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A web application for finding and comparing bioinformatics training materials on GitHub and GitLab

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Glittr

Glittr is a web app to find bioinformatics training materials on GitHub and GitLab based on Laravel.

Requirement

  • PHP 8.1+
  • MySQL or Postgres database
  • Redis
  • Github PAT (Personal access token)
  • Gitlab Access Token

Installation

Copy .env.example to .env and set your access tokens and server configuration.

Local

You can run in local using DDEV.

ddev start
ddev composer install
ddev artisan migrate:fresh --seed
ddev artisan repo:import
ddev npm install
ddev npm run dev

To have repositories updated when added/modified you need to run the queue worker.

ddev artisan queue:work

Production

composer install --no-dev -o
npm install
npm run build
artisan migrate:fresh --seed
artisan repo:import

See Laravel documentation for jobs task runner configuration and cron job.

API

The API endpoint is available at /api/repositories. It is using Spatie Query Builder to filter the data with the following parameters:

Filters

Example of filters usage

// Search repositories with author name containing "sib" and license containing "cc"
GET /api/repositories?filter[author.name]=sib&filter[license]=cc

// Search respositories taged with "r" or "machine learning"
GET /api/repositories?filter[tags.name]=r,machine%20learning
Fiter Exact match Description
name No Repository name
licence No Repository license
description No Repository description
author.name Yes Author Github/Gitlab username
author.display_name No Author Github/Gitlab display name
tags.name Yes Repository tags
tags.category.name No Repository with a tag from this category

To retrieve the list of tags and categories you can use the /api/tags endpoint which retunr the list of tags grouped by category with repositories count.

Sorting

Default sorting is by number of stars in descending order. You can change the sorting direction by adding - before the sort field.

// Sorting by most recently updated (last push)
GET /api/repositories?sort=-last_push
Sort Description
name Repository name
stargazers Number of stars
last_push Last push
author.name Author Github/Gitlab username

Pagination

By default, the API will return all results. You can retrieve paginated results by adding the page parameter. It will use spatie/laravel-json-api-paginate package which follow the JSON API spcec (max results per page is set to 100).

// Page 2 with 10 results per page
GET /api/repositories?page[size]=10&page[number]=2

Repositories List

There is an additional endpoint /api/list which returns the list of repositories grouped by their main category, as presented on the sib-swiss/training-collection repository.

Bioschemas

Endpoints /api/bioschemas is available to retrieve the list of repositories in Bioschemas TrainingMaterial Profiles format. The endpoint is using the same filters, sorting ang pagination optiopns than /api/repositories endpoint.

License

Glittr is licensed under The MIT License (MIT). Please see License File for more information.

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A web application for finding and comparing bioinformatics training materials on GitHub and GitLab

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