Modifications from testing apptainer locally (Martin)

.gitignore

@@ -38,4 +38,8 @@ api/*.js.map
 
 # ssl certs we ignore the content of the folder but keep the folder around.
 nginx/ssl/*
-!nginx/ssl/.gitkeep
+!nginx/ssl/.gitkeep
+
+# apptainer tmp dir
+tmp/
+

api/package.json

@@ -0,0 +1,58 @@
+{
+    "name": "ezbids",
+    "version": "1.1.0",
+    "description": "",
+    "main": "index.js",
+    "scripts": {
+        "uidev": "cd ui && lite-server",
+        "tsc": "tsc",
+        "dev": "ts-node-dev --respawn ./ezbids.ts",
+        "prod": "tsc && node ./build/ezbids.js",
+        "deploy": "ssh -t hayashis@test.brainlife.io \"sudo su - -c 'cd /root/docker/ezbids && ./update.sh'\"",
+        "deploy-prod": "ssh -t -J hayashis@brainlife.io ubuntu@ezbids \"sudo su - -c 'cd /root/docker/ezbids && ./update.sh'\"",
+        "style-check": "prettier --config .prettierrc.json --check",
+        "lint-check": "eslint --ext .ts,.vue,.js",
+        "lint-staged": "lint-staged --config .lintstagedrc.json",
+        "prepare-husky": "husky install"
+    },
+    "author": "",
+    "license": "MIT",
+    "dependencies": {
+        "@types/express": "^4.17.13",
+        "@types/jsonwebtoken": "^9.0.4",
+        "archiver": "^5.3.0",
+        "async": "^3.2.3",
+        "body-parser": "^1.19.2",
+        "compression": "^1.7.4",
+        "cors": "^2.8.5",
+        "express": "^4.17.3",
+        "express-fileupload": "^1.3.1",
+        "express-jwt": "^8.4.1",
+        "jsonwebtoken": "^9.0.2",
+        "mkdirp": "^1.0.4",
+        "mongoose": "^6.2.7",
+        "multer": "1.4.4-lts.1",
+        "nan": "^2.17.0",
+        "nocache": "^2.1.0",
+        "node-pty": "^0.10.1",
+        "range-stream": "^1.1.0",
+        "send-seekable": "^1.0.4",
+        "swagger-jsdoc": "^6.2.8",
+        "swagger-ui-express": "^5.0.0"
+    },
+    "devDependencies": {
+        "@types/async": "^3.2.12",
+        "@types/cors": "^2.8.12",
+        "@types/node": "^20.17.46",
+        "@typescript-eslint/eslint-plugin": "^6.9.1",
+        "@typescript-eslint/parser": "^6.9.1",
+        "eslint": "^8.52.0",
+        "eslint-config-prettier": "^9.0.0",
+        "eslint-plugin-prettier": "^5.0.1",
+        "lint-staged": "^15.0.2",
+        "prettier": "^3.3.3",
+        "ts-node-dev": "^2.0.0",
+        "tsc-watch": "^6.0.4",
+        "typescript": "^4.9.5"
+    }
+}

apptainer/.gitignore

@@ -0,0 +1,2 @@
+*.sif
+.env

apptainer/README.md

@@ -0,0 +1,49 @@
+# Apptainer for ezBIDS
+
+This guide provides steps to convert Docker containers into Apptainer images and run them.
+
+## Converting Docker to Apptainer
+
+### Step 1: Build and Stop Docker Containers
+Run the following command to build and start the Docker containers:
+```sh
+docker-compose up --build
+```
+
+If the containers are running, stop them with:
+```sh
+docker-compose down
+```
+
+### Step 2: Export Docker Images
+Save the running images to `.tar` files:
+```sh
+docker save -o api_image.tar ezbids-api
+docker save -o handler_image.tar ezbids-handler
+docker save -o ui_image.tar ezbids-ui
+docker save -o telemetry_image.tar ezbids-telemetry
+```
+For more information, refer to the Docker documentation: [Docker Save Command](https://docs.docker.com/reference/cli/docker/image/save/)
+
+### Step 3: Convert Docker Images to Apptainer Images
+Use the following commands to convert each exported Docker image to an Apptainer `.sif` image:
+```sh
+apptainer build api.sif docker-archive:api_image.tar
+apptainer build handler.sif docker-archive:handler_image.tar
+apptainer build ui.sif docker-archive:ui_image.tar
+apptainer build telemetry.sif docker-archive:telemetry_image.tar
+```
+
+## Usage
+
+### Starting the Containers
+Run the following command to start the Apptainer containers:
+```sh
+./run_apptainer.sh
+```
+
+### Stopping the Containers
+To stop the Apptainer containers, execute:
+```sh
+./stop_apptainer.sh
+```

apptainer/dev_apptainer.sh

@@ -0,0 +1,62 @@
+#!/usr/bin/env bash
+
+cd "$(dirname "$0")/.."
+
+set -ex
+
+# Explicitly check if a .env file exists in the correct location explicitly:
+ENV_PATH="apptainer/.env"
+if [ -f "$ENV_PATH" ]; then
+    echo ".env file exists at $ENV_PATH, loading environment variables."
+else
+    echo ".env file does not exist at $ENV_PATH. Creating it explicitly now."
+    cat << EOF > "$ENV_PATH"
+SERVER_NAME=localhost
+BRAINLIFE_PRODUCTION=false
+SSL_CERT_PATH=./nginx/ssl/sslcert.cert
+SSL_KEY_PATH=./nginx/ssl/sslcert.key
+SSL_PASSWORD_PATH=./nginx/ssl/sslpassword
+BRAINLIFE_AUTHENTICATION=false
+BRAINLIFE_DEVELOPMENT=false
+COMPOSE_PROFILES=
+VITE_APIHOST=http://localhost:8082
+EOF
+    echo "Explicitly created .env file at $ENV_PATH explicitly."
+fi
+
+# Ensure SERVER_NAME=localhost exists in .env explicitly
+if ! grep -q "^SERVER_NAME=" "$ENV_PATH"; then
+    echo "SERVER_NAME=localhost" >> "$ENV_PATH"
+    echo "Added SERVER_NAME=localhost to $ENV_PATH explicitly."
+fi
+
+# Explicitly create required directories explicitly:
+required_dirs=("tmp" "tmp/data" "tmp/ezbids-workdir" "tmp/upload" "tmp/workdir")
+
+for dir in "${required_dirs[@]}"; do
+    [ ! -d "$dir" ] && mkdir -p "$dir"
+done
+
+# Parse arguments explicitly for authentication flag explicitly
+BRAINLIFE_AUTHENTICATION=true
+while getopts "d" flag; do
+ case $flag in
+   d) BRAINLIFE_AUTHENTICATION=false ;;
+ esac
+done
+export BRAINLIFE_AUTHENTICATION
+
+# Check Node.js version explicitly
+REQUIRED_NODE_VERSION="18"
+CURRENT_NODE_VERSION=$(node -v | cut -d '.' -f 1 | sed 's/v//')
+
+if [ "$CURRENT_NODE_VERSION" -ne "$REQUIRED_NODE_VERSION" ]; then
+    echo "Warning: You are explicitly using Node.js version $CURRENT_NODE_VERSION. Explicitly recommended version is $REQUIRED_NODE_VERSION."
+fi
+
+# Update git submodules and explicitly install dependencies explicitly:
+git submodule update --init --recursive
+(cd api && npm install)
+(cd ui && npm install)
+
+./generate_keys.sh

apptainer/mongo_host

@@ -0,0 +1 @@
+127.0.0.1 localhost mongodb

apptainer/run_apptainer.sh

@@ -0,0 +1,74 @@
+#!/usr/bin/env bash
+
+EZBIDS_DIR=/home/martinnorgaard/Documents/GitHub/ezbids
+cd "$EZBIDS_DIR"
+
+# Load environment variables explicitly from the .env file
+source "$EZBIDS_DIR/apptainer/.env"
+
+"$EZBIDS_DIR/apptainer/dev_apptainer.sh"
+
+if [ ! -e "$EZBIDS_DIR/apptainer/mongodb.sif" ]; then
+    apptainer build "$EZBIDS_DIR/apptainer/mongodb.sif" docker://mongo:4.4.15
+fi
+
+# Stop previously running instances explicitly
+apptainer instance stop mongodb api handler ui >/dev/null 2>&1
+
+# Explicitly start MongoDB container (port 27017 explicitly exposed)
+echo "Starting MongoDB container..."
+apptainer instance run \
+  --fakeroot --writable-tmpfs \
+  --bind "$EZBIDS_DIR/tmp":/tmp \
+  --bind "$EZBIDS_DIR/tmp/data":/data/db \
+  --bind "$EZBIDS_DIR/apptainer":/app \
+  --hostname mongodb \
+  "$EZBIDS_DIR/apptainer/mongodb.sif" mongodb bash -c "cd /app && ./start_mongodb.sh --bind_ip_all" &
+
+sleep 5
+
+# Explicitly start API container (port 8082 explicitly exposed)
+echo "Starting API container..."
+apptainer instance run \
+  --fakeroot \
+  --writable-tmpfs \
+  --bind "$EZBIDS_DIR/api":/app/api \
+  --bind "$EZBIDS_DIR/apptainer":/app/apptainer \
+  --bind "$EZBIDS_DIR/tmp":/tmp \
+  "$EZBIDS_DIR/apptainer/api.sif" api bash -c "cd /app/api && npm install && npm install --save-dev ts-node-dev typescript @types/node && npm run dev" &
+
+sleep 5
+
+# Explicitly start Handler container explicitly
+echo "Starting Handler container..."
+apptainer instance run \
+  --fakeroot \
+  --writable-tmpfs \
+  --env "PRESORT=$PRESORT" \
+  --bind "$EZBIDS_DIR/handler":/app/handler \
+  --bind "$EZBIDS_DIR/apptainer":/app/apptainer \
+  --bind "$EZBIDS_DIR/tmp":/tmp \
+  "$EZBIDS_DIR/apptainer/handler.sif" handler bash -c "cd /app/handler && chmod +x ./start.sh && ./start.sh" &
+
+sleep 5
+
+# Explicitly start UI container explicitly (port 3000 explicitly exposed)
+echo "Starting UI container explicitly..."
+apptainer instance run \
+  --bind "$EZBIDS_DIR/ui":/ui \
+  --bind "$EZBIDS_DIR/tmp":/tmp \
+  --env "VITE_APIHOST=http://localhost:8082" \
+  --env "BRAINLIFE_PRODUCTION=false" \
+  "$EZBIDS_DIR/apptainer/ui.sif" ui bash -c "cd /ui && ./entrypoint.sh"
+
+sleep 5
+
+if [ "$PROFILE" == "development" ]; then
+    echo "Starting Telemetry container..."
+    apptainer instance run \
+      --bind "$EZBIDS_DIR":/app \
+      "$EZBIDS_DIR/apptainer/telemetry.sif" telemetry bash -c "cd /app/apptainer && ./start_telemetry.sh" &
+fi
+
+echo "All containers are running explicitly"
+

apptainer/start_api.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+cd ..
+cd api/
+./dev.sh

apptainer/start_handler.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+cd ..
+cd handler/
+./start.sh

apptainer/start_mongodb.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+mongod --bind_ip_all --dbpath /data/db

apptainer/start_telementry.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+cd ..
+cd telementry/
+npm start

apptainer/start_ui.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+cd ../ui
+npm install
+npm run dev -- --host 0.0.0.0

apptainer/stop_apptainer.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+echo "Stopping containers..."
+apptainer instance stop api
+apptainer instance stop handler
+apptainer instance stop mongodb
+apptainer instance stop ui
+if [ "$PROFILE" == "development" ]; then
+    apptainer instance stop telementry
+fi

apptainer/ui_container.log

@@ -0,0 +1,5 @@
+INFO:    squashfuse not found, will not be able to mount SIF or other squashfs files
+INFO:    fuse2fs not found, will not be able to mount EXT3 filesystems
+INFO:    gocryptfs not found, will not be able to use gocryptfs
+INFO:    Converting SIF file to temporary sandbox...
+INFO:    instance started successfully

docker-compose-production.yml

@@ -20,6 +20,7 @@ services:
 
     api:
         container_name: brainlife_ezbids-api
+        image: ezbids-api   # <-- explicitly set this
         build: .
         platform: linux/amd64
         volumes:
@@ -41,6 +42,7 @@ services:
 
     handler:
         container_name: brainlife_ezbids-handler
+        image: ezbids-handler   # <-- explicitly set this
         build: ./handler
         platform: linux/amd64
         volumes:
@@ -73,6 +75,7 @@ services:
     # by default this is not enabled, add COMPOSE_PROFILES=telemetry to your .env
     telemetry:
         container_name: brainlife_ezbids-telemetry
+        image: ezbids-telemetry   # <-- explicitly set this
         build: ./telemetry
         platform: linux/amd64
         depends_on: