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docker-compose.yml
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docker-compose.yml
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version: "3.3"
networks:
clarity:
driver: bridge
volumes:
mssql-data:
idp-signing-creds:
redisdata:
nlp-solrdata:
nlp-pgdata:
nlp-mongodata:
ingest-files:
ingest-mongodata:
luigi-frontend:
luigi-state:
luigi-logs:
letsencrypt:
nlp-api-data:
services:
mssql:
container_name: IDP_MSSQL
hostname: ${IDP_DB_HOSTNAME}
image: mcr.microsoft.com/mssql/server:2017-latest
expose:
- ${IDP_DB_CONTAINER_PORT}
volumes:
- mssql-data:/var/opt/mssql
environment:
- ACCEPT_EULA=Y
- SA_PASSWORD=${IDP_DB_PASSWORD}
- MSSQL_PID=Developer
networks:
- clarity
identity-provider:
container_name: IDENTITY_PROVIDER
hostname: ${IDENTITY_PROVIDER_HOSTNAME}
image: claritynlp/identity-provider
expose:
- ${IDENTITY_PROVIDER_CONTAINER_PORT}
volumes:
- idp-signing-creds:/app/creds
entrypoint:
- /app/wait-for-it-extra.sh
- ${IDP_DB_HOSTNAME}:${IDP_DB_CONTAINER_PORT}
- --timeout=420
- --extra=15
- --
- docker-entrypoint.sh
command: dotnet IdentityServer.dll
environment:
- ASPNETCORE_ENVIRONMENT=Production
- ASPNETCORE_URLS=${ASPNETCORE_URLS}
- PROTOCOL=${PROTOCOL}
- HOST=${HOST}
- IDP_URL=${HOST}:${ENTRYPOINT_SSL}/${IDP_PREFIX}
- DASHBOARD_URL=${HOST}:${ENTRYPOINT_SSL}/${DASHBOARD_PREFIX}
- INGEST_URL=${HOST}:${ENTRYPOINT_SSL}/${INGEST_PREFIX}
- RESULTS_URL=${HOST}:${ENTRYPOINT_SSL}/${RESULTS_PREFIX}
- ADMIN_USERNAME=${ADMIN_USERNAME}
- ADMIN_PASSWORD=${ADMIN_PASSWORD}
- CLIENT_CLI_SECRET=${CLIENT_CLI_SECRET}
- CLIENT_NLPASS_SECRET=${CLIENT_NLPASS_SECRET}
- IDP_DB_PASSWORD=${IDP_DB_PASSWORD}
- IDP_DATABASE=${IDP_DATABASE}
- IDP_SIGNING_CREDS_PASSPHRASE=${IDP_SIGNING_CREDS_PASSPHRASE}
- IS_VHOST=false
depends_on:
- mssql
networks:
- clarity
identity-and-access-proxy:
container_name: IDENTITY_AND_ACCESS_PROXY
hostname: identity-and-access-proxy
image: claritynlp/identity-and-access-proxy
expose:
- ${IDENTITY_AND_ACCESS_PROXY_CONTAINER_PORT}
entrypoint: pm2-runtime
command: proxy.js
environment:
- IDENTITY_PROVIDER_HOSTNAME=${IDENTITY_PROVIDER_HOSTNAME}
- IDENTITY_PROVIDER_CONTAINER_PORT=${IDENTITY_PROVIDER_CONTAINER_PORT}
networks:
- clarity
nlp-api:
restart: always
container_name: NLP_API
hostname: ${NLP_API_HOSTNAME}
image: claritynlp/nlp-api
volumes:
- nlp-api-data:/tmp
expose:
- ${NLP_API_CONTAINER_PORT}
entrypoint:
- /api/wait-for-it-extra.sh
- ${NLP_SOLR_HOSTNAME}:${NLP_SOLR_CONTAINER_PORT}
- ${NLP_MONGO_HOSTNAME}:${NLP_MONGO_CONTAINER_PORT}
- ${SCHEDULER_HOSTNAME}:${SCHEDULER_CONTAINER_PORT}
- ${NLP_PG_HOSTNAME}:${NLP_PG_CONTAINER_PORT}
- ${REDIS_HOSTNAME}:${REDIS_CONTAINER_PORT}
- --timeout=420
- --
command: gunicorn api --config config.py --timeout 500 -b :5000
environment:
- NLP_API_TMP_DIR=${NLP_API_TMP_DIR}
- NLP_API_LOG_DIR=${NLP_API_LOG_DIR}
- NLP_SOLR_URL=${NLP_SOLR_URL}
- NLP_API_DEBUG_MODE=${NLP_API_DEBUG_MODE}
- NLP_EXPRESSION_EVALUATOR=${NLP_EXPRESSION_EVALUATOR}
- NLP_API_URL=${NLP_API_URL}
- BATCH_SIZE=${BATCH_SIZE}
- RESULTS_CLIENT_URL=${RESULTS_URL}
- USE_MEMORY_CACHING=${USE_MEMORY_CACHING}
- USE_PRECOMPUTED_SEGMENTATION=${USE_PRECOMPUTED_SEGMENTATION}
- USE_REORDERED_NLPQL=${USE_REORDERED_NLPQL}
- USE_REDIS_CACHING=${USE_REDIS_CACHING}
- OHDSI_WEBAPI_URL=${OHDSI_WEBAPI_URL}
- SOLR_TEXT_FIELD=${SOLR_TEXT_FIELD}
- SOLR_ID_FIELD=${SOLR_ID_FIELD}
- SOLR_REPORT_ID_FIELD=${SOLR_REPORT_ID_FIELD}
- SOLR_SOURCE_FIELD=${SOLR_SOURCE_FIELD}
- SOLR_REPORT_DATE_FIELD=${SOLR_REPORT_DATE_FIELD}
- SOLR_SUBJECT_FIELD=${SOLR_SUBJECT_FIELD}
- SOLR_REPORT_TYPE_FIELD=${SOLR_REPORT_TYPE_FIELD}
- NLP_PG_HOSTNAME=${NLP_PG_HOSTNAME}
- NLP_PG_DATABASE=${NLP_PG_DATABASE}
- NLP_PG_USER=${NLP_PG_USER}
- NLP_PG_PASSWORD=${NLP_PG_PASSWORD}
- NLP_PG_CONTAINER_PORT=${NLP_PG_CONTAINER_PORT}
- NLP_MONGO_HOSTNAME=${NLP_MONGO_HOSTNAME}
- NLP_MONGO_CONTAINER_PORT=${NLP_MONGO_CONTAINER_PORT}
- NLP_MONGO_DATABASE=${NLP_MONGO_DATABASE}
- NLP_MONGO_WORKING_INDEX=${NLP_MONGO_WORKING_INDEX}
- NLP_MONGO_WORKING_COLLECTION=${NLP_MONGO_WORKING_COLLECTION}
- NLP_MONGO_USERNAME=${NLP_MONGO_USERNAME}
- NLP_MONGO_PASSWORD=${NLP_MONGO_PASSWORD}
- LUIGI_SCHEDULER_URL=${LUIGI_SCHEDULER_URL}
- LUIGI_URL=${LUIGI_URL}
- LUIGI_WORKERS=${LUIGI_WORKERS}
- REDIS_HOSTNAME=${REDIS_HOSTNAME}
- REDIS_HOST_PORT=${REDIS_HOST_PORT}
- REDIS_CONTAINER_PORT=${REDIS_CONTAINER_PORT}
networks:
- clarity
depends_on:
- redis
- nlp-solr
- nlp-mongo
- nlp-postgres
- luigid
luigid:
restart: always
container_name: scheduler
hostname: scheduler
image: axiom/docker-luigi:2.7.1
expose:
- ${SCHEDULER_CONTAINER_PORT}
volumes:
- luigi-frontend:/usr/local/lib/python2.7/site-packages/luigi/static/visualiser
- luigi-state:/luigi/state
- luigi-logs:/luigi/logs
networks:
- clarity
frontend-ctrl:
restart: always
image: claritynlp/front-ctrl
volumes:
- luigi-frontend:/usr/local/lib/python2.7/site-packages/luigi/static/visualiser
links:
- luigid:luigid
- identity-provider:identity-provider
labels:
- "traefik.enable=true"
- "traefik.http.routers.appsecure.rule=Host(`${HOST}`) && PathPrefix(`/luigi`,`/idp`,`/solr`,`/api`)"
- "traefik.http.routers.appsecure.entrypoints=websecure"
- "traefik.http.routers.appsecure.tls.certresolver=mytlschallenge"
- "traefik.http.routers.appsecure.tls=true"
- "traefik.http.middlewares.limit.buffering.maxRequestBodyBytes=10000000000"
- "traefik.http.middlewares.forwardProto.headers.sslproxyheaders.X-Forwarded-Proto=https"
- "traefik.http.routers.appsecure.middlewares=limit,forwardProto"
- "traefik.http.routers.app.rule=Host(`${HOST}`) && PathPrefix(`/luigi`,`/idp`,`/solr`,`/api`)"
- "traefik.http.routers.app.entrypoints=web"
- "traefik.http.middlewares.https-only.redirectscheme.scheme=https"
- "traefik.http.middlewares.https-only.redirectscheme.port=${ENTRYPOINT_SSL}"
- "traefik.http.routers.app.middlewares=https-only"
networks:
- clarity
nlp-solr:
restart: always
container_name: NLP_SOLR
hostname: ${NLP_SOLR_HOSTNAME}
image: claritynlp/nlp-solr
expose:
- ${NLP_SOLR_CONTAINER_PORT}
volumes:
- nlp-solrdata:/opt/solr/server/solr/mycores
environment:
- SOLR_HEAP=${SOLR_HEAP}
networks:
- clarity
nlp-mongo:
container_name: NLP_MONGO
hostname: ${NLP_MONGO_HOSTNAME}
image: claritynlp/nlp-mongo
expose:
- ${NLP_MONGO_CONTAINER_PORT}
volumes:
- nlp-mongodata:/data/db
environment:
- MONGO_DATA_DIR=/data/db
- MONGO_LOG_DIR=/dev/null
- MONGO_INITDB_DATABASE=${NLP_MONGO_DATABASE}
- MONGO_INITDB_ROOT_USERNAME=${NLP_MONGO_USERNAME}
- MONGO_INITDB_ROOT_PASSWORD=${NLP_MONGO_PASSWORD}
networks:
- clarity
nlp-postgres:
container_name: NLP_POSTGRES
hostname: ${NLP_PG_HOSTNAME}
image: claritynlp/nlp-postgres
command: postgres -c 'shared_buffers=512MB' -c 'max_connections=500'
environment:
POSTGRES_USER: ${NLP_PG_USER}
POSTGRES_PASSWORD: ${NLP_PG_PASSWORD}
POSTGRES_DB: ${NLP_PG_DATABASE}
INIT_OMOP: ${INIT_OMOP}
expose:
- ${NLP_PG_CONTAINER_PORT}
volumes:
- nlp-pgdata:/var/lib/postgresql/data/
networks:
- clarity
ingest-api:
container_name: INGEST_API
hostname: ${INGEST_API_HOSTNAME}
image: claritynlp/ingest-api
volumes:
- /app/node_modules/ #empties container node_modules, forces bcrypt to be built on container
- ingest-files:/var/lib/ingest-files
expose:
- ${INGEST_API_CONTAINER_PORT}
entrypoint:
- /app/wait-for-it-extra.sh
- ${NLP_SOLR_HOSTNAME}:${NLP_SOLR_CONTAINER_PORT}
- ${REDIS_HOSTNAME}:${REDIS_CONTAINER_PORT}
- ${INGEST_MONGO_HOSTNAME}:${INGEST_MONGO_CONTAINER_PORT}
- ${NLP_API_HOSTNAME}:${NLP_API_CONTAINER_PORT}
- --timeout=420
- --
- pm2-runtime
command: app.js
environment:
- NODE_ENV=production
- JOB_TYPES=ingest
- NLP_SOLR_HOSTNAME=${NLP_SOLR_HOSTNAME}
- NLP_SOLR_CONTAINER_PORT=${NLP_SOLR_CONTAINER_PORT}
- NLP_CORE_NAME=${NLP_CORE_NAME}
- NLP_SOLR_URL_TOP_LEVEL=${NLP_SOLR_URL_TOP_LEVEL}
- NLP_API_HOSTNAME=${NLP_API_HOSTNAME}
- NLP_API_CONTAINER_PORT=${NLP_API_CONTAINER_PORT}
- INTERVAL=${INTERVAL}
- INGEST_MONGO_USERNAME=${INGEST_MONGO_USERNAME}
- INGEST_MONGO_PASSWORD=${INGEST_MONGO_PASSWORD}
- INGEST_MONGO_HOSTNAME=${INGEST_MONGO_HOSTNAME}
- INGEST_MONGO_CONTAINER_PORT=${INGEST_MONGO_CONTAINER_PORT}
- INGEST_MONGO_DATABASE=${INGEST_MONGO_DATABASE}
- INGEST_CLIENT_HOST_PORT=${INGEST_CLIENT_HOST_PORT}
- INGEST_API_LOG_LEVEL=${INGEST_API_LOG_LEVEL}
- REDIS_HOSTNAME=${REDIS_HOSTNAME}
- REDIS_CONTAINER_PORT=${REDIS_CONTAINER_PORT}
- PROTOCOL=${PROTOCOL}
- DASHBOARD_HOST=${HOST}
- INGEST_HOST=${HOST}
- ENTRYPOINT=${ENTRYPOINT_SSL}
networks:
- clarity
depends_on:
- ingest-mongo
- redis
- nlp-solr
- nlp-api
labels:
- "traefik.enable=true"
- "traefik.http.routers.socket-secure.rule=Host(`${HOST}`) && PathPrefix(`/socket.io`,`/__getcookie`)"
- "traefik.http.routers.socket-secure.entrypoints=websecure"
- "traefik.http.routers.socket-secure.tls.certresolver=mytlschallenge"
- "traefik.http.routers.socket.rule=Host(`${HOST}`) && PathPrefix(`/socket.io`,`/__getcookie`)"
- "traefik.http.routers.socket.entrypoints=web"
- "traefik.http.middlewares.socket-https-only.redirectscheme.scheme=https"
- "traefik.http.routers.socket.middlewares=socket-https-only"
ingest-mongo:
container_name: ${INGEST_MONGO_CONTAINER_NAME}
hostname: ${INGEST_MONGO_HOSTNAME}
image: claritynlp/ingest-mongo
environment:
- MONGO_DATA_DIR=/data/db
- MONGO_LOG_DIR=/dev/null
- MONGO_INITDB_DATABASE=${INGEST_MONGO_DATABASE}
- MONGO_INITDB_ROOT_USERNAME=${INGEST_MONGO_USERNAME}
- MONGO_INITDB_ROOT_PASSWORD=${INGEST_MONGO_PASSWORD}
expose:
- ${INGEST_MONGO_CONTAINER_PORT}
volumes:
- ingest-mongodata:/data/db
networks:
- clarity
redis:
container_name: REDIS
hostname: ${REDIS_HOSTNAME}
image: redis:4.0.10
expose:
- ${REDIS_CONTAINER_PORT}
volumes:
- redisdata:/data
networks:
- clarity
ingest-client:
container_name: INGEST_CLIENT
hostname: ${INGEST_CLIENT_HOSTNAME}
image: claritynlp/ingest-client
volumes:
- /app/node_modules
environment:
- PORT=${INGEST_CLIENT_CONTAINER_PORT}
- IDENTITY_PROVIDER_URL=${HOST}:${ENTRYPOINT_SSL}/${IDP_PREFIX}
- API_HOST=${HOST}:${ENTRYPOINT_SSL}/${IAAP_PREFIX}
- DASHBOARD_URL=${HOST}:${ENTRYPOINT_SSL}/${DASHBOARD_PREFIX}
- RESULTS_URL=${HOST}:${ENTRYPOINT_SSL}/${RESULTS_PREFIX}
- INGEST_URL=${HOST}:${ENTRYPOINT_SSL}/${INGEST_PREFIX}
- SOCKET_URL=${HOST}:${ENTRYPOINT_SSL}
labels:
- "traefik.enable=true"
- "traefik.port=${INGEST_CLIENT_CONTAINER_PORT}"
- "traefik.http.routers.ingest-secure.rule=Host(`${HOST}`) && PathPrefix(`/${INGEST_PREFIX}`)"
- "traefik.http.routers.ingest-secure.entrypoints=websecure"
- "traefik.http.routers.ingest-secure.tls.certresolver=mytlschallenge"
- "traefik.http.middlewares.ingest-secure-stripprefix.stripprefix.prefixes=/${INGEST_PREFIX}"
- "traefik.http.routers.ingest-secure.middlewares=ingest-secure-stripprefix"
- "traefik.http.routers.ingest.rule=Host(`${HOST}`) && PathPrefix(`/${INGEST_PREFIX}`)"
- "traefik.http.routers.ingest.entrypoints=web"
- "traefik.http.middlewares.ingest-https-only.redirectscheme.scheme=https"
- "traefik.http.middlewares.ingest-https-only.redirectscheme.port=${ENTRYPOINT_SSL}"
- "traefik.http.routers.ingest.middlewares=ingest-https-only"
networks:
- clarity
results-client:
container_name: RESULTS_CLIENT
hostname: ${RESULTS_CLIENT_HOSTNAME}
image: claritynlp/viewer-client
volumes:
- /app/node_modules
environment:
- PORT=${RESULTS_CLIENT_CONTAINER_PORT}
- IDENTITY_PROVIDER_URL=${HOST}:${ENTRYPOINT_SSL}/${IDP_PREFIX}
- API_HOST=${HOST}:${ENTRYPOINT_SSL}/${IAAP_PREFIX}
- DASHBOARD_URL=${HOST}:${ENTRYPOINT_SSL}/${DASHBOARD_PREFIX}
- INGEST_URL=${HOST}:${ENTRYPOINT_SSL}/${INGEST_PREFIX}
- RESULTS_URL=${HOST}:${ENTRYPOINT_SSL}/${RESULTS_PREFIX}
- SOLR_URL=${HOST}:${ENTRYPOINT_SSL}/${SOLR_PREFIX}
- LUIGI_URL=${HOST}:${ENTRYPOINT_SSL}/${SCHEDULER_PREFIX}
labels:
- "traefik.enable=true"
- "traefik.port=${RESULTS_CLIENT_CONTAINER_PORT}"
- "traefik.http.routers.results-secure.rule=Host(`${HOST}`) && PathPrefix(`/${RESULTS_PREFIX}`)"
- "traefik.http.routers.results-secure.entrypoints=websecure"
- "traefik.http.routers.results-secure.tls.certresolver=mytlschallenge"
- "traefik.http.middlewares.results-secure-stripprefix.stripprefix.prefixes=/${RESULTS_PREFIX}"
- "traefik.http.routers.results-secure.middlewares=results-secure-stripprefix"
- "traefik.http.routers.results.rule=Host(`${HOST}`) && PathPrefix(`/${RESULTS_PREFIX}`)"
- "traefik.http.routers.results.entrypoints=web"
- "traefik.http.middlewares.results-https-only.redirectscheme.scheme=https"
- "traefik.http.middlewares.results-https-only.redirectscheme.port=${ENTRYPOINT_SSL}"
- "traefik.http.routers.results.middlewares=results-https-only"
networks:
- clarity
dashboard-client:
container_name: DASHBOARD_CLIENT
hostname: ${DASHBOARD_CLIENT_HOSTNAME}
image: claritynlp/dashboard-client
volumes:
- /app/node_modules
environment:
- PORT=${DASHBOARD_CLIENT_CONTAINER_PORT}
- IDENTITY_PROVIDER_URL=${HOST}:${ENTRYPOINT_SSL}/${IDP_PREFIX}
- API_HOST=${HOST}:${ENTRYPOINT_SSL}/${IAAP_PREFIX}
- INGEST_URL=${HOST}:${ENTRYPOINT_SSL}/${INGEST_PREFIX}
- RESULTS_URL=${HOST}:${ENTRYPOINT_SSL}/${RESULTS_PREFIX}
- DASHBOARD_URL=${HOST}:${ENTRYPOINT_SSL}/${DASHBOARD_PREFIX}
- SOCKET_URL=${HOST}:${ENTRYPOINT_SSL}
- REACT_APP_DOCUMETATION_URL=https://claritynlp.readthedocs.io/en/latest/index.html
labels:
- "traefik.enable=true"
- "traefik.port=${DASHBOARD_CLIENT_CONTAINER_PORT}"
- "traefik.http.routers.dashboard-secure.rule=Host(`${HOST}`) && PathPrefix(`/${DASHBOARD_PREFIX}`)"
- "traefik.http.routers.dashboard-secure.entrypoints=websecure"
- "traefik.http.routers.dashboard-secure.tls.certresolver=mytlschallenge"
- "traefik.http.middlewares.dashboard-secure-stripprefix.stripprefix.prefixes=/${DASHBOARD_PREFIX}"
- "traefik.http.routers.dashboard-secure.middlewares=dashboard-secure-stripprefix"
- "traefik.http.routers.dashboard.rule=Host(`${HOST}`) && PathPrefix(`/${DASHBOARD_PREFIX}`)"
- "traefik.http.routers.dashboard.entrypoints=web"
- "traefik.http.middlewares.dashboard-https-only.redirectscheme.scheme=https"
- "traefik.http.middlewares.dashboard-https-only.redirectscheme.port=${ENTRYPOINT_SSL}"
- "traefik.http.routers.dashboard.middlewares=dashboard-https-only"
networks:
- clarity
traefik:
image: "traefik:v2.1.2"
container_name: "traefik"
command:
- "--log.level=INFO"
- "--api=true"
- "--providers.docker=true"
- "--providers.docker.exposedbydefault=false"
- "--entrypoints.web.address=:80"
- "--entrypoints.websecure.address=:443"
- "--certificatesresolvers.mytlschallenge.acme.tlschallenge=true"
- "--certificatesresolvers.mytlschallenge.acme.email=${ACME_EMAIL}"
- "--certificatesresolvers.mytlschallenge.acme.storage=/letsencrypt/acme.json"
ports:
- "${ENTRYPOINT_NON_SSL}:80"
- "${ENTRYPOINT_SSL}:443"
- "8080:8080"
volumes:
- "/var/run/docker.sock:/var/run/docker.sock:ro"
- letsencrypt:/letsencrypt
networks:
- clarity