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.managers.configuration

Managers, serializers for Galaxy config file data. ConfigSerializer for all users
and a more expanded set of data for admin in AdminConfigSerializer.

Used by both the API and bootstrapped data.
import json
import logging
import os
import sys
from typing import (

from galaxy.managers import base
from galaxy.managers.context import ProvidesUserContext
from galaxy.managers.markdown_util import weasyprint_available
from galaxy.schema import SerializationParams
from galaxy.schema.fields import EncodedDatabaseIdField
from galaxy.structured_app import StructuredApp
from galaxy.web.framework.base import server_starttime

log = logging.getLogger(__name__)

VERSION_JSON_FILE = "version.json"

[docs]class ConfigurationManager: """Interface/service object for interacting with configuration and related data."""
[docs] def __init__(self, app: StructuredApp): self._app = app
[docs] def get_configuration( self, trans: ProvidesUserContext, serialization_params: SerializationParams ) -> Dict[str, Any]: is_admin = trans.user_is_admin host = getattr(trans, "host", None) serializer_class = AdminConfigSerializer if is_admin else ConfigSerializer serializer = serializer_class(self._app) return serializer.serialize_to_view(self._app.config, host=host, **serialization_params.dict())
[docs] def version(self) -> Dict[str, Any]: version_info = { "version_major": self._app.config.version_major, "version_minor": self._app.config.version_minor, } # Try loading extra version info json_file = os.path.join(self._app.config.root, VERSION_JSON_FILE) # TODO: add this to schema json_file = os.environ.get("GALAXY_VERSION_JSON_FILE", json_file) try: with open(json_file) as f: extra_info = json.load(f) except OSError: log.info("Galaxy extra version JSON file %s not loaded.", json_file) else: version_info["extra"] = extra_info return version_info
[docs] def decode_id( self, encoded_id: EncodedDatabaseIdField, ) -> Dict[str, int]: # Handle the special case for library folders if (len(encoded_id) % 16 == 1) and encoded_id.startswith("F"): encoded_id = cast(EncodedDatabaseIdField, encoded_id[1:]) decoded_id = self._app.security.decode_id(encoded_id) return {"decoded_id": decoded_id}
[docs] def tool_lineages(self) -> List[Dict[str, Dict]]: rval = [] for id, tool in self._app.toolbox.tools(): try: lineage_dict = tool.lineage.to_dict() except AttributeError: pass else: entry = {"id": id, "lineage": lineage_dict} rval.append(entry) return rval
[docs] def dynamic_tool_confs(self) -> List[Dict[str, str]]: # WARNING: If this method is ever changed so as not to require admin privileges, update the nginx proxy # documentation, since this path is used as an authentication-by-proxy method for securing other paths on the # server. A dedicated endpoint should probably be added to do that instead. def tool_conf_to_dict(conf): return dict( config_filename=conf["config_filename"], tool_path=conf["tool_path"], ) confs = self._app.toolbox.dynamic_confs(include_migrated_tool_conf=True) return list(map(tool_conf_to_dict, confs))
[docs] def reload_toolbox(self): self._app.queue_worker.send_control_task("reload_toolbox")
# TODO: this is a bit of an odd duck. It uses the serializer structure from managers # but doesn't have a model like them. It might be better in config.py or a # totally new area, but I'm leaving it in managers for now for class consistency.
[docs]class ConfigSerializer(base.ModelSerializer): """Configuration (galaxy.ini) settings viewable by all users"""
[docs] def __init__(self, app): super().__init__(app) self.default_view = "all" self.add_view("all", list(self.serializers.keys()))
[docs] def default_serializer(self, config, key): return getattr(config, key, None)
[docs] def add_serializers(self): def _defaults_to(default) -> base.Serializer: return lambda item, key, **context: getattr(item, key, default) def _use_config(item, key: str, **context): """Let config object determine the value for key""" assert hasattr(item, key) return item.config_value_for_host(key, context.get("host")) def _config_is_truthy(item, key, **context): return True if item.get(key) else False self.serializers: Dict[str, base.Serializer] = { # TODO: this is available from user data, remove "is_admin_user": lambda *a, **c: False, "brand": _use_config, "display_galaxy_brand": _use_config, "logo_url": _use_config, "logo_src": _use_config, "logo_src_secondary": _use_config, "terms_url": _use_config, "myexperiment_target_url": _use_config, "wiki_url": _use_config, "screencasts_url": _use_config, "citation_url": _use_config, "support_url": _use_config, "quota_url": _use_config, "helpsite_url": _use_config, "lims_doc_url": _defaults_to("https://usegalaxy.org/u/rkchak/p/sts"), "default_locale": _use_config, "enable_tool_recommendations": _use_config, "enable_account_interface": _use_config, "tool_recommendation_model_path": _use_config, "admin_tool_recommendations_path": _use_config, "overwrite_model_recommendations": _use_config, "topk_recommendations": _use_config, "allow_user_impersonation": _use_config, "allow_user_creation": _defaults_to(False), # schema default is True "use_remote_user": _defaults_to(None), # schema default is False; or config.single_user "single_user": _config_is_truthy, "enable_oidc": _use_config, "oidc": _use_config, "prefer_custos_login": _use_config, "enable_quotas": _use_config, "remote_user_logout_href": _use_config, "datatypes_disable_auto": _use_config, "allow_user_dataset_purge": _defaults_to(False), # schema default is True "ga_code": _use_config, "plausible_server": _use_config, "plausible_domain": _use_config, "markdown_to_pdf_available": lambda item, key, **context: weasyprint_available(), "matomo_server": _use_config, "matomo_site_id": _use_config, "enable_unique_workflow_defaults": _use_config, "enable_beta_markdown_export": _use_config, "use_legacy_history": _use_config, "simplified_workflow_run_ui": _use_config, "simplified_workflow_run_ui_target_history": _use_config, "simplified_workflow_run_ui_job_cache": _use_config, "simplified_workflow_run_ui": _use_config, "has_user_tool_filters": _defaults_to(False), # TODO: is there no 'correct' way to get an api url? controller='api', action='tools' is a hack # at any rate: the following works with path_prefix but is still brittle # TODO: change this to (more generic) upload_path and incorporate config.nginx_upload_path into building it "nginx_upload_path": lambda item, key, **context: getattr(item, key, False), "chunk_upload_size": _use_config, "ftp_upload_site": _use_config, "version_major": _defaults_to(None), "version_minor": _defaults_to(None), "require_login": _use_config, "inactivity_box_content": _use_config, "visualizations_visible": _use_config, "interactivetools_enable": _use_config, "aws_estimate": _use_config, "message_box_content": _use_config, "message_box_visible": _use_config, "message_box_class": _use_config, "server_startttime": lambda item, key, **context: server_starttime, "mailing_join_addr": _defaults_to("galaxy-announce-join@bx.psu.edu"), # should this be the schema default? "server_mail_configured": lambda item, key, **context: bool(item.smtp_server), "registration_warning_message": _use_config, "welcome_url": _use_config, "show_welcome_with_login": _defaults_to(True), # schema default is False "cookie_domain": _use_config, "python": _defaults_to((sys.version_info.major, sys.version_info.minor)), "select_type_workflow_threshold": _use_config, "file_sources_configured": lambda item, key, **context: self.app.file_sources.custom_sources_configured, "panel_views": lambda item, key, **context: self.app.toolbox.panel_view_dicts(), "default_panel_view": _use_config, "upload_from_form_button": _use_config, "release_doc_base_url": _use_config, "expose_user_email": _use_config, "enable_tool_source_display": _use_config, "enable_celery_tasks": _use_config, "user_library_import_dir_available": lambda item, key, **context: bool(item.get("user_library_import_dir")), "welcome_directory": _use_config, }
[docs]class AdminConfigSerializer(ConfigSerializer): """Configuration attributes viewable only by admin users"""
[docs] def add_serializers(self): super().add_serializers() def _defaults_to(default): return lambda config, key, **context: getattr(config, key, default) self.serializers.update( { # TODO: this is available from user serialization: remove "is_admin_user": lambda *a, **context: True, "library_import_dir": _defaults_to(None), "user_library_import_dir": _defaults_to(None), "allow_library_path_paste": _defaults_to(False), "allow_user_deletion": _defaults_to(False), } )