review list of properties for find_trees and find_studies - Githubissues

OpenTreeOfLife / otindex

opentree index using postgres and pyramid

BSD 2-Clause "Simplified" License

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review list of properties for find_trees and find_studies #31

Closed kcranston closed 7 years ago

kcranston commented 8 years ago

Draft documentation of searchable properties for trees and studies in otindex.

Review requested. @jar398 @jimallman @josephwb

josephwb commented 8 years ago

Is there a timeframe on this?

kcranston commented 8 years ago

Within the next week would be good. Should have the NeXSON changes for preferred trees / ot:candidateTreeForSynthesis worked out by then and ready to implement.

josephwb commented 8 years ago

I'm not sure how to review: the math on the new vs. deprecated properties does not seem to add up (e.g. the page mentions 53 study properties, but running the script reports only 51; page says 32 tree properties, but script says 28).

Can all of the new vs. old properties be posted on that page rather than running a script? Presumably we might want to consider deprecating more?

josephwb commented 8 years ago

Is this repo not hooked up to gitter yet? Should do that so other people can note issues, etc.

josephwb commented 8 years ago

It would be nice on that page to list the property types as well.

kcranston commented 8 years ago

Ok, made the following changes:

added otindex to the gitter integrations
put the full result of the API call in the doc (and removed the link to the peyotl script, because that was confusing)
included links to NexSON / NeXML docs that have full descriptions of the properties that aren't specific to otindex

josephwb commented 8 years ago

Thanks!

kcranston commented 7 years ago

Assuming that there aren't any concerns, given lack of comment. Closing.

jar398 commented 7 years ago

Since the focal clade is found using the TNRS, it seems a lost opportunity for the curator app to fail to put the OTT id in the study ( ot:focalCladeOTTId). Minor thing.

kcranston commented 7 years ago

Since the focal clade is found using the TNRS, it seems a lost opportunity for the curator app to fail to put the OTT id in the study ( ot:focalCladeOTTId). Minor thing.

Not relevant for otindex. I suggest moving the request to opentree repo if you want this addressed. If the property exists in the NeXSON, otindex will return it.