CoL of November 2023 - Githubissues

yroskov commented 8 months ago

[x] WoRMS of 2023-11-01 (check auths/eds in WoRMS Mollusca & Nemys); all syncs of 2023-11-03 failed (https://github.com/CatalogueOfLife/backend/issues/1269); synced 2023-11-07
[x] ITIS of 2023-10-31 (incl. a new global checklist for the mite superfamily Anystoidea); imported 2023-11-02; synced 2023-11-03 - CHECK ITIS SYNC! = all 122 failed; synced 2023-11-07
[x] Scarabs of 2023-11-06; imported 2023-11-06; synced 2023-11-07
[x] 3i Auchenorrhyncha of Nov 2023; imported 2023-11-08; synced 2023-11-10
[x] Entiminae of Nov 2023; imported 2023-11-09; synced 2023-11-09
[x] SF Isoptera of 2023-11-08; imported 2023-11-09; synced 2023-11-09
[x] WCO (Opiliones) of 2023-11-08; imported 2023-11-09; synced 2023-11-09
[x] WOL (Odonata) of 2023-11-08; imported 2023-11-09; synced 2023-11-10
[x] GLI synced 2023-11-07, re-synced 2023-11-13
[x] Gelechiidae ver 1.1.23.315 (11 Nov 2023) / 2023-11-11; imported 2023-11-11; synced 2023-11-13
[ ] Pterophoroidea = There is no update since CoL of Oct 2023. No need to re-sync.
[x] Hepialidae (Lepidoptera), new; ver 1.0 of ?; imported 2023-10-01; synced 2023-10-27
[x] PaleoBioDB replaced with previous version of Feb 2018 / 2018-02-16 (id 268676); synced 2023-11-06 = Need to be re-imported when 'extinct' flag appear in Options for import. This will resolve issue of non-extinct genera in PaleoBioDB sectors.
[x] World Plants ver 18.1 of 2023-11-08; imported 2023-11-15; synced 2023-11-15
[x] World Ferns ver 18.1 of 2023-11-08; imported 2023-11-14; synced 2023-11-15
[x] WCVP-Fabaceae ver. 2023v.4 / 2023-08-02; synced 2023-11-13
[x] SF Orthoptera ver. 0.35.2 / 2023-11-09; imported 2023-11-14; synced 2023-11-15

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Conifers as a part of WFO - Nov?
UCD in Nov?
WCVP ver 11.0 / 2023-04-20
ScaleNet
LPSN
Species Files via TW (in Nov - Dec) - check with Heidi on a new SF Permopsocida (39 paleospp)
FishBase - ?
Paris/DBTNT - ?
Species Fungorum via API (should be confirmed by Paul)
LDL Neuropterida

=============================

Filling gaps:

Suborder Symphyta (Hymenoptera) https://github.com/CatalogueOfLife/data/issues/579 Class/order Diplura https://github.com/CatalogueOfLife/data/issues/577 Order †Permopsocida (Insecta) https://github.com/CatalogueOfLife/data/issues/578 Family Promecheilidae (Tenebrionoidea, Coleoptera) https://github.com/CatalogueOfLife/data/issues/580

dhobern commented 8 months ago

The COL TG has approved the replacement of the family Hepialidae (Lepidoptera) with this new dataset:

https://www.checklistbank.org/dataset/265709/about

yroskov commented 8 months ago

[x] WCO (Opiliones): check authorstrings with extinct taxa (https://github.com/CatalogueOfLife/data/issues/569) = FIXED, PREVIEW 2023-11-13

yroskov commented 8 months ago

[x] PaleoBioDB update of Oct: missing "extinct" flag with 4615 spp (data absent in CLB source). Consider reverting to a previous cleaned version.

Replaced with previous version of Feb 2018 / 2018-02-16 (id 268676)

sergbolshakov commented 8 months ago

Hello! In the latest version for names from Bryonames in the status of synonyms there are no links. But online in the link field there are links to the name page in Tropicos. E. g. https://www.checklistbank.org/dataset/272972/name/4a2f4d14-e255-4c55-a8a4-b5df5608bf6c vs grep Takakiophyta NameUsage.tsv Is this a bug or a feature?

yroskov commented 8 months ago

[x] Fixed a bug which caused unstable UUID identifiers. Now need to re-sync all sectors in: https://github.com/CatalogueOfLife/backend/issues/1277

The list of GSDs awaiting re-sync: https://github.com/CatalogueOfLife/backend/issues/1277

key	modified	count	alias	date of re-sync
2317	2023-10-04	68033	3i Auchenorrhyncha	2023-11-10
55434	2023-10-12	1341	GLI	2023-11-07
2144	2023-10-02	315280	ITIS	~~2023-11-03~~ 2023-11-07
XXXX	2023-10-03	4260	all WoRMS	2023-11-07
1141	2023-09-28	8708	World Plants	2023-11-07
1021	2023-05-12	70	SF Orthoptera	2023-11-07
1101	2023-06-14	48	Systema Dipterorum	2023-11-07

yroskov commented 8 months ago

Donald, 2023-10-29: _... I needed to confirm to you that the Taxonomy Group supports the two decisions here: https://docs.google.com/document/d/1YLcC7dHrMA40UKViZ5ww39Yc99IcgGCo/edit?usp=sharing&ouid=113140186902620905250&rtpof=true&sd=true https://docs.google.com/document/d/1HUkQxthfXSb6Sr8BNv2837T7bUGas95-3XE73GS_X-w/edit Please do anything else that needs to happen to replace these sections in COL._

[x] Hepialidae (ghost moths)
[ ] WFO conifers = Not in November; see email from Olaf, 2023-11-07: -Before the conifer database from WFO can be included into the COL Checklist, several issues need to be resolved. -However, we have no current model to allocate the proper metadata to the conifer database. A thought could be to assign metadata to a sector. It needs to be worked out more what the implications would be, and what needs to be implemented.
-Given that discussion and implementation may take some time, it is probably best if we find a pragmatic solution for now so that the inclusion of the conifer database from WFO into the COL Checklist does not have to wait too long.

gdower commented 8 months ago

@sergbolshakov, that's likely an exporter bug. Please open a ticket here.

yroskov commented 8 months ago

PREVIEW release started 2023-11-07, 11:06 pm (server time) Finished as COL23.11, id 276829, 2023-11-07 Deployed to the preview website 2023-10-08

[x] PaleoBioDB
[x] Lepidoptera & Hepialidae
[x] Other GSD stats: WoRMS Myxozoa spp 761 in Oct vs 1494 in Nov = ? = I did not spot overlaps neither inside GSD (checked on species level) nor between GSDs (checked on genus level https://www.checklistbank.org/catalogue/3/duplicates?catalogueKey=3&limit=500&rank=genus&status=accepted&status=provisionally%20accepted). Also, confirmed by Bart.
[ ] https://github.com/CatalogueOfLife/portal/issues/207

yroskov commented 8 months ago

[ ] Check GSD logos (they disappeared in Oct release or earlier), see https://github.com/CatalogueOfLife/portal/issues/206
No logos in preview 2023-11-13