Bug #945
Updated by Aaron Marcuse-Kubitza over 9 years ago
_this is "TNRS-195":https://pods.iplantcollaborative.org/jira/browse/TNRS-195 on the TNRS JIRA bug tracker_
TNRS's synonym-selection algorithm incorrectly considers taxonomic_status when sorting names, which causes a worse Tropicos synonym to be selected instead of a better TPL synonym (when TPL is ranked before Tropicos in the source sort order)
the fix for this is to remove lines 784-786 of "@class.tnrs_aggregator.php@":https://github.com/iPlantCollaborativeOpenSource/TNRS/blob/master/taxamatch-webservice-read-only/api/classes/class.tnrs_aggregator.php#L766 (on the dev server):
<pre><code class="PHP">
if ($aa != $ba) {
return (self::$acceptance_array[$aa] > self::$acceptance_array[$ba]) ? -1 : +1;
}
</code></pre>
(note that the vars @$aa@, @$ba@ are set on lines 766-767)
h3. test case
p(. "_from Brad_":mailto:bboyleATemail.arizona.edu?Brad_Boyle.2014-9-2.14:57PT.Test_names_for_TNRS_fix:
> Here’s a pair of names that are still a problem: [test these with the sources set to TPL, Tropicos (in that order)]
>
> Glandularia quadrangulata
> Verbena quadrangulata
>
> The second name (Verbena quadrangular) is a synonym of the first, according to Tropicos’s website. But computedAcceptance returns both as accepted. This is the result you get if you submit the names to the TNRS (either the production version or toad):
>
> Glandularia quadrangulata —> Accepted, =Glandularia quadrangulata (A. Heller) Umber, Tropicos
> Verbena quadrangulata —> Accepted, =Verbena quadrangulata A. Heller, Tropicos
>
> The suggested fix should result in:
>
> Glandularia quadrangulata —> Accepted, =Glandularia quadrangulata (A. Heller) Umber, Tropicos
> Verbena quadrangulata —> Synonym, =Glandularia quadrangulata (A.Heller) Umber, TPL
>
> …which is what we want.