Customizing dccvalidator

dccvalidator is intended to be customizable for different settings. The Shiny application uses a configuration file to set details such as where to store uploaded files, which metadata templates to validate against, whom to contact with questions, etc.

To create a custom version of the app, you’ll need to follow these steps:

  1. Create a Synapse project or folder with the appropriate permissions to store uploaded files. In AMP-AD, we created a folder to which consortium members have permissions to read and write, but not download. Only the curation team has the ability to download files (in order to assist with debugging). See this example of how to create a project with appropriate permissions.
  2. Fork the dccvalidator GitHub repository.
  3. Create a new configuration in the config.yml file. Note that any values you do not customize will be inherited from the default configuration. The configuration file must have a default configuration.
  4. (Optional): create a pull request with your configuration back to the upstream dccvalidator repository.
  5. Within the file app.R, replace the "default" configuration with the name of your new configuration.
  6. Deploy the application as described in the Deploying dccvalidator vignette.

To install the dccvalidator instead of forking the repository:

  1. Create an app.R file containing the following:
library("dccvalidator")
run_app()
  1. Create a config.yml file using the configuration options specified below and name the parameters “default”.
default:
  parent: "syn20400157"
  1. Create a Synapse project or folder with the appropriate permissions to store uploaded files. In AMP-AD, we created a folder to which consortium members have permissions to read and write, but not download. Only the curation team has the ability to download files (in order to assist with debugging). See this example of how to create a project with appropriate permissions.

Configuration options