mx-bluesky 1.4.1a0__py3-none-any.whl → 1.4.2__py3-none-any.whl

mx_bluesky/hyperion/experiment_plans/robot_load_and_change_energy.py

@@ -10,7 +10,7 @@ import bluesky.preprocessors as bpp
 import pydantic
 from blueapi.core import BlueskyContext
 from bluesky.utils import Msg
-from dodal.devices.aperturescatterguard import ApertureScatterguard
+from dodal.devices.aperturescatterguard import ApertureScatterguard, ApertureValue
 from dodal.devices.attenuator import Attenuator
 from dodal.devices.dcm import DCM
 from dodal.devices.focusing_mirror import FocusingMirrorWithStripes, MirrorVoltages
@@ -94,7 +94,11 @@ def take_robot_snapshots(oav: OAV, webcam: Webcam, directory: Path):
 def prepare_for_robot_load(
     aperture_scatterguard: ApertureScatterguard, smargon: Smargon
 ):
-    yield from bps.trigger(aperture_scatterguard.move_out, group="prepare_robot_load")
+    yield from bps.abs_set(
+        aperture_scatterguard,
+        ApertureValue.ROBOT_LOAD,
+        group="prepare_robot_load",
+    )
 
     yield from bps.mv(smargon.stub_offsets, StubPosition.RESET_TO_ROBOT_LOAD)  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
 
@@ -124,11 +128,7 @@ def do_robot_load(
         group="robot_load",
     )
 
-    if demand_energy_ev:
-        yield from set_energy_plan(
-            demand_energy_ev / 1000,
-            cast(SetEnergyComposite, composite),
-        )
+    yield from set_energy_plan(demand_energy_ev, cast(SetEnergyComposite, composite))
 
     yield from bps.wait("robot_load")
 
@@ -214,24 +214,28 @@ def robot_load_and_change_energy_plan(
     yield from prepare_for_robot_load(
         composite.aperture_scatterguard, composite.smargon
     )
-    yield from bpp.run_wrapper(
-        robot_load_and_snapshots(
-            composite,
-            sample_location,
-            params.snapshot_directory,
-            params.thawing_time,
-            params.demand_energy_ev,
-        ),
-        md={
-            "subplan_name": CONST.PLAN.ROBOT_LOAD,
-            "metadata": {
-                "visit": params.visit,
-                "sample_id": params.sample_id,
-                "sample_puck": sample_location.puck,
-                "sample_pin": sample_location.pin,
+
+    yield from bpp.set_run_key_wrapper(
+        bpp.run_wrapper(
+            robot_load_and_snapshots(
+                composite,
+                sample_location,
+                params.snapshot_directory,
+                params.thawing_time,
+                params.demand_energy_ev,
+            ),
+            md={
+                "subplan_name": CONST.PLAN.ROBOT_LOAD,
+                "metadata": {
+                    "visit": params.visit,
+                    "sample_id": params.sample_id,
+                    "sample_puck": sample_location.puck,
+                    "sample_pin": sample_location.pin,
+                },
+                "activate_callbacks": [
+                    "RobotLoadISPyBCallback",
+                ],
             },
-            "activate_callbacks": [
-                "RobotLoadISPyBCallback",
-            ],
-        },
+        ),
+        CONST.PLAN.ROBOT_LOAD_AND_SNAPSHOTS,
     )

mx_bluesky/hyperion/experiment_plans/robot_load_then_centre_plan.py

@@ -1,10 +1,12 @@
 from __future__ import annotations
 
+from math import isclose
 from typing import cast
 
 import bluesky.preprocessors as bpp
 import pydantic
 from blueapi.core import BlueskyContext
+from bluesky import plan_stubs as bps
 from bluesky.utils import MsgGenerator
 from dodal.devices.aperturescatterguard import ApertureScatterguard
 from dodal.devices.attenuator import Attenuator
@@ -56,6 +58,10 @@ from mx_bluesky.hyperion.experiment_plans.robot_load_and_change_energy import (
     pin_already_loaded,
     robot_load_and_change_energy_plan,
 )
+from mx_bluesky.hyperion.experiment_plans.set_energy_plan import (
+    SetEnergyComposite,
+    set_energy_plan,
+)
 from mx_bluesky.hyperion.parameters.constants import CONST
 
 
@@ -170,20 +176,33 @@ def robot_load_then_xray_centre(
         yield from pin_already_loaded(composite.robot, sample_location)
     )
 
-    doing_chi_change = parameters.chi_start_deg is not None
+    current_chi = yield from bps.rd(composite.smargon.chi)
+    LOGGER.info(f"Read back current smargon chi of {current_chi} degrees.")
+    doing_chi_change = parameters.chi_start_deg is not None and not isclose(
+        current_chi, parameters.chi_start_deg, abs_tol=0.001
+    )
 
     if doing_sample_load:
+        LOGGER.info("Pin not loaded, loading and centring")
         plan = _robot_load_then_flyscan_plan(
             composite,
             parameters,
         )
-        LOGGER.info("Pin not loaded, loading and centring")
-    elif doing_chi_change:
-        plan = _flyscan_plan_from_robot_load_params(composite, parameters)
-        LOGGER.info("Pin already loaded but chi changed so centring")
     else:
-        LOGGER.info("Pin already loaded and chi not changed so doing nothing")
-        return
+        # Robot load normally sets the energy so we should do this explicitly if no load is
+        # being done
+        demand_energy_ev = parameters.demand_energy_ev
+        LOGGER.info(f"Setting the energy to {demand_energy_ev}eV")
+        yield from set_energy_plan(
+            demand_energy_ev, cast(SetEnergyComposite, composite)
+        )
+
+        if doing_chi_change:
+            plan = _flyscan_plan_from_robot_load_params(composite, parameters)
+            LOGGER.info("Pin already loaded but chi changed so centring")
+        else:
+            LOGGER.info("Pin already loaded and chi not changed so doing nothing")
+            return
 
     detector_params = yield from fill_in_energy_if_not_supplied(
         composite.dcm, parameters.detector_params

mx_bluesky/hyperion/experiment_plans/rotation_scan_plan.py

@@ -331,13 +331,6 @@ def _move_and_rotation(
         yield from setup_beamline_for_OAV(
             composite.smargon, composite.backlight, composite.aperture_scatterguard
         )
-        yield from bps.wait(group=CONST.WAIT.READY_FOR_OAV)
-        if params.selected_aperture:
-            yield from bps.abs_set(
-                composite.aperture_scatterguard.aperture_outside_beam,
-                params.selected_aperture,
-                group=CONST.WAIT.ROTATION_READY_FOR_DC,
-            )
         yield from oav_snapshot_plan(composite, params, oav_params)
     yield from rotation_scan_plan(
         composite,

mx_bluesky/hyperion/experiment_plans/set_energy_plan.py

@@ -48,12 +48,13 @@ def _set_energy_plan(
 
 
 def set_energy_plan(
-    energy_kev,
+    energy_ev: float | None,
     composite: SetEnergyComposite,
 ):
-    yield from transmission_and_xbpm_feedback_for_collection_wrapper(
-        _set_energy_plan(energy_kev, composite),
-        composite.xbpm_feedback,
-        composite.attenuator,
-        DESIRED_TRANSMISSION_FRACTION,
-    )
+    if energy_ev:
+        yield from transmission_and_xbpm_feedback_for_collection_wrapper(
+            _set_energy_plan(energy_ev / 1000, composite),
+            composite.xbpm_feedback,
+            composite.attenuator,
+            DESIRED_TRANSMISSION_FRACTION,
+        )

mx_bluesky/hyperion/external_interaction/callbacks/__init__.py

@@ -4,7 +4,3 @@ execution of an experimental plan.
 
 Callbacks used for the Hyperion fast grid scan are prefixed with 'FGS'.
 """
-
-from .__main__ import main
-
-__all__ = ["main"]

mx_bluesky/hyperion/external_interaction/callbacks/__main__.py

@@ -20,6 +20,9 @@ from mx_bluesky.hyperion.external_interaction.callbacks.rotation.ispyb_callback
 from mx_bluesky.hyperion.external_interaction.callbacks.rotation.nexus_callback import (
     RotationNexusFileCallback,
 )
+from mx_bluesky.hyperion.external_interaction.callbacks.sample_handling.sample_handling_callback import (
+    SampleHandlingCallback,
+)
 from mx_bluesky.hyperion.external_interaction.callbacks.xray_centre.ispyb_callback import (
     GridscanISPyBCallback,
 )
@@ -49,6 +52,7 @@ def setup_callbacks():
         RotationISPyBCallback(emit=zocalo),
         LogUidTaggingCallback(),
         RobotLoadISPyBCallback(),
+        SampleHandlingCallback(),
     ]
 
 

mx_bluesky/hyperion/external_interaction/callbacks/common/callback_util.py

@@ -11,6 +11,9 @@ from mx_bluesky.hyperion.external_interaction.callbacks.rotation.ispyb_callback
 from mx_bluesky.hyperion.external_interaction.callbacks.rotation.nexus_callback import (
     RotationNexusFileCallback,
 )
+from mx_bluesky.hyperion.external_interaction.callbacks.sample_handling.sample_handling_callback import (
+    SampleHandlingCallback,
+)
 from mx_bluesky.hyperion.external_interaction.callbacks.xray_centre.ispyb_callback import (
     GridscanISPyBCallback,
 )
@@ -53,6 +56,7 @@ def create_load_centre_collect_callbacks() -> (
         RobotLoadISPyBCallback,
         RotationNexusFileCallback,
         RotationISPyBCallback,
+        SampleHandlingCallback,
     ]
 ):
     return (
@@ -61,4 +65,5 @@ def create_load_centre_collect_callbacks() -> (
         RobotLoadISPyBCallback(),
         RotationNexusFileCallback(),
         RotationISPyBCallback(emit=ZocaloCallback()),
+        SampleHandlingCallback(),
     )

mx_bluesky/hyperion/external_interaction/callbacks/robot_load/ispyb_callback.py

@@ -2,8 +2,6 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING
 
-from event_model.documents import EventDescriptor
-
 from mx_bluesky.hyperion.external_interaction.callbacks.common.ispyb_mapping import (
     get_proposal_and_session_from_visit_string,
 )
@@ -11,6 +9,7 @@ from mx_bluesky.hyperion.external_interaction.callbacks.plan_reactive_callback i
     PlanReactiveCallback,
 )
 from mx_bluesky.hyperion.external_interaction.ispyb.exp_eye_store import (
+    BLSampleStatus,
     ExpeyeInteraction,
     RobotActionID,
 )
@@ -25,6 +24,7 @@ class RobotLoadISPyBCallback(PlanReactiveCallback):
     def __init__(self) -> None:
         ISPYB_LOGGER.debug("Initialising ISPyB Robot Load Callback")
         super().__init__(log=ISPYB_LOGGER)
+        self._metadata: dict | None = None
         self.run_uid: str | None = None
         self.descriptors: dict[str, EventDescriptor] = {}
         self.action_id: RobotActionID | None = None
@@ -35,16 +35,17 @@ class RobotLoadISPyBCallback(PlanReactiveCallback):
         if doc.get("subplan_name") == CONST.PLAN.ROBOT_LOAD:
             ISPYB_LOGGER.debug(f"ISPyB robot load callback received: {doc}")
             self.run_uid = doc.get("uid")
-            assert isinstance(metadata := doc.get("metadata"), dict)
+            self._metadata = doc.get("metadata")
+            assert isinstance(self._metadata, dict)
             proposal, session = get_proposal_and_session_from_visit_string(
-                metadata["visit"]
+                self._metadata["visit"]
             )
             self.action_id = self.expeye.start_load(
                 proposal,
                 session,
-                metadata["sample_id"],
-                metadata["sample_puck"],
-                metadata["sample_pin"],
+                self._metadata["sample_id"],
+                self._metadata["sample_puck"],
+                self._metadata["sample_pin"],
             )
         return super().activity_gated_start(doc)
 
@@ -77,10 +78,17 @@ class RobotLoadISPyBCallback(PlanReactiveCallback):
             assert (
                 self.action_id is not None
             ), "ISPyB Robot load callback stop called unexpectedly"
-            exit_status = (
-                doc.get("exit_status") or "Exit status not available in stop document!"
-            )
+            exit_status = doc.get("exit_status")
+            assert exit_status, "Exit status not available in stop document!"
+            assert self._metadata, "Metadata not received before stop document."
             reason = doc.get("reason") or "OK"
+
             self.expeye.end_load(self.action_id, exit_status, reason)
+            self.expeye.update_sample_status(
+                self._metadata["sample_id"],
+                BLSampleStatus.LOADED
+                if exit_status == "success"
+                else BLSampleStatus.ERROR_BEAMLINE,
+            )
             self.action_id = None
         return super().activity_gated_stop(doc)

mx_bluesky/hyperion/external_interaction/callbacks/sample_handling/sample_handling_callback.py

@@ -0,0 +1,84 @@
+import dataclasses
+from collections.abc import Generator
+from functools import partial
+from typing import Any
+
+import bluesky.plan_stubs as bps
+from bluesky.preprocessors import contingency_wrapper
+from bluesky.utils import Msg, make_decorator
+from event_model import Event, EventDescriptor, RunStart
+
+from mx_bluesky.hyperion.exceptions import CrystalNotFoundException, SampleException
+from mx_bluesky.hyperion.external_interaction.callbacks.common.abstract_event import (
+    AbstractEvent,
+)
+from mx_bluesky.hyperion.external_interaction.callbacks.plan_reactive_callback import (
+    PlanReactiveCallback,
+)
+from mx_bluesky.hyperion.external_interaction.ispyb.exp_eye_store import (
+    BLSampleStatus,
+    ExpeyeInteraction,
+)
+from mx_bluesky.hyperion.log import ISPYB_LOGGER
+from mx_bluesky.hyperion.parameters.constants import CONST
+
+# TODO remove this event-raising shenanigans once
+# https://github.com/bluesky/bluesky/issues/1829 is addressed
+
+
+@dataclasses.dataclass(frozen=True)
+class _ExceptionEvent(AbstractEvent):
+    exception_type: str
+
+
+def _exception_interceptor(exception: Exception) -> Generator[Msg, Any, Any]:
+    yield from bps.create(CONST.DESCRIPTORS.SAMPLE_HANDLING_EXCEPTION)
+    yield from bps.read(_ExceptionEvent(type(exception).__name__))
+    yield from bps.save()
+
+
+sample_handling_callback_decorator = make_decorator(
+    partial(contingency_wrapper, except_plan=_exception_interceptor)
+)
+
+
+class SampleHandlingCallback(PlanReactiveCallback):
+    """Intercepts exceptions from experiment plans and updates the ISPyB BLSampleStatus
+    field according to the type of exception raised."""
+
+    def __init__(self):
+        super().__init__(log=ISPYB_LOGGER)
+        self._sample_id: int | None = None
+        self._descriptor: str | None = None
+
+    def activity_gated_start(self, doc: RunStart):
+        if not self._sample_id:
+            sample_id = doc.get("metadata", {}).get("sample_id")
+            self.log.info(f"Recording sample ID at run start {sample_id}")
+            self._sample_id = sample_id
+
+    def activity_gated_descriptor(self, doc: EventDescriptor) -> EventDescriptor | None:
+        if doc.get("name") == CONST.DESCRIPTORS.SAMPLE_HANDLING_EXCEPTION:
+            self._descriptor = doc["uid"]
+        return super().activity_gated_descriptor(doc)
+
+    def activity_gated_event(self, doc: Event) -> Event | None:
+        if doc["descriptor"] == self._descriptor:
+            exception_type = doc["data"]["exception_type"]
+            self.log.info(
+                f"Sample handling callback intercepted exception of type {exception_type}"
+            )
+            self._record_exception(exception_type)
+        return doc
+
+    def _record_exception(self, exception_type: str):
+        expeye = ExpeyeInteraction()
+        assert self._sample_id, "Unable to record exception due to no sample ID"
+        sample_status = self._decode_sample_status(exception_type)
+        expeye.update_sample_status(self._sample_id, sample_status)
+
+    def _decode_sample_status(self, exception_type: str) -> BLSampleStatus:
+        match exception_type:
+            case SampleException.__name__ | CrystalNotFoundException.__name__:
+                return BLSampleStatus.ERROR_SAMPLE
+        return BLSampleStatus.ERROR_BEAMLINE

mx_bluesky/hyperion/external_interaction/callbacks/xray_centre/ispyb_callback.py

@@ -53,13 +53,16 @@ if TYPE_CHECKING:
 
 
 def ispyb_activation_wrapper(plan_generator: MsgGenerator, parameters):
-    return bpp.run_wrapper(
-        plan_generator,
-        md={
-            "activate_callbacks": ["GridscanISPyBCallback"],
-            "subplan_name": CONST.PLAN.GRID_DETECT_AND_DO_GRIDSCAN,
-            "hyperion_parameters": parameters.model_dump_json(),
-        },
+    return bpp.set_run_key_wrapper(
+        bpp.run_wrapper(
+            plan_generator,
+            md={
+                "activate_callbacks": ["GridscanISPyBCallback"],
+                "subplan_name": CONST.PLAN.GRID_DETECT_AND_DO_GRIDSCAN,
+                "hyperion_parameters": parameters.model_dump_json(),
+            },
+        ),
+        CONST.PLAN.ISPYB_ACTIVATION,
     )
 
 

mx_bluesky/hyperion/external_interaction/exceptions.py

@@ -1,13 +1,4 @@
-from mx_bluesky.hyperion.exceptions import WarningException
-
-
 class ISPyBDepositionNotMade(Exception):
     """Raised when the ISPyB or Zocalo callbacks can't access ISPyB deposition numbers."""
 
     pass
-
-
-class NoCentreFoundException(WarningException):
-    """Error for if zocalo is unable to find the centre during a gridscan."""
-
-    pass

mx_bluesky/hyperion/external_interaction/ispyb/exp_eye_store.py

@@ -1,4 +1,6 @@
 import configparser
+from dataclasses import dataclass
+from enum import StrEnum
 
 from requests import patch, post
 from requests.auth import AuthBase
@@ -29,20 +31,44 @@ def _get_base_url_and_token() -> tuple[str, str]:
     return expeye_config["url"], expeye_config["token"]
 
 
+def _send_and_get_response(auth, url, data, send_func) -> dict:
+    response = send_func(url, auth=auth, json=data)
+    if not response.ok:
+        raise ISPyBDepositionNotMade(f"Could not write {data} to {url}: {response}")
+    return response.json()
+
+
+@dataclass
+class BLSample:
+    container_id: int
+    bl_sample_id: int
+    bl_sample_status: str | None
+
+
+class BLSampleStatus(StrEnum):
+    # The sample has been loaded
+    LOADED = "LOADED"
+    # Problem with the sample e.g. pin too long/short
+    ERROR_SAMPLE = "ERROR - sample"
+    # Any other general error
+    ERROR_BEAMLINE = "ERROR - beamline"
+
+
+assert all(
+    len(value) <= 20 for value in BLSampleStatus
+), "Column size limit of 20 for BLSampleStatus"
+
+
 class ExpeyeInteraction:
+    """Exposes functionality from the Expeye core API"""
+
     CREATE_ROBOT_ACTION = "/proposals/{proposal}/sessions/{visit_number}/robot-actions"
     UPDATE_ROBOT_ACTION = "/robot-actions/{action_id}"
 
     def __init__(self) -> None:
         url, token = _get_base_url_and_token()
-        self.base_url = url
-        self.auth = BearerAuth(token)
-
-    def _send_and_get_response(self, url, data, send_func) -> dict:
-        response = send_func(url, auth=self.auth, json=data)
-        if not response.ok:
-            raise ISPyBDepositionNotMade(f"Could not write {data} to {url}: {response}")
-        return response.json()
+        self._base_url = url
+        self._auth = BearerAuth(token)
 
     def start_load(
         self,
@@ -66,7 +92,7 @@ class ExpeyeInteraction:
         Returns:
             RobotActionID: The id of the robot load action that is created
         """
-        url = self.base_url + self.CREATE_ROBOT_ACTION.format(
+        url = self._base_url + self.CREATE_ROBOT_ACTION.format(
             proposal=proposal_reference, visit_number=visit_number
         )
 
@@ -77,7 +103,7 @@ class ExpeyeInteraction:
             "containerLocation": container_location,
             "dewarLocation": dewar_location,
         }
-        response = self._send_and_get_response(url, data, post)
+        response = _send_and_get_response(self._auth, url, data, post)
         return response["robotActionId"]
 
     def update_barcode_and_snapshots(
@@ -95,14 +121,14 @@ class ExpeyeInteraction:
             snapshot_before_path (str): Path to the snapshot before robot load
             snapshot_after_path (str): Path to the snapshot after robot load
         """
-        url = self.base_url + self.UPDATE_ROBOT_ACTION.format(action_id=action_id)
+        url = self._base_url + self.UPDATE_ROBOT_ACTION.format(action_id=action_id)
 
         data = {
             "sampleBarcode": barcode,
             "xtalSnapshotBefore": snapshot_before_path,
             "xtalSnapshotAfter": snapshot_after_path,
         }
-        self._send_and_get_response(url, data, patch)
+        _send_and_get_response(self._auth, url, data, patch)
 
     def end_load(self, action_id: RobotActionID, status: str, reason: str):
         """Finish an existing robot action, providing final information about how it went
@@ -113,13 +139,37 @@ class ExpeyeInteraction:
                           otherwise error
             reason (str): If the status is in error than the reason for that error
         """
-        url = self.base_url + self.UPDATE_ROBOT_ACTION.format(action_id=action_id)
+        url = self._base_url + self.UPDATE_ROBOT_ACTION.format(action_id=action_id)
 
         run_status = "SUCCESS" if status == "success" else "ERROR"
 
         data = {
             "endTimestamp": get_current_time_string(),
             "status": run_status,
-            "message": reason,
+            "message": reason[:255] if reason else "",
         }
-        self._send_and_get_response(url, data, patch)
+        _send_and_get_response(self._auth, url, data, patch)
+
+    def update_sample_status(
+        self, bl_sample_id: int, bl_sample_status: BLSampleStatus
+    ) -> BLSample:
+        """Update the blSampleStatus of a sample.
+        Args:
+            bl_sample_id: The sample ID
+            bl_sample_status: The sample status
+            status_message: An optional message
+        Returns:
+             The updated sample
+        """
+        data = {"blSampleStatus": (str(bl_sample_status))}
+        response = _send_and_get_response(
+            self._auth, self._base_url + f"/samples/{bl_sample_id}", data, patch
+        )
+        return self._sample_from_json(response)
+
+    def _sample_from_json(self, response) -> BLSample:
+        return BLSample(
+            bl_sample_id=response["blSampleId"],
+            bl_sample_status=response["blSampleStatus"],
+            container_id=response["containerId"],
+        )

mx_bluesky/hyperion/utils/validation.py

@@ -9,7 +9,7 @@ import bluesky.preprocessors as bpp
 from bluesky.run_engine import RunEngine
 from dodal.beamlines import i03
 from dodal.devices.oav.oav_parameters import OAVConfig
-from ophyd_async.core import set_mock_value
+from ophyd_async.testing import set_mock_value
 
 from mx_bluesky.hyperion.device_setup_plans.read_hardware_for_setup import (
     read_hardware_during_collection,

{mx_bluesky-1.4.1a0.dist-info → mx_bluesky-1.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mx-bluesky
-Version: 1.4.1a0
+Version: 1.4.2
 Summary: Bluesky tools for MX Beamlines at DLS
 Author-email: Dominic Oram <dominic.oram@diamond.ac.uk>
 License:                                  Apache License
@@ -239,7 +239,7 @@ Requires-Dist: daq-config-server>=0.1.1
 Requires-Dist: ophyd==1.9.0
 Requires-Dist: ophyd-async>=0.8a5
 Requires-Dist: bluesky>=1.13.0a4
-Requires-Dist: dls-dodal==1.36.1a
+Requires-Dist: dls-dodal==1.36.3
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: build; extra == "dev"