docker-compose.yml

services:

  biosamples-webapps-core:
    build: .
    image: biosamples:latest
    mem_limit: 1g
    restart: on-failure:5
    depends_on:
      mongo:
        condition: service_healthy
      schema-store:
        condition: service_started
      json-schema-validator:
        condition: service_started
      rabbitmq:
        condition: service_started
      solr:
        condition: service_started
      neo4j:
        condition: service_started
    links:
    - solr
    - mongo
    - rabbitmq
    - neo4j
    - json-schema-validator
    - schema-store
    volumes:
    - logs:/logs
    - "/mnt/c/Users/dgupta/secrets:/secrets"
    command:
    - java
    - -jar
    - webapps-core-5.3.15-SNAPSHOT.war
    environment:
    - env=local
    #application properties
    - biosamples.bulksubmisison.webin.superuser.validation=true
    #configure other services
    - spring.data.solr.host=http://solr:8983/solr
    - spring.data.mongodb.uri=mongodb://mongo:27017/biosamples
    - spring.data.mongodb.auto-index-creation=true
    - biosamples.mongo.sample.writeConcern=1
    - BIOSAMPLES_NEO_URL=bolt://neo4j:7687
    - biosamples.schema.validator.url=http://json-schema-validator:3020/validate
    - biosamples.schema.store.url=https://wwwdev.ebi.ac.uk/biosamples/schema-store
    - biosamples.search.host=biosamples-search
    - SPRING_RABBITMQ_HOST=rabbitmq
    - SPRING_RABBITMQ_PUBLISHER-CONFIRMS=true
    - SPRING_RABBITMQ_PUBLISHER-RETURNS=true
    - SPRING_RABBITMQ_LISTENER_SIMPLE_PREFETCH=100
    - SPRING_RABBITMQ_LISTENER_SIMPLE_TRANSACTION-SIZE=25
    - spring.jackson.serialization-inclusion=non_null
    - spring.jackson.serialization.WRITE_NULL_MAP_VALUES=false
    - spring.jackson.serialization.indent_output=true
    - management.health.solr.enabled=false
    - management.health.neo4j.enabled=false
    - management.endpoint.health.show-details=always
    - management.metrics.enable.all=false
    - management.metrics.enable.http=true
    - management.metrics.web.server.request.autotime.percentiles-histogram=true
    - management.metrics.web.server.request.autotime.percentiles=0.50,0.90,0.99
    #buckets(in ms to match base Time Unit)
    - management.metrics.distribution.sla.http.server.requests.duration.buckets=50,100,250,500,1000,5000,10000,15000,30000,60000,120000,180000,240000,300000
    # Micrometer
    - spring.cloud.gcp.project-id=prj-int-dev-omics-apps-mon
    - management.metrics.export.stackdriver.projectId=prj-int-dev-omics-apps-mon
    - management.metrics.export.stackdriver.useSemanticMetricTypes=true
    - management.metrics.export.stackdriver.step=5m
    #Configure root path to server from
    - server.servlet.context-path=/biosamples
    - server.context-path=/biosamples
    #Enable use behind a proxy with original urls
    - server.use-forward-headers=true
    # show error messages
    - server.error.include-binding-errors=always
    - server.error.include-message=always
    # server session timeout
    - server.servlet.session.timeout=1m
    #Improve logging
    - LOGGING_FILE=/logs/webapps-core.log
    - server.tomcat.accesslog.enabled=true
    - server.tomcat.accesslog.directory=/logs
    - server.tomcat.accesslog.prefix=webapps-core.access
    - server.tomcat.accesslog.pattern=- %l %u %t \"%r\" %s %b %D %{Content-Type}o
    #Enable gzip compression of responses
    - server.compression.enabled=true
    - server.compression.mime-types=application/json,application/hal+json,application/xml,text/html,application/javascript,text/css
    #Don't waste CPU compressing very small responses
    - server.compression.min-response-size=2048
    # Charset of HTTP requests and responses. Added to the "Content-Type" header if not set explicitly.
    - spring.http.encoding.charset=UTF-8
    # Enable http encoding support.
    - spring.http.encoding.enabled=true
    # Force the encoding to the configured charset on HTTP requests and responses.
    - spring.http.encoding.force=true
    - spring.mvc.pathmatch.use-suffix-pattern=true
    - spring.mvc.pathmatch.matching-strategy=ant-path-matcher
    # File upload
    - spring.servlet.multipart.location=/data/upload_tmp
    # gcp monitoring servoce account key.
    - GOOGLE_APPLICATION_CREDENTIALS=/secrets/prj-int-dev-omics-apps-mon-1fba094e79b2.json
    ports:
    - 8081:8080
    - 8000:8000

  biosamples-webapps-core-v2:
    build: .
    image: biosamples:latest
    mem_limit: 1g
    restart: on-failure:5
    depends_on:
      mongo:
        condition: service_healthy
      schema-store:
        condition: service_started
      json-schema-validator:
        condition: service_started
      rabbitmq:
        condition: service_started
    links:
      - mongo
      - json-schema-validator
      - schema-store
      - rabbitmq
    volumes:
      - logs:/logs
      - "/mnt/c/Users/dgupta/secrets:/secrets"
    command:
      - java
      - -jar
      - webapps-core-v2-5.3.15-SNAPSHOT.jar
    environment:
      #application properties
      - biosamples.bulksubmisison.webin.superuser.validation=true
      #configure other services
      - spring.data.solr.host=http://solr:8983/solr
      - spring.data.mongodb.uri=mongodb://mongo:27017/biosamples
      - spring.data.mongodb.auto-index-creation=true
      - SPRING_RABBITMQ_HOST=rabbitmq
      - SPRING_RABBITMQ_PUBLISHER-CONFIRMS=true
      - SPRING_RABBITMQ_PUBLISHER-RETURNS=true
      - SPRING_RABBITMQ_LISTENER_SIMPLE_PREFETCH=100
      - SPRING_RABBITMQ_LISTENER_SIMPLE_TRANSACTION-SIZE=25
      - BIOSAMPLES_NEO_URL=bolt://neo4j:7687
      - biosamples.schema.validator.url=http://json-schema-validator:3020/validate
      - biosamples.schema.store.url=https://wwwdev.ebi.ac.uk/biosamples/schema-store
      - spring.jackson.serialization-inclusion=non_null
      - spring.jackson.serialization.WRITE_NULL_MAP_VALUES=false
      - spring.jackson.serialization.indent_output=true
      - management.health.solr.enabled=false
      - management.health.neo4j.enabled=false
      - management.health.rabbit.enabled=false
      - management.endpoint.health.show-details=always
      - management.metrics.enable.all=false
      - management.metrics.enable.http=true
      - management.metrics.web.server.request.autotime.percentiles-histogram=true
      - management.metrics.web.server.request.autotime.percentiles=0.50,0.90,0.99
      #buckets(in ms to match base Time Unit)
      - management.metrics.distribution.sla.http.server.requests.duration.buckets=50,100,250,500,1000,5000,10000,15000,30000,60000,120000,180000,240000,300000
      # Micrometer
      - spring.cloud.gcp.project-id=prj-int-dev-omics-apps-mon
      - management.metrics.export.stackdriver.projectId=prj-int-dev-omics-apps-mon
      - management.metrics.export.stackdriver.useSemanticMetricTypes=true
      - management.metrics.export.stackdriver.step=5m
      #Configure root path to server from
      - server.servlet.context-path=/biosamples/v2
      - server.context-path=/biosamples/v2
      # show error messages
      - server.error.include-binding-errors=always
      - server.error.include-message=always
      #Enable use behind a proxy with original urls
      - server.use-forward-headers=true
      #Improve logging
      - LOGGING_FILE=/logs/webapps-core-v2.log
      - server.tomcat.accesslog.enabled=true
      - server.tomcat.accesslog.directory=/logs
      - server.tomcat.accesslog.prefix=webapps-core.access
      - server.tomcat.accesslog.pattern=- %l %u %t \"%r\" %s %b %D %{Content-Type}o
      #Enable gzip compression of responses
      - server.compression.enabled=true
      - server.compression.mime-types=application/json,application/hal+json,application/xml,text/html,application/javascript,text/css
      #Don't waste CPU compressing very small responses
      - server.compression.min-response-size=2048
      # Charset of HTTP requests and responses. Added to the "Content-Type" header if not set explicitly.
      - spring.http.encoding.charset=UTF-8
      # Enable http encoding support.
      - spring.http.encoding.enabled=true
      # Force the encoding to the configured charset on HTTP requests and responses.
      - spring.http.encoding.force=true
      - spring.mvc.pathmatch.use-suffix-pattern=true
      - spring.mvc.pathmatch.matching-strategy=ant-path-matcher
      # gcp monitoring servoce account key.
      - GOOGLE_APPLICATION_CREDENTIALS=/secrets/prj-int-dev-omics-apps-mon-1fba094e79b2.json
    ports:
      - 8082:8080

  biosamples-agents-solr:
    image: biosamples:latest
    mem_limit: 500m
    links:
    - solr
    - rabbitmq
    volumes:
    - logs:/logs
    command:
    - java
    - -jar
    - agents-solr-5.3.15-SNAPSHOT.jar
    environment:
    - SPRING_RABBITMQ_HOST=rabbitmq
    - SPRING_RABBITMQ_PUBLISHER-CONFIRMS=true
    - SPRING_RABBITMQ_PUBLISHER-RETURNS=true
    - SPRING_RABBITMQ_LISTENER_CONCURRENCY=16
    - SPRING_RABBITMQ_LISTENER_MAX-CONCURRENCY=32
    - SPRING_RABBITMQ_LISTENER_SIMPLE_PREFETCH=128
    - SPRING_RABBITMQ_LISTENER_SIMPLE_TRANSACTION-SIZE=32
    - SPRING_DATA_SOLR_HOST=http://solr:8983/solr
    - BIOSAMPLES_AGENT_SOLR_STAYALIVE=true
    - LOGGING_FILE=/logs/agents-solr.log
    - spring.cache.cache-names=ols_ancestors_synonyms
    - spring.cache.caffeine.spec=maximumSize=500,expireAfterAccess=600s

  biosamples-agents-upload-workers:
    image: biosamples:latest
    mem_limit: 500m
    links:
      - rabbitmq
    volumes:
      - logs:/logs
    command:
      - java
      - -jar
      - agents-uploadworkers-5.3.15-SNAPSHOT.jar
    environment:
      - SPRING_RABBITMQ_HOST=rabbitmq
      - SPRING_RABBITMQ_PUBLISHER-CONFIRMS=true
      - SPRING_RABBITMQ_PUBLISHER-RETURNS=true
      - SPRING_RABBITMQ_LISTENER_CONCURRENCY=16
      - SPRING_RABBITMQ_LISTENER_MAX-CONCURRENCY=32
      - SPRING_RABBITMQ_LISTENER_SIMPLE_PREFETCH=128
      - SPRING_RABBITMQ_LISTENER_SIMPLE_TRANSACTION-SIZE=32
      - spring.data.mongodb.uri=mongodb://mongo:27017/biosamples
      - LOGGING_FILE=/logs/agents-uploadworkers.log
      - spring.cache.cache-names=ols_ancestors_synonyms
      - spring.cache.caffeine.spec=maximumSize=500,expireAfterAccess=600s

  biosamples-pipelines-ena:
    image: biosamples:latest
    mem_limit: 500m
    volumes:
    - logs:/logs
    links:
    - biosamples-webapps-core
    command:
    - java
    - -jar
    - pipelines-ena-5.3.15-SNAPSHOT.jar
    environment:
    - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
    - LOGGING_FILE=/logs/pipelines-ena.log

  biosamples-pipelines-ncbi:
    image: biosamples:latest
    mem_limit: 500m
    volumes:
    - logs:/logs
    links:
    - biosamples-webapps-core
    command:
    - java
    - -jar
    - pipelines-ncbi-5.3.15-SNAPSHOT.jar
    environment:
    - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
    - LOGGING_FILE=/logs/pipelines-ncbi.log

  biosamples-pipelines-accession:
    image: biosamples:latest
    mem_limit: 500m
    volumes:
    - logs:/logs
    links:
    - biosamples-webapps-core
    command:
    - java
    - -jar
    - pipelines-accession-5.3.15-SNAPSHOT.jar
    environment:
    - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
    - LOGGING_FILE=/logs/pipelines-accession.log

  biosamples-pipelines-copydown:
    image: biosamples:latest
    mem_limit: 500m
    volumes:
    - logs:/logs
    links:
    - biosamples-webapps-core
    command:
    - java
    - -jar
    - pipelines-copydown-5.3.15-SNAPSHOT.jar
    environment:
    - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
    - LOGGING_FILE=/logs/pipelines-copydown.log

  biosamples-pipelines-curation:
    volumes:
    - logs:/logs
    image: biosamples:latest
    mem_limit: 500m
    links:
    - biosamples-webapps-core
    command:
    - java
    - -jar
    - pipelines-curation-5.3.15-SNAPSHOT.jar
    environment:
    - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
    - LOGGING_FILE=/logs/pipelines-curation.log
    - spring.cache.cache-names=ols_short
    - spring.cache.caffeine.spec=maximumSize=50000

  biosamples-pipelines-zooma:
    volumes:
    - logs:/logs
    image: biosamples:latest
    mem_limit: 500m
    links:
    - biosamples-webapps-core
    command:
    - java
    - -jar
    - pipelines-zooma-5.3.15-SNAPSHOT.jar
    environment:
    - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
    - LOGGING_FILE=/logs/pipelines-zooma.log
    - spring.cache.cache-names=zooma,ols_short
    - spring.cache.caffeine.spec=maximumSize=50000

  biosamples-pipelines-reindex:
    volumes:
    - logs:/logs
    image: biosamples:latest
    mem_limit: 500m
    links:
    - biosamples-webapps-core
    command:
    - java
    - -jar
    - pipelines-reindex-5.3.15-SNAPSHOT.jar
    environment:
    - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
    - LOGGING_FILE=/logs/pipelines-reindex.log
    - spring.data.mongodb.uri=mongodb://mongo/biosamples
    - SPRING_RABBITMQ_HOST=rabbitmq

  biosamples-pipelines-export:
    volumes:
    - logs:/logs
    - ./docker/export:/export
    image: biosamples:latest
    mem_limit: 500m
    links:
    - biosamples-webapps-core
    command:
    - java
    - -jar
    - pipelines-export-5.3.15-SNAPSHOT.jar
    - --gzip
    - /export/export.json.gzip
    environment:
    - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
    - LOGGING_FILE=/logs/pipelines-export.log

  biosamples-integration:
    volumes:
    - logs:/logs
    image: biosamples:latest
    mem_limit: 500m
    depends_on:
      mongo:
        condition: service_healthy
      biosamples-webapps-core:
        condition: service_started
      biosamples-webapps-core-v2:
        condition: service_started
    links:
    - biosamples-webapps-core
    - neo4j
    - mongo
    command:
    - java
    - -jar
    - integration-5.3.15-SNAPSHOT.jar
    environment:
    - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
    - BIOSAMPLES_CLIENT_URI_V2=http://biosamples-webapps-core-v2:8080/biosamples/v2
    - LOGGING_FILE=/logs/integration.log
    - BIOSAMPLES_LEGACYAPIKEY=fooqwerty
    - BIOSAMPLES_NEO_URL=bolt://neo4j:7687
    - spring.data.mongodb.uri=mongodb://mongo:27017/biosamples

  json-schema-validator:
    image: quay.io/ebi-ait/biovalidator:2.0.1
    ports:
      - 3020:3020

  schema-store:
    image: biosamples/json-schema-store:1.1.0
    depends_on:
      mongo:
        condition: service_healthy
      json-schema-validator:
        condition: service_started
    ports:
      - 8085:8085
    links:
      - mongo
      - json-schema-validator
    environment:
      - spring.data.mongodb.uri=mongodb://mongo:27017/schemastore
      - elixirValidator.hostUrl=http://json-schema-validator:3020/validate

  mongo:
    image: mongo:4.4.22
    command: ["mongod", "--bind_ip_all"]
    mem_limit: 2g
    healthcheck:
      test: ["CMD", "mongo", "--quiet", "--eval", "db.runCommand({ ping: 1 }).ok"]
      interval: 10s
      timeout: 5s
      retries: 10
      start_period: 20s
    volumes:
    - mongo_data:/data/db
    - ./docker/mongoarchive:/mongoarchive
    ports:
    - 27017:27017

  rabbitmq:
    image: rabbitmq:3.10.7-management-alpine
    mem_limit: 1g
    hostname: biosamples-rabbitmq
    ports:
    - 5672:5672
    - 15672:15672
    volumes:
    - rabbitmq_data:/var/lib/rabbitmq/mnesia

  solr:
    image: solr:8.11.2
    mem_limit: 1g
    ports:
    - 8983:8983
    volumes:
    - solr_data:/var/solr
    environment:
    - VERBOSE=yes
    - SOLR_HEAP=1g
    entrypoint:
    - docker-entrypoint.sh
    - solr-precreate
    - samples

  neo4j:
    image: neo4j:4.0.3
    mem_limit: 1g
    ports:
      - 7474:7474
      - 7687:7687
    environment:
      - NEO4J_AUTH=neo4j/neo5j
    volumes:
      - neo_plugins:/plugins
      - neo_data:/data
      - neo_import:/import
      - logs:/logs


  biosamples-search:
    image: biosamples-search:latest
    ports:
      - "8083:8080"
      - "9090:9090"
    environment:
      - spring.elasticsearch.username=elastic
      - spring.elasticsearch.password=elastic
      - spring.elasticsearch.uris=http://elastic:9200
      - spring.rabbitmq.host=rabbitmq
    links:
      - elastic
  elastic-setup:
    image: docker.elastic.co/elasticsearch/elasticsearch:${STACK_VERSION}
    user: "0"
    command: >
      bash -c '
        if [ x${ELASTIC_PASSWORD} == x ]; then
          echo "Set the ELASTIC_PASSWORD environment variable in the .env file";
          exit 1;
        elif [ x${KIBANA_PASSWORD} == x ]; then
          echo "Set the KIBANA_PASSWORD environment variable in the .env file";
          exit 1;
        fi;
        echo "Waiting for Elasticsearch availability";
        until curl -s http://elastic:9200 | grep -q "missing authentication credentials"; do sleep 30; done;
        echo "Setting kibana_system password";
        until curl -s -X POST -u "elastic:${ELASTIC_PASSWORD}" -H "Content-Type: application/json" http://elastic:9200/_security/user/kibana_system/_password -d "{\"password\":\"${KIBANA_PASSWORD}\"}" | grep -q "^{}"; do sleep 10; done;
        echo "All done!";
      '
    healthcheck:
      test: [ "CMD-SHELL", "[ -f config/certs/es01/es01.crt ]" ]
      interval: 1s
      timeout: 5s
      retries: 120
  elastic:
    image: docker.elastic.co/elasticsearch/elasticsearch:${STACK_VERSION}
    volumes:
      - es_data1:/usr/share/elasticsearch/data
    ports:
      - ${ES_PORT}:9200
    environment:
      - node.name=elastic
      - discovery.type=single-node
      - ELASTIC_PASSWORD=${ELASTIC_PASSWORD}
      - bootstrap.memory_lock=true
      - xpack.security.http.ssl.enabled=false
    mem_limit: 1g
    ulimits:
      memlock:
        soft: -1
        hard: -1
    healthcheck:
      test:
        [
          "CMD-SHELL",
          "curl -s http://localhost:9200 | grep -q 'missing authentication credentials'",
        ]
      interval: 10s
      timeout: 10s
      retries: 120


volumes:
  solr_data: null
  mongo_data: null
  rabbitmq_data: null
  logs: null
  neo_plugins: null
  neo_data: null
  neo_import: null
  es_data1:
    driver: local
  kibana_data:
    driver: local