CU-8699k4eem sync demo webapp

.github/workflows/medcat-demo-app_build.yml

@@ -0,0 +1,35 @@
+name: medcat-demo - Test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+defaults:
+  run:
+    working-directory: ./medcat-demo-app
+
+jobs:
+  integration-test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Docker Compose
+      run: sudo apt-get update && sudo apt-get install -y docker-compose
+
+    - name: Build and start containers
+      run: docker-compose -f docker-compose-test.yml up -d --build
+
+    - name: Run integration test
+      run: ./tests/test_integration.sh
+
+    - name: Check container logs for errors
+      run: |
+        docker-compose logs medcatweb
+        docker-compose logs medcatweb | grep -i 'error' && exit 1 || true
+
+    - name: Tear down
+      run: docker-compose -f docker-compose-test.yml down

medcat-demo-app/docker-compose-test.yml

@@ -0,0 +1,16 @@
+version: '3.4'
+
+services:
+  medcatweb:
+    build:
+      context: ./webapp
+    command: >
+      bash -c "/etc/init.d/cron start &&
+               python /webapp/manage.py runserver 0.0.0.0:8000"
+    volumes:
+      - ../medcat-v2/tests/resources:/webapp/models
+    ports:
+      - "8000:8000"
+    env_file:
+      - ./envs/env_medmen_test
+    tty: true

medcat-demo-app/envs/env_medmen_test

@@ -0,0 +1 @@
+MODEL_PACK_PATH=/webapp/models/mct2_model_pack.zip

medcat-demo-app/tests/test_integration.py

@@ -0,0 +1,33 @@
+# tests/test_integration.py
+
+import requests
+
+from bs4 import BeautifulSoup
+
+URL = "http://localhost:8000/"
+session = requests.Session()
+
+# GET the page to get the CSRF token
+resp = session.get(URL)
+soup = BeautifulSoup(resp.text, "html.parser")
+csrf = soup.find("input", {"name": "csrfmiddlewaretoken"}).get("value")
+
+disease = "kidney failure"
+
+text = f"Patient had been diagnosed with acute {disease} the week before"
+
+# POST with the token and same session (cookies preserved)
+resp = session.post(URL, data={
+    "text": text,
+    "csrfmiddlewaretoken": csrf})
+
+print(f"RESPOONSE:\n{resp.text}")
+
+soup = BeautifulSoup(resp.text, "html.parser")
+
+annotations = soup.select("div.entities mark.entity")
+assert annotations, "No annotations found in the response"
+assert any(disease in mark.text.lower() for mark in annotations), (
+    f"Disease '{disease}' not found in annotations")
+
+assert disease in resp.text

medcat-demo-app/tests/test_integration.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+set -euo pipefail
+
+echo "Waiting for service to start..."
+
+# install bs4 for tests
+python -m pip install beautifulsoup4
+
+# Wait until curl doesn't fail
+for i in {1..60}; do
+  if curl -s --fail http://localhost:8000 > /dev/null; then
+    echo "Service is up"
+    break
+  else
+    echo "Waiting ($i)..."
+    sleep 2
+  fi
+done
+
+python tests/test_integration.py

medcat-demo-app/webapp/Dockerfile

@@ -1,37 +1,69 @@
-FROM python:3.7
+# Stage 1: Build stage (dependencies and compilation)
+FROM python:3.12-slim as build
 
 # Create the required folders
 RUN mkdir -p /webapp/models
 
-# Copy everything
+# Copy the application code
 COPY . /webapp
 
+# Install dependencies for building (git, etc.)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    git \
+    build-essential \
+    apt-utils \
+    cron \
+    sqlite3 \
+    libsqlite3-dev
+
+# Install Python dependencies
+ARG USE_CPU_TORCH=false
+# NOTE: Allow building without GPU so as to lower image size (disabled by default)
+RUN pip install -U pip && if [ "$USE_CPU_TORCH" = "true" ]; then \
+                              pip install -r /webapp/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu/; \
+                          else \
+                              pip install -r /webapp/requirements.txt; \
+                          fi
+
+# Get the spacy model (for later copy)
+RUN python -m spacy download en_core_web_md
+
+# Stage 2: Final (production) image
+FROM python:3.12-slim as final
+
+# Install runtime dependencies (you don’t need git in production)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    cron \
+    sqlite3 \
+    libsqlite3-dev && apt-get autoremove
+
+# Create the required folders (if not created already)
+RUN mkdir -p /webapp/models && mkdir -p /medcat_data
+
+# Copy only necessary files from build stage
+COPY --from=build /webapp /webapp
+# COPY --from=build /root/.cache /root/.cache  # Copy pip cache if needed
+
+# Copy Python site-packages (installed by pip) from build stage
+COPY --from=build /usr/local/lib/python3.12/site-packages /usr/local/lib/python3.12/site-packages
+
+# Set environment variables
 ENV VOCAB_URL=https://medcat.rosalind.kcl.ac.uk/media/vocab.dat
 ENV CDB_URL=https://medcat.rosalind.kcl.ac.uk/media/cdb-medmen-v1.dat
 
 ENV CDB_PATH=/webapp/models/cdb.dat
 ENV VOCAB_PATH=/webapp/models/vocab.dat
 
-# Create the data directory
-RUN mkdir -p /medcat_data
-
 # Set the pythonpath
 WORKDIR /webapp
 
-RUN pip install -r requirements.txt
-
-# Get the spacy model
-RUN python -m spacy download en_core_web_md
+# Create the db backup cron job (copied from your setup)
+COPY etc/cron.d/db-backup-cron /etc/cron.d/db-backup-cron
+RUN chmod 0644 /etc/cron.d/db-backup-cron && crontab /etc/cron.d/db-backup-cron
 
-# Build the db
+# Run migrations and collect static (could be in entrypoint script)
 RUN python manage.py makemigrations && \
     python manage.py makemigrations demo && \
     python manage.py migrate && \
     python manage.py migrate demo && \
     python manage.py collectstatic --noinput
-
-# Create the db backup cron job
-RUN apt-get update && apt-get install -y --no-install-recommends apt-utils cron sqlite3 libsqlite3-dev
-COPY etc/cron.d/db-backup-cron /etc/cron.d/db-backup-cron
-RUN chmod 0644 /etc/cron.d/db-backup-cron
-RUN crontab /etc/cron.d/db-backup-cron

medcat-demo-app/webapp/demo/forms.py

@@ -46,3 +46,8 @@ class Meta:
             "funder": forms.TextInput(attrs={"size": 40}),
             "use_case": forms.Textarea(attrs={"rows": 5, "cols": 40}),
         }
+
+
+class UMLSApiKeyForm(forms.Form):
+    apikey = forms.CharField(label='UMLS API Key',
+                             widget=forms.TextInput(attrs={'size': 50}))

medcat-demo-app/webapp/demo/templates/base.html

@@ -15,7 +15,7 @@
 	</head>
 	<body>
 		<nav class="navbar navbar-expand-lg navbar-light bg-light">
-			<a class="navbar-brand" href="/">MedCAT</a>
+			<a class="navbar-brand" href="/">MedCAT v2 (running v{{ medcat_version|default:"N/A" }})</a>
 
 			<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
 				<span class="navbar-toggler-icon"></span>

medcat-demo-app/webapp/demo/templates/umls_api_key_entry.html

@@ -0,0 +1,49 @@
+{% extends 'base.html' %}
+{% load static %}
+
+{% block style %}
+<link rel="stylesheet" href="{% static 'css/home.css' %}">
+<link rel="stylesheet" href="{% static 'css/annotations.css' %}">
+<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.8.2/css/all.css" integrity="sha384-oS3vJWv+0UjzBfQzYUhtDYW+Pj2yciDJxpsK1OYPAYjqT085Qq/1cq5FLXAZQ7Ay" crossorigin="anonymous">
+<link rel="icon" href="{% static 'image/favicon.ico' %}">
+{% endblock %}
+
+{% block body %}
+<div class="container-fluid">
+    <h5>Please enter your UMLS API key to verify your license:</h5>
+
+    {% if message %}
+        <div class="alert alert-info">
+            {{ message }}
+        </div>
+    {% endif %}
+
+    {% if form.errors %}
+        <div class="alert alert-danger">
+            <ul>
+                {% for field in form %}
+                    {% for error in field.errors %}
+                        <li><strong>{{ field.label }}:</strong> {{ error }}</li>
+                    {% endfor %}
+                {% endfor %}
+                {% for error in form.non_field_errors %}
+                    <li>{{ error }}</li>
+                {% endfor %}
+            </ul>
+        </div>
+    {% endif %}
+
+    <form method="post">
+        {% csrf_token %}
+        <div class="form-group">
+            {{ form.apikey.label_tag }}
+            {{ form.apikey }}
+        </div>
+        <button type="submit" class="btn btn-primary">Verify API Key</button>
+    </form>
+
+    <p class="mt-3 text-muted">
+        You can find your API key by logging into your UMLS account and visiting your <a href="https://uts.nlm.nih.gov/uts/profile" target="_blank">UMLS Profile</a>.
+    </p>
+</div>
+{% endblock %}

medcat-demo-app/webapp/demo/urls.py

@@ -5,5 +5,6 @@
 urlpatterns = [
     path('', show_annotations, name='train_annotations'),
     path('auth-callback', validate_umls_user, name='validate-umls-user'),
+    path('auth-callback-api', validate_umls_api_key, name='validate-umls-api-key'),
     path('download-model', download_model, name="download-model")
 ]