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Source code for galaxy.webapps.tool_shed.config

"""
Universe configuration builder.
"""
import logging
import logging.config
import os
import re
from datetime import timedelta

from six.moves import configparser

from galaxy.config import BaseAppConfiguration
from galaxy.util import string_as_bool
from galaxy.version import VERSION, VERSION_MAJOR
from galaxy.web.formatting import expand_pretty_datetime_format

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 ToolShedAppConfiguration(BaseAppConfiguration): default_config_file_name = 'tool_shed.yml'
[docs] def __init__(self, **kwargs): self.config_dict = kwargs self.root = kwargs.get('root_dir', '.') self._set_config_base(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 self.version = VERSION # Database related configuration self.database_connection = kwargs.get("database_connection", False) self.database_connection = kwargs.get("database_connection", "sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path("community.sqlite", self.data_dir)) self.database_engine_options = get_database_engine_options(kwargs) self.database_create_tables = string_as_bool(kwargs.get("database_create_tables", "True")) # Repository and Tool search API self.toolshed_search_on = string_as_bool(kwargs.get("toolshed_search_on", True)) self.whoosh_index_dir = kwargs.get("whoosh_index_dir", 'database/toolshed_whoosh_indexes') self.repo_name_boost = kwargs.get("repo_name_boost", 0.9) self.repo_description_boost = kwargs.get("repo_description_boost", 0.6) self.repo_long_description_boost = kwargs.get("repo_long_description_boost", 0.5) self.repo_homepage_url_boost = kwargs.get("repo_homepage_url_boost", 0.3) self.repo_remote_repository_url_boost = kwargs.get("repo_remote_repository_url_boost", 0.2) self.repo_owner_username_boost = kwargs.get("repo_owner_username_boost", 0.3) self.tool_name_boost = kwargs.get("tool_name_boost", 1.2) self.tool_description_boost = kwargs.get("tool_description_boost", 0.6) self.tool_help_boost = kwargs.get("tool_help_boost", 0.4) self.tool_repo_owner_username = kwargs.get("tool_repo_owner_username", 0.3) # Analytics self.ga_code = kwargs.get("ga_code", None) self.session_duration = int(kwargs.get('session_duration', 0)) # Where dataset files are stored self.file_path = resolve_path(kwargs.get("file_path", "database/community_files"), self.root) self.new_file_path = resolve_path(kwargs.get("new_file_path", "database/tmp"), self.root) self.cookie_path = kwargs.get("cookie_path", None) self.cookie_domain = kwargs.get("cookie_domain", None) self.enable_quotas = string_as_bool(kwargs.get('enable_quotas', False)) self.id_secret = kwargs.get("id_secret", "changethisinproductiontoo") # Tool stuff self.tool_path = resolve_path(kwargs.get("tool_path", "tools"), self.root) self.tool_secret = kwargs.get("tool_secret", "") self.tool_data_path = resolve_path(kwargs.get("tool_data_path", "shed-tool-data"), os.getcwd()) self.tool_data_table_config_path = None self.integrated_tool_panel_config = resolve_path(kwargs.get('integrated_tool_panel_config', 'integrated_tool_panel.xml'), self.root) self.builds_file_path = resolve_path(kwargs.get("builds_file_path", os.path.join(self.tool_data_path, 'shared', 'ucsc', 'builds.txt')), self.root) self.len_file_path = resolve_path(kwargs.get("len_file_path", os.path.join(self.tool_data_path, 'shared', 'ucsc', 'chrom')), self.root) self.ftp_upload_dir = kwargs.get('ftp_upload_dir', None) self.update_integrated_tool_panel = False # Galaxy flavor Docker Image self.enable_galaxy_flavor_docker_image = string_as_bool(kwargs.get("enable_galaxy_flavor_docker_image", "False")) self.use_remote_user = string_as_bool(kwargs.get("use_remote_user", "False")) self.user_activation_on = None self.registration_warning_message = kwargs.get('registration_warning_message', None) self.terms_url = kwargs.get('terms_url', None) self.blacklist_location = kwargs.get('blacklist_file', None) self.blacklist_content = None self.remote_user_maildomain = kwargs.get("remote_user_maildomain", None) self.remote_user_header = kwargs.get("remote_user_header", 'HTTP_REMOTE_USER') self.remote_user_logout_href = kwargs.get("remote_user_logout_href", None) self.remote_user_secret = kwargs.get("remote_user_secret", None) self.require_login = string_as_bool(kwargs.get("require_login", "False")) 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.template_path = resolve_path(kwargs.get("template_path", "templates"), self.root) self.template_cache_path = resolve_path(kwargs.get("template_cache_path", "database/compiled_templates/community"), self.root) self.admin_users = kwargs.get("admin_users", "") self.admin_users_list = [u.strip() for u in self.admin_users.split(',') if u] self.mailing_join_addr = kwargs.get('mailing_join_addr', "galaxy-announce-join@bx.psu.edu") self.error_email_to = kwargs.get('error_email_to', None) self.smtp_server = kwargs.get('smtp_server', None) self.smtp_username = kwargs.get('smtp_username', None) self.smtp_password = kwargs.get('smtp_password', None) self.smtp_ssl = kwargs.get('smtp_ssl', None) self.email_from = kwargs.get('email_from', None) self.nginx_upload_path = kwargs.get('nginx_upload_path', False) self.log_actions = string_as_bool(kwargs.get('log_actions', 'False')) self.brand = kwargs.get('brand', None) self.pretty_datetime_format = expand_pretty_datetime_format(kwargs.get('pretty_datetime_format', '$locale (UTC)')) # 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.support_url = kwargs.get('support_url', 'https://galaxyproject.org/support') 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.cloud_controller_instance = False self.server_name = '' # Error logging with sentry self.sentry_dsn = kwargs.get('sentry_dsn', None) # Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory. self.hgweb_config_dir = resolve_path(kwargs.get('hgweb_config_dir', ''), self.root) # Proxy features self.apache_xsendfile = kwargs.get('apache_xsendfile', False) self.nginx_x_accel_redirect_base = kwargs.get('nginx_x_accel_redirect_base', False) self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script', None) # Parse global_conf and save the parser global_conf = kwargs.get('global_conf', None) global_conf_parser = configparser.ConfigParser() self.global_conf_parser = global_conf_parser if global_conf and "__file__" in global_conf and ".yml" not in global_conf["__file__"]: global_conf_parser.read(global_conf['__file__']) self.running_functional_tests = string_as_bool(kwargs.get('running_functional_tests', False)) self.citation_cache_type = kwargs.get("citation_cache_type", "file") self.citation_cache_data_dir = resolve_path(kwargs.get("citation_cache_data_dir", "database/tool_shed_citations/data"), self.root) self.citation_cache_lock_dir = resolve_path(kwargs.get("citation_cache_lock_dir", "database/tool_shed_citations/locks"), self.root) self.password_expiration_period = timedelta(days=int(kwargs.get("password_expiration_period", 0))) # Security/Policy Compliance self.redact_username_during_deletion = False self.redact_email_during_deletion = False self.redact_username_in_logs = False self.enable_beta_gdpr = string_as_bool(kwargs.get("enable_beta_gdpr", False)) if self.enable_beta_gdpr: self.redact_username_during_deletion = True self.redact_email_during_deletion = True self.redact_username_in_logs = True self.allow_user_deletion = True
@property def shed_tool_data_path(self): return self.tool_data_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 """ # TODO refactor this to a common place between toolshed/galaxy config, along # with other duplicated methods. 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): defaults = dict( auth_config_file=[self._in_config_dir('config/auth_conf.xml')], datatypes_config_file=[self._in_config_dir('datatypes_conf.xml'), self._in_sample_dir('datatypes_conf.xml.sample')], shed_tool_data_table_config=[self._in_mutable_config_dir('shed_tool_data_table_conf.xml')], ) self._parse_config_file_options(defaults, dict(), kwargs) # Backwards compatibility for names used in too many places to fix self.datatypes_config = self.datatypes_config_file
[docs] def get(self, key, default=None): return self.config_dict.get(key, default)
[docs] def get_bool(self, key, default): if key in self.config_dict: return string_as_bool(self.config_dict[key]) else: return default
[docs] def check(self): # Check that required directories exist. paths_to_check = [self.root, self.file_path, self.hgweb_config_dir, self.tool_data_path, self.template_path] 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, e)) # Create the directories that it makes sense to create. for path in self.file_path, \ self.template_cache_path, \ os.path.join(self.tool_data_path, 'shared', 'jars'): 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, e)) # Check that required files exist. if not os.path.isfile(self.datatypes_config): raise ConfigurationError("File not found: %s" % self.datatypes_config)
[docs] def is_admin_user(self, user): """ Determine if the provided user is listed in `admin_users`. """ admin_users = self.get("admin_users", "").split(",") return user is not None and user.email in admin_users
Configuration = ToolShedAppConfiguration
[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, 'server_side_cursors': 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