Fixes for recent MO PR

mxcubecore/HardwareObjects/ALBA/ALBACollect.py

@@ -390,6 +390,8 @@ def write_image_headers(self, start_angle):
         )
         self.image_headers["Detector_Voffset"] = "0 m"
 
+        # NBNB TODO check if get_beam_position() (should be pixels)
+        # matches beamx, beamy (should be mm)
         beamx, beamy = HWR.beamline.detector.get_beam_position()
         self.image_headers["Beam_xy"] = "(%.2f, %.2f) pixels" % (beamx, beamy)
 

mxcubecore/HardwareObjects/ALBA/ALBAPilatus.py

@@ -104,6 +104,9 @@ def has_shutterless(self):
 
     def get_beam_position(self, distance=None, wavelength=None):
         """Returns beam center coordinates"""
+
+        # NBNB TODO check if pixels or mm, and adjust code
+        # Should be pixels
         beam_x = 0
         beam_y = 0
         try:

mxcubecore/HardwareObjects/EMBLFlexHCD.py

@@ -403,7 +403,8 @@ def load(self, sample):
             res = SampleChanger.load(self, sample)
         finally:
             for msg in self.get_robot_exceptions():
-                logging.getLogger("HWR").error(msg)
+                if msg is not None:
+                    logging.getLogger("HWR").error(msg)
 
         if res:
             self.prepare_centring()
@@ -541,7 +542,8 @@ def _do_load(self, sample=None):
                 gevent.sleep(2)
 
         for msg in self.get_robot_exceptions():
-            logging.getLogger("HWR").error(msg)
+            if msg is not None:
+                logging.getLogger("HWR").error(msg)
 
         return self._set_loaded_sample_and_prepare(loaded_sample, previous_sample)
 
@@ -559,7 +561,8 @@ def _do_unload(self, sample=None):
         )
 
         for msg in self.get_robot_exceptions():
-            logging.getLogger("HWR").error(msg)
+            if msg is not None:
+                logging.getLogger("HWR").error(msg)
 
         if loaded_sample == (-1, -1, -1):
             self._reset_loaded_sample()

mxcubecore/HardwareObjects/ISPyBRestClient.py

@@ -183,7 +183,7 @@ def get_dc(self, dc_id):
             response = json.loads(get(url).text)[0]
         except Exception as ex:
             response = None
-            logging.getLogger("ispyb_client").exception(str(ex))
+            # logging.getLogger("ispyb_client").exception(str(ex))
 
         lims_dc = {}
         lims_dc["workflow_result_url_list"] = []

mxcubecore/HardwareObjects/LimaEigerDetector.py

@@ -149,8 +149,8 @@ def prepare_acquisition(
 
         beam_x, beam_y = HWR.beamline.detector.get_beam_position()
         header_info = [
-            "beam_center_x=%s" % (beam_x / 7.5000003562308848e-02),
-            "beam_center_y=%s" % (beam_y / 7.5000003562308848e-02),
+            "beam_center_x=%s" % (beam_x),
+            "beam_center_y=%s" % (beam_y),
             "detector_distance=%s"
             % (HWR.beamline.detector.distance.get_value() / 1000.0),
             "omega_start=%0.4f" % start,

mxcubecore/HardwareObjects/LimaPilatusDetector.py

@@ -194,8 +194,8 @@ def prepare_acquisition(
         self.header["Transmission"] = HWR.beamline.transmission.get_value()
 
         self.header["Flux"] = HWR.beamline.flux.get_value()
-        self.header["Beam_xy"] = "(%.2f, %.2f) pixels" % tuple(
-            [value / 0.172 for value in HWR.beamline.detector.get_beam_position()]
+        self.header["Beam_xy"] = (
+            "(%.2f, %.2f) pixels" % HWR.beamline.detector.get_beam_position()
         )
         self.header["Detector_Voffset"] = "0.0000 m"
         self.header["Energy_range"] = "(0, 0) eV"

mxcubecore/HardwareObjects/abstract/AbstractCollect.py

@@ -599,8 +599,9 @@ def update_data_collection_in_lims(self):
             params["resolution"] = HWR.beamline.resolution.get_value()
             params["transmission"] = HWR.beamline.transmission.get_value()
             beam_centre_x, beam_centre_y = HWR.beamline.detector.get_beam_position()
-            params["xBeam"] = beam_centre_x
-            params["yBeam"] = beam_centre_y
+            pixel_x, pixel_y = self.get_pixel_size()
+            params["xBeam"] = beam_centre_x * pixel_x
+            params["yBeam"] = beam_centre_y * pixel_y
             und = self.get_undulators_gaps()
             i = 1
             for jj in self.bl_config.undulators:

mxcubecore/HardwareObjects/queue_model_objects.py

@@ -2159,9 +2159,7 @@ def set_pre_strategy_params(
             distance = HWR.beamline.resolution.resolution_to_distance(
                 resolution, wavelength
             )
-            orgxy = HWR.beamline.detector.get_beam_position(
-                distance, wavelength
-            )
+            orgxy = HWR.beamline.detector.get_beam_position(distance, wavelength)
 
             self.detector_setting = GphlMessages.BcsDetectorSetting(
                 resolution, orgxy=orgxy, Distance=distance
@@ -2500,6 +2498,13 @@ def get_files_to_be_written(self):
         return self.acquisitions[0].path_template.get_files_to_be_written()
 
 
+def addXrayCentring(parent_node, **centring_parameters):
+    """Add Xray centring to queue."""
+    xc_model = XrayCentring2(**centring_parameters)
+    HWR.beamline.queue_model.add_child(parent_node, xc_model)
+    #
+    return xc_model
+
 #
 # Collect hardware object utility function.
 #

mxcubecore/configuration/esrf_id30a2/gphl-setup.yml

@@ -0,0 +1,91 @@
+
+_initialise_class:
+    class: mxcubecore.HardwareObjects.GphlWorkflowConnection.GphlWorkflowConnection
+
+directory_locations:
+    # Directory locations. Can also be used with ${} syntax in this file
+    GPHL_INSTALLATION: /users/blissadm/applications/GPhL_WorkFlow_beta-academic_20220601
+    # GPHL_WRAPPERS: /data/users/p3l-gleb1/gphl/
+
+
+# If set, run workflow through ssh with selected options
+# and quote parameters as appropriate
+# NB The Host option is mandatory
+# ConfigFile is the ssh configuration file, passed to ssh with the -F option
+#ssh_options:
+#    Host: lonsdale
+#    IdentityFile: /home/rhfogh/.ssh/wf_test_id
+#    User: rhfogh
+#    StrictHostKeyChecking: no
+#    ConfigFile: /path/to/ssh/config/file
+
+#    Directory used for GPhL workflow persistence data and workflow logs:
+#    Used to set the wdir workflow option
+#    If relative designates a subdirectory under Session.get_process_directory()
+#    If absolute taken as it stands
+gphl_subdir: GPHL
+#    root name of persistence layer file; suffix'.xml. is added
+gphl_persistname: persistence
+
+#Hosts and ports for py4j java-python gateway, all OPTIONAL
+#If not set will use py4j default values, which are as given below
+#NB python_host is set automatically to localhost or socket.gethostname()
+#NB java_host is not needed as all communication is effectively one-way 
+#connection_parameters:
+#    python_port: 25334
+#    java_port: 25333
+
+#NB Non-absolute file names are interpreted relative to one of the
+#HardwareRepository directories on the lookup path
+
+software_paths:
+    # Mandatory. Directory with workflow config input, e.g. instrumentation.nml
+    gphl_beamline_config: gphl/config_esrf_id30a1
+
+    # MANDATORY for CCP4 => $GPHL_CCP4_PATH/bin/ccp4.setup-sh,
+    # unless already sourced in environment
+    GPHL_CCP4_PATH: /opt/pxsoft/ccp4/v7.1/ubuntu20.04-x86_64/ccp4-7.1/bin
+
+    # MANDATORY for XDS => $GPHL_XDS_PATH/xds_par
+    # unless already sourced in environment
+    GPHL_XDS_PATH: /opt/pxsoft/bin
+
+    GPHL_INSTALLATION: /home/opid30/GPhL_WorkFlow_beta-academic
+
+    # OPTIONAL for java binary => defaults to just 'java'
+#    java_binary: "/alt/rhfogh/Software/GPhL/mxcube_setup/jre1.8.0_144/bin/java"
+
+    # gphl test samples directory - for collection emulation
+#    gphl_test_samples: gphl/test_samples
+
+    #Location of installation used for processing queue (if not reachable from BCS computer.
+    #Passed as environmental variable GPHL_PROC_INSTALLATION. Optional
+#    gphl_wf_processing_installation: /users/pkeller/GPhL-ESRF/exe
+
+# Software paths that are passed to global phasing workflow as java properties
+# Used to specify locations of alternative executables (wrappers)
+# More (unused) properties are described in the ASTRA workflow documentation
+software_properties:
+    #Location of GPhL .license directory
+    #defaults to GPHL_INSTALLATION
+    #Only needed if you do NOT use the gphl installation wrapper scripts in .../exe :
+    #        co.gphl.wf.bdg_licence_dir: "{GPHL_RELEASE}/gphl_release/latest"
+
+    # MANDATORY pending change in workflow
+    co.gphl.wf.stratcal.bin: "{GPHL_INSTALLATION}/exe/run_stratcal_wrap.py"
+
+    # OPTIONAL location of alternative executables (wrappers) supported by the workflow
+    # Each has an option (rarely used)  to specify a specific license directory -->
+    # co.gphl.wf.process.bin: {GPHL_WRAPPERS}/scripts/aP_wf_process
+    # co.gphl.wf.process.bdg_licence_dir/fill/me/in
+    # co.gphl.wf.diffractcal.bin: {GPHL_WRAPPERS}/scripts/aP_wf_rotcal
+    # co.gphl.wf.diffractcal.bdg_licence_dir/fill/me/in
+    # co.gphl.wf.simcal_predict.bin: {GPHL_WRAPPERS}/scripts/simcal_predict
+    # co.gphl.wf.simcal_predict.bdg_licence_dir/fill/me/in
+    # co.gphl.wf.transcal.bin: {GPHL_WRAPPERS}/scripts/transcal
+    # co.gphl.wf.transcal.bdg_licence_dir/fill/me/in
+    # co.gphl.wf.recen.bin: {GPHL_WRAPPERS}/scripts/recen
+    # co.gphl.wf.recen.bdg_licence_dir/fill/me/in
+
+    # OPTIONAL. simcal *binary* For Mock collection emulation only. Not used by ASTRA workflow
+#    co.gphl.wf.simcal.bin: "{GPHL_INSTALLATION}/autoPROC/bin/linux64/simcal"