WIP Added MXLIMS v. 0.3.0 exporter code

mxcubecore/HardwareObjects/Beamline.py

@@ -882,7 +882,7 @@ 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:
             logging.getLogger("HWR").warning(
                 "get_default_acquisition_parameters: "

mxcubecore/HardwareObjects/Gphl/GphlQueueEntry.py

@@ -27,6 +27,9 @@
 from mxcubecore import HardwareRepository as HWR
 from mxcubecore.queue_entry.base_queue_entry import BaseQueueEntry
 
+from mxlims.pydantic import mxmodel
+from mxcubecore.utils import mxlims as mxutils
+
 __credits__ = ["MXCuBE collaboration"]
 __license__ = "LGPLv3+"
 __category__ = "queue"
@@ -54,7 +57,7 @@ def pre_execute(self):
 
     def post_execute(self):
         BaseQueueEntry.post_execute(self)
-        msg = "Finishing GΦL workflow (%s)" % (self.get_data_model().strategy_name)
+        msg = "Finishing GΦL workflow (%s)" % self.get_data_model().strategy_name
         logging.getLogger("user_level_log").info(msg)
         HWR.beamline.gphl_workflow.post_execute()
 
@@ -63,3 +66,15 @@ def stop(self):
         BaseQueueEntry.stop(self)
         logging.getLogger("HWR").info("MXCuBE aborting current GΦL workflow")
         self.get_view().setText(1, "Stopped")
+
+    def init_mxlims(self):
+        """Initialise MXLIMS MxExperimentMessage if it is not already set"""
+
+        mxexperiment: mxmodel.MxExperimentMessage = self.get_mxlims_record()
+        if mxexperiment is None:
+            data_model = self.get_data_model()
+            self._mxlims_record = mxutils.create_mxrecord(
+                sample=data_model.get_sample_node(),
+                tracking_data=data_model.tracking_data,
+                measured_flux = HWR.beamline.flux.get_value()
+            )

mxcubecore/HardwareObjects/Gphl/GphlWorkflow.py

@@ -37,8 +37,8 @@
 import socket
 import subprocess
 import time
-import uuid
 from collections import OrderedDict
+from uuid import uuid1
 
 import f90nml
 import gevent
@@ -77,7 +77,6 @@ class GphlWorkflowStates(enum.Enum):
     COMPLETED = 4
     UNKNOWN = 5
 
-
 __copyright__ = """ Copyright © 2016 - 2019 by Global Phasing Ltd. """
 __license__ = "LGPLv3+"
 __author__ = "Rasmus H Fogh"
@@ -260,6 +259,7 @@ def init(self):
             "WorkflowAborted": self.workflow_aborted,
             "WorkflowCompleted": self.workflow_completed,
             "WorkflowFailed": self.workflow_failed,
+            "StartEnactment": self.start_enactment,
         }
 
         # Set standard configurable file paths
@@ -729,7 +729,6 @@ def query_pre_strategy_params(self, choose_lattice=None):
             dispatcher.connect(
                 self.receive_pre_strategy_data,
                 self.PARAMETER_RETURN_SIGNAL,
-                dispatcher.Any,
             )
             responses = dispatcher.send(
                 self.PARAMETERS_NEEDED,
@@ -752,7 +751,6 @@ def query_pre_strategy_params(self, choose_lattice=None):
             dispatcher.disconnect(
                 self.receive_pre_strategy_data,
                 self.PARAMETER_RETURN_SIGNAL,
-                dispatcher.Any,
             )
             self._return_parameters = None
 
@@ -851,6 +849,34 @@ def pre_execute(self, queue_entry):
 
         self._workflow_queue = gevent.queue.Queue()
 
+    def start_enactment(self, enactment_id:str, correlation_id:str):
+        """Set enactment_id and initialise MXLIMS MxExperimentMessage"""
+        data_model = self._queue_entry.get_data_model()
+        tracking_data = data_model.tracking_data
+        workflow_parameters = data_model.workflow_parameters
+        tracking_data.uuid = enactment_id
+        tracking_data.workflow_uid = (
+            workflow_parameters.get("workflow_uid") or enactment_id
+        )
+        # NB it is not set it will be overwritten later
+        tracking_data.workflow_name = workflow_parameters.get("workflow_name")
+        tracking_data.workflow_type = (
+            workflow_parameters.get("workflow_type")
+            or data_model.strategy_type
+        )
+        tracking_data.location_id = (
+            workflow_parameters.get("workflow_position_id")
+            or str(uuid1())
+        )
+        # NB first orientation only:
+        tracking_data.orientation_id = workflow_parameters.get(
+            "workflow_kappa_settings_id"
+        )
+        tracking_data.characterisation_id = workflow_parameters.get(
+            "characterisation_id"
+        )
+        self._queue_entry.init_mxlims()
+
     def execute(self):
 
         if self._workflow_queue is None:
@@ -1261,10 +1287,9 @@ def query_collection_strategy(self, geometric_strategy):
             raise ValueError(
                 "invalid default recentring mode '%s' " % default_recentring_mode
             )
-        use_modes = ["sweep"]
+        use_modes = ["sweep", "none"]
         if len(orientations) > 1:
             use_modes.append("start")
-            use_modes.append("none")
         if is_interleaved:
             use_modes.append("scan")
         for indx in range(len(modes) - 1, -1, -1):
@@ -1378,7 +1403,6 @@ def query_collection_strategy(self, geometric_strategy):
             dispatcher.connect(
                 self.receive_pre_collection_data,
                 self.PARAMETER_RETURN_SIGNAL,
-                dispatcher.Any,
             )
             responses = dispatcher.send(
                 self.PARAMETERS_NEEDED,
@@ -1398,7 +1422,6 @@ def query_collection_strategy(self, geometric_strategy):
             dispatcher.disconnect(
                 self.receive_pre_collection_data,
                 self.PARAMETER_RETURN_SIGNAL,
-                dispatcher.Any,
             )
             self._return_parameters = None
 
@@ -1949,6 +1972,7 @@ def collect_data(self, payload, correlation_id):
         last_orientation = ()
         maxdev = -1
         snapshotted_rotation_ids = set()
+        characterisation_id = None
         scan_numbers = {}
         for scan in scans:
             sweep = scan.sweep
@@ -2043,31 +2067,48 @@ def collect_data(self, payload, correlation_id):
 
             # Handle orientations and (re) centring
             goniostatRotation = sweep.goniostatSweepSetting
-            rotation_id = orientation_id = goniostatRotation.id_
-
-            model_workflow_parameters = gphl_workflow_model.workflow_parameters
-            if not model_workflow_parameters.get("workflow_name"):
-                model_workflow_parameters["workflow_name"] = gphl_workflow_model.wfname
-            if not model_workflow_parameters.get("workflow_type"):
-                model_workflow_parameters["workflow_type"] = gphl_workflow_model.wftype
-            if not model_workflow_parameters.get("workflow_uid"):
-                model_workflow_parameters["workflow_uid"] = str(
-                    HWR.beamline.gphl_connection._enactment_id
-                )
-            if not model_workflow_parameters.get("workflow_position_id"):
-                # As of 20240911 all workflows use a single position,
-                model_workflow_parameters["workflow_position_id"] = str(uuid.uuid1())
+            rotation_id = goniostatRotation.id_
+
+
+            # handle mxlims
+            # handle workflow parameters
+            new_workflow_parameters = gphl_workflow_model.workflow_parameters.copy()
+            wf_tracking_data = gphl_workflow_model.tracking_data
+            data_collection = queue_model_objects.DataCollection([acq], crystal)
+            # Workflow parameters for ICAT / external workflow
+            # The 'if' statement is to allow this to work in multiple versions
+            data_collection.workflow_parameters = new_workflow_parameters
+            tracking_data = data_collection.tracking_data
+            tracking_data.uuid = str(scan.id_)
+            tracking_data.workflow_name = wf_tracking_data.workflow_name
+            tracking_data.workflow_type = wf_tracking_data.workflow_type
+            tracking_data.workflow_uid = wf_tracking_data.uuid
+            tracking_data.location_id = wf_tracking_data.location_id
+            tracking_data.orientation_id = rotation_id
             if (
                 gphl_workflow_model.wftype == "acquisition"
                 and not gphl_workflow_model.characterisation_done
-                and not model_workflow_parameters.get("workflow_characterisation_id")
             ):
-                model_workflow_parameters["workflow_characterisation_id"] = str(
-                    sweep.id_
-                )
-            model_workflow_parameters["workflow_kappa_settings_id"] = str(
-                orientation_id
-            )
+                if characterisation_id is None:
+                    # NB this is a hack - forces tharacterisation to be a single sweep
+                    characterisation_id = str(sweep.id_)
+                tracking_data.characterisation_id = characterisation_id
+                wf_tracking_data.characterisation_id = characterisation_id
+                tracking_data.role = "Characterisation"
+                tracking_data.sweep_id = characterisation_id
+            else:
+                tracking_data.characterisation_id = wf_tracking_data.characterisation_id#
+                tracking_data.role = "Result"
+                tracking_data.sweep_id = str(sweep.id_)
+            tracking_data.scan_number = gphl_workflow_model.next_scan_number
+            gphl_workflow_model.next_scan_number += 1
+
+            new_workflow_parameters["workflow_name"] = tracking_data.workflow_name
+            new_workflow_parameters["workflow_type"] = tracking_data.workflow_type
+            new_workflow_parameters["workflow_uid"] = tracking_data.workflow_uid
+            new_workflow_parameters["workflow_position_id"] = tracking_data.location_id
+            new_workflow_parameters["characterisation_id"] = tracking_data.characterisation_id
+            new_workflow_parameters["workflow_kappa_settings_id"] = tracking_data.orientation_id
 
             initial_settings = sweep.get_initial_settings()
             orientation = (
@@ -2129,11 +2170,6 @@ def collect_data(self, payload, correlation_id):
                     acq_parameters.num_images_per_trigger * acq_parameters.osc_range
                     - sweep_offset
                 )
-            data_collection = queue_model_objects.DataCollection([acq], crystal)
-            # Workflow parameters for ICAT / external workflow
-            # The 'if' statement is to allow this to work in multiple versions
-            if hasattr(data_collection, "workflow_parameters"):
-                data_collection.workflow_parameters.update(model_workflow_parameters)
             data_collections.append(data_collection)
             data_collection.set_enabled(True)
             data_collection.ispyb_group_data_collections = True

mxcubecore/HardwareObjects/Gphl/GphlWorkflowConnection.py

@@ -619,6 +619,17 @@ def processMessage(self, py4j_message):
                         "GΦL - response=%s jobId=%s messageId=%s"
                         % (result.__class__.__name__, enactment_id, correlation_id)
                     )
+                if message_type == "ObtainPriorInformation":
+                    # At this point we have the enactment_id and can set the workflow_id
+                    self.workflow_queue.put_nowait(
+                        (
+                            "StartEnactment",
+                            self._enactment_id,
+                            None,
+                            None,
+                        )
+                    )
+
                 return self._response_to_server(result, correlation_id)
 
         elif message_type in ("WorkflowAborted", "WorkflowCompleted", "WorkflowFailed"):

mxcubecore/configuration/mockup/gphl/gphl-setup.yml

@@ -89,6 +89,6 @@ software_properties:
 
   # OPTIONAL. simcal *binary* For Mock collection emulation only. Not used by workflow
   co.gphl.wf.simcal.bin:
-    /alt/rhfogh/Software/GPhL/nightly_20240611/Files_workflow_TRUNK_alpha-bdg/autoPROC/bin/linux64/simcal
+    /alt/rhfogh/Software/GPhL/nightly_20241108/Files_workflow_TRUNK_alpha-bdg/autoPROC/bin/linux64/simcal
   co.gphl.wf.simcal.bdg_licence_dir:
-    /alt/rhfogh/Software/GPhL/nightly_20240611/Files_workflow_TRUNK_alpha-bdg
+    /alt/rhfogh/Software/GPhL/nightly_20241108/Files_workflow_TRUNK_alpha-bdg

mxcubecore/configuration/mockup/gphl/gphl-workflow.yml

@@ -42,7 +42,7 @@
   default_beam_energy_tag: Main
 
   # NB Temporary developer option. Defaults to 1
-  allow_duplicate_orientations: 0
+#  allow_duplicate_orientations: 0
 
   # Suppress log output of programs called from GPhL workflow
   # Default to False
@@ -240,6 +240,7 @@
 
       - title: Phasing (SAD)
         strategy_type: phasing
+        short_name: SAD
         wf_selection: mxexpt
         variants:
           - full
@@ -261,6 +262,7 @@
 
       - title: Two-wavelength MAD
         strategy_type: phasing
+        short_name: "2wvlMAD"
         wf_selection: mxexpt
         variants:
           - quick
@@ -291,6 +293,7 @@
 
       - title: Three-wavelength MAD
         strategy_type: phasing
+        short_name: "3wvlMAD"
         wf_selection: mxexpt
         variants:
           - quick