Update dependencies, update to Pydantic V2

.gitignore

@@ -37,3 +37,5 @@ coverage.xml
 .DS_Store
 .vscode/
 .python-version
+
+test/HardwareObjectsMockup.xml/

mxcubecore/BaseHardwareObjects.py

@@ -26,7 +26,6 @@
 from collections import OrderedDict
 import logging
 from gevent import event, Timeout
-import pydantic
 from typing import (
     TYPE_CHECKING,
     Callable,
@@ -43,12 +42,12 @@
 )
 from typing_extensions import Self, Literal
 
+from pydantic.v1 import BaseModel, Field, create_model
 from mxcubecore.dispatcher import dispatcher
 from mxcubecore.CommandContainer import CommandContainer
 
 if TYPE_CHECKING:
     from logging import Logger
-    from pydantic import BaseModel
     from .CommandContainer import CommandObject
 
 __copyright__ = """ Copyright © 2010-2020 by the MXCuBE collaboration """
@@ -656,11 +655,11 @@ def _get_type_annotations(self) -> None:
                 # Skipp return typehint
                 if _n != "return":
                     self._exports[attr_name].append(_n)
-                    fdict[_n] = (_t, pydantic.Field(alias=_n))
+                    fdict[_n] = (_t, Field(alias=_n))
 
             _models[attr_name] = (
-                pydantic.create_model(attr_name, **fdict),
-                pydantic.Field(alias=attr_name),
+                create_model(attr_name, **fdict),
+                Field(alias=attr_name),
             )
 
             self._pydantic_models[attr_name] = _models[attr_name][0]
@@ -670,7 +669,7 @@ def _get_type_annotations(self) -> None:
                 attr_name
             ].schema_json()
 
-        model = pydantic.create_model(self.__class__.__name__, **_models)
+        model = create_model(self.__class__.__name__, **_models)
         self._pydantic_models["all"] = model
 
     def execute_exported_command(self, cmd_name: str, args: Dict[str, Any]) -> Any:

mxcubecore/HardwareObjects/ANSTO/prefect_flows/schemas/grid_scan.py

@@ -1,4 +1,4 @@
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 from typing import Optional, Union
 
 

mxcubecore/HardwareObjects/ANSTO/prefect_flows/schemas/screening.py

@@ -1,4 +1,4 @@
-from pydantic import Field, BaseModel
+from pydantic.v1 import Field, BaseModel
 from typing import Union, Optional
 
 

mxcubecore/HardwareObjects/DataPublisher.py

@@ -21,6 +21,7 @@
 import gevent
 import logging
 
+from os import environ
 from enum import Enum, unique
 
 from mxcubecore.BaseHardwareObjects import HardwareObject
@@ -92,12 +93,35 @@ def init(self):
         """
         super(DataPublisher, self).init()
 
-        rhost = self.get_property("host", "localhost")
-        rport = self.get_property("port", 6379)
-        rdb = self.get_property("db", 11)
+        rhost = self.get_property(
+            "host",
+            environ.get("MXCUBE_REDIS_HOST", "localhost"),
+        )
+        rport = self.get_property(
+            "port",
+            int(environ.get("MXCUBE_REDIS_PORT", "6379")),
+        )
+        username = self.get_property(
+            "username",
+            environ.get("MXCUBE_REDIS_USERNAME"),
+        )
+        password = self.get_property(
+            "password",
+            environ.get("MXCUBE_REDIS_PASSWORD"),
+        )
+        rdb = self.get_property(
+            "db",
+            int(environ.get("MXCUBE_REDIS_DB", "11")),
+        )
 
         self._r = redis.Redis(
-            host=rhost, port=rport, db=rdb, charset="utf-8", decode_responses=True
+            host=rhost,
+            port=rport,
+            username=username,
+            password=password,
+            db=rdb,
+            charset="utf-8",
+            decode_responses=True,
         )
 
         if not self._subsribe_task:

mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_base_queue_entry.py

@@ -6,7 +6,7 @@
 import gevent
 
 from typing_extensions import Literal
-from pydantic import BaseModel, Field
+from pydantic.v1 import BaseModel, Field
 from devtools import debug
 
 from mxcubecore import HardwareRepository as HWR

mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_big_foil_collection.py

@@ -2,7 +2,7 @@
 
 from typing_extensions import Literal
 
-from pydantic import BaseModel, Field
+from pydantic.v1 import BaseModel, Field
 from devtools import debug
 
 from mxcubecore.model.common import (

mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_chip_collection.py

@@ -3,7 +3,7 @@
 import contextlib
 import enum
 import subprocess
-from pydantic import BaseModel, Field
+from pydantic.v1 import BaseModel, Field
 from devtools import debug
 
 from mxcubecore import HardwareRepository as HWR

mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_foil_collection.py

@@ -4,7 +4,7 @@
 
 from typing_extensions import Literal
 
-from pydantic import Field
+from pydantic.v1 import Field
 from devtools import debug
 
 from mxcubecore.model.common import (

mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_injector_collection.py

@@ -2,7 +2,7 @@
 import time
 import enum
 
-from pydantic import BaseModel, Field
+from pydantic.v1 import BaseModel, Field
 from devtools import debug
 
 from mxcubecore import HardwareRepository as HWR

mxcubecore/HardwareObjects/ESRF/queue_entry/test_collection.py

@@ -3,7 +3,7 @@
 
 from typing_extensions import Literal
 
-from pydantic import BaseModel, Field
+from pydantic.v1 import BaseModel, Field
 from devtools import debug
 
 from mxcubecore import HardwareRepository as HWR

mxcubecore/HardwareObjects/GenericDiffractometer.py

@@ -33,7 +33,7 @@
 import enum
 
 from typing import List, Tuple, Union, Dict
-from pydantic import BaseModel, Field, ValidationError
+from pydantic.v1 import BaseModel, Field, ValidationError
 
 from mxcubecore.HardwareObjects import sample_centring
 from mxcubecore.model import queue_model_objects

mxcubecore/HardwareObjects/MiniDiff.py

@@ -9,7 +9,7 @@
 import json
 
 from typing import Union
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 from mxcubecore.BaseHardwareObjects import Equipment
 from mxcubecore.TaskUtils import task

mxcubecore/HardwareObjects/TangoLimaMpegVideo.py

@@ -73,8 +73,6 @@ def start_video_stream_process(self, port):
             self._video_stream_process = subprocess.Popen(
                 [
                     "video-streamer",
-                    "-tu",
-                    self.get_property("tangoname").strip(),
                     "-hs",
                     "localhost",
                     "-p",

mxcubecore/HardwareObjects/mockup/BeamlineActionsMockup.py

@@ -1,6 +1,6 @@
 from typing_extensions import Literal
 
-from pydantic import BaseModel, Field
+from pydantic.v1 import BaseModel, Field
 from mxcubecore.TaskUtils import task
 from mxcubecore.CommandContainer import CommandObject
 from mxcubecore.HardwareObjects.BeamlineActions import (

mxcubecore/HardwareObjects/mockup/DiffractometerMockup.py

@@ -22,7 +22,7 @@
 import random
 import warnings
 
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 from mxcubecore.HardwareObjects.GenericDiffractometer import (
     GenericDiffractometer,

mxcubecore/HardwareObjects/mockup/MDCameraMockup.py

@@ -115,8 +115,6 @@ def start_video_stream_process(self, size):
             self._video_stream_process = subprocess.Popen(
                 [
                     "video-streamer",
-                    "-tu",
-                    "test",
                     "-hs",
                     "localhost",
                     "-p",

mxcubecore/configuration/ansto/mxcube-web/server.yaml

@@ -12,7 +12,9 @@ server:
     - "http://localhost:3000"
     - "ws://localhost:8000"
     - "https://mxcube.mx3.beamline.synchrotron.org.au"
+    - "wss://mxcube.mx3.beamline.synchrotron.org.au"
     - "http://mxcube.mx3.beamline.synchrotron.org.au"
+    - "ws://mxcube.mx3.beamline.synchrotron.org.au"
 
 mxcube:
   USE_EXTERNAL_STREAMER: False

mxcubecore/configuration/checkxml.py

@@ -2,7 +2,7 @@
 import xmltodict
 import argparse
 import pprint
-import pydantic
+from pydantic.v1 import ValidationError
 
 from colorama import Fore, Back, Style
 from mxcubecore.model import configmodel
@@ -40,7 +40,7 @@ def check_xml(rpath="."):
                     if config_model:
                         try:
                             config_model(**_data_to_validate)
-                        except pydantic.ValidationError as ex:
+                        except ValidationError as ex:
                             print(f"{Fore.RED}WARNING in: {fpath}")
                             print(f"{str(ex)}")
                             print(Style.RESET_ALL)

mxcubecore/model/common.py

@@ -1,6 +1,6 @@
 from datetime import datetime
 from typing import Optional, Union
-from pydantic import BaseModel, Field
+from pydantic.v1 import BaseModel, Field
 
 
 class CommonCollectionParamters(BaseModel):

mxcubecore/model/configmodel.py

@@ -1,4 +1,4 @@
-from pydantic import BaseModel, Field
+from pydantic.v1 import BaseModel, Field
 
 
 class ExporterNStateConfigModel(BaseModel):

mxcubecore/model/procedure_model.py

@@ -1,14 +1,13 @@
 # -*- coding: utf-8 -*-
 
-import pydantic
-from pydantic import Field
+from pydantic.v1 import BaseModel, Field
 
 
 class ValidationError(Exception):
     pass
 
 
-class BaseModel(pydantic.BaseModel):
+class BaseModel(BaseModel):
     def __init__(self, *args, **kwargs):
         try:
             super(BaseModel, self).__init__(*args, **kwargs)