Bugs import adds duplicate entries in taxa tree master

[roger-mahler]

Duplicates can be identified by this query:

with duplicates as (
	select distinct author_name, genus_name, species
	from tbl_taxa_tree_master
	join tbl_taxa_tree_genera using (genus_id)
	join tbl_taxa_tree_authors using (author_id)
	group by author_name, genus_name, species
	having count(*) > 1
), taxa as (
	select taxon_id, genus_id, author_id, author_name, genus_name, species
	from tbl_taxa_tree_master
	join tbl_taxa_tree_genera using (genus_id)
	join tbl_taxa_tree_authors using (author_id)
)
	select taxon_id, author_name, genus_name, species, bt.*
	from duplicates
	join taxa using ( author_name, genus_name, species)
	left join bugs_import.bugs_trace as bt
	  on bt.sead_table = 'tbl_taxa_tree_master'
	 and bt.sead_reference_id = taxon_id
	 -- and bt.bugs_table = 'INDEX'
	order by taxon_id

Bugs import	Records	Comment
Clean (no bugs import)	0 duplicates
sead_production_201912	78 duplicates	After import of bugsdata_20190303
sead_production_201912	1636 duplicates	After incremental import

[roger-mahler]

Sample duplicate data from sead_production_201912:
author_name = '(L.)', genus_name = 'Elaphrus', species = 'riparius'

select taxon_id, t.date_updated, author_id, genus_id, author_name, genus_name, species, bt.bugs_trace_id
from tbl_taxa_tree_master t
join tbl_taxa_tree_genera using (genus_id)
join tbl_taxa_tree_authors using (author_id)
left join bugs_import.bugs_trace as bt
  on bt.sead_table = 'tbl_taxa_tree_master'
 and bt.sead_reference_id = taxon_id
where author_name = '(L.)'
  and genus_name = 'Elaphrus'
  and species = 'riparius'

taxon_id	date_updated	author_id	genus_id	bugs_trace_id	comment
28965	2014-04-17 06:02:04	3103	12656		existing record
40204	2019-12-20 23:26:18	3103	12656	150283	added by import

Imported data seems to be assigned to existing taxon:

select *
from tbl_abundances
join tbl_analysis_entities using (analysis_entity_id)
join tbl_datasets using (dataset_id)
where taxon_id in (28965, 40204)

No item assigned to 40204.

[roger-mahler]

Same data from BugsCEP:

select *
from "INDEX"
where "AUTHORITY" = '(L.)'
  and "GENUS" = 'Elaphrus'
  and "SPECIES" = 'riparius'

CODE	FAMILY	GENUS	SPECIES	AUTHORITY
1.0120030000000000	CARABIDAE	Elaphrus	riparius	(L.)

This specie has a synonym:

select *
from "TSynonym"
where "SynAuthority" = '(L.)'
  and "SynGenus" = 'Elaphrus'
  and "SynSpecies" = 'riparius'

CODE	SynGenus	SynSpecies	SynAuthority	Ref	Notes	SynonymCODE
1.0120045000000000	Elaphrus	riparius	(L.)	Lindroth 1985	regards this as a synonym.	31

select *
from "INDEX"
where "CODE" in ('1.0120030000000000', '1.0120045000000000')

CODE	FAMILY	GENUS	SPECIES	AUTHORITY
1.0120030000000000	CARABIDAE	Elaphrus	riparius	(L.)
1.0120045000000000	CARABIDAE	Elaphrus	tuberculatus	Mäklin

Motsvarande poster i sead_production:

select taxon_id, family_name, genus_name, species, author_name, taxonomic_code 
from tbl_taxa_tree_master
join tbl_taxonomic_order using (taxon_id)
join tbl_taxa_tree_genera using (genus_id)
join tbl_taxa_tree_authors using (author_id)
join tbl_taxa_tree_families using (family_id)
where taxonomic_code in (1.0120030000, 1.0120045000)

taxon_id	family_name	genus_name	species	author_name	taxonomic_code
28965	CARABIDAE	Elaphrus	riparius	(L.)	1.0120030000
28966	CARABIDAE	Elaphrus	tuberculatus	Mäklin	1.0120045000

select taxon_id, family_name, genus_name, species, author_name, taxonomic_code 
from tbl_taxa_tree_master
left join tbl_taxonomic_order using (taxon_id)
join tbl_taxa_tree_genera using (genus_id)
join tbl_taxa_tree_authors using (author_id)
join tbl_taxa_tree_families using (family_id)
where family_name = 'CARABIDAE'
  and genus_name = 'Elaphrus'
  and author_name in ('(L.)', 'Mäklin')

taxon_id	family_name	genus_name	species	author_name	taxonomic_code
28965	CARABIDAE	Elaphrus	riparius	(L.)	1.0120030000
28966	CARABIDAE	Elaphrus	tuberculatus	Mäklin	1.0120045000
40204	CARABIDAE	Elaphrus	riparius	(L.)

select bugs_table, sead_table, sead_reference_id, bugs_data, manipulation_type
from bugs_import.bugs_trace
where translated_compressed_data like '%Elaphrus%'
  and bugs_table = 'TSynonym' 

bugs_table	sead_table	sead_reference_id	bugs_data	manipulation_type
TSynonym	tbl_taxa_tree_master	40204	{1.0120045,Elaphrus,riparius,(L.),Lindroth 1985,regards this as a synonym.}	INSERT
TSynonym	tbl_species_associations	2650	{1.0120045,Elaphrus,riparius,(L.),Lindroth 1985,regards this as a synonym.}	INSERT

[roger-mahler]

The bug can be reproduced with the following small BugsCEP database. The data is created using Jailer for sample SAMP000546, with a few data points from TFossil. A record with CODE 1.0120045 has been added to INDEX and TSynonym (these two records might be sufficient to reproduce the error).

insert into "INDEX" ("CODE", "FAMILY", "GENUS", "SPECIES", "AUTHORITY") values ('1.0120045000000000', 'CARABIDAE', 'Elaphrus', 'tuberculatus', 'Mäklin');
insert into "INDEX" ("CODE", "FAMILY", "GENUS", "SPECIES", "AUTHORITY") values ('1.0120030000000000', 'CARABIDAE', 'Elaphrus', 'riparius', '(L.)');
insert into "INDEX" ("CODE", "FAMILY", "GENUS", "SPECIES", "AUTHORITY") values ('23.028001499999998', 'STAPHYLINIDAE', 'Eucnecosum', 'brachypterum (grp)', '(Grav.)');
insert into "INDEX" ("CODE", "FAMILY", "GENUS", "SPECIES", "AUTHORITY") values ('93.015056999999999', 'CURCULIONIDAE', 'Otiorhynchus', 'nodosus', '(Möll.)');
insert into "INDEX" ("CODE", "FAMILY", "GENUS", "SPECIES", "AUTHORITY") values ('40.002102000000001', 'SCIRTIDAE', 'Ptilodactyla', 'exotica', 'Chapin');

insert into "TBiblio" ("REFERENCE", "AUTHOR", "TITLE", "Notes") values ('Bell & Walker (2005)', 'Bell, M. & Walker M.J.C. (1992)', 'Late Quaternary Environmental Change - Physical and Human Perspectives (Second Edition). Longman, Essex.', NULL);
insert into "TBiblio" ("REFERENCE", "AUTHOR", "TITLE", "Notes") values ('Bohme 2005', 'Böhme, J. (2005)', 'Die Köfer Mitteleuropas. K. Katalog (Faunistiche Übersicht) (2nd ed.). Spektrum Academic, Munich.', '(revised version of Lucht 1987)');
insert into "TBiblio" ("REFERENCE", "AUTHOR", "TITLE", "Notes") values ('Morris 2006', 'Morris, M. (2006)', 'Checklist of beetles of the British Isles, Curculionidae. <www.coleopterist.org.uk/curculionidae-list.htm>.', NULL);
insert into "TBiblio" ("REFERENCE", "AUTHOR", "TITLE", "Notes") values ('Strand 1946', 'Strand, A. (1946)', 'Nord Norges Coleoptera. Tromsö Museums Arshefter, Naturhistorisk Avd. Nr. 34, 67(1). (629pp.)', NULL);

insert into "TSite" ("SiteCODE", "SiteName", "Region", "Country", "NGR", "LatDD", "LongDD", "Alt", "IDBy", "Interp", "Specimens") values ('SITE000253', 'Håkulls Mosse, Kullaberg', 'Skåne', 'Sweden', NULL, 56.2999992, 12.5333338, 125, 'Lemdahl', 'Kullen Peninsula, see also Björkeröds mosse.', NULL);

insert into "TCountsheet" ("CountsheetCODE", "CountsheetName", "SiteCODE", "SheetContext", "SheetType") values ('COUN000144', 'Hakullsmosse_bugsdata.XLS', 'SITE000253', 'Stratigraphic sequence', 'Abundances');

insert into "TSample" ("SampleCODE", "SiteCODE", "X", "Y", "ZorDepthTop", "ZorDepthBot", "RefNrContext", "CountsheetCODE") values ('SAMP000546', 'SITE000253', NULL, NULL, NULL, NULL, 'B8:6/6', 'COUN000144');

insert into "TDatesMethods" ("Abbrev", "Method", "Type", "SortOrder") values ('GeolPer', 'Geological period', 'Period', 2);

insert into "TDatesPeriod" ("PeriodDateCODE", "SampleCODE", "Uncertainty", "PeriodCODE", "DatingMethod", "Notes") values ('PERI005175', 'SAMP000546', NULL, 'LG', 'GeolPer', NULL);

insert into "TFossil" ("FossilBugsCODE", "CODE", "SampleCODE", "Abundance") values ('FOSS014299', '93.015056999999999', 'SAMP000546', 3);
insert into "TFossil" ("FossilBugsCODE", "CODE", "SampleCODE", "Abundance") values ('FOSS144182', '23.028001499999998', 'SAMP000546', 30);

insert into "TLookupCountsheetContext" ("SheetContext", "SortOrder") values ('Stratigraphic sequence', 3);

insert into "TLookupCountsheetTypes" ("CountsheetType", "SortOrder") values ('Abundances', 1);

insert into "TPeriods" ("PeriodCODE", "PeriodName", "PeriodType", "PeriodDesc", "PeriodRef", "PeriodGeog", "Begin", "BeginBCAD", "End", "EndBCAD", "YearsType") values ('LG', 'Lateglacial', 'Geological', 'Cold period after the last Glaciation. Pollen Zones I-III', 'Bell & Walker (2005)', 'Europe', 13500, 'BP', 10000, 'BP', 'C14');

insert into "TSiteOtherProxies" ("OtherProxyID", "SiteCODE", "HasPollen", "HasPlantMacro", "HasDiatoms", "HasChironomids", "HasSoilChemistry", "HasIsotopes", "HasAnimalBones", "HasArchaeology", "HasMolluscs") values (1, 'SITE000253', 1, 0, 0, 0, 0, 0, 0, 0, 0);

insert into "TSynonym" ("CODE", "SynGenus", "SynSpecies", "SynAuthority", "Ref", "Notes") values ('93.015056999999999', 'Otiorhynchus', 'dubius', '(Ström.)', 'Bohme 2005', NULL);
insert into "TSynonym" ("CODE", "SynGenus", "SynSpecies", "SynAuthority", "Ref", "Notes") values ('93.015056999999999', 'Otiorhynchus', 'maurus', '(Gyllenhal) non (Marsham)', 'Morris 2006', NULL);
insert into "TSynonym" ("CODE", "SynGenus", "SynSpecies", "SynAuthority", "Ref", "Notes") values ('23.028001499999998', 'Arpedium', NULL, NULL, 'Strand 1946', NULL);
insert into "TSynonym" ("CODE", "SynGenus", "SynSpecies", "SynAuthority", "Ref", "Notes") values ('1.0120045000000000', 'Elaphrus', 'riparius', '(L.)', 'Lindroth 1985', 'regards this as a synonym.');

insert into "TTaxoNotes" ("CODE", "Ref", "Data") values ('40.002102000000001', 'Bohme 2005', 'Genus not listed.');

[roger-mahler]

This is a minimal BugsCEP database that reproduces the error:

insert into "INDEX" ("CODE", "FAMILY", "GENUS", "SPECIES", "AUTHORITY") values
    ('1.0120045000000000', 'CARABIDAE', 'Elaphrus', 'tuberculatus', 'Mäklin');
    ('1.0120030000000000', 'CARABIDAE', 'Elaphrus', 'riparius', '(L.)');

insert into "TSynonym" ("CODE", "SynGenus", "SynSpecies", "SynAuthority", "Ref", "Notes") values
    ('1.0120045000000000', 'Elaphrus', 'riparius', '(L.)', 'Lindroth 1985', 'regards this as a synonym.');

[roger-mahler]

Import INDEX items

The mapping between items in BugsCEP INDEX and SEAD taxon_id is kept in table tbl_taxonomic_order i.e. the first step is to find taxon_id where taxonomic_code equals INDEX.CODE.

The items already exists in the SEAD database, so no new items are inserted.

select *
from tbl_taxonomic_order
where taxonomic_code in (1.0120030000, 1.0120045000)

taxonomic_order_id	date_updated	taxon_id	taxonomic_code	taxonomic_order_system_id
20245	2014-04-17 06:02:04	28965	1.0120030000	1
20246	2014-04-17 06:02:04	28966	1.0120045000	1

[roger-mahler]

Import Synonym items

Each BugsCEP synonym item should have a corresponding record in SEAD table tbl_species_associations. The minimal test database has the following synonym item:

CODE	SynGenus	SynSpecies	SynAuthority	Ref	Notes
1.01200450	Elaphrus	riparius	(L.)	Lindroth 1985	regards this as a synonym.

If a synonym is previously imported (exists in the import trace) then nothing needs to be done. Otherwise a new species association is created comprising of:

• a new or existing source species (taxon_id)
• a new or existing target species (associated_taxon_id)
• a reference (biblio_id)
• an association type

The target species (tbl_taxa_tree_master ) is found by searching for synonym's CODE in tbl_taxa_tree_order. The source species (tbl_taxa_tree_master ) is found by searching for synonym's species, genus and author in species repository (tbl_taxa_tree_master ).

[roger-mahler]

Find or create association's target species

Fetch target species (tbl_taxa_tree_master ) using taxonomic_code in tbl_taxa_tree_order. This item should always exists - if not there is an inconsistency in the BugsCEP database.

select taxon_id
from tbl_taxonomic_order
where taxonomic_code in (1.0120045000)

taxonomic_order_id	date_updated	taxon_id	taxonomic_code	taxonomic_order_system_id
20246	2014-04-17 06:02:04	28966	1.0120045000	1

sead_bugs_import/src/main/java/se/sead/bugsimport/speciessynonyms/SynonymCreator.java

Lines 47 to 54 in 62a882c

	private void setTargetSpecies(){
	TaxaSpecies targetSpecies = taxonomicOrderRepository.findBugsSpeciesByCode(BigDecimalDefinition.convertToSeadCode(synonym.getCode()));
	if(targetSpecies == null){
	seadData.addError("No species found for code");
	return;
	}
	seadData.setTargetSpecies(targetSpecies);
	}

select taxon_id, author_name, genus_name, species
from tbl_taxa_tree_master
join tbl_taxa_tree_genera using (genus_id)
join tbl_taxa_tree_authors using (author_id)
where taxon_id = 28966    

taxon_id	author_name	genus_name	species
28966	Mäklin	Elaphrus	tuberculatus

[roger-mahler]

Find or create association's source species

Finding the source species is basically a simple search in SEAD of the given species name (riparius), genus name (Elaphrus) and authority name (Mäklin).

select taxon_id, author_name, genus_name, species
from tbl_taxa_tree_master
join tbl_taxa_tree_genera using (genus_id)
join tbl_taxa_tree_authors using (author_id)
where species = 'riparius'
  and genus_name = 'Elaphrus'
  and author_name = '(L.)'

Note that this species exists in the SEAD database. The bugs import, however, uses the authority name given by the target species ((L.)) instead of the authority given by the synonym item (Mäklin). This can be seen on line 149 in the following code snippet.

sead_bugs_import/src/main/java/se/sead/bugsimport/speciessynonyms/SynonymSpeciesManager.java

Lines 147 to 156 in 62a882c

	private TaxaSpecies getOrCreate(TaxaGenus synonymGenus, Synonym synonym, TaxaSpecies targetSpecies){
	String name = synonym.getSynSpecies() != null ? synonym.getSynSpecies() : targetSpecies.getSpeciesName();
	String authorName = targetSpecies.getAuthor() != null ? targetSpecies.getAuthor().getAuthorName() : null;
	TaxaSpecies found = speciesRepository.findBySpeciesNameAndGenusGenusNameAndAuthorAuthorName(name, synonymGenus.getGenusName(), authorName);
	if(found == null || !authorityManager.authorityMatches(found, targetSpecies)){
	return createBaseSynonymSpecies(synonymGenus, synonym, targetSpecies);
	} else {
	return found;
	}
	}

Since the combination (riparius, Elaphrus, (L.)) is missing in the database the system adds a new species.This species is however assigned the authority of the synonym (Mäklin), and not the authority used when searching for an existing species ((L.)).

This results in a duplicate species record (riparius, Elaphrus, Mäklin) in the database.

[roger-mahler]

We have two options to correct the issue:

1. When searching for existing source species the system should use the same autority as specified in the synonym (SynAuthor).
2. When creating a new source species then it should be assigned the same authority as the target species.