Remove the need for an ispyb environment variable (#435)

* Turned file path fields in Security BaseModel to Optional[Path]
* 'murfey_db_credentials' and 'rabbitmq_credentials' are mandatory Path fields

---------

Co-authored-by: Eu Pin Tien <[email protected]>

Author: stephen-riggs

src/murfey/server/ispyb.py

@@ -2,7 +2,6 @@
 
 import datetime
 import logging
-import os
 from typing import Callable, List, Literal, Optional
 
 import ispyb
@@ -31,9 +30,11 @@
     url,
 )
 
+from murfey.util.config import get_security_config
 from murfey.util.models import FoilHoleParameters, GridSquareParameters, Sample, Visit
 
 log = logging.getLogger("murfey.server.ispyb")
+security_config = get_security_config()
 
 try:
     Session = sqlalchemy.orm.sessionmaker(
@@ -60,7 +61,11 @@ def __init__(self, transport_type: Literal["PikaTransport"]):
         self.transport = workflows.transport.lookup(transport_type)()
         self.transport.connect()
         self.feedback_queue = ""
-        self.ispyb = ispyb.open() if os.getenv("ISPYB_CREDENTIALS") else None
+        self.ispyb = (
+            ispyb.open(credentials=security_config.ispyb_credentials)
+            if security_config.ispyb_credentials
+            else None
+        )
         self._connection_callback: Callable | None = None
 
     def reconnect(self):

src/murfey/util/config.py

@@ -82,8 +82,7 @@ def from_file(config_file_path: Path, instrument: str = "") -> Dict[str, Machine
 
 
 class Security(BaseModel):
-    rabbitmq_credentials: str
-    murfey_db_credentials: str
+    murfey_db_credentials: Path
     crypto_key: str
     auth_key: str = ""
     auth_algorithm: str = ""
@@ -93,9 +92,11 @@ class Security(BaseModel):
     session_token_timeout: Optional[int] = None
     auth_type: Literal["password", "cookie"] = "password"
     cookie_key: str = ""
+    rabbitmq_credentials: Path
     feedback_queue: str = "murfey_feedback"
     graylog_host: str = ""
     graylog_port: Optional[int] = None
+    ispyb_credentials: Optional[Path] = None
 
     @validator("graylog_port")
     def check_port_present_if_host_is(