10618
Reporter: mdoering
Assignee: mdoering
Type: Bug
Summary: Some nub usages have unstable ids
Priority: Blocker
Resolution: Fixed
Status: Closed
Created: 2012-01-10 11:15:03.724
Updated: 2013-12-09 13:40:39.346
Resolved: 2012-01-10 21:11:34.959
Description: Although the integration test for stable ids did not fail some names in the nub have changed their ids since the last version.
Those names are not homonyms and this should not happen as we must provide stable ids for external links.
Investigate why this happened and the quantity of changed ids since the last version.
Known names that have changed are:
Astragalus angustifolius
Trifolium repens http://ecat-dev.gbif.org/usage/10087471
Hydraena truncata Rey. http://ecat-dev.gbif.org/usage/10486431
Dracaena cinnabari Balf. f. http://ecat-dev.gbif.org/usage/10191773
Zeus faber http://ecat-dev.gbif.org/usage/10275863]]>
Author: mdoering@gbif.org
Created: 2012-01-10 12:41:03.016
Updated: 2012-01-10 12:41:25.191
diffing the outcome of subsequent nub builds of the testStableIds IT these names have changed their ids.
It seems they are all homonyms or child taxa of genus homonyms:
1010776 Acanthophora aokii Okamura f 600 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1008647 Acanthophora arborea Harvey f 600 Plantae \N \N \N \N Acanthophora
1010763 Acanthophora delilei Greville, nom. illeg. t 600 Animalia Echinodermata Crinoidea Comatulida Thalassometridae \N
1010780 Acanthophora dendroides Harvey f 600 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1010771 Acanthophora intermedia t 600 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1010777 Acanthophora muscoides (Linnaeus) Bory de Saint-Vincent f 600 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1010778 Acanthophora nayadiformis (Delile) Papenfuss f 600 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1010770 Acanthophora orientalis J. Agardh t 600 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1010773 Acanthophora orientalis wightii (J. Agardh) Sonder t 625 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1010779 Acanthophora pacifica (Setchell) Kraft f 600 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1010775 Acanthophora ramulosa Lindenberg ex Kützing f 600 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1008646 Acanthophora scandens Merr. f 600 Plantae \N \N \N \N Acanthophora
1010767 Acanthophora spicifera (M. Vahl) Børgesen f 600 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1010768 Acanthophora spicifera orientalis (J.Agardh) Weber-van Bosse t 625 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1010769 Acanthophora spicifera wightii (J. Agardh) Weber-van Bosse t 625 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1008645 Acanthophora tasmanica Sonder f 600 Plantae \N \N \N \N Acanthophora
1010774 Acanthophora thierryi J.V. Lamouroux t 600 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1010772 Acanthophora wightii J. Agardh t 600 Plantae Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Acanthophora
1010822 Amphibia hybrid × formula Perroud & Montrouzier, 1864 f 425 Animalia Arthropoda Insecta Coleoptera Carabidae Amphibia hybrid × formula Perroud & Montrouzier, 1864
1010749 Amphiporidae Oersted, 1844 f 325 Animalia Nemertea Enopla \N Amphiporidae \N
1010838 Amphiporidae Rukhin, 1938 f 325 Animalia Porifera \N \N Amphiporidae \N
1010809 1006640 Anura Hodgson, 1841 f 425 Animalia Chordata Aves \N \N Anura
1010815 Apodidae Burmeister, 1846 t 325 Animalia Arthropoda Branchiopoda Notostraca Triopsidae \N
1010794 Atyidae Thiele, 1925 t 325 Animalia Mollusca Gastropoda Cephalaspidea Haminoeidae \N
1010705 Atyidae de Haan, 1849 f 325 Animalia Arthropoda Malacostraca Decapoda Atyidae \N
1010792 Aulocystidae Sokolov, 1950 f 325 Animalia Cnidaria Anthozoa \N Aulocystidae \N
1002043 Aulocystidae Sollas, 1887 f 325 Animalia Porifera Hexactinellida Lychniscosida Aulocystidae \N
1010762 Axiidae Huxley, 1879 f 325 Animalia Arthropoda Malacostraca Decapoda Axiidae \N
1001566 Buliminidae Jones, 1875 f 325 Protozoa \N Granuloreticulosea Foraminiferida Buliminidae \N
1010796 Buliminidae Kobelt, 1880 t 325 Animalia Mollusca Gastropoda Pulmonata Enidae \N
1010832 Caeciliidae Kolbe, 1880 t 325 Animalia Arthropoda Insecta Psocoptera Caeciliusidae \N
1006496 Caeciliidae Rafinesque, 1814 f 325 Animalia Chordata Amphibia Gymnophiona Caeciliidae \N
1010839 Canuellidae t 325 Animalia Bryozoa Stenolaemata Cyclostomatida Cerioporidae \N
... more
Author: mdoering@gbif.org
Created: 2012-01-10 13:12:31.951
Updated: 2012-01-10 13:12:31.951
So definitely there is a problem with homonyms of higher ranks.
For example the families:
Cepheidae Claus, 1883
Cepheidae Berlese, 1896
or
Axiidae Rebel, 1919
Axiidae Huxley, 1879
Currenlty higher taxa ids are only based on the canonical name and the rank.
This needs to be changed to take the homonym reference usage id into account
Author: mdoering@gbif.org
Created: 2012-01-10 14:38:46.511
Updated: 2012-01-10 14:38:46.511
Another source for the same problem are hybrids and other non parable names.
The NubIdGenerator only dealt with parsable names so far. This is fixed in revision 4832
Author: mdoering@gbif.org
Created: 2012-01-10 14:43:49.782
Updated: 2012-01-10 14:43:49.782
Another source for the problem are "partial" homonyms, i.e. species or infraspecific names that have a genus which is a homonym.
In that case the id generator does only look for true species homonyms, but not for the usually unique canonical binomial.
In the above testStableIds IT this is the case for all Acanthophora species such as Acanthophora aokii
Author: mdoering@gbif.org
Comment: Fixed the unconfirmed partial homonym issue in revision 4833
Created: 2012-01-10 14:52:53.759
Updated: 2012-01-10 14:52:53.759
Author: mdoering@gbif.org
Created: 2012-01-10 21:11:26.801
Updated: 2012-01-10 21:11:26.801
revision 4835 also fixes the unstable ids for higher taxon homonyms with the same rank.
Good to close this issue with the new integration test assertion that no single new id is assigned when the test nub is rebuild.
http://code.google.com/p/gbif-ecat/source/detail?r=4835