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.webapps.reports.config

"""Universe configuration builder."""

import logging
import os
import re

from galaxy.util import string_as_bool

log = logging.getLogger(__name__)

[docs]def resolve_path(path, root): """If 'path' is relative make absolute by prepending 'root'""" if not (os.path.isabs(path)): path = os.path.join(root, path) return path
[docs]class ConfigurationError(Exception): pass
[docs]class Configuration:
[docs] def __init__(self, **kwargs): self.config_dict = kwargs self.root = kwargs.get("root_dir", ".") # Database related configuration self.database = resolve_path(kwargs.get("database_file", "database/universe.sqlite"), self.root) self.database_connection = kwargs.get("database_connection", False) self.database_engine_options = get_database_engine_options(kwargs) # Where dataset files are stored self.file_path = resolve_path(kwargs.get("file_path", "database/objects"), self.root) self.new_file_path = resolve_path(kwargs.get("new_file_path", "database/tmp"), self.root) self.id_secret = kwargs.get("id_secret", "USING THE DEFAULT IS NOT SECURE!") self.use_remote_user = string_as_bool(kwargs.get("use_remote_user", "False")) self.require_login = string_as_bool(kwargs.get("require_login", "False")) self.template_cache_path = resolve_path( kwargs.get("template_cache_path", "database/compiled_templates/reports"), self.root ) self.allow_user_creation = string_as_bool(kwargs.get("allow_user_creation", "True")) self.allow_user_deletion = string_as_bool(kwargs.get("allow_user_deletion", "False")) self.log_actions = string_as_bool(kwargs.get("log_actions", "False")) self.brand = kwargs.get("brand", None) # Configuration for the message box directly below the masthead. self.message_box_visible = string_as_bool(kwargs.get("message_box_visible", False)) self.message_box_content = kwargs.get("message_box_content", None) self.message_box_class = kwargs.get("message_box_class", "info") self.wiki_url = kwargs.get("wiki_url", "https://galaxyproject.org/") self.blog_url = kwargs.get("blog_url", None) self.screencasts_url = kwargs.get("screencasts_url", None) self.log_events = False self.cookie_path = kwargs.get("cookie_path", None) self.cookie_domain = kwargs.get("cookie_domain", None) # Error logging with sentry self.sentry_dsn = kwargs.get("sentry_dsn", None) # Security/Policy Compliance self.redact_username_in_logs = False self.redact_email_in_job_name = False self.enable_beta_gdpr = string_as_bool(kwargs.get("enable_beta_gdpr", False)) if self.enable_beta_gdpr: self.redact_username_in_logs = True self.redact_email_in_job_name = True self.allow_user_deletion = True
[docs] def get(self, key, default=None): return self.config_dict.get(key, default)
[docs] def check(self): # Check that required directories exist for path in (self.root,): if not os.path.isdir(path): raise ConfigurationError(f"Directory does not exist: {path}")
@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 get_database_engine_options(kwargs): """ 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, } 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