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Source code for tool_shed.webapp.config

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

from six.moves import configparser

from galaxy.config import (
    BaseAppConfiguration,
    CommonConfigurationMixin,
    get_database_engine_options,
)
from galaxy.config.schema import AppSchema
from galaxy.exceptions import ConfigurationError
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__)

ts_webapp_path = os.path.abspath(os.path.dirname(__file__))
templates_path = os.path.join(ts_webapp_path, 'templates')

TOOLSHED_APP_NAME = 'tool_shed'
TOOLSHED_CONFIG_SCHEMA_PATH = 'lib/tool_shed/webapp/config_schema.yml'


[docs]class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin): default_config_file_name = 'tool_shed.yml' def _load_schema(self): return AppSchema(TOOLSHED_CONFIG_SCHEMA_PATH, TOOLSHED_APP_NAME)
[docs] def __init__(self, **kwargs): super(ToolShedAppConfiguration, self).__init__(**kwargs) self._process_config(kwargs)
@property def shed_tool_data_path(self): return self.tool_data_path
[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_managed_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 check(self): # Check that required directories exist; attempt to create otherwise paths_to_check = [ self.file_path, self.hgweb_config_dir, self.template_path, self.tool_data_path, self.template_cache_path, os.path.join(self.tool_data_path, 'shared', 'jars'), ] for path in paths_to_check: self._ensure_directory(path) # Check that required files exist. if not os.path.isfile(self.datatypes_config): raise ConfigurationError('File not found: %s' % self.datatypes_config)
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 self.version = VERSION # Database related configuration if not self.database_connection: # Provide default if not supplied by user self.database_connection = 'sqlite:///%s?isolation_level=IMMEDIATE' % self._in_data_dir('community.sqlite') self.database_engine_options = get_database_engine_options(kwargs) self.database_create_tables = string_as_bool(kwargs.get('database_create_tables', 'True')) # Where dataset files are stored self.file_path = self._in_root_dir(self.file_path) self.new_file_path = self._in_root_dir(self.new_file_path) self.cookie_path = kwargs.get('cookie_path') self.cookie_domain = kwargs.get('cookie_domain') self.enable_quotas = string_as_bool(kwargs.get('enable_quotas', False)) # Tool stuff self.tool_path = self._in_root_dir(kwargs.get('tool_path', 'tools')) self.tool_secret = kwargs.get('tool_secret', '') self.tool_data_path = os.path.join(os.getcwd(), kwargs.get('tool_data_path', 'shed-tool-data')) self.tool_data_table_config_path = None self.integrated_tool_panel_config = self._in_root_dir(kwargs.get('integrated_tool_panel_config', 'integrated_tool_panel.xml')) self.builds_file_path = self._in_root_dir(kwargs.get('builds_file_path', os.path.join(self.tool_data_path, 'shared', 'ucsc', 'builds.txt'))) self.len_file_path = self._in_root_dir(kwargs.get('len_file_path', os.path.join(self.tool_data_path, 'shared', 'ucsc', 'chrom'))) self.ftp_upload_dir = kwargs.get('ftp_upload_dir') self.update_integrated_tool_panel = False # Galaxy flavor Docker Image self.user_activation_on = None self.registration_warning_message = kwargs.get('registration_warning_message') self.blacklist_location = kwargs.get('blacklist_file') self.blacklist_content = None self.whitelist_location = kwargs.get('whitelist_file') self.whitelist_content = None self.template_path = templates_path self.template_cache_path = self._in_root_dir(kwargs.get('template_cache_path', 'database/compiled_templates/community')) self.error_email_to = kwargs.get('error_email_to') self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format) # Configuration for the message box directly below the masthead. self.wiki_url = kwargs.get('wiki_url', 'https://galaxyproject.org/') self.blog_url = kwargs.get('blog_url') self.screencasts_url = kwargs.get('screencasts_url') self.log_events = False self.cloud_controller_instance = False self.server_name = '' # Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory. self.hgweb_config_dir = self._in_root_dir(self.hgweb_config_dir) or self.root # Proxy features self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script') # Parse global_conf and save the parser global_conf = kwargs.get('global_conf') 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_data_dir = self._in_root_dir(kwargs.get('citation_cache_data_dir', 'database/tool_shed_citations/data')) self.citation_cache_lock_dir = self._in_root_dir(kwargs.get('citation_cache_lock_dir', 'database/tool_shed_citations/locks')) self.password_expiration_period = timedelta(days=int(self.password_expiration_period)) # 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
Configuration = ToolShedAppConfiguration