Communities lost

[AlexanderPico]

We have a bug in our communities logic. Currently, when a communities text file is updated (e.g., a WPID is add to a community list), then the community is added to the md file for that pathways. This is the on_community_change.yml and it works fine, as outlined here.

However! If a pathway is edited later on, then the on_gpml_change.yml is triggered and it creates a new md file and doesn't access the communities lists, thus removing the community assignment!

@khanspers and others. If you've noticed pathways disappearing from communities, then this might be the cause.

I don't think this happens every time a pathway is edited, since it should just overwrite the changed parts, but it definitely happens sometimes. Need to dig deeper.

[AlexanderPico]

Here is an example of where the community "Rare diseases" was lost during an MD update of the authors. https://github.com/wikipathways/wikipathways.github.io/commit/3516ca12cdd7532c4386eb5e21642c772ef68090

[khanspers]

Yikes! I haven't noticed missing pathways but will look now.....

[AlexanderPico]

Community, CitedIn, and NDEx entries in the MD would be lost for the same reasons.

[AlexanderPico]

Yikes! I haven't noticed missing pathways but will look now.....

Two examples WP5105 and WP5130 are no longer in the Rare Diseases community, even though they are still in the text file lists.

Don't need additional examples to diagnose or fix issue.

[AlexanderPico]

I can simply run the actions for adding communities and ndex entries to md files. This will correct all the losses. But before doing that I want to fix the bug so we don't have to run those every time we run on_gpml_change.yml

[AlexanderPico]

Ok. Fixed create_frontmatter.py and am running actions for communities, NDEx, and CitedIn to refill lost entries.