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CoL of March 2024 #251

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23 of 32 tasks
yroskov opened this issue Feb 22, 2024 · 18 comments
Open
23 of 32 tasks

CoL of March 2024 #251

yroskov opened this issue Feb 22, 2024 · 18 comments

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@yroskov
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yroskov commented Feb 22, 2024 •
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  • WoRMS of 2024-03-01; imported 2024-03-02; synced 2024-03-04

  • ITIS of 2024-02-28 with new GSDs for mite superfamily Raphignathoidea, and beetle families Haliplidae & Noteridae; imported 2024-03-02; synced 2024-03-05

  • Scarabs of 2024-03-05; imported 2024-03-05; synced 2024-03-05

FROM TaxonWorks:

  • 3i Auchenorrhyncha - Nested sector Auchenorrhyncha? Hemiptera classification: temporary adjustment #250 (comment); imported 2024-03-08; synced 2024-03-19
  • Entiminae; imported 2024-03-08; synced 2024-03-19
  • WCO (Opiliones); imported 2024-03-08; synced 2024-03-19
  • WOL (Odonata); imported 2024-03-08; synced 2024-03-20
  • SF Isoptera; imported 2024-03-08; synced 2024-03-20
  • SF Orthoptera; imported 2024-03-08; synced 2024-03-20

monthly started from January 2024:

  • SF Dermaptera; imported 2024-03-09; synced 2024-03-20
  • SF Embioptera; imported 2024-03-09; synced 2024-03-20
  • SF Plecoptera; imported 2024-03-09; synced 2024-03-20
  • SF Psocodea; imported 2024-03-09; synced 2024-03-20

monthly started from March 2024:

  • SF Aphid = no new import
  • SF Chrysididae; imported 2024-03-09; synced 2024-03-21
  • SF Coreoidea; imported 2024-03-09; synced 2024-03-21
  • SF Lygaeoidea; imported 2024-03-09; synced 2024-03-21, re-synced 2024-03-22
  • SF Mantodea; imported 2024-03-09; synced 2024-03-21
  • SF Phasmida; imported 2024-03-09; synced 2024-03-21
  • Systema Dipterorum ver. 5.0, 2024-01-08 processed via TW by DD; second iteration (bring back extinct spp); imported 2024-03-07; synced 2024-03-18, re-synced 2024-03-22

LEPIDOPTERA:

  • GLI 1.1.24.040 / 2024-02-09; imported 2024-03-17; synced 2024-03-18
  • Alucitoidea (Lepidoptera) Alucitoidea update #252 (comment); ver. 1.1.24.60 (29 Feb 2024); synced 2024-03-18
  • Gelechiidae (Lepidoptera) ver 1.1.24.73 (13 Mar 2024); synced 2024-03-18
  • Hepialidae (Lepidoptera) = no new import
  • Pterophoroidea (Lepidoptera) = no new import
  • Sesiidae (Lepidoptera) = no new import

OTHER:

  • RJB Geranium received 2024-01-17

  • Cunaxidae database (as an update for one family in BdelloideaBase) received 2024-02-28

  • WSC (spiders) ver. 24.5 of 2024-01-15; received 2024-03-02

  • World Ferns ver. 19.1, 2024-03-09; received 2024-03-12; imported 2024-03-15; synced 2024-03-20

  • World Plants ver. 19.1, 2024-03-09; received 2024-03-12 -> update moved to April (19.2 of March 18th)

  • ReptileDB ver. 2023-09 / 2023-09-30; received 2024-03-21

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

  • SF Permopsocida is not yet in CoL; I have submitted its adoption to the CoL Taxon Group. (see email of 2023-11-10, Heidi)

  • Conifers as a part of WFO - Nov?

  • ScaleNet

  • UCD in Nov?

  • WCVP ver 11.0 / 2023-04-20

  • LPSN see Genome Taxonomy Database (GTDB) for prokaryotes data#202 (comment)

  • Rotifers

  • FishBase - ?

  • Paris/DBTNT - ?

  • Species Fungorum via API (should be confirmed by Paul) (2nd email sent 2024-02-28)

  • LDL Neuropterida

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

Filling gaps:

Suborder Symphyta (Hymenoptera) CatalogueOfLife/data#579
Class/order Diplura CatalogueOfLife/data#577
Order †Permopsocida (Insecta) CatalogueOfLife/data#578
Family Promecheilidae (Tenebrionoidea, Coleoptera) CatalogueOfLife/data#580
@yroskov
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yroskov commented Mar 4, 2024 •
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Geoff reported 3 broken WoRMS sectors with missing subjects. Sectors FIXED 2024-03-04 #254 (comment)

NEED TO BE RE-SYNCED:

  • WoRMS Octocorallia
  • WoRMS Myxozoa
  • WoRMS Ceriantharia

@yroskov
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yroskov commented Mar 4, 2024 •
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Weird name parsing in ReptileDB CatalogueOfLife/data#628

Cleaned up 2024-03-04.

NEED TO BE RE-SYNCED:

  • ReptileDB = Synced 2024-03-4

@yroskov
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yroskov commented Mar 20, 2024 •
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PREVIEW release started 2024-03-20, 9:33 pm (server time)
Finished as COL24.3, id 291318, 2024-03-20
Deployed to the preview website 2024-03-21

CHECKS 2024-03-21:

  • TAXREF (id 2008) is a new entry in CoL (0 spp in CoL) = Why & who?

image

https://www.checklistbank.org/catalogue/3/dataset/2008/metadata
TAXREF is the national taxonomic repository for the fauna, flora and fungus of mainland France and overseas, developed and distributed by the National Museum of Natural History (MNHN) as part of the implementation of the System of 'Information from the National Natural Heritage Inventory (SINP). This reference system is unique for France; its aim is to list and organize the scientific names of all living beings recorded in the territory.
207,826 spp in total

image

@mdoering, we cannot figure out TAXREF sectors in the CoL. We believe, this database appeared by mistake in the list of CoL Source Datasets

Looks like it came from Chrysididae Project. Why it jumped in CoL-3?

image

@yroskov
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yroskov commented Mar 21, 2024 •
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PREVIEW release started 2024-03-21, 8:26 pm (server time)
Finished as COL24.3, id 291420, 2024-03-21
Deployed to the preview website 2024-03-22

Checked 2024-03-22.

  • there is no TAXREF (id 2008) in the PREVIEW

@mdoering
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It is a artifact from testing an extended merge sector on prod. We have removed that sector now and it should not show up in subsequent releases any more. I am working on a fix in dev to avoid this before we try to add a merge sector again on prod

@yroskov
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yroskov commented Mar 22, 2024 •
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It is a artifact ... and it should not show up in subsequent releases any more.

It's gone from yesterday's release (id 291420). Thank you!

@yroskov
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yroskov commented Mar 22, 2024 •
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PREVIEW release started 2024-03-22, 7:58 pm (server time)
Finished as COL24.3, id 291532, 2024-03-22
Deployed to the preview website 2024-03-25

CHECKS 2024-03-25

  • Duplicated 3i vs FLOW families: Cixiidae, Coleoscytidae, Delphacidae, Dorytocidae, Fulgoridiidae, Jubisentidae, Lalacidae, Mimarachnidae, Neazoniidae, Perforissidae, Qiyangiricaniidae, Surijokocixiidae
    = 2024-03-25 blocked infraorder Fulgoromorpha in 3i. 3i re-synced

@yroskov
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yroskov commented Mar 25, 2024 •
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PREVIEW release started 2024-03-25, 3:31 pm (server time)
Finished as COL24.3, id 291964, 2024-03-25, 5:00 pm
Deployed to the preview website 2024-03-25

Checks 2024-03-25

  • Superfamily Fulgoroidea is out of suborder Auchenorrhyncha. FLOW sector is broken, missing target. = FIXED (target infraorder Fulgoromorpha Evans, 1946)

image

@yroskov
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yroskov commented Mar 25, 2024 •
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PREVIEW release started 2024-03-25, 5:23 pm (server time)
Finished as COL24.3, id 291968, 2024-03-25, 7:07 pm
Deployed to the preview website 2024-03-25

@yroskov
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yroskov commented Mar 25, 2024

For attention of @olafbanki & @mdoering: COL24.3, id 291968, 2024-03-25 is ready now for deployment as CoL of March 2024.

@yroskov
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yroskov commented Mar 26, 2024

Deployed to the portal 2024-03-26

@yroskov
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yroskov commented Mar 26, 2024 •
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@yroskov
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yroskov commented Mar 26, 2024 •
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It looks like, 3 cancelled GSDs need now re-sync:

  • WoRMS Mollusca,
  • WoRMS Isopoda
  • WoRMS Bryozoa.

Re-syncs started 2024-03-26

@yroskov
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yroskov commented Mar 26, 2024 •
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PREVIEW release started 2024-03-26, 10:27 pm (server time)
Finished as COL24.3, id 292011, 2024-03-27, 1:52 am
Deployed to the preview website 2024-03-26 (Champaign time)

Checked 2024-03-26

Total spp 2,024,876 (2024-03-25) vs 2,153,847 (2024-03-26)

@yroskov
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yroskov commented Mar 27, 2024

@mdoering, @olafbanki: it looks like WoRMS Mollusca is back now.

I would suggest to replace March edition with COL24.3, id 292011, 2024-03-26.

@mdoering
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done

@mdoering
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You could also tell by the total number of records that sth was weird in yesterdays release:
Screenshot 2024-03-27 at 08 06 34

@yroskov
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yroskov commented Mar 27, 2024

Thanks!

Total number "size" in that table is useful. I didn't know about this parameter. Now I'll include it in my routine. Thanks!

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