WIP update to work with MXLIMS 0.6.9 (rhfogh: rhfogh_mxlims_2025)

docs/source/dev/json-schema-generated-user-interface.md

@@ -9,7 +9,7 @@
 
 We have a system for code-generated interfaces that can be plugged in to both a Qt and a Web user interface. It is implemented for Qt5, and (as of 20240213) just about ready for testing with the web interface.
 
-The system is used to generate parameter queries from mxcubecore (for now from the GΦL workflow). It includes a wide range of widgets; multiple nested layout fields; support for custom update functions triggered when values are edited, that can reset values of other fields, change widget colouring and pulldown enums; field value validation; and colouring and disabling of action for invalid values. There are several examples of pulldown menu contents being modified depending on the values of other fields. The system is started with a `PARAMETERS_NEEDED` on signals being sent from the mxcubecore side with the JSON schemas as parameters. The UI side responds by sending a `PARAMETER_RETURN_SIGNAL` with the complete dictionary of parameter values. There is also a control parameter, that determines whether the response matches a Continue or Cancel click (closing the UI popup), or whether it is a request for a UI update. In the latter case the update is sent from the mxcubecore side with a `PARAMETER_UPDATE_SIGNAL`.
+The system is used to generate parameter queries from mxcubecore (for now from the GPhL workflow). It includes a wide range of widgets; multiple nested layout fields; support for custom update functions triggered when values are edited, that can reset values of other fields, change widget colouring and pulldown enums; field value validation; and colouring and disabling of action for invalid values. There are several examples of pulldown menu contents being modified depending on the values of other fields. The system is started with a `PARAMETERS_NEEDED` on signals being sent from the mxcubecore side with the JSON schemas as parameters. The UI side responds by sending a `PARAMETER_RETURN_SIGNAL` with the complete dictionary of parameter values. There is also a control parameter, that determines whether the response matches a Continue or Cancel click (closing the UI popup), or whether it is a request for a UI update. In the latter case the update is sent from the mxcubecore side with a `PARAMETER_UPDATE_SIGNAL`.
 
 The form of the JSON schemas used has been agreed between Rasmus Fogh, Jean-Baptiste Florial, and Marcus Oscarsson. Hopefully it fits with standard practices.
 

mxcubecore/HardwareObjects/ALBA/ALBAMiniDiff.py

@@ -281,6 +281,7 @@ def use_sample_changer(self):
         return True
 
     # TODO:Implement dynamically
+    @property
     def in_plate_mode(self):
         """
         Overrides GenericDiffracometer method.
@@ -349,7 +350,7 @@ def prepare_centring(self):
     #             {"X": (x - self.zoom_centre['x'])/ self.pixels_per_mm_x,
     #              "Y": (y - self.zoom_centre['y'])/ self.pixels_per_mm_y})
 
-    #        if self.in_plate_mode():
+    #        if self.in_plate_mode:
     #            dynamic_limits = self.phi_motor_hwobj.get_dynamic_limits()
     #            if click == 0:
     #                self.phi_motor_hwobj.set_value(dynamic_limits[0])

mxcubecore/HardwareObjects/ALBA/XalocMiniDiff.py

@@ -125,6 +125,7 @@ def getBeamInfo(self, update_beam_callback):
 
         update_beam_callback(data)
 
+    @property
     def in_plate_mode(self):
         return False
 
@@ -146,7 +147,7 @@ def manual_centring(self):
                 }
             )
 
-            if self.in_plate_mode():
+            if self.in_plate_mode:
                 dynamic_limits = self.phi_motor_hwobj.get_dynamic_limits()
                 if click == 0:
                     self.phi_motor_hwobj.set_value(dynamic_limits[0])

mxcubecore/HardwareObjects/Beamline.py

@@ -396,7 +396,7 @@ def get_default_acquisition_parameters(self, acquisition_type="default"):
             acq_parameters.detector_binning_mode = ""
 
         try:
-            acq_parameters.detector_roi_mode = self.detector.get_roi_mode()
+            acq_parameters.detector_roi_mode = self.detector.get_roi_mode_name()
         except Exception:
             self.log.warning(
                 "get_default_acquisition_parameters: "

mxcubecore/HardwareObjects/DESY/P11Collect.py

@@ -1264,5 +1264,5 @@ def take_crystal_snapshots(self):
                 self._take_crystal_snapshot(snapshot_filename)
                 time.sleep(1)  # needed, otherwise will get the same images
                 if number_of_snapshots > 1:
-                    HWR.beamline.diffractometer.move_omega_relative(90)
+                    HWR.beamline.diffractometer.omega.set_value_relative(90)
                     time.sleep(1)  # needed, otherwise will get the same images

mxcubecore/HardwareObjects/DESY/P11NanoDiff.py

@@ -338,7 +338,7 @@ def centring_done(self, centring_procedure, motor_p=None):
                 # if 3 click centring move -180. well. dont, in principle the calculated
                 # centred positions include omega to initial position
                 pass
-                # if not self.in_plate_mode():
+                # if not self.in_plate_mode:
                 #    self.log.debug("Centring finished. Moving omega back to initial position")
                 #    self.motor_hwobj_dict['phi'].set_value_relative(-180, timeout=None)
                 #    self.log.debug("         Moving omega done")

mxcubecore/HardwareObjects/EMBL/EMBLDoorInterlock.py

@@ -149,7 +149,7 @@ def unlock_door_interlock(self):
         """
         if HWR.beamline.diffractometer is not None:
             detector_distance = HWR.beamline.detector.distance
-            if HWR.beamline.diffractometer.in_plate_mode():
+            if HWR.beamline.diffractometer.in_plate_mode:
                 if detector_distance is not None:
                     if detector_distance.get_value() < 780:
                         detector_distance.set_value(800, timeout=None)

mxcubecore/HardwareObjects/EMBL/EMBLMiniDiff.py

@@ -178,7 +178,7 @@ def use_sample_changer(self):
 
         :return: bool
         """
-        return not self.in_plate_mode()
+        return not self.in_plate_mode
 
     def beam_position_changed(self, value):
         self.beam_position = value
@@ -301,7 +301,7 @@ def set_phase(self, phase, timeout=80):
                 "Diffractometer: Setting %s phase. Please wait..." % phase
             )
 
-        if self.in_plate_mode() and (
+        if self.in_plate_mode and (
             phase
             in (GenericDiffractometer.PHASE_TRANSFER, GenericDiffractometer.PHASE_BEAM)
             or self.current_phase
@@ -391,7 +391,7 @@ def manual_centring(self):
                     "Y": (y - self.beam_position[1]) / self.pixels_per_mm_y,
                 }
             )
-            if self.in_plate_mode():
+            if self.in_plate_mode:
                 dynamic_limits = self.get_osc_limits()
                 if click == 0:
                     self.motor_hwobj_dict["phi"].set_value(dynamic_limits[0] + 0.5)
@@ -601,7 +601,7 @@ def convert_from_obj_to_name(self, motor_pos):
         return motors
 
     def visual_align(self, point_1, point_2):
-        if self.in_plate_mode():
+        if self.in_plate_mode:
             self.log.info("EMBLMiniDiff: Visual align not available in Plate mode")
         else:
             t1 = [point_1.sampx, point_1.sampy, point_1.phiy]

mxcubecore/HardwareObjects/GenericDiffractometer.py

@@ -303,7 +303,6 @@ def __init__(self, name):
         self.fast_shutter_is_open = None
         self.centring_status = {"valid": False}
         self.centring_time = 0
-        self.user_confirms_centring = None
         self.user_clicked_event = None
         self.automatic_centring_try_count = 1
         self.omega_reference_par = None
@@ -327,7 +326,6 @@ def init(self):
         # Internal values -----------------------------------------------------
         self.ready_event = gevent.event.Event()
         self.user_clicked_event = gevent.event.AsyncResult()
-        self.user_confirms_centring = True
 
         self.beamstop = self.get_object_by_role("beamstop")
         self.aperture = self.get_object_by_role("aperture")
@@ -682,20 +680,14 @@ def execute_server_task(self, method, timeout=30, *args):
         self.wait_device_ready(timeout)
         self.ready_event.set()
 
+    @property
     def in_plate_mode(self):
         """Returns True if diffractometer in plate mod
 
         :returns: boolean
         """
         return self.head_type == GenericDiffractometer.HEAD_TYPE_PLATE
 
-    def get_head_type(self):
-        """Returns head type
-
-        :returns: string
-        """
-        return self.head_type
-
     def use_sample_changer(self):
         """Returns True if sample changer is in use
 
@@ -1000,7 +992,7 @@ def centring_done(self, centring_procedure):
                 # if 3 click centring move -180. well. dont, in principle the calculated
                 # centred positions include omega to initial position
                 pass
-                # if not self.in_plate_mode():
+                # if not self.in_plate_mode:
                 #    self.log.debug("Centring finished. Moving omega back to initial position")
                 #    self.motor_hwobj_dict['phi'].set_value_relative(-180, timeout=None)
                 #    self.log.debug("         Moving omega done")

mxcubecore/HardwareObjects/Gphl/CollectEmulator.py

@@ -236,10 +236,10 @@ def data_collection_hook(self):
         data_collect_parameters = self.current_dc_parameters
 
         if not HWR.beamline.gphl_workflow:
-            raise ValueError("Emulator requires GΦL workflow installation")
+            raise ValueError("Emulator requires GPhL workflow installation")
         gphl_connection = HWR.beamline.gphl_connection
         if not gphl_connection:
-            raise ValueError("Emulator requires GΦL connection installation")
+            raise ValueError("Emulator requires GPhL connection installation")
 
         # Get program locations
         simcal_executive = gphl_connection.get_executable("simcal")
@@ -326,7 +326,7 @@ def set_ulimit():
             # NBNB TODO put in time-out, somehow
             return_code = running_process.wait()
         except Exception:
-            self.log.error("Error in GΦL collection emulation")
+            self.log.error("Error in GPhL collection emulation")
             raise
         finally:
             fp1.close()

mxcubecore/HardwareObjects/Gphl/GphlQueueEntry.py

@@ -25,6 +25,7 @@
 
 from mxcubecore import HardwareRepository as HWR
 from mxcubecore.queue_entry.base_queue_entry import BaseQueueEntry
+from mxcubecore.utils import mxutils
 
 __credits__ = ["MXCuBE collaboration"]
 __license__ = "LGPLv3+"
@@ -35,7 +36,7 @@ class GphlWorkflowQueueEntry(BaseQueueEntry):
     def execute(self):
         BaseQueueEntry.execute(self)
 
-        msg = "Starting GΦL workflow (%s), please wait." % (
+        msg = "Starting GPhL workflow (%s), please wait." % (
             self.get_data_model().strategy_name
         )
         logging.getLogger("user_level_log").info(msg)
@@ -45,20 +46,59 @@ def pre_execute(self):
         BaseQueueEntry.pre_execute(self)
         if not HWR.beamline.gphl_workflow.is_ready():
             logging.getLogger("user_level_log").warning(
-                "WARNING: GΦL workflow was not ready - cleaning up"
+                "WARNING: GPhL workflow was not ready - cleaning up"
             )
             HWR.beamline.gphl_workflow.post_execute()
         HWR.beamline.gphl_workflow.pre_execute(self)
         logging.getLogger("HWR").debug("Done GphlWorkflowQueueEntry.pre_execute")
 
     def post_execute(self):
+        self.finalize_mxlims()
         BaseQueueEntry.post_execute(self)
-        msg = "Finishing GΦL workflow (%s)" % (self.get_data_model().strategy_name)
+        msg = "Finishing GPhL workflow (%s)" % (self.get_data_model().strategy_name)
         logging.getLogger("user_level_log").info(msg)
         HWR.beamline.gphl_workflow.post_execute()
 
     def stop(self):
         HWR.beamline.gphl_workflow.workflow_aborted("Dummy", "Dummy")
         BaseQueueEntry.stop(self)
-        logging.getLogger("user_level_log").info("MXCuBE aborting current GΦL workflow")
+        logging.getLogger("user_level_log").info(
+            "MXCuBE aborting current GPhL workflow"
+        )
         self.get_view().setText(1, "Stopped")
+
+    def init_mxlims(self):
+        """Initialise MXLIMS MxExperimentMessage if it is not already set"""
+
+        if self.get_mxlims_job() is None:
+            data_model = self.get_data_model()
+            self._mxlims_job, mxlims_sample = mxutils.make_mx_experiment(
+                sample=data_model.get_sample_node(),
+                tracking_data=data_model.tracking_data,
+                measured_flux=HWR.beamline.flux.get_value(),
+            )
+    def finalize_mxlims(self):
+        """Finalize MXLIMS MxExperimentMessage setting information  at end of execution
+        """
+        mx_experiment = self.get_mxlims_job()
+        if not mx_experiment:
+            # Only happens if there was an error upstream anyway
+            return
+        data_model = self.get_data_model()
+        workflow_name = data_model.workflow_name
+        if not mx_experiment.experiment_strategy:
+            mx_experiment.experiment_strategy = workflow_name
+        mx_experiment.radiation_dose = data_model.total_radiation_dose
+        mx_experiment.selected_space_group_name = data_model.space_group
+        cell_parameters = data_model.cell_parameters
+        if cell_parameters:
+            unit_cell = mxutils.make_unit_cell(*cell_parameters)
+            if unit_cell:
+                mx_experiment.selected_unit_cell = unit_cell
+        extensions = mx_experiment.extensions
+        if not extensions:
+            extensions = mx_experiment.extensions = {}
+        gphl_extensions = extensions.setdefault(data_model.GPHL_WORKFLOW_EXTENSION, {})
+        gphl_extensions.update(data_model.strategy_options)
+        gphl_extensions["experiment_strategy"] = workflow_name
+