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OpenTreeOfLife / otcetera

C++20 lib for manipulations of phylogenetic trees and supertree operations
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taxon info needs to report suppressed from synth correctly #104

Open mtholder opened 3 years ago

mtholder commented 3 years ago

see https://tree.opentreeoflife.org/taxonomy/browse?id=4130355

'is_suppressed': False, 'is_suppressed_from_synth': False,

bredelings commented 3 years ago

OK, so ott413055 is not present in labelled_ott.tre, but it is present in:

It is not in

So, presumably it is pruned because it is incertae sedis, but does not occur in a phylogeny.

bredelings commented 3 years ago

So the obvious way to handle this would just be to check the synth tree and see if it has the node.

If we have multiple synth trees, we could use the default synth tree.

I suppose we could allow a "synth_id" flag on the taxon_info call... which kind of points out that this isn't really a taxonomy property anymore.

bredelings commented 3 years ago

@mtholder Do you think we may have originally assumed that we could determine from the taxonomy alone whether a tree was suppressed from synth?

In theory people could check to see if taxon X exists using taxon_info, and then check to see if the summary tree node "ottX" exists using node_info.

Fixing this issue seems to be the same as doing that inside the server so people don't have to do two calls.