SF Orthoptera (id 1021): test report

yroskov commented 3 years ago

Data of 2021-08-20 taken from local machine http://10.194.234.20:3000/ File orthoptera_species_file(2021-08-20145630+0000)_coldp_otu_id_53_2021-10-04t114121-0500 imported 2021-10-05.

(see DEV report https://github.com/CatalogueOfLife/testing/issues/87 )

[x] Imported: 29135 spp (vs 27344 + 767† in ac19)
[x] Metadata: updated 2021-10-05
[x] Classification: OK
[x] Sector: order Orthoptera re-established (Replace)

yroskov commented 3 years ago

[x] ISSUES assessed

Classification Rank Order Invalid, 12: do not see a problem. No actions.

Rank Invalid, 30: the problem might be with "infrageneric name" and "unranked" ranks applied in the checklistbank. No actions taken.

Inconsistent Name, 471: portion "supersp" is interpreted as SpeciesEpithet; rank assigned as "species aggregate". No actions.

yroskov commented 3 years ago

-[ ] TASKS

yroskov commented 3 years ago

[x] ACC-SYN sp diff acc, same auth: binomial appears twice: as an accepted species and as a synonym to its child type subspecies (for attention of @gdower) = SYNs BLOCKED https://data.catalogueoflife.org/catalogue/3/dataset/1021/duplicates?acceptedDifferent=true&authorshipDifferent=false&category=binomial&limit=500&minSize=2&mode=STRICT&offset=0&status=accepted&status=synonym

Examples:
Aboilomimus sichuanensis Gorochov, 2001 is accepted species and a synonym to Aboilomimus sichuanensis sichuanensis Gorochov, 2001 Acanthacris ruficornis (Fabricius, 1787) is accepted species and a synonym to Acanthacris ruficornis ruficornis (Fabricius, 1787) Aclodes bora Desutter-Grandcolas, 1992 is accepted species and a synonym to Aclodes bora bora Desutter-Grandcolas, 1992

yroskov commented 3 years ago

[x] ACC-SYN infrasp diff acc, same auth: type trinomial appears twice: as an accepted subspecies and as a synonym to its parent species (for attention of @gdower) = SYNs BLOCKED https://data.catalogueoflife.org/catalogue/3/dataset/1021/duplicates?acceptedDifferent=true&authorshipDifferent=false&category=trinomial&limit=500&minSize=2&mode=STRICT&offset=0&status=accepted&status=synonym

Examples: Barytettix contilus contilus Cohn & Cantrall, 1974 is accepted subspecies and a synonym to its parent species Barytettix contilus Cohn & Cantrall, 1974 Biroella ornata ornata Bolívar, 1925 is accepted subspecies and a synonym to its parent species Biroella ornata Bolívar, 1925

yroskov commented 3 years ago

[x] ACC-SYN infrasp same acc, same auth: trinomial appears twice: as an accepted name and a synonym to itself with rank "infraspecies name" (for attention of @gdower) = SYNs BLOCKED

https://data.catalogueoflife.org/catalogue/3/dataset/1021/duplicates?acceptedDifferent=false&authorshipDifferent=false&category=trinomial&limit=500&minSize=2&mode=STRICT&offset=0&status=accepted&status=synonym&withDecision=false

Examples: Aglaothorax ovatus armiger Rehn & Hebard, 1920 is accepted subspecies and a synonym (with rank "infraspecific name") to itself: Aglaothorax ovatus armiger Rehn & Hebard, 1920 Celes variabilis carbonaria Uvarov, 1917 is accepted subspecies and a synonym (with rank "infraspecific name") to itself: Celes variabilis carbonaria Uvarov, 1917

yroskov commented 3 years ago

[ ] Few (two?) names with identical IDs, for example, Eyprepocnemis yunkweiensis Chang, 1937 (as a synonym of Shirakiacris yunkweiensis (Chang, 1937)). = NO ACTION (for attention of @gdower)

[x] Blocked 72 names with portion"[GENUS NOT SPECIFIED]" https://data.catalogueoflife.org/catalogue/3/dataset/1021/workbench?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&limit=50&offset=0&q=%5BGENUS%20NOT%20SPECIFIED%5D

yroskov commented 3 years ago

Resolved 2021-10-06:

yroskov commented 3 years ago

[ ] Unresolved issue [in the TW-COLDP export?]: Broken parent-child relationships between superspecies/species aggregate and species. Species are placed in NotAssigned species-aggregate-node, but not in the parent species aggregate, as expected. see: https://github.com/CatalogueOfLife/testing/issues/162#issuecomment-921844486 = ALL SF SUPERSPECIES EXCLUDED AS A RANK IN COL

Example names: Agnotecous supersp albifrons Agnotecous supersp robustus Agnotecous supersp tapinopus

@Geoff kindly FIXED the issue in the checklistbank. He excluded all taxa with "species aggregate" rank in SF Orthoptera through the following steps: go to Assembly, right click on the sector label, activate option EditSector, select all ranks which need to be kept (huge list) and leave unwanted ranks out, FinishEdit, do sync.

Synced 2021-10-06

yroskov commented 3 years ago

Re-imported, re-synced with Distribution Gazetteer "text" 2021-10-08

yroskov commented 3 years ago

How synonymy and combinations for subspecies Acanthacris ruficornis ruficornis (Fabricius, 1787) appear in different platforms:

Species Files: http://orthoptera.speciesfile.org/Common/basic/Taxa.aspx?TaxonNameID=1112599

subspecies Acanthacris ruficornis ruficornis (Fabricius, 1787) Citations (26): Fabricius. 1787. Mantissa insectorum exhibens species nuper in Etruria collectas a Ptro Rossio 1:237 www.animalbase.uni-goettingen.de >> Gryllus ruficornis Kirby, W.F. 1896. Ann. Mag. nat. Hist. 6 18:262 www.biodiversitylibrary.org >> Cyrtacanthacris ruficornis LSID icon urn:lsid:Orthoptera.speciesfile.org:TaxonName:50246 Rehn, J.A.G. 1901. Proc. Acad. Nat. Sci. Philad. 53:376 www.biodiversitylibrary.org >> Cyrtacanthacris ruficornis Giglio-Tos. 1907. Boll. Musei Zool. Anat. Comp. R. Univ. Torino 22(554):15 www.biodiversitylibrary.org >> Acridium ruficorne LSID icon urn:lsid:Orthoptera.speciesfile.org:TaxonName:50247 Giglio-Tos. 1907. Boll. Musei Zool. Anat. Comp. R. Univ. Torino 22(569):4 www.biodiversitylibrary.org >> Acridium ruficorne Bruner, L. 1910. Reise in Ostafrika 2:639 www.biodiversitylibrary.org >> Acridium ruficorne Bolívar, I. 1914. Mem. Soc. espan. Hist. nat. 8(5):207 bibdigital.rjb.csic.es >> Locusta ruficornis LSID icon urn:lsid:Orthoptera.speciesfile.org:TaxonName:510526 Giglio-Tos. 1916. Boll. Soc. entom. ital. 48:136 www.biodiversitylibrary.org >> Cyrtacanthacris ruficornis Bruner, L. 1920[1919]. Annals of the Carnegie Museum 13:106 www.biodiversitylibrary.org >> Cyrtacanthacris ruficornis Sjöstedt. 1929. Ark. Zool. 20 A(15):23 >> Acanthacris ruficornis ruficornis LSID icon urn:lsid:Orthoptera.speciesfile.org:TaxonName:50244 Werner. 1932. S.B. Akad. Wiss. Wien, Math.-Nat. Kl. (Abt. 1) 141:173 www.zobodat.at >> Orthacanthacris ruficornis LSID icon urn:lsid:Orthoptera.speciesfile.org:TaxonName:509917 Johnston, H.B. 1956. Annotated catalogue of African grasshoppers 371, 376 >> Acanthacris ruficornis ruficornis Dirsh. 1965. The African Genera of Acridoidea 388 >> Acanthacris ruficornis Kevan, D.K.M. 1967. J. Nat. Hist. 1:93 >> Note: misspelling of species name at A. r. lineata >> Acanthacris ruficornia Johnston, H.B. 1968. Annotated catalogue of African grasshoppers Suppl:281, 283 >> Acanthacris ruficornis Dirsh. 1970. Ann. Mus. Roy. Afr. Cent. 8(182):374 >> Acanthacris ruficornis ruficornis COPR (Centre for Overseas Pest Research). 1982. The Locust and Grasshopper Agricultural Manual 359 >> Acanthacris ruficornis Mungai. 1987. J. Nat. Hist. 21(4)(4):817 >> Note: redescription, neotype designation >> Acanthacris ruficornis ruficornis Hemp, C. & A. Hemp. 2003. Ecotropica 9:71-97 www.soctropecol.eu >> Acanthacris ruficornis ruficornis Roy, R. 2003. Mém. Mus. Nat. d'Hist. nat. 190:351 www.zin.ru >> Acanthacris ruficornis ruficornis Picker, M., Griffiths & Weaving. 2005. Field Guide to Insects of Southern Africa 102 books.google.com >> Acanthacris ruficornis Mestre & Chiffaud. 2006. Catalogue et atlas des acridiens d'Afrique de l'Ouest 31 >> Acanthacris ruficornis ruficornis Hemp, C. 2009. Jour. Orth. Res. 18(2):201 www.bioone.org >> Acanthacris ruficornis ruficornis Pronk, Pryke, Samways & Bazelet. 2017. J. Insect Conservation 21(1):97–109 link.springer.com >> Acanthacris ruficornis ruficornis Kooyman. 2019. In Lecoq & Long Zhang [Ed.]. Encyclopedia of Pest Orthoptera of the World 11 >> Ageneotettix deorum Hemp, C. & Rowell. 2020. Jago's Grasshoppers of East and North East Africa. Volume 4. Acrididae: Euryphyminae, Cyrtacanthacridinae, Oedipodinae 40 >> Acanthacris ruficornis ruficornis

synonym amoenula (Walker, 1870) synonym decisa (Walker, 1870) synonym fulvum (Sjöstedt, 1910) synonym gyldenstolpei (Sjöstedt, 1923) synonym lineatus (Stoll, 1813) synonym pallidicornis (Kirby, 1902) synonym subimmaculata (Finot, 1907) synonym yemenita Uvarov, 1936

TaxonWorks: https://sandcastle.taxonworks.org/tasks/nomenclature/browse?taxon_name_id=13311

subspecies Acanthacris ruficornis ruficornis (Fabricius, 1787) History (51) Gryllus ruficornis Fabricius, 1787: 237. Cyrtacanthacris amoenula Walker, 1870: 573.
Cyrtacanthacris decisa Walker, 1870: 485-594.
Cyrtacanthacris ruficornis (Fabricius, 1787) in Kirby, 1896: 262.
Cyrtacanthacris ruficornis (Fabricius, 1787) in Rehn, 1901: 376.
Cyrtacanthacris pallidicornis Kirby, 1902: 99.
Acridium ruficorne (Fabricius, 1787) in Giglio-Tos, 1907: 15.
Acridium ruficorne (Fabricius, 1787) in Giglio-Tos, 1907: 4.
Acridium [SPECIES NOT SPECIFIED] subimmaculata Finot, 1907: 305.
Acridium fulvum Sjöstedt, 1910: 187.
Acridium ruficorne (Fabricius, 1787) in Bruner, 1910: 639.Specimen or distribution
Cyrtacanthacris amoenula Walker, 1870 in Kirby, 1910: 452.
Locusta ruficornis (Fabricius, 1787) in Bolívar, 1914: 207.
Cyrtacanthacris ruficornis (Fabricius, 1787) in Giglio-Tos, 1916: 136.
Cyrtacanthacris ruficornis (Fabricius, 1787) in Bruner, 1920: 106.
Acridium gyldenstolpei Sjöstedt, 1923: 29.
Acanthacris ruficornis fulva in Uvarov, 1924: 15.
Acridium gyldenstolpei Sjöstedt, 1923 (synonym of Gryllus ruficornis Fabricius, 1787) in Uvarov, 1924: 17.
Cyrtacanthacris amoenula Walker, 1870 (subjective synonym of Gryllus ruficornis Fabricius, 1787) in Uvarov, 1924: 17.
Acanthacris ruficornis ruficornis (Fabricius, 1787) in Sjöstedt, 1929: 23.
Acridium fulvum Sjöstedt, 1910 (synonym of Acanthacris ruficornis fulva ) in Sjöstedt, 1929: 23.
Orthacanthacris ruficornis (Fabricius, 1787) in Werner, 1932: 173.
Acanthacris [SPECIES NOT SPECIFIED] yemenita Uvarov, 1936: 547.
Acridium fulvum Sjöstedt, 1910 (synonym of Acanthacris ruficornis fulva ) in Uvarov, 1938: 176.
Acridium fulvum Sjöstedt, 1910 (synonym of Acanthacris ruficornis fulva ) in Rehn, 1944: 7.
Acanthacris ruficornis ruficornis (Fabricius, 1787) in Johnston, 1956: 371, 376.
Acanthacris ruficornis (Fabricius, 1787) in Dirsh, 1965: 388.
Acanthacris ruficornia in Kevan, 1967: 93.
Acanthacris [SPECIES NOT SPECIFIED] yemenita Uvarov, 1936 in Weidner & Wagner, 1968: 127.
Acanthacris ruficornis (Fabricius, 1787) in Johnston, 1968: 281, 283.
Acanthacris ruficornis ruficornis (Fabricius, 1787) in Dirsh, 1970: 374.
Acanthacris ruficornis (Fabricius, 1787) in COPR (Centre for Overseas Pest Research), 1982: 359.
Acanthacris ruficornis ruficornis (Fabricius, 1787) in Mungai, 1987: 817.
Acridium gyldenstolpei Sjöstedt, 1923 (synonym of Gryllus ruficornis Fabricius, 1787) in Mungai, 1987: 817.
Cyrtacanthacris decisa Walker, 1870 (synonym of Gryllus ruficornis Fabricius, 1787) in Mungai, 1987: 817.
Cyrtacanthacris pallidicornis Kirby, 1902 (synonym of Gryllus ruficornis Fabricius, 1787) in Mungai, 1987: 817.
Acanthacris [SPECIES NOT SPECIFIED] yemenita Uvarov, 1936 (subjective synonym of Gryllus ruficornis Fabricius, 1787) in Mungai, 1987: 817.
Acridium [SPECIES NOT SPECIFIED] subimmaculata Finot, 1907 (subjective synonym of Gryllus ruficornis Fabricius, 1787) in Mungai, 1987: 817.
Acridium fulvum Sjöstedt, 1910 (subjective synonym of Gryllus ruficornis Fabricius, 1787) in Mungai, 1987: 817.
Cyrtacanthacris amoenula Walker, 1870 (subjective synonym of Gryllus ruficornis Fabricius, 1787) in Mungai, 1987: 817.
Acanthacris ruficornis ruficornis (Fabricius, 1787) in Roy, 2003: 351.
Acanthacris ruficornis ruficornis (Fabricius, 1787) in Hemp & Hemp, 2003
Acanthacris ruficornis (Fabricius, 1787) in Picker, Griffiths & Weaving, 2005: 102.
Acanthacris ruficornis ruficornis (Fabricius, 1787) in Mestre & Chiffaud, 2006: 31.
Acanthacris ruficornis ruficornis (Fabricius, 1787) in Hemp, 2009: 201.
Acanthacris ruficornis ruficornis (Fabricius, 1787) in Pronk, Pryke, Samways & Bazelet, 2017
Ageneotettix deorum in Kooyman, 2019: 11.
Acanthacris ruficornis ruficornis (Fabricius, 1787) in Hemp & Rowell, 2020: 40.
Acanthacris ruficornis fulva (unavailable or invalid, linked to Acridium fulvum Sjöstedt, 1910)
Acanthacris ruficornia (unavailable or invalid, linked to Gryllus ruficornis Fabricius, 1787)
Ageneotettix deorum (unavailable or invalid, linked to Gryllus ruficornis Fabricius, 1787)

CoL Preview: https://preview.catalogueoflife.org/data/taxon/5FCH8

Acanthacris ruficornis ruficornis (Fabricius, 1787) accepted subspecies = Cyrtacanthacris amoenula Walker, 1870 = Acridium fulvum Sjöstedt, 1910 = Cyrtacanthacris decisa Walker, 1870 = Cyrtacanthacris ruficornis (Fabricius, 1787) = Orthacanthacris ruficornis (Fabricius, 1787) = Cyrtacanthacris pallidicornis Kirby, 1902 = Acridium ruficornis (Fabricius, 1787) = Acridium gyldenstolpei Sjöstedt, 1923 = Acanthacris ruficornia = Locusta ruficornis (Fabricius, 1787) = Acanthacris ruficornis fulva = Ageneotettix deorum

yroskov commented 3 years ago

Maria Marta, 2021-10-25:

We have looked through the Tree, sample few species of Orthoptera SF in the Catalogue of Life, and except for finding that common names are repeated three times each, we did not find any major problem. So, you can go ahead and publish a new Orthoptera SF version in the CoL

[ ] Sometimes, common names are repeated on Species Details page

(So far, I failed to find a bug in 3 sampled species/subspecies: https://preview.catalogueoflife.org/data/taxon/7BSPW https://www.catalogueoflife.org/data/taxon/M8BT https://preview.catalogueoflife.org/data/taxon/P8ZP )

Examples from MM: (1) Schistocerca cancellata (Serville, 1838)

(2)Locusta migratoria migratoria (Linnaeus, 1758)

As in the CoL:

As on SF website: http://orthoptera.speciesfile.org/Common/basic/Taxa.aspx?TaxonNameID=1103075

As in TW: https://sandcastle.taxonworks.org/tasks/otus/browse?otu_id=3800#Common%20names

yroskov commented 2 years ago

[ ] Many common names are repeated many times with the exact same content: https://github.com/CatalogueOfLife/data/issues/388 - @gdower, could you pls add this to the list of required TW-CoL fixes?

https://data.catalogueoflife.org/dataset/1021/taxon/24313

yroskov commented 2 years ago

New versions exported/imported SF->TW 2022-09-05 = release date; imported TW->CLB 2022-09-14; re-imported with fixed extinct flag 2022-10-19 Data taken from localhost:3000.

[x] New importer used. Distribution added. "Looped synonymy" resolved.
[x] Imported: 29441 spp (vs 29135 spp in Aug 2021)
[x] Metadata: not updated yet. I was not able to update version & date: Request failed with status code 400 Dataset 1021 is registered in GBIF af66d4cf-0fd2-434b-9334-9806a5efa6f7 and updates are not allowed = UPDATED 2022-10-19
[x] Classification: family Legendreiidae Huang, Schubnel & Nel, 2020 in a Tree root of the order
[x] Sector: order Orthoptera broken; rematched successfully

yroskov commented 2 years ago

ISSUES assessed 2022-10-03

Classification Rank Order Invalid, 1: Acridomorpha flagged in CLB as nanorder. In SF Orthoptera: "superfamily group"
Rank Invalid, 24. For example, Ceuthophilus (Ceuthophilus) Scudder, 1862 or Ceuthophilus (Geotettix) Scudder, 1894 - rank "other"
Multi Word Epithet, 171: majority are names with portion "[sic]", for example, Acmophyllum nigro-punctatum [sic] Bolívar, 1905. All left as they are.
Inconsistent Name, 473: names with portion "supersp". All mistreated in CLB (flagged as "species aggregate" without children; appear in parallel with species with identical epithet; portion "supersp" parsed as specificEpithet). All blocked.
Indetermined, 528: set of names like this "synonym, Boopedon subsp. nigrum Thomas, 1870" (no species epithet). Left as they are.

yroskov commented 2 years ago

TASKS

Broken decisions, 1023 = Deleted all
ACC-ACC sp, same auth, 2 pairs of identical names with identical IDs (exmpl. 46063 accepted Clonia (Clonia) zernyi Kaltenbach, 1971 vs 46063 accepted Clonia (Clonia) zernyi Kaltenbach, 1971). Geoff: single record in the database. CLB problem? = No actions.
ACC-ACC infra, same auth, 103 pairs of identical names with different IDs (exmpl, 180538 accepted Acorypha clara clara (Walker, 1870) vs 13488 accepted Acorypha clara clara (Walker, 1870)). Geoff: Data in TW problem? = Names with highest IDs blocked.
SYN-SYN sp, same acc, same auth, 464 pairs. Not clear what it's mean and what blocking one name in a pair may cause.

Resolved 2022-10-04:

Synced 2022-10-19; re-synced 2022-10-20

yroskov commented 1 year ago

[ ] Need fixes with a new update: https://github.com/CatalogueOfLife/data/issues/541

gdower commented 1 year ago

It seems that the SF Orthoptera data access URL had been set to the IPT, when the data should be coming from TaxonWorks. As far as I can tell the gbifsync user did it because that's the dataset last modifiedBy user. At least it didn't seem to import because the IPT is in DWCA format whereas the dataset is configured as COLDP and I had import frequency set to never.

https://api.checklistbank.org/dataset/1021.json

{
  "created": "2019-11-20T11:07:46.255777",
  "createdBy": 102,
  "modified": "2023-06-02T07:51:36.849887",
  "modifiedBy": 12,
  "key": 1021,
  "type": "taxonomic",
  "origin": "external",
  "attempt": 13,
  "imported": "2022-10-20T15:12:08.941117",
  "gbifKey": "af66d4cf-0fd2-434b-9334-9806a5efa6f7",
  "gbifPublisherKey": "47a779a6-a230-4edd-b787-19c3d2c80ab5",
  "size": 76255,
  "doi": "10.15468/nn7jhc",
  "identifier": {
    "col": "1021"
  },
  "title": "Orthoptera Species File",
  "alias": "SF Orthoptera",
  "issued": "2022-09-05",
  "version": "Sep 2022",
  ...
  "geographicScope": "Global",
  "taxonomicScope": "Grasshoppers, locusts, katydids, crickets",
  "confidence": 5,
  "completeness": 100,
  "license": "cc by",
  "logo": "https://github.com/Sp2000/colplus-repo/raw/master/logos/SF_Orthoptera.png",
  "label": "Orthoptera Species File (Sep 2022)",
  "citation": "<div class=\"csl-entry\">Cigliano, M. M., Braun, H., Eades, D. C., &amp; Otte, D. (2022). <span style=\"font-style: italic\">Orthoptera Species File</span> (Sep 2022). Species File Group. https://doi.org/10.15468/nn7jhc</div>",
  "private": false
}

https://api.checklistbank.org/dataset/1021/settings

{
  "data format": "coldp",
  "csv quote": "\"",
  "csv delimiter": "\t",
  "csv quote escape": "\\",
  "nomenclatural code": "zoological",
  "data access": "http://IPT.speciesfile.org:8080/archive.do?r=orthoptera",
  "distribution gazetteer": "text",
  "import frequency": "never"
}

yroskov commented 1 year ago

SF Orthoptera ver. 0.35.2 / 2023-11-09; imported 2023-11-13; re-imported 2023-11-14 from Geoff's laptop

[x] Imported: 29749 spp (vs 29441 spp in Sep 2022)
[x] Metadata: version changed 0.35.2 / 2023-11-09 --> Nov 2023 / 2023-11-09
[x] Classification: family †Legendreiidae Huang, Schubnel & Nel, 2020 & genus †Tillyardiella Martynov, 1930 are in a Tree root of the order Orthoptera
[x] Sector: order Orthoptera broken - missing subject; fixed 2023-11-15
[x] Extinct flag: missing = FIXED in 2023-11-14 import
[x] Figure "1" present in authorstrings of paleo taxa: for example, Tillyardiella Martynov, 1930 1 = FIXED in 2023-11-14 import
[x] Superspecies: accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = 481 names BLOCKED via Workbench @gdower, would it be possible to exclude accepted superspecies from the export** for CoL (but keep their children species). Reasons: CLB recognise them as trinomials and misinterpriting portion "supersp" as a species epithet; superspecies adding problems with synonyms (their accepted children species repeated as a synonym with parent superspecies)
[ ] no URLs to species pages in TaxonPages

yroskov commented 1 year ago

ISSUES (SF Orthoptera ver. 0.35.2 / 2023-11-09) https://www.checklistbank.org/dataset/1021/issues

Rank Invalid, 23: rank interpreted as "other" = NO ACTION in CoL, need to be seen in TW https://www.checklistbank.org/dataset/1021/names?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&issue=rank%20invalid&limit=50&offset=0

Examples:

CoL status	Name	Rank
accepted	Ceuthophilus (Ceuthophilus) Scudder, 1862	other
accepted	Ceuthophilus (Ceuthophilus) (Burmeister, 1838)	other
accepted	Ceuthophilus (Ceuthophilus) Thomas, 1876	other
accepted	Chorthippus (Glyptobothrus) (Thunberg, 1815)	other
accepted	Cycloptilum Love & Walker, 1979	other
accepted	Eupholidoptera (Çiplak, Heller & Willemse, 2010)	other
accepted	Eupholidoptera (Brunner von Wattenwyl, 1882)	other

Classification Rank Order Invalid, 1: accepted | Acridomorpha MacLeay, 1821 | nanorder = NO ACTION, need to be checked in PREVIEW
Inconsistent Name, 943: accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = BLOCKED in CoL (see above); and synonyms with portion "subsp" correctly interpreted = NO ACTION https://www.checklistbank.org/dataset/1021/names?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&issue=inconsistent%20name&limit=50&offset=0

yroskov commented 1 year ago

TASKS (SF Orthoptera ver. 0.35.2 / 2023-11-09)

Broken decisions, 3654: deleted
[x] ACC-ACC infraspecies and infraspecies marker (same authors), 98: 98 type accepted subspecies are listed there. For example, accepted Acorypha clara clara (Walker, 1870); accepted Acorypha nigrovariegata nigrovariegata (Bolívar, 1889) https://www.checklistbank.org/catalogue/3/dataset/1021/duplicates?authorshipDifferent=false&catalogueKey=3&category=trinomial&limit=500&minSize=2&mode=STRICT&offset=0&status=accepted = BLOCKED in CoL
[x] ACC-SYN species (different accepted, different authors), 176: this might be an interest for SF editors (=synonyms flagged as Ambiguous in CoL) https://www.checklistbank.org/catalogue/3/dataset/1021/duplicates?acceptedDifferent=true&authorshipDifferent=true&catalogueKey=3&category=binomial&limit=500&minSize=2&mode=STRICT&offset=0&status=accepted&status=synonym
[x] ACC-SYN species (different accepted, same authors), 192: the report contains a mix of conflicting 'synonyms" in accepted superspecies and type subspecies. (= all synonyms blocked in CoL; accepted superspecies were blocked in previous steps). For example:

accepted Amphiacusta mona Desutter-Grandcolas, 1997 synonym Amphiacusta mona Desutter-Grandcolas, 1997 to acc Amphiacusta supersp mona Desutter-Grandcolas, 1997

accepted Bohemanella frigida (Boheman, 1846) synonym Bohemanella frigida (Boheman, 1846) to acc Bohemanella frigida frigida (Boheman, 1846)

https://www.checklistbank.org/catalogue/3/dataset/1021/duplicates?acceptedDifferent=true&authorshipDifferent=false&catalogueKey=3&category=binomial&limit=500&minSize=2&mode=STRICT&offset=0&status=accepted&status=synonym

[ ] Cases of "looped synonymy" between type subspecies and its parent species: ACC-SYN infraspecies (different accepted, same authors), 40 (https://www.checklistbank.org/catalogue/3/dataset/1021/duplicates?acceptedDifferent=true&authorshipDifferent=false&catalogueKey=3&category=trinomial&limit=500&minSize=2&mode=STRICT&offset=0&status=accepted&status=synonym) SYN-SYN species (different accepted, same authors), 360 (https://www.checklistbank.org/catalogue/3/dataset/1021/duplicates?acceptedDifferent=true&authorshipDifferent=false&catalogueKey=3&category=binomial&limit=500&minSize=2&mode=STRICT&offset=0&status=synonym)
[ ] SYN-SYN species (different accepted, same authors), 360 = difficult mix related to superspecies, looped synonymy in type subspecies, cases where species is a synonym to subgenus, and cases where "ambig syn" status need to be applied (resolved!) = unable to resolve subspecies yet (https://www.checklistbank.org/catalogue/3/dataset/1021/duplicates?acceptedDifferent=true&authorshipDifferent=false&catalogueKey=3&category=binomial&limit=500&minSize=2&mode=STRICT&offset=0&status=synonym)
[x] SYN-SYN species (same accepted, same authors), 519 = a lot of manual work involved; completed
[x] SYN-SYN infraspecies (different accepted, same authors), 24 = require resolution "line by line" = completed https://www.checklistbank.org/catalogue/3/dataset/1021/duplicates?acceptedDifferent=true&authorshipDifferent=false&catalogueKey=3&category=trinomial&limit=500&minSize=2&mode=STRICT&offset=0&status=synonym
[x] Suspicious duplicates: two subfamilies Schizodactylinae Blanchard, 1845 & Tettigoniinae Krauss, 1902 and one tribe Tettigoniini Krauss, 1902 = might be an interest for SF editors = one entry in each pair has no children, blocked in CoL

Resolved 2023-11-15:

Synced 2023-11-15

yroskov commented 11 months ago

SF Orthoptera ver. 0.36.0 / 2023-12-08; imported 2023-12-07; re-imported 2023-12-11 from Geoff's laptop

[x] Imported: 29840 spp (vs 29749 spp in Nov 2023)
[x] Metadata: version changed 0.36.0 / 2023-12-08 --> Dec 2023 / 2023-12-08
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: missing = FIXED in iteration of 2023-12-08
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] Figure "1" in authorstrings: no
[x] Superspecies: accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = 481 names blocked with IGNORE decision 2023-12-08 = UNFINISHED!: for unknown reasons the software left 7 names without decisions (e.g. Amblycorypha supersp uhleri; Uromenus supersp poncyi) = 2023-12-11, all names have decision
[ ] no URLs to species pages in TaxonPages

ISSUES assessed 2023-12-11

Rank Invalid, 24 (https://www.checklistbank.org/catalogue/3/dataset/1021/workbench?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&issue=rank%20invalid&limit=100&offset=0): what's happened to acc with rank "other" Ceuthophilus (Ceuthophilus) (Burmeister, 1838); Ceuthophilus (Ceuthophilus) Thomas, 1876 after sync?

@gdower, could you pls have a look on how subgenera exported from TW into CoLDP (see above, and after sync: https://www.checklistbank.org/catalogue/3/assembly?assemblyTaxonKey=ZPcH5zqLgwNu3GmJCyH-L1)

Uninomial Field Misplaced, 64 (https://www.checklistbank.org/catalogue/3/dataset/1021/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): all synonyms. What's happened?

TASKS

Broken decisions, 19: deleted

Resolved 2023-12-11:

Synced 2023-12-11

yroskov commented 10 months ago

SF Orthoptera ver. 0.37.0 / 2024-01-02; imported 2024-01-02 from Geoff's laptop

[x] Imported: 29844 spp (vs 29840 spp in Dec 2023)
[x] Metadata: version changed 0.37.0 / 2024-01-02 --> Jan 2024 / 2024-01-02
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: OK
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] Figure "1" in authorstrings: no
[x] Superspecies: (accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = 481 names blocked with IGNORE decision) = all names have decision
[ ] no URLs to species pages in TaxonPages
[ ] DOI: incorrect; doi 10.15468/nn7jhc points to GBIF page https://www.gbif.org/dataset/af66d4cf-0fd2-434b-9334-9806a5efa6f7 and refers to January 14, 2019

TASKS

Broken decisions, 33: deleted
Outdated decisions, 11: deleted

Resolved 2024-01-03:

Synced 2024-01-03

yroskov commented 9 months ago

SF Orthoptera ver. 0.38.1 / 2024-02-06; imported 2024-02-06 from Geoff's laptop

[x] Imported: 29857 spp (vs 29844 spp)
[x] Metadata: version changed 0.38.1 / 2024-02-06 --> Feb 2024 / 2024-02-06
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: OK
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] ~~Figure "1" in authorstrings: no~~
[ ] Superspecies: (accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = 481 names blocked with IGNORE decision) = decisions are not shown. GSD - Options - Re-index dataset = Request failed with status code 403 - User not authorized. https://github.com/CatalogueOfLife/backend/issues/1290#issuecomment-1944494473
[x] Block names with portion [species not specified] = 3 new blocked; name (supergen. Perugryllae) Cadena-Castañeda & García García, 2020 = ignore
[ ] no URLs to species pages in TaxonPages
[ ] DOI: incorrect; doi 10.15468/nn7jhc points to GBIF page https://www.gbif.org/dataset/af66d4cf-0fd2-434b-9334-9806a5efa6f7 and refers to January 14, 2019

ISSUES assessed 2024-02-14

Uninomial Field Misplaced, 64 https://www.checklistbank.org/catalogue/3/dataset/1021/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, could you please have a look, what might be wrong with names in this report

TASKS

Broken decisions, 54 = deleted
Outdated decisions, 24 = deleted

Resolved 2024-02-14

Synced 2024-02-14

yroskov commented 8 months ago

SF Orthoptera ver. 0.39.0 / 2024-03-08; imported 2024-03-08 from Geoff's laptop

[x] Imported: 29885 spp (vs 29857 spp)
[x] Metadata: version changed 0.39.0 / 2024-03-08 --> Mar 2024 / 2024-03-08
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: OK
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] Superspecies: (accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = rank excluded through Edit Sector option in Assembly
[x] Block names with portion [species not specified] = 3 blocked; 1 name (supergen. Perugryllae) Cadena-Castañeda & García García, 2020 = ignore
[ ] no URLs to species pages in TaxonPages
[ ] DOI: incorrect; doi 10.15468/nn7jhc points to GBIF page https://www.gbif.org/dataset/af66d4cf-0fd2-434b-9334-9806a5efa6f7 and refers to January 14, 2019

Metrics

ISSUES assessed 2024-03-20

Uninomial Field Misplaced, 64: https://www.checklistbank.org/catalogue/3/dataset/1021/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, perhaps, there is a sense to look on this. The issue present through different SFs (e.g. SF Coreoidea, SF Orthoptera, SF Lygaeoidea, etc.)

TASKS

Broken decisions, 16 = deleted
Outdated decisions, 2 = deleted

Resolved 2024-03-20

Synced 2024-03-20

yroskov commented 6 months ago

SF Orthoptera ver. 0.40.3 / 2024-04-18; imported 2024-04-19 from Geoff's laptop

[x] Imported: 29942 spp (vs 29885 spp)
[x] Metadata: version changed 0.40.3 / 2024-04-18 --> Apr 2024 / 2024-04-18
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: OK
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] Superspecies: (accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = rank excluded through Edit Sector option in Assembly
[x] Block names with portion [species not specified] = 3 blocked; 1 name (supergen. Perugryllae) Cadena-Castañeda & García García, 2020 = ignore
[ ] no URLs to species pages in TaxonPages
[ ] DOI: absent

Metrics:

TASKS

Broken decisions, 52 = deleted
Outdated decisions, 10 = deleted

Resolved 2024-04-22:

Synced 2024-04-22

yroskov commented 6 months ago

SF Orthoptera ver. 0.41.0 / 2024-05-06; imported 2024-05-06 from Geoff's laptop

[x] Imported: 29984 spp (vs 29942 spp)
[x] Metadata: version changed 0.41.0 / 2024-05-06 -> May 2024 / 2024-05-06
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: OK
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] Superspecies: (accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = rank excluded through Edit Sector option in Assembly
[x] Block names with portion [species not specified] = 3 blocked; 1 name (supergen. Perugryllae) Cadena-Castañeda & García García, 2020 = ignore THE SAME NAMES AS IN PREVIOUS IMPORT. DECISIONS ARE NOT SHOWN IN THE INTERFACE
[ ] no URLs to species pages in TaxonPages
[ ] DOI: absent

Metrics:

ISSUES assessed 2024-05-09

TASKS

Broken decisions, 44 = blocked
Outdated decisions, 6 = blocked

Resolved 2024-05-09:

Synced 2024-05-09

yroskov commented 5 months ago

SF Orthoptera ver. 0.41.1 / 2024-06-03; imported 2024-06-03 from Geoff's laptop

[x] Imported: 30005 spp (vs 29984 spp)
[x] Metadata: version changed 0.41.1 / 2024-06-03 -> Jun 2024 / 2024-06-03
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: OK
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] Superspecies: (accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = rank excluded through Edit Sector option in Assembly
[x] Block names with portion [species not specified] = 3 blocked; 1 name (supergen. Perugryllae) Cadena-Castañeda & García García, 2020 = din't find THE SAME NAMES AS IN PREVIOUS IMPORT. DECISIONS ARE NOT SHOWN IN THE INTERFACE
[ ] no URLs to species pages in TaxonPages
[ ] DOI: absent

Metrics

ISSUES

TASKS

Broken decisions, 26 = deleted all
Outdated decisions, 8 = no action

Resolved 2024-06-04:

Synced 2024-06-04

yroskov commented 4 months ago

SF Orthoptera ver. 0.42.0 / 2024-07-05; imported 2024-07-05 from Geoff's laptop

[x] Imported: 30016 spp (vs 30005 spp)
[x] Metadata: version corrected 0.42.0 / 2024-07-05 -> Jul 2024 / 2024-07-05
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: OK
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] Superspecies: (accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = rank excluded through Edit Sector option in Assembly
[x] Block names with portion [species not specified] = 3 blocked, 0 new; 1 name (supergen. Perugryllae) Cadena-Castañeda & García García, 2020 = ignored
[ ] no URLs to species pages in TaxonPages
[ ] DOI: absent

Metrics

TASKS

Broken decisions, 24 = deleted
Outdated decisions, 17 = no action

Resolved 2024-07-16:

Synced 2024-07-16

yroskov commented 3 months ago

SF Orthoptera ver. 0.43.1 / 2024-08-06; imported 2024-08-06 from Geoff's laptop

[x] Imported: 30031 spp (vs 30016 spp)
[x] Metadata: version corrected 0.43.1 / 2024-08-06 -> Aug 2024 / 2024-08-06
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: OK
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] Superspecies: (accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = rank excluded through Edit Sector option in Assembly
[x] Block names with portion [species not specified] = 3 blocked, 0 new; but interface does not show applied decisions
[ ] no URLs to species pages in TaxonPages
[ ] DOI: absent

Metrics

ISSUES assessed 2024-08-09

Rank Invalid, 24 = @gdower, _it looks like all names in this report supposed to have a rank subgenus. Now they have rank "other". Plus, there are 2 different style of parsing: subgenus as a combination (i.e. Ceuthophilus (Geotettix) Scudder, 1894) and subgenus as an uninomial (i.e. Eupholidoptera Kaltenbach, 1969)_

TASKS

Broken decisions, 5 = deleted
Outdated decisions, 12 = no action

Resolved 2024-08-09:

Synced 2024-08-09

yroskov commented 2 months ago

SF Orthoptera ver. 0.43.2 / 2024-09-06; imported from Geoff's laptop

[x] Imported: 30049 spp (vs 30031 spp)
[x] Metadata: version corrected 0.43.2 / 2024-09-06 -> Sep 2024 / 2024-09-06
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: OK
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] Superspecies: (accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = rank excluded through Edit Sector option in Assembly
[x] Block names with portion [species not specified] = 3 blocked, 0 new; but interface does not show applied decisions
[ ] no URLs to species pages in TaxonPages
[ ] DOI:

Metrics

TASKS

Broken decisions, 36 = deleted
Outdated decisions, 27 = no action

Resolved 2024-09-13:

Synced 2024-09-13

yroskov commented 1 month ago

SF Orthoptera ver. Oct 2024 / 2024-10-08; imported 2024-10-09 from Geoff's laptop

[x] Imported: 30076 spp (vs 30049 spp)
[x] Metadata: OK
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: OK
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] Superspecies: (accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = rank excluded through Edit Sector option in Assembly
[x] Block names with portion [species not specified] = 3 blocked, 0 new; but interface does not show applied decisions, decisions re-applied: Request failed with status code 400
[x] URLs to species pages: OK
[ ] DOI:

Metrics

ISSUES assessed 2024-10-11

TASKS

Broken decisions, 9 = deleted
Outdated decisions, 20 = no action

Resolved 2024-10-11:

Synced 2024-10-11

yroskov commented 1 month ago

Metrics - Timeline 2024-10-11

yroskov commented 4 days ago

SF Orthoptera ver. Nov 2024 / 2024-11-04; imported 2024-11-05 from Geoff's laptop

[x] Imported: 30099 spp (vs 30076 spp)
[x] Metadata: OK
[x] Classification: OK (as above)
[x] Sector: OK
[x] Extinct flag: OK
[x] Environment: OK (test names Abmisha coiblemmoides; Acanthoprion aztecum)
[x] Superspecies: (accepted names with portion "supersp" interpreted as "species aggregate" plus "supersp" as species epithet = rank excluded through Edit Sector option in Assembly
[x] Block names with portion [species not specified] = 3 blocked, 0 new; but interface does not show applied decisions, decisions re-applied: Request failed with status code 400
[x] URLs to species pages: OK
[ ] DOI:

Metrics

TASKS

Broken decisions, 69 = deleted
Outdated decisions, 17 = no action
[ ] SYN-SYN species (different accepted, same authors) 341 of 388 - binomial name is a synonym of the species and its type subspecies - 47 pairs reported Example: Acheta reticulata Fabricius, 1781 syn of Homoeogryllus reticulatus (Fabricius, 1781)
Acheta reticulata Fabricius, 1781 syn of Homoeogryllus reticulatus reticulatus (Fabricius, 1781) = blocked

Resolved 2024-11-11:

Synced 2024-11-11

CatalogueOfLife / testing

SF Orthoptera (id 1021): test report #166