Windmill data portal

A generic data portal that supports some basic interaction with Gen3 services like peregrine, sheepdog and fence.

Get Started

Prerequisites

• npm

Installing

npm install

Then, update schema from gdcapi by running npm run-script schema. This command will update the latest schema that is used by Relay and GraphiQL. Without parameter, it will point to the endpoint at local API (http://localhost:5000/v0/submission/getschema). Use the parameter to point to remote url (e.g. https://dev.bionimbus.org/api/v0/submission/getschema) as follow:

npm run-script schema -- https://dev.bionimbus.org/api/v0/submission/getschema

Local development and dev.html

The portal's /dev.html path loads javascript and most css from localhost. Test code under local development with this procedure:

• npm install
• launch the webpack dev server, and configure local code with the same configuration as the server to test against. For example - if we intend to test against dev.planx-pla.net, then:

HOSTNAME=dev.planx-pla.net NODE_ENV=auto bash ./runWebpack.sh

, or for qa-brain:

HOSTNAME=qa-brain.planx-pla.net NODE_ENV=auto bash ./runWebpack.sh

NOTE: To locally test Tiered Access features, you must include the additional environment variables TIER_ACCESS_LEVEL and TIER_ACCESS_LIMIT, with should have the same values as the server's "global.tier_access_level" and "global.tier_access_limit" properties in its manifest.json.

Example:HOSTNAME=qa-brain.planx-pla.net TIER_ACCESS_LEVEL=regular TIER_ACCESS_LIMIT=50 NODE_ENV=auto bash ./runWebpack.sh

• Accept the self-signed certificate at https://localhost:9443/bundle.js

• Load the test environment's /dev.html - ex: https://qa-brian.planx-pla.net/dev.html

Local development and gitops

Most production commons currently load custom configuration via gitops. The configuration for a production commons is available in that commons' gitops repository (mostly https://github.com/uc-cdis/cdis-manifest), and can be copied for local development. The runWebpack.sh script automates this process when NODE_ENV is set to auto - ex:

HOSTNAME=qa-brain.planx-pla.net NODE_ENV=auto bash ./runWebpack.sh

Note: the legacy dev NODE_ENV is still available, but the APP environment must also be manually set to load the configuration that matches the dictionary from HOSTNAME - ex:

HOSTNAME=dev.planx-pla.net NODE_ENV=dev APP=dev bash ./runWebpack.sh

Component story books

To run Storybook: npm run storybook

To run with Arranger components:

1. Set local environment variables:

• $STORYBOOK_ARRANGER_API: localhost:3000
• $STORYBOOK_PROJECT_ID: search
• $REACT_APP_ARRANGER_API: /api/v0/flat-search
• $REACT_APP_PROJECT_ID: search

2. Run ElasticSearch at localhost:9200
3. Clone and cd into gen3-arranger. Run:

docker-compose -f esearch.yml up -d
export ESHOST=localhost:9200
source esearch/indexSetup.sh
es_indices
es_delete_all
es_setup_index
es_gen_data 0 20

4. Follow the Arranger setup steps - run the server and the dashboard.
5. At the Arranger Dashboard (localhost:6060), add a new version called 'dev'.
6. Click on 'dev' and add a new index. Name: subject, Index: gen3-dev-subject, ES Type: subject.
7. Go back to Versions and hit the lightning bolt. The endpoint should go from a red arrow to a green arrow.
8. At this point, running the Data Portal from our Storybook should work.

Docker Build for Local Development

Build the container image first

docker build -t windmill .

Then run the container

docker run --rm -e HOSTNAME=dev.example.net -e APP=dev -p 443:443 -ti windmill

You will then need to visit https://localhost and accept the self-signed certificate warnings

Deployment

docker run -d --name=dataportal -p 80:80 quay.io/cdis/data-portal

GraphQL configuration

All the configurations of Homepage and Explorer page are specified data/config/.json. For each common, we need to specify the following json entities:

"graphql": {
  "boardCounts": [
    {
      "graphql": "_case_count",
      "name": "Case",
      "plural": "Cases"
    },
    {
      "graphql": "_experiment_count",
      "name": "Experiment",
      "plural": "Experiments"
    },
    {
      "graphql": "_aliquot_count",
      "name": "Aliquot",
      "plural": "Aliquots"
    }
  ],
  "chartCounts": [
    {
      "graphql": "_case_count",
      "name": "Case"
    },
    {
      "graphql": "_experiment_count",
      "name": "Experiment"
    },
    {
      "graphql": "_aliquot_count",
      "name": "Aliquot"
    }
  ],
  "projectDetails": "boardCounts"
}

• boardCounts are the counts that you want to display in the top-left of dashboard's
• chartCounts are the counts that you want to display in the bar chart of dashboard's
• projectDetails are the counts that you want to display in the list of projects. It could be same as boardCounts, in this case, you only need to point to boardCounts.

Certificates configuration

All the configurations of necessary certificates are define in src/.json. For each common, we need to specify the following json entities:

"components": {
  "certs": {
    "<certificate-name>": {
      "title": "BloodPAC User agreement",
      "description": "The agreement on what you can and need to do in a Commons.",
      "questions": [
        {
          "name": "Things you can do after registration",
          "question": "As a registered user, I can do the following things without any problem. Is it true or not:",
          "options": ["Browse public Project", "Upload file", "Download file", "Invite people"],
          "answer": 0,
          "hint": "Some information about this question"
        },
        {
          "name": "Things you need to do to become the registered user",
          "question": "In order to be a register user, I must do the following things otherwise:",
          "options": ["Agree the user agreement", "Accept a consent", "None of them", "Both of them"],
          "answer": 2,
          "hint": "Some information about this question"
        },
        {
          "name": "Things you can do with data",
          "question": "How can I share data with other people according to the policy of the commons",
          "options": ["I can not share data", "I can only share data with BPA memebers", "I can share data with family", "I can share data with my wife"],
          "answer": 1,
          "hint": "Some information about this question"
        }
      ]
    }
  }
}

Then, specify all the required certificates that need to be completed before using the portal in following entry:

"requiredCerts": ["<certificate-name>"]

Default is an empty list.

Style Guide

When styling components, we adhere to a few rules. We style using class selectors (.class-name instead of #class-name), and separate class names with hypens instead of camel case (.class-name instead of .className). The CSS file should be named {component}.css, and be in the same folder as the component. It is then imported into the component's .jsx file.

We are moving toward using the BEM methodology in terms of CSS organizational conventions. This means we are dividing chunks of code within a component into blocks, are avoiding nesting components, and are using the naming convention of {block}__{elements}--{modifer}. {element} and {modifier} are optional depending on the situation - see the BEM guidelines for more examples.

For our example, say we have a simple component called Component:

import './Component.css';

class Component extends React.Component {
  render() {
    return (
      <div>
        <h1>This is my component</h1>
        <button>Submit</button>
        <button>Cancel</button>
      </div>
    );
  }
}

Our block would be .component, and elements in that block would consist of the buttons and the title. So our CSS would look like this, based on the BEM naming conventions:

.component { }
.component__title { }
.component__button { }

And the code would look like this:

import './Component.css';

class Component extends React.Component {
  render() {
    return (
      <div className="component">
        <h1 className="component__title">This is my component</h1>
        <button className="component__button">Submit</button>
        <button className="component__button">Cancel</button>
      </div>
    );
  }
}

The buttons can also have modifiers - let's say we want two different colors depending on if the button is a submit button or a cancel button. Then our CSS and code would look something like this, respectively:

.component { }
.component__title { }
.component__button { }
.component__button--submit {
  color: blue;
}
.component__button--cancel {
  color: red;
}

import './Component.css';

class Component extends React.Component {
  render() {
    return (
      <div className="component">
        <h1 className="component__title">This is my component</h1>
        <button className="component__button component__button--submit">Submit</button>
        <button className="component__button component__button--cancel">Cancel</button>
      </div>
    );
  }
}