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OpenTreeOfLife / opentree

Opentree browsing and curation web site. For overarching or cross-repo concerns, please see the 'germinator' repo.
http://tree.opentreeoflife.org/
BSD 2-Clause "Simplified" License
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Show duplicated tip labels #1117

Open josephwb opened 7 years ago

josephwb commented 7 years ago

Recently, the "show duplicated tips" only appear if a tree is Included in synthesis. This is a bit of a bummer, since this is a good way to to doublecheck mapping: if there are duplicate mapped tips when they are not expected, then probably mapped a bad synonym.

This seems important, as a tree may be mapped in the curator, but added to synthesis by another route, such that the duplicate tips is not detected (and which of the duplicates survives to synthesis may adversely impact downstream synthesis).

josephwb commented 7 years ago

For my purposes, I want to use trees for something other than synthesis.

jimallman commented 7 years ago

Recently, the "show duplicated tips" only appear if a tree is Included in synthesis. This is a bit of a bummer, since this is a good way to to doublecheck mapping: if there are duplicate mapped tips when they are not expected, then probably mapped a bad synonym.

Yes, things are different now. The old "preferred" flag represented intent to use a tree in synthesis, so we have time to clean up in response to stricter quality checks. The new include-in-synth-collections feature takes immediate action, so I think it makes sense to impose stricter quality checks up-front, for all trees.

A side effect of this is that it might complain about "unimportant" trees. Not sure if that's a practical problem or just an annoyance.

josephwb commented 7 years ago

Could there possibly be a dry-run "Include"? That is, run the check before it is actually added to the synth collection. If it passes, can click "Confirm" to, er, confirm.

jimallman commented 7 years ago

We already have a very minimal validator that runs (quickly) on all trees before they can be added to synthesis. It would be cleaner to add tests there.