Warning
This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.config
"""
Universe configuration builder.
"""
# absolute_import needed for tool_shed package.
from __future__ import absolute_import
import collections
import errno
import ipaddress
import logging
import logging.config
import os
import re
import signal
import socket
import string
import sys
import tempfile
import threading
import time
from datetime import timedelta
import yaml
from beaker.cache import CacheManager
from beaker.util import parse_cache_config_options
from six import string_types
from six.moves import configparser
from galaxy.config.schema import AppSchema
from galaxy.containers import parse_containers_config
from galaxy.exceptions import ConfigurationError
from galaxy.model import mapping
from galaxy.model.tool_shed_install.migrate.check import create_or_verify_database as tsi_create_or_verify_database
from galaxy.util import (
ExecutionTimer,
listify,
string_as_bool,
unicodify,
)
from galaxy.util.custom_logging import LOGLV_TRACE
from galaxy.util.dbkeys import GenomeBuilds
from galaxy.util.properties import (
find_config_file,
read_properties_from_file,
running_from_source,
)
from galaxy.web.formatting import expand_pretty_datetime_format
from galaxy.web_stack import (
get_stack_facts,
register_postfork_function
)
from ..version import VERSION_MAJOR
log = logging.getLogger(__name__)
GALAXY_APP_NAME = 'galaxy'
GALAXY_CONFIG_SCHEMA_PATH = 'lib/galaxy/webapps/galaxy/config_schema.yml'
LOGGING_CONFIG_DEFAULT = {
'disable_existing_loggers': False,
'version': 1,
'root': {
'handlers': ['console'],
'level': 'DEBUG',
},
'loggers': {
'paste.httpserver.ThreadPool': {
'level': 'WARN',
'qualname': 'paste.httpserver.ThreadPool',
},
'routes.middleware': {
'level': 'WARN',
'qualname': 'routes.middleware',
},
'amqp': {
'level': 'INFO',
'qualname': 'amqp',
},
},
'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]class BaseAppConfiguration(object):
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 (IOError, 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')
# mutable_config_dir is intentionally not configurable. You can
# override individual mutable configs with config options, but they
# should be considered Galaxy-controlled data files and will by default
# just live in the data dir
self.sample_config_dir = os.path.join(os.path.dirname(__file__), 'sample')
if running_from_source:
if self.config_dir is None:
self.config_dir = os.path.join(self.root, 'config')
if self.data_dir is None:
self.data_dir = os.path.join(self.root, 'database')
self.mutable_config_dir = self.config_dir
else:
if self.config_dir is None:
self.config_dir = os.getcwd()
if self.data_dir is None:
self.data_dir = os.path.join(self.config_dir, 'data')
self.mutable_config_dir = os.path.join(self.data_dir, 'config')
# TODO: do we still need to support ../shed_tools when running_from_source?
self.shed_tools_dir = os.path.join(self.data_dir, 'shed_tools')
log.debug("Configuration directory is %s", self.config_dir)
log.debug("Data directory is %s", self.data_dir)
log.debug("Mutable config directory is %s", self.mutable_config_dir)
_set_global_conf()
_set_config_directories()
def _in_mutable_config_dir(self, path):
return os.path.join(self.mutable_config_dir, path)
def _in_config_dir(self, path):
return os.path.join(self.config_dir, path)
def _in_sample_dir(self, path):
return os.path.join(self.sample_config_dir, path)
def _parse_config_file_options(self, defaults, listify_defaults, config_kwargs):
for var, values in defaults.items():
if config_kwargs.get(var) is not None:
path = config_kwargs.get(var)
setattr(self, var + '_set', True)
else:
for value in values:
if os.path.exists(os.path.join(self.root, value)):
path = value
break
else:
path = values[-1]
setattr(self, var + '_set', False)
setattr(self, var, os.path.join(self.root, path))
for var, values in listify_defaults.items():
paths = []
if config_kwargs.get(var) is not None:
paths = listify(config_kwargs.get(var))
setattr(self, var + '_set', True)
else:
for value in values:
for path in listify(value):
if not os.path.exists(os.path.join(self.root, path)):
break
else:
paths = listify(value)
break
else:
paths = listify(values[-1])
setattr(self, var + '_set', False)
setattr(self, var, [os.path.join(self.root, x) for x in paths])
[docs]class GalaxyAppConfiguration(BaseAppConfiguration):
deprecated_options = ('database_file', 'track_jobs_in_database')
default_config_file_name = 'galaxy.yml'
# {key: config option, value: deprecated directory name}
# If value == first dir in a user path that resolves to key, it will be stripped from the path
deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
[docs] def __init__(self, **kwargs):
self._load_schema() # Load schema from schema definition file
self._load_config_from_schema() # Load default propery values from schema
self._validate_schema_paths() # check that paths can be resolved
self._update_raw_config_from_kwargs(kwargs) # Overwrite default values passed as kwargs
self._create_attributes_from_raw_config() # Create attributes for LOADED properties
self.config_dict = kwargs
self.root = find_root(kwargs)
self._set_config_base(kwargs) # must be called prior to _resolve_paths()
self._resolve_paths(kwargs) # Overwrite attributes (not _raw_config) w/resolved paths
self._process_config(kwargs) # Finish processing configuration
def _load_schema(self):
self.schema = AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
self.appschema = self.schema.app_schema
def _load_config_from_schema(self):
self._raw_config = {} # keeps track of startup values (kwargs or schema default)
self.reloadable_options = set() # config options we can reload at runtime
self._paths_to_resolve = {} # {config option: referenced config option}
for key, data in self.appschema.items():
self._raw_config[key] = data.get('default')
if data.get('reloadable'):
self.reloadable_options.add(key)
if data.get('path_resolves_to'):
self._paths_to_resolve[key] = data.get('path_resolves_to')
def _validate_schema_paths(self):
def check_exists(option, key):
if not option:
message = "Invalid schema: property '{}' listed as path resolution target " \
"for '{}' does not exist".format(resolves_to, key)
raise_error(message)
def check_type_is_str(option, key):
if option.get('type') != 'str':
message = "Invalid schema: property '{}' should have type 'str'".format(key)
raise_error(message)
def check_is_dag():
visited = set()
for key in self._paths_to_resolve:
visited.clear()
while key:
visited.add(key)
key = self.appschema[key].get('path_resolves_to')
if key and key in visited:
raise_error('Invalid schema: cycle detected')
def raise_error(message):
log.error(message)
raise ConfigurationError(message)
for key, resolves_to in self._paths_to_resolve.items():
parent = self.appschema.get(resolves_to)
check_exists(parent, key)
check_type_is_str(parent, key)
check_type_is_str(self.appschema[key], key)
check_is_dag() # must be called last: walks entire graph
def _update_raw_config_from_kwargs(self, kwargs):
def convert_datatype(key, value):
datatype = self.appschema[key].get('type')
# check for `not None` explicitly (value can be falsy)
if value is not None and datatype in type_converters:
return type_converters[datatype](value)
return value
def strip_deprecated_dir(key, value):
resolves_to = self.appschema[key].get('path_resolves_to')
if resolves_to: # value is a path that will be resolved
first_dir = value.split(os.sep)[0] # get first directory component
if first_dir == self.deprecated_dirs[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, value
)
return value[len(ignore):]
return value
type_converters = {'bool': string_as_bool, 'int': int, 'float': float, 'str': str}
for key, value in kwargs.items():
if key in self.appschema:
value = convert_datatype(key, value)
if value:
value = strip_deprecated_dir(key, value)
self._raw_config[key] = value
def _create_attributes_from_raw_config(self):
for key, value in self._raw_config.items():
if hasattr(self, key):
raise ConfigurationError("Attempting to override existing attribute '%s'" % key)
setattr(self, key, value)
def _resolve_paths(self, kwargs):
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.appschema[key].get('path_resolves_to')
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._paths_to_resolve:
resolve(key)
def _process_config(self, kwargs):
# Resolve paths of other config files
self.parse_config_file_options(kwargs)
# 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
# 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 = os.path.join(self.data_dir, 'universe.sqlite')
self.database_connection = 'sqlite:///%s?isolation_level=IMMEDIATE' % db_path
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.database_log_query_counts = string_as_bool(kwargs.get("database_log_query_counts", 'False'))
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_")
override_tempdir = string_as_bool(kwargs.get("override_tempdir", "True"))
if override_tempdir:
tempfile.tempdir = self.new_file_path
self.shared_home_dir = kwargs.get("shared_home_dir")
self.cookie_path = kwargs.get("cookie_path")
self.tool_path = os.path.join(self.root, self.tool_path)
self.tool_data_path = os.path.join(self.root, self.tool_data_path)
if not running_from_source and kwargs.get("tool_data_path") is None:
self.tool_data_path = os.path.join(self.data_dir, "tool-data")
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)
# Galaxy OIDC settings.
self.oidc_config = kwargs.get("oidc_config_file", self.oidc_config_file)
self.oidc_backends_config = kwargs.get("oidc_backends_config_file", self.oidc_backends_config_file)
self.oidc = []
self.integrated_tool_panel_config = os.path.join(self.mutable_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 = os.path.join(self.root, 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(self.password_expiration_period))
if self.shed_tool_data_path:
self.shed_tool_data_path = os.path.join(self.root, 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, string_types):
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_whitelist_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_whitelist", "").split(',')
if len(ip.strip()) > 0
]
self.template_path = os.path.join(self.root, kwargs.get("template_path", "templates"))
self.job_queue_cleanup_interval = int(kwargs.get("job_queue_cleanup_interval", "5"))
self.cluster_files_directory = self.resolve_path(self.cluster_files_directory)
# Fall back to legacy job_working_directory config variable if set.
self.jobs_directory = os.path.join(self.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")
# Older default container cache path, I don't think anyone is using it anymore and it wasn't documented - we
# should probably drop the backward compatiblity to save the path check.
self.container_image_cache_path = os.path.join(self.data_dir, kwargs.get("container_image_cache_path", "container_images"))
if not os.path.exists(self.container_image_cache_path):
self.container_image_cache_path = self.resolve_path(kwargs.get("container_image_cache_path", os.path.join(self.data_dir, "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
# Get the disposable email domains blacklist file and its contents
self.blacklist_content = None
if self.blacklist_file:
self.blacklist_file = os.path.join(self.root, self.blacklist_file)
try:
with open(self.blacklist_file) as f:
self.blacklist_content = [line.rstrip() for line in f]
except IOError:
log.error("CONFIGURATION ERROR: Can't open supplied blacklist file from path: %s", self.blacklist_file)
self.persistent_communication_rooms = listify(self.persistent_communication_rooms, do_strip=True)
# The transfer manager and deferred job queue
self.enable_beta_job_managers = string_as_bool(kwargs.get('enable_beta_job_managers', 'False'))
# 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'))
workflow_resource_params_mapper = kwargs.get("workflow_resource_params_mapper")
if not workflow_resource_params_mapper:
workflow_resource_params_mapper = None
elif ":" not in workflow_resource_params_mapper:
# Assume it is not a Python function, so a file
workflow_resource_params_mapper = self.resolve_path(workflow_resource_params_mapper)
# else: a Python a function!
self.workflow_resource_params_mapper = 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', "")
self.sanitize_whitelist_file = os.path.join(self.root, self.sanitize_whitelist_file)
self.allowed_origin_hostnames = self._parse_allowed_origin_hostnames(kwargs)
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_whitelist = listify(self.user_library_import_symlink_whitelist, 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", os.path.join(self.root, "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:
conda_mapping_files = [
self.local_conda_mapping_file,
os.path.join(self.root, "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"] = conda_mapping_files
if self.containers_resolvers_config_file:
self.containers_resolvers_config_file = os.path.join(self.config_dir, self.containers_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.appschema['tool_dependency_dir'].get('default')
self.involucro_path = os.path.join(self.data_dir, target_dir, "involucro")
self.involucro_path = os.path.join(self.root, self.involucro_path)
if self.mulled_channels:
self.mulled_channels = [c.strip() for c in self.mulled_channels.split(',')]
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)
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.resolve_path(kwargs.get("object_store_cache_path", os.path.join(self.data_dir, "object_store_cache")))
# 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 = os.path.join(self.root, 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']
if self.heartbeat_log is None:
self.heartbeat_log = 'heartbeat_{server_name}.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 = "sqlalchemy+" + self.database_connection
else:
self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % os.path.join(self.data_dir, "control.sqlite")
self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format)
try:
with open(self.user_preferences_extra_conf_path, 'r') as stream:
self.user_preferences_extra = yaml.safe_load(stream)
except Exception:
if self.user_preferences_extra_conf_path_set:
log.warning('Config file (%s) could not be found or is malformed.' % self.user_preferences_extra_conf_path)
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:
self.logging = kwargs.get('logging')
# 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 += ",%s" % 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.resolve_path(kwargs.get("interactivetools_map", os.path.join(self.data_dir, "interactivetools_map.sqlite")))
self.interactivetools_prefix = kwargs.get("interactivetools_prefix", "interactivetool")
self.interactivetools_proxy_host = kwargs.get("interactivetools_proxy_host", None)
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")
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': kwargs['log_destination'],
'filters': ['stack']
}
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 "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
})
@property
def admin_users(self):
return self._admin_users
@admin_users.setter
def admin_users(self, value):
self._admin_users = value
if value:
self.admin_users_list = [u.strip() for u in value.split(',') if u]
else: # provide empty list for convenience (check membership, etc.)
self.admin_users_list = []
@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)
else:
return None
[docs] def parse_config_file_options(self, kwargs):
"""
Backwards compatibility for config files moved to the config/ dir.
"""
defaults = dict(
auth_config_file=[self._in_config_dir('auth_conf.xml')],
build_sites_config_file=[self._in_config_dir('build_sites.yml'), self._in_sample_dir('build_sites.yml.sample')],
containers_config_file=[self._in_config_dir('containers_conf.yml')],
data_manager_config_file=[self._in_config_dir('data_manager_conf.xml')],
datatypes_config_file=[self._in_config_dir('datatypes_conf.xml'), self._in_sample_dir('datatypes_conf.xml.sample')],
dependency_resolvers_config_file=[self._in_config_dir('dependency_resolvers_conf.xml')],
error_report_file=[self._in_config_dir('error_report.yml')],
job_config_file=[self._in_config_dir('job_conf.xml')],
job_metrics_config_file=[self._in_config_dir('job_metrics_conf.xml'), self._in_sample_dir('job_metrics_conf.xml.sample')],
job_resource_params_file=[self._in_config_dir('job_resource_params_conf.xml')],
local_conda_mapping_file=[self._in_config_dir('local_conda_mapping.yml')],
migrated_tools_config=[self._in_mutable_config_dir('migrated_tools_conf.xml')],
modules_mapping_files=[self._in_config_dir('environment_modules_mapping.yml')],
object_store_config_file=[self._in_config_dir('object_store_conf.xml')],
oidc_backends_config_file=[self._in_config_dir('oidc_backends_config.xml')],
oidc_config_file=[self._in_config_dir('oidc_config.xml')],
shed_data_manager_config_file=[self._in_mutable_config_dir('shed_data_manager_conf.xml')],
shed_tool_config_file=[self._in_mutable_config_dir('shed_tool_conf.xml')],
shed_tool_data_table_config=[self._in_mutable_config_dir('shed_tool_data_table_conf.xml')],
tool_destinations_config_file=[self._in_config_dir('tool_destinations.yml')],
tool_sheds_config_file=[self._in_config_dir('tool_sheds_conf.xml')],
user_preferences_extra_conf_path=[self._in_config_dir('user_preferences_extra_conf.yml')],
workflow_resource_params_file=[self._in_config_dir('workflow_resource_params_conf.xml')],
workflow_schedulers_config_file=[self._in_config_dir('workflow_schedulers_conf.xml')],
markdown_export_css=[self._in_config_dir('markdown_export.css')],
markdown_export_css_pages=[self._in_config_dir('markdown_export_pages.css')],
markdown_export_css_invocation_reports=[self._in_config_dir('markdown_export_invocation_reports.css')],
)
listify_defaults = {
'tool_data_table_config_path': [
self._in_config_dir('tool_data_table_conf.xml'),
self._in_sample_dir('tool_data_table_conf.xml.sample')],
'tool_config_file': [
self._in_config_dir('tool_conf.xml'),
self._in_sample_dir('tool_conf.xml.sample')]
}
self._parse_config_file_options(defaults, listify_defaults, 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
[docs] def reload_sanitize_whitelist(self, explicit=True):
self.sanitize_whitelist = []
try:
with open(self.sanitize_whitelist_file, 'rt') as f:
for line in f.readlines():
if not line.startswith("#"):
self.sanitize_whitelist.append(line.strip())
except IOError:
if explicit:
log.warning("Sanitize log file explicitly specified as '%s' but does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
[docs] def get_bool(self, key, default):
if key in self.config_dict:
return string_as_bool(self.config_dict[key])
else:
return 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("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
[docs] def check(self):
paths_to_check = [self.tool_data_path, self.data_dir, self.mutable_config_dir]
# Check that required directories exist
for path in paths_to_check:
if path not in [None, False] and not os.path.isdir(path):
try:
os.makedirs(path)
except Exception as e:
raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
# Create the directories that it makes sense to create
for path in (self.new_file_path, self.template_cache_path, self.ftp_upload_dir,
self.library_import_dir, self.user_library_import_dir,
self.nginx_upload_store, self.object_store_cache_path):
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("Tool config file not found: %s" % path)
for datatypes_config in listify(self.datatypes_config):
if not os.path.isfile(datatypes_config):
raise ConfigurationError("Datatypes config file not found: %s" % datatypes_config)
# Check for deprecated options.
for key in self.config_dict.keys():
if key in self.deprecated_options:
log.warning("Config option '%s' is deprecated and will be removed in a future release. Please consult the latest version of the sample configuration file." % key)
[docs] def is_admin_user(self, user):
"""
Determine if the provided user is listed in `admin_users`.
NOTE: This is temporary, admin users will likely be specified in the
database in the future.
"""
return user is not None and user.email in self.admin_users_list
[docs] def resolve_path(self, path):
""" Resolve a path relative to Galaxy's root.
"""
return os.path.join(self.root, path)
@staticmethod
def _parse_allowed_origin_hostnames(kwargs):
"""
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 = listify(kwargs.get('allowed_origin_hostnames'))
if not allowed_origin_hostnames:
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 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.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('Reloaded %s' % 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 = {
'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 = "%sdatabase_engine_option_" % model_prefix
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
[docs]def init_models_from_config(config, map_install_models=False, object_store=None, trace_logger=None):
db_url = get_database_url(config)
model = mapping.init(
config.file_path,
db_url,
config.database_engine_options,
map_install_models=map_install_models,
database_query_profiling_proxy=config.database_query_profiling_proxy,
object_store=object_store,
trace_logger=trace_logger,
use_pbkdf2=config.get_bool('use_pbkdf2', True),
slow_query_log_threshold=config.slow_query_log_threshold,
thread_local_log=config.thread_local_log,
log_query_counts=config.database_log_query_counts,
)
return model
[docs]def configure_logging(config):
"""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.
"""
# Get root logger
logging.addLevelName(LOGLV_TRACE, "TRACE")
root = logging.getLogger()
# 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(**get_stack_facts(config=config))
logging_conf['handlers'][name] = conf
logging.config.dictConfig(logging_conf)
if getattr(config, "sentry_dsn", None):
from raven.handlers.logging import SentryHandler
sentry_handler = SentryHandler(config.sentry_dsn)
sentry_handler.setLevel(logging.WARN)
register_postfork_function(root.addHandler, sentry_handler)
[docs]class ConfiguresGalaxyMixin(object):
""" Shared code for configuring Galaxy-like app objects.
"""
def _configure_genome_builds(self, data_table_name="__dbkeys__", load_old_style=True):
self.genome_builds = GenomeBuilds(self, data_table_name=data_table_name, load_old_style=load_old_style)
[docs] def wait_for_toolbox_reload(self, old_toolbox):
timer = ExecutionTimer()
log.debug('Waiting for toolbox reload')
# Wait till toolbox reload has been triggered (or more than 60 seconds have passed)
while timer.elapsed < 60:
if self.toolbox.has_reloaded(old_toolbox):
log.debug('Finished waiting for toolbox reload %s', timer)
break
time.sleep(0.1)
else:
log.warning('Waiting for toolbox reload timed out after 60 seconds')
def _configure_tool_config_files(self):
if self.config.shed_tool_config_file not in self.config.tool_configs:
self.config.tool_configs.append(self.config.shed_tool_config_file)
# The value of migrated_tools_config is the file reserved for containing only those tools that have been
# eliminated from the distribution and moved to the tool shed. If migration checking is disabled, only add it if
# it exists (since this may be an existing deployment where migrations were previously run).
if ((self.config.check_migrate_tools or os.path.exists(self.config.migrated_tools_config))
and self.config.migrated_tools_config not in self.config.tool_configs):
self.config.tool_configs.append(self.config.migrated_tools_config)
def _configure_toolbox(self):
from galaxy import tools
from galaxy.managers.citations import CitationsManager
from galaxy.tool_util.deps import containers
from galaxy.tool_util.deps.dependencies import AppInfo
import galaxy.tools.search
self.citations_manager = CitationsManager(self)
from galaxy.managers.tools import DynamicToolManager
self.dynamic_tools_manager = DynamicToolManager(self)
self._toolbox_lock = threading.RLock()
self.toolbox = tools.ToolBox(self.config.tool_configs, self.config.tool_path, self)
galaxy_root_dir = os.path.abspath(self.config.root)
file_path = os.path.abspath(getattr(self.config, "file_path"))
app_info = AppInfo(
galaxy_root_dir=galaxy_root_dir,
default_file_path=file_path,
tool_data_path=self.config.tool_data_path,
shed_tool_data_path=self.config.shed_tool_data_path,
outputs_to_working_directory=self.config.outputs_to_working_directory,
container_image_cache_path=self.config.container_image_cache_path,
library_import_dir=self.config.library_import_dir,
enable_mulled_containers=self.config.enable_mulled_containers,
containers_resolvers_config_file=self.config.containers_resolvers_config_file,
involucro_path=self.config.involucro_path,
involucro_auto_init=self.config.involucro_auto_init,
mulled_channels=self.config.mulled_channels,
)
mulled_resolution_cache = None
if self.config.mulled_resolution_cache_type:
cache_opts = {
'cache.type': self.config.mulled_resolution_cache_type,
'cache.data_dir': self.config.mulled_resolution_cache_data_dir,
'cache.lock_dir': self.config.mulled_resolution_cache_lock_dir,
}
mulled_resolution_cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache('mulled_resolution')
self.container_finder = containers.ContainerFinder(app_info, mulled_resolution_cache=mulled_resolution_cache)
self._set_enabled_container_types()
index_help = getattr(self.config, "index_tool_help", True)
self.toolbox_search = galaxy.tools.search.ToolBoxSearch(self.toolbox, index_help)
self.reindex_tool_search()
[docs] def reindex_tool_search(self):
# Call this when tools are added or removed.
self.toolbox_search.build_index(tool_cache=self.tool_cache)
self.tool_cache.reset_status()
def _set_enabled_container_types(self):
container_types_to_destinations = collections.defaultdict(list)
for destinations in self.job_config.destinations.values():
for destination in destinations:
for enabled_container_type in self.container_finder._enabled_container_types(destination.params):
container_types_to_destinations[enabled_container_type].append(destination)
self.toolbox.dependency_manager.set_enabled_container_types(container_types_to_destinations)
self.toolbox.dependency_manager.resolver_classes.update(self.container_finder.container_registry.resolver_classes)
self.toolbox.dependency_manager.dependency_resolvers.extend(self.container_finder.container_registry.container_resolvers)
def _configure_tool_data_tables(self, from_shed_config):
from galaxy.tools.data import ToolDataTableManager
# Initialize tool data tables using the config defined by self.config.tool_data_table_config_path.
self.tool_data_tables = ToolDataTableManager(tool_data_path=self.config.tool_data_path,
config_filename=self.config.tool_data_table_config_path)
# Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables.
try:
self.tool_data_tables.load_from_config_file(config_filename=self.config.shed_tool_data_table_config,
tool_data_path=self.tool_data_tables.tool_data_path,
from_shed_config=from_shed_config)
except (OSError, IOError) as exc:
# Missing shed_tool_data_table_config is okay if it's the default
if exc.errno != errno.ENOENT or self.config.shed_tool_data_table_config_set:
raise
def _configure_datatypes_registry(self, installed_repository_manager=None):
from galaxy.datatypes import registry
# Create an empty datatypes registry.
self.datatypes_registry = registry.Registry(self.config)
if installed_repository_manager:
# Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool shed repositories. We
# load proprietary datatypes before datatypes in the distribution because Galaxy's default sniffers include some
# generic sniffers (eg text,xml) which catch anything, so it's impossible for proprietary sniffers to be used.
# However, if there is a conflict (2 datatypes with the same extension) between a proprietary datatype and a datatype
# in the Galaxy distribution, the datatype in the Galaxy distribution will take precedence. If there is a conflict
# between 2 proprietary datatypes, the datatype from the repository that was installed earliest will take precedence.
installed_repository_manager.load_proprietary_datatypes()
# Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config.
datatypes_configs = self.config.datatypes_config
for datatypes_config in listify(datatypes_configs):
# Setting override=False would make earlier files would take
# precedence - but then they wouldn't override tool shed
# datatypes.
self.datatypes_registry.load_datatypes(self.config.root, datatypes_config, override=True)
def _configure_object_store(self, **kwds):
from galaxy.objectstore import build_object_store_from_config
self.object_store = build_object_store_from_config(self.config, **kwds)
def _configure_security(self):
from galaxy.security import idencoding
self.security = idencoding.IdEncodingHelper(id_secret=self.config.id_secret)
def _configure_tool_shed_registry(self):
import galaxy.tool_shed.tool_shed_registry
# Set up the tool sheds registry
if os.path.isfile(self.config.tool_sheds_config_file):
self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry(self.config.tool_sheds_config_file)
else:
self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry()
def _configure_models(self, check_migrate_databases=False, check_migrate_tools=False, config_file=None):
"""
Preconditions: object_store must be set on self.
"""
db_url = get_database_url(self.config)
install_db_url = self.config.install_database_connection
# TODO: Consider more aggressive check here that this is not the same
# database file under the hood.
combined_install_database = not(install_db_url and install_db_url != db_url)
install_db_url = install_db_url or db_url
install_database_options = self.config.database_engine_options if combined_install_database else self.config.install_database_engine_options
if self.config.database_wait:
self._wait_for_database(db_url)
if getattr(self.config, "max_metadata_value_size", None):
from galaxy.model import custom_types
custom_types.MAX_METADATA_VALUE_SIZE = self.config.max_metadata_value_size
if check_migrate_databases:
# Initialize database / check for appropriate schema version. # If this
# is a new installation, we'll restrict the tool migration messaging.
from galaxy.model.migrate.check import create_or_verify_database
create_or_verify_database(db_url, config_file, self.config.database_engine_options, app=self, map_install_models=combined_install_database)
if not combined_install_database:
tsi_create_or_verify_database(install_db_url, install_database_options, app=self)
if check_migrate_tools:
# Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed.
from galaxy.tool_shed.galaxy_install.migrate.check import verify_tools
verify_tools(self, install_db_url, config_file, install_database_options)
self.model = init_models_from_config(
self.config,
map_install_models=combined_install_database,
object_store=self.object_store,
trace_logger=getattr(self, "trace_logger", None)
)
if combined_install_database:
log.info("Install database targetting Galaxy's database configuration.")
self.install_model = self.model
else:
from galaxy.model.tool_shed_install import mapping as install_mapping
install_db_url = self.config.install_database_connection
log.info("Install database using its own connection %s" % install_db_url)
self.install_model = install_mapping.init(install_db_url,
install_database_options)
def _configure_signal_handlers(self, handlers):
for sig, handler in handlers.items():
signal.signal(sig, handler)
def _wait_for_database(self, url):
from sqlalchemy_utils import database_exists
attempts = self.config.database_wait_attempts
pause = self.config.database_wait_sleep
for i in range(1, attempts):
try:
database_exists(url)
break
except Exception:
log.info("Waiting for database: attempt %d of %d" % (i, attempts))
time.sleep(pause)
@property
def tool_dependency_dir(self):
return self.toolbox.dependency_manager.default_base_path