❗ As of 2024-07-17 the code that updates the EL metadata dictionary and publishes the GH pages website has been movved to https://github.com/eliteportal/data-models to simplify the maintanence. This repository may be revived and used again later but for now is not the source of the EL metadata dictionary.

EL Data Model

This is the repository hosting ELITE data model and a set of standardized metadata terms that can be used to describe attributes in the data model. The data model defines attributes that are associated with a dataset type (e.g. clinical metadata) and their interdependencies. Data Curator App (DCA) pulls the data model when generating metadata template and validates manifests against it. This repository also houses the pipelines and workflows to streamline data model update and metadata dictonary management.

EL Metadata Dictionary Site

EL Metadata Dictionary is a Jekyll site utilizing Just the Docs theme and is published on GitHub Pages.

• index.md is the home page
• _config.yml can be used to tweak Jekyll settings, such as theme, title
• _data/ folder stores data for Jekyll to use when generating the site
• files in docs/ will be accessed by GitHub Actions workflow to build the site

Setup

a. Change the configuration yaml file to point to correct data model

b. Have poetry installed. Created poetry environment with poetry install.

Create CSVs to Organize Website

Run create_CSVs.py. It will create a CSV for each unique Module found in the data model.

Updata Data Model and Metadata Dictionary

Prerequisites:

a. Grant workflows "have read and write permissions" in the repository for all scopes.

b. Allow deploying the GitHub pages using the workflow (see Publish site on GitHub pages below).

Step 1. Pull most recent changes from the Main branch and create a new branch

Step 2. On the new branch, edit the EL.data.model.csv. The following columns are required to be filled: Attribute, Description, Required, Parent, Source. (See Data Model Schema for details).If you'd like to clarify valid values of an attribute in the metadata dictionary, the Module and Type are required to be filled.

Step 3. Push the changes to the remote branch and create a pull request (PR) to the Main branch. Creating a PR will trigger several GitHub Actions to:

1. Convert the EL.data.model.csv to jsonld file (i.e. EL.data.model.jsonld) that can be read by DCA and commit the changes to the PR via ci-convert.yml
2. Add and update metadata term/template csv and markdown files that are used in the metadata dictionary static site and commit the changes to the PR via update_metadata_dictionary.yml.
3. Build and publish the metadata dictionary site on GitHub pages via pages.yml

Update Metadata Dictionary Only

Step 1. Pull most recent changes from the Main branch and create a new branch

Step 2. On the new branch, edit terms csv files under .\_data\ by adding Key Description and Source information.

Step 3. Push the changes to the remote branch and create a pull request (PR) to the Main branch. Creating a PR will trigger several GitHub Actions to:

1. Add and update metadata template csv and markdown files that are used in the metadata dictionary static site and commit the changes to the PR via update_metadata_dictionary.yml

2. Build and publish the metadata dictionary site on GitHub pages via pages.yml

Customization

You can add additional descriptions to home page or specific page by directly editing index.md or markdown files in docs/.

Building and previewing the site locally

1. Install Jekyll gem install bundler jekyll
2. Install Bundler bundle install
3. Run bundle exec jekyll serve to build your site and preview it at http://localhost:4000. The built site is stored in the directory _site.

Publish site on GitHub pages

In addition to setting up the GitHub Actions workflow (i.e pages.yml), you need to allow deploying the GitHub pages using the workflow. Go to Settings-> Pages -> Build and deployment, then select Source: GitHub Actions.

Making Changes to the Data Model

Any changes should be done in this repo. Then run _scripts/get_data_model.py to get the updated model.

To Do

• Fix template names on side bar
• For each module besides Template, create a table in that side bar menu
• Update data model attributes with descriptions, types and source
• Remove terms from side bar with no values in table
• (SEP-19-2023): Handling when there is no module
• (SEP-19-2023): Only pages to generate are ones with key values, empty tables should not be shown
• (SEP-19-2023): Add full table page