docker-compose.yml

# The reasons behind these settings are in doc/deployment-rationale.md; read the
# relevant section there before changing one. Instance-specific values go into
# docker-compose.override.yml and .env (see docker-compose.override.yml.template).
# The fleet deploys from nanopub-infrastructure/nanopub-query/; keep the two in sync.

services:
  query:
    build: .
    image: nanopub/query:${NANOPUB_QUERY_IMAGE_TAG:-latest}
    restart: unless-stopped
    ports:
      # Localhost only: no authentication, and /repo requests of every method
      # reach RDF4J (rationale: #ports-bound-to-localhost).
      - "127.0.0.1:9393:9393"
      # :9394 is only accessible from localhost as it is used for the /metrics endpoint
      - "127.0.0.1:9394:9394"
    volumes:
      # For the local nanopub loader (optional).
      # If not used, Query will load the nanopubs from the Registry with Jelly.
      - ./load:/app/load
    environment:
      - ENDPOINT_TYPE=rdf4j
      - ENDPOINT_BASE=http://rdf4j:8080/rdf4j-server/
      - REGISTRY_FIXED_URL=https://registry.knowledgepixels.com/
      - RDF4J_PROXY_HOST=rdf4j
      # Server-side SPARQL evaluation limit in seconds; 0 disables
      # (rationale: #query-timeout).
      - RDF4J_QUERY_TIMEOUT_SECONDS=${RDF4J_QUERY_TIMEOUT_SECONDS:-60}
      # Socket timeout (ms) for the app's own reads from RDF4J; keep in step with
      # the default in Utils.getHttpRequestConfig (rationale: #fetching-socket-timeout).
      - NANOPUB_QUERY_FETCHING_SOCKET_TIMEOUT=${NANOPUB_QUERY_FETCHING_SOCKET_TIMEOUT:-30000}
      # One-shot repair: re-stream the whole registry at startup. Only on a wiped
      # or out-of-rotation instance, for one `up -d` (rationale: #force_resync).
      - FORCE_RESYNC=${FORCE_RESYNC:-false}
    # Stop the app before RDF4J, so no write is in flight when the store goes down
    # (rationale: #shutdown-order-and-grace-periods).
    depends_on:
      - rdf4j
    # Must stay above NANOPUB_QUERY_SHUTDOWN_QUIESCE_SECONDS (90 s); raise both
    # together (rationale: #shutdown-order-and-grace-periods).
    stop_grace_period: 150s
    logging:
      options:
        max-size: "10m"
        max-file: "3"

  rdf4j:
    # rdf4j 6.0.0 with the eclipse-rdf4j/rdf4j#5974 fixes. Neither stock 6.0.0 (store
    # corruption) nor 6.1.0 (query-planning regression) is safe for this workload;
    # 5.x -> 6.x needs a wipe and re-ingest (rationale: #rdf4j-version). Override
    # RDF4J_IMAGE and RDF4J_IMAGE_TAG together: official releases are published as
    # eclipse/rdf4j-workbench.
    image: ${RDF4J_IMAGE:-nanopub/rdf4j-workbench}:${RDF4J_IMAGE_TAG:-6.0.0-lmdbpool4}
    restart: unless-stopped
    # Root, so init.sh can install curl and re-chown the volumes; it drops to the
    # tomcat user before starting the JVM.
    user: "0"
    environment:
      # Pool sizes for federated SERVICE calls: lowering them makes the federation
      # deadlock MORE likely (rationale: #federation-connection-pool-and-tomcat-threads).
      # OOM handling, heap size and lock diagnostics: #jvm-options-for-rdf4j.
      - JAVA_OPTS=-XX:+ExitOnOutOfMemoryError -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=/var/info/ -XX:MaxRAMPercentage=${RDF4J_MAX_RAM_PERCENTAGE:-50} -XX:+PrintConcurrentLocks -Dorg.eclipse.rdf4j.client.http.connectionTimeout=10000 -Dorg.eclipse.rdf4j.client.http.connectionRequestTimeout=10000 -Dorg.eclipse.rdf4j.client.http.socketTimeout=10000 -Dorg.eclipse.rdf4j.client.http.maxConnPerRoute=${RDF4J_MAX_CONN_PER_ROUTE:-120} -Dorg.eclipse.rdf4j.client.http.maxConnTotal=${RDF4J_MAX_CONN_TOTAL:-240}
      # Tomcat worker threads (set by init.sh); must stay >= 2x maxConnPerRoute.
      - RDF4J_TOMCAT_MAX_THREADS=${RDF4J_TOMCAT_MAX_THREADS:-240}
      # For the healthcheck's federation probe; explicitly empty disables it.
      - NANOPUB_QUERY_INTERNAL_URL=${NANOPUB_QUERY_INTERNAL_URL-http://query:9393/}
      # Whether a failing healthcheck may restart Tomcat; off by default
      # (rationale: #healthcheck).
      - RDF4J_HEALTHCHECK_RESTART=${RDF4J_HEALTHCHECK_RESTART:-off}
    volumes:
      - ./data/rdf4j/data:/var/rdf4j
      - ./data/rdf4j/logs:/usr/local/tomcat/logs
      - ./data/info:/var/info
      - ./entrypoint:/var/entrypoint
    ports:
      # Localhost only: no authentication, and every repository is writable
      # (rationale: #ports-bound-to-localhost).
      - "127.0.0.1:8081:8080"
    entrypoint: /var/entrypoint/init.sh
    # A clean shutdown closes thousands of LMDB repos and takes ~100 s
    # (rationale: #shutdown-order-and-grace-periods).
    stop_grace_period: 120s
    healthcheck:
        # Direct-query probe plus federation-route probe; restarts are suppressed
        # unless RDF4J_HEALTHCHECK_RESTART=on (rationale: #healthcheck).
        test: |
          restart_tomcat() {
            if [ "$$RDF4J_HEALTHCHECK_RESTART" != "on" ]; then
              date >> /var/info/restart-suppressed
              return
            fi
            if [ -f /var/info/restart ]; then
              last_s=$$(date -d "$$(tail -1 /var/info/restart)" +%s 2>/dev/null || echo 0)
              if [ $$(( $$(date +%s) - last_s )) -lt 600 ]; then
                return
              fi
            fi
            date >> /var/info/restart
            pkill -15 java
            i=0
            while [ $$i -lt 12 ] && pgrep java > /dev/null; do
              sleep 5
              i=$$((i + 1))
            done
            if pgrep java > /dev/null; then
              pkill -9 java
            fi
          }
          if ! curl -fsS --retry 2 --max-time 10 --retry-delay 2 --retry-max-time 10 --retry-connrefused \
              "http://localhost:8080/rdf4j-server/repositories/full?query=select%2Awhere%7B%3Fs%3Cx%3A%3E%3Fo%7Dlimit1" > /dev/null; then
            if [ -f /var/info/ready ]; then
              restart_tomcat
            fi
            exit 1
          fi
          touch /var/info/ready
          if [ -n "$$NANOPUB_QUERY_INTERNAL_URL" ]; then
            if ! curl -fsS --retry 2 --max-time 12 --retry-delay 2 \
                --data-urlencode "query=select ?s where { service <$${NANOPUB_QUERY_INTERNAL_URL}repo/meta> { select ?s where { ?s ?p ?o } limit 1 } }" \
                "http://localhost:8080/rdf4j-server/repositories/spaces" > /dev/null; then
              date >> /var/info/federation-restart
              restart_tomcat
              exit 1
            fi
          fi
          exit 0
        interval: 60s
        timeout: 60s
        start_period: 300s