GlowingBear

A cohort selection user interface for TranSMART.

Development

This project was generated with Angular CLI version 1.0.0.

Development server

Run ng serve for a dev server. Navigate to http://localhost:4200/. The app will automatically reload if you change any of the source files.

Code scaffolding

Run ng generate component component-name to generate a new component. You can also use ng generate directive/pipe/service/class/module.

Build

Run ng build to build the project. The build artifacts will be stored in the dist/ directory. Use the -prod flag for a production build.

Running unit tests

Run ng test to execute the unit tests via Karma, run ng test --code-coverage to test with generated coverage documents, which are located in the coverage folder.

Running end-to-end tests

For e2e test we use Cypress in combination with the cypress-cucumber-preprocessor. Cypress is install as part of the your npm install command. To run the tests using the headless browser npm run e2e or npm run cypress to launch the GUI. by default the tests expect a glowing bear instance to be running at http://localhost:4200/. This can be changed in cypress.json WARNING: tests alter state. All saved queries are deleted.

Further help

To get more help on the Angular CLI use ng help or go check out the Angular CLI README.

Publishing

We use Gradle to create bundles that are suitable for deployment:

# Create a tar bundle in build/distributions
gradle assemble

# Publish the bundle to Nexus
gradle publish

Deployment

Published snapshot bundles are available in the snapshots repository on https://repo.thehyve.nl with id nl.thehyve:glowing-bear:0.0.1-SNAPSNOT:tar.

Untar the archive in a directory where it can be served by a web server, e.g., Apache or nginx.

Configuration

The application can be configured by changing the env.json and config.*.json files in app/config.

Example env.json:

{
  "env": "default"
}

Example config.prod.json:

{
  "api-url": "https://transmart.thehyve.net",
  "api-version": "v2",
  "app-url": "https://glowingbear.thehyve.net",
  "tree-node-counts-update": true,
  "autosave-subject-sets": false
}

Supported properties in the config.*.json files:

Property	Default	Description
api-url		URL of the TranSMART API to connect to.
api-version	v2	TranSMART API version. Only v2 is supported.
app-url		URL where the Glowing Bear is accessible for the user.
tree-node-counts-update	true	Fetch counts for study nodes in step 2 of Data Selection.
autosave-subject-sets	false	Persist subject selection as subject set automatically.
export-data-view	default	Shape of the export (default, surveyTable).
show-observation-counts	true
instant-counts-update-1	false
instant-counts-update-2	false
instant-counts-update-3	false
authentication-service-type	oidc	Authentication service type (oidc, transmart)
oidc-server-url		E.g., https://keycloak.example.com/auth/realms/{realm}/protocol/openid-connect
oidc-client-id	glowingbear-js
api-type	transmart	API type to use (transmart or picsure)
picsure-resource-name		Name of the PIC-SURE resource to use if relevant (e.g. i2b2-local)
enable-query-saving	true	Enable query saving feature
enable-variable-selection	true	Enable variable selection step
enable-data-table	true	Enable data table step
enable-analysis	true	Enable analysis features
enable-export	true	Enable data export features
force-i2b2-nesting-style	false	Enforce the AND/OR i2b2 query format (if false, format is free)
enable-greedy-tree-loading	true	Enable greedy tree loading (load whole tree at startup)

License

Copyright © 2017–2018   The Hyve B.V.

This program is free software: you can redistribute it and/or modify it under the terms of the Mozilla Public License 2.0.

You should have received a copy of the license along with this program. If not, see https://opensource.org/licenses/MPL-2.0.