mxcubecore 1.391.0__py3-none-any.whl → 1.393.0__py3-none-any.whl

mxcubecore/HardwareObjects/GenericDiffractometer.py

@@ -363,7 +363,7 @@ class GenericDiffractometer(HardwareObject):
             try:
                 self.used_channels_list = eval(ss0)
             except Exception:
-                pass  # used the default value
+                logging.getLogger("HWR").exception("")
 
         for channel_name in self.used_channels_list:
             self.channel_dict[channel_name] = self.get_channel_object(channel_name)
@@ -392,7 +392,7 @@ class GenericDiffractometer(HardwareObject):
         try:
             self.used_commands_list = eval(self.get_property("used_commands", "[]"))
         except Exception:
-            pass  # used the default value
+            logging.getLogger("HWR").exception("")
         for command_name in self.used_commands_list:
             self.command_dict[command_name] = self.get_command_object(command_name)
 
@@ -479,12 +479,12 @@ class GenericDiffractometer(HardwareObject):
                     self.motor_hwobj_dict["sampy"]
                 )
         except Exception:
-            pass  # used the default value
+            logging.getLogger("HWR").exception("")
 
         try:
             self.delay_state_polling = self.get_property("delay_state_polling")
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
         # Other parameters ---------------------------------------------------
         try:
@@ -610,6 +610,22 @@ class GenericDiffractometer(HardwareObject):
         """
         return self.motor_hwobj_dict.get("phiz")
 
+    @property
+    def zoom(self):
+        """zoom motor object
+
+        NBNB TBD This is supposedly now living in AbstractSampleView,
+        And the property was removed in an earlier PR (20251021, 15:24 Elmir Jagudin)
+        BUT 1) there does not seem to be any mechanism to set it from config there
+        2) it is configured on the diffractometer according to available config files
+        3) accessing diffractometer.zoom is all through the code
+        This needs global refactoring, but meanwhile this property should remain
+
+        Returns:
+            AbstractActuator
+        """
+        return self.motor_hwobj_dict.get("zoom")
+
     def is_ready(self):
         """
         Detects if device is ready
@@ -1396,7 +1412,7 @@ class GenericDiffractometer(HardwareObject):
                 self.sample_is_loaded_changed,
             )
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
         if (
             head_type == GenericDiffractometer.HEAD_TYPE_MINIKAPPA

mxcubecore/HardwareObjects/Gphl/GphlMessages.py

@@ -1310,7 +1310,8 @@ class SampleCentred(Payload):
             self._wavelengths = tuple((data_model.wavelengths[0],))
             # if data_model.wftype != "diffractcal":
             #     self._detectorSetting = data_model.detector_setting
-        self._detectorSetting = data_model.detector_setting
+        if data_model.wftype != "diffractcal":
+            self._detectorSetting = data_model.detector_setting
 
     @property
     def imageWidth(self):

mxcubecore/HardwareObjects/Gphl/GphlWorkflow.py

@@ -844,6 +844,7 @@ class GphlWorkflow(HardwareObject):
         HWR.beamline.gphl_connection.open_connection()
 
         if data_model.wftype == "transcal":
+            self._workflow_queue = gevent.queue.Queue()
             return
         elif data_model.automation_mode:
             params = data_model.auto_acq_parameters[0]

mxcubecore/HardwareObjects/LNLS/LNLSCollect.py

@@ -262,6 +262,8 @@ class LNLSCollect(AbstractMultiCollect, HardwareObject):
             ft = ft / 100  # [0, 1]
         except Exception as e:
             print("Error on setting Pilatus transmission: {}".format(str(e)))
+
+            logging.getLogger("HWR").exception("")
             return False
 
         # Write to det (values will be on the cbf header)

mxcubecore/HardwareObjects/LNLS/LNLSPilatusDet.py

@@ -119,6 +119,8 @@ class LNLSPilatusDet(AbstractDetector):
             logging.getLogger("HWR").error(
                 "Error while setting Pilatus threshold. Value must be float."
             )
+
+            logging.getLogger("HWR").exception("")
             return False
 
         target_threshold = energy / 2
@@ -178,6 +180,8 @@ class LNLSPilatusDet(AbstractDetector):
             logging.getLogger("HWR").error(
                 "Error while setting Pilatus wavelength. Value must be float."
             )
+
+            logging.getLogger("HWR").exception("")
             return False
 
         # if abs(self.wavelength - wavelength) < 0.0001:
@@ -223,6 +227,8 @@ class LNLSPilatusDet(AbstractDetector):
             logging.getLogger("HWR").error(
                 "Error while setting Pilatus det distance. Value must be float."
             )
+
+            logging.getLogger("HWR").exception("")
             return False
 
         # if abs(self.det_distance - det_distance) < 0.001:
@@ -380,6 +386,8 @@ class LNLSPilatusDet(AbstractDetector):
             logging.getLogger("HWR").error(
                 "Error while setting Pilatus transmission. Value must be float."
             )
+
+            logging.getLogger("HWR").exception("")
             return False
 
         logging.getLogger("HWR").info(
@@ -417,6 +425,8 @@ class LNLSPilatusDet(AbstractDetector):
             logging.getLogger("HWR").error(
                 "Error while setting Pilatus start angle. Value must be float."
             )
+
+            logging.getLogger("HWR").exception("")
             return False
 
         logging.getLogger("HWR").info(
@@ -454,6 +464,8 @@ class LNLSPilatusDet(AbstractDetector):
             logging.getLogger("HWR").error(
                 "Error while setting Pilatus angle increment. Value must be float."
             )
+
+            logging.getLogger("HWR").exception("")
             return False
 
         logging.getLogger("HWR").info(

mxcubecore/HardwareObjects/LimaEigerDetector.py

@@ -239,7 +239,7 @@ class LimaEigerDetector(AbstractDetector):
         try:
             self.get_command_object("stop_acq")()
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
         time.sleep(1)
         self.get_command_object("reset")()

mxcubecore/HardwareObjects/Marvin.py

@@ -871,7 +871,7 @@ class Marvin(AbstractSampleChanger.SampleChanger):
                         Container.Pin.get_sample_address(basket_no, sample_no)
                     )
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
         self._set_selected_component(basket)
         self._set_selected_sample(sample)
 
@@ -1042,7 +1042,7 @@ class Marvin(AbstractSampleChanger.SampleChanger):
                         self.emit("progressStep", self._progress)
                         self._info_dict["progress"] = self._progress
                 except Exception:
-                    pass
+                    logging.getLogger("HWR").exception("")
             elif prop_name == "CPuck":
                 if prop_value == "1":
                     centre_puck = True

mxcubecore/HardwareObjects/MicrodiffActuator.py

@@ -54,7 +54,7 @@ class MicrodiffActuator(AbstractActuator):
             tt = float(self.get_property("timeout"))
             self.timeout = tt
         except TypeError:
-            pass
+            logging.getLogger("HWR").exception("")
 
         if self.get_property("use_hwstate"):
             self.hwstate_attr = self.add_channel(

mxcubecore/HardwareObjects/MicrodiffBeamstop.py

@@ -1,3 +1,5 @@
+import logging
+
 from mxcubecore.BaseHardwareObjects import HardwareObject
 
 """
@@ -92,7 +94,7 @@ class MicrodiffBeamstop(HardwareObject):
         try:
             pos = self.beamstop.states[pos]
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
         if not noEmit:
             if pos:

mxcubecore/HardwareObjects/MicrodiffInOut.py

@@ -57,7 +57,7 @@ class MicrodiffInOut(HardwareObject):
             tt = float(self.get_property("timeout"))
             self.timeout = tt
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
         if self.get_property("use_hwstate"):
             self.hwstate_attr = self.add_channel(

mxcubecore/HardwareObjects/MiniDiff.py

@@ -142,7 +142,7 @@ class MiniDiff(HardwareObject):
             try:
                 self.lightWago = hwr.get_hardware_object(wl_prop)
             except Exception:
-                pass
+                logging.getLogger("HWR").exception("")
 
         if self.phiMotor is not None:
             self.connect(self.phiMotor, "stateChanged", self.phiMotorStateChanged)

mxcubecore/HardwareObjects/MotorWPositions.py

@@ -67,6 +67,8 @@ class MotorWPositions(AbstractMotor, Device):
             self.motor = self.get_object_by_role(role)
         except KeyError:
             logging.getLogger("HWR").error("MotorWPositions: motor not defined")
+
+            logging.getLogger("HWR").exception("")
             return
         try:
             self.delta = self["deltas"].get_property(role)

mxcubecore/HardwareObjects/PlateManipulator.py

@@ -242,7 +242,7 @@ class PlateManipulator(SampleChanger):
                     self.num_drops,
                 ) = cmd_get_config.get_value()
             except Exception:
-                pass
+                logging.getLogger("HWR").exception("")
         else:
             self.num_cols = self.get_property("numCols")
             self.num_rows = self.get_property("numRows")
@@ -323,7 +323,7 @@ class PlateManipulator(SampleChanger):
             self.plate_location_changed(self.chan_plate_location.get_value())
             self._on_state_changed(state)
         except AttributeError:
-            pass
+            logging.getLogger("HWR").exception("")
 
     def _on_state_changed(self, state):
         """

mxcubecore/HardwareObjects/QtGraphicsLib.py

@@ -466,7 +466,7 @@ class GraphicsItemPoint(GraphicsItem):
                 self.__centred_position.kappa_phi,
             )
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
         return full_name
 
     def get_centred_position(self):
@@ -602,7 +602,7 @@ class GraphicsItemLine(GraphicsItem):
                 start_cpos.kappa_phi,
             )
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
         return full_name
 
     def paint(self, painter, option, widget):

mxcubecore/HardwareObjects/QtGraphicsManager.py

@@ -294,7 +294,7 @@ class QtGraphicsManager(AbstractSampleView):
                 self.image_scale = self.get_property("default_image_scale")
                 self.set_image_scale(self.image_scale, self.image_scale is not None)
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
         """
         if self.get_property("store_graphics_config") == True:
@@ -335,7 +335,7 @@ class QtGraphicsManager(AbstractSampleView):
                 eval(self.get_property("magnification_tool"))
             )
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
         # try:
         #    self.set_view_scale(self.get_property("view_scale"))
@@ -797,7 +797,7 @@ class QtGraphicsManager(AbstractSampleView):
             date_time_str = datetime.now().strftime("%Y_%m_%d_%H_%M_%S")
             result_image.save("/opt/embl-hh/var/crystal_images/%s.png" % date_time_str)
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
     def diffractometer_centring_failed(self, method, centring_status):
         """CleanUp method after centring failed

mxcubecore/HardwareObjects/QueueManager.py

@@ -168,7 +168,7 @@ class QueueManager(HardwareObject, QueueEntryContainer):
                         qe.handle_exception(ex)
                         self.stop()
                     except gevent.GreenletExit:
-                        pass
+                        logging.getLogger("HWR").exception("")
 
                     if isinstance(ex, base_queue_entry.QueueAbortedException):
                         logging.getLogger("user_level_log").warning(
@@ -276,9 +276,9 @@ class QueueManager(HardwareObject, QueueEntryContainer):
                     qe.stop()
                     qe.post_execute()
                 except base_queue_entry.QueueAbortedException:
-                    pass
+                    logging.getLogger("HWR").exception("")
                 except Exception:
-                    pass
+                    logging.getLogger("HWR").exception("")
 
         if self._root_task:
             self._root_task.kill(block=False)

mxcubecore/HardwareObjects/RedisClient.py

@@ -88,7 +88,7 @@ class RedisClient(HardwareObject):
         try:
             self.connect(HWR.beamline.flux, "fluxChanged", self.flux_changed)
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
         self.proposal_id = HWR.beamline.session.get_proposal()
         self.beamline_name = HWR.beamline.session.beamline_name
@@ -162,7 +162,7 @@ class RedisClient(HardwareObject):
                 )
                 logging.getLogger("HWR").debug("RedisClient: Graphics loaded")
             except Exception:
-                pass
+                logging.getLogger("HWR").exception("")
 
     def save_queue_history_item(self, item):
         """Saves queue history in redisDB"""
@@ -187,7 +187,7 @@ class RedisClient(HardwareObject):
                 for item in items:
                     result.append(eval(item))
             except Exception:
-                pass
+                logging.getLogger("HWR").exception("")
         return result
 
     def clear_db(self):

mxcubecore/HardwareObjects/SC3.py

@@ -1,3 +1,4 @@
+import logging
 import xml.sax
 from xml.sax.handler import ContentHandler
 
@@ -374,7 +375,7 @@ class SC3(SampleChanger):
                         Pin.get_sample_address(basket_no, sample_no)
                     )
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
         self._set_selected_component(basket)
         self._set_selected_sample(sample)
 

mxcubecore/HardwareObjects/SOLEIL/PX1/PX1BeamInfo.py

@@ -85,7 +85,7 @@ class PX1BeamInfo(HardwareObject):
                     self.beam_info_dict["size_x"] = self.beam_size[0] = float(beamx)
                     self.beam_info_dict["size_y"] = self.beam_size[1] = float(beamy)
             except Exception:
-                pass
+                logging.getLogger("HWR").exception("")
 
     def connect_notify(self, signal):
         if signal == "beamInfoChanged":

mxcubecore/HardwareObjects/SOLEIL/PX1/PX1Cryotong.py

@@ -104,7 +104,7 @@ class PX1Cryotong(Cats90):
                     self._cmdAckSampleMemory()
                 except Exception:
                     """ do nothing if cmd not to acknowledge not in xml """
-                    pass
+                    logging.getLogger("HWR").exception("")
             self.incoherent_state = value
 
     def _dry_and_soak_needed(self, value=None):

mxcubecore/HardwareObjects/SOLEIL/PX1/PX1Pilatus.py

@@ -111,7 +111,7 @@ class PX1Pilatus(AbstractDetector, HardwareObject):
                 beam_x = value[0]
                 beam_y = value[1]
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
         return beam_x, beam_y
 
     def get_manufacturer(self):

mxcubecore/HardwareObjects/SOLEIL/PX2/PX2Collect.py

@@ -89,7 +89,7 @@ class PX2Collect(AbstractCollect, HardwareObject):
             for undulator in self["undulators"]:
                 undulators.append(undulator)
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
         beam_div_hor, beam_div_ver = HWR.beamline.beam.get_beam_divergence()
 

mxcubecore/HardwareObjects/SOLEIL/SOLEILISPyBClient.py

@@ -45,7 +45,7 @@ class SOLEILISPyBClient(ISPyBClient):
             hdlr.setFormatter(formatter)
             logger.addHandler(hdlr)
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
         logger.setLevel(logging.INFO)
 
@@ -111,19 +111,19 @@ class SOLEILISPyBClient(ISPyBClient):
                 try:
                     self._translations[code]["ldap"] = proposal.ldap
                 except AttributeError:
-                    pass
+                    logging.getLogger("HWR").exception("")
                 try:
                     self._translations[code]["ispyb"] = proposal.ispyb
                 except AttributeError:
-                    pass
+                    logging.getLogger("HWR").exception("")
                 try:
                     self._translations[code]["gui"] = proposal.gui
                 except AttributeError:
-                    pass
+                    logging.getLogger("HWR").exception("")
         except IndexError:
-            pass
+            logging.getLogger("HWR").exception("")
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
     def translate(self, code, what):
         """
@@ -187,7 +187,7 @@ class SOLEILISPyBClient(ISPyBClient):
                 logging.debug("SOLEIL ISPyBClient - %s is %s " % (prop, ispyb_path))
                 mx_collect_dict[prop] = ispyb_path
             except Exception:
-                pass
+                logging.getLogger("HWR").exception("")
 
     def prepare_image_for_lims(self, image_dict):
         for prop in ["jpegThumbnailFileFullPath", "jpegFileFullPath"]:
@@ -196,7 +196,7 @@ class SOLEILISPyBClient(ISPyBClient):
                 ispyb_path = HWR.beamline.session.path_to_ispyb(path)
                 image_dict[prop] = ispyb_path
             except Exception:
-                pass
+                logging.getLogger("HWR").exception("")
 
 
 def test_hwo(hwo):

mxcubecore/HardwareObjects/SOLEIL/SOLEILRuche.py

@@ -27,7 +27,7 @@ class SOLEILRuche(HardwareObject):
             if HWR.beamline.session.user_id is None:
                 return
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
         if os.path.isdir(path):
             path_to_sync = path
         elif os.path.exists(path):

mxcubecore/HardwareObjects/SOLEIL/TangoDCMotor.py

@@ -60,7 +60,7 @@ class TangoDCMotor(HardwareObject):
             try:
                 self.threshold = float(threshold)
             except Exception:
-                pass
+                logging.getLogger("HWR").exception("")
 
         self.set_is_ready(True)
         try:

mxcubecore/HardwareObjects/Session.py

@@ -5,6 +5,7 @@ Contains information regarding the current session and methods to
 access and manipulate this information.
 """
 
+import logging
 import os
 import socket
 import time
@@ -93,7 +94,7 @@ class Session(HardwareObject):
                 domain = socket.getfqdn().split(".")
                 self.email_extension = ".".join((domain[-2], domain[-1]))
             except (TypeError, IndexError):
-                pass
+                logging.getLogger("HWR").exception("")
 
         self.set_base_data_directories(
             file_info["base_directory"],

mxcubecore/HardwareObjects/SpecShell.py

@@ -155,7 +155,7 @@ class SpecShell(HardwareObject):
                 try:
                     buf_list = buf.split()
                 except Exception:
-                    pass
+                    logging.getLogger("HWR").exception("")
                 else:
                     i = 0
                     while i < len(buf_list):
@@ -163,20 +163,20 @@ class SpecShell(HardwareObject):
                         try:
                             cmd_aux = buf_list[i + 1]
                         except Exception:
-                            pass
+                            logging.getLogger("HWR").exception("")
                         else:
                             try:
                                 left_par = cmd_aux[0]
                                 right_par = cmd_aux[-1]
                                 midle_num = cmd_aux[1:-1]
                             except Exception:
-                                pass
+                                logging.getLogger("HWR").exception("")
                             else:
                                 if left_par == "(" and right_par == ")":
                                     try:
                                         int(midle_num)
                                     except Exception:
-                                        pass
+                                        logging.getLogger("HWR").exception("")
                                     else:
                                         commands_list.append(cmd_name.lstrip("*"))
                         i += 2
@@ -222,7 +222,7 @@ class SpecShell(HardwareObject):
             try:
                 self.specShellCommand.abort()
             except SpecClient.SpecClientError.SpecClientError as diag:
-                pass
+                logging.getLogger("HWR").exception("")
 
     def outputReceived(self, output):
         if self.lsdefRunning:
@@ -250,7 +250,7 @@ class SpecShell(HardwareObject):
                 else:
                     cmds.append(cmd.method)
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
         return cmds
 
     def getAllCommands(self):

mxcubecore/HardwareObjects/SpecState.py

@@ -63,7 +63,7 @@ class SpecState(Procedure):
         try:
             cmd = self.get_command_object("SpecStateMacro")
         except KeyError:
-            pass
+            logging.getLogger("HWR").exception("")
         else:
             if cmd is not None:
                 cmd.disconnect_signal("commandReady", self.commandReady)

mxcubecore/HardwareObjects/TangoLimaMpegVideo.py

@@ -117,7 +117,7 @@ class TangoLimaMpegVideo(TangoLimaVideo):
                 for p in ps:
                     p.kill()
             except psutil.NoSuchProcess:
-                pass
+                logging.getLogger("HWR").exception("")
 
             self._video_stream_process = None
 

mxcubecore/HardwareObjects/TangoMotor.py

@@ -20,6 +20,8 @@
 TangoMotor class defines motor in the Tango control system (used and tested in DESY/P11
 """
 
+import logging
+
 import gevent
 
 from mxcubecore.HardwareObjects.abstract.AbstractMotor import AbstractMotor
@@ -106,7 +108,7 @@ class TangoMotor(AbstractMotor):
                 if self.get_property("default_limits"):
                     self.update_limits(eval(self.get_property("default_limits")))
             except Exception:
-                pass
+                logging.getLogger("HWR").exception("")
 
         self.cmd_stop = self.get_command_object("stopAxis")
         if self.cmd_stop is None:

mxcubecore/HardwareObjects/UserTypeISPyBLims.py

@@ -185,7 +185,7 @@ class UserTypeISPyBLims(ISPyBAbstractLIMS):
                                         session.endDate, "%Y-%m-%d %H:%M:%S"
                                     )
                                 except Exception:
-                                    pass
+                                    logging.getLogger("HWR").exception("")
                                 sessions.append(utf_encode(asdict(session)))
 
                     except WebFault as e:
@@ -281,7 +281,7 @@ class UserTypeISPyBLims(ISPyBAbstractLIMS):
                                 session.endDate, "%Y-%m-%d %H:%M:%S"
                             )
                         except Exception:
-                            pass
+                            logging.getLogger("HWR").exception("")
 
                         sessions.append(utf_encode(asdict(session)))
 
@@ -291,6 +291,8 @@ class UserTypeISPyBLims(ISPyBAbstractLIMS):
 
         except URLError:
             logging.getLogger("ispyb_client").warning(_CONNECTION_ERROR_MSG)
+
+            logging.getLogger("HWR").exception("")
             return empty_dict
 
         logging.getLogger("ispyb_client").info(str(sessions))

mxcubecore/HardwareObjects/XMLRPCServer.py

@@ -88,7 +88,7 @@ class XMLRPCServer(HardwareObject):
             self._server.server_close()
             del self._server
         except AttributeError:
-            pass
+            logging.getLogger("HWR").exception("")
 
     def open(self):
         # The value of the member self.port is set in the xml configuration
@@ -691,7 +691,7 @@ class XMLRPCServer(HardwareObject):
                         module_name + "." + sub_module[1], recurse=False, prefix=prefix
                     )
                 except StopIteration:
-                    pass
+                    logging.getLogger("HWR").exception("")
 
     def set_token(self, token):
         SecureXMLRpcRequestHandler.setReferenceToken(token)

mxcubecore/HardwareObjects/abstract/AbstractCollect.py

@@ -106,7 +106,7 @@ class AbstractCollect(HardwareObject, object):
             for undulator in self.config.undulators:
                 undulators.append(undulator)
         except Exception:
-            pass
+            logging.getLogger("HWR").exception("")
 
         beam_div_hor, beam_div_ver = HWR.beamline.beam.get_beam_divergence()