feat: add python-dotenv (#494)

Add `python-dotenv` to backend entry points.

This is a simple quality-of-life improvement driven by my unending
frustration with the mountain of environment variables upon which metakb
sits. Store a `.env` file in `server/` and it'll load env vars from
there.

* I have aspirations for a more featureful configuration experience. I'd
made an initial attempt
[here](GenomicMedLab/software-templates#78) but
I'm not totally happy with it. I have an issue
[here](GenomicMedLab/software-templates#106)
to take up someday where I try and do something better, but I think that
would entail implementation in all of the library dependencies first.
For now I think this PR is just fine though.

Author: jsstevenson

server/.env.example

@@ -0,0 +1,10 @@
+METAKB_EB_PROD=
+METAKB_DB_URL=bolt://localhost:7687
+METAKB_DB_USERNAME=neo4j
+METAKB_DB_PASSWORD=neo4j
+METAKB_DB_SECRET=
+DISEASE_NORM_DB_URL=http://localhost:8000
+THERAPY_NORM_DB_URL=http://localhost:8000
+GENE_NORM_DB_URL=http://localhost:8000
+UTA_DB_URL=postgresql://uta_admin:password@localhost:5432/uta/uta_20210129b
+SEQREPO_ROOT_DIR=/usr/local/share/seqrepo/latest

server/pyproject.toml

@@ -40,6 +40,7 @@ dependencies = [
     "boto3",
     "botocore",
     "asyncclick",
+    "python-dotenv",
 ]
 dynamic = ["version"]
 

server/src/metakb/cli.py

@@ -16,6 +16,7 @@
 import boto3
 from boto3.exceptions import ResourceLoadException
 from botocore.config import Config
+from dotenv import load_dotenv
 from neo4j import Driver
 
 from metakb import APP_ROOT, DATE_FMT
@@ -38,6 +39,8 @@
 
 _logger = logging.getLogger(__name__)
 
+load_dotenv()
+
 
 def _echo_info(msg: str) -> None:
     """Log (as INFO) and echo given message.

server/src/metakb/database.py

@@ -49,7 +49,7 @@ def _get_credentials(
     :return: tuple containing host, and a second tuple containing username/password
     """
     if not (uri and credentials[0] and credentials[1]):
-        if "METAKB_EB_PROD" in environ:
+        if environ.get("METAKB_EB_PROD"):
             secret = ast.literal_eval(_get_secret())
             uri = f"bolt://{secret['host']}:{secret['port']}"
             credentials = (secret["username"], secret["password"])

server/src/metakb/log_handle.py

@@ -36,7 +36,7 @@ def configure_logs(log_level: int = logging.DEBUG, quiet_upstream: bool = True)
     if quiet_upstream:
         _quiet_upstream_libs()
     log_filename = (
-        "/tmp/metakb.log" if "METAKB_EB_PROD" in os.environ else "metakb.log"  # noqa: S108
+        "/tmp/metakb.log" if os.environ.get("METAKB_EB_PROD") else "metakb.log"  # noqa: S108
     )
     logging.basicConfig(
         filename=log_filename,

server/src/metakb/main.py

@@ -4,6 +4,7 @@
 from contextlib import asynccontextmanager
 from typing import Annotated
 
+from dotenv import load_dotenv
 from fastapi import FastAPI, Query
 from fastapi.openapi.utils import get_openapi
 
@@ -18,6 +19,8 @@
     ServiceMeta,
 )
 
+load_dotenv()
+
 query = QueryHandler()