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CatalogueOfLife / testing

Editorial tests and discussion to prepare for COL releases
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CoL of February 2024 #245

Open yroskov opened 5 months ago

yroskov commented 5 months ago

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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

yroskov commented 5 months ago

3 new suborders Auchenorrhyncha, Heteroptera & Sternorrhyncha in addition to existing Coleorrhyncha.

dhobern commented 5 months ago

World Wide Wattle has been updated (as has the Global Lepidoptera Index)

yroskov commented 5 months ago

World Wide Wattle has been updated (as has the Global Lepidoptera Index)

I have tried to process WWW on 2024-01-19 (see https://github.com/CatalogueOfLife/testing/issues/213#issuecomment-1900944688 for identified issues). However, final sync failed (code 400)

OK, it's clear, "Source license OTHER... is not compatible with license CC_BY of project 3". License changed to CC-BY. = FIXED

Synced 2024-02-14.

dhobern commented 5 months ago

@yroskov - can you please offer an update on the shift to the pruned higher classification for vertebrates? This was shared a couple of months ago - is something holding up its adoption?

https://www.checklistbank.org/dataset/279229/classification?taxonKey=21

dhobern commented 5 months ago

The Gelechiidae dataset has been updated following the move of a genus from Gelechiidae to Depressariidae. GLI has also been updated to include the genus.

yroskov commented 5 months ago

@yroskov - can you please offer an update on the shift to the pruned higher classification for vertebrates? This was shared a couple of months ago - is something holding up its adoption?

https://www.checklistbank.org/dataset/279229/classification?taxonKey=21

@dhobern, there were no actions after I sent you this email:

-----Original Message----- From: Roskov, Yury Sent: Tuesday, November 28, 2023 15:32 To: 'Markus Döring'; Donald Hobern Cc: Camila Plata; Diana Hernandez; Olaf Banki Subject: RE: Chordate classification

Dear Donald,

I had a look through the dataset id279229 in CLB: https://www.checklistbank.org/dataset/279229/classification. (Could you please confirm that you were referring to this dataset in your email below? I picked up the link from Markus' email).

Here is my assessment of your classification vs Nicolas version implemented in the CoL: https://github.com/CatalogueOfLife/testing/issues/186#issuecomment-1828674947. As I can see, there are only few changes which need to be made in the CoL via CLB Tree editor. That is easy task*.

The main problem, your version (as well as Nicolas version) does not match classification used by ReptileDB: http://www.reptile-database.org/db-info/taxa.html#Sau. If we implement your version, we'll have the same (i.e. identical) names for reptile classes and orders in the CoL, or we will lose order as a rank in all reptile data (like now). Do you have any solution for this?

*) Changes might be made in December edition, if I'll get green light to do the work and have a clear order on what to do with orders.

Yours, Yury

dhobern commented 5 months ago

Sorry @yroskov - this is incorrect. The version of the COL Chordata list that was uploaded on 27 November has the four reptile orders at the same rank as ReptileDB:

image

https://www.checklistbank.org/dataset/279229/classification?taxonKey=21

This isssue was fixed, so I believe the new Chordata classification should be ready to use.

dhobern commented 5 months ago

Maybe you understood this already and were just concerned that we have no named classes for the reptile orders. For the time being, I think we should just do as shown - treat these orders as siblings for the other classes in the megaclass. We will have a conversation with ReptileDB about whether they expect to add classes.

yroskov commented 5 months ago

Complete CoL of Feb before 22-23 February

yroskov commented 5 months ago
yroskov commented 5 months ago

PREVIEW release started 2024-02-01, 7:40 pm (server time) Fixed Progonocimicidae duplication = FIXED Finished as COL24.2, id 287018, 2024-02-01 Deployed to the preview website 2024-02-02

dhobern commented 5 months ago

Sesiidae have been updated with 10 more species

yroskov commented 5 months ago

(1) Subphylum Vertebrata - infraphylum Gnathostomata - parvphylum Osteichthyes = EXCLUDE gigaclass Actinopterygii & create class Actinopterygii with FishBase orders as they are in CoL; EXCLUDE gigaclass Sarcopterygii = DONE 2024-02-05 (2) Subphylum Vertebrata - infraphylum Gnathostomata - parvphylum Osteichthyes - gigaclass Sarcopterygii - megaclass Tetrapoda = EXCLUDE superclass Amniota = DONE 2024-02-05 (3) Synonym "Reptilia" with 4 orders Rhynchocephalia, Squamata, Crocodylia & Testudines. Implemented 2024-02-05: these four orders established as new sectors from the resource id 279229, synced; ReptileDB children taxa re-established as sectors under orders of resource id 279229. = NEED TO BE CHECKED IN THE PREVIEW

AS A RESULT of implementing the classification from the resource id 279229 "COL Checklist Chordata Higher Classification, ver 1.0 / 2023-11-27", rank Class is missing now for all reptiles.

yroskov commented 5 months ago

= Option "delete all" in World Plants ver. 18.4, Jan 2024 / 2024-01-31 (3195 names) = DOES NOT WORK. They should be deleted one-by-one - 1959 left - 1403 left - 801 left - 400 left - 0 = DELETED 2024-02-05

2024-02-07: 1,351 left; mainly in ReptileDB. The same subspecies is accepted name and synonym to its parent species image

yroskov commented 5 months ago

PREVIEW release started 2024-02-05, 9:39 pm (server time) Changes in Vertebrata classification. Reptilia as a synonym. = CHECKED 2024-02-06 Finished as COL24.2, id 287332, 2024-02-05 Deployed to the preview website 2024-02-06

yroskov commented 5 months ago

PREVIEW release started 2024-02-07, 2:51 pm (server time) Finished as COL24.2, id 287465, 2024-02-07, 4:16 pm Deployed to the preview website 2024-02-07

CHECKS 2024-02-07

Next:

yroskov commented 5 months ago

PREVIEW release started 2024-02-07, 8:10 pm (server time) Finished as COL24.2, id 287567, 2024-02-07, 9:39 pm Deployed to the preview website 2024-02-07

yroskov commented 4 months ago

PREVIEW release started 2024-02-14, 10:00 pm (server time) Finished as COL24.2, id 288269, 2024-02-14 Deployed to the preview website 2024-02-15

CHECKS of 2024-02-15

Systema Dipterorum +5,233 spp in total WWW 1088-6200 = -422 spp - WHY?

yroskov commented 4 months ago

PREVIEW release started 2024-02-16, 5:09 pm (server time) Check WWW & Hemiptera classification Finished as COL24.2, id 288480, 2024-02-16, 1:57 pm Deployed to the preview website 2024-02-16

CHECKS 2024-02-16

Hemiptera: 3i Auchenorrhyncha -3,424 spp ITIS -2,784 spp

yroskov commented 4 months ago

PREVIEW release started 2024-02-19, 8:31 pm (server time) Check missed spp/taxa in Hemiptera Finished as COL24.2, id 288771, 2024-02-19, 10:01 pm Deployed to the preview website 2024-02-19

CHECKS 2024-02-19 Hemiptera fixed.

yroskov commented 4 months ago

PREVIEW release started 2024-02-20, 8:38 pm (server time) Finished as COL24.2, id 288827, 2024-02-20, 10:06 pm Deployed to the preview website 2024-02-20

yroskov commented 4 months ago

PREVIEW release started 2024-02-21, 7:36 pm (server time) Finished as COL24.2, id 288937, 2024-02-21, 9:02 pm Deployed to the preview website 2024-02-21

yroskov commented 4 months ago

PREVIEW release started 2024-02-22, 2:13 pm (server time) Check ver in metadata Finished as COL24.2, id 288943, 2024-02-22, 4:40 pm Deployed to the preview website 2024-02-22

yroskov commented 4 months ago

For attention of @olafbanki & @mdoering: COL24.2, id 288943, 2024-02-22 is ready now for deployment as CoL of February 2024.

yroskov commented 4 months ago

Deployed to the portal 2024-02-28

yroskov commented 4 months ago

2024-03-01, problems with the portal:

https://www.catalogueoflife.org/data/source-datasets image

The same problem is on the PREVIEW: https://www.catalogueoflife.org/data/source-datasets (At the time of PREVIEW tests (Feb 22 & 23) all worked fine).