docker-compose.yml

version: '3'

services:
  # A local instance of dynamodb, based on sqlite which persists data between instances
  # dynamodb:
  #   image: amazon/dynamodb-local
  #   hostname: dynamodb
  #   container_name: dynamodb
  #   ports:
  #     # map port 8000 in the container to port 8000 in the host
  #     - "8000:8000"
  #   # tell dynamo to persist data  
  #   command: -jar DynamoDBLocal.jar -sharedDb -dbPath /home/dynamodblocal/data/
  #   # map a directory in the host OS to this container
  #   volumes:
  #    - ./data/dynamodb:/home/dynamodblocal/data
  # Run scylladb in dynamodb mode to provide a performant local store. Save data to ./data/scylla
  dynamodb:
    image: scylladb/scylla
    hostname: dynamodb
    container_name: dynamodb
    ports:
      # map port 8000 in the container to port 8000 in the host
      - "8000:8000"
    # tell scylla to run in dynamodb mode, see http://scylla.docs.scylladb.com/master/alternator/alternator.html#write-isolation-policies
    command: --smp 1 --memory=750M --overprovisioned 1 --alternator-port=8000 --alternator-write-isolation=only_rmw_uses_lwt
    # map a directory in the host OS to this container
    volumes:
     - ./data/scylla:/var/lib/scylla  
  # The therapy service
  therapy:
    build: therapy-normalization
    hostname: therapy
    container_name: therapy
    environment: 
      - THERAPY_NORM_DB_URL=http://dynamodb:8000
      # read from .env file
      - RXNORM_API_KEY=${RXNORM_API_KEY}
      - AWS_DEFAULT_REGION=${AWS_DEFAULT_REGION:-dev}
      - AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID:-foo}
      - AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY:-bar}
      - DRUGBANK_USER=${DRUGBANK_USER}
      - DRUGBANK_PWD=${DRUGBANK_PWD}
    ports:
      # map port 80 in the container to free port in the host
      - "8001:80"
    volumes:
     - ./data/therapy:/app/therapy/data          
    depends_on:
      - "dynamodb"  
  # The gene service
  gene:
    build: gene-normalization
    hostname: gene
    container_name: gene
    environment: 
      - GENE_NORM_DB_URL=http://dynamodb:8000
      # read from .env file
      - AWS_DEFAULT_REGION=${AWS_DEFAULT_REGION:-dev}
      - AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID:-foo}
      - AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY:-bar}
    ports:
      # map port 80 in the container to free port in the host
      - "8002:80"
    depends_on:
      - "dynamodb"
    volumes:
     - ./data/gene:/app/gene/data
  # The variant service
  variant:
    build: variant-normalization
    hostname: variant
    container_name: variant
    environment:
      # variant shares gene's db 
      - GENE_NORM_DB_URL=http://dynamodb:8000
      # read from .env file
      - AWS_DEFAULT_REGION=${AWS_DEFAULT_REGION:-dev}
      - AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID:-foo}
      - AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY:-bar}
    ports:
      # map port 80 in the container to free port in the host
      - "8003:80"
    depends_on:
      - "dynamodb"
    volumes:
     # The variant service has packaged data at variant/data,
     # so we do not map a host directory to variant/data.
     # We do share seqrepo already harvested for gene
     - ./data/gene/seqrepo:/app/variant/data/seqrepo
  # The disease service
  disease:
    build: disease-normalization
    hostname: disease
    container_name: disease
    environment: 
      - DISEASE_NORM_DB_URL=http://dynamodb:8000
      # read from .env file
      - AWS_DEFAULT_REGION=${AWS_DEFAULT_REGION:-dev}
      - AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID:-foo}
      - AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY:-bar}
    ports:
      # map port 80 in the container to free port in the host
      - "8004:80"
    depends_on:
      - "dynamodb"
    volumes:
     - ./data/disease:/app/disease/data
  # The neo4j service see https://github.com/grand-stack/grand-stack-starter
  neo4j:
    build: ./neo4j
    # image: neo4j:4.2.5
    volumes:
      - ./data/neo4j:/data
      # wget https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/4.2.5/apoc-4.2.5-all.jar
      # - ./data/neo4j-plugins:/plugins
    ports:
      - 7474:7474
      - 7687:7687
    environment:
      - NEO4J_dbms_security_procedures_unrestricted=apoc.*
      - NEO4J_apoc_import_file_enabled=true
      - NEO4J_apoc_export_file_enabled=true
      # - NEO4J_dbms_shell_enabled=true
      - NEO4J_apoc_import_file_use__neo4j__config=true
      - NEO4JLABS_PLUGINS=["apoc"]
  # The metakb service
  metakb:
    build: metakb
    hostname: metakb
    container_name: metakb
    environment: 
      - GENE_NORM_DB_URL=http://dynamodb:8000
      - THERAPY_NORM_DB_URL=http://dynamodb:8000
      - DISEASE_NORM_DB_URL=http://dynamodb:8000
      # read from .env file
      - AWS_DEFAULT_REGION=${AWS_DEFAULT_REGION:-dev}
      - AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID:-foo}
      - AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY:-bar}
      - METAKB_DB_URL=bolt://neo4j:7687
      - METAKB_DB_USERNAME=${METAKB_DB_USERNAME}
      - METAKB_DB_PASSWORD=${METAKB_DB_PASSWORD}
    ports:
      # map port 80 in the container to free port in the host
      - "8005:80"
    depends_on:
      - "neo4j"
      - "disease"
      - "variant"
      - "gene"
      - "therapy"      
    volumes:
     - ./metakb/metakb:/app/metakb
     - ./data/metakb:/app/metakb/data
     - ./data/therapy:/app/therapy/data          
     - ./data/gene:/app/gene/data
     - ./data/disease:/app/disease/data

  # A generic python instance to run tests
  test:
    build: test
    hostname: test
    container_name: test
    volumes:
    # map tests source so we can add/modify tests w/out needing to re-build
     - ./test/tests:/app/tests
    depends_on:
      - "disease"
      - "variant"
      - "gene"
      - "therapy"