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VEuPathDB / EdaSubsettingService

A REST service to provide data and subsetting in the Exploratory Data Analysis Workspace
Apache License 2.0
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Backend: include "scale" annotation #64

Closed danicahelb closed 1 year ago

danicahelb commented 2 years ago

The scale annotation property in the .owl files is not currently included in the JSON returned by the back end. EdaSubsettingService should include the scale annotation, so that it can be added to display labels.

The front end ticket for adding scale to display labels is: https://github.com/VEuPathDB/web-monorepo/issues/450

Edit: Danica clarifies on Slack:

“scale” (EUPATH_0001014) is annotated in the owl file for each study, following these rules: Used to identify terms that are on the log scale or natural log scale, as opposed to on the linear scale. Study specific. Set to “log” if data is on the log base 10 scale Set to “log2” if data is on the log base 2 scale Set to “ln” if data is on the natural log scale Leave blank for: All continuous terms on the linear scale, all categorical terms, all categories

danicahelb commented 2 years ago

slack communication with @jbrestel:

I don't think that will be a minor change. It will be similar to what we do with units but we'll need to add tables and rebuild the database. (in addition to adding all of the annotation properties). I have a bunch of features in the mega study branch which will need to be incorporated and will also force a rebuild so we should do that at the same time (a few release cycles away)

I've added a b59 label as a reminder to check back in with john

danicahelb commented 2 years ago

the ticket for data dev is: https://redmine.apidb.org/issues/47689 this git ticket is a reminder to make sure the redmine ticket gets completed

jaycolin commented 1 year ago

Scale is loaded, this issue can be closed. Following up in UI issue https://github.com/VEuPathDB/web-monorepo/issues/450

danicahelb commented 1 year ago

Slack convo from @dmfalke and @ryanrdoherty:

Dave Falke 1 hour ago @Ryan Doherty do you know if scale is being included in variable metadata, by the subsetting service?

Ryan Doherty 1 hour ago Looks like it is not. Not in the raml types anyway

danicahelb commented 1 year ago

"scale" (EUPATH_0001014) is annotated in the owl file for each study, following these rules:

Used to identify terms that are on the log scale or natural log scale, as opposed to on the linear scale. Study specific.

danicahelb commented 1 year ago

Related ticket: https://github.com/VEuPathDB/web-eda/issues/1055

ryanrdoherty commented 1 year ago

Column is now present in eda-rbld and that DB is configured on dev and qa stacks. The backend code is now updated to read the value and display it in the API in dev. Will be in QA once qa tagger branch is updated to 3.11.0. Waiting on client ticket https://github.com/VEuPathDB/web-monorepo/issues/450 to actually view in the UI.