Bug #945
Updated by Aaron Marcuse-Kubitza about 10 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) 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. h3. fix # -in "@class.tnrs_aggregator.php@":https://github.com/iPlantCollaborativeOpenSource/TNRS/blob/master/taxamatch-webservice-read-only/api/classes/class.tnrs_aggregator.php#L21 "@class.tnrs_aggregator.php@":https://github.com/iPlantCollaborativeOpenSource/TNRS/blob/master/taxamatch-webservice-read-only/api/classes/class.tnrs_aggregator.php#L746 (on the dev server), change the sort order of accepted vs. synonym so that a (TPL) synonym is chosen in preference to a (Tropicos) accepted name:- name- <pre><code class="PHP"> - static $acceptance_array=array("Accepted" => 3, "Synonym" => 2, "Illegitimate" => 1, "Invalid" => 1, "Rejected name" => 1, "Orth. var." => 1, "Misapplied name" => 1, "Synonym? (unresolved)" => 1, "No opinion" => 0, "" => 0); + static $acceptance_array=array("Synonym" => 3, "Accepted" => 2, "Illegitimate" => 1, "Invalid" => 1, "Rejected name" => 1, "Orth. var." => 1, "Misapplied name" => 1, "Synonym? (unresolved)" => 1, "No opinion" => 0, "" => 0); </code></pre>_this _this has now been fixed on the TNRS dev server (tested with "Brad's test case":https://projects.nceas.ucsb.edu/nceas/issues/945#test-case above)_ # rescrub names where this is an issue