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bendhouseartTim BudrasAnthony Galassiaebuti1021
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Updating bendhouseart/ezbids:master from buti1021/ezbids:add-nginx-forwarding (#1)
* updating docker compose to use nginx for forwarding * added nginx config and updated docker file works on mac * added folder for certs * had to bodge npm installs, husky, and vite to get healthy containers on osx * updated docker compose, health checks all pass. CORS still an issue * add nginx config * ssl works with the addition of a cert, key, and the password for it * create standalone production config * consolidating variables and options into 1 launch script and 1 .env file * updated lint check to use prettier instead of npm 'style-check' and 'lint-check' * update package-lock.json * bringing more in line with buti1021's PR, while 'stream-lining' env and entrypoints * update docker ignore and build * Update example.env * certs and keys path as environment * enable telemetry via build in compose_profile env var * revert vite config changes * remove old files --------- Co-authored-by: Tim Budras <[email protected]> Co-authored-by: Anthony Galassiae <[email protected]> Co-authored-by: buti1021 <[email protected]>
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‎.dockerignore‎

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ui
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handler
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workdir
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test
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bids-specification

‎.gitignore‎

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# local env files
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.env.local
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.env.*.local
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.env
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# Log files
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npm-debug.log*
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api/*.key
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api/ezbids.key
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api/*.js
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api/*.js.map
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api/*.js.map
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# ssl certs we ignore the content of the folder but keep the folder around.
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nginx/ssl/*
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!nginx/ssl/.gitkeep

‎.lintstagedrc.json‎

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{
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"**/*.{js,json,ts,vue}": ["npm run style-check", "npm run lint-check"]
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"**/*.{js,json,ts,vue}": ["prettier --write"]
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}

‎Dockerfile‎

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WORKDIR /app
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RUN npm install -g [email protected]
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RUN npm install -g [email protected] pm2 typescript tsc-watch
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RUN npm install -g pm2 typescript tsc-watch
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# build the api and the ui
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RUN cd /app/api && npm install
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RUN cd /app/ui && npm install

‎dev.sh‎

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‎docker-compose-production.yml‎

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version: "3"
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networks:
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ezbids:
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services:
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mongodb:
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container_name: brainlife_ezbids-mongodb
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image: mongo:4.4.15
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platform: linux/amd64
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volumes:
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- /data/db
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healthcheck:
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test: echo 'db.runCommand("ping").ok' | mongo localhost:27017/test --quiet
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interval: 10s
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timeout: 10s
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retries:
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5
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networks:
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- ezbids
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api:
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container_name: brainlife_ezbids-api
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build: .
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platform: linux/amd64
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volumes:
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- ./api:/app/api
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- /tmp:/tmp
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depends_on:
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mongodb:
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condition: service_healthy
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healthcheck:
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test: ["CMD", "curl", "-f", "http://localhost:8082/health"]
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working_dir: /app/api
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command:
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./dev.sh
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environment:
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MONGO_CONNECTION_STRING: mongodb://mongodb:27017/ezbids
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BRAINLIFE_AUTHENTICATION: ${BRAINLIFE_AUTHENTICATION}
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networks:
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- ezbids
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handler:
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container_name: brainlife_ezbids-handler
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build: ./handler
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platform: linux/amd64
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volumes:
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- .:/app
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- /tmp:/tmp
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depends_on:
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mongodb:
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condition: service_healthy
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api:
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condition: service_healthy
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environment:
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MONGO_CONNECTION_STRING: mongodb://mongodb:27017/ezbids
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networks:
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- ezbids
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tty: true #turn on color for bids-validator output
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command: pm2 start handler.js --attach
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ui:
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container_name: brainlife_ezbids-ui-builder
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env_file:
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- .env
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build: ./ui
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platform: linux/amd64
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volumes:
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- ./ui/dist:/ui/dist
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environment:
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VITE_APIHOST: https://${SERVER_NAME}/api
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VITE_BRAINLIFE_AUTHENTICATION: ${BRAINLIFE_AUTHENTICATION}
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# by default this is not enabled, add COMPOSE_PROFILES=telemetry to your .env
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telemetry:
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container_name: brainlife_ezbids-telemetry
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build: ./telemetry
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platform: linux/amd64
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depends_on:
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- mongodb
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profiles: ["telemetry"]
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networks:
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- ezbids
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nginx:
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env_file:
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- .env
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container_name: brainlife_ezbids-nginx
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depends_on:
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- ui
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- api
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image: nginx:latest
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platform: linux/amd64
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ports:
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- 443:443
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networks:
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- ezbids
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volumes:
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- ${SSL_CERT_PATH}:/etc/nginx/conf.d/ssl/sslcert.cert
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- ${SSL_KEY_PATH}:/etc/nginx/conf.d/ssl/sslcert.key
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- ${SSL_PASSWORD_PATH}:/etc/nginx/conf.d/ssl/sslpassword
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- ./nginx/production_nginx.conf:/etc/nginx/conf.d/default.conf
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- ./ui/dist:/usr/share/nginx/html/ezbids:ro

‎docker-compose.yml‎

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# version: "3"
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version: "3"
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networks:
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ezbids:
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services:
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mongodb:
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ports:
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- 27417:27017 #for local debugging
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networks:
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- ezbids
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api:
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container_name: brainlife_ezbids-api
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BRAINLIFE_AUTHENTICATION: ${BRAINLIFE_AUTHENTICATION}
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ports:
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- 8082:8082 #localhost runs on local browser to it needs to access api via host port
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networks:
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- ezbids
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handler:
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container_name: brainlife_ezbids-handler
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condition: service_healthy
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environment:
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MONGO_CONNECTION_STRING: mongodb://mongodb:27017/ezbids
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networks:
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- ezbids
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tty: true #turn on color for bids-validator output
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command: pm2 start handler.js --attach --watch --ignore-watch "ui **/node_modules"
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ui:
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container_name: brainlife_ezbids-ui
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env_file:
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- .env
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build: ./ui
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platform: linux/amd64
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volumes:
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test: ["CMD", "curl", "-f", "http://localhost:3000"]
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ports:
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- 3000:3000 #vite wants to be exposed on the host for HMR?
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networks:
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- ezbids
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# by default this is not enabled, need to run docker compose with --profile development to enable this service
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telemetry:
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container_name: brainlife_ezbids-telemetry
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build: ./telemetry
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platform: linux/amd64
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depends_on:
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- mongodb
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profiles: ["development"]
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profiles: ["telemetry"]
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ports:
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- 8000:8000 #for local debugging
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- 8000:8000 #for local debugging
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networks:
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- ezbids
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‎example.env‎

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# Create/Copy this file as .env in the root of the project to set default environment variables
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# insert your host name here, it should match your ssl certificate and/or the output
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# of echo $HOSTNAME
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SERVER_NAME=localhost
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# Set the BRAINLIFE_PRODUCTION environment variable to true to use https"
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# (this will launch the services on port 443) and run with nginx/production_nginx.conf"
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# this will require providing the correct paths for the SSL_CERT_PATH, SSL_KEY_PATH and SSL_PASSWORD_PATH
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# with false the UI will run on 3000"
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BRAINLIFE_PRODUCTION=false
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SSL_CERT_PATH=./nginx/ssl/sslcert.cert
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SSL_KEY_PATH=./nginx/ssl/sslcert.key
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SSL_PASSWORD_PATH=./nginx/ssl/sslpassword #if your key is not encrypted use an arbitrary path here
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# Set the BRAINLIFE_AUTHENTICATION environment variable to true, if you're not running"
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# this with brainlife don't use."
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BRAINLIFE_AUTHENTICATION=false
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# Set the BRAINLIFE_DEVELOPMENT enables additional debugging output and mounts
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# the ezbids repo/folder into the various containers default is false"
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BRAINLIFE_DEVELOPMENT=false
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# Define which profiles to use, e.g. set to COMPOSE_PROFILES=telemetry to enable telemetry
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COMPOSE_PROFILES=

‎handler/Dockerfile‎

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FROM neurodebian:nd20.04-non-free
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COPY . /app
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SHELL ["/bin/bash", "-c"]
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ENV DEBIAN_FRONTEND noninteractive
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RUN apt update && \
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apt-get update && apt-get upgrade -y
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RUN apt install -y parallel python3 python3-pip tree curl unzip git jq python libgl-dev python-numpy bc
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RUN apt update && apt install -y parallel python3 python3-pip tree curl unzip git jq python libgl-dev python-numpy bc
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RUN pip3 install numpy==1.23.0 nibabel==4.0.0 pandas matplotlib pyyaml==5.4.1 pydicom==2.3.1 natsort pydeface && \
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pip3 install quickshear mne mne-bids

‎launch.sh‎

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#!/usr/bin/env bash
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# check to see if a .env file exists
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if [ -f .env ]; then
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echo ".env file exists, loading environment variables from .env file"
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else
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echo ".env file does not exist, copying example.env to .env"
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cp example.env .env
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fi
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# load the environment variables from the .env file
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source .env
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echo "Setting Environment Variables from .env file:"
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# display the environment variables read in from .env, could be a gotcha if
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# the user is unclear about if the .env variables are being used. The .env variables
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# will override environment variables set in the shell as they're set once this script
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# is run.
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while read line
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do
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# if line does not start with # then echo the line
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if [[ $line != \#* ]]; then
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if [[ $line != "" ]]; then
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echo " ${line}"
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fi
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fi
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done < .env
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if [ $BRAINLIFE_DEVELOPMENT == true ]; then
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# enable or disable debugging output
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set -ex
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else
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set -e
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fi
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# build local changes and mount them directly into the containers
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# api/ and ui/ are mounted as volumes at /app within the docker-compose.yml
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(cd api && npm install)
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(cd ui && npm install)
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# update the bids submodule
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git submodule update --init --recursive
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# The main differences between the production and development docker-compose files are that the production
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# files uses https via nginx and the development file uses http.
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if [[ $BRAINLIFE_PRODUCTION == true ]]; then
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DOCKER_COMPOSE_FILE=docker-compose-production.yml
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else
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DOCKER_COMPOSE_FILE=docker-compose.yml
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fi
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mkdir -p /tmp/upload
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mkdir -p /tmp/workdir
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#npm run prepare-husky
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./generate_keys.sh
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# ok docker compose is now included in docker as an option for docker
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if [[ $(command -v docker-compose) ]]; then
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# if the older version is installed use the dash
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docker-compose --file ${DOCKER_COMPOSE_FILE} up
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else
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# if the newer version is installed don't use the dash
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docker compose --file ${DOCKER_COMPOSE_FILE} up
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fi

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