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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.app import MinimalManagerApp
from galaxy.managers import base
from galaxy.managers.context import ProvidesUserContext
from galaxy.managers.markdown_util import weasyprint_available
from galaxy.schema.fields import EncodedDatabaseIdField
from galaxy.schema.types import SerializationParams
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: MinimalManagerApp): 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)
[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 JSON version file not loaded') 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): return lambda config, key, **context: getattr(config, key, default) def _use_config(config, key, **context): """Let config object determine the value for key""" assert hasattr(config, key) return config.config_value_for_host(key, context.get("host")) def _config_is_truthy(config, key, **context): return True if config.get(key) else False self.serializers = { # 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, 'search_url': _use_config, 'mailing_lists': _defaults_to(self.app.config.mailing_lists_url), '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_openid': _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, '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 config, 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, '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 config, key, **context: getattr(config, 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 config, 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 config, key, **context: bool(config.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 config, key, **context: self.app.file_sources.custom_sources_configured, 'panel_views': lambda config, key, **content: 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, 'user_library_import_dir_available': lambda config, key, **context: bool(config.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), })