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cytomine.template
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# -------------------------------------------------- #
# Update these to configure your instance
global:
urls:
constant:
CORE: cytomine.local
IMAGE_SERVER: ims.cytomine.local
UPLOAD: upload.cytomine.local
urls_with_scheme:
constant:
CORE: http://cytomine.local
IMAGE_SERVER: http://ims.cytomine.local
UPLOAD: http://upload.cytomine.local
host_paths:
constant:
PROJECT_DATA_PATH: ./data
DATASET_PATH: ./dataset
smtp:
constant:
HOST: mail.smtp
PORT: 587
USER: user
PASS: password
# -------------------------------------------------- #
# Only update variables below if you know what you are doing
versions:
constant:
CYTOMINE_COMMERCIAL: BP2024.1
images:
constant:
BIOFORMAT: cytomineuliege/bioformat:v3.1.0
CORE: cytomineuliege/core:bp-0.2.0-ms
ELASTICSEARCH: docker.elastic.co/elasticsearch/elasticsearch:8.6.2
LOGSTASH: docker.elastic.co/logstash/logstash:8.6.2
MONGO: mongo:4.4.18-focal
NGINX: cytomineuliege/nginx:1.22.1-1.0.0
PIMS: cytomineuliege/pims:bp-0.2.0
PIMS_CACHE: redis:7.0.8
POSTGIS: cytomineuliege/postgis:15-3.3-alpine-1.0.0
RABBITMQ: rabbitmq:3.10
WEB_UI: cytomineuliege/web_ui:bp-0.2.2-ms
internal_docker_urls: # must match respective container hostnames from compose file
constant:
WEB_UI: web_ui
CORE: core:8080
ELASTICSEARCH: elasticsearch
LOGSTASH: logstash
PIMS: pims:5000
RABBITMQ: rabbitmq
BIOFORMAT: bioformat
MONGO: mongo
NGINX: nginx
PIMS_CACHE: pims_cache
POSTGIS: postgis
container_paths:
constant:
DATASET: /dataset
IMAGES: /data/images
UPLOADED: /tmp/uploaded
elasticsearch:
constant:
PORT: 9200
javamelody:
constant:
DATA_PATH: /javamelody-core # inside container
USER: admin
auto:
PASS:
type: openssl
length: 32
postgres:
constant:
PORT: 5432
DB_NAME: docker
USER: docker
auto:
PASS:
type: openssl
length: 32
mongodb:
constant:
USER: mongoadmin
DB_NAME: cytomine
PORT: 27017
auto:
PASS:
type: openssl
length: 32
keys:
constant:
CRYPT4GH_PUBLIC_KEY: crypt4gh_sender_public_key
CRYPT4GH_PRIVATE_KEY: crypt4gh_private_key
auto:
IMAGE_SERVER_PRIVATE: random_uuid
IMAGE_SERVER_PUBLIC: random_uuid
image_metadata:
constant:
PREFIXES: |-
APERIO=APERIO.
TIFF=TIFF.
HAMAMATSU=HAMAMATSU.
OPENSLIDE=OPENSLIDE.
EXIF=EXIF.
LEICA=LEICA.
JFIF=JFIF.
FILE=FILE.
PNG=PNG.
XMP=XMP.
VENTANA=VENTANA.
DICOM=DICOM.
MIRAX=MIRAX.
ICC_PROFILE=ICC_PROFILE.
services:
default:
core:
constant:
METADATA_PREFIXES_FILE_URI: /app/metaPrefix.properties
auto:
SERVER_ID: random_uuid
JWT_SECRET:
type: secret
length: 256
whitelist: abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789'+.;^_~
ADMIN_PASSWORD:
type: openssl
length: 32
ADMIN_PRIVATE_KEY: random_uuid
ADMIN_PUBLIC_KEY: random_uuid
SUPER_ADMIN_PRIVATE_KEY: random_uuid
SUPER_ADMIN_PUBLIC_KEY: random_uuid
RABBITMQ_PRIVATE_KEY: random_uuid
RABBITMQ_PUBLIC_KEY: random_uuid
global:
ELASTICSEARCH_HOST: internal_docker_urls.ELASTICSEARCH
ELASTICSEARCH_PORT: elasticsearch.PORT
IMAGE_SERVER_PRIVATE_KEY: keys.IMAGE_SERVER_PRIVATE
IMAGE_SERVER_PUBLIC_KEY: keys.IMAGE_SERVER_PUBLIC
POSTGIS_HOST: internal_docker_urls.POSTGIS
POSTGIS_PORT: postgres.PORT
POSTGIS_DB_NAME: postgres.DB_NAME
POSTGIS_USER: postgres.USER
POSTGIS_PASS: postgres.PASS
SMTP_HOST: smtp.HOST
SMTP_PORT: smtp.PORT
SMTP_USER: smtp.USER
SMTP_PASS: smtp.PASS
MONGO_HOST: internal_docker_urls.MONGO
MONGO_PORT: mongodb.PORT
MONGO_USER: mongodb.USER
MONGO_PASS: mongodb.PASS
MONGO_DB_NAME: mongodb.DB_NAME
JAVAMELODY_PATH: javamelody.DATA_PATH
JAVAMELODY_USER: javamelody.USER
JAVAMELODY_PASS: javamelody.PASS
SERVER_URL: urls_with_scheme.CORE
REVERSE_PROXY_URL: internal_docker_urls.NGINX
IMAGE_SERVER_URL: urls_with_scheme.IMAGE_SERVER
URL_CORE: urls.CORE
URL_IMS1: urls.IMAGE_SERVER
INSTANCE_HOST_WEBSITE_URL: urls_with_scheme.CORE
STORAGE_PATH: container_paths.IMAGES
METADATA_PREFIXES: image_metadata.PREFIXES
logstash:
global:
ELASTICSEARCH_HOST: internal_docker_urls.ELASTICSEARCH
ELASTICSEARCH_PORT: elasticsearch.PORT
POSTGIS_DB_NAME: postgres.DB_NAME
POSTGIS_HOST: internal_docker_urls.POSTGIS
POSTGIS_PASS: postgres.PASS
POSTGIS_PORT: postgres.PORT
POSTGIS_USER: postgres.USER
mongo:
global:
MONGO_INITDB_ROOT_USERNAME: mongodb.USER
MONGO_INITDB_ROOT_PASSWORD: mongodb.PASS
MONGO_INIT_DATABASE: mongodb.DB_NAME
bioformat:
constant:
BIOFORMAT_PORT: 4321
pims:
constant:
WEB_CONCURRENCY: 16
MAX_REQUESTS: 0
LOG_CONFIG_FILE: /app/logging.yml
DEFAULT_IMAGE_SIZE_SAFETY_MODE: SAFE_REJECT
DEFAULT_ANNOTATION_ORIGIN: LEFT_TOP
OUTPUT_SIZE_LIMIT: 10000
task_queue_enabled: false
cache_enabled: true
global:
CRYPT4GH_PUBLIC_KEY: keys.CRYPT4GH_PUBLIC_KEY
CRYPT4GH_PRIVATE_KEY: keys.CRYPT4GH_PRIVATE_KEY
CYTOMINE_PUBLIC_KEY: keys.IMAGE_SERVER_PUBLIC
CYTOMINE_PRIVATE_KEY: keys.IMAGE_SERVER_PRIVATE
ROOT: container_paths.IMAGES
DATASET_PATH: container_paths.DATASET
PENDING_PATH: container_paths.UPLOADED
PIMS_URL: urls_with_scheme.IMAGE_SERVER
REVERSE_PROXY_URL: internal_docker_urls.NGINX
URL_CORE: urls.CORE
URL_IMAGE_SERVER: urls.IMAGE_SERVER
URL_UPLOAD: urls.UPLOAD
web_ui:
global:
URL_CORE: urls_with_scheme.CORE
URL_UPLOAD: urls_with_scheme.UPLOAD
CYTOMINE_COMMERCIAL_VERSION: versions.CYTOMINE_COMMERCIAL
METADATA_PREFIXES: image_metadata.PREFIXES
postgis:
global:
POSTGRES_USER: postgres.USER
POSTGRES_PASSWORD: postgres.PASS
POSTGRES_DB: postgres.DB_NAME
nginx:
global:
INTERNAL_URLS_WEB_UI: internal_docker_urls.WEB_UI
INTERNAL_URLS_CORE: internal_docker_urls.CORE
INTERNAL_URLS_IMS: internal_docker_urls.PIMS
URLS_CORE: urls.CORE
URLS_IMAGE_SERVER: urls.IMAGE_SERVER
URLS_UPLOAD: urls.UPLOAD
UPLOAD_PATH: container_paths.UPLOADED
etc_hosts_rewriter:
constant:
PROXY_HOSTNAME: nginx
global:
URL_CORE: urls.CORE
URL_IMS1: urls.IMAGE_SERVER
URL_UPLOAD: urls.UPLOAD