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Source code for galaxy.webapps.galaxy.api.configuration

API operations allowing clients to determine Galaxy instance's capabilities
and configuration settings.
import json
import logging
import os

from galaxy.managers import configuration, users
from galaxy.queue_worker import send_control_task
from galaxy.web import (
    _future_expose_api as expose_api,
    _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless,
from galaxy.web.base.controller import BaseAPIController

log = logging.getLogger(__name__)

[docs]class ConfigurationController(BaseAPIController):
[docs] def __init__(self, app): super(ConfigurationController, self).__init__(app) self.config_serializer = configuration.ConfigSerializer(app) self.admin_config_serializer = configuration.AdminConfigSerializer(app) self.user_manager = users.UserManager(app)
[docs] @expose_api def whoami(self, trans, **kwd): """ GET /api/whoami Return information about the current authenticated user. :returns: dictionary with user information :rtype: dict """ current_user = self.user_manager.current_user(trans) rval = None if current_user: # None for master API key for instance rval = current_user.to_dict() return rval
[docs] @expose_api_anonymous_and_sessionless def index(self, trans, **kwd): """ GET /api/configuration Return an object containing exposable configuration settings. Note: a more complete list is returned if the user is an admin. """ is_admin = trans.user_is_admin serialization_params = self._parse_serialization_params(kwd, 'all') return self.get_config_dict(trans, is_admin, **serialization_params)
[docs] @expose_api_anonymous_and_sessionless def version(self, trans, **kwds): """ GET /api/version Return a description of the major version of Galaxy (e.g. 15.03). :rtype: dict :returns: dictionary with major version keyed on 'version_major' """ extra = {} try: version_file = os.environ.get("GALAXY_VERSION_JSON_FILE", self.app.container_finder.app_info.galaxy_root_dir + "/version.json") with open(version_file, "r") as f: extra = json.load(f) except Exception: pass return {"version_major": self.app.config.version_major, "extra": extra}
[docs] def get_config_dict(self, trans, return_admin=False, view=None, keys=None, default_view='all'): """ Return a dictionary with (a subset of) current Galaxy settings. If `return_admin` also include a subset of more sensitive keys. Pass in `view` (String) and comma seperated list of keys to control which configuration settings are returned. """ serializer = self.config_serializer if return_admin: # TODO: this should probably just be under a different route: 'admin/configuration' serializer = self.admin_config_serializer serialized = serializer.serialize_to_view(self.app.config, view=view, keys=keys, default_view=default_view) return serialized
[docs] @expose_api @require_admin def dynamic_tool_confs(self, trans): # 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. confs = self.app.toolbox.dynamic_confs(include_migrated_tool_conf=True) return list(map(_tool_conf_to_dict, confs))
[docs] @expose_api @require_admin def decode_id(self, trans, encoded_id, **kwds): """Decode a given id.""" decoded_id = None # Handle the special case for library folders if ((len(encoded_id) % 16 == 1) and encoded_id.startswith('F')): decoded_id = trans.security.decode_id(encoded_id[1:]) else: decoded_id = trans.security.decode_id(encoded_id) return {"decoded_id": decoded_id}
[docs] @expose_api @require_admin def tool_lineages(self, trans): rval = [] for id, tool in self.app.toolbox.tools(): if hasattr(tool, 'lineage'): lineage_dict = tool.lineage.to_dict() else: lineage_dict = None entry = dict( id=id, lineage=lineage_dict ) rval.append(entry) return rval
[docs] @expose_api @require_admin def reload_toolbox(self, trans, **kwds): """ PUT /api/configuration/toolbox Reload the Galaxy toolbox (but not individual tools). """ send_control_task(self.app.toolbox.app, 'reload_toolbox')
def _tool_conf_to_dict(conf): return dict( config_filename=conf['config_filename'], tool_path=conf['tool_path'], )