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Fix the open parser issues #209 to #225 - #226
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"Festuca rubra/arenaria" and "Bombus terrestris or lucorum" name no one
species: the identification stopped at several. The second epithet was
read as a combination author, or the "or" dropped, so name matching took
the first species as the identification. With one genus the name is now
INFORMAL, anchored on that genus (and subgenus), the rest its phrase,
left partial. A qualifier may stand before the epithet ("Agabus cf.
lutosus/griseipennis"). A rank hint changes nothing; a separate authorship
joins the phrase, as on any informal name without an epithet.
With two genera there is no one taxon to claim: "Uria aalge/Alca torda",
"Anser/Branta" and "Zea mays/Aspergillus flavus mixed library" are
unparsable OTHER. "Larus marinus or Larus hyboreus" in one genus moves
from OTHER to informal. A capital alone may be an author ("Festuca
rubra/Hackel"), a strain code is no epithet, a hybrid formula stays one,
and "Tethea or hibernica" keeps the moth's epithet "or".
ChecklistBank verbatim names: about 2,280 distinct names become informal,
about 330 unparsable.
Closes #225
Closes #212
"Apidae-223957883" and "Acrocirridae_gen1" were rejected as junk, like any
single word with a digit, although "Apidae 223957883" parses. A capitalised
word, a dash and a number, or an underscore and a lower-case label with a
digit, is now that taxon with the label as its phrase. So is the first word
of "Abies_01 sp_01" and "Strat_genus3 sp. 1", whose genus held the label.
An underscored indet marker stands for the space: "Sus_spec_2" reads as
"Sus spec_2", and "spec_2" joins "sp_2" as an indet designation instead of a
species epithet. "Entodinium_1" and "Oxalis_barrelieri" are unchanged, as is
a virus ("Crucivirus-112").
Closes #209
Closes #210
The first word of "ADN Suelo" and "Wurm-8005097" and a herbarium record
("HNT_Specimen:5625_Accession:29540") are no name, OTHER. The word "Genus"
before anything else ("Genus sp.", "Genus B sp. 1") and "unpublished name"
are placeholders.
"accession", "parasite", "sample", "specimen" and "western" join the epithet
blacklist, and flag a name doubtful. "Stomoxys parasite Fabricius, 1781" and
"Halodactyle parasite Van Beneden, 1845" are real and go on the whitelist.
Closes #211
"Fisher & Orth, 1978" lost its second author to a nomenclatural note "Orth.", as the note's abbreviation is matched in any case, with or without its dot. "Orth" with no dot and no lower-case word behind it is a surname now. "Orth. var." stays a note, and so does a capitalised "Nomen". About 100 distinct ChecklistBank names, mostly American dipterists. Closes #222
In "Heliconia waoraniana W.J. Kress, sp. nov. ined. 2013" the "sp." became an author and "nov. 2013" was left unparsed, as the note was only recognised at the end of the string or before certain words. "ined." may now follow it after a comma, and the year may follow any note without one. The year goes to the authorship, the note stays "sp. nov. ined.". Closes #220
"Arenaria ciliata L.s.l." and "Placynthium pulvinatum Øvst.ined" had one author "L.s.l." and "Øvst.ined". A sensu note (s.l., s.str., s.s., s.lat., s.ampl.), "ined" or "auct" right after the dot of a capitalised abbreviation now stands as if a space were there, on the name string and in a separate authorship. Closes #217
"Aphidius tarsalis vanAchterberg 2006" had the infraspecific epithet "vanAchterberg", and "(deGeer, 1778)" stayed unparsed. A lower-case van, von, de, der, den, del, du, di, da, la or le right before a capitalised surname stands as if a space were there, on the name string and in a separate authorship. About 460 distinct ChecklistBank names, mostly deLoriol, deMeijere, deGeer and duPont. A capital belongs to the surname: LeConte. Closes #218
"Panaeolus cyanescens (Berk. | Broome) Sacc." and "Macrolepiota olivascens Singer | M.M. Moser" read the two authors as one. A pipe between two capitalised words, past the genus, is now an ampersand, on the name string and in a separate authorship. Elsewhere it stays a word break: "Rosa rubiginosa| L. s.l.". A pipe between epithets or names reads as the slash does: "Salicornia pusilla|Salicornia disarticulata" keeps only the genus, "Abramis brama|Blicca bjoerkna" and "Bilderdykia|Polygonum" are unparsable. Closes #219
"Allium bourgeaui Rech. fil. subsp. bourgeaui" left the subspecies unparsed, as only "f." was known to continue a species author before a rank marker. Closes #221
"Priscula Dup9", "Actia Janzen05" and "Priscula Ven02/80-085" had a code for an author, as had "Agrobacterium pusense L2/2/1": about 3,500 and 1,500 distinct ChecklistBank names. A capitalised word with a digit, all that follows a uninomial, is its phrase now, and a code after a binomial may hold a slash and follow a genus in square brackets, as in "[Eubacterium] rectale M104/1". A year glued to its author is split off: "(Linnaeus1758)", "Totton1930". Any author that still holds a digit gets the new warning "author with attached number". Closes #213
"Aegialites debilis (BIN BOLD:ADH3884)" had the basionym author "BIN Bold". A BOLD BIN or SH code after a name may stand in brackets now, with or without its BIN label, and goes to the phrase as it does without them. Closes #216
… too "Youngia japonica (L.) DC. subp. japonica" left the subspecies unparsed. Of the markers one letter off, only "subsp" has all its letters, and a dropped letter is the usual slip. A misspelt marker is now also repaired after a species author, not only between two epithets. Closes #215
"Canis lupus familiaris cf." had "cf" for an epithet of a quadrinomial, "Amanita
gilbertii Beauseign. cf." an author "Beauseign.cf.", and "Protium giganteum Engl.
cf. var. giganteum" lost the variety to it. A cf., aff. or nr. trailing a name
with more than a species epithet, in a bracket at the end ("(cf.)"), or between
the species author and an infraspecific epithet is now the epithet qualifier of
the name's last epithet, on the name string and in a separate authorship. After
the author only with a rank marker or as an autonym: others are mostly second
names ("Septifer bilocularis Brachidontes cf. variabilis").
A bare qualifier on a genus ("Ulnaria cf.") stays the phrase of an unnamed species,
like "sp.".
Closes #214
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Fixes every open issue except #30 (help wanted). One commit per issue, or per group where the issues share a fix.
Read together, the issues overlapped in five groups: separators and blacklists (#209, #210, #211), notes in the authorship (#217, #220, #222), author tokens (#213, #218, #219, #221), qualifiers and ranks (#214, #215), and alternatives (#212, #225, plus the pipe from #219).
Changes
Festuca rubra/arenaria: species with authorarenariaFestuca, phraserubra/arenaria, state partialBombus terrestris or lucorum: trinomialterrestris or lucorumUria aalge/Alca torda,Anser/Branta: first name with an authorApidae-223957883: unparsableApidae, phrase223957883Sus_spec_2,Acrocirridae_gen1: unparsableSus, phrasespec_2; uninomialAcrocirridae, phrasegen1Genus sp.,ADN Suelo,Wurm-8005097Priscula Dup9,Actia Janzen05: code as author(Linnaeus1758)splits off the year; new warning for an author still holding a digitCanis lupus familiaris cf.: quadrinomial(cf.)andEngl. cf. var. giganteumDC. subp. japonica: unparsed(BIN BOLD:ADH3884): basionym authorBIN BoldBOLD:ADH3884L.s.l.,Øvst.ined: one authorvanAchterberg,(deGeer, 1778): epithet, unparsedvan Achterberg,de GeerSinger | M.M. Moser: one authorW.J. Kress, sp. nov., ined. 2013: authorsp.sp. nov. ined., year 2013Rech. fil. subsp. bourgeaui: unparsedFisher & Orth, 1978: noteOrth.Fisher,OrthDecisions to check
Ulnaria cf.andNeobisium aff.stay the phrase of an unnamed species, as decided in fix(parser): review batch 4 — six FIXME(review) markers #57. The issue asked for an epithet qualifier here too. Changing it is one branch inname_tokens.rsif you prefer the issue's reading.rubra/arenaria Hack.), so it matches the embedded form and nothing is lost. The issue's "same result" could also mean dropping it.orwith one genus:Larus marinus or Larus hyboreusmoves from OTHER (Name parser: Treatment of alternative names #194) to informal, to match the slash.Bubo virginianus pallescens / Bubo virginianus pinorum intergradeanchors on the genus, asTachybaptus ruficollis tricolor/vulcanorumdoes in Slash between epithets: parse as an informal name with the genus and the rest as phrase #225. treat slash as unparsable if it occurs after first or second word #212 wished for the species level.duPontbecomesdu Pont. One test ingna_01and two golden rows changed for this.Word1234is a code (Capitonius Malaise1924), because nearly all of the 562 such rows in the candidate set are trap or interim codes. The three that look like real authors (Thiele1928,Navas1919,Dirsh1953) become phrases too.author with attached numberexists only in this engine. It travels as a string, so there is no ABI or model change, butname-parser-api'sWarningsclass has no constant for it.Left as they are
Belaustium/microsmaris,Hypsithocus / hynsithocus Bergroth, 1927.Sorbus udvardyana Somlyay et Sennikov / S. pelsoensis Németh,Viola curtisii ssp. coniophila|Viola tricolor.Sus_spec_2renders asSus sp. spec_2inname-parser-api's ownNameFormatter, which has a separate copy of the phrase marker. No ChecklistBank name has this shape.Impact
Anon.ined.(now an anonymous author with the note), 85 glued particles, 49Orth, 19 with the new warning, 10Genus …and 4 others.