myLIMS
Electronic lab notebook for open science
Installation
The following commands will respectively install the dependencies and build the core app.
npm installConfiguration
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 devIf 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:runConfiguration
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:createProduction
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:createDesign
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
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