search

KarrLab / datanator_rest_api

A OAS3 compliant REST API for the Datanator integrated database
MIT License
0 stars 3 forks source link

Bug with taxonomic distance calculation in /proteins/proximity_abundance #133

Closed jonrkarr closed 3 years ago

jonrkarr commented 3 years ago

Examples:

jonrkarr commented 3 years ago

The error appears to be with the taxonomic distance calculation because the query succeeds without the species. Example: https://testapi.datanator.info/proteins/proximity_abundance/proximity_abundance_kegg/?kegg_id=997616at2&distance=40

lzy7071 commented 3 years ago

Cases where two different species have the same canonical common ancestors were not properly accounted for. It has now been fixed. Performance should also be greatly improved now the endpoint leverage native canonical ancestor information.

Note: having the keyword fixed in commit message in front of the issue link seems to automatically close the referenced issue.

jonrkarr commented 3 years ago

This looks to be fixed in the API, but the test API still has the error.

I learned about these shortcuts from Bilal. He's been using them. This works in comments on pull requests too. GitHub recognizes several keywords. See https://docs.github.com/en/free-pro-team@latest/github/managing-your-work-on-github/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword.

lzy7071 commented 3 years ago

This looks to be fixed in the API, but the test API still has the error.

I didn't deploy the test API. Should be fixed once the deployment is done. I also found out a big part of the performance issue for this endpoint is due to MongoDB's handling of sparse compound indexes. I've trying different combinations to see if performance can be improved.

jonrkarr commented 3 years ago

Improvement to the performance would be great

lzy7071 commented 3 years ago

Original issue is working now. Moved performance improvement issue to other repo.