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Source code for tool_shed.webapp.config

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

from galaxy.config import (
    BaseAppConfiguration,
    CommonConfigurationMixin,
    expand_pretty_datetime_format,
    get_database_engine_options,
    TOOL_SHED_CONFIG_SCHEMA_PATH,
)
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,
    VERSION_MINOR,
)

log = logging.getLogger(__name__)

TOOLSHED_APP_NAME = "tool_shed"


[docs]class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin): default_config_file_name = "tool_shed.yml" add_sample_file_to_defaults = {"datatypes_config_file"} def _load_schema(self): return AppSchema(TOOL_SHED_CONFIG_SCHEMA_PATH, TOOLSHED_APP_NAME)
[docs] def __init__(self, **kwargs): super().__init__(**kwargs) self._process_config(kwargs)
@property def shed_tool_data_path(self): return self.tool_data_path
[docs] def check(self): # Check that required directories exist; attempt to create otherwise paths_to_check = [ self.file_path, self.hgweb_config_dir, 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(f"File not found: {self.datatypes_config}")
def _process_config(self, kwargs): # Backwards compatibility for names used in too many places to fix self.datatypes_config = self.datatypes_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 self.version = VERSION # Database related configuration if not self.database_connection: # Provide default if not supplied by user self.database_connection = f"sqlite:///{self._in_data_dir('community.sqlite')}?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")) # 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.email_domain_blocklist_content = None self.email_domain_allowlist_content = None 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.citation_cache_url = kwargs.get("citation_cache_lock_dir", None) self.citation_cache_schema_name = kwargs.get("citation_cache_schema_name", None) self.citation_cache_table_name = kwargs.get("citation_cache_table_name", None) 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