Prototype

[cbizon]

Consumes the synonym files created by the synonym_prototype branch of Babel.

The input structure is now quite different. Rather than a single document per (curie,label) pair, we now make one doc per curie. We remove the id and length parameters, and add in biolink types and a preferred name.

This has an extra benefit of making the lookup code simpler, and reducing 3 solr calls to 1.

Fixes #39, fixes #43.
Fixes #24 by returning a list sorted by ElasticSearch scores instead of a dictionary.
Fixes #32 by adding types and canonical information to NameRes.

[cbizon]

It may not be worth reviewing yet @gaurav - I realized that I need to update the openapi examples and the documentation.

[gaurav]

It may not be worth reviewing yet @gaurav - I realized that I need to update the openapi examples and the documentation.

Sounds good! Let me know once this is ready for review.

[cbizon]

I think it is ready now - the docs will need to be updated for the load, but probably after the makefile is sorted, and I think the openapi doesn't have an example anyway.

[gaurav]

• Filtering by Biolink type doesn't seem to be working at the moment.
  • This is because I had accidentally indexed types as a LowerTextField; changing it to a string fixed this issue.

[gaurav]

@cbizon I've got this working now! I made some changes to the queries; could you please check them and make sure they still make sense? You can see all the changes made since your last commit by going here: 48aa659...prototype

I've left preferred_name as a string field for now, but I think we should change it into a LowerTextField so that we can boost results that include the query in the preferred_name as compared to the names list. What do you think?

Apart from that question, I'm good to merge!

[gaurav]

Works for me! (You can try it out at http://name-resolution-sri-dev.apps.renci.org/docs within the RENCI VPN).

[gaurav]

• Not all documents in Solr have a "names" key, so we should modify the code to handle the case where there is no "names" key in doc (e.g. on line 130 in server.py). (fixed in 6f46b71 in PR Added a GitHub Action to build and publish NameRes Docker images in GitHub #36)
• Report an error if the limit is negative, since this is no longer supported. (filed in Add check for a negative limit #60 to be fixed separately)