README.md

Moka Panel App (mokapapp)

mokapapp imports Panel App panels into the Viapath Genetics LIMS system (Moka).

Simply install, create a configuration file and run:

$ mokapapp-import -c config.ini

Features

• Deactviates any deprecated Panel App panels in the Moka database
• Builds MokaPanel objects with a unique hash for each panel's green and amber genes, required for import into Moka.
• Performs data validation checks before import:
  • Are all panel hashes in dbo.Item?
  • Are all panel versions in dbo.Item?
  • Are all panel HGNC IDs in dbo.GenesHGNC_Current?
• Raises an error if the Moka HGNC snapshot is outdated

Installation

Clone this repository and install with pip (tested on a Linux OS with python v3.6.5):

$ git clone https://github.com/moka-guys/mokapapp.git
$ pip install ./mokapapp

Usage

usage: mokapapp-import [-h] [-c CONFIG] [--logfile LOGFILE] [--head HEAD]

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        A mokapapp config.ini file
  --logfile LOGFILE     A file to write application log outputs
  --head HEAD           An integer limit for the number of PanelApp panels to process

Config file

mokapapp-import requires a config.ini file with Moka database connection details:

# Example config.ini
[mokadb]
server = 10.10.10.10
db = dbname
user = username
password = password

Tests

Unit tests in the tests/ directory are run using pytest. An auth.py file containing test server details must be present in tests/:

# Example auth.py
MOKADB = {
    'server': '10.10.10.100',
    'db': 'database',
    'user': 'username',
    'password': 'password'
}

Once this file has been created run all tests:

$ pytest .

Notes

• Panel App gene confidence levels are converted to Green, Amber and Red colours as specified in Appendix A p.29 of the Panel App Handbook v5.5.

License

MIT License © 2019 Nana Mensah