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Implement the middle panes for EU Galaxy servers #1380

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NickSto opened this issue May 11, 2022 · 3 comments
Open

Implement the middle panes for EU Galaxy servers #1380

NickSto opened this issue May 11, 2022 · 3 comments
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hosted Content hosted for inclusion in other sites (like Galaxy instances) new-feature Issue making a feature request, or a PR implementing a new feature. unification

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@NickSto
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NickSto commented May 11, 2022 •
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I'm copying this here from #1117, since it outgrew that list.

Basics

galaxyproject.eu provides the middle panes for all the *.usegalaxy.eu servers.

Each of the index-*.md files in the root directory generates a page that's hotlinked from an iframe in a Galaxy instance.

For instance:
index-rna.md generates
https://usegalaxy-eu.github.io/index-rna.html, which is the center pane of
https://rna.usegalaxy.eu/

Most (all?) of them seem to be for subdomains of usegalaxy.eu.

Static content

The most common pattern seems to be that they contain some intro text, a table with links to relevant GTN tutorials, tables that list relevant tools, and things like acknowledgments, a list of contributors, and citation guidelines.

Dynamic features

But there are a number of elements in these pages which are not contained in the Markdown files, and are instead dynamic features injected by the framework:

  • Header: Things like server maintenance announcements or the Ukraine support message
    • These seem to be the same on every page.
  • {{ page.website }}
    • Many pages use this variable notation, which expands to the galaxy server's domain (e.g. https://rna.usegalaxy.eu).
      • This is set in the .md file metadata header.
    • We could just replace these with hardcoded strings. It's pretty easy to Replace All if the domain ever changes.
    • Or we could use a similar syntax that vue-remark provides: {{ $frontmatter.website }}
  • page.subdomain
    • This is also set in some pages' metadata, and not directly referenced in the content. But it's used in the tool.html include.
  • Footer: Things like the data retention policy and a widget showing the currently running jobs (jobs_graph.html)
    • Same on every page.
  • They also include the site-wide footer present on every galaxyproject.eu page.
  • Finally, 11 of the middle panes use the tool.html function to generate tool urls (see below)

Exceptions

28 of these 32 pages follow the above patterns, but 4 do not:

  • galaxy/index.md: This includes the header and footer, but the body is dynamic, not static content: the homepage carousel, plus recent news and events.
  • index-metabolomics.md: Normal except that it also includes the same dynamic stuff that galaxy/index.md does.
  • index-proteomics.md: Same. It also includes a Twitter widget, but using static HTML.
  • index-live.md: Ditches the header and footer, replacing it with a totally custom page. At least it's all static. But it's all HTML.

tool.html

11 pages use _includes/tool.html to translate a tool id to its url on the Galaxy instance:

  • index-cheminformatics.md
  • index-climate.md
  • index-erasmusmc.md
  • index-graphclust.md
  • index-humancellatlas.md
  • index-ml.md
  • index-nanopore.md
  • index-rna.md
  • index-singlecell.md
  • index-spatialomics.md
  • index-virology.md

This requires looking up the id in the https://github.com/usegalaxy-eu/website/blob/master/_data/tools.yml database (and knowing the domain name of the Galaxy instance).

Details are here: #1410
@NickSto NickSto mentioned this issue May 11, 2022
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NickSto commented May 11, 2022 •
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The tool.html/tools.yml issue is now tracked in #1410.

@NickSto
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NickSto commented May 12, 2022 •
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Links

One major consideration: navigation from the middle panes. I.e. what happens when a user clicks an internal link in the middle pane?

Currently, on the .eu-hosted pages, they get taken to a navbar-less plain.html version of the post. The response to #1385 will determine if we need to also do this. Otherwise, we could just add target="_blank" to every link.

Implementation

So how would we actually add the target="_blank" to every link? It's actually not trivial when you think about it.

Option 1

Just add {: target="_blank" } to every link in each Markdown file.

Pros: Simple, allows maximum customization (we can choose which links to apply it to).
Cons: Painstaking, manual, verbose.

Option 2

Add a <base> tag to the HTML?

Apparently you can use this element to set a default target on every link in the document.

But I'm not even sure if this would work. It looks like it's only allowed in the <head>, meaning we can't just stick it in the BareArticle template. Instead we'd have to do messy things to get it into the <head>, but only on BareArticles.

Pros: Automatically applies to all links on the page
Cons: Hidden magic, no per-link customization, hacky or impossible to get it into the <head>.

Option 3

Add a client-side bit of Javascript that adds target="_blank" to every link in the Markdown.

Pros: Relatively simple, automatically applies to all links, slightly customizable
Cons: Kludgy

@NickSto NickSto added the new-feature Issue making a feature request, or a PR implementing a new feature. label Jun 1, 2022
This was referenced Jun 24, 2022
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NickSto commented Jun 30, 2022 •
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Update: Apparently almost* every EU Member Site has its own middle pane, and they all seem to list news and events.

*elixir-it doesn't have one.

Site Galaxy instance Notes
freiburg ?
erasmusmc erasmusmc.usegalaxy.eu Landing page doesn't use the middle pane.
belgium usegalaxy.be Instance currently serving a redirect loop.
pasteur galaxy.pasteur.fr Landing page doesn't use the middle pane.
genouest galaxy.genouest.org Private instance.
ifb usegalaxy.fr Landing page doesn't use the middle pane.

@bgruening @beatrizserrano Do you know if/where these middle panes are used in these Galaxy instance? Because I haven't found them in use yet. Maybe traffic stats for each of the middle panes could show whether they're used.

@NickSto NickSto added the hosted Content hosted for inclusion in other sites (like Galaxy instances) label Jul 7, 2022
@NickSto NickSto mentioned this issue Jul 7, 2022
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