PORI Python Adaptor

This repository is part of the Platform for Oncogenomic Reporting and Interpretation (PORI).

This is a python adaptor package for querying the GraphKB API and IPR API.

This python tool takes in variant inputs as tab-delimited files and annotates them using GraphKB. The resulting output is uploaded to IPR as a report. Additional report content such as images and metadata can be passed to be included in the report upload.

For documentation on how to create reports using the IPR adaptor, see the main documentation site for the platform. For the GraphKB adaptor, see the user manual.

• Getting Started
  • Install (For developers)
  • JSON Validate and Upload to IPR
• Documentation
• Deployment (Publishing)

Getting Started

Install (For developers)

clone this repository

git clone https://github.com/bcgsc/pori_python.git
cd pori_python

create a virtual environment

python3 -m venv venv
source venv/bin/activate

install the package and its development dependencies

pip install -U pip setuptools
pip install -e .[dev]

Run the tests:

Export usernames, passwords, and test options.

IPR_URL and GRAPHKB_URL values must also be set.

Set EXCLUDE vars to 1 if you don't want to run these tests. ONCOKB and BCGSC tests are enabled by default.

export IPR_USER='pori_admin'
export IPR_PASS='pori_admin'
export IPR_URL='http://localhost:8081/api'
export GRAPHKB_USER='pori_admin'
export GRAPHKB_PASS='pori_admin'
export GRAPHKB_URL='http://localhost:8080/api'
export EXCLUDE_BCGSC_TESTS=1
export EXCLUDE_ONCOKB_TESTS=1

If you want to run tests that upload reports to a live IPR instance, specify the url of the IPR API you want to use and set the test var INCLUDE_UPLOAD_TESTS to 1. These tests are disabled by default.

The created reports are deleted by default. If you want to keep them, set DELETE_UPLOAD_TEST_REPORTS to 0.

export IPR_TEST_URL='http://localhost:8081/api'
export INCLUDE_UPLOAD_TESTS=1
export DELETE_UPLOAD_TEST_REPORTS=0

pytest tests

JSON Validate and Upload to IPR

An IPR_URL must be provided either as an environment variable or an arg.

If you only want to validate the json content, use

ipr --password $IPR_PASS -c 'path/to/content.json' --validate_json --ipr_url $IPR_URL

If you only want to upload the json directly to ipr and skip all the preprocessing, use

ipr --password $IPR_PASS -c 'path/to/content.json' --upload_json --ipr_url $IPR_URL

Documentation

The user documentation for this tool is hosted with the main documentation site.

Developers: Any updates to this tool should be edited and reflected in the main site documentation as well.

Deployment (Publishing)

Install the deployment dependencies

pip install .[deploy]

Build the distribution files

python setup.py install sdist bdist_wheel

Upload the distibutions to the package server (-r is defined in your pypirc)

twine upload -r bcgsc dist/*