Version 1.2.0

.dockerignore

@@ -0,0 +1,2 @@
+# React env files (dev-only, must never go into prod image)
+src/client/.env*

.env.example

@@ -11,4 +11,7 @@ DB_DUMP_HOST_PATH=/srv/backups/bionexus.dump
 
 # Paths to models used by the backend
 PARAS_MODEL_PATH=/app/models/all_substrates_model.paras.gz
-PARAS_MODEL_HOST_PATH=/srv/models/all_substrates_model.paras.gz
+PARAS_MODEL_HOST_PATH=/srv/models/all_substrates_model.paras.gz
+
+PFAM_HMM_DIR_PATH=/app/hmms/
+PFAM_HMM_DIR_HOST_PATH=/Users/davidmeijer/repos/RetroMol-GUI/hmms/

.gitignore

@@ -2,4 +2,5 @@
 .env
 cache/
 models/
+hmms/
 .DS_Store

README.md

@@ -149,6 +149,12 @@ curl -i http://localhost:4000/api/health
 
 ### Run the frontend locally
 
+Make sure to add `.env.development.local` to `src/client` and add the follwing line for SSE:
+
+```
+REACT_APP_SSE_BASE=http://localhost:4000
+```
+
 From the React client directory `src/client`, install dependencies and start the development server:
 
 ```bash

docker-compose.yml

@@ -53,8 +53,10 @@ services:
       - ./docker/backend.env
     environment:
       PARAS_MODEL_PATH: ${PARAS_MODEL_PATH}
+      PFAM_HMM_DIR_PATH: ${PFAM_HMM_DIR_PATH}
     volumes:
       - ${PARAS_MODEL_HOST_PATH}:${PARAS_MODEL_PATH}:ro
+      - ${PFAM_HMM_DIR_HOST_PATH}:${PFAM_HMM_DIR_PATH}:ro
     depends_on:
       db:
         condition: service_healthy

docker/backend.Dockerfile

@@ -15,7 +15,7 @@ RUN groupadd --gid $USER_GID $USERNAME \
 WORKDIR /app
 
 # System deps (psycopg binary + git)
-RUN apt-get update && apt-get install -y --no-install-recommends build-essential libpq-dev git && rm -rf /var/lib/apt/lists/*
+RUN apt-get update && apt-get install -y --no-install-recommends build-essential libpq-dev git libxrender1 libxext6 libsm6 && rm -rf /var/lib/apt/lists/*
 
 # Copy env + requirements before env creation for caching
 COPY src/server/environment.backend.yml /app/

docker/nginx.conf

@@ -22,9 +22,20 @@ server {
 
     location /api/ {
         proxy_pass http://retromol_backend:4000;
+
         proxy_set_header Host $host;
         proxy_set_header X-Real-IP $remote_addr;
 
+        # Important for SSE
+        proxy_buffering off;
+        proxy_cache off;
+        proxy_read_timeout 3600;
+        proxy_send_timeout 3600;
+        proxy_set_header Connection "";
+
+        # Tell nginx not to buffer even if upstream sets headers weirdly
+        add_header X-Accel-Buffering "no" always;
+
         client_max_body_size 100M;  # Max upload size
 
         # CORS headers

scripts/dev_backend.sh

@@ -25,6 +25,7 @@ export CACHE_DIR="$(pwd)/cache"
 
 # Define model paths
 export PARAS_MODEL_PATH="$(pwd)/models/all_substrates_model.paras.gz"
+export PFAM_HMM_DIR_PATH="$(pwd)/hmms/"
 
 # Make sure Flask can find the app
 export PYTHONPATH="$(pwd)/src/server"