Closed pkalita-lbl closed 2 months ago
Thanks for the review. My plan is to wait for the initial feedback from https://github.com/geneontology/go-site/issues/2255 before merging this.
@kltm I pushed some changes in accordance with https://github.com/geneontology/go-site/issues/2255 and updated the PR description/screenshots. Do you want to give this one last glance before I merge?
Looking at your changes, I still approve. @pgaudet If you look at the images above, is this sufficient?
@pkalita-lbl , talking to @pgaudet , she said that she's good to move ahead.
Fixes #506
Summary
These changes add a
Makefile
with a target to fetch the latestgorefs.yaml
file from thego-site
repo. From this file a single GO REFs page is generated.Details
Makefile
with a single target,_data/gorefs.yaml
, which fetches the latestgorefs.yaml
from the head of themaster
branch of thego-site
repo._data/gorefs.yaml
file to.gitignore
. This file will never be checked into this repo to maintaingo-site
as the source of truth. TheMakefile
target should be run before doing any development or making a production build.Add a singlegorefs.html
page which lists all GO REFs. The format of this page is largely based on the existingREADME
file (https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md). One notable difference is that this page does not include the "table of contents" at the top of the page. It wasn't clear how much value that really provides. Each GO REF title links to its own page anchor (e.g./gorefs#GO_REF:0000008
).gorefs.html
which lists the ID and title of each GO REF. This is modeled on the "table of contents" at the top of https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md. Each item links to a separate page for the individual GO_REF. Based on feedback in https://github.com/geneontology/go-site/issues/2255, obsolete GO REFs are listed in a separate list at the bottom of the page.gorefs/go_ref0000003.html
)Screenshots
Index page:![image](https://github.com/geneontology/geneontology.github.io/assets/102547565/7897295d-01ec-4361-9527-5de46d8b0add)
Individual GO REF page:![image](https://github.com/geneontology/geneontology.github.io/assets/102547565/330d8efa-7922-4b28-9fc0-f81652e67f85)
Comments
README
file did. In particular the following fields are part of the GO_REF YAML file specification, but not displayed on the page:alt_id
,evidence_codes
,url
. If we want to take this opportunity to display that information we could.You'll notice that plain URLs don't render as links in this page, whereas they did in theUPDATE: Jekyll's Markdown renderer does not turn plain URLs into links, which are somewhat pervasive in the GO REF descriptions. I added a custom Liquid filter to turn these URLs into links.README
(as displayed on GitHub anyway). This is due to a difference in the Markdown renderers used by GitHub vs Jekyll (further reading here and here). I can keep looking at technical solutions to get them linked. But if all else fails the descriptions may need to be updated to enclose the URLs in angle brackets (<http://example.org>
).I talked briefly with @kltm about one long page vs individual pages for GO REFs (or both) and decided to do one long page with anchor links for now. However I'll throw out the standard caveat that anchor links can be a little confusing for sections near the bottom of the page (i.e. when there isn't enough content below the desired section to scroll it all the way to the top of the view).UPDATE: After feedback in https://github.com/geneontology/go-site/issues/2255 we reversed course and did make an index page and individual pages.