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Ability to launch blueapi and run Hyperion plans (#1389)
* Add load_centre_collect, robot_unload and udc_default_state blueapi plans * Add some documentation for hyperion-blueapi * Updates to work with DeviceManager, BartRobot changes
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‎docs/developer/hyperion/hyperion-blueapi.rst‎

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Hyperion on BlueAPI
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===================
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This document describes the migration of Hyperion from a monolithic service that contains its own application server
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and is only partially dependent on BlueAPI,
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to a standard BlueAPI application deployment.
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Architecture
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------------
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Hyperion on BlueAPI consists of two components:
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* hyperion-blueapi: This is intended to ultimately be a standard blueapi installation, consisting of a beamline
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module and a dodal plan module. In the interim, deployment may vary from the standard method until such time as
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monolithic operation can be desupported. ``hyperion-blueapi`` exposes a minimal set of bluesky plans for UDC data
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collection.
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* hyperion-supervisor: This will be a separate service that is responsible for fetching instructions from
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Agamemnon, decoding them and sending corresponding requests to ``hyperion-blueapi`` for execution. The supervisor
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also monitors the state of ``hyperion-blueapi``, manages the Hyperion baton and provides endpoints for status
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monitoring.
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Deployment
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----------
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``hyperion-blueapi`` is automatically available in a standard Hyperion deployment.
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Launching
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---------
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``hyperion-blueapi`` can be launched in using the ``run_hyperion.sh`` script, using the ``--blueapi`` option:
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::
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./run_hyperion.sh --beamline=i03 --dev --blueapi

‎docs/developer/hyperion/index.rst‎

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@@ -17,6 +17,7 @@ Documentation specific for the Hyperion module within MX-Bluesky
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reference/param-hierarchy
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reference/coordinate-systems
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system-tests
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hyperion-blueapi
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+++
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‎run_hyperion.sh‎

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IN_DEV=false
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MODE=gda
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CONFIG_DIR=`dirname $0`/src/mx_bluesky/hyperion
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BLUEAPI_CONFIG=$CONFIG_DIR/blueapi_config.yaml
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for option in "$@"; do
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case $option in
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-b=*|--beamline=*)
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;;
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--dev)
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IN_DEV=true
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BLUEAPI_CONFIG=$CONFIG_DIR/blueapi_dev_config.yaml
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;;
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--udc)
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MODE=udc
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;;
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--blueapi)
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MODE=blueapi
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;;
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--help|--info|--h)
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source .venv/bin/activate
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echo "`basename $0` [options]"
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--stop Used to stop a currently running instance of Hyperion. Will override any other operations
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options.
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--no-start Used to specify that the script should be run without starting the server.
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--skip-startup-connection
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Do not connect to devices at startup
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--dev Enable dev mode to run from a local workspace on a development machine.
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--udc Start hyperion in UDC mode instead of taking commands from GDA
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--blueapi Start hyperion in blueapi mode instead of taking commands from GDA
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--help This help
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By default this script will start an Hyperion server unless the --no-start flag is specified.
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echo "Killing active instances of hyperion and hyperion-callbacks..."
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pkill -e -f "python.*hyperion"
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pkill -e -f "SCREEN.*hyperion"
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blueapi controller stop 2>/dev/null
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echo "done."
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}
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source .venv/bin/activate
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#Add future arguments here
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declare -A h_and_cb_args=( ["IN_DEV"]="$IN_DEV" )
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declare -A h_and_cb_arg_strings=( ["IN_DEV"]="--dev" )
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done
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unset PYEPICS_LIBCA
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echo "Starting hyperion with hyperion $h_commands, start_log is $start_log_path"
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hyperion `echo $h_commands;`>$start_log_path 2>&1 &
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if [ $MODE = "blueapi" ]; then
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echo "Starting hyperion in blueapi mode, start log is $start_log_path"
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blueapi --config $BLUEAPI_CONFIG serve > $start_log_path 2>&1 &
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HEALTHCHECK_ENDPOINT="healthz"
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else
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echo "Starting hyperion with hyperion $h_commands, start_log is $start_log_path"
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hyperion `echo $h_commands;`>$start_log_path 2>&1 &
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HEALTHCHECK_ENDPOINT="status"
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fi
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echo "Starting hyperion-callbacks with hyperion-callbacks $cb_commands, start_log is $callback_start_log_path"
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hyperion-callbacks `echo $cb_commands;`>$callback_start_log_path 2>&1 &
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echo "$(date) Waiting for Hyperion to start"
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for i in {1..30}
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do
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echo "$(date)"
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curl --head -X GET http://localhost:5005/status >/dev/null
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curl --head -X GET http://localhost:5005/$HEALTHCHECK_ENDPOINT >/dev/null
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ret_value=$?
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if [ $ret_value -ne 0 ]; then
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sleep 1

‎src/mx_bluesky/common/device_setup_plans/robot_load_unload.py‎

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from bluesky.utils import MsgGenerator
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from dodal.devices.aperturescatterguard import ApertureScatterguard, ApertureValue
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from dodal.devices.motors import XYZStage
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from dodal.devices.robot import BartRobot
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from dodal.devices.robot import SAMPLE_LOCATION_EMPTY, BartRobot
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from dodal.devices.smargon import CombinedMove, Smargon, StubPosition
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from dodal.plan_stubs.motor_utils import MoveTooLargeError, home_and_reset_wrapper
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yield from bps.save()
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def _unload():
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yield from bps.abs_set(robot, None, wait=True)
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yield from bps.abs_set(robot, SAMPLE_LOCATION_EMPTY, wait=True)
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yield from wait_for_smargon_not_disabled(smargon)
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gonio_finished = yield from do_plan_while_lower_gonio_at_home(

‎src/mx_bluesky/hyperion/blueapi_config.yaml‎

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env:
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sources:
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- kind: deviceManager
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module: dodal.beamlines.i03
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- kind: planFunctions
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module: mx_bluesky.hyperion.blueapi_plans
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events:
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broadcast_status_events: false
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api:
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url: http://localhost:5005
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cors:
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allow_credentials: True
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origins:
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- "*"
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logging:
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graylog:
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url: "tcp://graylog-log-target.diamond.ac.uk:12232"
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enabled: true

‎src/mx_bluesky/hyperion/blueapi_dev_config.yaml‎

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env:
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sources:
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- kind: deviceManager
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module: dodal.beamlines.i03
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mock: true
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- kind: planFunctions
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module: mx_bluesky.hyperion.blueapi_plans
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events:
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broadcast_status_events: false
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api:
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url: http://localhost:5005
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cors:
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allow_credentials: True
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origins:
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- "*"
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logging:
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level: DEBUG

‎src/mx_bluesky/hyperion/blueapi_plans/__init__.py‎

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"""
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This module contains the bluesky plan entry points for use with hyperion-blueapi.
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The json schema and documentation therein generated by the blueapi /plans endpoint
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from this file constitutes the hyperion-blueapi interface to the hyperion supervisor
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process.
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"""
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from bluesky.utils import MsgGenerator
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from dodal.common import inject
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from dodal.devices.aperturescatterguard import ApertureScatterguard
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from dodal.devices.motors import XYZStage
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from dodal.devices.robot import BartRobot
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from dodal.devices.smargon import Smargon
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from mx_bluesky.common.device_setup_plans.robot_load_unload import (
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robot_unload as _robot_unload,
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)
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from mx_bluesky.hyperion.experiment_plans.load_centre_collect_full_plan import (
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LoadCentreCollectComposite,
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)
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from mx_bluesky.hyperion.experiment_plans.load_centre_collect_full_plan import (
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load_centre_collect_full as _load_centre_collect_full,
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)
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from mx_bluesky.hyperion.experiment_plans.udc_default_state import (
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UDCDefaultDevices,
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)
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from mx_bluesky.hyperion.experiment_plans.udc_default_state import (
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move_to_udc_default_state as _move_to_udc_default_state,
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)
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from mx_bluesky.hyperion.parameters.load_centre_collect import LoadCentreCollect
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__all__ = [
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"LoadCentreCollectComposite",
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"LoadCentreCollect",
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"UDCDefaultDevices",
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"load_centre_collect",
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"move_to_udc_default_state",
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"robot_unload",
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]
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def load_centre_collect(
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parameters: LoadCentreCollect, composite: LoadCentreCollectComposite = inject()
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) -> MsgGenerator:
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"""
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Attempt a complete data collection experiment, consisting of the following:
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* Load the sample if necessary
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* Move to the specified goniometer start angles
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* Perform optical centring, then X-ray centring
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* If X-ray centring finds one or more diffracting centres then for each centre
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that satisfies the chosen selection function,
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move to that centre and do a collection with the specified parameters.
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"""
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yield from _load_centre_collect_full(composite, parameters)
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def robot_unload(
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visit: str,
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robot: BartRobot = inject("robot"),
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smargon: Smargon = inject("smargon"),
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aperture_scatterguard: ApertureScatterguard = inject("aperture_scatterguard"),
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lower_gonio: XYZStage = inject("lower_gonio"),
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) -> MsgGenerator:
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"""
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Unload the currently mounted pin into the location that it was loaded from.
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This is to be invoked as the final step upon successful completion of the UDC queue.
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"""
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yield from _robot_unload(robot, smargon, aperture_scatterguard, lower_gonio, visit)
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def move_to_udc_default_state(
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composite: UDCDefaultDevices = inject(),
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) -> MsgGenerator:
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"""
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Move beamline hardware to known positions prior to UDC start.
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"""
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yield from _move_to_udc_default_state(composite)

‎tests/test_data/hyperion_blueapi/move_to_udc_default_state.json‎

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{
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"name": "move_to_udc_default_state",
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"params": {},
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"instrument_session": "cm12345-1"
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}

‎tests/test_data/hyperion_blueapi/robot_unload.json‎

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{
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"name": "robot_unload",
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"params": {
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"visit": "cm12345-1"
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},
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"instrument_session": "cm12345-1"
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}

‎tests/test_data/hyperion_blueapi/test_load_centre_collect.json‎

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{
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"name": "load_centre_collect",
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"params": {
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"parameters": {
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"parameter_model_version": "5.0.0",
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"beamline": "BL03S",
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"det_dist_to_beam_converter_path": "tests/test_data/test_lookup_table.txt",
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"insertion_prefix": "SR03S",
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"visit": "cm31105-4",
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"detector_distance_mm": 255,
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"sample_id": 12345,
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"sample_puck": 40,
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"sample_pin": 3,
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"robot_load_then_centre": {
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"storage_directory": "{tmp_data}/123458/xraycentring",
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"file_name": "robot_load_centring_file",
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"comment": "Robot load and centre",
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"exposure_time_s": 0.004,
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"use_roi_mode": false,
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"demand_energy_ev": 11100,
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"run_number": 0,
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"panda_runup_distance_mm": 0.17,
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"box_size_um": 20
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},
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"multi_rotation_scan": {
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"comment": "Rotation",
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"storage_directory": "{tmp_data}/123458/",
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"file_name": "file_name",
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"exposure_time_s": 0.004,
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"selected_aperture": "SMALL_APERTURE",
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"transmission_frac": 1.0,
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"demand_energy_ev": 11100,
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"rotation_increment_deg": 0.1,
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"shutter_opening_time_s": 0.6,
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"snapshot_omegas_deg": [
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0,
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90,
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180,
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270
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],
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"run_number": 1,
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"rotation_scans": [
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{
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"rotation_axis": "omega",
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"rotation_direction": "Negative",
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"scan_width_deg": 180.0,
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"omega_start_deg": 0,
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"phi_start_deg": 0.47,
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"chi_start_deg": 23.85
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}
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]
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}
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}
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},
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"instrument_session": "cm12345-1"
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}

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