adding health testing

Dockerfile

@@ -1,11 +1,17 @@
-FROM continuumio/miniconda3:4.10.3
+FROM ubuntu:22.04
 MAINTAINER Mingxun Wang "[email protected]"
 
 WORKDIR /app
 RUN apt-get update -y && \
         apt-get install -y libxrender-dev && \
-        apt-get install -y git-core libarchive-dev
-RUN conda install -c conda-forge mamba
+        apt-get install -y git-core libarchive-dev build-essential wget vim curl
+
+# Install Mamba
+ENV CONDA_DIR /opt/conda
+RUN wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O ~/miniforge.sh && /bin/bash ~/miniforge.sh -b -p /opt/conda
+ENV PATH=$CONDA_DIR/bin:$PATH
+RUN echo "export PATH=$CONDA_DIR:$PATH" >> ~/.bashrc
+
 RUN mamba create -y -n usi -c conda-forge -c bioconda -c defaults celery==5.3.6 \
         dash=1.20.0 dash-bootstrap-components=0.9.2 flask gunicorn \
         joblib matplotlib==3.6.3 numba numpy openssl qrcode rdkit requests \

docker-compose-production.yml

@@ -20,6 +20,26 @@ services:
         max-size: "10m"
         max-file: "3"
 
+  metabolomicsusi-api1:
+    networks:
+      - default
+      - nginx-net
+    environment:
+      VIRTUAL_HOST: ${HOSTNAME:-api.metabolomics-usi.gnps2.org}
+      VIRTUAL_PORT: 5000
+      LETSENCRYPT_HOST: ${HOSTNAME:-api.metabolomics-usi.gnps2.org}
+      LETSENCRYPT_EMAIL: [email protected]
+    command: /app/run_server.sh
+    deploy:
+      resources:
+        limits:
+          memory: 16000M
+    logging:
+      driver: "json-file"
+      options:
+        max-size: "10m"
+        max-file: "3"
+
   metabolomicsusi-worker:
     deploy:
       resources:

docker-compose.yml

@@ -14,6 +14,37 @@ services:
       - default
     restart: always
     command: /app/run_dev_server.sh
+    labels:
+      autoheal: true
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:5000/heartbeat"]
+      interval: 30s
+      timeout: 10s
+      retries: 3
+      start_period: 60s
+
+  metabolomicsusi-api1:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    container_name: metabolomicsusi-api1
+    ports:
+    - "5088:5000"
+    volumes:
+        - ./tmp:/app/tmp:rw
+        - ./logsapi/:/app/logs:rw
+    networks:
+      - default
+    restart: always
+    command: /app/run_dev_server.sh
+    labels:
+      autoheal: true
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:5000/heartbeat"]
+      interval: 30s
+      timeout: 10s
+      retries: 3
+      start_period: 60s
 
   metabolomicsusi-worker:
     build:

metabolomics_spectrum_resolver/views.py

@@ -39,7 +39,6 @@
 def render_homepage():
     return flask.render_template("homepage.html")
 
-
 @blueprint.route("/contributors", methods=["GET"])
 def render_contributors():
     return flask.render_template("contributors.html")