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pori_ipr_python's Introduction

IPR

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

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 this adaptor, see the main documentation site for the platform.

Getting Started

Install (For developers)

clone this repository

git clone https://github.com/bcgsc/pori_ipr_python.git
cd pori_ipr_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

pytest tests

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.

pori_ipr_python's People

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pori_ipr_python's Issues

Missing required expression comparators

When running pori ipr python adapter using expression data as input I receive the following error:

Traceback (most recent call last):
File "/projects/cgrisdale_prj/POG/GraphKB/PORI_python_adapter/pori_ipr_python/venv/bin/ipr", line 11, in
load_entry_point('ipr', 'console_scripts', 'ipr')()
File "/projects/cgrisdale_prj/POG/GraphKB/PORI_python_adapter/pori_ipr_python/ipr/main.py", line 133, in command_interface
generate_therapeutics=args.therapeutics,
File "/projects/cgrisdale_prj/POG/GraphKB/PORI_python_adapter/pori_ipr_python/ipr/main.py", line 219, in create_report
check_comparators(optional_content or {}, expression_variants)
File "/projects/cgrisdale_prj/POG/GraphKB/PORI_python_adapter/pori_ipr_python/ipr/inputs.py", line 551, in check_comparators
raise ValueError(f'missing required comparator definitions ({missing})')
ValueError: missing required comparator definitions (expression (biopsy site); expression (disease); expression (primary site))

Command:
ipr --username 'cgrisdale' --password 'myPass' -e tests/test_data/expression.tab --patient_id 'ExpTest02' -d 'colorectal cancer' -o ./ExpTest02_output.json

OS: centos7
Python: 3.6.9

Missing property 'template' error

I tried running the pori ipr python adapter using provided small mutation test data and received the following error message:

Traceback (most recent call last): File "/projects/cgrisdale_prj/POG/GraphKB/PORI_python_adapter/pori_ipr_python/ipr/main.py", line 331, in create_report ipr_result = ipr_conn.upload_report(output) File "/projects/cgrisdale_prj/POG/GraphKB/PORI_python_adapter/pori_ipr_python/ipr/connection.py", line 66, in upload_report return self.post('/reports', content) File "/projects/cgrisdale_prj/POG/GraphKB/PORI_python_adapter/pori_ipr_python/ipr/connection.py", line 62, in post **kwargs, File "/projects/cgrisdale_prj/POG/GraphKB/PORI_python_adapter/pori_ipr_python/ipr/connection.py", line 53, in request raise requests.exceptions.HTTPError(message) requests.exceptions.HTTPError: 400 Client Error: Bad Request for url: https://iprstaging-api.bcgsc.ca/api//reports There was an error validating the report content Error: should have required property 'template' [missingProperty: template]

Command run:
ipr --username 'cgrisdale' --password 'myPass' -m tests/test_data/small_mutations_probe.tab --patient_id 'SmMuTest02' -d 'colorectal cancer' -o ./SmMutTest02_output.json

OS: centos7
Python: 3.6.9

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