Analysis Reports

Introduction

This repository provides a script ar.py to generate analysis reports to accompany released data.

Getting Started

Installation

Clone this repository into a folder on the cluster.

git clone git@github.com:oicr-gsi/Analysis_Reports.git

Dependenices

Separately, confirm that you have access to the QC-ETL caches under the folder /scratch2/groups/gsi/production/qcetl_v1, or else the report will not be able to pull data.

The file requirements.txt has the dependenices required for the script to work. It is recomended that you install these in a new python virtual environment. One option is to use Anaconda, a popular package management software that was used in the development of this repository.

After installing Anaconda and setting up a new virtual environment, run the following command in the root directory of this repo

conda create -c conda-forge --prefix /path/to/conda/env --file requirements.txt

If you opt to use a different package manager like Pyenv, you will most likely run

pip install -r requirements.txt

Usage

Two examples of using the script are as follows:

Example 1

python3 ar.py -i infile.json -o outfile.pdf

This will pull data from infile.json and, using data from QC-ETL files located under /scratch2/groups/gsi/production/qcetl_v1, will create an Analysis Report in the current directory named outfile.pdf

Example 2

python3 ar.py -i infile.json -o /reports/outfile.pdf --stage

This will pull data from infile.json and, using data from QC-ETL files located under /scratch2/groups/gsi/staging/qcetl_v1, will create an Analysis Report in the reports directory named outfile.pdf.

Parameters

argument	abbreviation	purpose	required/optional	default
--infile	-i	The input file to be read	required	ar_input.json
--outfile	-o	Name of the report generated	required	"Analysis_Report.pdf"
--staging, --stage		If used, data will be pulled from stage. optional	Leaving out the flag will pull data from production

Input json structure

Still being developed. (JSON below is a placeholder.)

{"cases":
   {workflow_1:
      {"workflow_id": "19168526", "workflow_version":"2.0.2"},
    workflow_2:
      {"workflow_id":"16962244", "workflow_version":"2.0.2"}
   }
}