From 371ac4d8f83fb8fb4762e6e2bd1ce726d7895a18 Mon Sep 17 00:00:00 2001
From: Daniel Hatton <daniel.hatton@diamond.ac.uk>
Date: Wed, 13 Nov 2024 11:54:05 +0000
Subject: [PATCH 1/3] Directly pass configuration file from Murfey security
 configuration to workflows transport object rather than relying on the Zocalo
 configuration

---
 src/murfey/server/__init__.py | 5 +++--
 src/murfey/util/config.py     | 1 +
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/murfey/server/__init__.py b/src/murfey/server/__init__.py
index 0165bf992..2dae882e9 100644
--- a/src/murfey/server/__init__.py
+++ b/src/murfey/server/__init__.py
@@ -283,7 +283,9 @@ def run():
     LogFilter.install()
 
     zc.add_command_line_options(parser)
-    workflows.transport.add_command_line_options(parser, transport_argument=True)
+
+    security_config = get_security_config()
+    workflows.transport.load_configuration_file(security_config.rabbitmq_credentials)
 
     args = parser.parse_args()
 
@@ -296,7 +298,6 @@ def run():
     # Set up logging now that the desired verbosity is known
     _set_up_logging(quiet=args.quiet, verbosity=args.verbose)
 
-    security_config = get_security_config()
     if not args.temporary and _transport_object:
         _transport_object.feedback_queue = security_config.feedback_queue
     rabbit_thread = Thread(
diff --git a/src/murfey/util/config.py b/src/murfey/util/config.py
index fc058cca8..9e4d2a867 100644
--- a/src/murfey/util/config.py
+++ b/src/murfey/util/config.py
@@ -82,6 +82,7 @@ def from_file(config_file_path: Path, instrument: str = "") -> Dict[str, Machine
 
 
 class Security(BaseModel):
+    rabbitmq_credentials: str
     murfey_db_credentials: str
     crypto_key: str
     auth_key: str = ""

From b412491574a5765cdc6fba7d5f41a37f078b1bab Mon Sep 17 00:00:00 2001
From: Daniel Hatton <daniel.hatton@diamond.ac.uk>
Date: Wed, 13 Nov 2024 12:11:01 +0000
Subject: [PATCH 2/3] Setup graylog logging outside of Zocalo configuration

This should remove the need for the ZOCALO_CONFIG environment variable to be set when starting a Murfey server
---
 src/murfey/server/__init__.py | 16 ++++++++--------
 src/murfey/util/config.py     | 12 +++++++++++-
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/src/murfey/server/__init__.py b/src/murfey/server/__init__.py
index 2dae882e9..766edcc5a 100644
--- a/src/murfey/server/__init__.py
+++ b/src/murfey/server/__init__.py
@@ -13,11 +13,11 @@
 from threading import Thread
 from typing import Any, Dict, List, NamedTuple, Tuple
 
+import graypy
 import mrcfile
 import numpy as np
 import uvicorn
 import workflows
-import zocalo.configuration
 from backports.entry_points_selectable import entry_points
 from fastapi import Request
 from fastapi.templating import Jinja2Templates
@@ -273,18 +273,18 @@ def run():
         default=0,
     )
 
+    security_config = get_security_config()
     # setup logging
-    zc = zocalo.configuration.from_file()
-    zc.activate()
+    if security_config.graylog_host:
+        handler = graypy.GELFUDPHandler(
+            security_config.graylog_host, security_config.graylog_port, level_names=True
+        )
+        root_logger = logging.getLogger()
+        root_logger.addHandler(handler)
 
     # Install a log filter to all existing handlers.
-    # At this stage this will exclude console loggers, but will cover
-    # any Graylog logging set up by the environment activation
     LogFilter.install()
 
-    zc.add_command_line_options(parser)
-
-    security_config = get_security_config()
     workflows.transport.load_configuration_file(security_config.rabbitmq_credentials)
 
     args = parser.parse_args()
diff --git a/src/murfey/util/config.py b/src/murfey/util/config.py
index 9e4d2a867..5cab20733 100644
--- a/src/murfey/util/config.py
+++ b/src/murfey/util/config.py
@@ -8,7 +8,7 @@
 
 import yaml
 from backports.entry_points_selectable import entry_points
-from pydantic import BaseModel, BaseSettings, Extra
+from pydantic import BaseModel, BaseSettings, Extra, validator
 
 
 class MachineConfig(BaseModel, extra=Extra.allow):  # type: ignore
@@ -94,6 +94,16 @@ class Security(BaseModel):
     auth_type: Literal["password", "cookie"] = "password"
     cookie_key: str = ""
     feedback_queue: str = "murfey_feedback"
+    graylog_host: str = ""
+    graylog_port: Optional[int] = None
+
+    @validator("graylog_port")
+    def check_port_present_if_host_is(
+        cls, v: Optional[int], values: dict, **kwargs
+    ) -> Optional[int]:
+        if values["graylog_host"] and v is None:
+            raise ValueError("The Graylog port must be set if the Graylog host is")
+        return v
 
 
 def security_from_file(config_file_path: Path) -> Security:

From 220988f9703c1716611361bad2577c4312203828 Mon Sep 17 00:00:00 2001
From: Daniel Hatton <daniel.hatton@diamond.ac.uk>
Date: Wed, 13 Nov 2024 13:23:34 +0000
Subject: [PATCH 3/3] Add rabbitmq_credentials default for tests

---
 src/murfey/util/config.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/murfey/util/config.py b/src/murfey/util/config.py
index 5cab20733..56f51978a 100644
--- a/src/murfey/util/config.py
+++ b/src/murfey/util/config.py
@@ -144,6 +144,7 @@ def get_security_config() -> Security:
         if machine_config.security_configuration_path:
             return security_from_file(machine_config.security_configuration_path)
     return Security(
+        rabbitmq_credentials="",
         session_validation="",
         murfey_db_credentials="",
         crypto_key="",