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:"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 = return {"decoded_id": decoded_id}
[docs] def tool_lineages(self) -> List[Dict[str, Dict]]: rval = [] for id, tool in 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 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(""), "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(""), # 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:, "panel_views": lambda item, key, **context:, "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), } )