Merge pull request #119 from fractal-analytics-platform/new-example-for-testing

Add `staging-full-stack` example

Author: tcompa

examples/staging-full-stack/docker-compose.yml

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+services:
+  db:
+    cpus: 1.0
+    mem_limit: "1G"
+    container_name: fractal-db
+    image: postgres:15.4-alpine
+    restart: always
+    ports:
+      - 5433:5433
+    command: -p 5433
+    environment:
+      POSTGRES_USER: fractal
+      POSTGRES_PASSWORD: fractal
+      POSTGRES_DB: fractal
+      # required for the check below - otherwise postgresql
+      # will use undefined 'root' user and raise errors
+      PGUSER: fractal
+    healthcheck:
+      # postgresql starts up, stops, and then restarts
+      # => errors if the server connects before the stop
+      # this checks if the system is ready
+      test: pg_isready -p 5433
+      interval: 5s
+      timeout: 5s
+      retries: 5
+    volumes:
+      - postgres_db:/var/lib/postgresql/data
+    networks:
+      - fractal
+
+  server:
+    hostname: server
+    container_name: server
+    cpus: 3.0
+    mem_limit: 5g
+    build:
+      context: server
+      dockerfile: Dockerfile
+      args:
+        - FRACTAL_SERVER_VERSION=2.14.0a0
+    depends_on:
+      db:
+        condition: service_healthy
+    volumes:
+      - data:/data
+    ports:
+      - 8000:8000
+    healthcheck:
+      test: wget http://server:8000/api/alive/ > /dev/null 2>&1
+      interval: 5s
+      timeout: 2s
+      retries: 5
+    networks:
+      - fractal
+
+  web:
+    container_name: fractal-web
+    build:
+      context: ./web
+      dockerfile: Dockerfile
+      args:
+        - FRACTAL_WEB_VERSION=1.17.0-a0
+    depends_on:
+      server:
+        condition: service_healthy
+    ports:
+      - 5173:5173
+    networks:
+      - fractal
+
+  server-config:
+    container_name: server-config
+    build:
+      context: ./server-config
+      args:
+        - FRACTAL_CLIENT_VERSION=2.7.1
+    depends_on:
+      server:
+        condition: service_healthy
+    volumes:
+      - data:/data
+    networks:
+      - fractal
+
+  fractal-filebrowser:
+    container_name: fractal-filebrowser
+    build:
+      context: ./filebrowser
+    ports:
+      - 8080:80
+    networks:
+      - fractal
+    volumes:
+      - data:/data
+
+  vizarr:
+    container_name: vizarr
+    image: ghcr.io/fractal-analytics-platform/fractal-vizarr-viewer:stable
+    environment:
+      - FRACTAL_SERVER_URL=http://server:8000
+      - AUTHORIZATION_SCHEME=fractal-server
+    ports:
+      - 3000:3000
+    networks:
+      - fractal
+    volumes:
+      - data:/data:ro
+
+volumes:
+  data:
+  postgres_db:
+
+networks:
+  fractal:
+    driver: bridge

examples/staging-full-stack/filebrowser/Dockerfile

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+FROM filebrowser/filebrowser:v2
+RUN apk update
+RUN apk add inotify-tools openrc
+COPY check_file.sh /usr/check_file.sh
+COPY monitord /etc/init.d/monitord
+RUN chmod +x /usr/check_file.sh
+RUN chmod +x /etc/init.d/monitord
+COPY conf_files/filebrowser.db database.db
+COPY conf_files/filebrowser.json .filebrowser.json
+RUN mkdir -p /branding/img/icons
+ADD conf_files/favicon-16x16.png branding/img/icons
+ADD conf_files/favicon-32x32.png branding/img/icons
+ADD conf_files/logo.svg branding/img
+RUN /filebrowser config set --auth.method=noauth
+RUN /filebrowser config set --branding.name "Fractal FileBrowser" --branding.files "/branding" --branding.disableExternal
+RUN /filebrowser users update 1 --perm.admin=false
+COPY entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
+ENTRYPOINT /entrypoint.sh

examples/staging-full-stack/filebrowser/README.md

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+Note: To make the files uploaded/created in the `/data` dir broadly accessible, we added a service called `monitord` into the `fractal-filebrowser` container. This service uses `inotifywait` tool to check when a new file or dir is created within the `/data` folder, and modify its permission from 0644 to 0666.

examples/staging-full-stack/filebrowser/check_file.sh

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+#!/bin/sh
+DIRECTORY_TO_WATCH="/data"
+echo $$ > /run/monitord.pid
+# Monitor the directory and change permissions
+inotifywait -m -e create --format '%w%f' "$DIRECTORY_TO_WATCH" | while read NEW_FILE; do
+  chmod -R 0666 "$NEW_FILE"
+  echo "Changed permissions for $NEW_FILE"
+done

examples/staging-full-stack/filebrowser/conf_files/favicon-16x16.png

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+{
+  "port": 80,
+  "log": "stdout",
+  "database": "/database.db",
+  "root": "/data"
+}

examples/staging-full-stack/filebrowser/conf_files/favicon-32x32.png

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+#!/bin/sh
+
+openrc default                 # set runlevel to default
+rc-update add monitord default # add monitord service to system services
+service monitord start
+
+/filebrowser

examples/staging-full-stack/filebrowser/conf_files/filebrowser.db

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+#!/sbin/openrc-run
+
+name="Monitor data dir and change Permissions"
+description="Monitor data and change permissions for newly created files"
+command="/usr/check_file.sh"
+command_background=true
+pidfile="/run/monitord.pid"

examples/staging-full-stack/filebrowser/conf_files/filebrowser.json

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+# Auxiliary targets
+
+up:
+	docker compose up
+
+build:
+	docker compose build --progress=plain
+
+build-no-cache:
+	docker compose build --no-cache --progress=plain
+
+clean:
+	docker compose down -v --timeout 1
+
+clean-with-volumes:
+	docker compose down --volumes -v --timeout 1

examples/staging-full-stack/filebrowser/conf_files/logo.svg

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+FRACTAL_USER=[email protected]
+FRACTAL_PASSWORD=1234
+FRACTAL_SERVER=http://localhost:8000

examples/staging-full-stack/filebrowser/entrypoint.sh

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+venv
+.cache

examples/staging-full-stack/filebrowser/monitord

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+#!/bin/bash
+
+# Set cache path to the local directory, remove it if it exists
+FRACTAL_CACHE_PATH=$(pwd)/".cache"
+export FRACTAL_CACHE_PATH="$FRACTAL_CACHE_PATH"
+if [ -d "$FRACTAL_CACHE_PATH" ]; then
+    rm -rv "$FRACTAL_CACHE_PATH"  2> /dev/null
+fi
+
+fractal task collect fractal-tasks-core --package-extras fractal-tasks

examples/staging-full-stack/makefile

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+#!/bin/bash
+
+# Exit immediately if a command exits with a non-zero status
+set -e
+
+LABEL="cardiac"
+
+PROJECT_NAME="proj-$LABEL"
+DS_NAME="ds-$LABEL"
+WF_NAME="Workflow $LABEL"
+ZARR_DIR=/data/zarrs/${LABEL}
+
+
+# Set cache path to the local directory, remove it if it exists
+FRACTAL_CACHE_PATH=$(pwd)/".cache"
+export FRACTAL_CACHE_PATH="$FRACTAL_CACHE_PATH"
+if [ -d "$FRACTAL_CACHE_PATH" ]; then
+    rm -rv "$FRACTAL_CACHE_PATH"  2> /dev/null
+fi
+
+
+# Create project
+PROJECT_ID=$(fractal --batch project new "$PROJECT_NAME")
+echo "PROJECT_ID=$PROJECT_ID created"
+
+# Add input dataset, and add a resource to it
+DS_ID=$(fractal --batch project add-dataset "$PROJECT_ID" "$DS_NAME" --zarr-dir "$ZARR_DIR")
+echo "DS_IN_ID=$DS_ID created"
+
+# Import workflow
+WF_ID=$(fractal --batch workflow import --project-id "$PROJECT_ID" --json-file workflow.json --workflow-name "$WF_NAME")
+echo "WF_ID=$WF_ID created"