FEGA Sweden Helpdesk Acceptance Testing

The purpose of this repository is to keep track of issues resulting from acceptance testing carried out by the by FEGA Sweden's Helpdesk team.

See open issues

We are currently testing the following products:

• File upload -- software for uploading files the FEGA Sweden
• Submitter Portal -- FEGA Sweden's instance of the FEGA Submitter Portal, which is currently hosted by central EGA.
• Helpdesk Portal -- FEGA Sweden's instance of the FEGA Helpdesk Portal, which is currently hosted by central EGA.

Generating reports

A script can be used for compiling reports to be sent to developers. Prerequisites and use is described below.

Prerequisites

You need to have Python 3 installed on your computer, as well as the following Python packages:

• pandas
• PyGithub

1. Use the Python script generate_report.py to export non-draft issues to Quarto markdown.

Usage:

./generate_report.py [CONFIG-FILE] [PRODUCT-NAME]

For example, to generate a report file, type something like this in the terminal:

./generate_report.py ~/my-config.ini "Submitter Portal" > ~/report.qmd

The config file should contain a valid GitHub access token and be formatted like this:

[github]
token={your access token}

2. Open and edit the resulting markdown file in RStudio.

3. From within RStudio, render a pdf of the report (you will need to have LaTeX installed on your computer in order to do this).

Generating FASTQ test files

A Snakemake workflow for generating unique test files is available in a separate GitHub repo: https://github.com/NBISweden/fega-sweden-helpdesk-generate-files