is " "deprecated and will be no longer checked in a future release. Please consult " "the latest version of the sample configuration file." % deprecated ) _sanitize_allowlist_path = deprecated break self.sanitize_allowlist_file = _sanitize_allowlist_path self.allowed_origin_hostnames = self._parse_allowed_origin_hostnames(self.allowed_origin_hostnames) if "trust_jupyter_notebook_conversion" not in kwargs: # if option not set, check IPython-named alternative, falling back to schema default if not set either _default = self.trust_jupyter_notebook_conversion self.trust_jupyter_notebook_conversion = string_as_bool( kwargs.get("trust_ipython_notebook_conversion", _default) ) # Configuration for the message box directly below the masthead. self.blog_url = kwargs.get("blog_url") self.user_library_import_symlink_allowlist = listify(self.user_library_import_symlink_allowlist, do_strip=True) self.user_library_import_dir_auto_creation = ( self.user_library_import_dir_auto_creation if self.user_library_import_dir else False ) # Searching data libraries self.ftp_upload_dir_template = kwargs.get( "ftp_upload_dir_template", "${ftp_upload_dir}%s${ftp_upload_dir_identifier}" % os.path.sep ) # Support older library-specific path paste option but just default to the new # allow_path_paste value. self.allow_library_path_paste = string_as_bool(kwargs.get("allow_library_path_paste", self.allow_path_paste)) self.disable_library_comptypes = kwargs.get("disable_library_comptypes", "").lower().split(",") self.check_upload_content = string_as_bool(kwargs.get("check_upload_content", True)) # On can mildly speed up Galaxy startup time by disabling index of help, # not needed on production systems but useful if running many functional tests. self.index_tool_help = string_as_bool(kwargs.get("index_tool_help", True)) self.tool_labels_boost = kwargs.get("tool_labels_boost", 1) default_tool_test_data_directories = os.environ.get("GALAXY_TEST_FILE_DIR", self._in_root_dir("test-data")) self.tool_test_data_directories = kwargs.get("tool_test_data_directories", default_tool_test_data_directories) # Deployers may either specify a complete list of mapping files or get the default for free and just # specify a local mapping file to adapt and extend the default one. if "conda_mapping_files" not in kwargs: _default_mapping = self._in_root_dir( os.path.join("lib", "galaxy", "tool_util", "deps", "resolvers", "default_conda_mapping.yml") ) # dependency resolution options are consumed via config_dict - so don't populate # self, populate config_dict self.config_dict["conda_mapping_files"] = [self.local_conda_mapping_file, _default_mapping] if self.container_resolvers_config_file: self.container_resolvers_config_file = self._in_config_dir(self.container_resolvers_config_file) # tool_dependency_dir can be "none" (in old configs). If so, set it to None if self.tool_dependency_dir and self.tool_dependency_dir.lower() == "none": self.tool_dependency_dir = None if self.mulled_channels: self.mulled_channels = [c.strip() for c in self.mulled_channels.split(",")] # type: ignore[attr-defined] default_job_resubmission_condition = kwargs.get("default_job_resubmission_condition", "") if not default_job_resubmission_condition.strip(): default_job_resubmission_condition = None self.default_job_resubmission_condition = default_job_resubmission_condition # Configuration options for taking advantage of nginx features if self.nginx_upload_store: self.nginx_upload_store = os.path.abspath(self.nginx_upload_store) if self.tus_upload_store: self.tus_upload_store = os.path.abspath(self.tus_upload_store) self.object_store = kwargs.get("object_store", "disk") self.object_store_check_old_style = string_as_bool(kwargs.get("object_store_check_old_style", False)) self.object_store_cache_path = self._in_root_dir( kwargs.get("object_store_cache_path", self._in_data_dir("object_store_cache")) ) self._configure_dataset_storage() # Handle AWS-specific config options for backward compatibility if kwargs.get("aws_access_key") is not None: self.os_access_key = kwargs.get("aws_access_key") self.os_secret_key = kwargs.get("aws_secret_key") self.os_bucket_name = kwargs.get("s3_bucket") self.os_use_reduced_redundancy = kwargs.get("use_reduced_redundancy", False) else: self.os_access_key = kwargs.get("os_access_key") self.os_secret_key = kwargs.get("os_secret_key") self.os_bucket_name = kwargs.get("os_bucket_name") self.os_use_reduced_redundancy = kwargs.get("os_use_reduced_redundancy", False) self.os_host = kwargs.get("os_host") self.os_port = kwargs.get("os_port") self.os_is_secure = string_as_bool(kwargs.get("os_is_secure", True)) self.os_conn_path = kwargs.get("os_conn_path", "/") self.object_store_cache_size = float(kwargs.get("object_store_cache_size", -1)) self.distributed_object_store_config_file = kwargs.get("distributed_object_store_config_file") if self.distributed_object_store_config_file is not None: self.distributed_object_store_config_file = self._in_root_dir(self.distributed_object_store_config_file) self.irods_root_collection_path = kwargs.get("irods_root_collection_path") self.irods_default_resource = kwargs.get("irods_default_resource") # Heartbeat log file name override if self.global_conf is not None and "heartbeat_log" in self.global_conf: self.heartbeat_log = self.global_conf["heartbeat_log"] # Determine which 'server:' this is self.server_name = "main" for arg in sys.argv: # Crummy, but PasteScript does not give you a way to determine this if arg.lower().startswith("--server-name="): self.server_name = arg.split("=", 1)[-1] # Allow explicit override of server name in config params if "server_name" in kwargs: self.server_name = kwargs["server_name"] # The application stack code may manipulate the server name. It also needs to be accessible via the get() method # for galaxy.util.facts() self.config_dict["base_server_name"] = self.base_server_name = self.server_name # Store all configured server names for the message queue routing self.server_names = [] for section in self.global_conf_parser.sections(): if section.startswith("server:"): self.server_names.append(section.replace("server:", "", 1)) self._set_host_related_options(kwargs) # Asynchronous execution process pools - limited functionality for now, attach_to_pools is designed to allow # webless Galaxy server processes to attach to arbitrary message queues (e.g. as job handlers) so they do not # have to be explicitly defined as such in the job configuration. self.attach_to_pools = kwargs.get("attach_to_pools", []) or [] # Store advanced job management config self.job_handlers = [x.strip() for x in kwargs.get("job_handlers", self.server_name).split(",")] self.default_job_handlers = [ x.strip() for x in kwargs.get("default_job_handlers", ",".join(self.job_handlers)).split(",") ] # Galaxy internal control queue configuration. # If specified in universe, use it, otherwise we use whatever 'real' # database is specified. Lastly, we create and use new sqlite database # (to minimize locking) as a final option. if "amqp_internal_connection" in kwargs: self.amqp_internal_connection = kwargs.get("amqp_internal_connection") # TODO Get extra amqp args as necessary for ssl elif "database_connection" in kwargs: self.amqp_internal_connection = f"sqlalchemy+{self.database_connection}" else: self.amqp_internal_connection = ( f"sqlalchemy+sqlite:///{self._in_data_dir('control.sqlite')}?isolation_level=IMMEDIATE" ) self._process_celery_config() self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format) try: with open(self.user_preferences_extra_conf_path) as stream: self.user_preferences_extra = yaml.safe_load(stream) except Exception: if self.is_set("user_preferences_extra_conf_path"): log.warning( f"Config file ({self.user_preferences_extra_conf_path}) could not be found or is malformed." ) self.user_preferences_extra = {"preferences": {}} # Experimental: This will not be enabled by default and will hide # nonproduction code. # The api_folders refers to whether the API exposes the /folders section. self.api_folders = string_as_bool(kwargs.get("api_folders", False)) # This is for testing new library browsing capabilities. self.new_lib_browse = string_as_bool(kwargs.get("new_lib_browse", False)) # Logging configuration with logging.config.configDict: # Statistics and profiling with statsd self.statsd_host = kwargs.get("statsd_host", "") self.proxy_session_map = self.dynamic_proxy_session_map self.manage_dynamic_proxy = self.dynamic_proxy_manage # Set to false if being launched externally # InteractiveTools propagator mapping file self.interactivetools_map = self._in_root_dir( kwargs.get("interactivetools_map", self._in_data_dir("interactivetools_map.sqlite")) ) # Compliance/Policy variables self.redact_username_during_deletion = False self.redact_email_during_deletion = False self.redact_ip_address = False self.redact_username_in_logs = False self.redact_email_in_job_name = False self.redact_user_details_in_bugreport = False self.redact_user_address_during_deletion = False # GDPR compliance mode changes values on a number of variables. Other # policies could change (non)overlapping subsets of these variables. if self.enable_beta_gdpr: self.expose_user_name = False self.expose_user_email = False self.redact_username_during_deletion = True self.redact_email_during_deletion = True self.redact_ip_address = True self.redact_username_in_logs = True self.redact_email_in_job_name = True self.redact_user_details_in_bugreport = True self.redact_user_address_during_deletion = True self.allow_user_deletion = True LOGGING_CONFIG_DEFAULT["formatters"]["brief"] = { "format": "%(asctime)s %(levelname)-8s %(name)-15s %(message)s" } LOGGING_CONFIG_DEFAULT["handlers"]["compliance_log"] = { "class": "logging.handlers.RotatingFileHandler", "formatter": "brief", "filename": "compliance.log", "backupCount": 0, } LOGGING_CONFIG_DEFAULT["loggers"]["COMPLIANCE"] = { "handlers": ["compliance_log"], "level": "DEBUG", "qualname": "COMPLIANCE", } log_destination = kwargs.get("log_destination") log_rotate_size = size_to_bytes(unicodify(kwargs.get("log_rotate_size", 0))) log_rotate_count = int(kwargs.get("log_rotate_count", 0)) if log_destination == "stdout": LOGGING_CONFIG_DEFAULT["handlers"]["console"] = { "class": "logging.StreamHandler", "formatter": "stack", "level": "DEBUG", "stream": "ext://sys.stdout", "filters": ["stack"], } elif log_destination: LOGGING_CONFIG_DEFAULT["handlers"]["console"] = { "class": "logging.handlers.RotatingFileHandler", "formatter": "stack", "level": "DEBUG", "filename": log_destination, "filters": ["stack"], "maxBytes": log_rotate_size, "backupCount": log_rotate_count, } if galaxy_daemon_log_destination := os.environ.get("GALAXY_DAEMON_LOG"): LOGGING_CONFIG_DEFAULT["handlers"]["files"] = { "class": "logging.handlers.RotatingFileHandler", "formatter": "stack", "level": "DEBUG", "filename": galaxy_daemon_log_destination, "filters": ["stack"], "maxBytes": log_rotate_size, "backupCount": log_rotate_count, } LOGGING_CONFIG_DEFAULT["root"]["handlers"].append("files") # Load and flatten themes into css variables def _load_theme(path: str, theme_dict: dict): if self._path_exists(path): with open(path) as f: themes = yaml.safe_load(f) for key, val in themes.items(): theme_dict[key] = flatten_theme(val) self.themes = {} if "themes_config_file_by_host" in self.config_dict: self.themes_by_host = {} resolve_to_dir = self.schema.paths_to_resolve["themes_config_file"] resolve_dir_path = getattr(self, resolve_to_dir) for host, file_name in self.config_dict["themes_config_file_by_host"].items(): self.themes_by_host[host] = {} file_path = self._in_dir(resolve_dir_path, file_name) _load_theme(file_path, self.themes_by_host[host]) else: _load_theme(self.themes_config_file, self.themes) def _process_celery_config(self): if self.celery_conf and self.celery_conf.get("result_backend") is None: # If the result_backend is not set, use a SQLite database in the data directory result_backend = f"db+sqlite:///{self._in_data_dir('results.sqlite')}?isolation_level=IMMEDIATE" self.celery_conf["result_backend"] = result_backend def _check_database_connection_strings(self): """ Verify connection URI strings in galaxy's configuration are parseable with urllib. """ def try_parsing(value, name): try: urlparse(value) except ValueError as e: msg = f"The `{name}` configuration property cannot be parsed as a connection URI." if "Invalid IPv6 URL" in str(e): msg += ( "\nBesides an invalid IPv6 format, this may be caused by a bracket character in the `netloc` part of " "the URI (most likely, the password). In this case, you should percent-encode that character: for `[` " "use `%5B`, for `]` use `%5D`. For example, if your URI is `postgresql://user:pass[word@host/db`, " "change it to `postgresql://user:pass%5Bword@host/db`. " ) raise ConfigurationError(msg) from e try_parsing(self.database_connection, "database_connection") try_parsing(self.install_database_connection, "install_database_connection") try_parsing(self.amqp_internal_connection, "amqp_internal_connection") def _configure_dataset_storage(self): # The default for `file_path` has changed in 20.05; we may need to fall back to the old default self._set_alt_paths("file_path", self._in_data_dir("files")) # this is called BEFORE guessing id/uuid ID, UUID = "id", "uuid" if self.is_set("object_store_store_by"): if self.object_store_store_by not in [ID, UUID]: raise Exception(f"Invalid value for object_store_store_by [{self.object_store_store_by}]") elif os.path.basename(self.file_path) == "objects": self.object_store_store_by = UUID else: self.object_store_store_by = ID def _load_list_from_file(self, filepath): with open(filepath) as f: return [line.strip() for line in f] def _set_host_related_options(self, kwargs): # The following 3 method calls must be made in sequence self._set_galaxy_infrastructure_url(kwargs) self._set_hostname() self._set_email_from() def _set_galaxy_infrastructure_url(self, kwargs): # indicate if this was not set explicitly, so dependending on the context a better default # can be used (request url in a web thread, Docker parent in IE stuff, etc.) self.galaxy_infrastructure_url_set = kwargs.get("galaxy_infrastructure_url") is not None if "HOST_IP" in self.galaxy_infrastructure_url: self.galaxy_infrastructure_url = string.Template(self.galaxy_infrastructure_url).safe_substitute( {"HOST_IP": socket.gethostbyname(socket.gethostname())} ) if "GALAXY_WEB_PORT" in self.galaxy_infrastructure_url: port = os.environ.get("GALAXY_WEB_PORT") if not port: raise Exception("$GALAXY_WEB_PORT set in galaxy_infrastructure_url, but environment variable not set") self.galaxy_infrastructure_url = string.Template(self.galaxy_infrastructure_url).safe_substitute( {"GALAXY_WEB_PORT": port} ) if "UWSGI_PORT" in self.galaxy_infrastructure_url: raise Exception("UWSGI_PORT is not supported anymore") def _set_hostname(self): if self.galaxy_infrastructure_url_set: self.hostname = urlparse(self.galaxy_infrastructure_url).hostname else: self.hostname = socket.getfqdn() def _set_email_from(self): if not self.email_from: self.email_from = f"{DEFAULT_EMAIL_FROM_LOCAL_PART}@{self.hostname}"
[docs] def reload_sanitize_allowlist(self, explicit=True): self.sanitize_allowlist = [] if not os.path.exists(self.sanitize_allowlist_file): if explicit: log.warning( "Sanitize log file explicitly specified as '%s' but does not exist, continuing with no tools allowlisted.", self.sanitize_allowlist_file, ) else: with open(self.sanitize_allowlist_file) as f: self.sanitize_allowlist = sorted( line.strip() for line in f.readlines() if line.strip() and not line.startswith("#") )
[docs] def ensure_tempdir(self): self._ensure_directory(self.new_file_path)
[docs] def check(self): # Check that required directories exist; attempt to create otherwise paths_to_check = [ self.data_dir, self.ftp_upload_dir, self.library_import_dir, self.managed_config_dir, self.new_file_path, self.nginx_upload_store, self.tus_upload_store, self.object_store_cache_path, self.template_cache_path, self.tool_data_path, self.user_library_import_dir, ] for path in paths_to_check: self._ensure_directory(path) # Check that required files exist tool_configs = self.tool_configs for path in tool_configs: if not os.path.exists(path) and path not in (self.shed_tool_config_file, self.migrated_tools_config): raise ConfigurationError(f"Tool config file not found: {path}") for datatypes_config in listify(self.datatypes_config): if not os.path.isfile(datatypes_config): raise ConfigurationError(f"Datatypes config file not found: {datatypes_config}") # Check for deprecated options. for key in self.config_dict.keys(): if key in self.deprecated_options: log.warning( f"Config option '{key}' is deprecated and will be removed in a future release. Please consult the latest version of the sample configuration file." )
[docs] def is_fetch_with_celery_enabled(self): """ True iff celery is enabled and celery_conf["task_routes"]["galaxy.fetch_data"] != DISABLED_FLAG. """ celery_enabled = self.enable_celery_tasks try: fetch_disabled = self.celery_conf["task_routes"]["galaxy.fetch_data"] == DISABLED_FLAG except (TypeError, KeyError): # celery_conf is None or sub-dictionary is none or either key is not present fetch_disabled = False return celery_enabled and not fetch_disabled
@staticmethod def _parse_allowed_origin_hostnames(allowed_origin_hostnames): """ Parse a CSV list of strings/regexp of hostnames that should be allowed to use CORS and will be sent the Access-Control-Allow-Origin header. """ allowed_origin_hostnames_list = listify(allowed_origin_hostnames) if not allowed_origin_hostnames_list: return None def parse(string): # a string enclosed in fwd slashes will be parsed as a regexp: e.g. /<some val>/ if string[0] == "/" and string[-1] == "/": string = string[1:-1] return re.compile(string, flags=(re.UNICODE)) return string return [parse(v) for v in allowed_origin_hostnames_list if v]
# legacy naming Configuration = GalaxyAppConfiguration
[docs]def reload_config_options(current_config): """Reload modified reloadable config options.""" modified_config = read_properties_from_file(current_config.config_file) for option in current_config.schema.reloadable_options: if option in modified_config: # compare to raw value, as that one is set only on load and reload if current_config._raw_config[option] != modified_config[option]: current_config._raw_config[option] = modified_config[option] setattr(current_config, option, modified_config[option]) log.info(f"Reloaded {option}")
[docs]def get_database_engine_options(kwargs, model_prefix=""): """ Allow options for the SQLAlchemy database engine to be passed by using the prefix "database_engine_option". """ conversions: Dict[str, Callable[[Any], Union[bool, int]]] = { "convert_unicode": string_as_bool, "pool_timeout": int, "echo": string_as_bool, "echo_pool": string_as_bool, "pool_recycle": int, "pool_size": int, "max_overflow": int, "pool_threadlocal": string_as_bool, "server_side_cursors": string_as_bool, } prefix = f"{model_prefix}database_engine_option_" prefix_len = len(prefix) rval = {} for key, value in kwargs.items(): if key.startswith(prefix): key = key[prefix_len:] if key in conversions: value = conversions[key](value) rval[key] = value return rval