Flake/ Black reformatted

Add default timeout 0

mxcubecore/HardwareObjects/Beamline.py

@@ -486,9 +486,9 @@ def harvester_maintenance(self):
     def plate_manipulator(self):
         """**DEPRECATED**
         Plate Manuipulator Hardware object
-        NBNB TODO REMOVE THIS From qt version usage and 
-        and call HWR.beamline.sample_changer instead as plate_manipulator being 
-        treated as an alternative sample changer .
+        NBNB TODO REMOVE THIS From qt version usage and
+        and call HWR.beamline.sample_changer instead as plate_manipulator being
+        treated as an alternative sample changer.
 
         Returns:
             Optional[AbstractSampleChanger]:

mxcubecore/HardwareObjects/Harvester.py

@@ -134,7 +134,7 @@ def _execute_cmd_exporter(self, cmd, *args, **kwargs):
         return : respond
         """
         ret = None
-        timeout = kwargs.pop("timeout", 900)
+        timeout = kwargs.pop("timeout", 0)
         if args:
             args_str = "%s" % "\t".join(map(str, args))
         if kwargs.pop("command", None):
@@ -164,7 +164,7 @@ def _execute_cmd_exporter(self, cmd, *args, **kwargs):
             if cmd.startswith("set"):
                 ret = exp_attr.set_value(args_str)
 
-        # self._wait_ready(timeout=timeout)
+        self._wait_ready(timeout=timeout)
         return ret
 
     # ---------------------- State --------------------------------

mxcubecore/HardwareObjects/mockup/HarvesterMockup.py

@@ -11,19 +11,20 @@
 
  - getSampleList : Get list of available sample from Harvester
  - Harvest : load sample from Harvester
- 
+
 -----------------------------------------------------------------------
 """
 import gevent
 import logging
 
 from mxcubecore.BaseHardwareObjects import HardwareObject
 
+
 class HarvesterMockup(HardwareObject):
     """Harvester functionality
 
-      The Harvester Class consists of methods executing exporter commands
-      to communicate with the Crystal Direct Harvester Machine
+    The Harvester Class consists of methods executing exporter commands
+    to communicate with the Crystal Direct Harvester Machine
 
     """
 
@@ -38,10 +39,9 @@ def __init__(self, name):
         self.room_temperature_mode = False
 
     def init(self):
-        """ Init """
+        """Init"""
         self.exporter_addr = self.get_property("exporter_address")
 
-
     def set_calibrate_state(self, state):
         """Set Calibration state
 
@@ -65,9 +65,11 @@ def _wait_ready(self, timeout=None):
 
         with gevent.Timeout(timeout, RuntimeError(err_msg)):
             while not self._ready():
-                logging.getLogger("user_level_log").info("Waiting Harvester to be Ready")
+                logging.getLogger("user_level_log").info(
+                    "Waiting Harvester to be Ready"
+                )
                 gevent.sleep(3)
-    
+
     def _wait_sample_transfer_ready(self, timeout=None):
         """Wait Harvester to be ready to transfer a sample
 
@@ -82,7 +84,9 @@ def _wait_sample_transfer_ready(self, timeout=None):
 
         with gevent.Timeout(timeout, RuntimeError(err_msg)):
             while not self._ready_to_transfer():
-                logging.getLogger("user_level_log").info("Waiting Harvester to be ready to transfer")
+                logging.getLogger("user_level_log").info(
+                    "Waiting Harvester to be ready to transfer"
+                )
                 gevent.sleep(3)
 
     def _execute_cmd_exporter(self, cmd, *args, **kwargs):
@@ -91,11 +95,10 @@ def _execute_cmd_exporter(self, cmd, *args, **kwargs):
         Args:
         cmd (string) : command type
         args, kwargs (string): commands arguments, and  command or attribute
-        
+
         return : respond
         """
         ret = None
-        timeout = kwargs.pop("timeout", 900)
         if args:
             args_str = "%s" % "\t".join(map(str, args))
         if kwargs.pop("command", None):
@@ -126,16 +129,16 @@ def _execute_cmd_exporter(self, cmd, *args, **kwargs):
                 ret = exp_attr.set_value(args_str)
 
         return ret
-    
+
     # ---------------------- State --------------------------------
 
     def get_state(self):
         """Get the Harvester State
 
         Return (str):  state "Ready, Running etc.."
-        """ 
+        """
         return "Ready"
-    
+
     def get_status(self):
         """Get the Harvester Status
 
@@ -157,7 +160,7 @@ def _busy(self):
         Return (bool):  True if Harvester is not Ready otherwise False
         """
         return not self._ready()
-    
+
     def _ready_to_transfer(self):
         """Same as Get Harvester Status
 
@@ -166,24 +169,22 @@ def _ready_to_transfer(self):
         # return self._execute_cmd_exporter("getStatus", attribute=True) == "Waiting Sample Transfer"
         return "Waiting Sample Transfer"
 
-
     def get_samples_state(self):
         """Get the Harvester Sample State
 
         Return (List):  list of crystal state "waiting_for_transfer, Running etc.."
-        """ 
+        """
         # return self._execute_cmd_exporter("getSampleStates", command=True)
         return "Ready"
-    
+
     def get_current_crystal(self):
         """Get the Harvester current harvested crystal
 
         Return (str): crystal uuid
-        """ 
+        """
         # return self._execute_cmd_exporter("getCurrentSampleID", attribute=True)
         return None
-
-
+
     def is_crystal_harvested(self, crystal_uuid):
         """Same as Get Harvester Status
 
@@ -198,7 +199,7 @@ def is_crystal_harvested(self, crystal_uuid):
             if crystal_uuid == Current_SampleID:
                 res = True
         return res
-    
+
     def current_crystal_state(self, crystal_uuid):
         """Wait Harvester to be ready to transfer a sample
 
@@ -214,9 +215,8 @@ def current_crystal_state(self, crystal_uuid):
             if crystal_uuid == x_tal:
                 return sample_states[index]
 
-
         return None
-    
+
     def check_crystal_state(self, crystal_uuid):
         """Check wether if a Crystal is in pending_and_current or not
 
@@ -228,19 +228,20 @@ def check_crystal_state(self, crystal_uuid):
         crystal_uuids = self.get_crystal_uuids()
 
         for index, x_tal in enumerate(crystal_uuids):
-            if crystal_uuid == x_tal and sample_states[index] == 'waiting_for_transfer':
-                return 'pending_and_current'
-            elif crystal_uuid != x_tal and sample_states[index] == 'waiting_for_transfer':
-                return 'pending_not_current'
+            if crystal_uuid == x_tal and sample_states[index] == "waiting_for_transfer":
+                return "pending_and_current"
+            elif (
+                crystal_uuid != x_tal and sample_states[index] == "waiting_for_transfer"
+            ):
+                return "pending_not_current"
             else:
                 return None
-
 
     def get_crystal_uuids(self):
         """Get the Harvester Sample List uuid
 
         Return (List):  list of crystal by uuid from the current processing plan"
-        """ 
+        """
         # harvester_crystal_list = self._execute_cmd_exporter("getSampleList",  attribute=True)
         return []
 
@@ -251,7 +252,7 @@ def get_sample_names(self):
         """
         # harvester_sample_names = self._execute_cmd_exporter("getSampleNames", attribute=True)
         return []
-    
+
     def get_crystal_images_urls(self, crystal_uuid):
         """Get the Harvester Sample List Images
 
@@ -262,15 +263,14 @@ def get_crystal_images_urls(self, crystal_uuid):
         # crystal_images_url = self._execute_cmd_exporter("getImageURL", crystal_uuid, command=True)
         return []
 
-
     def get_sample_acronyms(self):
         """Get the Harvester Sample List by Acronyms
 
         Return (List):  list of crystal by Acronyms from the current processing plan"
         """
         # harvester_sample_acronyms = self._execute_cmd_exporter("getSampleAcronyms", attribute=True)
         return []
-    
+
     # ------------------------------------------------------------------------------------
 
     def abort(self):
@@ -279,7 +279,7 @@ def abort(self):
         """
         # return self._execute_cmd_exporter("abort", command=True)
         return None
-    
+
     def harvest_crystal(self, crystal_uuid):
         """Harvester crystal
 
@@ -288,20 +288,16 @@ def harvest_crystal(self, crystal_uuid):
         # return self._execute_cmd_exporter("harvestCrystal", crystal_uuid, command=True)
         return False
 
-
     def transfer_sample(self):
-        """Transfer the current Harvested Crystal
-        """
+        """Transfer the current Harvested Crystal"""
         # return self._execute_cmd_exporter("startTransfer", command=True)
         return False
-    
+
     def trash_sample(self):
-        """ Trash the current Harvested Crystal
-        """
+        """Trash the current Harvested Crystal"""
         # return self._execute_cmd_exporter("trashSample", command=True)
         return False
 
-
     # -----------------------------------------------------------------------------
 
     def load_plate(self, plate_id):
@@ -330,8 +326,7 @@ def get_image_target_x(self, crystal_uuid):
         """
         # return self._execute_cmd_exporter("getImageTargetX", crystal_uuid, command=True)
         return ""
-
-
+
     def get_image_target_y(self, crystal_uuid):
         """Wait Harvester to be ready to transfer a sample
 
@@ -341,7 +336,7 @@ def get_image_target_y(self, crystal_uuid):
         """
         # return self._execute_cmd_exporter("getImageTargetY", crystal_uuid, command=True)
         return ""
-    
+
     def get_room_temperature_mode(self):
         # return self._execute_cmd_exporter("getRoomTemperatureMode", attribute=True)
         return True
@@ -352,7 +347,7 @@ def set_room_temperature_mode(self, value):
         Args: (bool) set room temperature when true
         """
         # self._execute_cmd_exporter("setRoomTemperatureMode", value, command=True)
-        print("setting HA Room temperature to: %s" %value)
+        print("setting HA Room temperature to: %s" % value)
         return self.get_room_temperature_mode()
 
     # -------------------- Calibrate  Drift Shape offset ----------------------------
@@ -386,24 +381,23 @@ def get_last_pin_cut_shape_offset_x(self):
         """
         # pin_last_cut_shape_offset_x = self._execute_cmd_exporter("getLastSampleCutShapeOffsetX", attribute=True)
         pass
-    
+
     def get_last_pin_cut_shape_offset_y(self):
         """Pin shape Offset Y position when
-         Return (float):  last pin cut shape offset y
+        Return (float):  last pin cut shape offset y
         """
         # pin_last_cut_shape_offset_y = self._execute_cmd_exporter("getLastSampleCutShapeOffsetY", attribute=True)
         pass
 
     # =============== Pin / Calibration -----------------------------
 
     def load_calibrated_pin(self):
-        """Start Pin Calibration Procedure
-        """
+        """Start Pin Calibration Procedure"""
         # return self._execute_cmd_exporter("loadCalibratedPin", command=True)
         pass
 
     def store_calibrated_pin(self, x, y, z):
-        """ Store x , y , z offsets position after calibration procedure
+        """Store x , y , z offsets position after calibration procedure
 
         Args: (float) x, y, z offsets
         """
@@ -425,10 +419,8 @@ def get_number_of_available_pin(self):
         """
         # return self._execute_cmd_exporter("getNbRemainingPins", command=True)
         return 1
-
-
-    def get_offsets_for_sample_centering(self):
 
+    def get_offsets_for_sample_centering(self):
         pin_to_beam = tuple(self.get_calibrated_pin_offset())
 
         sample_drift_x = float(self.get_last_sample_drift_offset_x())
@@ -438,10 +430,10 @@ def get_offsets_for_sample_centering(self):
         pin_cut_shape_x = float(self.get_last_pin_cut_shape_offset_x())
         pin_cut_shape_y = float(self.get_last_pin_cut_shape_offset_y())
 
-        phiy_offset = sample_drift_x - pin_cut_shape_x +  float(pin_to_beam[1])
+        phiy_offset = sample_drift_x - pin_cut_shape_x + float(pin_to_beam[1])
 
-        centringFocus = sample_drift_z  + float(pin_to_beam[0])
+        centringFocus = sample_drift_z + float(pin_to_beam[0])
 
-        centringTableVertical = sample_drift_y  - pin_cut_shape_y + float(pin_to_beam[2])
+        centringTableVertical = sample_drift_y - pin_cut_shape_y + float(pin_to_beam[2])
 
-        return (phiy_offset, centringFocus, centringTableVertical)
+        return (phiy_offset, centringFocus, centringTableVertical)