SenNet Data Portal

Working with submodule

This repository relies on the search-ui as a submodule to function. The file .gitmodules contains the configuration for the URL and specific branch of the submodule that is to be used. Once you already have cloned this repository and switched to the target branch, to load the latest search-ui submodule:

git submodule update --init --remote

For Local Development

Create a file called .env.local in /src with the same structure as example.env. Modify the variables as needed.

Required services

The ingest-api must be running locally and for the time being you must change the variable GLOBUS_CLIENT_APP_URI in app.cfg to be 'http://localhost:3000/' for redirects to work properly. You can start the ingest-api with the following command:

$ ingest-api/src/python app.py

The search-api and entity-api must be running via Docker to avoid CORS related problems. You can start the search-api with the following command:

$ ./search-api-docker.sh localhost start

To start the application run the following commands inside /src:
Note: This application requires Node.js 18 or later

$ pnpm install
$ pnpm run run

Docker deployment

For docker deployment, first create .env.local file base on example.env file in the same src directory.

Docker build for DEV development

There are a few configurable environment variables to keep in mind:

• HOST_UID: the user id on the host machine to be mapped to the container. Default to 1000 if not set or null.
• HOST_GID: the user's group id on the host machine to be mapped to the container. Default to 1000 if not set or null.
• PORTAL_UI_CLOUDWATCH_LOG_GROUP='/aws/ec2/sennet-dev/portal-ui/next-server': The Cloudwatch log group that saves the nodejs/next-js server logs

cd docker
./docker-development.sh [check|config|build|start|stop|down]

To run the image just built edit docker-compose.deployment.dev.yml and set it to the name of the image just built like sennet/portal-ui:<version_number>

Docker build for deployment on TEST/STAGE/PROD

cd docker
docker pull hubmap/portal-ui:1.0.0 (replace with the actual released version number)
./docker-deployment.sh [start|stop|down]

Environment vars

• PORTAL_UI_CLOUDWATCH_LOG_GROUP='/aws/ec2/sennet-prod/portal-ui/next-server': The Cloudwatch log group that saves the nodejs/next-js server logs

Vitessce

Visual integration tool for exploration of spatial single cell experiments

Vitessce docs

Vitessce is embedded in the view dataset page for sn-RNA-seq data types. The React component takes 3 props as input, a json object named config that describes the visualizations, a theme, and the height.

Vitessce View Config

The view config is responsible for which views are rendered, what data is fetched, and the layout of the views. Vitessce can render many views for each individual dataset. The files are served by the assets service

An example json view config is src/SNT753.WGBZ.884-snRNA-seq-large-intestine.js

Hint The view config is logged in the browser console for HubMAP and SenNet.

You can copy/paste the json object into the Vitessce app.

Vitessce JS view config API

Vitessce App to validate view configs

During development, we can use the vitessce app to validate view configs. It will tell us if there are any errors in the config and then load the visualizations in the browser.

Vitessce app

Usage

const Vitessce = React.lazy(() => import ('../components/custom/VitessceWrapper.js'))
<Vitessce config={config} theme={'light'} height={800}/>

Common Coordination Framework Registration User Interface (CCF-RUI)

The CCF-RUI allows a user to locate and record 3D coordinates of tissue blocks sampled from organs. Example HubMAP RUI

CCF-UI github repo

The tool is integrated as a web component with a react component wrapping it. The web component is

<ccf-rui
  ref={this.ruiRef}
  base-href="https://cdn.jsdelivr.net/gh/hubmapconsortium/ccf-ui@3/rui/"
  theme={'sennet'}
/>

The react component is src/components/custom/edit/sample/rui/RUIIntegration.js

The tool is only available for human Block tissue samples with an ancestor of Organ

The Register location button will display on the edit sample page and launch the CCF-RUI tool.

Content Management

Banner

Currently, two locations offer adding a banner via adding/updating public/content/banners/index.json file without having to rebuild the image. To specify that both locations use the same banner, use the key default as property name. To use different banners per location, specify the property name login and/or homepage.

login Located before the Login section

{
  "login": {
    "content": "..."
  }
}

homepage Located on the homepage

{
  "homepage": {
    "content": "..."
  }
}

default This banner will be used for locations not specified.

{
  "default": {
    "content": "..."
  }
}

Configure the json object with the following properties:

Property	Type	Description
theme	enum string	["info", "danger", "warning"] Default: warning.
title	html string	A title for the Alert, which is the actual banner. (Going forward we will call this just 'banner'.)
content	html string	Required. The main banner content.
dismissible	boolean	Add a close button to the banner.
keepDismissed	boolean	Keep the banner dismissed on close. The banner will show again on refresh if this is set to false or undefined.
className	string	A class name for the banner. Default: mt-4.
innerClassName	string	A class name for inner wrapper of the banner.
outerWrapperClassName	string	A class name for the div that wraps the banner.
beforeBanner	html string	Set some content before the banner.
beforeBannerClassName	string	Set a class name on div of beforeBanner.
afterBanner	html string	Set some content after the banner.
afterBannerClassName	string	Set a class name on div of afterBanner.
sectionClassName	string	A class name for the c-SenNetBanner section. Default: sui-layout-body.
ariaLabel	string	For accessibility, add a unique label to the c-SenNetBanner section

Custom Plugins

There are some custom JS plugins located in src/components/custom/js/addons which adds additional functionality to the UI on HTML elements with classes or properties like js-{app}--{component} or data-js-{app} respectively. The ES6 classes have been excluded from docker build time and are automatically rebuilt to main-plugins.js when developing under pnpm run run or pnpm run plugins-watch. Use pnpm run plugins to manually rebuild.