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)
@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