biodiversity 3.0.1 → 3.1.0
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.
- data/CHANGELOG +3 -0
- data/LICENSE +3 -1
- data/README.md +44 -10
- data/VERSION +1 -1
- data/lib/biodiversity/parser.rb +19 -0
- data/spec/parser/test_data.txt +29 -22
- metadata +2 -5
data/CHANGELOG
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data/LICENSE
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@@ -1,4 +1,6 @@
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The MIT License (MIT)
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Copyright (c) 2008-2013 Marine Biological Laboratory
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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data/README.md
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@@ -46,7 +46,8 @@ you can use a socket server
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parserver -h
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Usage: parserver [options]
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-r, --canonical_with_rank Adds infraspecies rank
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-r, --canonical_with_rank Adds infraspecies rank
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to canonical forms
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-o, --output=output Specifies the type of the output:
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json - parsed results in json
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@@ -116,15 +117,18 @@ You can use it as a library in Ruby, JRuby etc.
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parser.parse(" Plantago major ")[:scientificName][:normalized]
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# to get only cleaned up latin part of the name
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parser.parse("Pseudocercospora dendrobii (H.C. Burnett) U.
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parser.parse("Pseudocercospora dendrobii (H.C. Burnett) U. \
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Braun & Crous 2003")[:scientificName][:canonical]
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# to get detailed information about elements of the name
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parser.parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U.
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parser.parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. \
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Braun & Crous 2003")[:scientificName][:details]
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Returned result is not always linear, if name is complex. To get simple linear
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representation of the name you can use:
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parser.parse("Pseudocercospora dendrobii (H.C. Burnett)
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parser.parse("Pseudocercospora dendrobii (H.C. Burnett) \
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U. Braun & Crous 2003")[:scientificName][:position]
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# returns {0=>["genus", 16], 17=>["species", 26],
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# 28=>["author_word", 32], 33=>["author_word", 40],
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# 42=>["author_word", 44], 45=>["author_word", 50],
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# of the word, second element of the value is the character index
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# of end of the word
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'Surrogate' is a broad group which includes 'Barcode of Life' names, and various
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undetermined names with cf. sp. spp. nr. in them:
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parser.parse("Coleoptera BOLD:1234567")[:scientificName][:surrogate]
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To parse using several CPUs (4 seem to be optimal)
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parser = ParallelParser.new
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# ParallelParser.new(4) will try to run 4 processes if hardware allows
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array_of_names = ["Betula alba", "Homo sapiens"....]
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parser.parse(array_of_names)
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# Output: {"Betula alba" => {:scientificName...},
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# Output: {"Betula alba" => {:scientificName...},
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# "Homo sapiens" => {:scientificName...}, ...}
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parallel parser takes list of names and returns back a hash with names as
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parallel parser takes list of names and returns back a hash with names as
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keys and parsed data as values
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To get canonicals with ranks for infraspecific epithets:
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parser = ScientificNameParser.new(canonical_with_rank: true)
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parser.parse('Cola cordifolia var. puberula
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parser.parse('Cola cordifolia var. puberula \
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A. Chev.')[:scientificName][:canonical]
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# Output: Cola cordifolia var. puberula
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To resolve lsid and get back RDF file
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LsidResolver.resolve("urn:lsid:ubio.org:classificationbank:2232671")
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Troubleshooting
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---------------
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If nnparse or parserver do not start -- try to run
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gem uninstall biodiversity
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gem uninstall biodiversity19
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and make sure you remove all versions and all nnparse and parserver scripts.
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Then install biodiversity again
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gem install biodiversity
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It should fix the problem.
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Copyright
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---------
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Authors: [Dmitry Mozzherin][10],
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Copyright (c) 2008-2013 Marine Biological Laboratory. See LICENSE for
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further details.
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[1]: https://badge.fury.io/rb/
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[2]: http://badge.fury.io/rb/
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[1]: https://badge.fury.io/rb/biodiversity.png
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[2]: http://badge.fury.io/rb/biodiversity
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[3]: https://secure.travis-ci.org/GlobalNamesArchitecture/biodiversity.png
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[4]: http://travis-ci.org/GlobalNamesArchitecture/biodiversity
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[5]: https://codeclimate.com/github/GlobalNamesArchitecture/biodiversity.png
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[6]: https://codeclimate.com/github/GlobalNamesArchitecture/biodiversity
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[7]: https://gemnasium.com/GlobalNamesArchitecture/biodiversity.png
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[8]: https://gemnasium.com/GlobalNamesArchitecture/biodiversity
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[9]:
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[9]: http://bit.ly/149iLm5
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[10]: https://github.com/dimus
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data/VERSION
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3.0
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3.1.0
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data/lib/biodiversity/parser.rb
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res[:details][0][:infraspecies])
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ScientificNameParser.add_rank_to_canonical(res)
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end
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res[:surrogate] = true if ScientificNameParser.surrogate?(res)
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res = {:scientificName => res}
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end
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private
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def self.surrogate?(parsed_data)
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return false unless parsed_data[:parsed]
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name = parsed_data[:verbatim]
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pos = parsed_data[:positions].to_a.flatten
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surrogate1 = /BOLD:|[\d]{5,}/i
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surrogate2 = /(spp|sp|nr|cf)[\.]?[\s]*$/i
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is_surrogate = false
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ai_index = pos.index('annotation_identification')
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if ai_index
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ai = name[pos[ai_index - 1]..pos[ai_index + 1]]
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is_surrogate = true if ai.match(/^(spp|cf|sp|nr)/)
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end
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is_surrogate = true if !is_surrogate && (name.match(surrogate1) ||
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name.match(surrogate2))
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is_surrogate
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end
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def self.add_rank_to_canonical(parsed)
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parts = parsed[:canonical].split(' ')
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name_ary = parts[0..1]
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data/spec/parser/test_data.txt
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#species and infraspecies without epithets, comparisons
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Acarinina aff. pentacamerata|{"scientificName":{"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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Acarinina aff pentacamerata|{"scientificName":{"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":{"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]}}}
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Abturia cf alabamensis (Morton )|{"scientificName":{"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]}}}
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Abturia cf. alabamensis (Morton )|{"scientificName":{"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":{"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":{"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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Alyxia reinwardti var.|{"scientificName":{"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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Alyxia reinwardti ssp|{"scientificName":{"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":{"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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Alaria spp|{"scientificName":{"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]}}}
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Alaria spp.|{"scientificName":{"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]}}}
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Xenodon sp|{"scientificName":{"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]}}}
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Xenodon sp.|{"scientificName":{"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]}}}
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Formicidae cf.|{"scientificName":{"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]}}}
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Formicidae cf|{"scientificName":{"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]}}}
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Acastoides spp.|{"scientificName":{"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]}}}
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Sphingomonas sp. 37|{"scientificName":{"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]}}}
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Thryothorus leucotis spp. bogotensis|{"scientificName":{"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]}}}
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Endoxyla sp. GM-, 2003|{"scientificName":{"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]}}}
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Liopropoma sp.2 Not applicable|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Liopropoma sp.2 Not applicable", "normalized":"Liopropoma", "canonical":"Liopropoma", "hybrid":false, "details":[{"genus":{"string":"Liopropoma"}, "annotation_identification":"sp.", "ignored":{"unparsed":"2 Not applicable"}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["annotation_identification", 14]}}}
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Lacanobia nr. subjuncta Bold:Aab, 0925|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Lacanobia nr. subjuncta Bold:Aab, 0925", "normalized":"Lacanobia", "canonical":"Lacanobia", "hybrid":false, "details":[{"genus":{"string":"Lacanobia"}, "annotation_identification":"nr.", "ignored":{"species":{"string":"subjuncta", "authorship":"Bold:Aab", "basionymAuthorTeam":{"authorTeam":"Bold:Aab", "author":["Bold:Aab"]}}}}], "parser_run":2, "positions":{"0":["genus", 9], "10":["annotation_identification", 13]}}}
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Lacanobia sp. nr. subjuncta Bold:Aab, 0925|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Lacanobia sp. nr. subjuncta Bold:Aab, 0925", "normalized":"Lacanobia", "canonical":"Lacanobia", "hybrid":false, "details":[{"genus":{"string":"Lacanobia"}, "annotation_identification":"sp. nr.", "ignored":{"species":{"string":"subjuncta", "authorship":"Bold:Aab", "basionymAuthorTeam":{"authorTeam":"Bold:Aab", "author":["Bold:Aab"]}}}}], "parser_run":2, "positions":{"0":["genus", 9], "10":["annotation_identification", 17]}}}
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Alyxia reinwardti ssp|{"scientificName":{"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]}, "surrogate": true}}
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Alyxia reinwardti ssp.|{"scientificName":{"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]}, "surrogate": true}}
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Alaria spp|{"scientificName":{"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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Alaria spp.|{"scientificName":{"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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Xenodon sp|{"scientificName":{"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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Xenodon sp.|{"scientificName":{"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}}
|
|
184
|
+
Formicidae cf.|{"scientificName":{"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}}
|
|
185
|
+
Formicidae cf|{"scientificName":{"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}}
|
|
186
|
+
Acastoides spp.|{"scientificName":{"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}}
|
|
187
|
+
Sphingomonas sp. 37|{"scientificName":{"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}}
|
|
188
|
+
Thryothorus leucotis spp. bogotensis|{"scientificName":{"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}}
|
|
189
|
+
Endoxyla sp. GM-, 2003|{"scientificName":{"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}}
|
|
190
|
+
Liopropoma sp.2 Not applicable|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Liopropoma sp.2 Not applicable", "normalized":"Liopropoma", "canonical":"Liopropoma", "hybrid":false, "details":[{"genus":{"string":"Liopropoma"}, "annotation_identification":"sp.", "ignored":{"unparsed":"2 Not applicable"}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["annotation_identification", 14]}, "surrogate": true}}
|
|
191
|
+
Lacanobia nr. subjuncta Bold:Aab, 0925|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Lacanobia nr. subjuncta Bold:Aab, 0925", "normalized":"Lacanobia", "canonical":"Lacanobia", "hybrid":false, "details":[{"genus":{"string":"Lacanobia"}, "annotation_identification":"nr.", "ignored":{"species":{"string":"subjuncta", "authorship":"Bold:Aab", "basionymAuthorTeam":{"authorTeam":"Bold:Aab", "author":["Bold:Aab"]}}}}], "parser_run":2, "positions":{"0":["genus", 9], "10":["annotation_identification", 13]}, "surrogate": true}}
|
|
192
|
+
Lacanobia sp. nr. subjuncta Bold:Aab, 0925|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Lacanobia sp. nr. subjuncta Bold:Aab, 0925", "normalized":"Lacanobia", "canonical":"Lacanobia", "hybrid":false, "details":[{"genus":{"string":"Lacanobia"}, "annotation_identification":"sp. nr.", "ignored":{"species":{"string":"subjuncta", "authorship":"Bold:Aab", "basionymAuthorTeam":{"authorTeam":"Bold:Aab", "author":["Bold:Aab"]}}}}], "parser_run":2, "positions":{"0":["genus", 9], "10":["annotation_identification", 17]}, "surrogate": true}}
|
|
193
193
|
#Larus occidentalis cf. wymani|{}
|
|
194
|
-
Calidris cf. cooperi|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Calidris cf. cooperi", "normalized":"Calidris cf. cooperi", "canonical":"Calidris cooperi", "hybrid":false, "details":[{"genus":{"string":"Calidris"}, "annotation_identification":"cf.", "species":{"species":{"string":"cooperi"}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["annotation_identification", 12], "13":["species", 20]}}}
|
|
194
|
+
Calidris cf. cooperi|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Calidris cf. cooperi", "normalized":"Calidris cf. cooperi", "canonical":"Calidris cooperi", "hybrid":false, "details":[{"genus":{"string":"Calidris"}, "annotation_identification":"cf.", "species":{"species":{"string":"cooperi"}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["annotation_identification", 12], "13":["species", 20]}, "surrogate": true}}
|
|
195
195
|
#TODO:Gemmula cf. cosmoi NP-2008 -- generates wrong authorship
|
|
196
196
|
|
|
197
197
|
#unknown authorship
|
|
@@ -393,12 +393,12 @@ Zygaena witti Wiegel [1973]|{"scientificName":{"parsed":true, "parser_version":"
|
|
|
393
393
|
Deyeuxia coarctata Kunth, 1815 [1816]|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":2,"verbatim":"Deyeuxia coarctata Kunth, 1815 [1816]","normalized":"Deyeuxia coarctata Kunth 1815 (1816)","canonical":"Deyeuxia coarctata","hybrid":false,"details":[{"genus":{"string":"Deyeuxia"},"species":{"string":"coarctata","authorship":"Kunth, 1815 [1816]","basionymAuthorTeam":{"authorTeam":"Kunth","author":["Kunth"],"year":"1815","approximate_year":"(1816)"}}}],"positions":{"0":["genus",8],"9":["species",18],"19":["author_word",24],"26":["year",30],"32":["year",36]}}}
|
|
394
394
|
|
|
395
395
|
#names with garbage at the end
|
|
396
|
-
Morea (Morea) Burt 2342343242 23424322342 23424234|{"scientificName":{"parsed":true, "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"]}}}],
|
|
396
|
+
Morea (Morea) Burt 2342343242 23424322342 23424234|{"scientificName":{"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}}
|
|
397
397
|
Nautilus asterizans von|{"scientificName":{"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]}}}
|
|
398
398
|
|
|
399
399
|
#salvage canonical
|
|
400
|
-
Morea ssjjlajajaj324$33 234243242|{"scientificName":{"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]}}}
|
|
401
|
-
Morea (Morea) burtius 2342343242 23424322342 23424234|{"scientificName":{"parsed":true, "parser_version":"test_version", "
|
|
400
|
+
Morea ssjjlajajaj324$33 234243242|{"scientificName":{"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}}
|
|
401
|
+
Morea (Morea) burtius 2342343242 23424322342 23424234|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Morea (Morea) burtius 2342343242 23424322342 23424234", "normalized":"Morea (Morea) burtius", "canonical":"Morea burtius", "hybrid":false, "details":[{"genus":{"string":"Morea"}, "infragenus":{"string":"Morea"}, "species":{"string":"burtius"}}], "parser_run":2, "positions":{"0":["genus", 5], "7":["infragenus", 12], "14":["species", 21]}, "surrogate":true}}
|
|
402
402
|
Verpericola megasoma ""Dall" Pils.|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":2,"verbatim":"Verpericola megasoma \"\"Dall\" Pils.","normalized":"Verpericola megasoma","canonical":"Verpericola megasoma","hybrid":false,"details":[{"genus":{"string":"Verpericola"},"species":{"string":"megasoma"}}],"positions":{"0":["genus",11],"12":["species",20]}}}
|
|
403
403
|
Verpericola megasoma "Dall" Pils.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Verpericola megasoma \"Dall\" Pils.", "normalized":"Verpericola megasoma", "canonical":"Verpericola megasoma", "hybrid":false, "details":[{"genus":{"string":"Verpericola"}, "species":{"string":"megasoma"}}], "parser_run":2, "positions":{"0":["genus", 11], "12":["species", 20]}}}
|
|
404
404
|
Moraea spathulata ( (L. f. Klatt|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":2,"verbatim":"Moraea spathulata ( (L. f. Klatt","normalized":"Moraea spathulata","canonical":"Moraea spathulata","hybrid":false,"details":[{"genus":{"string":"Moraea"},"species":{"string":"spathulata"}}],"positions":{"0":["genus",6],"7":["species",17]}}}
|
|
@@ -412,5 +412,12 @@ Kerana var. cameroni|{"scientificName":{"parsed":true, "parser_version":"test_ve
|
|
|
412
412
|
#should parse names which previously caused prolems:
|
|
413
413
|
Buteo borealis ? ventralis|{"scientificName":{"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]}}}
|
|
414
414
|
Cetraria islandica ? islandica|{"scientificName":{"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]}}}
|
|
415
|
-
Euxoa nr. idahoensis sp. 1clay|{"scientificName":{"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]}}}
|
|
415
|
+
Euxoa nr. idahoensis sp. 1clay|{"scientificName":{"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}}
|
|
416
416
|
Parus caeruleus species complex|{"scientificName":{"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]}}}
|
|
417
|
+
|
|
418
|
+
#should flag surrogate names
|
|
419
|
+
Coleoptera sp. BOLD:AAV0432|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Coleoptera sp. BOLD:AAV0432", "normalized":"Coleoptera", "canonical":"Coleoptera", "hybrid":false, "details":[{"genus":{"string":"Coleoptera"}, "annotation_identification":"sp.", "ignored":{"unparsed":"BOLD:AAV0432"}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["annotation_identification", 14]}, "surrogate":true}}
|
|
420
|
+
Coleoptera Bold:AAV0432|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Coleoptera Bold:AAV0432", "normalized":"Coleoptera", "canonical":"Coleoptera", "hybrid":false, "details":[{"uninomial":{"string":"Coleoptera"}}], "parser_run":2, "positions":{"0":["uninomial", 10]}, "surrogate":true}}
|
|
421
|
+
|
|
422
|
+
#should not flag as surrogates similar to surrogates names
|
|
423
|
+
Dryopteris X separabilis Small (pro sp.)|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Dryopteris X separabilis Small (pro sp.)", "normalized":"Dryopteris × separabilis Small", "canonical":"Dryopteris separabilis", "hybrid":false, "details":[{"genus":{"string":"Dryopteris"}, "species":{"string":"separabilis", "authorship":"Small", "basionymAuthorTeam":{"authorTeam":"Small", "author":["Small"]}}}], "parser_run":2, "positions":{"0":["genus", 10], "13":["species", 24], "25":["author_word", 30]}}}
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: biodiversity
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 3.0
|
|
4
|
+
version: 3.1.0
|
|
5
5
|
prerelease:
|
|
6
6
|
platform: ruby
|
|
7
7
|
authors:
|
|
@@ -9,7 +9,7 @@ authors:
|
|
|
9
9
|
autorequire:
|
|
10
10
|
bindir: bin
|
|
11
11
|
cert_chain: []
|
|
12
|
-
date: 2013-
|
|
12
|
+
date: 2013-06-17 00:00:00.000000000 Z
|
|
13
13
|
dependencies:
|
|
14
14
|
- !ruby/object:Gem::Dependency
|
|
15
15
|
name: rake
|
|
@@ -209,9 +209,6 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
|
209
209
|
- - ! '>='
|
|
210
210
|
- !ruby/object:Gem::Version
|
|
211
211
|
version: '0'
|
|
212
|
-
segments:
|
|
213
|
-
- 0
|
|
214
|
-
hash: -3305280802339019228
|
|
215
212
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
216
213
|
none: false
|
|
217
214
|
requirements:
|