biodiversity 3.4.6 → 3.5.0
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- 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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---
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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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SHA512:
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metadata.gz:
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data.tar.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
CHANGED
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@@ -1 +1 @@
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1
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2.
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1
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2.4.4
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data/.travis.yml
CHANGED
data/CHANGELOG
CHANGED
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@@ -1,91 +1,95 @@
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1
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-
3.
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1
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3.5.0 -- add the tail cut by preprocessing to the results. The tail usually
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2
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contains annotations about the name.
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3
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3.4.6 -- gems update.
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5
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3
6
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3.4.5 -- fix "fil." and "filius" with infraspecies after them, add "'t" as a
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4
7
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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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10
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3.4.4 -- support "del" as part of authorship, do not truncate epithets that
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8
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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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15
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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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29
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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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85
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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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88
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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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@@ -96,7 +100,7 @@ multiplication sign for hybrids.
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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
CHANGED
data/README.md
CHANGED
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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
CHANGED
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@@ -23,13 +23,15 @@ module PreProcessor
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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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@@ -174,6 +176,7 @@ class ScientificNameParser
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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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@@ -198,7 +201,7 @@ class ScientificNameParser
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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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@@ -230,6 +233,7 @@ class ScientificNameParser
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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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+
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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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@@ -263,7 +267,9 @@ class ScientificNameParser
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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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@@ -285,4 +291,4 @@ class ScientificNameParser
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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
CHANGED
data/spec/files/test_data.txt
CHANGED
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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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@@ -202,17 +202,17 @@ Acarinina aff. pentacamerata|{"scientificName":{"id":"c4ab66ee-79a2-5100-8b87-20
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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
|