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Installation

Project is still under active development

Please consider this project in it's current state just as a draft. The api is not yet stable and there may still be important security vulnerabilities. Documentation is still far from being complete.

Installation of SciCat4daphne

Requirements

The described installation has been tested on the following systems:

  • Virtual machine running Ubuntu 20.04

Tested dependency Versions:

  • docker version 24
  • docker-compose version 1.29, installed via pip

Getting started

Just navigate into the scicatlive4daphne directory and run

docker-compose up -d

to look at log messages use

docker-compose logs

to stop all services use

docker-compose down

Necessary adoptions

  • configuration of upload frontend
  • password of MongoExpress
  • passwords of default users

configuration templates are provided in scicatlive4daphne/config

Services in detail

This is an overview of the different services invoked through docker-compose together with the most important configuration options.

SciCat Backend

the configuration file is located in 

/scicat4daphne/scicatlive4daphne/config/backend/config.env

but should not need site-specific changes for a basic installation. For a production environment e.g. the entries pidPrefix and site should be specified.

SciCat Frontend

this service uses the configuration file

scicatlive4daphne/config/frontend/config.json

where e.g. the appearance of the scientific metadata (tree view vs. simple tabular view) and the columns of the dataset table can be configured.

Reverse Proxy (Traefik)

this service is used to stitch the different services in docker-compose together

Database (MongoDB)

all configuration happens in the docker-compose.yaml. Most important is the mounting point for the _ mongoDB_ on the host system which is specified at

    volumes:
      - "/srv/mongodb:/bitnami/mongodb"     # check that is mount exists on local file-system

in the docker-compose.yaml there are also some hints for database backups using the provided script.

Upload Frontend

Can be found at http://scicat-host/upload with configuration in scicatlive4daphne/config/upload/env.js. This file needs to be adopted for each running SciCat instance.

window.env = {
  "REACT_APP_API_URL": "http://your-scicat-domain.org/api/v3",
  "REACT_APP_API_URL2": "http://your-scicat-domain.org",
  "REACT_APP_STORE_KEY": "scicat",
  "REACT_APP_EXTERNAL_DATASETS_URL": "http://your-scicat-domain.org/datasets",
  "REACT_APP_ROUTER_BASENAME": "/upload",
  "PUBLIC_URL": "http://your-scicat-domain.org/upload",
  "REACT_APP_SCICAT_DEFAULT_DS_OWNER": "a_owner",
  "REACT_APP_SCICAT_DEFAULT_DS_GROUP": "a_group",
  "REACT_APP_SCICAT_DEFAULT_DS_OWNER_GROUP": "a_owner_group"
}

the primary change needed is to exchange your-scicat-domain.org according to the local conditions. For test installation e.g. replace with localhost

Addon API

Currently there is no configuration for this service. An interactive api-documentation can be found at http://scicat-host/swagger-ui.

Not Secure

  • calls to this additional backend api currently do not rely on any authentication

MongoDB Web GUI (MongoExpress)

Mainly intended for those who are managing the installation and for inspection of the DB. By default this service is deactivated (commented out in docker-compose.yaml). The login for this service is specified in the docker-compose.yaml and managed by traefik. The password is hashed using 🔴 which can e.g. be generated at 🔴.

Maintenance and House Keeping

Backup

The current backup strategy is to run the script scicatlive4daphne\backup.sh periodically e.g. in a cron job running it via docker inside an already running container via

docker exec scicatlive4daphne_mongodb_1 /backup.sh

from the host system. This script basically relies on mongodump.

Restore from backup

Please have a look at the documentation of mongorestore. In case you want to import an existing dump please do so starting from a clean Mongo DB before starting the SciCat backend for the first time.