myLIMS

Electronic lab notebook for open science

• Installation
• Configuration
• Run
  • Development
  • Production
• Design
  • Core
  • Addons

Installation

The following commands will respectively install the dependencies and build the core app.

npm install

Configuration

Edit it as needed. Example: auth config for ldap provider.

Run

Development

The following commands will start mongodb and ldap (to test the ldap provider) containers, setup a replica set on the mongodb server (to support migrations) and start the development server.

docker-compose up -d
node scripts/init-db.mjs
npm run dev

If it's the first time, don't forget to copy or create the .env file and is necessary to run the migration command

cp .env.example .env
npm i
node ace mongodb:migration:run

Configuration

Is necessary to have running the frontend server in order con administrate de system. For this in the localhost:3333/admin server configuration is possible to administrate the addons, including the login methods. After is required to have created an user:

node ace user:create

Production

cp .env.example .env.prod
docker-compose -f ./docker-compose.prod.yml build
docker-compose -f ./docker-compose.prod.yml up -d
docker-compose -f ./docker-compose.prod.yml exec backend node ace user:create

Design

The new ELN is meant to be highly modular, allowing developers to add new functionalities by creating addons.

Core

The core part is built on top of AdonisJS framework. The core provides commons parts such as addons loading, user model and ELN routes.

New ELN uses MongoDB as the default database system using the adonis-mongodb provider.

Addons

Addons can provide functionalities to the platform by exposing the following components:

• API routes in routes.ts
• Adonis providers providers/*
• Migrations migrations/*

An addons should be stored as a subfolder in the addons folder. It can be named as anything valid for the filesystem.

Models

classDiagram
  class User {
    +ObjectId _id
    +String firstName
    +String lastName
    +String[] usernames
    +String[] emails
    +String role
    +AuthMethods authMethods
  }

  class File {
    +String _id
    +String filename
    +Number size
    +String collection
  }

  class SampleKind {
    +String _id
    +String name
    +String description
    +String color
    +JSON schema

    +fromInput(sampleKind ,input)
  }

  class Sample {
    +ObjectId _id
    +String[] sampleCode
    +String uuid10
    +ObjectId userId
    +String kind
    +String[] labels
    +String project
    +JSON meta
    +String title
    +String description
    +String comment
    +MeasurementLink[] measurements
    +SampleAttachment[] attachments
    +ObjectId[] parents

    +fromInput(sample, input)
  }
  Sample "1" --> "*" Sample
  Sample "*" --> "1" SampleKind
  Sample "*" --> "1" File

  class Measurement {
    +ObjectId _id
    +String username
    +ObjectId sampleId
    +String title
    +String fileId
    +ObjectId eventId
    +String comment
    +ObjectId createdBy
    +String description
  }
  Measurement "*" --> "*" User
  Measurement "*" --> "1" Sample
  Measurement "*" --> "1" Event

  class Notebook {
    +ObjectId _id
    +String title
    +String description
    +ObjectId userId
    +String[] labels
    +ObjectId[] samples
    +MeasurementLink[] measurements
    +String project
    +String content
  }
  Notebook "*" --> "*" Measurement
  Notebook "*" --> "*" Sample
  Notebook "*" --> "1" User
  Sample "*" --> "1" User

  class Event {
    +ObjectId _id
    +String topic
    +EventData data
    +EventProcessor[] processors
  }
  class EventProcessor {
    +String processorId
    +EventHistory[] history
  }
  class EventHistory {
    +String processId
    +String status
    +Date date
    +String message
  }
  class EventData {
    +String type
    +String fileId
  }
  Event --* EventData
  Event --* EventProcessor
  EventProcessor --* EventHistory
  EventData --> File