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Source code for galaxy.config
"""
Universe configuration builder.
"""
# absolute_import needed for tool_shed package.
import configparser
import ipaddress
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 (
Any,
Callable,
cast,
Dict,
List,
Optional,
Set,
SupportsInt,
TypeVar,
Union,
)
import yaml
from galaxy.config.schema import AppSchema
from galaxy.containers import parse_containers_config
from galaxy.exceptions import ConfigurationError
from galaxy.util import (
listify,
string_as_bool,
unicodify,
)
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 (
find_config_file,
read_properties_from_file,
running_from_source,
)
from ..version import VERSION_MAJOR, VERSION_MINOR
try:
from importlib.resources import files # type: ignore[attr-defined]
except ImportError:
# Python < 3.9
from importlib_resources import files # type: ignore[no-redef]
log = logging.getLogger(__name__)
DEFAULT_LOCALE_FORMAT = '%a %b %e %H:%M:%S %Y'
ISO_DATETIME_FORMAT = "%Y-%m-%d %H:%M:%S"
GALAXY_APP_NAME = "galaxy"
GALAXY_SCHEMAS_PATH = files("galaxy.config") / "schemas"
GALAXY_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "config_schema.yml"
REPORTS_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "reports_config_schema.yml"
TOOL_SHED_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "tool_shed_config_schema.yml"
UWSGI_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "uwsgi_schema.yml"
LOGGING_CONFIG_DEFAULT: Dict[str, Any] = {
'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',
},
},
'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`"""
[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 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
[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 = find_config_file('galaxy')
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.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 type(value) is 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 '{0}' option should be relative to '{1}'. To suppress this warning, "
"move '{0}' into '{1}', or set it's value to an absolute path.".format(key, resolves_to)
)
return new_path
return current_path
current_value = getattr(self, key) # resolved path or list of resolved paths
if type(current_value) is 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):
"""Determine if the provided user is listed in `admin_users`."""
return user 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):
deprecated_options = ('database_file', 'track_jobs_in_database', 'blacklist_file', 'whitelist_file',
'sanitize_whitelist_file', 'user_library_import_symlink_whitelist', 'fetch_url_whitelist',
'containers_resolvers_config_file')
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',
}
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',
'containers_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',
}
add_sample_file_to_defaults = {
'build_sites_config_file',
'datatypes_config_file',
'job_metrics_config_file',
'tool_data_table_config_path',
'tool_config_file',
}
listify_options = {
'tool_data_table_config_path',
'tool_config_file',
}
database_connection: str
tool_path: str
tool_data_path: str
builds_file_path: str
len_file_path: str
integrated_tool_panel_config: str
toolbox_filter_base_modules: List[str]
tool_filters: List[str]
tool_label_filters: List[str]
tool_section_filters: List[str]
user_tool_filters: List[str]
user_tool_section_filters: List[str]
user_tool_label_filters: List[str]
password_expiration_period: timedelta
shed_tool_data_path: str
hours_between_check: int
galaxy_data_manager_data_path: str
use_remote_user: bool
cluster_files_directory: str
preserve_python_environment: str
email_from: str
workflow_resource_params_mapper: str
sanitize_allowlist_file: str
allowed_origin_hostnames: List[str]
trust_jupyter_notebook_conversion: bool
user_library_import_symlink_allowlist: List[str]
user_library_import_dir_auto_creation: bool
container_resolvers_config_file: str
tool_dependency_dir: Optional[str]
involucro_path: str
mulled_channels: List[str]
nginx_upload_store: str
tus_upload_store: str
pretty_datetime_format: str
visualization_plugins_directory: str
galaxy_infrastructure_url: str
[docs] def __init__(self, **kwargs):
super().__init__(**kwargs)
self._override_tempdir(kwargs)
self._configure_sqlalchemy20_warnings(kwargs)
self._process_config(kwargs)
def _configure_sqlalchemy20_warnings(self, kwargs):
"""
This method should be deleted after migration to SQLAlchemy 2.0 is complete.
To enable warnings, set `GALAXY_CONFIG_SQLALCHEMY_WARN_20=1`,
"""
warn = string_as_bool(kwargs.get('sqlalchemy_warn_20', False))
if warn:
import sqlalchemy
sqlalchemy.util.deprecations.SQLALCHEMY_WARN_20 = True
self._setup_sqlalchemy20_warnings_filters()
def _setup_sqlalchemy20_warnings_filters(self):
import warnings
from sqlalchemy.exc import RemovedIn20Warning
# Always display RemovedIn20Warning warnings.
warnings.filterwarnings('always', category=RemovedIn20Warning)
# Optionally, enable filters for specific warnings (raise error, or log, etc.)
# messages = [
# r"replace with warning text to match",
# ]
# for msg in messages:
# warnings.filterwarnings('error', message=msg, category=RemovedIn20Warning)
#
# See documentation:
# https://docs.python.org/3.7/library/warnings.html#the-warnings-filter
# https://docs.sqlalchemy.org/en/14/changelog/migration_20.html#migration-to-2-0-step-three-resolve-all-removedin20warnings
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"
if per_host_option in self.config_dict:
per_host = self.config_dict[per_host_option] or {}
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):
# 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
# Database related configuration
self.check_migrate_databases = 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_create_tables = string_as_bool(kwargs.get('database_create_tables', 'True'))
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")
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 = {}
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 = [
ipaddress.ip_network(unicodify(ip.strip())) # If it has a slash, assume 127.0.0.1/24 notation
if '/' in ip else
ipaddress.ip_address(unicodify(ip.strip())) # Otherwise interpret it as an ip address.
for ip in kwargs.get("fetch_url_allowlist", "").split(',')
if len(ip.strip()) > 0
]
self.job_queue_cleanup_interval = int(kwargs.get("job_queue_cleanup_interval", "5"))
self.cluster_files_directory = self._in_root_dir(self.cluster_files_directory)
# 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))
# activation_email was used until release_15.03
activation_email = kwargs.get('activation_email')
self.email_from = self.email_from or activation_email
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.involucro_path is None:
target_dir = self.tool_dependency_dir or self.schema.defaults['tool_dependency_dir']
self.involucro_path = self._in_data_dir(os.path.join(target_dir, "involucro"))
self.involucro_path = self._in_root_dir(self.involucro_path)
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.get("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_galaxy_infrastructure_url(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.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', '')
ie_dirs = self.interactive_environment_plugins_directory
self.gie_dirs = [d.strip() for d in (ie_dirs.split(",") if ie_dirs else [])]
if ie_dirs:
self.visualization_plugins_directory += f",{ie_dirs}"
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")))
self.containers_conf = parse_containers_config(self.containers_config_file)
# 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")
galaxy_daemon_log_destination = os.environ.get('GALAXY_DAEMON_LOG')
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.FileHandler',
'formatter': 'stack',
'level': 'DEBUG',
'filename': log_destination,
'filters': ['stack']
}
if galaxy_daemon_log_destination:
LOGGING_CONFIG_DEFAULT['handlers']['files'] = {
'class': 'logging.FileHandler',
'formatter': 'stack',
'level': 'DEBUG',
'filename': galaxy_daemon_log_destination,
'filters': ['stack']
}
LOGGING_CONFIG_DEFAULT['root']['handlers'].append('files')
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_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:
import uwsgi
http = unicodify(uwsgi.opt['http'])
host, port = http.split(":", 1)
assert port, "galaxy_infrastructure_url depends on dynamic PORT determination but port unknown"
self.galaxy_infrastructure_url = string.Template(self.galaxy_infrastructure_url).safe_substitute({
'UWSGI_PORT': port
})
[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 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.")
@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