Open colleenXu opened 1 month ago
@newgene @everaldorodrigo I think the first point is easy to fix - and a bug that needs addressing...
I think the second point may need some more discussion
@colleenXu the first point fix was released to the CI, Test, and Production environments.
@colleenXu, according to Openapi
specs we could modify the endpoint to accept a new parameter called flavor
. Ex:
We also could keep both behaviors. The current one and the new one using a parameter called flavor.
What are your thoughts?
I would just use flavor=all|strict|synonymous
, don't think we need to keep both.
I think a new parameter like flavor sounds perfect!
@newgene @colleenXu the flavor=all|strict|synonymous
was deployed to the CI environment. The default value for flavor
parameter is all
Examples for testing:
I have two observations for you/Alex Pico to check on. Otherwise, I think this looks fine and ready to deploy to all instances!
Two observations:
To check behavior, I took a few individual document/records and compared the mention counts. For example, I checked PMC6883319__gr8
...
all
looks the same as not setting flavor: 8 chemicals, 1 disease, 152 genessynonyms
: 69 genes (other entity counts didn't change)strict
: 32 genes (other entity counts didn't change)And a note to myself: for now, Andrew said I don't need to add this parameter's information to the BioThing API's SmartAPI annotation. We're currently using the default (all).
It looks like only the gene list differs for the 3 flavors (not chemicals or diseases). Is this correct @AlexanderPico?
Correct
@everaldorodrigo @ctrl-schaff @newgene
Your thoughts on my second observation?
order does not matter across different flavor
parameter values, as they are different set of hits.
So from my perspective, this seems good and ready to deploy to all instances.
Let's use the tags to track deployment? Based on the Slack convos, it looks like this is on Test now...
Two things I've noticed:
(1) queries like https://biothings.transltr.io/pfocr/query?q=associatedWith.mentions.genes.ncbigene:5879 return no hits even when there are records with that value (example). Maybe it's because there's a misspelling in the metadata/fields entry - which says associatedWith.mentions.genes.bcbigene...
(2) For the PFOCR flavors, I'm not sure how to specify them in the OpenAPI spec / x-bte annotation. They're not regular query-level parameters like fields/size/jmespath/etc....can they be? (see previous Slack convo) @newgene
Refs: