Alert LCs of upcoming sessions

Author: gfrn

Dockerfile

@@ -19,7 +19,7 @@ WORKDIR /project
 
 # make the wheel outside of the venv so 'build' does not dirty requirements.txt
 RUN pip install --upgrade pip build && \
-    export SOURCE_DATE_EPOCH=$(git log -1 --pretty=%ct) && \
+    #export SOURCE_DATE_EPOCH=$(git log -1 --pretty=%ct) && \
     python -m build && \
     touch requirements.txt
 

MANIFEST.in

@@ -2,4 +2,5 @@ include src/scaup/assets/cut-here.png
 include src/scaup/assets/diamond-logo.jpg
 include src/scaup/assets/this-side-up.png
 include src/scaup/assets/DejaVuSans-Bold.ttf
-include src/scaup/assets/DejaVuSans.ttf
+include src/scaup/assets/DejaVuSans.ttf
+include src/scaup/assets/logo-light.png

config.json

@@ -9,6 +9,14 @@
     "backend_url": "https://sample-shipping-staging.diamond.ac.uk",
     "frontend_url": "https://sample-shipping-staging.diamond.ac.uk"
   },
+  "alerts": {
+    "contact_email": "pato@diamond.ac.uk",
+    "smtp_port": 26,
+    "smtp_server": "smtp.ac.uk",
+    "local_contacts": {
+      "Dr John Doe": "john@diamond.ac.uk"
+    }
+  },
   "db": { "pool": 3, "overflow": 6 },
   "ispyb_api": "http://127.0.0.1:8060/api",
   "frontend_url": "http://localtest.diamond.ac.uk:9000"

pyproject.toml

@@ -15,6 +15,7 @@ description = "Scaup's backend"
 
 dependencies = [
     "SQLAlchemy~=2.0.36",
+    "APScheduler~=3.11.0",
     "fastapi~=0.115.6",
     "psycopg[binary,pool]~=3.2.3",
     "pydantic~=2.10.5",
@@ -78,7 +79,8 @@ addopts = """
 # https://iscinumpy.gitlab.io/post/bound-version-constraints/#watch-for-warnings
 filterwarnings = "error"
 markers = [
-    "noregister: do not register HTTP mock responses"
+    "noregister: do not register HTTP mock responses",
+    "no_sample_response: do not register sample creation HTTP mock responses"
 ]
 
 [tool.coverage.run]

src/scaup/assets/logo-light.png

@@ -7,3 +7,4 @@
 THIS_SIDE_UP = os.path.join(ASSETS_PATH, "this-side-up.png")
 DEJAVU_SANS = os.path.join(ASSETS_PATH, "DejaVuSans.ttf")
 DEJAVU_SANS_BOLD = os.path.join(ASSETS_PATH, "DejaVuSans-Bold.ttf")
+COMPANY_LOGO_LIGHT = os.path.join(ASSETS_PATH, "logo-light.png")

src/scaup/assets/paths.py

@@ -1,3 +1,4 @@
+from fastapi.security import HTTPAuthorizationCredentials
 from lims_utils.auth import GenericUser
 from sqlalchemy import select
 from sqlalchemy.dialects.postgresql import insert
@@ -22,12 +23,12 @@ def create_pre_session_info(shipmentId: int, params: PreSessionIn):
     return pre_session
 
 
-def get_pre_session_info(shipment_id: int, user: GenericUser):
+def get_pre_session_info(shipment_id: int, user: GenericUser, token: HTTPAuthorizationCredentials):
     pre_session_info = inner_db.session.scalar(select(PreSession).filter(PreSession.shipmentId == shipment_id))
 
     validated_model = PreSessionOut(
         details=None if pre_session_info is None else pre_session_info.details,
-        isLocked=check_session_locked(shipment_id, user),
+        isLocked=check_session_locked(shipment_id, user, token=token),
     )
 
     return validated_model

src/scaup/crud/pre_sessions.py

@@ -1,9 +1,10 @@
 import re
+from typing import List
 
 from fastapi import HTTPException, status
 from lims_utils.logging import app_logger
 from lims_utils.models import Paged, ProposalReference
-from sqlalchemy import and_, insert, select
+from sqlalchemy import and_, insert, select, update
 
 from ..models.inner_db.tables import Container, Sample, SampleParentChild, Shipment
 from ..models.samples import OptionalSample, SampleIn, SampleOut
@@ -80,8 +81,18 @@ def create_sample(shipmentId: int, params: SampleIn, token: str):
         ],
     ).all()
 
+    full_samples: List[Sample] = []
+
     for sample in samples:
-        Expeye.upsert(token, sample, None)
+        expeye_sample = Expeye.upsert(token, sample, None)
+
+        full_sample = inner_db.session.scalar(
+            update(Sample)
+            .returning(Sample)
+            .filter(Sample.id == sample.id)
+            .values({"externalId": expeye_sample["externalId"]})
+        )
+        full_samples.append(full_sample)
 
     if params.parents:
         inner_db.session.execute(
@@ -90,7 +101,7 @@ def create_sample(shipmentId: int, params: SampleIn, token: str):
         )
 
     inner_db.session.commit()
-    return Paged(items=samples, total=params.copies, page=0, limit=params.copies)
+    return Paged(items=full_samples, total=params.copies, page=0, limit=params.copies)
 
 
 def edit_sample(sampleId: int, params: OptionalSample, token: str):

src/scaup/crud/samples.py

@@ -1,11 +1,10 @@
 import os
+from contextlib import asynccontextmanager
 
 from fastapi import FastAPI, HTTPException, Request, Response
 from fastapi.middleware.cors import CORSMiddleware
 from lims_utils.database import get_session
 from lims_utils.logging import app_logger, log_exception_handler, register_loggers
-from sqlalchemy import create_engine
-from sqlalchemy.orm import sessionmaker
 
 from . import __version__
 from .routes import (
@@ -16,9 +15,20 @@
     shipments,
     top_level_containers,
 )
+from .utils.alerts import session_alerts_scheduler
 from .utils.config import Config
+from .utils.database import inner_session
 
-app = FastAPI(version=__version__, title="Scaup API")
+
+@asynccontextmanager
+async def lifespan(app: FastAPI):
+    register_loggers()
+    session_alerts_scheduler.start()
+    yield
+    session_alerts_scheduler.shutdown()
+
+
+app = FastAPI(version=__version__, title="Scaup API", lifespan=lifespan)
 
 api = FastAPI()
 
@@ -32,24 +42,6 @@
     )
 
 
-inner_engine = create_engine(
-    url=os.environ.get(
-        "SQL_DATABASE_URL",
-        "postgresql+psycopg://sample_handling:sample_root@127.0.0.1:5432/sample_handling",
-    ),
-    pool_pre_ping=True,
-    pool_recycle=3600,
-    pool_size=Config.db.pool,
-    max_overflow=Config.db.overflow,
-)
-
-
-inner_session = sessionmaker(autocommit=False, autoflush=False, bind=inner_engine)
-
-
-register_loggers()
-
-
 @app.middleware("http")
 async def get_session_as_middleware(request, call_next):
     with get_session(inner_session):

src/scaup/main.py

@@ -0,0 +1,15 @@
+# ruff: noqa: E501
+
+EMAIL_HEADER = """
+<html>
+<body>
+    <div class="wrapper" style="padding: 0.5%; text-align:center; border-radius: 5px; border: 1px solid #efefef">
+	<div class="header" style="background: #001d55; text-align: center; padding-top: 15px; padding-bottom: 15px; border-top-left-radius: 5px; border-top-right-radius: 5px;">
+        <img src="cid:logo-light.png" height="45"/>
+	</div>
+	<div>
+"""
+
+EMAIL_FOOTER = """
+    <p style="border-top: 1px solid #001d55; background-color: #1040A1; padding: 10px; color: white;">© 2025, Diamond Light Source</p></div>
+"""