3i Auchenorrhyncha (id 2317): test report

[yroskov]

3i Auchenorrhyncha dev

https://data.catalogueoflife.org/dataset/2317/classification

• [x] Imported: 46305 spp (vs 10,455 spp in ac19). See below: https://github.com/CatalogueOfLife/testing/issues/135#issuecomment-877365142 Now CoL takes 21503 spp in agreed groups.

• [x] Classification: many taxa (genera, subgenera, species) are outside suborder Auchenorrhyncha:

[yroskov]

• [ ] Summary of remaining cases of "looped synonymy with type subspecies" in 3i@TW (@gdower, for future improvements):

Case 1 (ACC-SYN species, different accepted, same authors):

acc: Aceratagallia (Aceratagallia) siccifolius (Uhler, 1876)

acc: Aceratagallia (Aceratagallia) siccifolius siccifolius (Uhler, 1876) syn: Aceratagallia (Aceratagallia) siccifolius (Uhler, 1876)

Case 2a (SYN-SYN species, different accepted, same authors):

acc: Aceratagallia (Aceratagallia) humilis Oman, 1933 syn: Aceratagallia humilis Oman, 1933

acc: Aceratagallia (Aceratagallia) humilis humilis Oman, 1933 syn: Aceratagallia humilis Oman, 1933

Case 2b (SYN-SYN species, different accepted, same authors):

acc: Macropsidius niger (Matsumura, 1915)
syn: Agallia nigra Matsumura, 1915

acc: Macropsidius niger niger (Matsumura, 1915) syn: Agallia nigra Matsumura, 1915

[proceps]

Those are original combination, yes they are identical for the species and subspecies.

[proceps]

The only reason of duplicate OTUs, we do not have an easy was to delete (merge) two OTUs in TW. So yes, all duplicates are related to duplicated OTUs in TW.

[mjy]

Multiple OTUs should only be present if real. Perhaps there is an issue with the script.

[proceps]

Most common scenario is the same as in UCD. A duplicate species is discovered, and it has an OTU with some data, to delete a species name, the OTU needs to be reassigned to the second species.

[yroskov]

3i Auchenorrhyncha of 0.32.3 / 2023-05-10; imported 2023-05-10 from Geoff's laptop

• [x] Imported: 46868 spp (vs 46865 spp)
• [x] Metadata: version corrected 0.32.3 / 2023-05-10 -> May 2023 / 2023-05-10.
• [x] Classification: OK (i.e. inside suborder Auchenorrhyncha); remaining spp & ssp outside suborder)
• [x] Sectors: OK
• [x] flag "extinct" = OK

TASKS

• Broken decisions, 7: deleted all

Resolved 2023-05-11:

Synced 2023-05-11

[yroskov]

For attention of @proceps, @gdower. In the version of 2023-05-10, CLB reported following issues (among others):

• There are two entries for Oliarellus fulvus (Kusnezov, 1935)

• There are 3 accepted genera which appear twice in CoL tree, and they have no species: Hardya, Macrosteles, Scaphytopius (and, probably, Lycoderes). Example via production interface: https://preview.catalogueoflife.org/?taxonKey=B7YS4 - is it OK?

• There are 5 accepted subfamilies which appear twice in CoL tree, and they have no species: https://www.checklistbank.org/catalogue/3/dataset/2317/duplicates?catalogueKey=3&category=uninomial&limit=500&minSize=2&mode=STRICT&rank=subfamily&status=accepted Example via production interface: https://preview.catalogueoflife.org/?taxonKey=B6NCG

[yroskov]

3i Auchenorrhyncha of 0.33.1 / 2023-07-13; imported 2023-07-13 from Geoff's laptop

• [x] Imported: 47203 spp (vs 46868 spp)
• [x] Metadata: version corrected 0.33.1 / 2023-07-13 -> Jul 2023 / 2023-07-13.
• [x] Classification: OK (i.e. inside suborder Auchenorrhyncha); remaining spp outside suborder; there are no subspecies outside suborder now!)
• [x] Sectors: OK
• [x] flag "extinct" = OK
• [x] All accepted combinations with genus in square brackets (e.g. [Aphrodes] puella Curtis, 1837) are flagged as provisionally accepted (Workbench: reverse sorting, accepted, setting 540 p/p)

ISSUES assessed 2023-07-14

@proceps, @gdower, I am blocking "incomplete" synonyms like this "Acucephalus albifrons var. — Gistel, 1837" in the CoL. Are these variety names exported from TW correctly?

ISSUES report "Doubtful Name, 258" https://www.checklistbank.org/catalogue/3/dataset/2317/workbench?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&issue=doubtful%20name&limit=500&offset=0&reverse=false

There are also similar names (ISSUES Unusual Name Characters):

[yroskov]

(3i Auchenorrhyncha of Jul 2023 / 2023-07-13, continue)

TASKS

• Broken decisions, 46: deleted all

• [ ] @proceps, @gdower, just in case, two accepted species appear twice in CLB: Cercopis arcuata Fieber, 1844 and Macrosteles hizemus Hamilton, 2017 (unresolved OTU or for the purpose?)

• [ ] @proceps, @gdower, there are two entries for 3 generaHamata, Madagella & Projecta; both entries have no children species in CLB:

Resolved 2023-07-14:

Synced 2023-07-14

[yroskov]

3i Auchenorrhyncha of 0.34.1 / 2023-08-08; imported 2023-08-08 from Geoff's laptop

• [x] Imported: 47211 spp (vs 47203 spp)
• [x] Metadata: version corrected 0.34.1 / 2023-08-08 -> Aug 2023 / 2023-08-08.
• [x] Classification: OK (see above)
• [x] Sectors: OK
• [x] flag "extinct" = OK
• [x] All accepted combinations with genus in square brackets (e.g. [Aphrodes] puella Curtis, 1837) are flagged as provisionally accepted (Workbench: reverse sorting, accepted, setting 540 p/p) = checked

TASKS

• Broken decisions, 5: deleted all
• Report SYN-SYN sp, same acc, same auth failed

Resolved 2023-08-10:

Synced 2023-08-10

[yroskov]

3i Auchenorrhyncha of 0.34.1 / 2023-09-06; imported 2023-09-06; re-imported 2023-09-08 from Geoff's laptop

2023-09-12: Just in case of 2023-09-06 & 08: the import is not finished yet

Re-imported 2023-09-12

• [x] Imported: 47259 spp (vs 47211 spp)

• [x] Metadata: version corrected Aug 2023 / 2023-08-08 -> Sep 2023 / 2023-09-06

• [x] Classification: OK. No taxa outside infraorders!

• [x] Sectors: OK

• [x] flag "extinct" = OK

• [x] All accepted combinations with genus in square brackets (e.g. [Aphrodes] puella Curtis, 1837) are flagged as provisionally accepted (Workbench: reverse sorting, accepted, setting 540 p/p) = checked; 3 new flagged

TASKS

• Broken decisions, 16: deleted

Resolved 2023-09-12:

Synced 2023-09-12

[yroskov]

@proceps, it looks like Macropsis (Macropsis) notata (Prohaska, 1923) has double entry in CLB:

...actually, there double entries for 25 species. Full list is here: https://www.checklistbank.org/dataset/2317/duplicates?authorshipDifferent=false&category=binomial&limit=500&minSize=2&mode=STRICT&offset=0&status=accepted

[proceps]

@gdower When TN has two OTUs, pick one of them, any of the two, and not both of them. For now, I deleted OTU from one of the species.

[yroskov]

pick one of them, any of the two

Just in case: currently, I am blocking one species in each pair in CLB.

[yroskov]

See: https://github.com/CatalogueOfLife/data/issues/563

All of these do not affect a quality of 3i data in the CoL of September.

[yroskov]

3i Auchenorrhyncha of 0.34.5 / 2023-10-04; imported 2023-10-04 from Geoff's laptop

• [x] Imported: 47254 spp (vs 47259 spp)
• [x] Metadata: version corrected 0.34.5 / 2023-10-04 -> Oct 2023 / 2023-10-04
• [x] Classification: OK. (No taxa outside infraorders)
• [x] Sectors: OK
• [x] flag "extinct" = OK
• [x] All accepted combinations with genus in square brackets (e.g. [Aphrodes] puella Curtis, 1837) are flagged as provisionally accepted (Workbench: reverse sorting, accepted, setting 540 p/p) = checked; 0 new flagged

ISSUES assessed 2023-10-04

• Parent Species Missing, 3 subspecies without parent species: Graptopsaltria colorata colorata Stål, 1866; Graptopsaltria colorata badia Kato, 1925; Perophlepsius conjunctus conjunctus Heller & Linnavuori, 1968. However, binomials Graptopsaltria colorata & Perophlepsius conjunctus are present, but as bare names

TASKS

• Broken decisions, 81: deleted

Synced 2023-10-04

[yroskov]

3i Auchenorrhyncha of 0.35.2 / 2023-11-08; imported 2023-11-09 from Geoff's laptop

• [x] Imported: 47302 spp (vs 47254 spp)
• [x] Metadata: version corrected 0.35.2 / 2023-11-08 -> Nov 2023 / 2023-11-08
• [x] Classification: OK. (No taxa outside infraorders)
• [x] Sectors: OK
• [x] flag "extinct" = OK
• [ ] All accepted combinations with genus in square brackets (e.g. [Aphrodes] puella Curtis, 1837) are flagged as provisionally accepted (Workbench: reverse sorting, accepted, setting 540 p/p) = checked; No any names with square brackets present in this export - need to be checked with @gdower = done. @mdoering, could you please confirm that you have modified CLB to (1) remove square brackets from species names and (2) automatically apply provisionally accepted status? (what happens to such names in synonyms?)

ISSUES assessed 2023-11-10

• [ ] Parent Species Missing, 1: Perophlepsius conjunctus conjunctus Heller & Linnavuori, 1968. However, binomial Perophlepsius conjunctus Heller & Linnavuori, 1968 is present, but flagged as bare name

• [ ] Uninomial Field Misplaced, 70 - what it may mean? After triage with @proceps, it looks like names with a rank of genus are missing as "synonyms" to the subgenus with the same spelling (these names flagged as "genus" + "bare name" in the report and missing in synonymy to the genus for example, Belaunus Ribaut, 1952 - bare name - genus
  Subgenus page Adarrus (Belaunus) Ribaut, 1952 - no genus in synonymy (https://www.checklistbank.org/dataset/2317/taxon/27565)

TASKS

• Broken decisions, 37: deleted

Resolved 2023-11-10:

Synced 2023-11-10

[yroskov]

3i Auchenorrhyncha of 0.36.0 / 2023-12-07; imported 2023-12-07 from Geoff's laptop

• [x] Imported: 47329 spp (vs 47302 spp)
• [x] Metadata: version corrected 0.36.0 / 2023-12-07 -> Dec 2023 / 2023-12-07
• [x] Classification: OK. (No taxa outside infraorders)
• [x] Sectors: OK
• [x] flag "extinct" = OK
• [x] Names with square brackets (e.g. [Aphrodes] puella Curtis, 1837): no in the interpreted import

ISSUES

TASKS

• Broken decisions, 21: deleted

Resolved 2023-12-08:

Synced 2023-12-08

[yroskov]

3i Auchenorrhyncha of 0.37.0 / 2024-01-02; imported 2024-01-02 from Geoff's laptop

• [x] Imported: 47343 spp (vs 47329 spp)
• [x] Metadata: version corrected 0.37.0 / 2024-01-02 -> Jan 2024 / 2024-01-02
• [x] Classification: OK. (No taxa outside infraorders)
• [x] Sectors: OK
• [x] flag "extinct" = OK
• [x] Names with square brackets (e.g. [Aphrodes] puella Curtis, 1837): no in the interpreted import
• [ ] DOI: absent

TASKS

• Broken decisions, 21: deleted
• Outdated decisions, 86: deleted

Resolved 2024-01-03:

Synced 2023-01-03

[yroskov]

3i Auchenorrhyncha of 0.38.1 / 2024-02-06; imported 2024-02-06 from Geoff's laptop

• [x] Imported: 47396 spp (vs 47343 spp)
• [x] Metadata: version corrected 0.38.1 / 2024-02-06 -> Feb 2024 / 2024-02-06
• [x] Classification: OK. (No taxa outside infraorders)
• [x] Sectors: OK
• [x] flag "extinct" = OK
• [x] Names with square brackets (e.g. [Aphrodes] puella Curtis, 1837): no in the interpreted import
• [ ] DOI: absent

TASKS

• Broken decisions, 4 = deleted

Resolved 2024-02-19:

Synced 2024-02-19

[yroskov]

2024-02-23: switched to a single sector suborder Auchenorrhyncha with nested COOL, FLOW & MOWD.

Blocked in 3i Auchenorrhyncha: Cercopoidea, Fulgoroidea, Membracidae

[yroskov]

3i Auchenorrhyncha of 0.39.0 / 2024-03-08; imported 2024-03-08 from Geoff's laptop

• [x] Imported: 47429 spp (vs 47396 spp)
• [x] Metadata: version corrected 0.39.0 / 2024-03-08 -> March 2024 / 2024-03-08
• [x] Classification: OK
• [x] Sector: OK, suborder Auchenorrhyncha. Blocked Cercopoidea, Fulgoroidea, Membracidae.
• [x] flag "extinct": OK
• [x] Names with square brackets (e.g. [Aphrodes] puella Curtis, 1837): no in the interpreted import
• [x] Names with [sic] portion: no in the import
• [ ] DOI: absent

Metrics:

ISSUES assessed 2024-03-19

• Uninomial Field Misplaced, 72: https://www.checklistbank.org/catalogue/3/dataset/2317/workbench?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&issue=uninomial%20field%20misplaced&limit=100&offset=0 @gdower, I do not quite understand what's wrong here, and how this issue important

• Unusual Name Characters, 734: there are truncated(?) names with portion "var." in the list like these: Yarrana continuata var. Distant, 1906 Uysanus fluctuans var. Distant, 1910
  Typhlocyba blandula var. — Sahlberg, 1868 Trichogonia boliviana var. ― Distant, 1908 Tettigonia robusta var. – Johnson & Fox, 1892

https://www.checklistbank.org/dataset/2317/names?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nomCode&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&facet=sectorMode&issue=unusual%20name%20characters&limit=900&offset=0&reverse=true&sortBy=name

@proceps & @gdower, just in case, are we missing these names in CoL because they are incorrectly exported from TW or misinterpreted by CLB?

TASKS

• Outdated decisions, 5 = deleted
• Broken decisions, 51 = deleted

Resolved 2024-03-19: all resolved, but interface does not show results:

Another strange issue:

• Outdated decisions, 18

Synced 2024-03-19

[yroskov]

3i Auchenorrhyncha of 0.40.3 / 2024-04-18; imported 2024-04-19 from Geoff's laptop

• [x] Imported: 47428 spp (vs 47429 spp)
• [x] Metadata: version corrected 0.40.3 / 2024-04-18 -> Apr 2024 / 2024-04-18
• [x] Classification: OK
• [x] Sector: OK, suborder Auchenorrhyncha. Blocked Fulgoromorpha, Cercopoidea, Membracidae.
• [x] flag "extinct": OK
• [x] Names with square brackets (e.g. [Aphrodes] puella Curtis, 1837): no in the interpreted import
• [x] Names with [sic] portion: no in the import
• [ ] DOI: absent

Metrics:

TASKS

• Broken decisions, 10 = deleted

• Outdated decisions, 21 = deleted

• [ ] SYN-SYN species (different accepted, different authors). @proceps & @gdower, perhaps, there is sense to check what's happened with these entries: Repeated twice and in a "wrong report": synonym Cicadetta megerlei Fieber, 1872 of Cicadetta montana (Scopoli, 1772) synonym Cicadetta megerlei Fieber, 1876 of Cicadetta montana (Scopoli, 1772)

• [ ] SYN-SYN species (different accepted, same authors). _@proceps & @gdower, here also something strange (i.e. "different accepted") https://www.checklistbank.org/catalogue/3/dataset/2317/duplicatescceptedDifferent=true&authorshipDifferent=false&catalogueKey=3&category=binomial&limit=50&minSize=2&mode=STRICT&offset=0&status=synonym&withDecision=false 4 accepted names with strange duplicates: Balclutha incisa incisa (Matsumura, 1902) Cicadetta montana (Scopoli, 1772) Changeondelphax velitchkovskyi (Melichar, 1913) Nisia nervosa (Motschulsky, 1863)

Resolved 2024-04-19:

Synced 2024-04-19

[proceps]

four mentioned cases, are duplicate OTUs in TW. We do not have functionality to merge OTUs yet.

[yroskov]

3i Auchenorrhyncha of 0.41.0 / 2024-05-06; imported 2024-05-06 from Geoff's laptop

• [x] Imported: 47450 spp (vs 47428 spp)
• [x] Metadata: version corrected 0.41.0 / 2024-05-06 -> May 2024 / 2024-05-06
• [x] Classification: OK
• [x] Sector: OK, suborder Auchenorrhyncha. Blocked Fulgoromorpha, Cercopoidea, Membracidae.
• [x] flag "extinct": OK
• [x] Names with square brackets (e.g. [Aphrodes] puella Curtis, 1837): no in the interpreted import
• [x] Names with [sic] portion: no in the import
• [ ] DOI: absent

Metrics:

TASKS

Resolved 2024-05-09:

Synced 2024-05-09

[yroskov]

3i Auchenorrhyncha of 0.41.1 / 2024-06-03; imported 2024-06-03 from Geoff's laptop

• [x] Imported: 47479 spp (vs 47450 spp)
• [x] Metadata: version corrected 0.41.1 / 2024-06-03 -> Jun 2024 / 2024-06-03
• [x] Classification: OK
• [x] Sector: OK, suborder Auchenorrhyncha. Blocked Fulgoromorpha, Cercopoidea, Membracidae.
• [x] flag "extinct": OK
• [x] Names with square brackets (e.g. [Aphrodes] puella Curtis, 1837): no in the interpreted import
• [x] Names with [sic] portion: no in the import
• [ ] DOI: absent

Metrics:

ISSUES

TASKS

• Broken decisions, 24 = deleted all
• Outdated decisions, 8 = no action

Resolved 2024-06-04:

Synced 2024-06-04

[yroskov]

3i Auchenorrhyncha of 0.42.0 / 2024-07-05; imported 2024-07-05 from Geoff's laptop

• [x] Imported: 47518 spp (vs 47479 spp)
• [x] Metadata: version corrected 0.42.0 / 2024-07-05 -> Jul 2024 / 2024-07-05
• [x] Classification: OK
• [x] Sector: OK, suborder Auchenorrhyncha. Blocked Fulgoromorpha, Cercopoidea, Membracidae.
• [x] flag "extinct": OK
• [x] Names with square brackets (e.g. [Aphrodes] puella Curtis, 1837): no in the interpreted import
• [x] Names with [sic] portion: no in the import
• [ ] DOI: absent

Metrics:

TASKS

• Broken decisions, 16 = deleted
• Outdated decisions, 12 = no action

Resolved 2024-07-15:

Synced 2024-07-15

[yroskov]

3i Auchenorrhyncha of 0.43.1 / 2024-08-06; imported 2024-08-06 from Geoff's laptop

• [x] Imported: 47533 spp (vs 47518 spp)
• [x] Metadata: version corrected 0.43.1 / 2024-08-06 -> Aug 2024 / 2024-08-06
• [x] Classification: OK
• [x] Sector: OK, suborder Auchenorrhyncha. Blocked Fulgoromorpha, Cercopoidea, Membracidae.
• [x] flag "extinct": OK
• [x] Names with portion "sp." = blocked
• [x] Names with square brackets (e.g. [Aphrodes] puella Curtis, 1837): no in the interpreted import
• [x] Names with [sic] portion: no in the import
• [ ] DOI: absent

Metrics:

ISSUES assessed 2024-08-07

TASKS

• Broken decisions, 38 = deleted
• Outdated decisions, 19 = no action

Resolved 2024-08-07:

Synced 2024-08-07

[yroskov]

3i Auchenorrhyncha of 0.43.2 / 2024-09-06; imported 2024-09-06 from Geoff's laptop

• [x] Imported: 47536 spp (vs 47533 spp)
• [x] Metadata: version corrected 0.43.2 / 2024-09-06 -> Sep 2024 / 2024-09-06
• [x] Classification: OK
• [x] Sector: OK, suborder Auchenorrhyncha. Blocked Fulgoromorpha, Cercopoidea, Membracidae.
• [x] flag "extinct": OK
• [x] Names with portion "sp." = blocked
• [x] Names with square brackets (e.g. [Aphrodes] puella Curtis, 1837): no in the interpreted import
• [x] Names with [sic] portion: no in the import
• [ ] DOI:

Metrics:

TASKS

• Broken decisions, 10 = deleted
• Outdated decisions, 18 = no action

Resolved 2024-09-12:

Synced 2024-09-12