Merge branch 'main' into main

docker-compose-single.yml

@@ -0,0 +1,37 @@
+version: '3.8'
+
+services:
+  p2p:
+    container_name: ptp
+    image: ghcr.io/pharmbio/ptp:latest
+    build:
+      context: ./ptp/
+      dockerfile: Dockerfile
+    #command: sh -c /app/run.sh
+    #command: >
+    #  sh -c "python manage.py migrate &&
+    #         python manage.py collectstatic --noinput &&
+    #         python manage.py runserver 0.0.0.0:8000"
+
+    #gunicorn p2p.wsgi:application --bind 0.0.0.0:8000"
+    volumes:
+      - ./ptp/:/app  # Mount the current directory to the container for live development
+    ports:
+      - "8000:8000"
+    environment:
+      - MODEL_DIR=/app/tmp/models
+      - MAX_MODELS=5
+      - STAGE=True
+      #- DATABASE_URL=postgres://postgres:postgres@postgres:5432/postgres
+      #- REDIS_URL=redis://redis:6379/0
+      #- CELERY_BROKER_URL=redis://redis:6379/0
+      #- DEBUG=True
+      #- EMAIL_HOST=smtp.your-email-provider.com
+      #- EMAIL_PORT="587"
+      #- EMAIL_USE_TLS="True"
+      #- [email protected]
+      #- EMAIL_HOST_PASSWORD=your-email-password
+      - SITE_URL=http://localhost:8000
+
+#volumes:
+#  postgres_data:

ptp/Dockerfile

@@ -7,13 +7,15 @@ RUN mkdir /app
 WORKDIR /app
 
 # Install system dependencies
-RUN apt-get update && apt-get install -y gcc git-lfs python3-dev redis-server supervisor \
+RUN apt-get update && apt-get install -y gcc git-lfs python3-dev redis-server supervisor nginx \
     && apt-get clean
 
 # Install Java (OpenJDK)
 RUN apt-get update && apt-get install -y openjdk-17-jre-headless \
     && apt-get clean
 
+RUN mkdir -p /var/lib/nginx/body
+RUN chown -R www-data:www-data /var/lib/nginx
 # Set JAVA_HOME environment variable (optional)
 ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64
 ENV PATH=$JAVA_HOME/bin:$PATH
@@ -41,6 +43,8 @@ RUN useradd -u 1000 $USER
 RUN chown -R $USER:$USER /etc/supervisor/conf.d/supervisord.conf
 RUN chown -R $USER:$USER /app/
 RUN chown -R $USER:$USER /var/log/supervisor/
+RUN chown -R $USER:$USER /var/lib/nginx/
+RUN chown -R $USER:$USER /var/log/nginx/
 RUN chmod +x /app/start-script.sh
 RUN chmod +x /app/start-django.sh
 

ptp/inference/tasks.py

@@ -113,7 +113,10 @@ def run_inference(job_id):
     """
 
     print("Concatenating results...", flush=True)
-    result_file_path = f"resultfilepath-{job_id}.csv"
+
+    BASE_DIR = os.environ.get("BASE_DIR", "/app/")
+    os.makedirs(f"{BASE_DIR}/interim", exist_ok=True)
+    result_file_path = f"{BASE_DIR}/interim/resultfilepath-{job_id}.csv"
 
     try:
         # Paths for input and output