biodiversity 3.4.6 → 3.5.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.byebug_history +18 -0
- data/.ruby-version +1 -1
- data/.travis.yml +1 -1
- data/CHANGELOG +39 -35
- data/LICENSE +1 -1
- data/README.md +1 -1
- data/lib/biodiversity/parser.rb +10 -4
- data/lib/biodiversity/version.rb +1 -1
- data/spec/files/test_data.txt +42 -42
- data/spec/parser/scientific_name_spec.rb +7 -0
- metadata +4 -3
checksums.yaml
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 39237a14ed21c0cdf5ea9f7687240b3af4477e47
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data.tar.gz: 7d1d770ce5748b48f86cb0bebadb89307ef0a3bc
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metadata.gz:
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metadata.gz: d2eb0fa48343641f9c05ec8320834ddef60dc5794c058b91d813eed1db40991c0c865496fe6c39c485aabbe8d200a20aac71d67e3be58535e5972bf8b4d04697
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data.tar.gz: eda4fb5b701f8c1606285d2e90d64a82f59958e1cf0a56247be8e2f2cc1c30b6ff04ace786ba6e0e6e7e36ce4ce3b113ed1e83ad28fdbdc02df6a11c39938841
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data/.byebug_history
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data/.ruby-version
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@@ -1 +1 @@
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2.
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2.4.4
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data/.travis.yml
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data/CHANGELOG
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@@ -1,91 +1,95 @@
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3.
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3.5.0 -- add the tail cut by preprocessing to the results. The tail usually
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contains annotations about the name.
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3.4.6 -- gems update.
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3.4.5 -- fix "fil." and "filius" with infraspecies after them, add "'t" as a
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possible author prefix, add "emend." as "emendatum or rectified by" to
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authors
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authors.
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3.4.4 -- support "del" as part of authorship, do not truncate epithets that
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start with "nomen", add "nvar." as a rank
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start with "nomen", add "nvar." as a rank.
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3.4.3 -- add "fil." as a possible spelling of "filius", add "do" as an author
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prefix, add "apud" as an author separator, add possible second "ex" or
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"in"
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"in".
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3.4.2 -- update treetop to 1.6
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3.4.2 -- update treetop to 1.6.
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3.4.1 -- support for authors starting with "d'"
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3.4.1 -- support for authors starting with "d'".
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3.4.0 -- added ScientificNameParser.add_rank_to_canonical(parsed) method.
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This method allows to add infraspecific rank to a canonical form
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after the fact of parsing.
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3.3.0 -- parserver gets new option -- -H for host, default 127.0.0.1
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3.3.0 -- parserver gets new option -- -H for host, default 127.0.0.1.
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3.2.1 -- fix parserver -- it does remove new lines now (before it was not
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necessary as they were stripped in older versions by parser)
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necessary as they were stripped in older versions by parser)
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necessary as they were stripped in older versions by parser)
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necessary as they were stripped in older versions by parser).
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3.2.0 -- added UUID version 5 identifiers for every name string, better
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normalizing for the names with apostrophes, underscore-formatted
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supported. Verbatim field does mean nonchanged input now
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stripping empty spaces and new lines around name
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increase because of change in the output
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normalizing for the names with apostrophes, underscore-formatted
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names are supported. Verbatim field does mean nonchanged input now
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(before it was stripping empty spaces and new lines around name
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string). Minor version increase because of change in the output
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format ("id" field).
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3.1.10 -- NPV viruses added
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3.1.10 -- NPV viruses added.
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3.1.9 -- more virus keywords, better handling of apostrophes in
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species epithets
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species epithets.
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3.1.8 -- downgrading dependency on treetop to 1.4.1
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3.1.8 -- downgrading dependency on treetop to 1.4.1.
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3.1.7 -- fixed travis and dependencies
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3.1.7 -- fixed travis and dependencies.
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3.1.6 -- added forma. to ranks, tests for species epithets with apostrophe
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3.1.6 -- added forma. to ranks, tests for species epithets with apostrophe.
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3.1.5 -- updated depenencies
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3.1.5 -- updated depenencies.
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3.1.4 -- added files generated by tt to repository
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3.1.4 -- added files generated by tt to repository.
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3.1.3 -- removed dependency on jeweler
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3.1.3 -- removed dependency on jeweler.
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3.1.2 -- fixed problems with infraspecies epithets starting with fo,
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for example Peristernia nassatula forskali Tapparone-Canefri 1875
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for example Peristernia nassatula forskali Tapparone-Canefri 1875.
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3.1.1 -- fixed problem with names ending on sp
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3.1.1 -- fixed problem with names ending on sp.
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3.1.0 -- added surrogates: Genbank, Barcode of life names.
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Also cf., sp. spp are flagged as surrogates
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Also cf., sp. spp are flagged as surrogates.
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3.0.1 -- updated gems
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3.0.1 -- updated gems.
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3.0.0 -- removing support for ruby 1.8.7, making biodiversity gem be the same
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as biodiversity19, deprecating biodiversity19. A few newly discovered bugs
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are fixed.
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2.1.0 -- added ScientificNameParser.version method
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2.1.0 -- added ScientificNameParser.version method.
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2.0.0 -- backward incompatibe change in parserver, therefore new major number.
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In parserver removed option --output=canonical_with_rank, instead added -r
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option which allows to have canonical with rank with either json or canonical
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outputs
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outputs.
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1.2.0 -- changed method invocation signature ScientificNameParser.new
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Now it can take options
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Now it can take options.
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1.1.3 -- added 'fo' as rank
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1.1.3 -- added 'fo' as rank.
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1.1.2 -- static method for fixins all-caps canonical names, fixing caps
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for authors words, ampersand instead of 'et' in normalization
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for authors words, ampersand instead of 'et' in normalization.
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1.1.1 -- more multi-uninomials cases, expanded viruses detection, added
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abbreviated genera and a few small fixes
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abbreviated genera and a few small fixes.
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1.1.0 -- added multi-uninomials, fixes in identification annotations (aff.,
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cf., sp. etc), bug fixes, more robust salvage mode
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cf., sp. etc), bug fixes, more robust salvage mode.
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1.0.17 -- fixed a bug which prevented all diacritics be converted correctly
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1.0.17 -- fixed a bug which prevented all diacritics be converted correctly.
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1.0.16 -- dirty mode now converts ë to e
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1.0.16 -- dirty mode now converts ë to e.
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1.0.15 -- additional rules added for names ending with ssp. sp sp. and cf.
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1.0.13 -- canonical forms for cf. aff. qualifiers are modified: canonical for
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'Aus cf. bus' is now 'Aus bus'; canonical for 'Aus aff. bus' is now 'Aus'.
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Ranks at the end of the name like 'var', 'ssp', 'spp' are considered junk and
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are ignored
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are ignored.
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1.0.12 -- bug is fixed which prevented 'Cucurbita pepo' be parsed correctly,
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f., forma, fr. are now treated as any other ranks.
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data/LICENSE
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data/README.md
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@@ -222,7 +222,7 @@ Copyright
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Authors: [Dmitry Mozzherin][dimus]
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Copyright (c) 2008-
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Copyright (c) 2008-2018 Dmitry Mozzherin. See [LICENSE][license]
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for further details.
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[gem_svg]: https://badge.fury.io/rb/biodiversity.svg
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data/lib/biodiversity/parser.rb
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ssp\.|ssp|subsp|subgen|hybrid|hort\.|hort)\??\s*$/ix
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def self.clean(a_string)
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orig = a_string
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[NOTES, TAXON_CONCEPTS1, TAXON_CONCEPTS2,
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TAXON_CONCEPTS3, NOMEN_CONCEPTS, LAST_WORD_JUNK].each do |i|
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a_string = a_string.gsub(i, "")
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end
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tail = orig[a_string.size..-1]
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a_string = a_string.tr("ſ","s") #old "s"
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a_string = a_string.tr("_", " ") if a_string.strip.match(/\s/).nil?
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a_string
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[a_string, tail.strip]
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end
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end
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@dirty = ScientificNameDirtyParser.new
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@canonical = ScientificNameCanonicalParser.new
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@parsed = nil
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@tail = nil
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end
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def virus?(a_string)
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def parse(a_string)
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@verbatim = a_string
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a_string = PreProcessor::clean(a_string)
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a_string, @tail = PreProcessor::clean(a_string)
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if virus?(a_string)
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@parsed = { verbatim: @verbatim, virus: true }
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parsed = self.class != Hash
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res = { id: @id, parsed: parsed,
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parser_version: ScientificNameParser::version}
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if parsed
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hybrid = self.hybrid rescue false
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res.merge!({
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end
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@parsed.verbatim = @verbatim
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@parsed.all(canonical_with_rank: @canonical_with_rank)
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res = @parsed.all(canonical_with_rank: @canonical_with_rank)
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res[:scientificName].merge!(tail: @tail) if @tail && @tail != ""
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res
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end
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private
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name.match(surrogate2))
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is_surrogate
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end
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end
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end
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data/lib/biodiversity/version.rb
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data/spec/files/test_data.txt
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@@ -139,7 +139,7 @@ Hordeum vulgare cœrulescens Metzger|{"scientificName":{"id":"3029cf1f-da59-5955
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Hordeum vulgare f. cœrulescens|{"scientificName":{"id":"27dd2ab3-8bf9-5f72-90bb-5c94530822f2", "parsed":true, "parser_version":"test_version", "verbatim":"Hordeum vulgare f. cœrulescens", "normalized":"Hordeum vulgare f. coerulescens", "canonical":"Hordeum vulgare coerulescens", "hybrid":false, "details":[{"genus":{"string":"Hordeum"}, "species":{"string":"vulgare"}, "infraspecies":[{"string":"coerulescens", "rank":"f."}]}], "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 15], "16":["infraspecific_type", 18], "19":["infraspecies", 30]}}}
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# old style s (ſ)
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Musca domeſtica Linnaeus 1758 sec. Pemberton 1947|{"scientificName":{"id":"da29293e-5bc4-5e28-ac02-a0100e9f4d50", "parsed":true, "verbatim":"Musca domeſtica Linnaeus 1758 sec. Pemberton 1947", "normalized":"Musca domestica Linnaeus 1758", "canonical":"Musca domestica", "hybrid":false, "details":[{"genus":{"string":"Musca"}, "species":{"string":"domestica", "authorship":"Linnaeus 1758", "basionymAuthorTeam":{"authorTeam":"Linnaeus", "author":["Linnaeus"], "year":"1758"}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 15], "16":["author_word", 24], "25":["year", 29]}}}
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Musca domeſtica Linnaeus 1758 sec. Pemberton 1947|{"scientificName":{"id":"da29293e-5bc4-5e28-ac02-a0100e9f4d50", "tail": "sec. Pemberton 1947", "parsed":true, "verbatim":"Musca domeſtica Linnaeus 1758 sec. Pemberton 1947", "normalized":"Musca domestica Linnaeus 1758", "canonical":"Musca domestica", "hybrid":false, "details":[{"genus":{"string":"Musca"}, "species":{"string":"domestica", "authorship":"Linnaeus 1758", "basionymAuthorTeam":{"authorTeam":"Linnaeus", "author":["Linnaeus"], "year":"1758"}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 15], "16":["author_word", 24], "25":["year", 29]}}}
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Amphisbæna fuliginoſa Linnaeus 1758|{"scientificName":{"id":"d2f6423b-7a8f-5389-a286-c074fb634c5a", "parsed":true, "parser_version":"test_version", "verbatim":"Amphisbæna fuliginoſa Linnaeus 1758", "normalized":"Amphisbaena fuliginosa Linnaeus 1758", "canonical":"Amphisbaena fuliginosa", "hybrid":false, "details":[{"genus":{"string":"Amphisbaena"}, "species":{"string":"fuliginosa", "authorship":"Linnaeus 1758", "basionymAuthorTeam":{"authorTeam":"Linnaeus", "author":["Linnaeus"], "year":"1758"}}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 21], "22":["author_word", 30], "31":["year", 35]}}}
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#basionym author in parenthesis
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Acarinina aff pentacamerata|{"scientificName":{"id":"06a32183-0aa7-5a00-9753-46db1141daa4", "parsed":true, "parser_version":"test_version", "verbatim":"Acarinina aff pentacamerata", "normalized":"Acarinina", "canonical":"Acarinina", "hybrid":false, "details":[{"genus":{"string":"Acarinina"}, "annotation_identification":"aff", "ignored":{"species":{"string":"pentacamerata"}}}], "parser_run":1, "positions":{"0":["genus", 9], "10":["annotation_identification", 14]}}}
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Abturia cf. alabamensis (Morton )|{"scientificName":{"id":"5fd4ce59-98d3-50af-9e28-918adc47d264", "parsed":true, "parser_version":"test_version", "verbatim":"Abturia cf. alabamensis (Morton )", "normalized":"Abturia cf. alabamensis (Morton)", "canonical":"Abturia alabamensis", "hybrid":false, "details":[{"genus":{"string":"Abturia"}, "annotation_identification":"cf.", "species":{"species":{"string":"alabamensis", "authorship":"(Morton )", "basionymAuthorTeam":{"authorTeam":"Morton", "author":["Morton"]}}}}], "parser_run":1, "positions":{"0":["genus", 7], "8":["annotation_identification", 11], "12":["species", 23], "25":["author_word", 31]}, "surrogate": true}}
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Abturia cf alabamensis (Morton )|{"scientificName":{"id":"423cd26d-c6fd-54fb-937b-f98ba8056fc0", "parsed":true, "parser_version":"test_version", "verbatim":"Abturia cf alabamensis (Morton )", "normalized":"Abturia cf alabamensis (Morton)", "canonical":"Abturia alabamensis", "hybrid":false, "details":[{"genus":{"string":"Abturia"}, "annotation_identification":"cf", "species":{"species":{"string":"alabamensis", "authorship":"(Morton )", "basionymAuthorTeam":{"authorTeam":"Morton", "author":["Morton"]}}}}], "parser_run":1, "positions":{"0":["genus", 7], "8":["annotation_identification", 11], "11":["species", 22], "24":["author_word", 30]}, "surrogate": true}}
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-
Alyxia reinwardti var|{"scientificName":{"id":"2f0ee2be-8d37-5e43-9eed-776c17f47e93", "parsed":true, "parser_version":"test_version", "verbatim":"Alyxia reinwardti var", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
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206
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Alyxia reinwardti var.|{"scientificName":{"id":"aed34708-82ed-52e4-876f-d4468af73fc3", "parsed":true, "parser_version":"test_version", "verbatim":"Alyxia reinwardti var.", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
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207
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Alyxia reinwardti ssp|{"scientificName":{"id":"760486d1-93ed-55c5-ade1-ba2c5b2aa900", "parsed":true, "parser_version":"test_version", "verbatim":"Alyxia reinwardti ssp", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
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Alyxia reinwardti ssp.|{"scientificName":{"id":"72b5072a-d952-54f8-aea1-5b5bd3c65c45", "parsed":true, "parser_version":"test_version", "verbatim":"Alyxia reinwardti ssp.", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
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209
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Alaria spp|{"scientificName":{"id":"5b31e830-ccf6-5918-94c5-75c4db7ef302", "parsed":true, "parser_version":"test_version", "verbatim":"Alaria spp", "normalized":"Alaria", "canonical":"Alaria", "hybrid":false, "details":[{"uninomial":{"string":"Alaria"}}], "parser_run":1, "positions":{"0":["uninomial", 6]}, "surrogate": true}}
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210
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Alaria spp.|{"scientificName":{"id":"d1cd4f1a-f511-5d5a-8f41-64911995fdec", "parsed":true, "parser_version":"test_version", "verbatim":"Alaria spp.", "normalized":"Alaria", "canonical":"Alaria", "hybrid":false, "details":[{"uninomial":{"string":"Alaria"}}], "parser_run":1, "positions":{"0":["uninomial", 6]}, "surrogate": true}}
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211
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Xenodon sp|{"scientificName":{"id":"7b0cb348-7fe9-5248-b396-b0336225ba2a", "parsed":true, "parser_version":"test_version", "verbatim":"Xenodon sp", "normalized":"Xenodon", "canonical":"Xenodon", "hybrid":false, "details":[{"uninomial":{"string":"Xenodon"}}], "parser_run":1, "positions":{"0":["uninomial", 7]}, "surrogate": true}}
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212
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Xenodon sp.|{"scientificName":{"id":"77b6718f-a26e-5ddf-a4cf-119e972cd015", "parsed":true, "parser_version":"test_version", "verbatim":"Xenodon sp.", "normalized":"Xenodon", "canonical":"Xenodon", "hybrid":false, "details":[{"uninomial":{"string":"Xenodon"}}], "parser_run":1, "positions":{"0":["uninomial", 7]}, "surrogate": true}}
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213
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Formicidae cf.|{"scientificName":{"id":"61f9ebc4-346e-5857-ab45-38808ff1c960", "parsed":true, "parser_version":"test_version", "verbatim":"Formicidae cf.", "normalized":"Formicidae", "canonical":"Formicidae", "hybrid":false, "details":[{"uninomial":{"string":"Formicidae"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}, "surrogate": true}}
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214
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Formicidae cf|{"scientificName":{"id":"90473425-7ce1-5ec6-8160-737646816ea7", "parsed":true, "parser_version":"test_version", "verbatim":"Formicidae cf", "normalized":"Formicidae", "canonical":"Formicidae", "hybrid":false, "details":[{"uninomial":{"string":"Formicidae"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}, "surrogate": true}}
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215
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Acastoides spp.|{"scientificName":{"id":"9853f0a4-6324-5a7d-8108-e910578e612b", "parsed":true, "parser_version":"test_version", "verbatim":"Acastoides spp.", "normalized":"Acastoides", "canonical":"Acastoides", "hybrid":false, "details":[{"uninomial":{"string":"Acastoides"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}, "surrogate": true}}
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205
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+
Alyxia reinwardti var|{"scientificName":{"id":"2f0ee2be-8d37-5e43-9eed-776c17f47e93", "parsed":true, "tail": "var", "parser_version":"test_version", "verbatim":"Alyxia reinwardti var", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
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206
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+
Alyxia reinwardti var.|{"scientificName":{"id":"aed34708-82ed-52e4-876f-d4468af73fc3", "parsed":true, "tail": "var.", "parser_version":"test_version", "verbatim":"Alyxia reinwardti var.", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
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207
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+
Alyxia reinwardti ssp|{"scientificName":{"id":"760486d1-93ed-55c5-ade1-ba2c5b2aa900", "parsed":true, "tail": "ssp", "parser_version":"test_version", "verbatim":"Alyxia reinwardti ssp", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
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208
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+
Alyxia reinwardti ssp.|{"scientificName":{"id":"72b5072a-d952-54f8-aea1-5b5bd3c65c45", "parsed":true, "tail": "ssp.", "parser_version":"test_version", "verbatim":"Alyxia reinwardti ssp.", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
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209
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+
Alaria spp|{"scientificName":{"id":"5b31e830-ccf6-5918-94c5-75c4db7ef302", "parsed":true, "tail": "spp", "parser_version":"test_version", "verbatim":"Alaria spp", "normalized":"Alaria", "canonical":"Alaria", "hybrid":false, "details":[{"uninomial":{"string":"Alaria"}}], "parser_run":1, "positions":{"0":["uninomial", 6]}, "surrogate": true}}
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210
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+
Alaria spp.|{"scientificName":{"id":"d1cd4f1a-f511-5d5a-8f41-64911995fdec", "parsed":true, "tail": "spp.", "parser_version":"test_version", "verbatim":"Alaria spp.", "normalized":"Alaria", "canonical":"Alaria", "hybrid":false, "details":[{"uninomial":{"string":"Alaria"}}], "parser_run":1, "positions":{"0":["uninomial", 6]}, "surrogate": true}}
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211
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+
Xenodon sp|{"scientificName":{"id":"7b0cb348-7fe9-5248-b396-b0336225ba2a", "parsed":true, "tail": "sp", "parser_version":"test_version", "verbatim":"Xenodon sp", "normalized":"Xenodon", "canonical":"Xenodon", "hybrid":false, "details":[{"uninomial":{"string":"Xenodon"}}], "parser_run":1, "positions":{"0":["uninomial", 7]}, "surrogate": true}}
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212
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+
Xenodon sp.|{"scientificName":{"id":"77b6718f-a26e-5ddf-a4cf-119e972cd015", "parsed":true, "tail": "sp.", "parser_version":"test_version", "verbatim":"Xenodon sp.", "normalized":"Xenodon", "canonical":"Xenodon", "hybrid":false, "details":[{"uninomial":{"string":"Xenodon"}}], "parser_run":1, "positions":{"0":["uninomial", 7]}, "surrogate": true}}
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213
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+
Formicidae cf.|{"scientificName":{"id":"61f9ebc4-346e-5857-ab45-38808ff1c960", "parsed":true, "tail": "cf.", "parser_version":"test_version", "verbatim":"Formicidae cf.", "normalized":"Formicidae", "canonical":"Formicidae", "hybrid":false, "details":[{"uninomial":{"string":"Formicidae"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}, "surrogate": true}}
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214
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+
Formicidae cf|{"scientificName":{"id":"90473425-7ce1-5ec6-8160-737646816ea7", "parsed":true, "tail": "cf", "parser_version":"test_version", "verbatim":"Formicidae cf", "normalized":"Formicidae", "canonical":"Formicidae", "hybrid":false, "details":[{"uninomial":{"string":"Formicidae"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}, "surrogate": true}}
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215
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+
Acastoides spp.|{"scientificName":{"id":"9853f0a4-6324-5a7d-8108-e910578e612b", "parsed":true, "tail": "spp.", "parser_version":"test_version", "verbatim":"Acastoides spp.", "normalized":"Acastoides", "canonical":"Acastoides", "hybrid":false, "details":[{"uninomial":{"string":"Acastoides"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}, "surrogate": true}}
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216
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Sphingomonas sp. 37|{"scientificName":{"id":"1daffd3a-f4de-58d9-91e3-ae4d08a50ce0", "parsed":true, "parser_version":"test_version", "verbatim":"Sphingomonas sp. 37", "normalized":"Sphingomonas", "canonical":"Sphingomonas", "hybrid":false, "details":[{"genus":{"string":"Sphingomonas"}, "annotation_identification":"sp.", "ignored":{"unparsed":"37"}}], "parser_run":1, "positions":{"0":["genus", 12], "13":["annotation_identification", 16]}, "surrogate": true}}
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217
217
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Thryothorus leucotis spp. bogotensis|{"scientificName":{"id":"d2cb7212-ff62-5e31-9ab9-31214a9782d5", "parsed":true, "parser_version":"test_version", "verbatim":"Thryothorus leucotis spp. bogotensis", "normalized":"Thryothorus leucotis", "canonical":"Thryothorus leucotis", "hybrid":false, "details":[{"genus":{"string":"Thryothorus"}, "species":{"string":"leucotis"}, "infraspecies":[{"annotation_identification":"spp.", "ignored":{"infraspecies":{"string":"bogotensis", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 20], "21":["annotation_identification", 25]}, "surrogate": true}}
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218
218
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Endoxyla sp. GM-, 2003|{"scientificName":{"id":"8a80bfee-947d-5602-9958-a2338ff46a4d", "parsed":true, "parser_version":"test_version", "verbatim":"Endoxyla sp. GM-, 2003", "normalized":"Endoxyla", "canonical":"Endoxyla", "hybrid":false, "details":[{"genus":{"string":"Endoxyla"}, "annotation_identification":"sp.", "ignored":{"unparsed":"GM-, 2003"}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["annotation_identification", 12]}, "surrogate": true}}
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@@ -231,7 +231,7 @@ Lachenalia tricolor var. nelsonii (ht.) Baker|{"scientificName":{"id":"0f7ce439-
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Lachenalia tricolor var. nelsonii (hort.) Baker|{"scientificName":{"id":"cc118b05-14ff-5a42-8780-802f60eba565", "parsed":true, "parser_version":"test_version", "verbatim":"Lachenalia tricolor var. nelsonii (hort.) Baker", "normalized":"Lachenalia tricolor var. nelsonii (hort.) Baker", "canonical":"Lachenalia tricolor nelsonii", "hybrid":false, "details":[{"genus":{"string":"Lachenalia"}, "species":{"string":"tricolor"}, "infraspecies":[{"string":"nelsonii", "rank":"var.", "authorship":"(hort.) Baker", "combinationAuthorTeam":{"authorTeam":"Baker", "author":["Baker"]}, "basionymAuthorTeam":{"authorTeam":"hort.", "author":["unknown"]}}]}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 19], "20":["infraspecific_type", 24], "25":["infraspecies", 33], "35":["unknown_author", 40], "42":["author_word", 47]}}}
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Puya acris ht.|{"scientificName":{"id":"83c98b8e-f373-57df-92bf-5a39a56d9909", "parsed":true, "parser_version":"test_version", "parser_run":1,"verbatim":"Puya acris ht.","normalized":"Puya acris ht.","canonical":"Puya acris","hybrid":false,"details":[{"genus":{"string":"Puya"},"species":{"string":"acris","authorship":"ht.","basionymAuthorTeam":{"authorTeam":"ht.","author":["unknown"]}}}],"positions":{"0":["genus",4],"5":["species",10],"11":["unknown_author",14]}}}
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Puya acris anon.|{"scientificName":{"id":"2b5243d3-e8a7-5e6c-a2c1-beb2ee5c3020", "parsed":true, "parser_version":"test_version", "parser_run":1,"verbatim":"Puya acris anon.","normalized":"Puya acris anon.","canonical":"Puya acris","hybrid":false,"details":[{"genus":{"string":"Puya"},"species":{"string":"acris","authorship":"anon.","basionymAuthorTeam":{"authorTeam":"anon.","author":["unknown"]}}}],"positions":{"0":["genus",4],"5":["species",10],"11":["unknown_author",16]}}}
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Puya acris hort.|{"scientificName":{"id":"78228a5e-dcd3-58f9-bf21-b452c378f6ee", "parsed":true, "verbatim":"Puya acris hort.", "normalized":"Puya acris", "canonical":"Puya acris", "hybrid":false, "details":[{"genus":{"string":"Puya"}, "species":{"string":"acris"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 4], "5":["species", 10]}}}
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234
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+
Puya acris hort.|{"scientificName":{"id":"78228a5e-dcd3-58f9-bf21-b452c378f6ee", "parsed":true, "tail": "hort.", "verbatim":"Puya acris hort.", "normalized":"Puya acris", "canonical":"Puya acris", "hybrid":false, "details":[{"genus":{"string":"Puya"}, "species":{"string":"acris"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 4], "5":["species", 10]}}}
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Prunus mexicana S. Watson var. reticulata (Sarg.) Sarg.|{"scientificName":{"id":"5ba1cc96-ab40-51b3-951d-f91b5bff1da8", "parsed":true, "parser_version":"test_version", "verbatim":"Prunus mexicana S. Watson var. reticulata (Sarg.) Sarg.", "normalized":"Prunus mexicana S. Watson var. reticulata (Sarg.) Sarg.", "canonical":"Prunus mexicana reticulata", "hybrid":false, "details":[{"genus":{"string":"Prunus"}, "species":{"string":"mexicana", "authorship":"S. Watson", "basionymAuthorTeam":{"authorTeam":"S. Watson", "author":["S. Watson"]}}, "infraspecies":[{"string":"reticulata", "rank":"var.", "authorship":"(Sarg.) Sarg.", "combinationAuthorTeam":{"authorTeam":"Sarg.", "author":["Sarg."]}, "basionymAuthorTeam":{"authorTeam":"Sarg.", "author":["Sarg."]}}]}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 15], "16":["author_word", 18], "19":["author_word", 25], "26":["infraspecific_type", 30], "31":["infraspecies", 41], "43":["author_word", 48], "50":["author_word", 55]}}}
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#miscellaneous names
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@@ -321,19 +321,19 @@ Polypodium x vulgare nothosubsp. mantoniae (Rothm.) Schidlay|{"scientificName":
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321
321
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####
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322
322
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323
323
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#removing annotations
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324
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Acarospora cratericola cratericola Shenk 1974 group|{"scientificName":{"id":"0f466e31-7e23-5320-ac7e-4c1026bc8af6", "parsed":true, "verbatim":"Acarospora cratericola cratericola Shenk 1974 group", "normalized":"Acarospora cratericola cratericola Shenk 1974", "canonical":"Acarospora cratericola cratericola", "hybrid":false, "details":[{"genus":{"string":"Acarospora"}, "species":{"string":"cratericola"}, "infraspecies":[{"string":"cratericola", "rank":"n/a", "authorship":"Shenk 1974", "basionymAuthorTeam":{"authorTeam":"Shenk", "author":["Shenk"], "year":"1974"}}]}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 22], "23":["infraspecies", 34], "35":["author_word", 40], "41":["year", 45]}}}
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Acarospora cratericola cratericola Shenk 1974 species group|{"scientificName":{"id":"a7684260-ed99-5d55-9a35-fd97b67e8933", "parsed":true, "verbatim":"Acarospora cratericola cratericola Shenk 1974 species group", "normalized":"Acarospora cratericola cratericola Shenk 1974", "canonical":"Acarospora cratericola cratericola", "hybrid":false, "details":[{"genus":{"string":"Acarospora"}, "species":{"string":"cratericola"}, "infraspecies":[{"string":"cratericola", "rank":"n/a", "authorship":"Shenk 1974", "basionymAuthorTeam":{"authorTeam":"Shenk", "author":["Shenk"], "year":"1974"}}]}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 22], "23":["infraspecies", 34], "35":["author_word", 40], "41":["year", 45]}}}
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326
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Acarospora cratericola cratericola Shenk 1974 species complex|{"scientificName":{"id":"d227da04-7c89-50f7-8cf1-de09bc5aa903", "parsed":true, "verbatim":"Acarospora cratericola cratericola Shenk 1974 species complex", "normalized":"Acarospora cratericola cratericola Shenk 1974", "canonical":"Acarospora cratericola cratericola", "hybrid":false, "details":[{"genus":{"string":"Acarospora"}, "species":{"string":"cratericola"}, "infraspecies":[{"string":"cratericola", "rank":"n/a", "authorship":"Shenk 1974", "basionymAuthorTeam":{"authorTeam":"Shenk", "author":["Shenk"], "year":"1974"}}]}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 22], "23":["infraspecies", 34], "35":["author_word", 40], "41":["year", 45]}}}
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324
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+
Acarospora cratericola cratericola Shenk 1974 group|{"scientificName":{"id":"0f466e31-7e23-5320-ac7e-4c1026bc8af6", "parsed":true, "tail": "group", "verbatim":"Acarospora cratericola cratericola Shenk 1974 group", "normalized":"Acarospora cratericola cratericola Shenk 1974", "canonical":"Acarospora cratericola cratericola", "hybrid":false, "details":[{"genus":{"string":"Acarospora"}, "species":{"string":"cratericola"}, "infraspecies":[{"string":"cratericola", "rank":"n/a", "authorship":"Shenk 1974", "basionymAuthorTeam":{"authorTeam":"Shenk", "author":["Shenk"], "year":"1974"}}]}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 22], "23":["infraspecies", 34], "35":["author_word", 40], "41":["year", 45]}}}
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+
Acarospora cratericola cratericola Shenk 1974 species group|{"scientificName":{"id":"a7684260-ed99-5d55-9a35-fd97b67e8933", "parsed":true, "tail": "species group", "verbatim":"Acarospora cratericola cratericola Shenk 1974 species group", "normalized":"Acarospora cratericola cratericola Shenk 1974", "canonical":"Acarospora cratericola cratericola", "hybrid":false, "details":[{"genus":{"string":"Acarospora"}, "species":{"string":"cratericola"}, "infraspecies":[{"string":"cratericola", "rank":"n/a", "authorship":"Shenk 1974", "basionymAuthorTeam":{"authorTeam":"Shenk", "author":["Shenk"], "year":"1974"}}]}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 22], "23":["infraspecies", 34], "35":["author_word", 40], "41":["year", 45]}}}
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Acarospora cratericola cratericola Shenk 1974 species complex|{"scientificName":{"id":"d227da04-7c89-50f7-8cf1-de09bc5aa903", "parsed":true, "tail": "species complex", "verbatim":"Acarospora cratericola cratericola Shenk 1974 species complex", "normalized":"Acarospora cratericola cratericola Shenk 1974", "canonical":"Acarospora cratericola cratericola", "hybrid":false, "details":[{"genus":{"string":"Acarospora"}, "species":{"string":"cratericola"}, "infraspecies":[{"string":"cratericola", "rank":"n/a", "authorship":"Shenk 1974", "basionymAuthorTeam":{"authorTeam":"Shenk", "author":["Shenk"], "year":"1974"}}]}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 22], "23":["infraspecies", 34], "35":["author_word", 40], "41":["year", 45]}}}
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#ignoring sensu sec
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329
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Senecio legionensis sensu Samp., non Lange|{"scientificName":{"id":"948d73b7-499b-5060-ace4-dd061f2f4373", "parsed":true, "verbatim":"Senecio legionensis sensu Samp., non Lange", "normalized":"Senecio legionensis", "canonical":"Senecio legionensis", "hybrid":false, "details":[{"genus":{"string":"Senecio"}, "species":{"string":"legionensis"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 19]}}}
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Pseudomonas methanica (Söhngen 1906) sensu. Dworkin and Foster 1956|{"scientificName":{"id":"f4261966-4f80-52c1-a3ff-8eaece507964", "parsed":true, "verbatim":"Pseudomonas methanica (Söhngen 1906) sensu. Dworkin and Foster 1956", "normalized":"Pseudomonas methanica (Söhngen 1906)", "canonical":"Pseudomonas methanica", "hybrid":false, "details":[{"genus":{"string":"Pseudomonas"}, "species":{"string":"methanica", "authorship":"(Söhngen 1906)", "basionymAuthorTeam":{"authorTeam":"Söhngen", "author":["Söhngen"], "year":"1906"}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 21], "23":["author_word", 30], "31":["year", 35]}}}
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331
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Abarema scutifera sensu auct., non (Blanco)Kosterm.|{"scientificName":{"id":"59f4b32d-3f8c-569f-bc81-3fe49d708c88", "parsed":true, "verbatim":"Abarema scutifera sensu auct., non (Blanco)Kosterm.", "normalized":"Abarema scutifera", "canonical":"Abarema scutifera", "hybrid":false, "details":[{"genus":{"string":"Abarema"}, "species":{"string":"scutifera"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 17]}}}
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332
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Puya acris Auct.|{"scientificName":{"id":"926ec12b-a597-5842-92f2-4b0ae4989df1", "parsed":true, "verbatim":"Puya acris Auct.", "normalized":"Puya acris", "canonical":"Puya acris", "hybrid":false, "details":[{"genus":{"string":"Puya"}, "species":{"string":"acris"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 4], "5":["species", 10]}}}
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333
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Puya acris Auct non L.|{"scientificName":{"id":"6c11df68-9e9d-5e97-b0f0-3609e4f18121", "parsed":true, "verbatim":"Puya acris Auct non L.", "normalized":"Puya acris", "canonical":"Puya acris", "hybrid":false, "details":[{"genus":{"string":"Puya"}, "species":{"string":"acris"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 4], "5":["species", 10]}}}
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334
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Galium tricorne Stokes, pro parte|{"scientificName":{"id":"c4d3da85-86b7-5ca9-925b-6e09ffad3a30", "parsed":true, "verbatim":"Galium tricorne Stokes, pro parte", "normalized":"Galium tricorne Stokes", "canonical":"Galium tricorne", "hybrid":false, "details":[{"genus":{"string":"Galium"}, "species":{"string":"tricorne", "authorship":"Stokes", "basionymAuthorTeam":{"authorTeam":"Stokes", "author":["Stokes"]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 15], "16":["author_word", 22]}}}
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335
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Galium tricorne Stokes,pro parte|{"scientificName":{"id":"7166cbd9-2b0f-5537-9ac9-98157b60a395", "parsed":true, "verbatim":"Galium tricorne Stokes,pro parte", "normalized":"Galium tricorne Stokes", "canonical":"Galium tricorne", "hybrid":false, "details":[{"genus":{"string":"Galium"}, "species":{"string":"tricorne", "authorship":"Stokes", "basionymAuthorTeam":{"authorTeam":"Stokes", "author":["Stokes"]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 15], "16":["author_word", 22]}}}
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Senecio jacquinianus sec. Rchb.|{"scientificName":{"id":"e8ad283f-afa8-5fd2-ae8f-bbedf2fb0bb7", "parsed":true, "verbatim":"Senecio jacquinianus sec. Rchb.", "normalized":"Senecio jacquinianus", "canonical":"Senecio jacquinianus", "hybrid":false, "details":[{"genus":{"string":"Senecio"}, "species":{"string":"jacquinianus"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 20]}}}
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Senecio legionensis sensu Samp., non Lange|{"scientificName":{"id":"948d73b7-499b-5060-ace4-dd061f2f4373", "parsed":true, "tail": "sensu Samp., non Lange", "verbatim":"Senecio legionensis sensu Samp., non Lange", "normalized":"Senecio legionensis", "canonical":"Senecio legionensis", "hybrid":false, "details":[{"genus":{"string":"Senecio"}, "species":{"string":"legionensis"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 19]}}}
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Pseudomonas methanica (Söhngen 1906) sensu. Dworkin and Foster 1956|{"scientificName":{"id":"f4261966-4f80-52c1-a3ff-8eaece507964", "parsed":true, "tail": "sensu. Dworkin and Foster 1956", "verbatim":"Pseudomonas methanica (Söhngen 1906) sensu. Dworkin and Foster 1956", "normalized":"Pseudomonas methanica (Söhngen 1906)", "canonical":"Pseudomonas methanica", "hybrid":false, "details":[{"genus":{"string":"Pseudomonas"}, "species":{"string":"methanica", "authorship":"(Söhngen 1906)", "basionymAuthorTeam":{"authorTeam":"Söhngen", "author":["Söhngen"], "year":"1906"}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 21], "23":["author_word", 30], "31":["year", 35]}}}
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Abarema scutifera sensu auct., non (Blanco)Kosterm.|{"scientificName":{"id":"59f4b32d-3f8c-569f-bc81-3fe49d708c88", "parsed":true, "tail": "sensu auct., non (Blanco)Kosterm.", "verbatim":"Abarema scutifera sensu auct., non (Blanco)Kosterm.", "normalized":"Abarema scutifera", "canonical":"Abarema scutifera", "hybrid":false, "details":[{"genus":{"string":"Abarema"}, "species":{"string":"scutifera"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 17]}}}
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Puya acris Auct.|{"scientificName":{"id":"926ec12b-a597-5842-92f2-4b0ae4989df1", "parsed":true, "tail": "Auct.", "verbatim":"Puya acris Auct.", "normalized":"Puya acris", "canonical":"Puya acris", "hybrid":false, "details":[{"genus":{"string":"Puya"}, "species":{"string":"acris"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 4], "5":["species", 10]}}}
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Puya acris Auct non L.|{"scientificName":{"id":"6c11df68-9e9d-5e97-b0f0-3609e4f18121", "parsed":true, "tail": "Auct non L.", "verbatim":"Puya acris Auct non L.", "normalized":"Puya acris", "canonical":"Puya acris", "hybrid":false, "details":[{"genus":{"string":"Puya"}, "species":{"string":"acris"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 4], "5":["species", 10]}}}
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Galium tricorne Stokes, pro parte|{"scientificName":{"id":"c4d3da85-86b7-5ca9-925b-6e09ffad3a30", "parsed":true, "tail": ", pro parte", "verbatim":"Galium tricorne Stokes, pro parte", "normalized":"Galium tricorne Stokes", "canonical":"Galium tricorne", "hybrid":false, "details":[{"genus":{"string":"Galium"}, "species":{"string":"tricorne", "authorship":"Stokes", "basionymAuthorTeam":{"authorTeam":"Stokes", "author":["Stokes"]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 15], "16":["author_word", 22]}}}
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Galium tricorne Stokes,pro parte|{"scientificName":{"id":"7166cbd9-2b0f-5537-9ac9-98157b60a395", "parsed":true, "tail": ",pro parte", "verbatim":"Galium tricorne Stokes,pro parte", "normalized":"Galium tricorne Stokes", "canonical":"Galium tricorne", "hybrid":false, "details":[{"genus":{"string":"Galium"}, "species":{"string":"tricorne", "authorship":"Stokes", "basionymAuthorTeam":{"authorTeam":"Stokes", "author":["Stokes"]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 15], "16":["author_word", 22]}}}
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Senecio jacquinianus sec. Rchb.|{"scientificName":{"id":"e8ad283f-afa8-5fd2-ae8f-bbedf2fb0bb7", "parsed":true, "tail": "sec. Rchb.", "verbatim":"Senecio jacquinianus sec. Rchb.", "normalized":"Senecio jacquinianus", "canonical":"Senecio jacquinianus", "hybrid":false, "details":[{"genus":{"string":"Senecio"}, "species":{"string":"jacquinianus"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 20]}}}
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Acantholimon ulicinum s.l. (Schultes) Boiss.|{"scientificName":{"id":"cf4b7aa4-b78f-5b79-86c3-9416de24c918", "parsed":true, "verbatim":"Acantholimon ulicinum s.l. (Schultes) Boiss.", "normalized":"Acantholimon ulicinum", "canonical":"Acantholimon ulicinum", "hybrid":false, "details":[{"genus":{"string":"Acantholimon"}, "species":{"string":"ulicinum"}}], "parser_version":"test_version", "parser_run":2, "positions":{"0":["genus", 12], "13":["species", 21]}}}
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Acantholimon ulicinum s. l. (Schultes) Boiss.|{"scientificName":{"id":"3a0b0412-f076-5714-8537-62761718ca7c", "parsed":true, "verbatim":"Acantholimon ulicinum s. l. (Schultes) Boiss.", "normalized":"Acantholimon ulicinum", "canonical":"Acantholimon ulicinum", "hybrid":false, "details":[{"genus":{"string":"Acantholimon"}, "species":{"string":"ulicinum"}}], "parser_version":"test_version", "parser_run":2, "positions":{"0":["genus", 12], "13":["species", 21]}}}
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Acantholimon ulicinum S. L. Schultes|{"scientificName":{"id":"702f97e0-792b-5ed4-b2d5-d813544c4139", "parsed":true, "verbatim":"Acantholimon ulicinum S. L. Schultes", "normalized":"Acantholimon ulicinum S. L. Schultes", "canonical":"Acantholimon ulicinum", "hybrid":false, "details":[{"genus":{"string":"Acantholimon"}, "species":{"string":"ulicinum", "authorship":"S. L. Schultes", "basionymAuthorTeam":{"authorTeam":"S. L. Schultes", "author":["S. L. Schultes"]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 12], "13":["species", 21], "22":["author_word", 24], "25":["author_word", 27], "28":["author_word", 36]}}}
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@@ -343,24 +343,24 @@ Ammodramus caudacutus (s.s.) diversus|{"scientificName":{"id":"2fb79b29-1579-560
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Arenaria serpyllifolia L. s.str.|{"scientificName":{"id":"8a350298-0dfc-5ad0-9a10-60902587f335", "parsed":true, "verbatim":"Arenaria serpyllifolia L. s.str.", "normalized":"Arenaria serpyllifolia L.", "canonical":"Arenaria serpyllifolia", "hybrid":false, "details":[{"genus":{"string":"Arenaria"}, "species":{"string":"serpyllifolia", "authorship":"L.", "basionymAuthorTeam":{"authorTeam":"L.", "author":["L."]}}}], "parser_version":"test_version", "parser_run":2, "positions":{"0":["genus", 8], "9":["species", 22], "23":["author_word", 25]}}}
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Asplenium trichomanes L. s.lat. - Asplen trich|{"scientificName":{"id":"1687d870-6bea-5573-80ef-4e55eca3199f", "parsed":true, "verbatim":"Asplenium trichomanes L. s.lat. - Asplen trich", "normalized":"Asplenium trichomanes L.", "canonical":"Asplenium trichomanes", "hybrid":false, "details":[{"genus":{"string":"Asplenium"}, "species":{"string":"trichomanes", "authorship":"L.", "basionymAuthorTeam":{"authorTeam":"L.", "author":["L."]}}}], "parser_version":"test_version", "parser_run":2, "positions":{"0":["genus", 9], "10":["species", 21], "22":["author_word", 24]}}}
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Asplenium anisophyllum Kunze, s.l.|{"scientificName":{"id":"a0d7a55a-ffad-5243-905e-048177b440df", "parsed":true, "verbatim":"Asplenium anisophyllum Kunze, s.l.", "normalized":"Asplenium anisophyllum Kunze", "canonical":"Asplenium anisophyllum", "hybrid":false, "details":[{"genus":{"string":"Asplenium"}, "species":{"string":"anisophyllum", "authorship":"Kunze", "basionymAuthorTeam":{"authorTeam":"Kunze", "author":["Kunze"]}}}], "parser_version":"test_version", "parser_run":2, "positions":{"0":["genus", 9], "10":["species", 22], "23":["author_word", 28]}}}
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Abramis Cuvier 1816 sec. Dybowski 1862|{"scientificName":{"id":"1fddff95-f470-5c36-8bc5-4436fe727bda", "parsed":true, "verbatim":"Abramis Cuvier 1816 sec. Dybowski 1862", "normalized":"Abramis Cuvier 1816", "canonical":"Abramis", "hybrid":false, "details":[{"uninomial":{"string":"Abramis", "authorship":"Cuvier 1816", "basionymAuthorTeam":{"authorTeam":"Cuvier", "author":["Cuvier"], "year":"1816"}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["uninomial", 7], "8":["author_word", 14], "15":["year", 19]}}}
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Abramis brama subsp. bergi Grib & Vernidub 1935 sec Eschmeyer 2004|{"scientificName":{"id":"5ac5f7fd-0a42-5133-961e-df94a54fb75f", "parsed":true, "parser_version":"test_version", "verbatim":"Abramis brama subsp. bergi Grib & Vernidub 1935 sec Eschmeyer 2004", "normalized":"Abramis brama subsp. bergi Grib & Vernidub 1935", "canonical":"Abramis brama bergi", "hybrid":false, "details":[{"genus":{"string":"Abramis"}, "species":{"string":"brama"}, "infraspecies":[{"string":"bergi", "rank":"subsp.", "authorship":"Grib & Vernidub 1935", "basionymAuthorTeam":{"authorTeam":"Grib & Vernidub", "author":["Grib", "Vernidub"], "year":"1935"}}]}], "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 13], "14":["infraspecific_type", 20], "21":["infraspecies", 26], "27":["author_word", 31], "34":["author_word", 42], "43":["year", 47]}}}
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Abarema clypearia (Jack) Kosterm., P. P.|{"scientificName":{"id":"2e18b789-865b-55dc-831b-f1fdd6bf740d", "parsed":true, "verbatim":"Abarema clypearia (Jack) Kosterm., P. P.", "normalized":"Abarema clypearia (Jack) Kosterm.", "canonical":"Abarema clypearia", "hybrid":false, "details":[{"genus":{"string":"Abarema"}, "species":{"string":"clypearia", "authorship":"(Jack) Kosterm.", "combinationAuthorTeam":{"authorTeam":"Kosterm.", "author":["Kosterm."]}, "basionymAuthorTeam":{"authorTeam":"Jack", "author":["Jack"]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 17], "19":["author_word", 23], "25":["author_word", 33]}}}
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Abarema clypearia (Jack) Kosterm., p.p.|{"scientificName":{"id":"bc9b0feb-8a33-5f35-97a9-8ee93220fff8", "parsed":true, "verbatim":"Abarema clypearia (Jack) Kosterm., p.p.", "normalized":"Abarema clypearia (Jack) Kosterm.", "canonical":"Abarema clypearia", "hybrid":false, "details":[{"genus":{"string":"Abarema"}, "species":{"string":"clypearia", "authorship":"(Jack) Kosterm.", "combinationAuthorTeam":{"authorTeam":"Kosterm.", "author":["Kosterm."]}, "basionymAuthorTeam":{"authorTeam":"Jack", "author":["Jack"]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 17], "19":["author_word", 23], "25":["author_word", 33]}}}
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Abarema clypearia (Jack) Kosterm., p. p.|{"scientificName":{"id":"1fae34cb-12f4-5600-9589-672199934719", "parsed":true, "verbatim":"Abarema clypearia (Jack) Kosterm., p. p.", "normalized":"Abarema clypearia (Jack) Kosterm.", "canonical":"Abarema clypearia", "hybrid":false, "details":[{"genus":{"string":"Abarema"}, "species":{"string":"clypearia", "authorship":"(Jack) Kosterm.", "combinationAuthorTeam":{"authorTeam":"Kosterm.", "author":["Kosterm."]}, "basionymAuthorTeam":{"authorTeam":"Jack", "author":["Jack"]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 17], "19":["author_word", 23], "25":["author_word", 33]}}}
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Abramis Cuvier 1816 sec. Dybowski 1862|{"scientificName":{"id":"1fddff95-f470-5c36-8bc5-4436fe727bda", "parsed":true, "tail": "sec. Dybowski 1862", "verbatim":"Abramis Cuvier 1816 sec. Dybowski 1862", "normalized":"Abramis Cuvier 1816", "canonical":"Abramis", "hybrid":false, "details":[{"uninomial":{"string":"Abramis", "authorship":"Cuvier 1816", "basionymAuthorTeam":{"authorTeam":"Cuvier", "author":["Cuvier"], "year":"1816"}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["uninomial", 7], "8":["author_word", 14], "15":["year", 19]}}}
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Abramis brama subsp. bergi Grib & Vernidub 1935 sec Eschmeyer 2004|{"scientificName":{"id":"5ac5f7fd-0a42-5133-961e-df94a54fb75f", "parsed":true, "tail": "sec Eschmeyer 2004", "parser_version":"test_version", "verbatim":"Abramis brama subsp. bergi Grib & Vernidub 1935 sec Eschmeyer 2004", "normalized":"Abramis brama subsp. bergi Grib & Vernidub 1935", "canonical":"Abramis brama bergi", "hybrid":false, "details":[{"genus":{"string":"Abramis"}, "species":{"string":"brama"}, "infraspecies":[{"string":"bergi", "rank":"subsp.", "authorship":"Grib & Vernidub 1935", "basionymAuthorTeam":{"authorTeam":"Grib & Vernidub", "author":["Grib", "Vernidub"], "year":"1935"}}]}], "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 13], "14":["infraspecific_type", 20], "21":["infraspecies", 26], "27":["author_word", 31], "34":["author_word", 42], "43":["year", 47]}}}
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Abarema clypearia (Jack) Kosterm., P. P.|{"scientificName":{"id":"2e18b789-865b-55dc-831b-f1fdd6bf740d", "parsed":true, "tail": ", P. P.", "verbatim":"Abarema clypearia (Jack) Kosterm., P. P.", "normalized":"Abarema clypearia (Jack) Kosterm.", "canonical":"Abarema clypearia", "hybrid":false, "details":[{"genus":{"string":"Abarema"}, "species":{"string":"clypearia", "authorship":"(Jack) Kosterm.", "combinationAuthorTeam":{"authorTeam":"Kosterm.", "author":["Kosterm."]}, "basionymAuthorTeam":{"authorTeam":"Jack", "author":["Jack"]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 17], "19":["author_word", 23], "25":["author_word", 33]}}}
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Abarema clypearia (Jack) Kosterm., p.p.|{"scientificName":{"id":"bc9b0feb-8a33-5f35-97a9-8ee93220fff8", "parsed":true, "tail": ", p.p.", "verbatim":"Abarema clypearia (Jack) Kosterm., p.p.", "normalized":"Abarema clypearia (Jack) Kosterm.", "canonical":"Abarema clypearia", "hybrid":false, "details":[{"genus":{"string":"Abarema"}, "species":{"string":"clypearia", "authorship":"(Jack) Kosterm.", "combinationAuthorTeam":{"authorTeam":"Kosterm.", "author":["Kosterm."]}, "basionymAuthorTeam":{"authorTeam":"Jack", "author":["Jack"]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 17], "19":["author_word", 23], "25":["author_word", 33]}}}
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Abarema clypearia (Jack) Kosterm., p. p.|{"scientificName":{"id":"1fae34cb-12f4-5600-9589-672199934719", "parsed":true, "tail": ", p. p.", "verbatim":"Abarema clypearia (Jack) Kosterm., p. p.", "normalized":"Abarema clypearia (Jack) Kosterm.", "canonical":"Abarema clypearia", "hybrid":false, "details":[{"genus":{"string":"Abarema"}, "species":{"string":"clypearia", "authorship":"(Jack) Kosterm.", "combinationAuthorTeam":{"authorTeam":"Kosterm.", "author":["Kosterm."]}, "basionymAuthorTeam":{"authorTeam":"Jack", "author":["Jack"]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 17], "19":["author_word", 23], "25":["author_word", 33]}}}
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Indigofera phyllogramme var. aphylla R.Vig., p.p.B|{"scientificName":{"id":"04bb878e-4442-5b7c-86d7-a41f2f6aefd3", "parsed":true, "parser_version":"test_version", "verbatim":"Indigofera phyllogramme var. aphylla R.Vig., p.p.B", "normalized":"Indigofera phyllogramme var. aphylla R.Vig.", "canonical":"Indigofera phyllogramme aphylla", "hybrid":false, "details":[{"genus":{"string":"Indigofera"}, "species":{"string":"phyllogramme"}, "infraspecies":[{"string":"aphylla", "rank":"var.", "authorship":"R.Vig.", "basionymAuthorTeam":{"authorTeam":"R.Vig.", "author":["R.Vig."]}}]}], "parser_run":2, "positions":{"0":["genus", 10], "11":["species", 23], "24":["infraspecific_type", 28], "29":["infraspecies", 36], "37":["author_word", 43]}}}
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#removing nomenclatural annotations
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Amphiprora pseudoduplex (Osada & Kobayasi, 1990) comb. nov.|{"scientificName":{"id":"06b58578-d00c-5c90-b77a-bc2325694b51", "parsed":true, "parser_version":"test_version", "verbatim":"Amphiprora pseudoduplex (Osada & Kobayasi, 1990) comb. nov.", "normalized":"Amphiprora pseudoduplex (Osada & Kobayasi 1990)", "canonical":"Amphiprora pseudoduplex", "hybrid":false, "details":[{"genus":{"string":"Amphiprora"}, "species":{"string":"pseudoduplex", "authorship":"(Osada & Kobayasi, 1990)", "basionymAuthorTeam":{"authorTeam":"Osada & Kobayasi", "author":["Osada", "Kobayasi"], "year":"1990"}}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 23], "25":["author_word", 30], "33":["author_word", 41], "43":["year", 47]}}}
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Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.|{"scientificName":{"id":"2dcef387-edc3-55a1-9cfc-ee95200bff08", "parsed":true, "verbatim":"Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.", "normalized":"Arthopyrenia hyalospora (Nyl.) R.C. Harris", "canonical":"Arthopyrenia hyalospora", "hybrid":false, "details":[{"genus":{"string":"Arthopyrenia"}, "species":{"string":"hyalospora", "authorship":"(Nyl.) R.C. Harris", "combinationAuthorTeam":{"authorTeam":"R.C. Harris", "author":["R.C. Harris"]}, "basionymAuthorTeam":{"authorTeam":"Nyl.", "author":["Nyl."]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 12], "13":["species", 23], "25":["author_word", 29], "31":["author_word", 35], "36":["author_word", 42]}}}
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Acanthophis lancasteri WELLS & WELLINGTON (nomen nudum)|{"scientificName":{"id":"aa527c3b-972e-56e9-9b8b-0c61c497422d", "parsed":true, "parser_version":"test_version", "verbatim":"Acanthophis lancasteri WELLS & WELLINGTON (nomen nudum)", "normalized":"Acanthophis lancasteri Wells & Wellington", "canonical":"Acanthophis lancasteri", "hybrid":false, "details":[{"genus":{"string":"Acanthophis"}, "species":{"string":"lancasteri", "authorship":"WELLS & WELLINGTON", "basionymAuthorTeam":{"authorTeam":"WELLS & WELLINGTON", "author":["Wells", "Wellington"]}}}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 22], "23":["author_word", 28], "31":["author_word", 41]}}}
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Acontias lineatus WAGLER 1830: 196 (nomen nudum)|{"scientificName":{"id":"16afe3dd-7724-5dc0-817c-f6d138d27174", "parsed":true, "parser_version":"test_version", "verbatim":"Acontias lineatus WAGLER 1830: 196 (nomen nudum)", "normalized":"Acontias lineatus Wagler 1830", "canonical":"Acontias lineatus", "hybrid":false, "details":[{"genus":{"string":"Acontias"}, "species":{"string":"lineatus", "authorship":"WAGLER 1830: 196", "basionymAuthorTeam":{"authorTeam":"WAGLER", "author":["Wagler"], "year":"1830"}}}], "parser_run":2, "positions":{"0":["genus", 8], "9":["species", 17], "18":["author_word", 24], "25":["year", 29]}}}
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Akeratidae Nomen Nudum|{"scientificName":{"id":"6bd60fba-9b78-5e4e-b904-dda976085fc7", "parsed":true, "verbatim":"Akeratidae Nomen Nudum", "normalized":"Akeratidae", "canonical":"Akeratidae", "hybrid":false, "details":[{"uninomial":{"string":"Akeratidae"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["uninomial", 10]}}}
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Aster exilis Ell., nomen dubium|{"scientificName":{"id":"00884bdf-ca19-5c07-8e48-e1adef987844", "parsed":true, "verbatim":"Aster exilis Ell., nomen dubium", "normalized":"Aster exilis Ell.", "canonical":"Aster exilis", "hybrid":false, "details":[{"genus":{"string":"Aster"}, "species":{"string":"exilis", "authorship":"Ell.", "basionymAuthorTeam":{"authorTeam":"Ell.", "author":["Ell."]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 12], "13":["author_word", 17]}}}
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Abutilon avicennae Gaertn., nom. illeg.|{"scientificName":{"id":"366d9605-0686-5072-b025-6c7b3695f086", "parsed":true, "verbatim":"Abutilon avicennae Gaertn., nom. illeg.", "normalized":"Abutilon avicennae Gaertn.", "canonical":"Abutilon avicennae", "hybrid":false, "details":[{"genus":{"string":"Abutilon"}, "species":{"string":"avicennae", "authorship":"Gaertn.", "basionymAuthorTeam":{"authorTeam":"Gaertn.", "author":["Gaertn."]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 18], "19":["author_word", 26]}}}
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Achillea bonarota nom. in herb.|{"scientificName":{"id":"cae8ac71-b3c4-52f7-94cb-31e639081e0d", "parsed":true, "verbatim":"Achillea bonarota nom. in herb.", "normalized":"Achillea bonarota", "canonical":"Achillea bonarota", "hybrid":false, "details":[{"genus":{"string":"Achillea"}, "species":{"string":"bonarota"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 17]}}}
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Aconitum napellus var. formosum (Rchb.) W. D. J. Koch (nom. ambig.)|{"scientificName":{"id":"9f79b2b3-cfd1-541a-9898-b60829134b11", "parsed":true, "parser_version":"test_version", "verbatim":"Aconitum napellus var. formosum (Rchb.) W. D. J. Koch (nom. ambig.)", "normalized":"Aconitum napellus var. formosum (Rchb.) W. D. J. Koch", "canonical":"Aconitum napellus formosum", "hybrid":false, "details":[{"genus":{"string":"Aconitum"}, "species":{"string":"napellus"}, "infraspecies":[{"string":"formosum", "rank":"var.", "authorship":"(Rchb.) W. D. J. Koch", "combinationAuthorTeam":{"authorTeam":"W. D. J. Koch", "author":["W. D. J. Koch"]}, "basionymAuthorTeam":{"authorTeam":"Rchb.", "author":["Rchb."]}}]}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 17], "18":["infraspecific_type", 22], "23":["infraspecies", 31], "33":["author_word", 38], "40":["author_word", 42], "43":["author_word", 45], "46":["author_word", 48], "49":["author_word", 53]}}}
|
|
363
|
-
× Dialaeliopsis Hort.|{"scientificName":{"id":"70953b19-19cd-52a3-a766-551e74437d55", "parsed":true, "verbatim":"× Dialaeliopsis Hort.", "normalized":"× Dialaeliopsis", "canonical":"Dialaeliopsis", "hybrid":true, "details":[{"uninomial":{"string":"Dialaeliopsis"}}], "parser_version":"test_version", "parser_run":1, "positions":{"2":["uninomial", 15]}}}
|
|
354
|
+
Amphiprora pseudoduplex (Osada & Kobayasi, 1990) comb. nov.|{"scientificName":{"id":"06b58578-d00c-5c90-b77a-bc2325694b51", "parsed":true, "tail": "comb. nov.", "parser_version":"test_version", "verbatim":"Amphiprora pseudoduplex (Osada & Kobayasi, 1990) comb. nov.", "normalized":"Amphiprora pseudoduplex (Osada & Kobayasi 1990)", "canonical":"Amphiprora pseudoduplex", "hybrid":false, "details":[{"genus":{"string":"Amphiprora"}, "species":{"string":"pseudoduplex", "authorship":"(Osada & Kobayasi, 1990)", "basionymAuthorTeam":{"authorTeam":"Osada & Kobayasi", "author":["Osada", "Kobayasi"], "year":"1990"}}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 23], "25":["author_word", 30], "33":["author_word", 41], "43":["year", 47]}}}
|
|
355
|
+
Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.|{"scientificName":{"id":"2dcef387-edc3-55a1-9cfc-ee95200bff08", "parsed":true, "tail": "comb. nov.", "verbatim":"Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov.", "normalized":"Arthopyrenia hyalospora (Nyl.) R.C. Harris", "canonical":"Arthopyrenia hyalospora", "hybrid":false, "details":[{"genus":{"string":"Arthopyrenia"}, "species":{"string":"hyalospora", "authorship":"(Nyl.) R.C. Harris", "combinationAuthorTeam":{"authorTeam":"R.C. Harris", "author":["R.C. Harris"]}, "basionymAuthorTeam":{"authorTeam":"Nyl.", "author":["Nyl."]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 12], "13":["species", 23], "25":["author_word", 29], "31":["author_word", 35], "36":["author_word", 42]}}}
|
|
356
|
+
Acanthophis lancasteri WELLS & WELLINGTON (nomen nudum)|{"scientificName":{"id":"aa527c3b-972e-56e9-9b8b-0c61c497422d", "parsed":true, "tail": "(nomen nudum)", "parser_version":"test_version", "verbatim":"Acanthophis lancasteri WELLS & WELLINGTON (nomen nudum)", "normalized":"Acanthophis lancasteri Wells & Wellington", "canonical":"Acanthophis lancasteri", "hybrid":false, "details":[{"genus":{"string":"Acanthophis"}, "species":{"string":"lancasteri", "authorship":"WELLS & WELLINGTON", "basionymAuthorTeam":{"authorTeam":"WELLS & WELLINGTON", "author":["Wells", "Wellington"]}}}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 22], "23":["author_word", 28], "31":["author_word", 41]}}}
|
|
357
|
+
Acontias lineatus WAGLER 1830: 196 (nomen nudum)|{"scientificName":{"id":"16afe3dd-7724-5dc0-817c-f6d138d27174", "parsed":true, "tail": "(nomen nudum)", "parser_version":"test_version", "verbatim":"Acontias lineatus WAGLER 1830: 196 (nomen nudum)", "normalized":"Acontias lineatus Wagler 1830", "canonical":"Acontias lineatus", "hybrid":false, "details":[{"genus":{"string":"Acontias"}, "species":{"string":"lineatus", "authorship":"WAGLER 1830: 196", "basionymAuthorTeam":{"authorTeam":"WAGLER", "author":["Wagler"], "year":"1830"}}}], "parser_run":2, "positions":{"0":["genus", 8], "9":["species", 17], "18":["author_word", 24], "25":["year", 29]}}}
|
|
358
|
+
Akeratidae Nomen Nudum|{"scientificName":{"id":"6bd60fba-9b78-5e4e-b904-dda976085fc7", "parsed":true, "tail": "Nomen Nudum", "verbatim":"Akeratidae Nomen Nudum", "normalized":"Akeratidae", "canonical":"Akeratidae", "hybrid":false, "details":[{"uninomial":{"string":"Akeratidae"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["uninomial", 10]}}}
|
|
359
|
+
Aster exilis Ell., nomen dubium|{"scientificName":{"id":"00884bdf-ca19-5c07-8e48-e1adef987844", "parsed":true, "tail": ", nomen dubium", "verbatim":"Aster exilis Ell., nomen dubium", "normalized":"Aster exilis Ell.", "canonical":"Aster exilis", "hybrid":false, "details":[{"genus":{"string":"Aster"}, "species":{"string":"exilis", "authorship":"Ell.", "basionymAuthorTeam":{"authorTeam":"Ell.", "author":["Ell."]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 12], "13":["author_word", 17]}}}
|
|
360
|
+
Abutilon avicennae Gaertn., nom. illeg.|{"scientificName":{"id":"366d9605-0686-5072-b025-6c7b3695f086", "parsed":true, "tail": ", nom. illeg.", "verbatim":"Abutilon avicennae Gaertn., nom. illeg.", "normalized":"Abutilon avicennae Gaertn.", "canonical":"Abutilon avicennae", "hybrid":false, "details":[{"genus":{"string":"Abutilon"}, "species":{"string":"avicennae", "authorship":"Gaertn.", "basionymAuthorTeam":{"authorTeam":"Gaertn.", "author":["Gaertn."]}}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 18], "19":["author_word", 26]}}}
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361
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+
Achillea bonarota nom. in herb.|{"scientificName":{"id":"cae8ac71-b3c4-52f7-94cb-31e639081e0d", "parsed":true, "tail": "nom. in herb.", "verbatim":"Achillea bonarota nom. in herb.", "normalized":"Achillea bonarota", "canonical":"Achillea bonarota", "hybrid":false, "details":[{"genus":{"string":"Achillea"}, "species":{"string":"bonarota"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 17]}}}
|
|
362
|
+
Aconitum napellus var. formosum (Rchb.) W. D. J. Koch (nom. ambig.)|{"scientificName":{"id":"9f79b2b3-cfd1-541a-9898-b60829134b11", "parsed":true, "tail": "(nom. ambig.)", "parser_version":"test_version", "verbatim":"Aconitum napellus var. formosum (Rchb.) W. D. J. Koch (nom. ambig.)", "normalized":"Aconitum napellus var. formosum (Rchb.) W. D. J. Koch", "canonical":"Aconitum napellus formosum", "hybrid":false, "details":[{"genus":{"string":"Aconitum"}, "species":{"string":"napellus"}, "infraspecies":[{"string":"formosum", "rank":"var.", "authorship":"(Rchb.) W. D. J. Koch", "combinationAuthorTeam":{"authorTeam":"W. D. J. Koch", "author":["W. D. J. Koch"]}, "basionymAuthorTeam":{"authorTeam":"Rchb.", "author":["Rchb."]}}]}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 17], "18":["infraspecific_type", 22], "23":["infraspecies", 31], "33":["author_word", 38], "40":["author_word", 42], "43":["author_word", 45], "46":["author_word", 48], "49":["author_word", 53]}}}
|
|
363
|
+
× Dialaeliopsis Hort.|{"scientificName":{"id":"70953b19-19cd-52a3-a766-551e74437d55", "parsed":true, "tail": "Hort.", "verbatim":"× Dialaeliopsis Hort.", "normalized":"× Dialaeliopsis", "canonical":"Dialaeliopsis", "hybrid":true, "details":[{"uninomial":{"string":"Dialaeliopsis"}}], "parser_version":"test_version", "parser_run":1, "positions":{"2":["uninomial", 15]}}}
|
|
364
364
|
|
|
365
365
|
#should not parse incertae sedis
|
|
366
366
|
|
|
@@ -455,7 +455,7 @@ Deyeuxia coarctata Kunth, 1815 [1816]|{"scientificName":{"id":"2f479365-40be-518
|
|
|
455
455
|
|
|
456
456
|
#names with garbage at the end
|
|
457
457
|
Morea (Morea) Burt 2342343242 23424322342 23424234|{"scientificName":{"id":"ca23679f-f3d8-5194-a406-048f970c4020", "parsed":true, "parser_version":"test_version", "verbatim":"Morea (Morea) Burt 2342343242 23424322342 23424234", "normalized":"Morea (Morea) Burt", "canonical":"Morea", "hybrid":false, "details":[{"uninomial":{"string":"Morea", "infragenus":{"string":"Morea"}, "authorship":"Burt", "basionymAuthorTeam":{"authorTeam":"Burt", "author":["Burt"]}}}], "parser_run":2, "positions":{"0":["uninomial", 5], "7":["infragenus", 12], "14":["author_word", 18]}, "surrogate":true}}
|
|
458
|
-
Nautilus asterizans von|{"scientificName":{"id":"0716f658-c952-5415-b2ad-79a39c2b7b0d", "parsed":true, "verbatim":"Nautilus asterizans von", "normalized":"Nautilus asterizans", "canonical":"Nautilus asterizans", "hybrid":false, "details":[{"genus":{"string":"Nautilus"}, "species":{"string":"asterizans"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 19]}}}
|
|
458
|
+
Nautilus asterizans von|{"scientificName":{"id":"0716f658-c952-5415-b2ad-79a39c2b7b0d", "parsed":true, "tail": "von", "verbatim":"Nautilus asterizans von", "normalized":"Nautilus asterizans", "canonical":"Nautilus asterizans", "hybrid":false, "details":[{"genus":{"string":"Nautilus"}, "species":{"string":"asterizans"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 19]}}}
|
|
459
459
|
|
|
460
460
|
#salvage canonical
|
|
461
461
|
Morea ssjjlajajaj324$33 234243242|{"scientificName":{"id":"268627a4-0984-5b51-b5c1-1a6ad54bf9b9", "parsed":true, "parser_version":"test_version", "verbatim":"Morea ssjjlajajaj324$33 234243242", "normalized":"Morea", "canonical":"Morea", "hybrid":false, "details":[{"uninomial":{"string":"Morea"}}], "parser_run":2, "positions":{"0":["uninomial", 5]}, "surrogate":true}}
|
|
@@ -466,7 +466,7 @@ Moraea spathulata ( (L. f. Klatt|{"scientificName":{"id":"21cb8638-ff53-534f-b81
|
|
|
466
466
|
Stewartia micrantha (Chun) Sealy, Bot. Mag. 176: t. 510. 1967.|{"scientificName":{"id":"7a4ffc19-61a9-551b-bea2-ebb0f5fe9c5a", "parsed":true, "parser_version":"test_version", "verbatim":"Stewartia micrantha (Chun) Sealy, Bot. Mag. 176: t. 510. 1967.", "normalized":"Stewartia micrantha (Chun) Sealy, Bot. Mag.", "canonical":"Stewartia micrantha", "hybrid":false, "details":[{"genus":{"string":"Stewartia"}, "species":{"string":"micrantha", "authorship":"(Chun) Sealy, Bot. Mag.", "combinationAuthorTeam":{"authorTeam":"Sealy, Bot. Mag.", "author":["Sealy", "Bot. Mag."]}, "basionymAuthorTeam":{"authorTeam":"Chun", "author":["Chun"]}}}], "parser_run":2, "positions":{"0":["genus", 9], "10":["species", 19], "21":["author_word", 25], "27":["author_word", 32], "34":["author_word", 38], "39":["author_word", 43]}}}
|
|
467
467
|
Pyrobaculum neutrophilum V24Sta|{"scientificName":{"id":"6d0be585-ec54-5662-9d30-1d369ecf2a64", "parsed":true, "parser_version":"test_version", "verbatim":"Pyrobaculum neutrophilum V24Sta", "normalized":"Pyrobaculum neutrophilum", "canonical":"Pyrobaculum neutrophilum", "hybrid":false, "details":[{"genus":{"string":"Pyrobaculum"}, "species":{"string":"neutrophilum"}}], "parser_run":2, "positions":{"0":["genus", 11], "12":["species", 24]}}}
|
|
468
468
|
Rana aurora Baird and Girard, 1852; H.B. Shaffer et al., 2004|{"scientificName":{"id":"f0fa6cd1-8018-5fec-92ad-1bda9ac929ca", "parsed":true, "parser_version":"test_version", "verbatim":"Rana aurora Baird and Girard, 1852; H.B. Shaffer et al., 2004", "normalized":"Rana aurora Baird & Girard", "canonical":"Rana aurora", "hybrid":false, "details":[{"genus":{"string":"Rana"}, "species":{"string":"aurora", "authorship":"Baird and Girard", "basionymAuthorTeam":{"authorTeam":"Baird and Girard", "author":["Baird", "Girard"]}}}], "parser_run":2, "positions":{"0":["genus", 4], "5":["species", 11], "12":["author_word", 17], "22":["author_word", 28]}}}
|
|
469
|
-
Agropyron pectiniforme var. karabaljikji ined.?|{"scientificName":{"id":"e951b7d4-0009-54df-9de6-efbb392dc8d6", "parsed":true, "parser_version":"test_version", "verbatim":"Agropyron pectiniforme var. karabaljikji ined.?", "normalized":"Agropyron pectiniforme var. karabaljikji", "canonical":"Agropyron pectiniforme karabaljikji", "hybrid":false, "details":[{"genus":{"string":"Agropyron"}, "species":{"string":"pectiniforme"}, "infraspecies":[{"string":"karabaljikji", "rank":"var."}]}], "parser_run":1, "positions":{"0":["genus", 9], "10":["species", 22], "23":["infraspecific_type", 27], "28":["infraspecies", 40]}}}
|
|
469
|
+
Agropyron pectiniforme var. karabaljikji ined.?|{"scientificName":{"id":"e951b7d4-0009-54df-9de6-efbb392dc8d6", "parsed":true, "tail": "ined.?", "parser_version":"test_version", "verbatim":"Agropyron pectiniforme var. karabaljikji ined.?", "normalized":"Agropyron pectiniforme var. karabaljikji", "canonical":"Agropyron pectiniforme karabaljikji", "hybrid":false, "details":[{"genus":{"string":"Agropyron"}, "species":{"string":"pectiniforme"}, "infraspecies":[{"string":"karabaljikji", "rank":"var."}]}], "parser_run":1, "positions":{"0":["genus", 9], "10":["species", 22], "23":["infraspecific_type", 27], "28":["infraspecies", 40]}}}
|
|
470
470
|
Staphylococcus hyicus chromogenes Devriese et al. 1978 (Approved Lists 1980).|{"scientificName":{"id":"ec17eb44-742c-5325-aca6-e33a0888ef0d", "parsed":true, "parser_version":"test_version", "verbatim":"Staphylococcus hyicus chromogenes Devriese et al. 1978 (Approved Lists 1980).", "normalized":"Staphylococcus hyicus chromogenes Devriese et al. 1978", "canonical":"Staphylococcus hyicus chromogenes", "hybrid":false, "details":[{"genus":{"string":"Staphylococcus"}, "species":{"string":"hyicus"}, "infraspecies":[{"string":"chromogenes", "rank":"n/a", "authorship":"Devriese et al. 1978", "basionymAuthorTeam":{"authorTeam":"Devriese et al.", "author":["Devriese et al."], "year":"1978"}}]}], "parser_run":2, "positions":{"0":["genus", 14], "15":["species", 21], "22":["infraspecies", 33], "34":["author_word", 42], "43":["author_word", 49], "50":["year", 54]}}}
|
|
471
471
|
Kerana var. cameroni|{"scientificName":{"id":"d3ca40c3-28ed-51c5-8e87-a22c3e05e8d7", "parsed":true, "parser_version":"test_version", "verbatim":"Kerana var. cameroni", "normalized":"Kerana", "canonical":"Kerana", "hybrid":false, "details":[{"uninomial":{"string":"Kerana"}}], "parser_run":2, "positions":{"0":["uninomial", 6]}}}
|
|
472
472
|
|
|
@@ -474,7 +474,7 @@ Kerana var. cameroni|{"scientificName":{"id":"d3ca40c3-28ed-51c5-8e87-a22c3e05e8
|
|
|
474
474
|
Buteo borealis ? ventralis|{"scientificName":{"id":"d26a4791-4858-5239-8a57-c88957d40919", "parsed":true, "parser_version":"test_version", "verbatim":"Buteo borealis ? ventralis", "normalized":"Buteo borealis", "canonical":"Buteo borealis", "hybrid":false, "details":[{"genus":{"string":"Buteo"}, "species":{"string":"borealis"}, "infraspecies":[{"annotation_identification":"?", "ignored":{"infraspecies":{"string":"ventralis", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 14], "15":["annotation_identification", 17]}}}
|
|
475
475
|
Cetraria islandica ? islandica|{"scientificName":{"id":"01af8da5-3a16-5270-82bb-b0123048ec63", "parsed":true, "parser_version":"test_version", "verbatim":"Cetraria islandica ? islandica", "normalized":"Cetraria islandica", "canonical":"Cetraria islandica", "hybrid":false, "details":[{"genus":{"string":"Cetraria"}, "species":{"string":"islandica"}, "infraspecies":[{"annotation_identification":"?", "ignored":{"infraspecies":{"string":"islandica", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 18], "19":["annotation_identification", 21]}}}
|
|
476
476
|
Euxoa nr. idahoensis sp. 1clay|{"scientificName":{"id":"02a664be-422a-56cb-b431-99aecf793721", "parsed":true, "parser_version":"test_version", "verbatim":"Euxoa nr. idahoensis sp. 1clay", "normalized":"Euxoa idahoensis", "canonical":"Euxoa idahoensis", "hybrid":false, "details":[{"genus":{"string":"Euxoa"}, "species":{"string":"idahoensis"}, "infraspecies":[{"annotation_identification":"sp.", "ignored":{"infraspecies":{"string":"uniclay", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 5], "10":["species", 20], "21":["annotation_identification", 24]}, "surrogate": true}}
|
|
477
|
-
Parus caeruleus species complex|{"scientificName":{"id":"f3752c09-242f-501c-8c8c-0feaf86c4693", "parsed":true, "parser_version":"test_version", "verbatim":"Parus caeruleus species complex", "normalized":"Parus caeruleus", "canonical":"Parus caeruleus", "hybrid":false, "details":[{"genus":{"string":"Parus"}, "species":{"string":"caeruleus"}}], "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 15]}}}
|
|
477
|
+
Parus caeruleus species complex|{"scientificName":{"id":"f3752c09-242f-501c-8c8c-0feaf86c4693", "parsed":true, "tail": "species complex", "parser_version":"test_version", "verbatim":"Parus caeruleus species complex", "normalized":"Parus caeruleus", "canonical":"Parus caeruleus", "hybrid":false, "details":[{"genus":{"string":"Parus"}, "species":{"string":"caeruleus"}}], "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 15]}}}
|
|
478
478
|
Peristernia nassatula forskali Tapparone-Canefri 1875|{"scientificName":{"id":"5aa39b53-32ee-5e9f-aa29-c268a9662fd7", "parsed":true, "parser_version":"test_version", "verbatim":"Peristernia nassatula forskali Tapparone-Canefri 1875", "normalized":"Peristernia nassatula forskali Tapparone-Canefri 1875", "canonical":"Peristernia nassatula forskali", "hybrid":false, "details":[{"genus":{"string":"Peristernia"}, "species":{"string":"nassatula"}, "infraspecies":[{"string":"forskali", "rank":"n/a", "authorship":"Tapparone-Canefri 1875", "basionymAuthorTeam":{"authorTeam":"Tapparone-Canefri", "author":["Tapparone-Canefri"], "year":"1875"}}]}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 21], "22":["infraspecies", 30], "31":["author_word", 48], "49":["year", 53]}}}
|
|
479
479
|
|
|
480
480
|
#should flag surrogate names
|
|
@@ -131,6 +131,13 @@ describe ".add_rank_to_canonical" do
|
|
|
131
131
|
end
|
|
132
132
|
end
|
|
133
133
|
|
|
134
|
+
it "returns preprocessing tail if it exists" do
|
|
135
|
+
sn = "Stenometope laevissimus sensu Eschmeyer 2004"
|
|
136
|
+
res = parser.parse(sn)
|
|
137
|
+
expect(res).to_not be_nil
|
|
138
|
+
expect(res[:scientificName][:tail]).to eq "sensu Eschmeyer 2004"
|
|
139
|
+
end
|
|
140
|
+
|
|
134
141
|
it "does not work for hybrids yet" do
|
|
135
142
|
data = [["Corda X cordiflora var. puberula",
|
|
136
143
|
"Corda cordiflora puberula"]]
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: biodiversity
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 3.
|
|
4
|
+
version: 3.5.0
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Dmitry Mozzherin
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2018-
|
|
11
|
+
date: 2018-04-16 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: treetop
|
|
@@ -158,6 +158,7 @@ executables:
|
|
|
158
158
|
extensions: []
|
|
159
159
|
extra_rdoc_files: []
|
|
160
160
|
files:
|
|
161
|
+
- ".byebug_history"
|
|
161
162
|
- ".document"
|
|
162
163
|
- ".gitignore"
|
|
163
164
|
- ".rspec"
|
|
@@ -215,7 +216,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
215
216
|
version: '0'
|
|
216
217
|
requirements: []
|
|
217
218
|
rubyforge_project:
|
|
218
|
-
rubygems_version: 2.
|
|
219
|
+
rubygems_version: 2.6.14.1
|
|
219
220
|
signing_key:
|
|
220
221
|
specification_version: 4
|
|
221
222
|
summary: Parser of scientific names
|