biodiversity19 2.1.0 → 3.0.0
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- data/.travis.yml +1 -0
- data/CHANGELOG +4 -0
- data/README.md +27 -6
- data/Rakefile +16 -10
- data/VERSION +1 -1
- data/lib/biodiversity/parser/scientific_name_clean.treetop +223 -223
- data/spec/parser/test_data.txt +8 -2
- metadata +3 -3
data/spec/parser/test_data.txt
CHANGED
@@ -277,7 +277,7 @@ Polypodium x vulgare nothosubsp. mantoniae (Rothm.) Schidlay|{"scientificName":
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#empty spaces
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Asplenium Xinexpectatum(E. L. Braun ex Friesner )Morton |{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Asplenium Xinexpectatum(E. L. Braun ex Friesner )Morton", "normalized":"Asplenium × inexpectatum (E. L. Braun ex Friesner) Morton", "canonical":"Asplenium inexpectatum", "hybrid":true, "details":[{"genus":{"string":"Asplenium"}, "species":{"string":"inexpectatum", "authorship":"(E. L. Braun ex Friesner )Morton", "combinationAuthorTeam":{"authorTeam":"Morton", "author":["Morton"]}, "basionymAuthorTeam":{"authorTeam":"E. L. Braun", "author":["E. L. Braun"], "exAuthorTeam":{"authorTeam":"Friesner", "author":["Friesner"]}}}}], "parser_run":1, "positions":{"4":["genus", 13], "21":["species", 33], "34":["author_word", 36], "37":["author_word", 39], "40":["author_word", 45], "49":["author_word", 57], "64":["author_word", 70]}}}
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-
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+
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####
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#
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# Names with problems
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@@ -312,7 +312,7 @@ Abramis brama subsp. bergi Grib & Vernidub 1935 sec Eschmeyer 2004|{"scientificN
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Abarema clypearia (Jack) Kosterm., P. P.|{"scientificName":{"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":{"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":{"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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315
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-
Indigofera phyllogramme var. aphylla R.Vig., p.p.B|{"scientificName":{"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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+
Indigofera phyllogramme var. aphylla R.Vig., p.p.B|{"scientificName":{"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":{"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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@@ -408,3 +408,9 @@ Rana aurora Baird and Girard, 1852; H.B. Shaffer et al., 2004|{"scientificName":
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Agropyron pectiniforme var. karabaljikji ined.?|{"scientificName":{"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]}}}
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Staphylococcus hyicus chromogenes Devriese et al. 1978 (Approved Lists 1980).|{"scientificName":{"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]}}}
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Kerana var. cameroni|{"scientificName":{"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]}}}
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+
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+
#should parse names which previously caused prolems:
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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]}}}
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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]}}}
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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]}}}
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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]}}}
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metadata
CHANGED
@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: biodiversity19
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version: !ruby/object:Gem::Version
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version:
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version: 3.0.0
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prerelease:
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platform: ruby
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authors:
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2013-
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+
date: 2013-05-08 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rake
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@@ -211,7 +211,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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version: '0'
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segments:
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- 0
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-
hash:
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+
hash: 4298673073625550277
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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