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Remove the need for an ispyb environment variable #435

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Merged
tieneupin merged 6 commits into from
Feb 11, 2025
Merged

Remove the need for an ispyb environment variable #435

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1e4ca8c
Remove the need for an ispyb environment variable
stephen-riggs Jan 9, 2025
a5f1c6f
Use empty string to represent no file provided
tieneupin Jan 9, 2025
3a8c440
Turned file path fields in Security BaseModel to Optional[Path]
tieneupin Jan 10, 2025
e8b615a
Murfey database is essential, so 'murfey_db_credentials' isn't Optional
tieneupin Jan 10, 2025
21e96ce
RabbitMQ credentials are mandatory as well for Murfey to operate corr…
tieneupin Jan 10, 2025
4da0bc9
Merged recent changes from 'main' branch and resolved conflicts
tieneupin Jan 10, 2025
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9 changes: 7 additions & 2 deletions src/murfey/server/ispyb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@

import datetime
import logging
import os
from typing import Callable, List, Literal, Optional

import ispyb
Expand Down Expand Up @@ -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(
Expand All @@ -60,7 +61,11 @@
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 = (

Check warning on line 64 in src/murfey/server/ispyb.py

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src/murfey/server/ispyb.py#L64 

Added line #L64 was not covered by tests
ispyb.open(credentials=security_config.ispyb_credentials)
if security_config.ispyb_credentials
else None
)
self._connection_callback: Callable | None = None

def reconnect(self):
Expand Down
5 changes: 3 additions & 2 deletions src/murfey/util/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,8 +83,7 @@ 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 = ""
Expand All @@ -94,9 +93,11 @@ 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(
Expand Down
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