app_configuration.md

Schema Configuration

In the app, the required schemas is configured in the file www/config.json, which is used to adapt the dropdown data types list in the app.

All properties in the config.json are listed below:

• manifest schemas: defines the list of schemas displayed under the "Choose a Metadata Template Type:" dropdown in the application.
  • display_name : The display name for the dropdown. (e.g. scRNA-seq Level 1)
  • schema_name: The name of the manifest in the JSON-LD schema (e.g. ScRNA-seqLevel1)
  • type: The type of manifest, either file or record.
• service_version: The version of schematic service (Default is empty string if no value provided)
• schema_version: The version of data model (if no specific version or branch provided in the schematic_config.yml, default is to query the latest release of the schema repo)

Workflow Deployment

During the app deployment, the workflow will perform following steps to automatically generate the config.json file:

1. Clone the data model repo defined in the repo configuration in the schematic_config.yml file (if you would like to continue using download_url, please remove or comment out the repo key).

2. Run create_schema.py script to automatically generate the config.json file (filled DependsOn Component column of your data model is required)

Local Development

For the local developers, the config.json will be automatically generated after the app launches via below command in global.R. You can always manually modify the config.json or replace with your own existing config.json in the www folder.

python3 .github/config_schema.py \
  -c schematic_config.yml \
  --service_repo 'Sage-Bionetworks/schematic' \
  --overwrite

• -c is the path to the schematic configuration file
• --service_repo is the repo path for schematic, with the format as <repo-owner>/<repo-name>
• --overwrite is to set whether to overwrite the existing config.json file (please remove this flag if you would like to use your own config.json)