Glowing Bear MedCo

glowing-bear-medco is the web user interface of MedCo. You can find more information about the MedCo project here. For further details, support, and contacts, you can check the MedCo Technical Documentation.

Source code organization

• deployment: docker deployment files
• src: root of the source code
  • app: angular application
  • config: configuration of the application
  • models: models used in the application
  • modules: angular modules
    • gb-explore-module: explore query module, enabling the construction of an explore query
    • gb-explore-results-module: explore query results module, displaying the results of the explore queries
    • gb-main-module: angular main module
    • gb-navbar-module: navigation bar module, containing the menu with tabs
    • gb-side-panel-module: side panel module, containing the summary, ontology tree and saved cohorts
    • gb-analysis-module: analysis module, containing the analysis option (only survival at the current time) and settings for the analysis to run
    • gb-survival-results-module: survival results module, containing the results of the various operations run on survival data points in the context of survival analysis. An overview of this compenent's logic can be found in this file.
  • services: services handling data flow
  • utilities: utility tools: crypto, log, error, etc.
  • assets: static assets
  • environments: definition of production or test environment
  • styles: CSS styles

Getting started

glowing-bear-medco needs a MedCo deployment to be used. A description of the available deployment profiles, along with a detailed guide on how to use them, is available here.

Use the live development server

cd deployment
./dev-server.sh

The default configuration will attempt to use the local dev-local-3nodes deployment of MedCo. An alternative configuration is provided to use the deployment medco-demo.epfl.ch (if it is online). To use it, update src/app/config/env.json with the value medco-demo.

Build the Docker image

cd deployment
docker-compose build glowing-bear-medco

Generate the mapping table

The crypto utility has a point to integer mapping table present in the file src/app/utilities/crypto/point-to-int-mapping.ts. In order to regenerate this file, e.g. so that it contains more points, you can run the following command:

cd deployment
USER_ID=$(id -u):$(id -g) docker-compose -f docker-compose.gen-mapping-table.yml run gen-mapping-table

Note that the maximum value present in this mapping table is the maximum number that the library will be able to decrypt.

License

glowing-bear-medco is licensed under the MPL 2.0. If you need more information, please contact us.