DraftCoreDataModel

Welcome to the DraftCoreDataModel repository. This repository contains an alpha version of the CoreVariantClass and GoldStandardDatabase. The CoreVariantClass is an internal core class developed to facilitate seamless bidirectional translations between various standards, including FHIR, VRS, SPDI, and HGVS. This repository also includes bidirectional translations between VRS and SPDI, HGVS and VRS, and SPDI and HGVS. These translations are achieved using external packages and APIs acknowledged bellow. The GoldStandardDatabase (GSDB) is a human-curated database designed to provide reliable and accurate data for various applications. This repository is in the early stages of development and may undergo occasional changes as progress is made.

Interacting with Notebooks

To interact with the notebooks without installing or cloning the repository, you can utilize Codespaces. Instructions on how to use Codespaces tools are provided below.

If you're new to using Codespace, you may find the following resources helpful:

• GitHub Codespaces Documentation

Access Notebooks (Codespace)

1. Starting Codespace

• Start off by clicking the Codespaces badge above to get started.
• A prompt to build a code space will pop up with certain specifications.
• Click on Create Codespace.
• NOTE: This will take a few minutes to build your virtual machine.

2. Selecting Kernel:

• Navigate to notebooks and select a notebook you wish to run.
• Locate the "Select Kernel" option on the top right-hand side of the interface.
• Click on "Select Kernel".

3. Choosing Python Environment:

• After clicking "Select Kernel", choose "Python Environment...".
• From the dropdown menu, select the Pipenv Environment labeled: DraftCoreDataModel-.

4. Running Notebooks:

• Once the appropriate kernel is selected, you can proceed to run the cells inside of the Jupyter notebooks.

5. Deactivating Codespace

• On the bottom left corner of your browser, click on "CodeSpaces:".
• Then click "Stop Current Codespace".
• Once this is done, you have successfully deactivated your Codespace.

Running pytest scripts inside of Codespace

To run pytest scripts within a Codespace environment the following steps need to be followed:

1. Activate the pipenv virtual environment:

To execute the test scripts, it is essential to ensure that you are operating within the virtual environment configured by Pipenv.

# Activate pipenv virtual environment
pipenv shell

2. Run the pytest command:

Once the virutal environment is activated, navigate to the test directory via the terminal. You can then execute pytest by specifying the particular files you intend to test.

# Execute the specified test file 
pytest file_name.py

Acknowledgments

This project utilizes several external packages and APIs. The following packages were used:

• vrs-python:
• biocommons.seqrepo:
• biocommons.uta:
• hgvs:
• NCBI Variation Services:
• HL7 FHIR: