CoL of February 2023

[yroskov]

• [x] WoRMS ver. (02/2023) / 2023-02-01; imported 2023-02-02; synced 2023-02-03

• [x] ITIS of 2023-01-30 (incl. new global checklists for mite family Podocinidae and decapod suborder Dendrobranchiata); synced 2023-02-02

• [x] Scarabs of 2023-02-06; imported 2023-02-06; synced 2023-02-06

• [x] 3i Auchenorrhyncha of Feb 2023; imported 2023-02-02; synced 2023-02-03

• [x] SF Isoptera of 2023-02-02; imported 2023-02-02; synced 2023-02-03

• [x] WCO (Opiliones) of 2023-02-02; imported 2023-02-02; synced 2023-02-06 - failed; re-synced 2023-02-06

• [x] WOL (Odonata) of 2023-02-02; imported 2023-02-02; synced 2023-02-06 - failed; re-synced 2023-02-06

• [x] World Plants, ver. 14.7, Jan 2023, received 2023-01-12; synced 2023-01-19; re-synced 2023-02-03 with 376_new (received 2023-01-21) ! Ask Michael about deep links to species page: >Michael's deep links don't work properly anymore http://www.worldplants.de/?deeplink=Knautia-longifolia = KEEP links as they present; it will be fixed on their side. ! Ranunculus crenatus Descr. -> Ranunculus crenatus Waldst. & Kit. = re-synced sector Ranunculales 2023-02-07

• [x] World Ferns, ver. 14.7, Jan 2023, received 2023-01-12; synced 2023-01-18

• [x] Species Fungorum Plus received 2023-01-17; synced 2023-01-27; re-synced 2023-02-06 - failed; re-synced 2023-02-06

Other 11 GSDs for updates: https://docs.google.com/spreadsheets/d/1WRxfYQF8h2Xiu3gNUvQ3de-zRH-BSq3wYWIAbHHBrhY/edit?usp=sharing

[yroskov]

• [x] https://github.com/CatalogueOfLife/data/issues/502#issuecomment-1387163153; Fabriogenia diga -> Fabriogenia dilga; HymIS Pompilidae re-synced 2023-01-18.

[yroskov]

• [x] FLOW from ac19 re-imported; synced 2023-01-26 (https://github.com/CatalogueOfLife/data/issues/503) re-synced 2023-01-27 (with fixed URLs) IsIssus analis back? - It's back in FLOW@CLB, but not present in CoL-draft & CoL@CLB & PREVIEW

[yroskov]

PREVIEW release started 2023-01-27 (server time 1:14 am 2023-01-28 Finished as COL23.1, 2023-01-28, id 9871 Deployed to https://preview.catalogueoflife.org/ 2023-01-30

Checks 2023-01-30:

• [ ] 2,095,854 acc spp vs 2,087,774 in Jan; 1,980,160 sp syns vs 2,283,241 in Jan -? At least, 303,081 synonyms are missed

Among synonyms following ranks are missing completely: variety, form, subvariety, proles, abberation, forma specialis, morph: Preview: https://preview.catalogueoflife.org/data/search?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=extinct&facet=environment&limit=50&offset=0&rank=species&rank=subspecies&rank=infraspecific%20name&sortBy=taxonomic&status=synonym&status=ambiguous%20synonym&status=misapplied

Jan edition: https://www.catalogueoflife.org/data/search?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=extinct&facet=environment&limit=50&offset=0&rank=species&rank=variety&rank=subspecies&rank=form&rank=infraspecific%20name&rank=subvariety&rank=proles&rank=aberration&rank=forma%20specialis&rank=morph&sortBy=taxonomic&status=ambiguous%20synonym&status=synonym&status=misapplied

Check for synonym stats in synced GSDs: WPlants - 473,325 in preview vs 446,209 in Jan = OK WFerns - 51,261 in preview vs 51,224 in Jan = OK FLOW - 9,084 in preview vs 4,798 in Jan vs 9,089 in ac19 = OK

• [ ] Broken GSDs order in the list at https://preview.catalogueoflife.org/data/source-datasets ! Eumycetozoa.com has no ShortName = Metadata patch re-adjusted, re-synced 2023-01-30

• [ ] IsIssus analis back? = No: it's not present in CoL-draft & CoL@CLB & PREVIEW, but present in FLOW@CLB as a synonym of Zopherisca analis:

PREVIEW (no synonym; not available in search):

2023-01-30 FLOW re-synced again: Issus analis is not present in CoL-draft - @gdower, do you have a way to find why synonym Issus analis failed to be synced?

@gdower, I did find an answer: Issus analis was blocked. (But, I deleted decision before re-import, and didn't block it again. Strange. Looks like a "ghost decision"

Deleted decision, re-synced again. Woops, a new problem:

• [ ] CoL-draft Browse the Tree, search for Issus analis (FLOW), the interface shows "synonym of null":

Preview Search for Abaphospora alpina (Species Fungorum Plus), the interface says "synonym of (Ellis & Everh.) M.E. Barr" - i.e. accepted binomial is missing in the results:

Preview Search for Austrolycopodium assurgens (World Ferns), the interface says "synonym of (Phil.) Holub" - i.e. accepted binomial is missing in the results**:

[yroskov]

PREVIEW release started 2023-01-30 (server time 6:38 pm) - with fixed alias for Eumycetozoa.com & deleted decision for Issus analis Finished as COL23.1, 2023-01-30, id 9877 - still indexing (8.20 am in Champaign) Deployed to https://preview.catalogueoflife.org/ 2023-01-31: but search option does not work in Browse & Search tools. - for attention of @mdoering

Geoff: release is still indexing:

Tim: >I don’t know if this helps or not, but the checklistbank application was restarted following an issue earlier today. I could well imagine that could abort indexing

Tim: >An update:We have a memory leak in the indexing step (logged here). That will be fixed next week. With some adjustments, I was able to get the step to proceed despite the memory leak, but we were not confident of the final state. Following a quick call with Markus and we agreed the best course of action was to delete that release, and trigger a new release.

[yroskov]

PREVIEW release launched by Tim 2023-02-01. ...with fixed alias for Eumycetozoa.com & deleted decision for Issus analis; "new sectors from old ITIS" Finished as COL23.2, 2023-02-01, id 9878. Deployed to https://preview.catalogueoflife.org/ 2023-02-01.

Checks of 2023-02-01:

• 2,096,339 acc spp vs 2,087,774 in Jan = OK; 2,326,505 sp syns vs 2,283,241 in Jan = OK
• Eumycetozoa.com = OK
• Broken GSDs order in the list = Fixed
• IsIssus analis back? = Yes
• [ ] "synonym of null" bug (front end? back end? ) https://github.com/CatalogueOfLife/backend/issues/1197

[yroskov]

Syncs of 2023-02-06 failed?

Geoff notified me: Failed SectorSync{sectorKey=3:1808, subjectDatasetKey=125101, sector=Sector{1808, datasetKey=3, mode=ATTACH, subjectDatasetKey=125101, subject=ACCEPTED ORDER Odonata Fabricius, 1793 [604316]}, created=2023-02-06T15:43:11.262034 by yroskov}

Failed SectorSync{sectorKey=3:1204, subjectDatasetKey=2256, sector=Sector{1204, datasetKey=3, mode=ATTACH, subjectDatasetKey=2256, subject=ACCEPTED ORDER Opiliones Sundevall, 1833 [551110]}, created=2023-02-06T15:33:35.213429 by yroskov}

(What happened to Fungi sync?)

Interface shows:

https://www.checklistbank.org/catalogue/3/sector/sync?limit=25&offset=0

[yroskov]

PREVIEW release started 2023-02-07 (server time 2:55 pm) - with all GSDs & WP-376-2nd(not3rd) Cancelled by Markus.

[yroskov]

PREVIEW release started 2023-02-07 (server time 8:55 pm) - with all GSDs & WP-376-3rd Finished as COL23.2 2023-02-07 id 9880 (server time 10:13 pm = conversion took 1h 18m - extraordinary fast!) Deployed to the PREVIEW site 2023-02-08

CHECKS

• [x] Stats for accepted species matches expectation through all GSDs.
• [x] Stats for syns 1916396 vs 1886770 = +29,626
• [x] All applied fixes present.

[yroskov]

COL23.2 2023-02-07 id 9880 is ready for deployment as February edition - for attention of @olafbanki & @mdoering

[olafbanki]

@yroskov @gdower many thanks!