[LIMS-1842] Alert LCs 24 hours before session (#13)

* Use paginate function from lims-utils

* Alert LCs of upcoming sessions

* Add email template

* Fix link URL

* Fix dependencies

* Make contact email optional

* Typing fixes

* Update email contents

* Fix test error with pytest 8.4.2

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

@@ -14,11 +14,12 @@ classifiers = [
 description = "Scaup's backend"
 
 dependencies = [
+    "APScheduler~=3.11.0",
     "SQLAlchemy~=2.0.36",
     "fastapi~=0.116.1",
     "psycopg[binary,pool]~=3.2.9",
     "pydantic~=2.11.7",
-    "uvicorn~=0.35.0", 
+    "uvicorn~=0.35.0",
     "types-requests",
     "lims_utils~=0.4.2",
     "requests",
@@ -38,7 +39,7 @@ dev = [
     "mypy",
     "pipdeptree",
     "pre-commit",
-    "pytest~=8.4.1",
+    "pytest~=8.4.2",
     "pytest-cov",
     "ruff",
     "freezegun~=1.5.5",
@@ -77,7 +78,8 @@ 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

@@ -429,7 +429,7 @@ def generate_report(shipment_id: int, token: str):
         .join(Sample.container)
         .filter(Sample.shipmentId == shipment_id)
         .options(contains_eager(Sample.container))
-        .order_by(Sample.subLocation.desc(), Sample.container, Sample.location)
+        .order_by(Sample.subLocation.desc(), Sample.containerId, Sample.location)
     )
 
     # TODO: rethink this once we're using user-provided templates

src/scaup/crud/pdf.py

@@ -28,7 +28,7 @@ def get_pre_session_info(shipment_id: int, user: GenericUser, token: HTTPAuthori
 
     validated_model = PreSessionOut(
         details=None if pre_session_info is None else pre_session_info.details,
-        isLocked=check_session_locked(shipment_id, user, token),
+        isLocked=check_session_locked(shipment_id, user, token=token),
     )
 
     return validated_model

src/scaup/crud/pre_sessions.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 +15,23 @@
     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()
+    if Config.alerts.contact_email:
+        session_alerts_scheduler.start()
+        yield
+        session_alerts_scheduler.shutdown()
+    else:
+        yield
+
+
+app = FastAPI(version=__version__, title="Scaup API", lifespan=lifespan)
 
 api = FastAPI()
 
@@ -32,24 +45,6 @@
     )
 
 
-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 +1,40 @@
+# ruff: noqa: E501
+
+from string import Template
+
+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>
+"""
+
+SAMPLE_COLLECTION_LINK = Template("""
+<li><a href="$frontend_url/proposals/$proposal/sessions/$session/shipments/$shipment">$shipment_name</a></li>
+""")
+
+ALERT_BODY = Template("""
+<p>Dear $local_contact,</p>
+
+<p>The user(s) have submitted important information regarding the grids and pre-session data collection parameters for session $proposal-$session in SCAUP.</p>
+
+<p>To view this information, either head to the <a href="$frontend_url/proposals/$proposal/sessions/$session">session samples dashboard</a>, select a sample collection and click “Print contents as table” under the Actions section, or view one of the session sample collections directly:</p>
+
+<ul style="text-align: left;list-style: square;">
+$sample_collection_links
+</ul>
+
+<p>Before starting an EPU session, please ensure that grids are added to the Cassette positions in the Sample Collection Summary page. This step allows results from the auto-processing pipeline in PATo to be correctly linked to sample conditions in SCAUP.</p>
+
+<p>Note: If you are not the designated Local Contact for this session, kindly forward this email to the appropriate person.</p>
+
+<p>Many thanks,</p>
+<p>SCAUP team</p>
+""")