Bridgedb and Ovis aries

[AlexanderPico]

This pathway broke our latest sync attempt: https://classic.wikipathways.org/index.php/Pathway:WP5196

The error was in the webservice call to BridgeDb:

https://webservice.bridgedb.org/Ovis aries/xrefsBatch

And I don't see Ovis aries in the support list of organisms.

Plan to add it or should this pathway be flagged as not acceptable?

[egonw]

Mmm... weird. Yeah, BridgeDb supports it. But when I check https://webservice.bridgedb.org/Ovis%20aries/properties or https://webservice.bridgedb.org/Sheep/properties I indeed not get results.

But the pathways should be accepted; we have the ID mapping files. This is a bug.

And I don't see Ovis aries in the support list of organisms.

That is because in the NWO grant we were updating the Swagger infrastructure and hacking the old documentation has not been on our priority list.

[egonw]

I see sheep in our actions, line 80 and 100:

• https://github.com/wikipathways/wikipathways-database/blob/main/.github/workflows/scheduled_bridge_cache.yml#L80
• https://github.com/wikipathways/wikipathways-database/blob/main/.github/workflows/scheduled_bridge_cache.yml#L100

At the same time, I think I can confirm that our BridgeDb WS is not hosting it: https://webservice.bridgedb.org/Ovis%20aries/properties

[egonw]

Okay, the problem is that I am not running the latest BridgeDb on the webservices, but the older 3.0.13. I'll fix this this week.

[egonw]

I think we're back in business.

[AlexanderPico]

Thanks! I'll mark the pathway as approved (again) and see if it run through our pipeline to the new site.

[AlexanderPico]

Done!