World Ferns (id 1140): test report

[yroskov]

World Ferns of 2020-09-25 see https://github.com/CatalogueOfLife/testing/issues/22

World Ferns of 2020-12-08.

Metadata patched:

[yroskov]

TASKS fixed:

[yroskov]

Broken decisions after Rematch All

How to clean up a list of remaining 1140 broken decisions?

[yroskov]

Truncated authorstrings with Gabriel y Galán (mis-parsed author) have been corrected via complex decisions:

Lomariocycas moritziana (Klotzsch) Gabriel
Struthiopteris fallax (Lange) S. Molino & Gabriel
Struthiopteris spicant var. fallax (J. E. Lange) Wasowicz & Gabriel Struthiopteris spicant var. homophyllum (Merino) Gabriel
Struthiopteris spicant var. pradae S. Molino & Gabriel

https://data.catalogueoflife.org/catalogue/3/dataset/1140/workbench?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&limit=50&offset=0&q=Gabriel

[yroskov]

Issues report "Rank Invalid".

Majority of cases (9 of 10) caused by the infraspecific marker "nothossp." used in the source. (I have interpreted this as "subspecies" via complex decisions).

also, https://github.com/CatalogueOfLife/backend/issues/931

[yroskov]

2020-12-15: new crawling and import

TASKS:

Resolved:

[yroskov]

Synced 2020-12-17

[yroskov]

New version received on 2021-01-04. @gdower imported data in the clearinghouse.

• [ ] @gdower changed version and received date in metadata as 2021-01-04. However, the system shown it to me as 2020-12-08. It's not a first time of halted system.

Tasks & Issues checked.

Data synced on 2021-01-04.

[yroskov]

• [x] Subspecies case in World Ferns: checked against master file. There is a mistake in the master file with Taxon code: Physematium scopulinum ssp. appalachianum should have a code SS. Reported to the author: It would be nice to correct in next exports.

S | | Physematium scopulinum ssp. appalachianum (T.M.C.Taylor) Li Bing Zhang, N.T.Lu & X.F.Gao SS | | Physematium scopulinum Trevis. ssp. scopulinum Trevis. SS | | Physematium scopulinum Trevis. ssp. laurentianum (Windham) Li Bing Zhang, N.T.Lu & X.F.Gao

Trying to fix in the clearinghouse:

cleaned up previous complex decision (change rank)

Well, it looks now like that:

image

[yroskov]

World Ferns of 2021-01-07. Subspecies case fixed in the master file:

World Ferns of 2021-01-07: synced 2021-01-07

[yroskov]

World Ferns of 2021-03-02 received and imported (id 1140). fourth update since AC19 Metadata: ver. & date changed as 2021-03-02.

[yroskov]

TASKS of 2021-03-02

"Rematch all decisions" = 1396 remains broken. "Delete all broken decisions" = completed.

[yroskov]

ISSUES of 2021-03-02

• [ ] Multi Word Epithet, 1010 & Unusual Name Characters, 1010 - names with hybrid mark, e.g. Asplenium × aprutianum Lovis Left as they are.

[yroskov]

World Ferns of 2021-03-02 synced 2021-03-03.

[yroskov]

World Ferns of 2021-03-17 received and imported (id 1140). fifth update since AC19 Metadata: ver. & date changed as 2021-03-17.

• [x] No broken sectors

ISSUES

• [x] assessed

[yroskov]

TASKS 2021-03-18

Resolved:

[yroskov]

World Ferns of 2021-03-17 synced 2021-03-18

[yroskov]

World Ferns of 2021-05-10 imported 2021-05-12.

• [x] Imported 13584 spp
• [x] Metadata: organisation incorrectly parsed. Fixed 2021-05-19
• [x] Sectors: ok
• [x] ISSUES assessed 2021-05-19

[yroskov]

TASKS

-[x] Broken decision: 38. Rematched, 5 broken - deleted.

Resolved 2021-05-19:

[yroskov]

World Ferns of 2021-05-10 synced 2021-05-19

[yroskov]

World Ferns of 2021-05-26 imported 2021-05-26.

• [x] Imported 13584 spp
• [x] Metadata: updated.
• [x] Sectors: ok

ISSUES assessed 2021-05-26

TASKS

• [x] Broken decisions, 59. Re-matched, 0 remains.

Synced 2021-05-26

[yroskov]

World Ferns of 2021-08-06 imported 2021-08-19. First update after ac21.

• [x] Imported 13684 spp
• [x] Metadata: updated.
• [x] Sectors: ok

TASKS

• [x] Broken decisions, 89. Re-match all, 24 remains - deleted.

Resolved:

Synced 2021-08-19

[yroskov]

World Ferns of 2021-10-14 imported 2021-10-14. Second update after ac21.

• [x] Imported 13676 spp
• [x] Metadata: version & date updated.
• [x] Sectors: ok

TASKS

• [x] Broken decisions, 201. Re-match all, 60 remains - deleted.

Resolved:

Synced 2021-10-21

[yroskov]

World Ferns of 2021-11-27 imported 2021-11-29. Third update after ac21.

• [x] Imported 13631 spp
• [x] Metadata: version (12.7, Nov 2021) & date updated.
• [x] Sectors: ok

TASKS

• [x] Broken decisions, 181. Re-match all, 89 remains = deleted.
• [x] Manuscript names without decisions: 15 new unresolved acc names = resolved.

Resolved 2021-11-29

Synced 2021-11-29, 2021-12-01

[yroskov]

2021-11-30: TASK reports (manually composed spreadsheets due to https://github.com/CatalogueOfLife/checklistbank/issues/973) on ACC-SYN species (different accepted, same authors) SYN-SYN species (different accepted, same authors) ACC-SYN infraspecific taxa (different accepted, same authors) SYN-SYN infraspecific taxa (different accepted, same authors) have been sent to the author for assessment and possible fixes.

[yroskov]

World Ferns of 2021-12-08 as a replacement for 2021-11-27; imported 2021-12-09. Third update after ac21.

• [x] Imported 13629 spp
• [x] Metadata: version (12.8, Dec 2021) & date updated.
• [x] Sectors: ok

TASKS

• [x] Broken decisions, 241. Re-match all, 155 remains = deleted.
• [x] Manuscript names without decisions: 1 new unresolved acc names = resolved.

Resolved 2021-12-10:

Synced 2021-12-10

[yroskov]

Checks of World Ferns 2021-12-08 on PREVIEW 2021-12-14

• [x] Incomplete references: only Author is present -- for @gdower attention (the same in WPlants https://github.com/CatalogueOfLife/testing/issues/4#issuecomment-993932102)

Example:

[yroskov]

World Ferns of 2022-01-08 imported 2022-01-10. 4th update after ac21. (after duplicate fixes)

• [x] Imported 13,622 spp
• [x] Metadata: version (12.9, Jan 2022) & date (2022-01-08) updated.
• [x] Sectors: ok

TASKS

• [x] Broken decisions, 61. Re-match all, 23 remains = deleted.
• [x] Manuscript names without decisions: resolved.

Resolved 2022-01-11:

• [x] Incomplete references: FIXED (preview 2022-01-12)

Synced 2022-01-11

[yroskov]

World Ferns 12.10 of 2022-02-19; imported 2022-02-21. 5th update after ac21.

• [x] Imported 13,654 spp
• [x] Metadata: version (12.10, Feb 2022) & date (2022-02-19) updated.
• [x] Sectors: ok

TASKS

• [x] Broken decisions, 18. Re-match all, 5 remains = deleted.
• [x] Manuscript names without decisions: additional 15 resolved.

Resolved 2022-02-22:

Synced 2022-02-22

[yroskov]

World Plants 12.10 of 2022-02-19 - continue after fixes https://github.com/CatalogueOfLife/testing/issues/184#issuecomment-1055567444

TASKS 2022-03-03

Resolved 2022-03-03:

Synced 2022-03-03

[yroskov]

World Ferns of 2022-05-29 imported 2022-06-02

• [x] Imported: 13,702 spp
• [x] Metadata: ver # ? = 13.0, May 2022 as on the website
• [x] Classification: ok
• [x] Sectors: ok

ISSUES assessed 2022-06-02

TASKS

• [x] Manuscript names, 174 of 240. 53 new acc names flagged as Prov Acc
• [x] Broken decisions, 4440. Rematch all = 4492 remain broken; deleted all

Resolved 2022-06-03

Synced 2022-06-03

[yroskov]

Imported 2022-07-05

• [x] Imported: 13,717 spp

TASKS:

• [x] Manuscript names, 171 of 237. May be fixes of https://github.com/CatalogueOfLife/data/issues/448#issuecomment-1189355147 broke decisions with nothospecies names. As an illustration, 53 inedita names lost "prov. acc." status, all of them have hybrid mark: = RE-APPLIED

• [x] Broken decision, 4,044 = deleted all

Partly resolved 2022-07-25 (unable to get large reports https://github.com/CatalogueOfLife/backend/issues/1157):

[yroskov]

World Ferns, ver 14.3, Nov 2022, received 2022-11-08 (replacement for 2022-10-15)

• [x] Imported: 13,755 spp
• [x] Metadata: ver 14.2, Oct 2022, received 2022-11-08
• [x] Classification: ok
• [x] Sectors: ok

ISSUES assessed 2022-11-10

TASKS

• Broken decisions, 149; deleted all
• Manuscript names, 212 of 228: 3 new acc marked as prov acc

Resolved 2022-11-10

Synced 2022-11-10; re-synced 2022-11-14

[yroskov]

World Ferns, ver 14.7, Jan 2023, received 2023-01-12

• [x] Imported: 13,805 (vs 13,755 spp)
• [x] Metadata: "ver 14.7" corrected
• [x] Classification: ok
• [x] Sectors: ok; 14 orders

ISSUES assessed 2023-01-18

TASKS

• Broken decisions, 4372; rematch all = 4372 broken; deleted all
• Manuscript names, 213 of 228: 2 new marked as prov. acc.

Resolved 2023-01-18:

Synced 2023-01-18

[yroskov]

World Ferns, ver 15, Mar 2023, received 2023-03-06; new version with fixes 2023-03-07; imported 2023-03-08

• [x] Imported: 13,818 (vs 13,805 spp)
• [x] Metadata: OK
• [x] Classification: OK
• [x] Sectors: OK

ISSUES assessed 2023-03-07

TASKS as 2023-03-07

• Broken decisions, 4371 = deleted all
• Manuscript names, 213 of 228: added 3 prov acc

TASKS as 2023-03-08 (new export)

Resolved 2023-03-08:

Synced 2023-03-08

[yroskov]

World Ferns, ver 15.3, May 2023, received 2023-05-01; imported 2023-05-01

• [x] Imported: 13,843 (vs 13,818 spp)

• [x] Metadata: OK

• [x] Classification: OK

• [x] Sectors: OK

• [x] infraspecific names (synonyms) with portions "proles" (28), "lusus" (1), "unranked" (14) as 2nd epithet = blocked

ISSUES assessed 2023-05-05

TASKS

• Manuscript names, 165 of 193: 15 new prov acc names flagged
• Broken decisions, 4552: all deleted

Resolved 2023-05-05

Synced 2023-05-05

[yroskov]

MH, 2023-05-15: it is now about time to change the profile text for WorldPlants and WorldFerns databases. Could you exchange it as follows? I hope it is not too long. The last paragraph is only for WorldFerns. Possibly it might be time to issue the “5 stars”. What do you think?

WorldFerns and WorldPlants are synonymic checklists of the vascular plants of the world (including ferns and lycophytes). The data set has been compiled – independently from other catalogues - over the last 40 years by starting from the basic data of the Kew Index and the Index Filicum. These names (initially over 1 million) have been subsequently cross-checked against local or regional floras, checklists, monographies and treatments. Large subsets of the database have been cross-checked by experts for certain groups. In the current status almost all names have been verified, and distribution data, newer checklists and/or floras are available for almost all countries and regions. Over the years, about 400,000 names have been added to the basic subset, leading to a total of 1,380,000 names for all families. Only a small subset (about 50,000 names) of mostly old, unverified and unassignable (“unplaced”) names have been deliberately omitted. Newly described taxa are added on a regular basis through data exchange with IPNI. Special attention is given to arranging the genera in correct phylogenetic sequence, by inclusion of the most important phylogenetic papers and monographies. The linear sequence of genera can be seen on the original website worldplants.de. As of 2023, almost all countries and regions have recent checklists or floras of reasonable quality and completeness, and over 90 % of geographical distribution is probably known. Some remaining large gaps have been closed by the recent completion of checklists for Brazil and India. Remaining regions with some data deficiencies are parts of Malesia and Central Africa (the two Congos), and for some states of former Yugoslavia the distribution is not yet fully broken down. WorldFerns is proud to be the main data source for the new Pteridophyte Phylogeny Group initiative “PPG-II”, starting 2023. Results from this continuing revision of the WorldFerns catalogue by almost 300 experts worldwide are subsequently back-integrated in the existing dataset and almost immediately available.

MH, 2023-05-31: in WorldFerns there is currently still the old profile active. Can you also exchange against the profile currently being used in WorldPlants?

Abstract is up-to-date in CLB. Re-synced 2023-05-31

[yroskov]

World Ferns, ver 16.2, Jul 2023, received 2023-07-19, 2023-07-21; imported 2023-08-08

• [x] Imported: 13,871 (vs 13,843 spp)

• [x] Metadata: OK

• [x] Classification: OK

• [x] Sectors: OK (checked in the list https://www.checklistbank.org/catalogue/3/sector?broken=true&offset=0&subjectDatasetKey=1140)

• [x] infraspecific names (synonyms) with portions "proles" (0), "lusus" (0), "unranked" (0) as 2nd epithet = checked

ISSUES assessed 2023-08-09

TASKS

• Broken decisions, 4924: all deleted
• Manuscript names, 165 of 193: 12 new flagged as "prov acc"

Resolved 2023-08-09:

Synced 2023-08-09

[yroskov]

World Ferns, ver 16.2, Jul 2023; re-converrted & re-imported 2023-08-11 after this fix https://github.com/CatalogueOfLife/testing/issues/4#issuecomment-1674917064

TASKS

• Broken decisions, 4978: all deleted

Resolved 2023-08-11:

Re-synced 2023-08-11

[yroskov]

World Ferns, ver 16.4, Sep 2023, received 2023-09-20; imported 2023-09-21

• [x] Imported: 13,921 (vs 13,871 spp)
• [x] Metadata: OK
• [x] Classification: OK
• [x] Sectors: OK (checked in the list https://www.checklistbank.org/catalogue/3/sector?broken=true&offset=0&subjectDatasetKey=1140)
• [x] infraspecific names (synonyms) with portions "proles" (0), "lusus" (0), "unranked" (0) as 2nd epithet = checked

ISSUES assessed 2023-09-22

TASKS

• Broken decisions, 4861: deleted
• Manuscript names, 174 of 194: 4 new flagged as "prov acc"

Resolved 2023-09-22:

Synced 2023-09-22

[yroskov]

World Ferns, 18.1, Nov 2023 / 2023-11-08, received 2023-11-09; imported 2023-11-14

• [x] Imported: 13,890 (vs 13,921 spp)
• [x] Metadata: OK
• [x] Classification: OK
• [x] Sectors: OK
• [x] infraspecific names (synonyms) with portions "proles" (0), "lusus" (0), "unranked" (0) as 2nd epithet = checked

ISSUES assessed 2023-11-15

• [ ] Complex Decision does not work in CLB https://github.com/CatalogueOfLife/checklistbank/issues/1310#issuecomment-1813067989 - affected Blacklisted Epithet

TASKS

• Broken decisions, 4668: deleted
• [ ] Manuscript names, 22 of 185: 147 new accepted "comb. ined." names should be flagged as Prov acc = Unable to resolve. Decisions were not applied by CLB: https://github.com/CatalogueOfLife/checklistbank/issues/1310#issuecomment-1813090805

Resolved 2023-11-15:

Synced 2023-11-15

[yroskov]

World Ferns, 18.2, Nov 2023 / 2023-11-25, received 2023-11-25; imported 2023-11-30

• [x] Imported: 13,892 (vs 13,890 spp)
• [x] Metadata: OK
• [x] Classification: OK
• [x] Sectors: OK
• [x] infraspecific names (synonyms) with portions "proles" (0), "lusus" (0), "unranked" (0) as 2nd epithet = checked

ISSUES assessed 2023-12-04

• Infrageneric Field Misplaced, 94: there are only synonyms with portion "subgen." (e.g. subgen. Abacopteris K. Iwats.; subgen. Abacopteris (Fée) Panigrahi; etc.). Note: CLB identifies rank correctly as subgenus. @gdower, the portion "subgen." need to be removed from the names by the script https://www.checklistbank.org/catalogue/3/dataset/1140/workbench?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&issue=infrageneric%20field%20misplaced&limit=100&offset=0

TASKS

• Manuscript names, 168 of 185: one new name flagged as prov acc
• Broken decisions, 4667: deleted

Resolved 2023-12-04:

Synced 2023-12-04

[yroskov]

World Ferns, ver. 18.4, Jan 2024 / 2024-01-31; received 2024-01-31, replacement 2024-02-04; imported 2024-02-06

• [x] Imported: 13,912 (vs 13,892 spp)
• [x] Metadata: OK; corrected ver. 18.4, Jan 2024 / 2024-02-04
• [x] Classification: OK
• [x] Sectors: OK
• [x] infraspecific names (synonyms) with portions "proles" (26), "lusus" (1), "unranked" (14) as 2nd epithet = blocked

ISSUES assessed 2024-02-07

TASKS

• Manuscript names, 164 of 184 = 4 new Prov Acc applied
• Broken decisions, 4663 = deleted
• Outdated decisions, 4 = deleted

Resolved 2024-02-07:

Synced 2024-02-07

[yroskov]

World Ferns, ver.19.1, Mar 2024 / 2024-03-09; received 2024-03-12, imported 2024-03-15

• [x] Imported: 13,912 (vs 13,912 spp)
• [x] Metadata: OK
• [x] Classification: OK
• [x] Sectors: OK
• [x] infraspecific names (synonyms) with portions "proles" (26), "lusus" (1), "unranked" (14) as 2nd epithet = blocked

Metrics

ISSUES assessed 2024-03-20

TASKS

• Manuscript names, 26 of 181 = 139 new flagged as Prov Acc = decisions are not shown by the interface
• Broken decisions, 4664 = deleted

Resolved 2024-03-20:

Synced 2024-03-20

[yroskov]

2024-03-22: tried to apply "provisionally accepted" status again:

• Manuscript names, 26 of 181 = 139 needs decisions; so far "prov acc" isn't shown in the interface. = FIXED. Confirmed 2024-03-28: all prov acc statuses applied

Attempt to apply decision again caused error message:

[yroskov]

World Ferns, ver. 19.3, May 2024 / 2024-05-18; received 2024-05-18, imported 2024-05-21

• [x] Imported: 13,925 spp (vs 13,912 spp)
• [x] Metadata: OK
• [x] Classification: OK
• [x] Sectors: OK
• [x] infraspecific names (synonyms) with portions "proles" (28), "lusus" (1), "unranked" (14) as 2nd epithet = blocked (but interface didn't show applied decisions = Request failed with status code 400) @mdoering, something wrong here

Metrics

ISSUES assessed 2024-05-21

TASKS

• Manuscript names, 23 of 181 = 142 accepted without decision; Apply decisions = Request failed with status code 400 @mdoering, something wrong here
• Broken decisions, 4661 = deleted

Resolved 2024-05-21:

Synced 2024-05-21

[yroskov]

World Ferns, ver. 19.4, Jun 2024 / 2024-06-30; received 2024-07-01, imported 2024-07-08

• [x] Imported: 13,931 spp (vs 13,925 spp)
• [x] Metadata: OK
• [x] Classification: OK
• [x] Sectors: OK
• [x] infraspecific names (synonyms) with portions "proles" (0), "lusus" (0), "unranked" (0) as 2nd epithet

Metrics

TASKS

• Manuscript names, 23 of 183 = Prov Acc status applied to 144 acc names; 142 remain without decision after window refresh https://github.com/CatalogueOfLife/checklistbank/issues/1437#issuecomment-2217673653
• Broken decisions, 4714
• Outdated decisions, 4 = no actions

Resolved 2024-07-09:

Synced 2024-07-09

[yroskov]

World Ferns, 24.9, Sep 2024 / 2024-09-18; received 2024-09-18, imported 2024-09-18

• [x] Imported: 13,954 spp (vs 13,931 spp)
• [x] Metadata: (see a problem with GSD metadata: https://github.com/CatalogueOfLife/backend/issues/1358). Phrase added in the abstract: Attention! The style of World Plants & World Ferns versions was changed in June 2024. The new style reflects the year and month of release. Version 24.6 of 2024-06-30 in CoL immediately follows version 19.3 of 2024-05-16.
• [x] Classification: OK
• [x] Sectors: OK
• [x] infraspecific names (synonyms) with portions "proles" (28 syns), "lusus" (1 syn), "unranked" (14 syns) as 2nd epithet = BLOCKED

Metrics

ISSUES assessed 2024-09-30

• [ ] Infrageneric Field Misplaced, 95 = @gdower, adjustment in WPlants/Ferns script needed: remove portion "subgen." from scientific names of taxa with rank subgenus, e.g.

TASKS

• Manuscript names, 154 of 172 = 2 new accepted marked as prov. acc.
• Broken decisions, 4248 = deleted
• Outdated decisions, 38 = no actions

Resolved 2024-09-30:

Synced 2024-09-30

[yroskov]

New version for CoL of October: World Ferns, 24.10, Oct 2024 / 2024-10-07; received 2024-10-05, imported 2024-10-07 MH, 2024-10-05: if you still have time for the October update, please exchange the attached ferns file. I have spent major work on standardizing the literature citations, which resulted in the correction of numerous errors.

• [x] Imported: 13,960 spp (vs 13,954 spp)
• [x] Metadata: Phrase added in the abstract: Attention! The style of World Plants & World Ferns versions was changed in June 2024. The new style reflects the year and month of release. Version 24.6 of 2024-06-30 immediately follows version 19.3 of 2024-05-16.
• [x] Classification: OK
• [x] Sectors: OK
• [x] infraspecific names (synonyms) with portions "proles" (0 new), "lusus" (0 new), "unranked" (2 syns) as 2nd epithet = BLOCKED
• [ ] Infrageneric Field Misplaced, 95 - the same problem remains

Metrics

TASKS

• Manuscript names, 26 of 170 = added 130 new prov acc names. Request failed with status code 400 - no decisions shown in the interface
• Broken decisions, 4624 = deleted
• Outdated decisions, 9 = no actions

Resolved 2024-10-08:

Synced 2024-10-08

[yroskov]

World Ferns, 24.11, Nov 2024 / 2024-11-05; received 2024-11-06, imported 2024-11-14

Michael: because I did get a lot of negative responses about the recent split of Selaginella, I come to the conclusion that PPG-II most probably will not accept this, and certainly not with a 75% majority. So I am reverting this and list Selaginella sensu lato in the next update (coming in November).

Geoff used old converter with some improvements: new version of GN parser - 70 names (synonyms) of class 3 were rejected, incl monstr. & hybrid formula; synonyms of genera have got their ranks (not yet in species, families & orders)

• [x] Imported: 13,955 spp (vs 13,960 spp)
• [x] Metadata: Phrase added in the abstract: Attention! The style of World Plants & World Ferns versions was changed in June 2024. The new style reflects the year and month of release. Version 24.6 of 2024-06-30 immediately follows version 19.3 of 2024-05-16.
• [x] Classification: OK
• [x] Sectors: OK
• [x] infraspecific names (synonyms) with portions "proles" (block 10 new = Request failed with status code 400), "lusus" (0 new), "unranked" (block 6 syns = Request failed with status code 400) as 2nd epithet = BLOCK FAILED
• [ ] Infrageneric Field Misplaced, 95

Metrics

ISSUES assessed 2024-11-14

TASKS

• Manuscript names, 22 of 161 = applied "prov. acc." status to 125 accepted names = Request failed with status code 400
• Broken decisions, 4635 = deleted
• Outdated decisions, 14 = no action

Resolved 2024-11-14:

Synced 2024-11-14