ACDC Data Dictionary

This is the Gen3 data dictionary for the Australian Cardiovascular Disease Project.

The yamls and jsonschema is found in the dictionary/prod_dict folder.

• yamls
• jsonschema

Development Workflow

This repository includes a dictionary/test_dict folder for testing purposes. You can convert the input_dd.yaml into jsonschema files without overwriting anything in the dictionary/prod_dict folder:

1. Use the dictionary/test_dict folder to generate and validate your schema changes
2. Copy specific elements from dictionary/test_dict to dictionary/prod_dict as needed
3. The dictionary/prod_dict/acdc_schema.json file is what will be used for deployment

Copying Files Between Folders

To copy files between the test and production folders, you can use the provided scripts:

• Copy from test to production:

  bash dictionary/copy_to_prod.sh

• Copy from production to test:

  bash dictionary/copy_to_test.sh

Using Gen3SchemaDev's Simplified YAML Input

The data model can be defined using Gen3SchemaDev's simplified YAML input language via the input_dd.yaml file. This approach is particularly useful for:

• Creating the main structure of the data model
• Defining links between nodes in a more readable format

For more information, see the Gen3SchemaDev README.

Setup

To set up the environment, run:

pip install poetry
poetry install
eval $(poetry env activate)

Updating the Dictionary

1. Copy prod_dict to test_dict

   bash dictionary/copy_to_test.sh

When making changes to the data dictionary:

2. Update the dictionary version in the dictionary/test_dict/_settings.yaml file
3. Bundle the schema using:

   gen3schemadev bundle -i dictionary/test_dict -f dictionary/test_dict/acdc_schema.json

Validating the Dictionary

4. To validate a folder of jsonschema YAML files, use:

gen3schemadev validate -y dictionary/test_dict
gen3schemadev validate -b dictionary/test_dict/acdc_schema.json

For more details, see the Gen3SchemaDev validation documentation.

To visualise the dictionary

5. The dictionary can be visualised using Gen3SchemaDev.

gen3schemadev visualise -i dictionary/test_dict/acdc_schema.json

Copying back to the prod folder

6. After validating and visualising the dictionary, copy it back to the prod folder:

bash dictionary/copy_to_prod.sh

• Then commit and push the changes to github