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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.web import (
expose_api,
expose_api_anonymous_and_sessionless,
require_admin
)
from galaxy.webapps.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] @require_admin
@expose_api
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] @require_admin
@expose_api
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] @require_admin
@expose_api
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] @require_admin
@expose_api
def reload_toolbox(self, trans, **kwds):
"""
PUT /api/configuration/toolbox
Reload the Galaxy toolbox (but not individual tools).
"""
self.app.queue_worker.send_control_task('reload_toolbox')
def _tool_conf_to_dict(conf):
return dict(
config_filename=conf['config_filename'],
tool_path=conf['tool_path'],
)