Bioplatforms Data Portal User Support Guides

Content

User support articles for the Bioplatforms Data Portal.

1. How to register for an account and log-in
2. How to find, filter and bulk download data and meta-data
3. How to filter Australian Microbiome data
4. Programmatic access to the Bioplatforms Data Portal

For the production view for end users linked off the BPA Data Portal, this uses a Jekyll remote theme that is compatible with Github Pages.

For development/authoring of content, a local build is possible with Jekyll, or a simplified view with RMarkdown/RStudio

Image assets are located in the images/ directory

Jekyll

Remote theme

There is a Jekyll theme that matches the main Bioplatforms Australia Data Portal website. It is located in the following repository.

https://github.com/BioplatformsAustralia/jekyll-theme-bpa

Remote themes for GitHub Pages are discussed here:

https://github.blog/2017-11-29-use-any-theme-with-github-pages/

This was used as a reference implementation during the process of getting it working:

https://github.com/MichaelCurrin/jekyll-theme-quickstart

Navigation

The navigation for the site is built based on the contents of _config.yml

If further User Support articles are added, they must be included here.

Local build using Jekyll

The site can be built locally for development and testing.

A local ruby install is required. Use of rbenv to setup a development environment, with the bundler gem needed to install Jekyll and associated plugins.

A Makefile is provided with the following targets:

• install - install the necessary gems
• serve - run a local web server to view the content
• build - build a static HTML render of the content

The build uses same remote theme as the production render. Render output will end up in the _site directory

Production render on Github Pages

The Remote Theme is specified in _config.yml file

The repository for the theme must have public access enable on Github.

The site is configured on the Github Pages settings page at:

https://github.com/BioplatformsAustralia/dataportal-usersupport/settings/pages

The Source is set on the master branch, with root specified as the relevant directory. No theme is chosen here as it is picked up from the _config.yml file.

RMarkdown

Local build using RStudio / RMarkdown

The site can be built locally for development under RStudio with RMarkdown.
A different theme is applied. The RMarkdown render is configured in _site.yml

Navigation

Navigation links are defined under _includes/header.html

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Attributions for the Jekyll render

Attributions for building the RMarkdown render

• Rmarkdown
  • Cookbook
  • Site
  • Appearance & style
  • Rstudio lesson for rmarkdown: lesson 13
  • HTML-CSS
• GitHub & Rstudio whitepaper
• Image hyperlinks
• Google Analytics
• Prevent body / navbar overlap
• Side nav bar
• CSS website layout
• CSS page width
• Add elements to header - including favicon

Xie Yihui, Dervieux Christophe, Riederer Emily. 2020. R Markdown Cookbook. https://bookdown.org/yihui/rmarkdown-cookbook/

Xie Yihui, Allaire J. J., Grolemund Garrett. 2020. R Markdown: The Definitive Guide. https://bookdown.org/yihui/rmarkdown/

R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.