docker-compose.yaml

# MYSQL_VER=8.0 docker compose up -d
version: "2.4"
services:
  db:
    image: datajoint/mysql:${MYSQL_VER}
    environment:
      - MYSQL_ROOT_PASSWORD=${PHARUS_PASSWORD}
    healthcheck:
      test: ["CMD", "mysqladmin", "ping", "-h", "localhost"]
      timeout: 30s
      retries: 5
      interval: 15s
  pharus:
    depends_on:
      db:
        condition: service_healthy
      fakeservices.datajoint.io:
        condition: service_healthy
    image: datajoint/pharus:0.8.0
    environment:
      - PHARUS_SPEC_PATH=/main/specs/sciviz_spec.yaml # SciViz spec file location
      - PHARUS_HOST
      - PHARUS_USER
      - PHARUS_PASSWORD
    volumes:
      - ./sciviz_spec.yaml:/main/specs/sciviz_spec.yaml # mount SciViz spec file
      - ./initialize.ipynb:/main/initialize.ipynb # initialize test pipeline
      - ./pip_requirements.txt:/tmp/pip_requirements.txt # dependencies for test pipeline
    command:
      - sh
      - -c
      - |
        set -e
        # initialize test data
        ipython --TerminalIPythonApp.file_to_run=initialize.ipynb
        # live reload
        pharus_update() {
            sleep 2  # delaying to ensure pharus is up
            [ -z "$$PRIMARY_PID" ] || kill $$PRIMARY_PID || echo "restarting"
            export DEBUG=1
            export FLASK_ENV=development
            pharus &
            PRIMARY_PID=$$!
        }
        pharus_update
        echo "[$$(date -u '+%Y-%m-%d %H:%M:%S')][DataJoint]: Monitoring Pharus updates..."
        INIT_TIME=$$(date +%s)
        LAST_MOD_TIME=$$(date -r $$PHARUS_SPEC_PATH +%s)
        DELTA=$$(expr $$LAST_MOD_TIME - $$INIT_TIME)
        while true; do
           CURR_LAST_MOD_TIME=$$(date -r $$PHARUS_SPEC_PATH +%s)
           CURR_DELTA=$$(expr $$CURR_LAST_MOD_TIME - $$INIT_TIME)
           if [ "$$DELTA" -lt "$$CURR_DELTA" ]; then
               echo "[$$(date -u '+%Y-%m-%d %H:%M:%S')][DataJoint]: Reloading Pharus since \`$$DJSCIVIZ_SPEC_PATH\` changed."
               pharus_update
               DELTA=$$CURR_DELTA
           else
               sleep 1
           fi
        done
  sci-viz:
    image: datajoint/sci-viz:1.1.0
    environment:
      - REACT_APP_DJSCIVIZ_BACKEND_PREFIX=/api # Pharus API prefix
      - DJSCIVIZ_SPEC_PATH=sciviz_spec.yaml # SciViz spec file location
      - NODE_OPTIONS="--max-old-space-size=4000" # increase build memory for larger apps
    volumes:
      - ./sciviz_spec.yaml:/main/sciviz_spec.yaml # mount SciViz spec file
    command:
      - sh
      - -c
      - |
        set -e
        # live reload
        sciviz_update() {
            sleep 3  # delaying to ensure pharus is up
            [ -z "$$PRIMARY_PID" ] || kill $$PRIMARY_PID || echo "restarting"
            python frontend_gen.py
            yarn run start &
            PRIMARY_PID=$$!
        }
        sciviz_update
        echo "[$$(date -u '+%Y-%m-%d %H:%M:%S')][DataJoint]: Monitoring SciViz updates..."
        INIT_TIME=$$(date +%s)
        LAST_MOD_TIME=$$(date -r $$DJSCIVIZ_SPEC_PATH +%s)
        DELTA=$$(expr $$LAST_MOD_TIME - $$INIT_TIME)
        while true; do
           CURR_LAST_MOD_TIME=$$(date -r $$DJSCIVIZ_SPEC_PATH +%s)
           CURR_DELTA=$$(expr $$CURR_LAST_MOD_TIME - $$INIT_TIME)
           if [ "$$DELTA" -lt "$$CURR_DELTA" ]; then
               echo "[$$(date -u '+%Y-%m-%d %H:%M:%S')][DataJoint]: Reloading SciViz since \`$$DJSCIVIZ_SPEC_PATH\` changed."
               sciviz_update
               DELTA=$$CURR_DELTA
           else
               sleep 2
           fi
        done
    healthcheck:
      test:
        [
          "CMD",
          "wget",
          "--no-verbose",
          "--tries=1",
          "--spider",
          "http://localhost:3000",
        ]
      timeout: 30s
      retries: 10
      interval: 15s
  fakeservices.datajoint.io:
    image: datajoint/nginx:v0.2.4
    environment:
      - ADD_db_TYPE=DATABASE
      - ADD_db_ENDPOINT=db:3306
      - ADD_pharus_TYPE=REST
      - ADD_pharus_ENDPOINT=pharus:5000
      - ADD_pharus_PREFIX=/api
      - ADD_sciviz_TYPE=REST
      - ADD_sciviz_ENDPOINT=sci-viz:3000
      - ADD_sciviz_PREFIX=/
      - HTTPS_PASSTHRU=TRUE
    ports:
      - "443:443"
      - "80:80"
      - "3306:3306"