VEuPathDB / VEuPathDB/lib-eda-subsetting
Map - default variable for bubble markers in megastudy is super-slow - think about improving default variable configuration
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Description
Despite the work done in https://github.com/VEuPathDB/EdaDataService/pull/320 for https://github.com/VEuPathDB/EdaNewIssues/issues/690 it still seems to take a long time to calculate the all/all proportion for the megastudy's species variable.
The current choice of default variable is the "first compatible featured variable".
We need to think about either adding new variable annotations, or some other way to select default variables?
Perhaps we could add more featured variables but in bubble marker mode the client filters out variables with a lot of values. The problem there is that any such featured variables have to be "below" sample.species in the entity tree, or they'll be picked up by donut/bar markers as the new default. I think we really want to keep species default for those.
TBH there isn't an obvious choice for a default bubble marker mode. Especially variables with 100% coverage. There are some great choices for specialised questions, such as mortality rate, genotype prevalences etc.
Tricky...
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Research direction
Start by reviewing the default-variable selection used for megastudy bubble marker mode and the related EdaDataService pull 320 and EdaNewIssues issue 690. Compare species with other featured variables and the client’s value-count filtering. Done means an agreed configuration or annotation approach that avoids the slow all/all proportion calculation while preserving species as the default for donut and bar markers.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- backend-api-design
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100