docker-compose.yml

version: '3.9'

volumes:
  atlasdb-postgres-data:
    name: atlasdb-postgres-data
  rstudio-home-data:
    name: rstudio-home-data
  rstudio-tmp-data:
    name: rstudio-tmp-data
  openldap-data:
    name: openldap-data
  jdbc-drivers-data:
    name: jdbc-drivers-data
  cdm-postprocessing-data:
    name: cdm-postprocessing-data
  perseus-shareddb:
    name: perseus-shareddb
  perseus-vocabularydb:
    name: perseus-vocabularydb
  perseus-solr:
    name: perseus-solr
  jupyter-notebook:
    name: jupyter-notebook
  pgadmin-data:
    name: pgadmin-data

services:
  
  traefik:
    image: docker.io/library/traefik:v2.11.2
    container_name: traefik
    restart: unless-stopped
    ipc: none
    read_only: true
    environment:
      BROADSEA_HOST: ${BROADSEA_HOST}
    labels:
     - "traefik.enable=true"
    ports:
      - "80:80"
      - "443:443"
    volumes:
      - ./traefik/traefik_${HTTP_TYPE}.yml:/etc/traefik/traefik.yml:ro
      - ./traefik/tls_${HTTP_TYPE}.yml:/etc/traefik/dynamic/tls.yml:ro
      - ./traefik/routers.yml:/etc/traefik/dynamic/routers.yml:ro
      - ${BROADSEA_CERTS_FOLDER}:/etc/certs:ro
      - /var/run/docker.sock:/var/run/docker.sock:ro

  broadsea-content:
    profiles: [ "default", "content" ]
    container_name: broadsea-content
    platform: "linux/amd64"
    build:
      context: ./content
      args:
        CONTENT_TITLE: ${CONTENT_TITLE}
        CONTENT_ARES_DISPLAY: ${CONTENT_ARES_DISPLAY}
        CONTENT_ATLAS_DISPLAY: ${CONTENT_ATLAS_DISPLAY}
        CONTENT_HADES_DISPLAY: ${CONTENT_HADES_DISPLAY}
        CONTENT_PERSEUS_DISPLAY: ${CONTENT_PERSEUS_DISPLAY}
        CONTENT_OPENSHINYSERVER_DISPLAY: ${CONTENT_OPENSHINYSERVER_DISPLAY}
        CONTENT_POSITCONNECT_DISPLAY: ${CONTENT_POSITCONNECT_DISPLAY}
    restart: unless-stopped
    labels:
      - "traefik.enable=true"

  broadsea-hades:
    profiles: [ "default", "hades" ]
    container_name: broadsea-hades
    image: ohdsi/broadsea-hades:4.2.1
    platform: "linux/amd64"
    secrets:
      - HADES_PASSWORD
    environment:
      USER: ${HADES_USER}
    volumes:
      - rstudio-home-data:/home
      - rstudio-tmp-data:/tmp
      - ./hades/00_set_secrets:/etc/cont-init.d/00_set_secrets
    labels:
      - "traefik.enable=true"

  # WebAPI and Atlas services based on the standard Docker Hub images -------------
  ohdsi-webapi-from-image:
    profiles: [ "default", "webapi-from-image" ]
    image: docker.io/ohdsi/webapi:latest
    extends: 
      file: "./compose/ohdsi-webapi.yml"
      service: ohdsi-webapi

  ohdsi-atlas-from-image:
    profiles: [ "default", "atlas-from-image" ]
    image: docker.io/ohdsi/atlas:latest
    extends: 
      file: "./compose/ohdsi-atlas.yml"
      service: ohdsi-atlas

  # WebAPI and Atlas services based on git repo (for developers) -------------
  ohdsi-webapi-from-git:
    profiles: [ "webapi-from-git" ]
    build: 
      context: ${WEBAPI_GITHUB_URL}
      args:
        MAVEN_PARAMS: -DskipTests=true -DskipUnitTests=true
        MAVEN_PROFILE: ${WEBAPI_MAVEN_PROFILE}
    extends: 
      file: "./compose/ohdsi-webapi.yml"
      service: ohdsi-webapi

  ohdsi-atlas-from-git:
    profiles: [ "atlas-from-git" ]
    build: ${ATLAS_GITHUB_URL}
    extends: 
      file: "./compose/ohdsi-atlas.yml"
      service: ohdsi-atlas

  # -----------------------------------------------------------------

  broadsea-atlasdb:
    profiles: [ "default", "atlasdb" ]
    image: ohdsi/broadsea-atlasdb:2.1.0-secret
    container_name: broadsea-atlasdb
    platform: linux/amd64
    restart: unless-stopped
    cpus: 2
    mem_limit: "2G"
    environment:
      POSTGRES_PASSWORD: mypass
    ports:
      - "5432:5432"
    volumes:
      - atlasdb-postgres-data:/var/lib/postgresql/data
      - ./atlasdb/100_populate_source_source_daimon.sql:/docker-entrypoint-initdb.d/100_populate_source_source_daimon.sql:ro
    healthcheck:
      test: ["CMD-SHELL", "pg_isready -U postgres"]
      interval: 5s
      timeout: 5s
      retries: 10

  broadsea-solr-vocab:
    profiles: [ "solr-vocab-no-import", "solr-vocab-with-import" ]
    container_name: solr-vocab
    restart: unless-stopped
    image: solr:8.11.1
    secrets:
      - SOLR_VOCAB_JDBC_PASSWORD
    environment: 
      SOLR_VOCAB_VERSION: ${SOLR_VOCAB_VERSION}
      SOLR_VOCAB_JDBC_DRIVER_PATH: ${SOLR_VOCAB_JDBC_DRIVER_PATH}
      SOLR_VOCAB_JDBC_URL: ${SOLR_VOCAB_JDBC_URL}
      SOLR_VOCAB_JDBC_USER: ${SOLR_VOCAB_JDBC_USER}
    volumes:
      - ${SOLR_VOCAB_JDBC_FILE_PATH}:/opt/solr-8.11.1/server/lib/solr_jdbc_driver.jar:ro
      - ./solr:/tmp/solr_config:ro
      - ./solr/docker-entrypoint.sh:/entrypoint.sh
    entrypoint: ["/bin/sh", "/entrypoint.sh"]
    labels:
      - "traefik.enable=true"
    healthcheck:
      test: curl --fail ${SOLR_VOCAB_ENDPOINT} || exit 1
      interval: 10s
      timeout: 5s
      retries: 5

  broadsea-solr-vocab-run-import:
    profiles: [ "solr-vocab-with-import" ]
    container_name: solr-vocab-run-import
    image: curlimages/curl
    depends_on:
      broadsea-solr-vocab:
        condition: service_healthy
    command: curl -d "vocab_database_schema=${SOLR_VOCAB_DATABASE_SCHEMA}" -X POST ${SOLR_VOCAB_ENDPOINT}/${SOLR_VOCAB_VERSION}/dataimport?command=full-import&entity=concept

  broadsea-ares:
    profiles: [ "ares" ]
    container_name: broadsea-ares
    restart: unless-stopped
    build:
      context: https://github.com/OHDSI/Ares.git
    volumes:
      - ${ARES_DATA_FOLDER}:/usr/share/nginx/html/ares/data:ro
    labels:
      - "traefik.enable=true"


  broadsea-omop-vocab-load:
    profiles: [ "omop-vocab-pg-load" ]
    container_name: omop-vocab-load
    extends:
      file: "./compose/postgres-load.yml"
      service: broadsea-postgres-load
    secrets:
      - VOCAB_PG_PASSWORD
      - UMLS_API_KEY
    environment:
      VOCAB_PG_HOST: ${VOCAB_PG_HOST}
      VOCAB_PG_DATABASE: ${VOCAB_PG_DATABASE}
      VOCAB_PG_SCHEMA: ${VOCAB_PG_SCHEMA}
      VOCAB_PG_USER: ${VOCAB_PG_USER}
    volumes:
      - ./omop_vocab/scripts:/tmp/scripts
      - ${VOCAB_PG_FILES_PATH}:/tmp/files
    entrypoint: ["sh", "/tmp/scripts/load_omop_vocab.sh" ]


  broadsea-phoebe-load:
    profiles: [ "phoebe-pg-load" ]
    container_name: broadsea-phoebe-load
    extends:
      file: "./compose/postgres-load.yml"
      service: broadsea-postgres-load
    secrets:
      - PHOEBE_PG_PASSWORD
    environment:
      PHOEBE_PG_HOST: ${PHOEBE_PG_HOST}
      PHOEBE_PG_DATABASE: ${PHOEBE_PG_DATABASE}
      PHOEBE_PG_SCHEMA: ${PHOEBE_PG_SCHEMA}
      PHOEBE_PG_USER: ${PHOEBE_PG_USER}
    volumes:
      - ./phoebe:/tmp
    entrypoint: ["sh", "/tmp/load_phoebe.sh" ]

  # Security providers for testing purposes

  broadsea-openldap:
    profiles: [ "openldap" ]
    image: docker.io/bitnami/openldap:2.6
    container_name: broadsea-openldap
    restart: unless-stopped
    secrets:
      - OPENLDAP_ADMIN_PASSWORD
      - OPENLDAP_ACCOUNT_PASSWORDS
    volumes:
      - ./openldap/entrypoint.sh:/tmp/entrypoint.sh
    environment:
      LDAP_ADMIN_USERNAME: ${SECURITY_LDAP_SYSTEM_USERNAME}
      LDAP_ADMIN_PASSWORD_FILE: /run/secrets/OPENLDAP_ADMIN_PASSWORD
      LDAP_USERS: ${OPENLDAP_USERS}
    ports:
      - '1389:1389'
      - '1636:1636'
    entrypoint: ["/bin/bash", "/tmp/entrypoint.sh"]
    command: [ "/opt/bitnami/scripts/openldap/run.sh" ]

  # shiny server options (open-source and commercial)

  broadsea-open-shiny-server:
    profiles: [ "open-shiny-server" ]
    image: rocker/shiny:4.3.0
    platform: "linux/amd64"
    container_name: broadsea-open-shiny-server
    restart: unless-stopped
    expose:
      - "3838:3838"
    volumes:
      - ${OPEN_SHINY_SERVER_APP_ROOT}:/srv/shiny-server/apps:ro
    labels:
      - "traefik.enable=true" 

  broadsea-posit-connect:
    profiles: [ "posit-connect" ]
    image: rstudio/rstudio-connect
    platform: "linux/amd64"
    container_name: broadsea-posit-connect
    restart: unless-stopped
    expose:
      - "3939:3939"
    privileged: true
    environment:
      RSC_LICENSE_SERVER: ${POSIT_CONNECT_LICENSE_SERVER}
      R_VERSION: ${POSIT_CONNECT_R_VERSION}
    volumes:
      - ${POSIT_CONNECT_LICENSE_FILE}:/etc/rstudio-connect/license.lic:ro
      - ${POSIT_CONNECT_GCFG_FILE}:/etc/rstudio-connect/rstudio-connect.gcfg:ro
    labels:
      - "traefik.enable=true"

# CDM Post-Processing ---------------

  broadsea-run-achilles:
    profiles: [ "cdm-postprocessing", "achilles" ]
    build: 
      context: ./achilles
      secrets:
        - GITHUB_PAT
    platform: "linux/amd64"
    container_name: broadsea-run-achilles
    secrets:
      - CDM_CONNECTIONDETAILS_PASSWORD
    volumes:
      - jdbc-drivers-data:/jdbc
      - cdm-postprocessing-data:/postprocessing
      - ./postprocessing/init.R:/postprocessing/init.R
      - ./achilles/run_achilles.R:/postprocessing/achilles/scripts/${CDM_DATABASE_SCHEMA}.R
    environment:
      CDM_CONNECTIONDETAILS_DBMS: ${CDM_CONNECTIONDETAILS_DBMS}
      CDM_CONNECTIONDETAILS_USER: ${CDM_CONNECTIONDETAILS_USER}
      CDM_CONNECTIONDETAILS_SERVER: ${CDM_CONNECTIONDETAILS_SERVER}
      CDM_CONNECTIONDETAILS_PORT: ${CDM_CONNECTIONDETAILS_PORT}
      CDM_CONNECTIONDETAILS_EXTRA_SETTINGS: ${CDM_CONNECTIONDETAILS_EXTRA_SETTINGS}
      CDM_VERSION: ${CDM_VERSION}
      CDM_SOURCE_NAME: ${CDM_SOURCE_NAME}
      CDM_DATABASE_SCHEMA: ${CDM_DATABASE_SCHEMA}
      RESULTS_DATABASE_SCHEMA: ${RESULTS_DATABASE_SCHEMA}
      SCRATCH_DATABASE_SCHEMA: ${SCRATCH_DATABASE_SCHEMA}
      VOCAB_DATABASE_SCHEMA: ${VOCAB_DATABASE_SCHEMA}
      TEMP_EMULATION_SCHEMA: ${TEMP_EMULATION_SCHEMA}

      ACHILLES_ANALYSIS_IDS: ${ACHILLES_ANALYSIS_IDS}
      ACHILLES_CREATE_TABLE: ${ACHILLES_CREATE_TABLE}
      ACHILLES_SMALL_CELL_COUNT: ${ACHILLES_SMALL_CELL_COUNT}
      ACHILLES_CREATE_INDICES: ${ACHILLES_CREATE_INDICES}
      ACHILLES_NUM_THREADS: ${ACHILLES_NUM_THREADS}
      ACHILLES_TEMP_ACHILLES_PREFIX: ${ACHILLES_TEMP_ACHILLES_PREFIX}
      ACHILLES_DROP_SCRATCH_TABLES: ${ACHILLES_DROP_SCRATCH_TABLES}
      ACHILLES_VERBOSE_MODE: ${ACHILLES_VERBOSE_MODE}
      ACHILLES_OPTIMIZE_ATLAS_CACHE: ${ACHILLES_OPTIMIZE_ATLAS_CACHE}
      ACHILLES_DEFAULT_ANALYSES_ONLY: ${ACHILLES_DEFAULT_ANALYSES_ONLY}
      ACHILLES_UPDATE_GIVEN_ANALYSES_ONLY: ${ACHILLES_UPDATE_GIVEN_ANALYSES_ONLY}
      ACHILLES_EXCLUDE_ANALYSIS_IDS: ${ACHILLES_EXCLUDE_ANALYSIS_IDS}
      ACHILLES_SQL_ONLY: ${ACHILLES_SQL_ONLY}
    entrypoint: ["Rscript", "/postprocessing/achilles/scripts/${CDM_DATABASE_SCHEMA}.R" ]

  broadsea-run-dqd:
    profiles: [ "cdm-postprocessing", "dqd" ]
    build: 
      context: ./dqd
      secrets:
        - GITHUB_PAT
    platform: "linux/amd64"
    container_name: broadsea-run-dqd
    secrets:
      - CDM_CONNECTIONDETAILS_PASSWORD
    volumes:
      - jdbc-drivers-data:/jdbc
      - cdm-postprocessing-data:/postprocessing
      - ./postprocessing/init.R:/postprocessing/init.R
      - ./dqd/run_dqd.R:/postprocessing/dqd/scripts/${CDM_DATABASE_SCHEMA}.R
    environment:
      CDM_CONNECTIONDETAILS_DBMS: ${CDM_CONNECTIONDETAILS_DBMS}
      CDM_CONNECTIONDETAILS_USER: ${CDM_CONNECTIONDETAILS_USER}
      CDM_CONNECTIONDETAILS_SERVER: ${CDM_CONNECTIONDETAILS_SERVER}
      CDM_CONNECTIONDETAILS_PORT: ${CDM_CONNECTIONDETAILS_PORT}
      CDM_CONNECTIONDETAILS_EXTRA_SETTINGS: ${CDM_CONNECTIONDETAILS_EXTRA_SETTINGS}
      CDM_VERSION: ${CDM_VERSION}
      CDM_SOURCE_NAME: ${CDM_SOURCE_NAME}
      CDM_DATABASE_SCHEMA: ${CDM_DATABASE_SCHEMA}
      RESULTS_DATABASE_SCHEMA: ${RESULTS_DATABASE_SCHEMA}
      VOCAB_DATABASE_SCHEMA: ${VOCAB_DATABASE_SCHEMA}

      DQD_NUM_THREADS: ${DQD_NUM_THREADS}
      DQD_SQL_ONLY: ${DQD_SQL_ONLY}
      DQD_SQL_ONLY_UNION_COUNT: ${DQD_SQL_ONLY_UNION_COUNT}
      DQD_SQL_ONLY_INCREMENTAL_INSERT: ${DQD_SQL_ONLY_INCREMENTAL_INSERT}
      DQD_VERBOSE_MODE: ${DQD_VERBOSE_MODE}
      DQD_WRITE_TO_TABLE: ${DQD_WRITE_TO_TABLE}
      DQD_WRITE_TABLE_NAME: ${DQD_WRITE_TABLE_NAME}
      DQD_WRITE_TO_CSV: ${DQD_WRITE_TO_CSV}
      DQD_CSV_FILE: ${DQD_CSV_FILE}
      DQD_CHECK_LEVELS: ${DQD_CHECK_LEVELS}
      DQD_CHECK_NAMES: ${DQD_CHECK_NAMES}
      DQD_COHORT_DEFINITION_ID: ${DQD_COHORT_DEFINITION_ID}
      DQD_COHORT_DATABASE_SCHEMA: ${DQD_COHORT_DATABASE_SCHEMA}
      DQD_COHORT_TABLE_NAME: ${DQD_COHORT_TABLE_NAME}
      DQD_TABLES_TO_EXCLUDE: ${DQD_TABLES_TO_EXCLUDE}
      DQD_TABLE_CHECK_THRESHOLD_LOC: ${DQD_TABLE_CHECK_THRESHOLD_LOC}
      DQD_FIELD_CHECK_THRESHOLD_LOC: ${DQD_FIELD_CHECK_THRESHOLD_LOC}
      DQD_CONCEPT_CHECK_THRESHOLD_LOC: ${DQD_CONCEPT_CHECK_THRESHOLD_LOC}
    entrypoint: ["Rscript", "/postprocessing/dqd/scripts/${CDM_DATABASE_SCHEMA}.R" ]

  broadsea-run-aresindexer-only:
    profiles: [ "aresindexer" ]
    extends: 
      file: "./compose/aresindexer.yml"
      service: broadsea-run-aresindexer

  broadsea-run-aresindexer-after:
    profiles: [ "cdm-postprocessing" ]
    extends: 
      file: "./compose/aresindexer.yml"
      service: broadsea-run-aresindexer
    depends_on:
      broadsea-run-achilles:
        condition: service_completed_successfully
      broadsea-run-dqd:
        condition: service_completed_successfully

  broadsea-dbt:
    profiles: [ "dbt" ]
    image: ohdsi/broadsea-dbt
    container_name: broadsea-dbt
    platform: "linux/amd64"
    restart: unless-stopped
    volumes:
      - ${DBT_PROJECT_PATH}:/usr/app
      - ${DBT_PROFILE_PATH}:/root/.dbt/


  
  ### Perseus

  perseus-shareddb:
    profiles: [ "perseus-shareddb", "perseus" ]
    image: perseushub/shareddb:latest
    platform: "linux/amd64"
    container_name: perseus-shareddb
    restart: unless-stopped
    volumes:
      - perseus-shareddb:/data/postgres

  perseus-files-manager:
    profiles: [ "perseus-files-manager", "perseus" ]
    image: perseushub/files-manager:latest
    platform: "linux/amd64"
    container_name: perseus-files-manager
    restart: unless-stopped
    expose:
      - "10500:10500"
    environment:
      SPRING_PROFILES_ACTIVE: docker
      SPRING_DATASOURCE_URL: jdbc:postgresql://perseus-shareddb:5432/shared
    depends_on:
      - perseus-shareddb

  perseus-user:
    profiles: [ "perseus-user", "perseus" ]
    image: perseushub/user:latest
    platform: linux/amd64
    container_name: perseus-user
    environment:
      SMTP_SERVER: ${PERSEUS_SMTP_SERVER}
      SMTP_PORT: ${PERSEUS_SMTP_PORT}
      SMTP_EMAIL: ${PERSEUS_SMTP_EMAIL}
      SMTP_USER: ${PERSEUS_SMTP_USER}
      SMTP_PWD: ${PERSEUS_SMTP_PWD}
      USER_ENV: Docker
      TOKEN_SECRET_KEY: ${PERSEUS_TOKEN_SECRET_KEY}
      EMAIL_SECRET_KEY: ${PERSEUS_EMAIL_SECRET_KEY}
      SERVER_ADDRESS: ${BROADSEA_HOST}
    volumes:
      - ./perseus/user/config.py:/app/config.py
    expose:
      - "5001:5001"
    labels:
      - "traefik.enable=true"
    depends_on:
      - perseus-shareddb

  perseus-backend:
    profiles: [ "perseus-backend", "perseus" ]
    image: perseushub/backend:latest
    platform: linux/amd64
    container_name: perseus-backend
    environment:
      PERSEUS_ENV: Docker
    volumes:
      - ./perseus/backend/config.py:/app/config.py
    expose:
      - "5004:5004"
    depends_on:
      - perseus-shareddb
      - perseus-files-manager
  
  perseus-frontend:
    profiles: [ "perseus-frontend", "perseus" ]
    image: ohdsi/perseus-frontend:0.2.0
    platform: linux/amd64
    container_name: perseus-frontend
    expose:
      - "4200:4200"
    labels:
      - "traefik.enable=true"

  perseus-vocabularydb:
    profiles: [ "perseus-vocabularydb", "perseus" ]
    image: perseushub/vocabularydb:latest
    platform: linux/amd64
    container_name: perseus-vocabularydb
    healthcheck:
      test: [ "CMD", "pg_isready", "-q", "-d", "vocabulary", "-U", "admin" ]
      timeout: 60s
      interval: 30s
      retries: 10
    volumes:
      - perseus-vocabularydb:/data/postgres
      - ${PERSEUS_VOCAB_FILES_PATH}:/vocabulary
    expose:
      - "5431:5432"

  perseus-cdm-builder:
    profiles: [ "perseus-cdm-builder", "perseus" ]
    image: perseushub/cdm-builder:latest
    platform: linux/amd64
    container_name: perseus-cdm-builder
    expose:
      - "9000:9000"
    volumes:
      - ./perseus/cdm-builder/appsettings.Docker.json:/app/appsettings.Docker.json
    environment:
      - ASPNETCORE_ENVIRONMENT=Docker
    depends_on:
      - perseus-shareddb
      - perseus-files-manager
      - perseus-vocabularydb

  perseus-solr:
    profiles: [ "perseus-solr", "perseus" ]
    image: perseushub/solr:latest
    platform: linux/amd64
    container_name: perseus-solr
    expose:
      - "8983:8983"
    volumes:
      - perseus-solr:/var/solr
    depends_on:
      - perseus-vocabularydb
  
  perseus-athena:
    profiles: [ "perseus-athena", "perseus" ]
    image: perseushub/athena:latest
    platform: linux/amd64
    container_name: perseus-athena
    environment:
      ATHENA_ENV: Docker
    volumes:
      - ./perseus/athena/config.py:/app/config.py
    expose:
      - "5002:5002"
    depends_on:
      - perseus-solr


  perseus-usagi:
    profiles: [ "perseus-usagi", "perseus" ]
    image: perseushub/usagi:latest
    platform: linux/amd64
    command: python /app/main.py
    container_name: perseus-usagi
    environment:
      USAGI_ENV: Docker
    volumes:
      - ./perseus/usagi/config.py:/app/config.py
    expose:
      - "5003:5003"
    depends_on:
      - perseus-shareddb
      - perseus-solr

  perseus-r-serve:
    profiles: [ "perseus-r-serve", "perseus" ]
    image: perseushub/r-serve:latest
    platform: linux/amd64
    container_name: perseus-r-serve
    expose:
      - "6311:6311"
    depends_on:
      - perseus-shareddb
  
  perseus-data-quality-dashboard:
    profiles: [ "perseus-dqd", "perseus" ]
    image: perseushub/data-quality-dashboard:latest
    platform: linux/amd64
    container_name: perseus-data-quality-dashboard
    expose:
      - "8001:8001"
    environment:
      SPRING_PROFILES_ACTIVE: docker
      SPRING_DATASOURCE_URL: jdbc:postgresql://perseus-shareddb:5432/shared
      FILES_MANAGER_URL: http://perseus-files-manager:10500/files-manager
    depends_on:
      - perseus-shareddb
      - perseus-files-manager
      - perseus-r-serve

  perseus-swagger:
    profiles: [ "perseus-swagger", "perseus" ]
    image: perseushub/swagger:latest
    platform: linux/amd64
    container_name: perseus-swagger
    expose:
      - 8080:8080

  perseus-white-rabbit:
    profiles: [ "perseus-white-rabbit", "perseus" ]
    image: ohdsi/perseus-white-rabbit:latest
    platform: "linux/amd64"
    container_name: perseus-white-rabbit
    restart: unless-stopped
    expose:
      - "8000:8000"
    environment:
      SPRING_PROFILES_ACTIVE: docker
      SPRING_DATASOURCE_URL: jdbc:postgresql://perseus-shareddb:5432/shared
      files-manager-url: "http://perseus-files-manager:10500/files-manager"
    depends_on:
      - perseus-shareddb
      - perseus-files-manager

  broadsea-jupyter-notebook:
    profiles: [ "jupyter-notebook" ]
    image: quay.io/jupyter/datascience-notebook:latest
    platform: ${DOCKER_ARCH}
    restart: unless-stopped
    container_name: broadsea-jupyter-notebook
    environment:
      JUPYTERHUB_SERVICE_PREFIX: /jupyter/
      JUPYTERHUB_BASE_URL: ${HTTP_TYPE}://${BROADSEA_HOST}
    volumes:
      - jupyter-notebook:/home/jovyan/work:rw
    command:
      - jupyter-lab
      - --ip=*
      - --NotebookApp.token=
      - --NotebookApp.password=
      - --NotebookApp.base_url=/jupyter
    labels:
      - "traefik.enable=true"


  broadsea-pgadmin4:
    profiles: [ "pgadmin4" ]
    user: "5050:5050"
    image: dpage/pgadmin4:8.5
    platform: ${DOCKER_ARCH}
    secrets:
      - PGADMIN_DEFAULT_PASSWORD
    restart: unless-stopped
    container_name: broadsea-pgadmin4
    environment:
      PGADMIN_DEFAULT_EMAIL: ${PGADMIN_ADMIN_USER}
      PGADMIN_DEFAULT_PASSWORD_FILE: /run/secrets/PGADMIN_DEFAULT_PASSWORD
      SCRIPT_NAME: /pgadmin4
    volumes:
      - pgadmin-data:/var/lib/pgadmin
    labels:
      - "traefik.enable=true"


secrets:
  GITHUB_PAT:
    file: ${GITHUB_PAT_SECRET_FILE}
  WEBAPI_DATASOURCE_PASSWORD:
    file: ${WEBAPI_DATASOURCE_PASSWORD_FILE}
  SECURITY_LDAP_SYSTEM_PASSWORD:
    file: ${SECURITY_LDAP_SYSTEM_PASSWORD_FILE}
  SECURITY_DB_DATASOURCE_PASSWORD:
    file: ${SECURITY_DB_DATASOURCE_PASSWORD_FILE}
  SECURITY_AD_SYSTEM_PASSWORD:
    file: ${SECURITY_AD_SYSTEM_PASSWORD_FILE}
  SECURITY_OAUTH_GOOGLE_APISECRET:
    file: ${SECURITY_OAUTH_GOOGLE_APISECRET_FILE}
  SECURITY_OAUTH_FACEBOOK_APISECRET:
    file: ${SECURITY_OAUTH_FACEBOOK_APISECRET_FILE}
  SECURITY_OAUTH_GITHUB_APISECRET:
    file: ${SECURITY_OAUTH_GITHUB_APISECRET_FILE}
  SECURITY_SAML_KEYMANAGER_STOREPASSWORD:
    file: ${SECURITY_SAML_KEYMANAGER_STOREPASSWORD_FILE}
  SECURITY_SAML_KEYMANAGER_PASSWORDS_ARACHNENETWORK:
    file: ${SECURITY_SAML_KEYMANAGER_PASSWORDS_ARACHNENETWORK_FILE}
  HADES_PASSWORD:
    file: ${HADES_PASSWORD_FILE}
  SOLR_VOCAB_JDBC_PASSWORD:
    file: ${SOLR_VOCAB_JDBC_PASSWORD_FILE}
  VOCAB_PG_PASSWORD:
    file: ${VOCAB_PG_PASSWORD_FILE}
  OPENLDAP_ADMIN_PASSWORD:
    file: ${OPENLDAP_ADMIN_PASSWORD_FILE}
  OPENLDAP_ACCOUNT_PASSWORDS:
    file: ${OPENLDAP_ACCOUNT_PASSWORDS_FILE}
  PHOEBE_PG_PASSWORD:
    file: ${PHOEBE_PG_PASSWORD_FILE}
  UMLS_API_KEY:
    file: ${UMLS_API_KEY_FILE}
  CDM_CONNECTIONDETAILS_PASSWORD:
    file: ${CDM_CONNECTIONDETAILS_PASSWORD_FILE}
  WEBAPI_CDM_SNOWFLAKE_PRIVATE_KEY:
    file: ${WEBAPI_CDM_SNOWFLAKE_PRIVATE_KEY_FILE}
  PGADMIN_DEFAULT_PASSWORD:
    file: ${PGADMIN_DEFAULT_PASSWORD_FILE}