biodiversity 3.5.1 → 4.0.0
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- checksums.yaml +5 -5
- data/.gitignore +1 -0
- data/.rubocop.yml +9 -6
- data/.ruby-version +1 -1
- data/.travis.yml +1 -6
- data/CHANGELOG +3 -0
- data/Gemfile +2 -0
- data/README.md +37 -178
- data/Rakefile +15 -48
- data/biodiversity.gemspec +18 -21
- data/clib/linux/libgnparser.h +93 -0
- data/clib/linux/libgnparser.so +0 -0
- data/clib/mac/libgnparser.h +93 -0
- data/clib/mac/libgnparser.so +0 -0
- data/lib/biodiversity.rb +4 -9
- data/lib/biodiversity/parser.rb +65 -281
- data/lib/biodiversity/version.rb +8 -1
- data/spec/lib/biodiversity_spec.rb +9 -0
- data/spec/lib/parser_spec.rb +38 -0
- data/spec/spec_helper.rb +4 -81
- metadata +27 -102
- data/.byebug_history +0 -18
- data/.document +0 -5
- data/examples/socket_client.rb +0 -25
- data/lib/biodiversity/guid.rb +0 -1
- data/lib/biodiversity/guid/lsid.rb +0 -16
- data/lib/biodiversity/parser/scientific_name_canonical.rb +0 -528
- data/lib/biodiversity/parser/scientific_name_canonical.treetop +0 -120
- data/lib/biodiversity/parser/scientific_name_clean.rb +0 -8991
- data/lib/biodiversity/parser/scientific_name_clean.treetop +0 -1632
- data/lib/biodiversity/parser/scientific_name_dirty.rb +0 -1298
- data/lib/biodiversity/parser/scientific_name_dirty.treetop +0 -264
- data/spec/biodiversity_spec.rb +0 -11
- data/spec/files/test_data.txt +0 -490
- data/spec/files/todo.txt +0 -55
- data/spec/guid/lsid.spec.rb +0 -15
- data/spec/parser/scientific_name_canonical_spec.rb +0 -36
- data/spec/parser/scientific_name_clean_spec.rb +0 -1137
- data/spec/parser/scientific_name_dirty_spec.rb +0 -165
- data/spec/parser/scientific_name_spec.rb +0 -193
data/spec/files/todo.txt
DELETED
@@ -1,55 +0,0 @@
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Rana aurora Baird and Girard, 1852; H.B. Shaffer et al., 2004 <---- WRONG CANONICAL FORM!!!!!!!!
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Gemmula cf. cosmoi NP-2008 <--- WRONG CANONICAL FORM
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Eupithecia cf. E. maestosa
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Eupithecia cf. maestosa
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Aleiodes Tetrasphaeropyx chumashanus => Aleiodes [subgenus] chumashanus
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Cucurbita pepo subsp. ovifera x subsp. fraterna
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Döringina Ihering 1929 (synonym) Dzzringina
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Doringina Ihering, 1929 (synonym) Döringina
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Lacanobia nr. subjuncta Bold:Aab, 0925 Lacanobia nr
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Lacanobia sp. nr. subjuncta Bold:Aab, 0925 Lacanobia sp
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Agropyron pectiniforme var. karabaljikji ined.? Agropyron pectiniforme
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Shaanxilithes Xing, Yue & Zhang, 1984 Shaanxilithes ing
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Parapandorina Xue, Tang, Yu & Zhou 1995 Parapandorina ue
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Potamogeton iilinoensis var. ventanicola (Hicken) Horn af Rantzien Potamogeton iilinoensis var. ventanicola af
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Rhododendron weyrichii Maxim. f. albiflorum T.Yamaz. Rhododendron
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23
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Polypodium pectinatum L. f. typica Rosenst. Polypodium
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Polypodium lineare C.Chr. f. caudatoattenuatum Takeda Polypodium
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26
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Rosa gallica × tomentosa var. eglandulosa R.Keller Rosa gallica
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Rosa gallica × afzeliana subsp. vosagiaca forma subcomplicata R.Keller Rosa gallica
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30
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Salmonella sp. (ser.) brancaster Macdonald, Sivell, Emms and Taylor 1948
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Stanhopea tigrina Bateman ex Lindl. x S. ecornuta Lem.
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35
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Junellia o'donelli Moldenke, 1946
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119052670 | Human rhinovirus A11 |
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38
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39
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Rubus idaeus monst. obtusifolius (Willd.) Focke | Rubus idaeus
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40
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41
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Kerana var. cameroni |Kerana var
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A. alba
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A.alba
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Bangalaia viridis sbsp. distinctemaculata Lepesme & Breuning, 1956
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Clostridium sp. enrichment culture clone M4C16
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000913765 Rubus x gracilidens Sudre
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Rubus gracilidens | 1
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Salix myrtilloides x starkeana ssp. starkeana
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data/spec/guid/lsid.spec.rb
DELETED
@@ -1,15 +0,0 @@
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describe LsidResolver do
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describe '.resolve' do
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let(:lsid) { 'urn:lsid:ubio.org:classificationbank:2232671' }
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it 'resolves lsid using tdwg service' do
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stub_request(:get,
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%r|#{Biodiversity::LSID_RESOLVER_URL + lsid}|).to_return do
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{ body: File.read(File.expand_path('../../files/lsid.xml', __FILE__)) }
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end
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expect(LsidResolver.resolve lsid).
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to match %r|<dc:title>Pternistis Wagler 1832</dc:title>|
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end
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end
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end
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# encoding: UTF-8
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describe ScientificNameCanonical do
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before(:all) do
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set_parser(ScientificNameCanonicalParser.new)
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end
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it "parses names with valid name part and unparseable rest" do
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[
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["Morea ssjjlajajaj324$33 234243242","Morea",
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[{ uninomial: { string: "Morea" }}], { 0 => ["uninomial", 5]}],
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["Morea (Morea) Burt 2342343242 23424322342 23424234",
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"Morea (Morea)", [{ genus: { string: "Morea" },
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infragenus: { string: "Morea" }}],
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{ 0 => ["genus", 5], 7 => ["infragenus", 12] }],
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["Morea (Morea) burtius 2342343242 23424322342 23424234",
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"Morea (Morea) burtius", [{ genus: { string: "Morea" },
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infragenus: { string: "Morea" },
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species: { string: "burtius" }}],
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{ 0 => ["genus", 5], 7 => ["infragenus", 12], 14 => ["species", 21] }],
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21
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["Moraea spathulata ( (L. f. Klatt","Moraea spathulata",
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[{ genus: { string: "Moraea" }, species: { string: "spathulata"}}],
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{ 0 => ["genus", 6], 7 => ["species", 17] } ],
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["Verpericola megasoma \"Dall\" Pils.","Verpericola megasoma",
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[{ genus: { string: "Verpericola" },
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species: { string: "megasoma"}}],
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{ 0 => ["genus", 11], 12 => ["species", 20] }]
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].each do |n|
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expect(parse(n[0])).not_to be_nil
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expect(value(n[0])).to eq n[1]
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expect(details(n[0])).to eq n[2]
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expect(pos(n[0])).to eq n[3]
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expect(parse(n[0]).hybrid).to be false
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end
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end
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end
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# encoding: UTF-8
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describe ScientificNameClean do
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before(:all) do
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set_parser(ScientificNameCleanParser.new)
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end
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it "parses uninomial" do
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sn = "Pseudocercospora"
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expect(parse(sn)).to_not be_nil
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expect(value(sn)).to eq "Pseudocercospora"
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expect(canonical(sn)).to eq "Pseudocercospora"
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expect(details(sn)).to eq [{ uninomial: { string: "Pseudocercospora" } }]
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expect(pos(sn)).to eq({ 0 => ["uninomial", 16] })
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end
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it "parses uninomial with author and year" do
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sn = "Pseudocercospora Speg."
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expect(parse(sn)).to_not be_nil
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expect(details(sn)).to eq [{ uninomial:
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{ string: "Pseudocercospora",
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authorship: "Speg.",
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basionymAuthorTeam:
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{ authorTeam: "Speg.", author: ["Speg."] } } }]
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expect(pos(sn)).to eq({ 0 => ["uninomial", 16], 17 => ["author_word", 22] })
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sn = "Pseudocercospora Spegazzini, 1910"
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expect(parse(sn)).to_not be_nil
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expect(value(sn)).to eq "Pseudocercospora Spegazzini 1910"
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expect(details(sn)).to eq [{ uninomial:
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{ string: "Pseudocercospora",
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authorship: "Spegazzini, 1910",
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basionymAuthorTeam:
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{ authorTeam: "Spegazzini",
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author: ["Spegazzini"], year: "1910" } } }]
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expect(pos(sn)).to eq({ 0 => ["uninomial", 16],
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17 => ["author_word", 27], 29 => ["year", 33] })
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end
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it "parses uninomials with uninomial ranks" do
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sn = "Epacridaceae trib. Archerieae Crayn & Quinn"
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expect(parse(sn)).to_not be_nil
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expect(details(sn)).to eq [{ uninomial:
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{ string: "Epacridaceae" },
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rank_uninomials: "trib.",
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:uninomial2 => { string: "Archerieae",
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authorship: "Crayn & Quinn",
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basionymAuthorTeam:
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{ authorTeam: "Crayn & Quinn",
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author: ["Crayn", "Quinn"] } } }]
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end
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it "parses names with a valid 2 letter genus" do
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["Ca Dyar 1914",
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"Ea Distant 1911",
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"Ge Nicéville 1895",
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"Ia Thomas 1902",
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"Io Lea 1831",
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"Io Blanchard 1852",
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"Ix Bergroth 1916",
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"Lo Seale 1906",
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61
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"Oa Girault 1929",
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62
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"Ra Whitley 1931",
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"Ty Bory de St. Vincent 1827",
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"Ua Girault 1929",
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"Aa Baker 1940",
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66
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"Ja Uéno 1955",
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"Zu Walters & Fitch 1960",
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"La Bleszynski 1966",
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"Qu Durkoop",
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"As Slipinski 1982",
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"Ba Solem 1983"].each do |name|
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expect(parse(name)).to_not be_nil
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end
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expect(canonical("Quoyula")).to eq "Quoyula"
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end
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it "parses canonical" do
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sn = "Pseudocercospora dendrobii"
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expect(parse(sn)).to_not be_nil
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expect(value(sn)).to eq "Pseudocercospora dendrobii"
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expect(canonical(sn)).to eq "Pseudocercospora dendrobii"
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expect(details(sn)).to eq [{ genus:
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{ string: "Pseudocercospora" },
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species: { string: "dendrobii" } }]
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expect(pos(sn)).to eq({ 0 => ["genus", 16], 21 => ["species", 30] })
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end
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it "parses abbreviated canonical" do
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sn = "P. dendrobii"
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expect(parse(sn)).to_not be_nil
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expect(value(sn)).to eq "P. dendrobii"
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sn = "Ps. dendrobii"
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expect(parse(sn)).to_not be_nil
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expect(value(sn)).to eq "Ps. dendrobii"
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expect(details(sn)).to eq [{ genus:
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{ string: "Ps." },
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species: { string: "dendrobii" } }]
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end
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100
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101
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it "parses species name with author and year" do
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sn = "Platypus bicaudatulus Schedl 1935"
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expect(parse(sn)).to_not be_nil
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expect(value(sn)).to eq "Platypus bicaudatulus Schedl 1935"
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sn = "Platypus bicaudatulus Schedl, 1935h"
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expect(parse(sn)).to_not be_nil
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expect(value(sn)).to eq "Platypus bicaudatulus Schedl 1935"
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expect(details(sn)).to eq [{ genus:
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{ string: "Platypus" },
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species: { string: "bicaudatulus",
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authorship: "Schedl, 1935h",
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basionymAuthorTeam:
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{ authorTeam: "Schedl", author: ["Schedl"],
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year: "1935" } } }]
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expect(pos(sn)).to eq({ 0 => ["genus", 8],
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9 => ["species", 21], 22 => ["author_word", 28],
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30 => ["year", 35] })
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expect(parse("Platypus bicaudatulus Schedl, 1935B")).to_not be_nil
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sn = "Platypus bicaudatulus Schedl (1935h)"
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expect(parse(sn)).to_not be_nil
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expect(details(sn)).to eq [{ genus: { string: "Platypus" },
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species: { string: "bicaudatulus", authorship: "Schedl (1935h)",
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basionymAuthorTeam: { authorTeam: "Schedl", author: ["Schedl"],
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year: "1935" } } }]
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125
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expect(parse("Platypus bicaudatulus Schedl 1935")).to_not be_nil
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126
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end
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127
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128
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it "parses species name with abbreviated genus, author and year" do
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129
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sn = "P. bicaudatulus Schedl 1935"
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expect(parse(sn)).to_not be_nil
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expect(value(sn)).to eq "P. bicaudatulus Schedl 1935"
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sn = "Pl. bicaudatulus Schedl, 1935h"
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expect(parse(sn)).not_to be_nil
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expect(value(sn)).to eq "Pl. bicaudatulus Schedl 1935"
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expect(details(sn)).to eq [{ genus: { string: "Pl." },
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species: { string: "bicaudatulus", authorship: "Schedl, 1935h",
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137
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basionymAuthorTeam: { authorTeam: "Schedl",
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author: ["Schedl"], year: "1935" } } }]
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139
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sn = "Pla. bicaudatulus Schedl, 1935h"
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140
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expect(parse(sn)).to_not be_nil
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141
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expect(value(sn)).to eq "Pla. bicaudatulus Schedl 1935"
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142
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end
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143
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-
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144
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it "parses species name with author\'s postfix f., filius (son of)" do
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145
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names = [
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146
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["Platypus bicaudatulus Schedl f. 1935", [{ genus: { string: "Platypus" },
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147
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species: { string: "bicaudatulus", authorship: "Schedl f. 1935",
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148
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basionymAuthorTeam: { authorTeam: "Schedl f.",
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149
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author: ["Schedl f."], year: "1935" } } }],
|
150
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"Platypus bicaudatulus Schedl f. 1935"],
|
151
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["Platypus bicaudatulus Schedl filius 1935",
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152
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[{ genus: { string: "Platypus" },
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153
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species: { string: "bicaudatulus",
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154
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authorship: "Schedl filius 1935",
|
155
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basionymAuthorTeam: { authorTeam: "Schedl filius",
|
156
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author: ["Schedl filius"], year: "1935" } } }],
|
157
|
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"Platypus bicaudatulus Schedl filius 1935"],
|
158
|
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["Fimbristylis ovata (Burm. f.) J. Kern",
|
159
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[{ genus: { string: "Fimbristylis" }, species: { string: "ovata",
|
160
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authorship: "(Burm. f.) J. Kern",
|
161
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combinationAuthorTeam: { authorTeam: "J. Kern",
|
162
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author: ["J. Kern"] },
|
163
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basionymAuthorTeam: { authorTeam: "Burm. f.",
|
164
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author: ["Burm. f."] } } }], "Fimbristylis ovata (Burm. f.) J. Kern"],
|
165
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["Carex chordorrhiza Ehrh. ex L. f.",
|
166
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[{ genus: { string: "Carex" }, species: { string: "chordorrhiza",
|
167
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authorship: "Ehrh. ex L. f.",
|
168
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basionymAuthorTeam: { authorTeam: "Ehrh.",
|
169
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author: ["Ehrh."], exAuthorTeam: { authorTeam: "L. f.",
|
170
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author: ["L. f."] } } } }], "Carex chordorrhiza Ehrh. ex L. f."],
|
171
|
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["Amelanchier arborea var. arborea (Michx. f.) Fernald",
|
172
|
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[{ genus: { string: "Amelanchier" }, species: { string: "arborea"},
|
173
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infraspecies: [{ string: "arborea", rank: "var.",
|
174
|
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authorship: "(Michx. f.) Fernald", combinationAuthorTeam: {
|
175
|
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authorTeam: "Fernald", author: ["Fernald"] },
|
176
|
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basionymAuthorTeam: { authorTeam: "Michx. f.",
|
177
|
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author: ["Michx. f."] } }]}],
|
178
|
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"Amelanchier arborea var. arborea (Michx. f.) Fernald"],
|
179
|
-
["Cerastium arvense var. fuegianum Hook. f.",
|
180
|
-
[{ genus: { string: "Cerastium" }, species: { string: "arvense"},
|
181
|
-
infraspecies: [{ string: "fuegianum", rank: "var.",
|
182
|
-
authorship: "Hook. f.",
|
183
|
-
basionymAuthorTeam: { authorTeam: "Hook. f.",
|
184
|
-
author: ["Hook. f."] } }]}],
|
185
|
-
"Cerastium arvense var. fuegianum Hook. f."],
|
186
|
-
["Cerastium arvense var. fuegianum Hook.f.",
|
187
|
-
[{ genus: { string: "Cerastium" }, species: { string: "arvense"},
|
188
|
-
infraspecies: [{ string: "fuegianum", rank: "var.",
|
189
|
-
authorship: "Hook.f.", basionymAuthorTeam: {
|
190
|
-
authorTeam: "Hook.f.", author: ["Hook.f."] } }]}],
|
191
|
-
"Cerastium arvense var. fuegianum Hook.f."],
|
192
|
-
["Cerastium arvense ssp. velutinum var. velutinum (Raf.) Britton f.",
|
193
|
-
[{ genus: { string: "Cerastium" }, species: { string: "arvense"},
|
194
|
-
infraspecies: [{ string: "velutinum", rank: "ssp." },
|
195
|
-
{ string: "velutinum", rank: "var.",
|
196
|
-
authorship: "(Raf.) Britton f.",
|
197
|
-
combinationAuthorTeam: { authorTeam: "Britton f.",
|
198
|
-
author: ["Britton f."] }, basionymAuthorTeam: { authorTeam: "Raf.",
|
199
|
-
author: ["Raf."] } }]}],
|
200
|
-
"Cerastium arvense ssp. velutinum var. velutinum (Raf.) Britton f."],
|
201
|
-
["Amelanchier arborea f. hirsuta (Michx. f.) Fernald",
|
202
|
-
[{ infraspecies: [{ basionymAuthorTeam: { author: ["Michx. f."],
|
203
|
-
authorTeam: "Michx. f." }, string: "hirsuta", rank: "f.",
|
204
|
-
combinationAuthorTeam: { author: ["Fernald"], authorTeam: "Fernald" },
|
205
|
-
authorship: "(Michx. f.) Fernald" }], genus: { string: "Amelanchier"},
|
206
|
-
species: { string: "arborea" } }],
|
207
|
-
"Amelanchier arborea f. hirsuta (Michx. f.) Fernald"],
|
208
|
-
["Betula pendula fo. dalecarlica (L. f.) C.K. Schneid.",
|
209
|
-
[{ infraspecies: [{ basionymAuthorTeam: { author: ["L. f."],
|
210
|
-
authorTeam: "L. f." }, string: "dalecarlica", rank: "fo.",
|
211
|
-
combinationAuthorTeam: { author: ["C.K. Schneid."],
|
212
|
-
authorTeam: "C.K. Schneid." }, authorship: "(L. f.) C.K. Schneid."}],
|
213
|
-
genus: { string: "Betula" }, species: { string: "pendula"} }],
|
214
|
-
"Betula pendula fo. dalecarlica (L. f.) C.K. Schneid."],
|
215
|
-
["Racomitrium canescens f. ericoides (F. Weber ex Brid.) Mönk.",
|
216
|
-
[{ genus: { string: "Racomitrium" }, species: { string: "canescens"},
|
217
|
-
infraspecies: [{ string: "ericoides", rank: "f.",
|
218
|
-
authorship: "(F. Weber ex Brid.) Mönk.",
|
219
|
-
combinationAuthorTeam: { authorTeam: "Mönk.", author: ["Mönk."] },
|
220
|
-
basionymAuthorTeam: { authorTeam: "F. Weber",
|
221
|
-
author: ["F. Weber"], exAuthorTeam: { authorTeam: "Brid.",
|
222
|
-
author: ["Brid."] } } }]}],
|
223
|
-
"Racomitrium canescens f. ericoides (F. Weber ex Brid.) Mönk."],
|
224
|
-
["Racomitrium canescens forma ericoides (F. Weber ex Brid.) Mönk.",
|
225
|
-
[{ genus: { string: "Racomitrium" }, species: { string: "canescens"},
|
226
|
-
infraspecies: [{ string: "ericoides", rank: "forma",
|
227
|
-
authorship: "(F. Weber ex Brid.) Mönk.",
|
228
|
-
combinationAuthorTeam: { authorTeam: "Mönk.", author: ["Mönk."] },
|
229
|
-
basionymAuthorTeam: { authorTeam: "F. Weber", author: ["F. Weber"],
|
230
|
-
exAuthorTeam: { authorTeam: "Brid.", author: ["Brid."] } } }]}],
|
231
|
-
"Racomitrium canescens forma ericoides (F. Weber ex Brid.) Mönk."],
|
232
|
-
["Peristernia nassatula forskali Tapparone-Canefri 1875",
|
233
|
-
[{ genus: { string: "Peristernia" }, species: { string: "nassatula"},
|
234
|
-
infraspecies: [{ string: "forskali", rank: "n/a",
|
235
|
-
authorship: "Tapparone-Canefri 1875", basionymAuthorTeam: {
|
236
|
-
authorTeam: "Tapparone-Canefri", author: ["Tapparone-Canefri"],
|
237
|
-
year: "1875" } }]}],
|
238
|
-
"Peristernia nassatula forskali Tapparone-Canefri 1875"],
|
239
|
-
]
|
240
|
-
names.each do |sn, sn_details, sn_value|
|
241
|
-
expect(parse(sn)).to_not be_nil
|
242
|
-
expect(details(sn)).to eq sn_details
|
243
|
-
expect(value(sn)).to eq sn_value
|
244
|
-
end
|
245
|
-
end
|
246
|
-
|
247
|
-
it "parses genus with '?'" do
|
248
|
-
sn = "Ferganoconcha? oblonga"
|
249
|
-
expect(parse(sn)).to_not be_nil
|
250
|
-
expect(value(sn)).to eq "Ferganoconcha oblonga"
|
251
|
-
expect(details(sn)).to eq [{ genus: { string: "Ferganoconcha" },
|
252
|
-
species: { string: "oblonga" } }]
|
253
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 14], 15 => ["species", 22] })
|
254
|
-
end
|
255
|
-
|
256
|
-
it "parses æ in the name" do
|
257
|
-
names = [
|
258
|
-
["Læptura laetifica Dow, 1913", "Laeptura laetifica Dow 1913"],
|
259
|
-
["Leptura lætifica Dow, 1913", "Leptura laetifica Dow 1913"],
|
260
|
-
["Leptura leætifica Dow, 1913", "Leptura leaetifica Dow 1913"],
|
261
|
-
["Leæptura laetifica Dow, 1913", "Leaeptura laetifica Dow 1913"],
|
262
|
-
["Leœptura laetifica Dow, 1913", "Leoeptura laetifica Dow 1913"],
|
263
|
-
["Ærenea cognata Lacordaire, 1872", "Aerenea cognata Lacordaire 1872"],
|
264
|
-
["Œdicnemus capensis", "Oedicnemus capensis"],
|
265
|
-
["Œnanthæ œnanthe","Oenanthae oenanthe"],
|
266
|
-
["Œnanthe œnanthe","Oenanthe oenanthe"],
|
267
|
-
["Cerambyx thomæ Gmelin J. F., 1790", "Cerambyx thomae Gmelin J. F. 1790"]
|
268
|
-
]
|
269
|
-
names.each do |name_pair|
|
270
|
-
expect(parse(name_pair[0])).to_not be_nil
|
271
|
-
expect(value(name_pair[0])).to eq name_pair[1]
|
272
|
-
end
|
273
|
-
end
|
274
|
-
|
275
|
-
it "parses names with e-umlaut" do
|
276
|
-
sn = "Kalanchoë tuberosa"
|
277
|
-
expect(canonical(sn)).to eq "Kalanchoe tuberosa"
|
278
|
-
sn = "Isoëtes asplundii H. P. Fuchs"
|
279
|
-
expect(canonical(sn)).to eq "Isoetes asplundii"
|
280
|
-
end
|
281
|
-
|
282
|
-
it "parses infragenus (ICZN code)" do
|
283
|
-
sn = "Hegeter (Hegeter) intercedens Lindberg H 1950"
|
284
|
-
expect(parse(sn)).to_not be_nil
|
285
|
-
expect(value(sn)).to eq "Hegeter (Hegeter) intercedens Lindberg H 1950"
|
286
|
-
expect(canonical(sn)).to eq "Hegeter intercedens"
|
287
|
-
expect(details(sn)).to eq [{ genus: { string: "Hegeter" },
|
288
|
-
infragenus: { string: "Hegeter" }, species: { string: "intercedens",
|
289
|
-
authorship: "Lindberg H 1950",
|
290
|
-
basionymAuthorTeam: { authorTeam: "Lindberg H",
|
291
|
-
author: ["Lindberg H"], year: "1950" } } }]
|
292
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 7], 9 => ["infragenus", 16],
|
293
|
-
18 => ["species", 29], 30 => ["author_word", 38],
|
294
|
-
39 => ["author_word", 40], 41 => ["year", 45] })
|
295
|
-
sn = "Ixodes (Ixodes) hexagonus hexagonus Neumann, 1911"
|
296
|
-
expect(canonical(sn)).to eq "Ixodes hexagonus hexagonus"
|
297
|
-
sn = "Brachytrypus (B.) grandidieri"
|
298
|
-
expect(canonical(sn)).to eq "Brachytrypus grandidieri"
|
299
|
-
expect(details(sn)).to eq [{ genus: { string: "Brachytrypus" },
|
300
|
-
infragenus: { string: "B." }, species: { string: "grandidieri"} }]
|
301
|
-
sn = "Empis (Argyrandrus) Bezzi 1909"
|
302
|
-
expect(details(sn)).to eq [{ uninomial: { string: "Empis",
|
303
|
-
infragenus: { string: "Argyrandrus" }, authorship: "Bezzi 1909",
|
304
|
-
basionymAuthorTeam: { authorTeam: "Bezzi",
|
305
|
-
author: ["Bezzi"], year: "1909" } } }]
|
306
|
-
sn = "Platydoris (Bergh )"
|
307
|
-
expect(details(sn)).to eq [{ uninomial: { string: "Platydoris",
|
308
|
-
infragenus: { string: "Bergh" } } }]
|
309
|
-
expect(value(sn)).to eq "Platydoris (Bergh)"
|
310
|
-
sn = "Platydoris (B.)"
|
311
|
-
expect(details(sn)).to eq [{ uninomial: { string: "Platydoris",
|
312
|
-
infragenus: { string: "B." } } }]
|
313
|
-
end
|
314
|
-
|
315
|
-
it "parses several authors without a year" do
|
316
|
-
sn = "Pseudocercospora dendrobii U. Braun & Crous"
|
317
|
-
expect(parse(sn)).to_not be be_nil
|
318
|
-
expect(value(sn)).to eq "Pseudocercospora dendrobii U. Braun & Crous"
|
319
|
-
expect(canonical(sn)).to eq "Pseudocercospora dendrobii"
|
320
|
-
expect(details(sn)).to eq [{ genus: { string: "Pseudocercospora" },
|
321
|
-
species: { string: "dendrobii", authorship: "U. Braun & Crous",
|
322
|
-
basionymAuthorTeam: { authorTeam: "U. Braun & Crous",
|
323
|
-
author: ["U. Braun", "Crous"] } } }]
|
324
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 16], 17 => ["species", 26],
|
325
|
-
27 => ["author_word", 29], 30 => ["author_word", 35],
|
326
|
-
38 => ["author_word", 43] })
|
327
|
-
sn = "Pseudocercospora dendrobii U. Braun and Crous"
|
328
|
-
expect(parse(sn)).to_not be_nil
|
329
|
-
expect(value(sn)).to eq "Pseudocercospora dendrobii U. Braun & Crous"
|
330
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 16], 17 => ["species", 26],
|
331
|
-
27 => ["author_word", 29], 30 => ["author_word", 35],
|
332
|
-
40 => ["author_word", 45] })
|
333
|
-
sn = "Pseudocercospora dendrobii U. Braun et Crous"
|
334
|
-
expect(parse(sn)).to_not be_nil
|
335
|
-
expect(value(sn)).to eq "Pseudocercospora dendrobii U. Braun & Crous"
|
336
|
-
sn = "Arthopyrenia hyalospora(Nyl.)R.C. Harris"
|
337
|
-
expect(parse(sn)).to_not be_nil
|
338
|
-
expect(value(sn)).to eq "Arthopyrenia hyalospora (Nyl.) R.C. Harris"
|
339
|
-
expect(canonical(sn)).to eq "Arthopyrenia hyalospora"
|
340
|
-
expect(details(sn)).to eq [{ genus: { string: "Arthopyrenia" },
|
341
|
-
species: { string: "hyalospora", authorship: "(Nyl.)R.C. Harris",
|
342
|
-
combinationAuthorTeam: { authorTeam: "R.C. Harris",
|
343
|
-
author: ["R.C. Harris"] },
|
344
|
-
basionymAuthorTeam: { authorTeam: "Nyl.", author: ["Nyl."] } } }]
|
345
|
-
end
|
346
|
-
|
347
|
-
it "parses several authors with a year" do
|
348
|
-
sn = "Pseudocercospora dendrobii U. Braun & Crous 2003"
|
349
|
-
expect(parse(sn)).to_not be_nil
|
350
|
-
expect(value(sn)).to eq "Pseudocercospora dendrobii U. Braun & Crous 2003"
|
351
|
-
expect(canonical(sn)).to eq "Pseudocercospora dendrobii"
|
352
|
-
expect(details(sn)).to eq [{ genus: { string: "Pseudocercospora" },
|
353
|
-
species: { string: "dendrobii", authorship: "U. Braun & Crous 2003",
|
354
|
-
basionymAuthorTeam: { authorTeam: "U. Braun & Crous",
|
355
|
-
author: ["U. Braun", "Crous"], year: "2003" } } }]
|
356
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 16], 17 => ["species", 26],
|
357
|
-
27 => ["author_word", 29], 30 => ["author_word", 35],
|
358
|
-
38 => ["author_word", 43], 44 => ["year", 48] })
|
359
|
-
sn = "Pseudocercospora dendrobii Crous, 2003"
|
360
|
-
expect(parse(sn)).to_not be_nil
|
361
|
-
end
|
362
|
-
|
363
|
-
it "parses basionym authors in parenthesis" do
|
364
|
-
sn = "Zophosis persis (Chatanay, 1914)"
|
365
|
-
expect(parse(sn)).to_not be_nil
|
366
|
-
expect(details(sn)).to eq [{ genus: { string: "Zophosis" },
|
367
|
-
species: { string: "persis", authorship: "(Chatanay, 1914)",
|
368
|
-
basionymAuthorTeam: { authorTeam: "Chatanay",
|
369
|
-
author: ["Chatanay"], year: "1914" } } }]
|
370
|
-
sn = "Zophosis persis (Chatanay 1914)"
|
371
|
-
expect(parse(sn)).to_not be_nil
|
372
|
-
expect(details(sn)).to eq [{ genus: { string: "Zophosis" },
|
373
|
-
species: { string: "persis", authorship: "(Chatanay 1914)",
|
374
|
-
basionymAuthorTeam: { authorTeam: "Chatanay",
|
375
|
-
author: ["Chatanay"], year: "1914" } } }]
|
376
|
-
sn = "Zophosis persis (Chatanay), 1914"
|
377
|
-
expect(parse(sn)).to_not be_nil
|
378
|
-
expect(value(sn)).to eq "Zophosis persis (Chatanay 1914)"
|
379
|
-
expect(details(sn)).to eq [{ genus: { string: "Zophosis" },
|
380
|
-
species: { string: "persis", authorship: "(Chatanay), 1914",
|
381
|
-
basionymAuthorTeam: { author_team: "(Chatanay), 1914",
|
382
|
-
author: ["Chatanay"], year: "1914" } } }]
|
383
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 8], 9 => ["species", 15],
|
384
|
-
17 => ["author_word", 25], 28 => ["year", 32] })
|
385
|
-
expect(parse("Zophosis persis (Chatanay) 1914")).to_not be_nil
|
386
|
-
#parse("Zophosis persis Chatanay (1914)")).to_not be_nil
|
387
|
-
end
|
388
|
-
|
389
|
-
it "parses name with identificaation annotation -- aff cf sp spp" do
|
390
|
-
sn = "Diplocephalus aff. procerus Thaler, 1972"
|
391
|
-
expect(details(sn)).to eq [{ genus: { string: "Diplocephalus" },
|
392
|
-
annotation_identification: "aff.",
|
393
|
-
ignored: { species: { string: "procerus", authorship: "Thaler, 1972",
|
394
|
-
basionymAuthorTeam: { authorTeam: "Thaler",
|
395
|
-
author: ["Thaler"], year: "1972" } } } }]
|
396
|
-
sn = "Diplocephalus aff procerus Thaler, 1972"
|
397
|
-
expect(details(sn)).to eq [{ genus: { string: "Diplocephalus" },
|
398
|
-
annotation_identification: "aff", ignored: { species:
|
399
|
-
{ string: "procerus", authorship: "Thaler, 1972",
|
400
|
-
basionymAuthorTeam: { authorTeam: "Thaler",
|
401
|
-
author: ["Thaler"], year: "1972" } } } }]
|
402
|
-
sn = "Diplocephalus affprocerus Thaler, 1972"
|
403
|
-
expect(details(sn)).to eq [{ genus: { string: "Diplocephalus" },
|
404
|
-
species: { string: "affprocerus", authorship: "Thaler, 1972",
|
405
|
-
basionymAuthorTeam: { authorTeam: "Thaler",
|
406
|
-
author: ["Thaler"], year: "1972" } } }]
|
407
|
-
sn = "Diplocephalus cf. procerus Thaler, 1972"
|
408
|
-
expect(details(sn)).to eq [{ genus: { string: "Diplocephalus" },
|
409
|
-
annotation_identification: "cf.", species: { species:
|
410
|
-
{ string: "procerus", authorship: "Thaler, 1972",
|
411
|
-
basionymAuthorTeam: { authorTeam: "Thaler",
|
412
|
-
author: ["Thaler"], year: "1972" } } } }]
|
413
|
-
sn = "Diplocephalus cf procerus Thaler, 1972"
|
414
|
-
expect(details(sn)).to eq [{ genus: { string: "Diplocephalus" },
|
415
|
-
annotation_identification: "cf", species:
|
416
|
-
{ species: { string: "procerus", authorship: "Thaler, 1972",
|
417
|
-
basionymAuthorTeam: { authorTeam: "Thaler",
|
418
|
-
author: ["Thaler"], year: "1972" } } } }]
|
419
|
-
sn = "Sphingomonas sp. 37"
|
420
|
-
expect(details(sn)).to eq [{ genus: { string: "Sphingomonas" },
|
421
|
-
annotation_identification: "sp.", ignored: { unparsed: "37" } }]
|
422
|
-
sn = "Thryothorus leucotis spp. bogotensis"
|
423
|
-
expect(details(sn)).to eq [{ genus: { string: "Thryothorus" },
|
424
|
-
species: { string: "leucotis" }, infraspecies:
|
425
|
-
[{ annotation_identification: "spp.",
|
426
|
-
ignored: { infraspecies: { string: "bogotensis", rank: "n/a" } } }]}]
|
427
|
-
end
|
428
|
-
|
429
|
-
it "parses scientific name" do
|
430
|
-
sn = "Pseudocercospora dendrobii(H.C. Burnett)U. Braun & Crous 2003"
|
431
|
-
expect(parse(sn)).to_not be_nil
|
432
|
-
expect(value(sn)).to eq "Pseudocercospora dendrobii (H.C. Burnett) "\
|
433
|
-
"U. Braun & Crous 2003"
|
434
|
-
expect(canonical(sn)).to eq "Pseudocercospora dendrobii"
|
435
|
-
expect(details(sn)).to eq [{ genus: { string: "Pseudocercospora" },
|
436
|
-
species: { string: "dendrobii",
|
437
|
-
authorship: "(H.C. Burnett)U. Braun & Crous 2003",
|
438
|
-
combinationAuthorTeam: { authorTeam: "U. Braun & Crous",
|
439
|
-
author: ["U. Braun", "Crous"], year: "2003" },
|
440
|
-
basionymAuthorTeam: { authorTeam: "H.C. Burnett",
|
441
|
-
author: ["H.C. Burnett"] } } }]
|
442
|
-
sn = "Pseudocercospora dendrobii(H.C. Burnett,1873)"\
|
443
|
-
"U. Braun & Crous 2003"
|
444
|
-
expect(parse(sn)).to_not be_nil
|
445
|
-
expect(value(sn)).to eq "Pseudocercospora dendrobii (H.C. Burnett 1873) "\
|
446
|
-
"U. Braun & Crous 2003"
|
447
|
-
expect(details(sn)).to eq [{ genus: { string: "Pseudocercospora" },
|
448
|
-
species: { string: "dendrobii",
|
449
|
-
authorship: "(H.C. Burnett,1873)U. Braun & Crous 2003",
|
450
|
-
combinationAuthorTeam: { authorTeam: "U. Braun & Crous",
|
451
|
-
author: ["U. Braun", "Crous"], year: "2003" },
|
452
|
-
basionymAuthorTeam: { authorTeam: "H.C. Burnett",
|
453
|
-
author: ["H.C. Burnett"], year: "1873" } } }]
|
454
|
-
end
|
455
|
-
|
456
|
-
it "parses several authors with several years" do
|
457
|
-
sn = "Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003"
|
458
|
-
expect(parse(sn)).to_not be_nil
|
459
|
-
expect(value(sn)).to eq "Pseudocercospora dendrobii (H.C. Burnett 1883) "\
|
460
|
-
"U. Braun & Crous 2003"
|
461
|
-
expect(canonical(sn)).to eq "Pseudocercospora dendrobii"
|
462
|
-
expect(details(sn)).to eq [{ genus: { string: "Pseudocercospora" },
|
463
|
-
species: { string: "dendrobii",
|
464
|
-
authorship: "(H.C. Burnett 1883) U. Braun & Crous 2003",
|
465
|
-
combinationAuthorTeam: { authorTeam: "U. Braun & Crous",
|
466
|
-
author: ["U. Braun", "Crous"], year: "2003" },
|
467
|
-
basionymAuthorTeam: { authorTeam: "H.C. Burnett",
|
468
|
-
author: ["H.C. Burnett"], year: "1883" } } }]
|
469
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 16], 17 => ["species", 26],
|
470
|
-
28 => ["author_word", 32], 33 => ["author_word", 40],
|
471
|
-
41 => ["year", 45], 47 => ["author_word", 49],
|
472
|
-
50 => ["author_word", 55], 58 => ["author_word", 63],
|
473
|
-
64 => ["year", 68] })
|
474
|
-
end
|
475
|
-
|
476
|
-
it "parses name with subspecies without rank Zoological Code" do
|
477
|
-
sn = "Hydnellum scrobiculatum zonatum (Banker) D. Hall & D.E. Stuntz 1972"
|
478
|
-
expect(parse(sn)).to_not be_nil
|
479
|
-
expect(value(sn)).to eq "Hydnellum scrobiculatum zonatum (Banker) "\
|
480
|
-
"D. Hall & D.E. Stuntz 1972"
|
481
|
-
expect(canonical(sn)).to eq "Hydnellum scrobiculatum zonatum"
|
482
|
-
expect(details(sn)).to eq [{ genus: { string: "Hydnellum" },
|
483
|
-
species: { string: "scrobiculatum" },
|
484
|
-
infraspecies: [{ string: "zonatum", rank: "n/a",
|
485
|
-
authorship: "(Banker) D. Hall & D.E. Stuntz 1972",
|
486
|
-
combinationAuthorTeam: { authorTeam: "D. Hall & D.E. Stuntz",
|
487
|
-
author: ["D. Hall", "D.E. Stuntz"], year: "1972" },
|
488
|
-
basionymAuthorTeam: { authorTeam: "Banker", author: ["Banker"] } }]}]
|
489
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 9], 10 => ["species", 23],
|
490
|
-
24 => ["infraspecies", 31], 33 => ["author_word", 39],
|
491
|
-
41 => ["author_word", 43], 44 => ["author_word", 48],
|
492
|
-
51 => ["author_word", 55], 56 => ["author_word", 62],
|
493
|
-
63 => ["year", 67] })
|
494
|
-
sn = "Begonia pingbienensis angustior"
|
495
|
-
expect(parse(sn)).to_not be_nil
|
496
|
-
expect(details(sn)).to eq [{ genus: { string: "Begonia" },
|
497
|
-
species: { string: "pingbienensis" },
|
498
|
-
infraspecies: [{ string: "angustior", rank: "n/a" }]}]
|
499
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 7],
|
500
|
-
8 => ["species", 21], 22 => ["infraspecies", 31] })
|
501
|
-
end
|
502
|
-
|
503
|
-
it "parses infraspecies with rank" do
|
504
|
-
sn = "Aus bus Linn. var. bus"
|
505
|
-
expect(parse(sn)).to_not be_nil
|
506
|
-
expect(details(sn)).to eq [{ genus: { string: "Aus" },
|
507
|
-
species: { string: "bus", authorship: "Linn.",
|
508
|
-
basionymAuthorTeam: { authorTeam: "Linn.",
|
509
|
-
author: ["Linn."] } }, infraspecies: [{ string: "bus", rank: "var."}]}]
|
510
|
-
sn = "Agalinis purpurea (L.) Briton var. borealis (Berg.) Peterson 1987"
|
511
|
-
expect(parse(sn)).to_not be_nil
|
512
|
-
expect(details(sn)).to eq [{ genus: { string: "Agalinis" },
|
513
|
-
species: { string: "purpurea", authorship: "(L.) Briton",
|
514
|
-
combinationAuthorTeam: { authorTeam: "Briton", author: ["Briton"] },
|
515
|
-
basionymAuthorTeam: { authorTeam: "L.",
|
516
|
-
author: ["L."] } }, infraspecies: [{ string: "borealis",
|
517
|
-
rank: "var.", authorship: "(Berg.) Peterson 1987",
|
518
|
-
combinationAuthorTeam: { authorTeam: "Peterson",
|
519
|
-
author: ["Peterson"], year: "1987" },
|
520
|
-
basionymAuthorTeam: { authorTeam: "Berg.", author: ["Berg."] } }]}]
|
521
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 8], 9 => ["species", 17],
|
522
|
-
19 => ["author_word", 21], 23 => ["author_word", 29],
|
523
|
-
30 => ["infraspecific_type", 34], 35 => ["infraspecies", 43],
|
524
|
-
45 => ["author_word", 50], 52 => ["author_word", 60],
|
525
|
-
61 => ["year", 65] })
|
526
|
-
sn = "Phaeographis inusta var. macularis(Leight.) A.L. Sm. 1861"
|
527
|
-
expect(parse(sn)).to_not be_nil
|
528
|
-
expect(value(sn)).to eq "Phaeographis inusta var. macularis (Leight.) "\
|
529
|
-
"A.L. Sm. 1861"
|
530
|
-
expect(canonical(sn)).to eq "Phaeographis inusta macularis"
|
531
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 12], 13 => ["species", 19],
|
532
|
-
20 => ["infraspecific_type", 24], 25 => ["infraspecies", 34],
|
533
|
-
35 => ["author_word", 42], 44 => ["author_word", 48],
|
534
|
-
49 => ["author_word", 52], 53 => ["year", 57] })
|
535
|
-
sn = "Cassytha peninsularis J. Z. Weber var. flindersii"
|
536
|
-
expect(canonical(sn)).to eq "Cassytha peninsularis flindersii"
|
537
|
-
sn = "Prunus armeniaca convar. budae (Pénzes) Soó"
|
538
|
-
|
539
|
-
expect(canonical(sn)).to eq "Prunus armeniaca budae"
|
540
|
-
sn = "Polypodium pectinatum L. f. typica Rosenst."
|
541
|
-
expect(canonical(sn)).to eq "Polypodium pectinatum typica"
|
542
|
-
# might get confused with forma vs filius
|
543
|
-
sn = "Polypodium pectinatum L.f. typica Rosenst."
|
544
|
-
expect(canonical(sn)).to eq "Polypodium pectinatum typica"
|
545
|
-
sn = "Polypodium pectinatum (L.) f. typica Rosenst."
|
546
|
-
expect(canonical(sn)).to eq "Polypodium pectinatum typica"
|
547
|
-
sn = "Polypodium pectinatum L. f., Rosenst."
|
548
|
-
expect(canonical(sn)).to eq "Polypodium pectinatum"
|
549
|
-
sn = "Polypodium pectinatum L. f."
|
550
|
-
expect(canonical(sn)).to eq "Polypodium pectinatum"
|
551
|
-
sn = "Polypodium pectinatum (L. f.) typica Rosent."
|
552
|
-
expect(canonical(sn)).to eq "Polypodium pectinatum typica"
|
553
|
-
sn = "Polypodium pectinatum L. f. thisisjunk Rosent."
|
554
|
-
expect(canonical(sn)).to eq "Polypodium pectinatum thisisjunk"
|
555
|
-
end
|
556
|
-
|
557
|
-
it "parsex unknown original authors (auct.)/(hort.)/(?)" do
|
558
|
-
sn = "Tragacantha leporina (?) Kuntze"
|
559
|
-
expect(parse(sn)).to_not be_nil
|
560
|
-
expect(value(sn)).to eq "Tragacantha leporina (?) Kuntze"
|
561
|
-
expect(details(sn)).to eq [{ genus: { string: "Tragacantha" },
|
562
|
-
species: { string: "leporina", authorship: "(?) Kuntze",
|
563
|
-
combinationAuthorTeam: { authorTeam: "Kuntze", author: ["Kuntze"] },
|
564
|
-
basionymAuthorTeam: { authorTeam: "(?)", author: ["?"] } } }]
|
565
|
-
sn = "Lachenalia tricolor var. nelsonii (auct.) Baker"
|
566
|
-
expect(parse(sn)).to_not be_nil
|
567
|
-
expect(value(sn)).to eq "Lachenalia tricolor var. nelsonii (auct.) Baker"
|
568
|
-
expect(details(sn)).to eq [{ genus: { string: "Lachenalia" },
|
569
|
-
species: { string: "tricolor" }, infraspecies: [{ string: "nelsonii",
|
570
|
-
rank: "var.", authorship: "(auct.) Baker",
|
571
|
-
combinationAuthorTeam: { authorTeam: "Baker",
|
572
|
-
author: ["Baker"] }, basionymAuthorTeam:
|
573
|
-
{ authorTeam: "auct.", author: ["unknown"] } }]}]
|
574
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 10], 11 => ["species", 19],
|
575
|
-
20 => ["infraspecific_type", 24], 25 => ["infraspecies", 33],
|
576
|
-
35 => ["unknown_author", 40], 42 => ["author_word", 47] })
|
577
|
-
end
|
578
|
-
|
579
|
-
it "parses unknown authors auct./anon./hort./ht." do
|
580
|
-
sn = "Puya acris ht."
|
581
|
-
expect(parse(sn)).to_not be_nil
|
582
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 4], 5 => ["species", 10],
|
583
|
-
11 => ["unknown_author", 14] })
|
584
|
-
end
|
585
|
-
|
586
|
-
it "parses normal names with hort or anon in them" do
|
587
|
-
sn = "Mus musculus hortulanus"
|
588
|
-
expect(parse(sn)).to_not be_nil
|
589
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 3], 4 => ["species", 12],
|
590
|
-
13 => ["infraspecies", 23] })
|
591
|
-
end
|
592
|
-
|
593
|
-
it "parses real world examples" do
|
594
|
-
sn = "Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934"
|
595
|
-
expect(parse(sn)).to_not be_nil
|
596
|
-
expect(value(sn)).
|
597
|
-
to eq "Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934"
|
598
|
-
expect(details(sn)).to eq [{ genus: { string: "Stagonospora" },
|
599
|
-
species: { string: "polyspora",
|
600
|
-
authorship: "M.T. Lucas & Sousa da Câmara 1934", basionymAuthorTeam:
|
601
|
-
{ authorTeam: "M.T. Lucas & Sousa da Câmara",
|
602
|
-
author: ["M.T. Lucas", "Sousa da Câmara"], year: "1934"} } }]
|
603
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 12], 13 => ["species", 22],
|
604
|
-
23 => ["author_word", 27], 28 => ["author_word", 33],
|
605
|
-
36 => ["author_word", 41], 42 => ["author_word", 44],
|
606
|
-
45 => ["author_word", 51], 52 => ["year", 56] })
|
607
|
-
expect(parse("Cladoniicola staurospora Diederich, "\
|
608
|
-
"van den Boom & Aptroot 2001")).to_not be_nil
|
609
|
-
sn = "Yarrowia lipolytica var. lipolytica (Wick., Kurtzman & E.A. Herrm.) "\
|
610
|
-
"Van der Walt & Arx 1981"
|
611
|
-
expect(parse(sn)).to_not be_nil
|
612
|
-
expect(value(sn)).to eq "Yarrowia lipolytica var. lipolytica "\
|
613
|
-
"(Wick., Kurtzman & E.A. Herrm.) Van der Walt & Arx 1981"
|
614
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 8], 9 => ["species", 19],
|
615
|
-
20 => ["infraspecific_type", 24], 25 => ["infraspecies", 35],
|
616
|
-
37 => ["author_word", 42], 44 => ["author_word", 52],
|
617
|
-
55 => ["author_word", 59], 60 => ["author_word", 66],
|
618
|
-
68 => ["author_word", 71], 72 => ["author_word", 75],
|
619
|
-
76 => ["author_word", 80], 83 => ["author_word", 86],
|
620
|
-
87 => ["year", 91] })
|
621
|
-
expect(parse("Physalospora rubiginosa (Fr.) anon.")).to_not be_nil
|
622
|
-
expect(parse("Pleurotus ëous (Berk.) Sacc. 1887")).to_not be_nil
|
623
|
-
expect(parse("Lecanora wetmorei Śliwa 2004")).to_not be_nil
|
624
|
-
# valid
|
625
|
-
# infraspecific
|
626
|
-
expect(parse("Calicium furfuraceum * furfuraceum (L.) Pers. 1797")).
|
627
|
-
to_not be_nil
|
628
|
-
expect(parse("Exobasidium vaccinii ** andromedae (P. Karst.) "\
|
629
|
-
"P. Karst. 1882")).to_not be_nil
|
630
|
-
expect(parse("Urceolaria scruposa **** clausa Flot. 1849")).to_not be_nil
|
631
|
-
expect(parse("Cortinarius angulatus B gracilescens Fr. 1838")).to_not be_nil
|
632
|
-
expect(parse("Cyathicula scelobelonium")).to_not be_nil
|
633
|
-
# single quote that did not show
|
634
|
-
# parse("Phytophthora hedraiandra De Cock & Man in ?t Veld 2004"
|
635
|
-
# Phthora vastatrix d?Hérelle 1909
|
636
|
-
# author is exception
|
637
|
-
sn = "Tuber liui A S. Xu 1999"
|
638
|
-
expect(parse(sn)).to_not be_nil
|
639
|
-
expect(details(sn)).to eq [{ genus: { string: "Tuber" },
|
640
|
-
species: { string: "liui", authorship: "A S. Xu 1999",
|
641
|
-
basionymAuthorTeam: { authorTeam: "A S. Xu",
|
642
|
-
author: ["A S. Xu"], year: "1999"} } }]
|
643
|
-
expect(parse("Xylaria potentillae A S. Xu")).to_not be_nil
|
644
|
-
expect(parse("Agaricus squamula Berk. & M.A. Curtis 1860")).to_not be_nil
|
645
|
-
expect(parse("Peltula coriacea Büdel, Henssen & Wessels 1986")).
|
646
|
-
to_not be_nil
|
647
|
-
#had to add no dot rule for trinomials without a rank to make it to work
|
648
|
-
sn = "Saccharomyces drosophilae anon."
|
649
|
-
expect(parse(sn)).to_not be_nil
|
650
|
-
expect(details(sn)).to eq [{ genus: { string: "Saccharomyces" },
|
651
|
-
species: { string: "drosophilae", authorship: "anon.",
|
652
|
-
basionymAuthorTeam: { authorTeam: "anon.", author: ["unknown"]} } }]
|
653
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 13],
|
654
|
-
14 => ["species", 25],
|
655
|
-
26 => ["unknown_author", 31] })
|
656
|
-
sn = "Abacetus laevicollis de Chaudoir, 1869"
|
657
|
-
expect(parse(sn)).to_not be_nil
|
658
|
-
expect(canonical(sn)).to eq "Abacetus laevicollis"
|
659
|
-
sn = "Gastrosericus eremorum van Beaumont 1955"
|
660
|
-
expect(canonical(sn)).to eq "Gastrosericus eremorum"
|
661
|
-
sn = "Gastrosericus eremorum von Beaumont 1955"
|
662
|
-
expect(canonical(sn)).to eq "Gastrosericus eremorum"
|
663
|
-
sn = "Cypraeovula (Luponia) amphithales perdentata"
|
664
|
-
expect(canonical(sn)).to eq "Cypraeovula amphithales perdentata"
|
665
|
-
expect(details(sn)).to eq [{ genus: { string: "Cypraeovula" },
|
666
|
-
infragenus: { string: "Luponia"}, species: { string: "amphithales"},
|
667
|
-
infraspecies: [{ string: "perdentata", rank: "n/a"}]}]
|
668
|
-
sn = "Polyrhachis orsyllus nat musculus Forel 1901"
|
669
|
-
expect(canonical(sn)).to eq "Polyrhachis orsyllus musculus"
|
670
|
-
sn = "Latrodectus 13-guttatus Thorell, 1875"
|
671
|
-
expect(canonical(sn)).to eq "Latrodectus tredecguttatus"
|
672
|
-
expect(value(sn)).to eq "Latrodectus tredecguttatus Thorell 1875"
|
673
|
-
sn = "Latrodectus 3-guttatus Thorell, 1875"
|
674
|
-
expect(canonical(sn)).to eq "Latrodectus triguttatus"
|
675
|
-
expect(value(sn)).to eq "Latrodectus triguttatus Thorell 1875"
|
676
|
-
sn = "Balaninus c-album Schönherr, CJ., 1836"
|
677
|
-
expect(canonical(sn)).to eq "Balaninus c-album"
|
678
|
-
end
|
679
|
-
|
680
|
-
it "parses name with morph." do
|
681
|
-
sn = "Callideriphus flavicollis morph. reductus Fuchs 1961"
|
682
|
-
expect(parse(sn)).to_not be_nil
|
683
|
-
expect(value(sn)).
|
684
|
-
to eq "Callideriphus flavicollis morph. reductus Fuchs 1961"
|
685
|
-
expect(canonical(sn)).to eq "Callideriphus flavicollis reductus"
|
686
|
-
expect(details(sn)).to eq [{ genus: { string: "Callideriphus" },
|
687
|
-
species: { string: "flavicollis"}, infraspecies: [{ string: "reductus",
|
688
|
-
rank: "morph.", authorship: "Fuchs 1961", basionymAuthorTeam:
|
689
|
-
{ authorTeam: "Fuchs", author: ["Fuchs"], year: "1961"} }]}]
|
690
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 13], 14 => ["species", 25],
|
691
|
-
26 => ["infraspecific_type", 32],
|
692
|
-
33 => ["infraspecies", 41],
|
693
|
-
42 => ["author_word", 47], 48 => ["year", 52] })
|
694
|
-
end
|
695
|
-
|
696
|
-
|
697
|
-
it "parses name with forma/fo./form./f." do
|
698
|
-
sn = "Caulerpa cupressoides forma nuda"
|
699
|
-
expect(parse(sn)).to_not be_nil
|
700
|
-
expect(value(sn)).to eq "Caulerpa cupressoides forma nuda"
|
701
|
-
expect(canonical(sn)).to eq "Caulerpa cupressoides nuda"
|
702
|
-
expect(details(sn)).to eq [{ genus: { string: "Caulerpa" },
|
703
|
-
species: { string: "cupressoides"},
|
704
|
-
infraspecies: [{ string: "nuda", rank: "forma"}]}]
|
705
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 8], 9 => ["species", 21],
|
706
|
-
22 => ["infraspecific_type", 27],
|
707
|
-
28 => ["infraspecies", 32] })
|
708
|
-
sn = "Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó"
|
709
|
-
expect(parse(sn)).to_not be_nil
|
710
|
-
expect(value("Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó")).
|
711
|
-
to eq "Chlorocyperus glaber form. fasciculariforme (Lojac.) Soó"
|
712
|
-
expect(canonical(sn)).to eq "Chlorocyperus glaber fasciculariforme"
|
713
|
-
expect(details(sn)).to eq [{ genus: { string: "Chlorocyperus" },
|
714
|
-
species: { string: "glaber"}, infraspecies:
|
715
|
-
[{ string: "fasciculariforme", rank: "form.",
|
716
|
-
authorship: "(Lojac.) Soó", combinationAuthorTeam: { authorTeam: "Soó",
|
717
|
-
author: ["Soó"]}, basionymAuthorTeam: { authorTeam: "Lojac.",
|
718
|
-
author: ["Lojac."]} }]}]
|
719
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 13], 14 => ["species", 20],
|
720
|
-
21 => ["infraspecific_type", 26],
|
721
|
-
27 => ["infraspecies", 43],
|
722
|
-
45 => ["author_word", 51],
|
723
|
-
53 => ["author_word", 56] })
|
724
|
-
sn = "Bambusa nana Roxb. fo. alphonse-karri (Mitford ex Satow) "\
|
725
|
-
"Makino ex Shiros."
|
726
|
-
expect(parse(sn)).to_not be_nil
|
727
|
-
expect(value(sn)).to eq "Bambusa nana Roxb. fo. alphonse-karri "\
|
728
|
-
"(Mitford ex Satow) Makino ex Shiros."
|
729
|
-
expect(canonical(sn)).to eq "Bambusa nana alphonse-karri"
|
730
|
-
expect(details(sn)).to eq [{ genus: { string: "Bambusa" },
|
731
|
-
species: { string: "nana", authorship: "Roxb.", basionymAuthorTeam:
|
732
|
-
{ authorTeam: "Roxb.", author: ["Roxb."]} },
|
733
|
-
infraspecies: [{ string: "alphonse-karri",
|
734
|
-
rank: "fo.", authorship: "(Mitford ex Satow) Makino ex Shiros.",
|
735
|
-
combinationAuthorTeam: { authorTeam: "Makino",
|
736
|
-
author: ["Makino"], exAuthorTeam: { authorTeam: "Shiros.",
|
737
|
-
author: ["Shiros."]} }, basionymAuthorTeam: { authorTeam: "Mitford",
|
738
|
-
author: ["Mitford"], exAuthorTeam: { authorTeam: "Satow",
|
739
|
-
author: ["Satow"]} } }]}]
|
740
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 7], 8 => ["species", 12],
|
741
|
-
13 => ["author_word", 18], 19 => ["infraspecific_type", 22],
|
742
|
-
23 => ["infraspecies", 37], 39 => ["author_word", 46],
|
743
|
-
50 => ["author_word", 55], 57 => ["author_word", 63],
|
744
|
-
67 => ["author_word", 74] })
|
745
|
-
sn = " Sphaerotheca fuliginea f. dahliae Movss. 1967 "
|
746
|
-
sn = "Sphaerotheca fuliginea f. dahliae Movss. 1967"
|
747
|
-
expect(parse(sn)).to_not be_nil
|
748
|
-
expect(value(sn)).to eq "Sphaerotheca fuliginea f. dahliae Movss. 1967"
|
749
|
-
expect(canonical(sn)).to eq "Sphaerotheca fuliginea dahliae"
|
750
|
-
expect(details(sn)).to eq [{ genus: { string: "Sphaerotheca" },
|
751
|
-
species: { string: "fuliginea"}, infraspecies:
|
752
|
-
[{ string: "dahliae", rank: "f.", authorship: "Movss. 1967",
|
753
|
-
basionymAuthorTeam: { authorTeam: "Movss.",
|
754
|
-
author: ["Movss."], year: "1967"} }]}]
|
755
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 12], 16 => ["species", 25],
|
756
|
-
29 => ["infraspecific_type", 31], 36 => ["infraspecies", 43],
|
757
|
-
47 => ["author_word", 53], 58 => ["year", 62] })
|
758
|
-
expect(parse("Polypodium vulgare nothosubsp. mantoniae (Rothm.) Schidlay")).
|
759
|
-
to_not be_nil
|
760
|
-
end
|
761
|
-
|
762
|
-
it "parses name with several subspecies names" do
|
763
|
-
# NOT BOTANICAL CODE BUT NOT INFREQUENT"
|
764
|
-
sn = "Hydnellum scrobiculatum var. zonatum f. "\
|
765
|
-
"parvum (Banker) D. Hall & D.E. Stuntz 1972"
|
766
|
-
expect(parse(sn)).to_not be_nil
|
767
|
-
expect(value(sn)).to eq "Hydnellum scrobiculatum var. zonatum f. "\
|
768
|
-
"parvum (Banker) D. Hall & D.E. Stuntz 1972"
|
769
|
-
expect(details(sn)).to eq [{ genus: { string: "Hydnellum" }, species:
|
770
|
-
{ string: "scrobiculatum"}, infraspecies: [{ string: "zonatum",
|
771
|
-
rank: "var."}, { string: "parvum", rank: "f.",
|
772
|
-
authorship: "(Banker) D. Hall & D.E. Stuntz 1972",
|
773
|
-
combinationAuthorTeam: { authorTeam: "D. Hall & D.E. Stuntz",
|
774
|
-
author: ["D. Hall", "D.E. Stuntz"], year: "1972"},
|
775
|
-
basionymAuthorTeam: { authorTeam: "Banker", author: ["Banker"]} }]}]
|
776
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 9], 10 => ["species", 23],
|
777
|
-
24 => ["infraspecific_type", 28], 29 => ["infraspecies", 36],
|
778
|
-
37 => ["infraspecific_type", 39], 40 => ["infraspecies", 46],
|
779
|
-
48 => ["author_word", 54], 56 => ["author_word", 58],
|
780
|
-
59 => ["author_word", 63], 66 => ["author_word", 70],
|
781
|
-
71 => ["author_word", 77], 78 => ["year", 82] })
|
782
|
-
expect(parse("Senecio fuchsii C.C.Gmel. subsp. fuchsii var. "\
|
783
|
-
"expansus (Boiss. & Heldr.) Hayek")).to_not be_nil
|
784
|
-
expect(parse("Senecio fuchsii C.C.Gmel. subsp. fuchsii var. fuchsii")).
|
785
|
-
to_not be_nil
|
786
|
-
end
|
787
|
-
|
788
|
-
|
789
|
-
it "parses status BOTANICAL RARE" do
|
790
|
-
#it is always latin abbrev often 2 words
|
791
|
-
sn = "Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov."
|
792
|
-
expect(parse(sn)).to_not be_nil
|
793
|
-
expect(value(sn)).to eq "Arthopyrenia hyalospora (Nyl.) "\
|
794
|
-
"R.C. Harris comb. nov."
|
795
|
-
expect(canonical(sn)).to eq "Arthopyrenia hyalospora"
|
796
|
-
expect(details(sn)).to eq [{ genus: { string: "Arthopyrenia" },
|
797
|
-
species: { string: "hyalospora", authorship: "(Nyl.) R.C. Harris",
|
798
|
-
combinationAuthorTeam: { authorTeam: "R.C. Harris",
|
799
|
-
author: ["R.C. Harris"]}, basionymAuthorTeam: { authorTeam: "Nyl.",
|
800
|
-
author: ["Nyl."]} }, status: "comb. nov."}]
|
801
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 12], 13 => ["species", 23],
|
802
|
-
25 => ["author_word", 29], 31 => ["author_word", 35],
|
803
|
-
36 => ["author_word", 42] })
|
804
|
-
end
|
805
|
-
|
806
|
-
it "parses revised (ex) names" do
|
807
|
-
#invalidly published
|
808
|
-
sn = "Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris"
|
809
|
-
expect(parse(sn)).to_not be_nil
|
810
|
-
expect(value(sn)).
|
811
|
-
to eq "Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris"
|
812
|
-
expect(canonical(sn)).to eq "Arthopyrenia hyalospora"
|
813
|
-
expect(details(sn)).to eq [{ genus: { string: "Arthopyrenia" },
|
814
|
-
species: { string: "hyalospora",
|
815
|
-
authorship: "(Nyl. ex Banker) R.C. Harris", combinationAuthorTeam:
|
816
|
-
{ authorTeam: "R.C. Harris", author: ["R.C. Harris"]},
|
817
|
-
basionymAuthorTeam: { authorTeam: "Nyl.", author: ["Nyl."],
|
818
|
-
exAuthorTeam: { authorTeam: "Banker", author: ["Banker"]} } } }]
|
819
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 12], 13 => ["species", 23],
|
820
|
-
25 => ["author_word", 29], 33 => ["author_word", 39],
|
821
|
-
41 => ["author_word", 45], 46 => ["author_word", 52] })
|
822
|
-
sn = "Arthopyrenia hyalospora Nyl. ex Banker"
|
823
|
-
expect(parse(sn)).to_not be_nil
|
824
|
-
expect(details(sn)).to eq [{ genus: { string: "Arthopyrenia" },
|
825
|
-
species: { string: "hyalospora", authorship: "Nyl. ex Banker",
|
826
|
-
basionymAuthorTeam: { authorTeam: "Nyl.", author: ["Nyl."],
|
827
|
-
exAuthorTeam: { authorTeam: "Banker", author: ["Banker"]} } } }]
|
828
|
-
sn = "Glomopsis lonicerae Peck ex C.J. Gould 1945"
|
829
|
-
expect(parse(sn)).to_not be_nil
|
830
|
-
expect(details(sn)).to eq [{ genus: { string: "Glomopsis" },
|
831
|
-
species: { string: "lonicerae", authorship: "Peck ex C.J. Gould 1945",
|
832
|
-
basionymAuthorTeam: { authorTeam: "Peck", author: ["Peck"],
|
833
|
-
exAuthorTeam: { authorTeam: "C.J. Gould", author: ["C.J. Gould"],
|
834
|
-
year: "1945"} } } }]
|
835
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 9], 10 => ["species", 19],
|
836
|
-
20 => ["author_word", 24], 28 => ["author_word", 32],
|
837
|
-
33 => ["author_word", 38], 39 => ["year", 43] })
|
838
|
-
expect(parse("Acanthobasidium delicatum (Wakef.) Oberw. ex Jülich 1979")).
|
839
|
-
to_not be_nil
|
840
|
-
sn = "Mycosphaerella eryngii (Fr. ex Duby) Johanson ex Oudem. 1897"
|
841
|
-
expect(parse(sn)).to_not be_nil
|
842
|
-
expect(details(sn)).to eq [{ genus: { string: "Mycosphaerella" },
|
843
|
-
species: { string: "eryngii",
|
844
|
-
authorship: "(Fr. ex Duby) Johanson ex Oudem. 1897",
|
845
|
-
combinationAuthorTeam: { authorTeam: "Johanson", author: ["Johanson"],
|
846
|
-
exAuthorTeam: { authorTeam: "Oudem.", author: ["Oudem."], year: "1897"} },
|
847
|
-
basionymAuthorTeam: { authorTeam: "Fr.", author: ["Fr."],
|
848
|
-
exAuthorTeam: { authorTeam: "Duby", author: ["Duby"]} } } }]
|
849
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 14], 15 => ["species", 22],
|
850
|
-
24 => ["author_word", 27], 31 => ["author_word", 35],
|
851
|
-
37 => ["author_word", 45], 49 => ["author_word", 55],
|
852
|
-
56 => ["year", 60] })
|
853
|
-
#invalid but happens
|
854
|
-
expect(parse("Mycosphaerella eryngii (Fr. Duby) ex Oudem. 1897")).
|
855
|
-
to_not be_nil
|
856
|
-
expect(parse("Mycosphaerella eryngii (Fr.ex Duby) ex Oudem. 1897")).
|
857
|
-
to_not be_nil
|
858
|
-
sn = "Salmonella werahensis (Castellani) Hauduroy and Ehringer "\
|
859
|
-
"in Hauduroy 1937"
|
860
|
-
expect(parse(sn)).to_not be_nil
|
861
|
-
expect(details(sn)).to eq [{ genus: { string: "Salmonella" },
|
862
|
-
species: { string: "werahensis",
|
863
|
-
authorship: "(Castellani) Hauduroy and Ehringer in Hauduroy 1937",
|
864
|
-
combinationAuthorTeam: { authorTeam: "Hauduroy and Ehringer",
|
865
|
-
author: ["Hauduroy", "Ehringer"], exAuthorTeam: {
|
866
|
-
authorTeam: "Hauduroy", author: ["Hauduroy"], year: "1937"} },
|
867
|
-
basionymAuthorTeam: { authorTeam: "Castellani",
|
868
|
-
author: ["Castellani"]} } }]
|
869
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 10], 11 => ["species", 21],
|
870
|
-
23 => ["author_word", 33], 35 => ["author_word", 43],
|
871
|
-
48 => ["author_word", 56], 60 => ["author_word", 68],
|
872
|
-
69 => ["year", 73] })
|
873
|
-
end
|
874
|
-
|
875
|
-
it "parses named hybrids" do
|
876
|
-
[
|
877
|
-
["×Agropogon P. Fourn. 1934", [{ uninomial: { string: "Agropogon",
|
878
|
-
authorship: "P. Fourn. 1934", basionymAuthorTeam:
|
879
|
-
{ authorTeam: "P. Fourn.", author: ["P. Fourn."], year: "1934" } } }]],
|
880
|
-
["xAgropogon P. Fourn.", [{ uninomial: { string: "Agropogon",
|
881
|
-
authorship: "P. Fourn.", basionymAuthorTeam: { authorTeam: "P. Fourn.",
|
882
|
-
author: ["P. Fourn."] } } }]],
|
883
|
-
["XAgropogon P.Fourn.", [{ uninomial: { string: "Agropogon",
|
884
|
-
authorship: "P.Fourn.", basionymAuthorTeam: { authorTeam: "P.Fourn.",
|
885
|
-
author: ["P.Fourn."] } } }]],
|
886
|
-
["× Agropogon", [{ uninomial: { string: "Agropogon" } }]],
|
887
|
-
["x Agropogon", [{ uninomial: { string: "Agropogon" } }]],
|
888
|
-
["X Agropogon", [{ uninomial: { string: "Agropogon" } }]],
|
889
|
-
["X Cupressocyparis leylandii", [{ genus: { string: "Cupressocyparis" },
|
890
|
-
species: { string: "leylandii"} }]],
|
891
|
-
["×Heucherella tiarelloides", [{ genus: { string: "Heucherella" },
|
892
|
-
species: { string: "tiarelloides"} }]],
|
893
|
-
["xHeucherella tiarelloides", [{ genus: { string: "Heucherella" },
|
894
|
-
species: { string: "tiarelloides"} }]],
|
895
|
-
["x Heucherella tiarelloides", [{ genus: { string: "Heucherella" },
|
896
|
-
species: { string: "tiarelloides"} }]],
|
897
|
-
["×Agropogon littoralis (Sm.) C. E. Hubb. 1946", [{ genus:
|
898
|
-
{ string: "Agropogon" }, species: { string: "littoralis",
|
899
|
-
authorship: "(Sm.) C. E. Hubb. 1946", combinationAuthorTeam:
|
900
|
-
{ authorTeam: "C. E. Hubb.", author: ["C. E. Hubb."], year: "1946"},
|
901
|
-
basionymAuthorTeam: { authorTeam: "Sm.", author: ["Sm."]} } }]]
|
902
|
-
].each do |res|
|
903
|
-
expect(parse(res[0])).to_not be_nil
|
904
|
-
expect(parse(res[0]).hybrid).to eq true
|
905
|
-
expect(details(res[0])).to eq res[1]
|
906
|
-
end
|
907
|
-
[
|
908
|
-
["Asplenium X inexpectatum (E.L. Braun 1940) Morton (1956)",
|
909
|
-
[{ genus: { string: "Asplenium" }, species: { string: "inexpectatum",
|
910
|
-
authorship: "(E.L. Braun 1940) Morton (1956)", combinationAuthorTeam:
|
911
|
-
{ authorTeam: "Morton", author: ["Morton"], year: "1956"},
|
912
|
-
basionymAuthorTeam: { authorTeam: "E.L. Braun", author: ["E.L. Braun"],
|
913
|
-
year: "1940"} } }]],
|
914
|
-
["Mentha ×smithiana R. A. Graham 1949",[{ genus: { string: "Mentha" },
|
915
|
-
species: { string: "smithiana", authorship: "R. A. Graham 1949",
|
916
|
-
basionymAuthorTeam: { authorTeam: "R. A. Graham",
|
917
|
-
author: ["R. A. Graham"], year: "1949"} } }]],
|
918
|
-
["Salix ×capreola Andersson (1867)",[{ genus: { string: "Salix" },
|
919
|
-
species: { string: "capreola", authorship: "Andersson (1867)",
|
920
|
-
basionymAuthorTeam: { authorTeam: "Andersson", author: ["Andersson"],
|
921
|
-
year: "1867"} } }]],
|
922
|
-
["Salix x capreola Andersson",[{ genus: { string: "Salix" },
|
923
|
-
species: { string: "capreola", authorship: "Andersson",
|
924
|
-
basionymAuthorTeam: { authorTeam: "Andersson",
|
925
|
-
author: ["Andersson"]} } }]]
|
926
|
-
].each do |res|
|
927
|
-
expect(parse(res[0])).to_not be_nil
|
928
|
-
expect(parse(res[0]).hybrid).to eq true
|
929
|
-
expect(details(res[0])).to eq res[1]
|
930
|
-
end
|
931
|
-
sn = "Rosa alpina x pomifera"
|
932
|
-
expect(canonical(sn)).to eq "Rosa alpina × pomifera"
|
933
|
-
expect(parse(sn).details).to eq [{ genus: { string: "Rosa" },
|
934
|
-
species: { string: "alpina"} }, { species: { string: "pomifera"},
|
935
|
-
genus: { string: "Rosa"} }]
|
936
|
-
end
|
937
|
-
|
938
|
-
it "parses hybrid combination" do
|
939
|
-
sn = "Arthopyrenia hyalospora X Hydnellum scrobiculatum"
|
940
|
-
expect(parse(sn)).to_not be_nil
|
941
|
-
expect(parse(sn).hybrid).to eq true
|
942
|
-
expect(value(sn)).
|
943
|
-
to eq "Arthopyrenia hyalospora \303\227 Hydnellum scrobiculatum"
|
944
|
-
expect(canonical(sn)).
|
945
|
-
to eq "Arthopyrenia hyalospora × Hydnellum scrobiculatum"
|
946
|
-
expect(details(sn)).to eq [{ genus: { string: "Arthopyrenia" },
|
947
|
-
species: { string: "hyalospora"} }, { genus: { string: "Hydnellum"},
|
948
|
-
species: { string: "scrobiculatum"} }]
|
949
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 12], 13 => ["species", 23],
|
950
|
-
26 => ["genus", 35], 36 => ["species", 49] })
|
951
|
-
sn = "Arthopyrenia hyalospora (Banker) D. Hall X Hydnellum "\
|
952
|
-
"scrobiculatum D.E. Stuntz"
|
953
|
-
expect(parse(sn)).to_not be_nil
|
954
|
-
expect(parse(sn).hybrid).to eq true
|
955
|
-
expect(value(sn)).to eq "Arthopyrenia hyalospora (Banker) "\
|
956
|
-
"D. Hall \303\227 Hydnellum scrobiculatum D.E. Stuntz"
|
957
|
-
expect(canonical(sn)).
|
958
|
-
to eq "Arthopyrenia hyalospora × Hydnellum scrobiculatum"
|
959
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 12], 13 => ["species", 23],
|
960
|
-
25 => ["author_word", 31], 33 => ["author_word", 35],
|
961
|
-
36 => ["author_word", 40], 43 => ["genus", 52],
|
962
|
-
53 => ["species", 66], 67 => ["author_word", 71],
|
963
|
-
72 => ["author_word", 78] })
|
964
|
-
expect(value("Arthopyrenia hyalospora X")).
|
965
|
-
to eq "Arthopyrenia hyalospora \303\227 ?"
|
966
|
-
sn = "Arthopyrenia hyalospora x"
|
967
|
-
expect(parse(sn)).to_not be_nil
|
968
|
-
expect(parse(sn).hybrid).to eq true
|
969
|
-
expect(canonical(sn)).to eq "Arthopyrenia hyalospora"
|
970
|
-
expect(details(sn)).to eq [{ genus: { string: "Arthopyrenia" },
|
971
|
-
species: { string: "hyalospora"} }, "?"]
|
972
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 12], 13 => ["species", 23] })
|
973
|
-
sn = "Arthopyrenia hyalospora × ?"
|
974
|
-
expect(parse(sn)).to_not be_nil
|
975
|
-
expect(parse(sn).hybrid).to eq true
|
976
|
-
expect(details(sn)).to eq [{ genus: { string: "Arthopyrenia" },
|
977
|
-
species: { string: "hyalospora"} }, "?"]
|
978
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 12], 13 => ["species", 23] })
|
979
|
-
end
|
980
|
-
|
981
|
-
it "parses names with taxon concept" do
|
982
|
-
sn = "Stenometope laevissimus sec. Eschmeyer 2004"
|
983
|
-
expect(details(sn)).to eq [{ genus: { string: "Stenometope" },
|
984
|
-
species: { string: "laevissimus"}, taxon_concept:
|
985
|
-
{ authorship: "Eschmeyer 2004",
|
986
|
-
basionymAuthorTeam: { authorTeam: "Eschmeyer",
|
987
|
-
author: ["Eschmeyer"], year: "2004"} } }]
|
988
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 11], 12 => ["species", 23],
|
989
|
-
29 => ["author_word", 38], 39 => ["year", 43] })
|
990
|
-
sn = "Stenometope laevissimus Bibron 1855 sec. Eschmeyer 2004"
|
991
|
-
expect(parse(sn)).to_not be_nil
|
992
|
-
expect(details(sn)).to eq [{ genus: { string: "Stenometope" },
|
993
|
-
species: { string: "laevissimus", authorship: "Bibron 1855",
|
994
|
-
basionymAuthorTeam: { authorTeam: "Bibron", author: ["Bibron"],
|
995
|
-
year: "1855"} }, taxon_concept: { authorship: "Eschmeyer 2004",
|
996
|
-
basionymAuthorTeam: { authorTeam: "Eschmeyer",
|
997
|
-
author: ["Eschmeyer"], year: "2004"} } }]
|
998
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 11], 12 => ["species", 23],
|
999
|
-
24 => ["author_word", 30], 31 => ["year", 35],
|
1000
|
-
41 => ["author_word", 50], 51 => ["year", 55] })
|
1001
|
-
end
|
1002
|
-
|
1003
|
-
it "parses names with spaces inconsistencies" do
|
1004
|
-
expect(parse(" Asplenium X inexpectatum (E.L. Braun 1940) "\
|
1005
|
-
"Morton (1956) ")).to_not be_nil
|
1006
|
-
end
|
1007
|
-
|
1008
|
-
it "parses names with any number of spaces" do
|
1009
|
-
sn = "Trematosphaeria phaeospora (E. Müll.)"\
|
1010
|
-
" L. Holm 1957"
|
1011
|
-
expect(parse(sn)).to_not be_nil
|
1012
|
-
expect(value(sn)).to eq "Trematosphaeria phaeospora (E. Müll.) L. Holm 1957"
|
1013
|
-
expect(canonical(sn)).to eq "Trematosphaeria phaeospora"
|
1014
|
-
expect(details(sn)).to eq [{ genus: { string: "Trematosphaeria" },
|
1015
|
-
species: { string: "phaeospora", authorship: "(E. Müll.) "\
|
1016
|
-
"L. Holm 1957",
|
1017
|
-
combinationAuthorTeam: { authorTeam: "L. Holm",
|
1018
|
-
author: ["L. Holm"], year: "1957"},
|
1019
|
-
basionymAuthorTeam: { authorTeam: "E. Müll.", author: ["E. Müll."]} } }]
|
1020
|
-
expect(pos(sn)).to eq({ 0 => ["genus", 15], 16 => ["species", 26],
|
1021
|
-
28 => ["author_word", 30], 31 => ["author_word", 36],
|
1022
|
-
46 => ["author_word", 48], 61 => ["author_word", 65],
|
1023
|
-
66 => ["year", 70] })
|
1024
|
-
end
|
1025
|
-
|
1026
|
-
it "does not parse serveral authors groups with several years NOT CORRECT" do
|
1027
|
-
expect(parse("Pseudocercospora dendrobii (H.C. Burnett 1883) "\
|
1028
|
-
"(Leight.) (Movss. 1967) U. Braun & Crous 2003")).to be_nil
|
1029
|
-
end
|
1030
|
-
|
1031
|
-
it "does not parse unallowed utf-8 chars in name part" do
|
1032
|
-
expect(parse("Érematosphaeria phaespora")).to be_nil
|
1033
|
-
expect(parse("Trematosphaeria phaeáapora")).to be_nil
|
1034
|
-
expect(parse("Trematоsphaeria phaeaapora")).to be_nil #cyrillic o
|
1035
|
-
end
|
1036
|
-
|
1037
|
-
it "parses new stuff" do
|
1038
|
-
sn = "Nesticus quelpartensis Paik & Namkung, in Paik, "\
|
1039
|
-
"Yaginuma & Namkung, 1969"
|
1040
|
-
expect(details(sn)).to eq [{ genus: { string: "Nesticus" },
|
1041
|
-
species: { string: "quelpartensis",
|
1042
|
-
authorship: "Paik & Namkung, in Paik, Yaginuma & Namkung, 1969",
|
1043
|
-
basionymAuthorTeam: { authorTeam: "Paik & Namkung",
|
1044
|
-
author: ["Paik", "Namkung"], exAuthorTeam:
|
1045
|
-
{ authorTeam: "Paik, Yaginuma & Namkung",
|
1046
|
-
author: ["Paik", "Yaginuma", "Namkung"], year: "1969"} } } }]
|
1047
|
-
expect(parse("Dipoena yoshidai Ono, in Ono et al., 1991")).to_not be_nil
|
1048
|
-
sn = "Latrodectus mactans bishopi Kaston, 1938"
|
1049
|
-
expect(details(sn)).to eq [{ genus: { string: "Latrodectus" },
|
1050
|
-
species: { string: "mactans"}, infraspecies: [{ string: "bishopi",
|
1051
|
-
rank: "n/a", authorship: "Kaston, 1938",
|
1052
|
-
basionymAuthorTeam: { authorTeam: "Kaston",
|
1053
|
-
author: ["Kaston"], year: "1938"} }]}]
|
1054
|
-
#have to figure out black lists for this one
|
1055
|
-
sn = "Thiobacillus x Parker and Prisk 1953"
|
1056
|
-
sn = "Bacille de Plaut, Kritchevsky and Séguin 1921"
|
1057
|
-
expect(details(sn)).to eq [{ uninomial: { string: "Bacille",
|
1058
|
-
authorship: "de Plaut, Kritchevsky and Séguin 1921",
|
1059
|
-
basionymAuthorTeam: { authorTeam: "de Plaut, Kritchevsky and Séguin",
|
1060
|
-
author: ["de Plaut", "Kritchevsky", "Séguin"], year: "1921" } } }]
|
1061
|
-
sn = "Araneus van bruysseli Petrunkevitch, 1911"
|
1062
|
-
expect(details(sn)).to eq [{ genus: { string: "Araneus" },
|
1063
|
-
species: { string: "van"}, infraspecies: [{ string: "bruysseli",
|
1064
|
-
rank: "n/a", authorship: "Petrunkevitch, 1911",
|
1065
|
-
basionymAuthorTeam: { authorTeam: "Petrunkevitch",
|
1066
|
-
author: ["Petrunkevitch"], year: "1911"} }]}]
|
1067
|
-
sn = "Sapromyces laidlawi ab Sabin 1941"
|
1068
|
-
expect(details(sn)).to eq [{ genus: { string: "Sapromyces" },
|
1069
|
-
species: { string: "laidlawi", authorship: "ab Sabin 1941",
|
1070
|
-
basionymAuthorTeam: { authorTeam: "ab Sabin", author: ["ab Sabin"],
|
1071
|
-
year: "1941"} } }]
|
1072
|
-
sn = "Nocardia rugosa di Marco and Spalla 1957"
|
1073
|
-
expect(details(sn)).to eq [{ genus: { string: "Nocardia" },
|
1074
|
-
species: { string: "rugosa", authorship: "di Marco and Spalla 1957",
|
1075
|
-
basionymAuthorTeam: { authorTeam: "di Marco and Spalla",
|
1076
|
-
author: ["di Marco", "Spalla"], year: "1957"} } }]
|
1077
|
-
sn = "Flexibacter elegans Lewin 1969 non Soriano 1945"
|
1078
|
-
expect(details(sn)).to eq [{ genus: { string: "Flexibacter" },
|
1079
|
-
species: { string: "elegans", authorship: "Lewin 1969 non Soriano 1945",
|
1080
|
-
basionymAuthorTeam: { authorTeam: "Lewin", author: ["Lewin"],
|
1081
|
-
year: "1969"} } }]
|
1082
|
-
sn = "Flexibacter elegans Soriano 1945, non Lewin 1969"
|
1083
|
-
expect(details(sn)).to eq [{ genus: { string: "Flexibacter" },
|
1084
|
-
species: { string: "elegans", authorship: "Soriano 1945, non Lewin 1969",
|
1085
|
-
basionymAuthorTeam: { authorTeam: "Soriano", author: ["Soriano"],
|
1086
|
-
year: "1945"} } }]
|
1087
|
-
sn = "Schottera nicaeënsis (J.V. Lamouroux ex Duby) Guiry & Hollenberg"
|
1088
|
-
expect(details(sn)).to eq [{ genus: { string: "Schottera" },
|
1089
|
-
species: { string: "nicaeensis",
|
1090
|
-
authorship: "(J.V. Lamouroux ex Duby) Guiry & Hollenberg",
|
1091
|
-
combinationAuthorTeam: { authorTeam: "Guiry & Hollenberg",
|
1092
|
-
author: ["Guiry", "Hollenberg"]}, basionymAuthorTeam:
|
1093
|
-
{ authorTeam: "J.V. Lamouroux", author: ["J.V. Lamouroux"],
|
1094
|
-
exAuthorTeam: { authorTeam: "Duby", author: ["Duby"]} } } }]
|
1095
|
-
sn = "Deschampsia cespitosa ssp pumila"
|
1096
|
-
expect(details(sn)).to eq [{ genus: { string: "Deschampsia" },
|
1097
|
-
species: { string: "cespitosa"},
|
1098
|
-
infraspecies: [{ string: "pumila", rank: "ssp"}]}]
|
1099
|
-
end
|
1100
|
-
|
1101
|
-
# Combination genus names merges without dash or capital letter
|
1102
|
-
it "parses hybrid names with capitalized second name in genus" do
|
1103
|
-
# (botanical code error)
|
1104
|
-
sn = "Anacampti-Platanthera P. Fourn."
|
1105
|
-
expect(parse(sn)).to_not be_nil
|
1106
|
-
expect(canonical(sn)).to eq "Anacamptiplatanthera"
|
1107
|
-
sn = "Anacampti-Platanthera vulgaris P. Fourn."
|
1108
|
-
expect(parse(sn)).to_not be_nil
|
1109
|
-
expect(canonical(sn)).to eq "Anacamptiplatanthera vulgaris"
|
1110
|
-
end
|
1111
|
-
|
1112
|
-
it "parses genus names starting with uppercase letters AE OE" do
|
1113
|
-
sn = "AEmona separata Broun 1921"
|
1114
|
-
expect(canonical(sn)).to eq "Aemona separata"
|
1115
|
-
sn = "OEmona simplex White, 1855"
|
1116
|
-
expect(canonical(sn)).to eq "Oemona simplex"
|
1117
|
-
end
|
1118
|
-
|
1119
|
-
|
1120
|
-
#"Arthrosamanea eriorhachis (Harms & sine ref. ) Aubrév."
|
1121
|
-
# -- ignore & sine ref. (means without reference)
|
1122
|
-
|
1123
|
-
=begin
|
1124
|
-
new stuff
|
1125
|
-
|
1126
|
-
sn = "Orchidaceae × Asconopsis hort."
|
1127
|
-
expect(canonical(sn)).to eq "Orchidaceae x Asconopsis"
|
1128
|
-
sn
|
1129
|
-
Tamiops swinhoei near hainanus|Tamiops swinhoei near hainanus
|
1130
|
-
Conus textile form archiepiscopus|Conus textile form archiepiscopus|
|
1131
|
-
Crypticus pseudosericeus ssp. olivieri Desbrochers des \
|
1132
|
-
Loges,1881|Crypticus pseudosericeus olivieri des
|
1133
|
-
Solanum nigrum subsp nigrum|Solanum nigrum subsp nigrum
|
1134
|
-
Protoglossus taeniatum author unknown|Protoglossus taeniatum author unknown
|
1135
|
-
Dupontiella (S. ?) bicolor|Dupontiella|
|
1136
|
-
=end
|
1137
|
-
end
|