biodiversity 3.1.8 → 3.1.9

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG

@@ -1,3 +1,6 @@
+3.1.8 -- more virus keywords, better handling of apostrophes in
+species epithets
+
 3.1.8 -- downgrading dependency on treetop to 1.4.1
 
 3.1.7 -- fixed travis and dependencies

data/lib/biodiversity/parser.rb

@@ -161,14 +161,18 @@ class ScientificNameParser
 
   def virus?(a_string)
     !!(a_string.match(/\sICTV\s*$/) ||
-       a_string.match(/\b(virus|viruses|
-                          phage|phages|viroid|viroids|
-                          satellite|satellites|prion|prions)\b/ix) ||
-       a_string.match(/[A-Z]?[a-z]+virus\b/))
+       a_string.match(/\b(virus|viruses|particle|particles|
+                          phage|phages|viroid|viroids|virophage|
+                          prion|prions|NPV)\b/ix) ||
+       a_string.match(/[A-Z]?[a-z]+virus\b/) ||
+       a_string.match(/\b[A-Za-z]*satellite[s]?\b/))
   end
 
-  def unknown_placement?(a_string)
-    !!(a_string.match(/incertae\s+sedis/i) || a_string.match(/inc\.\s*sed\./i))
+  def noparse?(a_string)
+    incertae_sedis = a_string.match(/incertae\s+sedis/i) ||
+      a_string.match(/inc\.\s*sed\./i)
+    rna = a_string.match(/[^A-Z]RNA[^A-Z]*/)
+    incertae_sedis || rna
   end
 
   def parsed
@@ -181,7 +185,7 @@ class ScientificNameParser
 
     if virus?(a_string)
       @parsed = { verbatim: a_string, virus: true }
-    elsif unknown_placement?(a_string)
+    elsif noparse?(a_string)
       @parsed = { verbatim: a_string }
     else
       begin

data/lib/biodiversity/parser/scientific_name_clean.treetop

@@ -1372,15 +1372,9 @@ grammar ScientificNameClean
       end
     }
     /
-    "o'donelli" {
+    a:valid_name_letter "'" b:latin_word {
       def value
-        "odonelli"
-      end
-    }
-    /
-    "o'neili" {
-      def value
-        "oneili"
+        a.value + "'" + b.value
       end
     }
     /
@@ -1388,7 +1382,7 @@ grammar ScientificNameClean
       def value
         a.value + b.value
       end
-     }
+    }
   end
 
   rule valid_name_letters

data/lib/biodiversity/version.rb

@@ -1,3 +1,3 @@
 module Biodiversity
-  VERSION = "3.1.8"
+  VERSION = "3.1.9"
 end

data/spec/files/test_data.txt

@@ -63,7 +63,13 @@ Mo. alpium (Osbeck, 1778)|{"scientificName":{"parsed":true, "parser_version":"te
 Mom.alpium (Osbeck, 1778)|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Mom.alpium (Osbeck, 1778)", "normalized":"Mom. alpium (Osbeck 1778)", "canonical":"Mom. alpium", "hybrid":false, "details":[{"genus":{"string":"Mom."}, "species":{"string":"alpium", "authorship":"(Osbeck, 1778)", "basionymAuthorTeam":{"authorTeam":"Osbeck", "author":["Osbeck"], "year":"1778"}}}], "parser_run":1, "positions":{"0":["genus", 4], "4":["species", 10], "12":["author_word", 18], "20":["year", 24]}}}
 
 #binomial with apostrophe in species epithet
-Junellia o'donelli Moldenke, 1946|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Junellia o'donelli Moldenke, 1946", "normalized":"Junellia odonelli Moldenke 1946", "canonical":"Junellia odonelli", "hybrid":false, "details":[{"genus":{"string":"Junellia"}, "species":{"string":"odonelli", "authorship":"Moldenke, 1946", "basionymAuthorTeam":{"authorTeam":"Moldenke", "author":["Moldenke"], "year":"1946"}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 18], "19":["author_word", 27], "29":["year", 33]}}}
+Junellia o'donelli Moldenke, 1946|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Junellia o'donelli Moldenke, 1946", "normalized":"Junellia o'donelli Moldenke 1946", "canonical":"Junellia o'donelli", "hybrid":false, "details":[{"genus":{"string":"Junellia"}, "species":{"string":"o'donelli", "authorship":"Moldenke, 1946", "basionymAuthorTeam":{"authorTeam":"Moldenke", "author":["Moldenke"], "year":"1946"}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 18], "19":["author_word", 27], "29":["year", 33]}}}
+Trophon d'orbignyi Carcelles, 1946|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Trophon d'orbignyi Carcelles, 1946", "normalized":"Trophon d'orbignyi Carcelles 1946", "canonical":"Trophon d'orbignyi", "hybrid":false, "details":[{"genus":{"string":"Trophon"}, "species":{"string":"d'orbignyi", "authorship":"Carcelles, 1946", "basionymAuthorTeam":{"authorTeam":"Carcelles", "author":["Carcelles"], "year":"1946"}}}], "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 18], "19":["author_word", 28], "30":["year", 34]}}}
+Arca m'coyi Tenison-Woods, 1878|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Arca m'coyi Tenison-Woods, 1878", "normalized":"Arca m'coyi Tenison-Woods 1878", "canonical":"Arca m'coyi", "hybrid":false, "details":[{"genus":{"string":"Arca"}, "species":{"string":"m'coyi", "authorship":"Tenison-Woods, 1878", "basionymAuthorTeam":{"authorTeam":"Tenison-Woods", "author":["Tenison-Woods"], "year":"1878"}}}], "parser_run":1, "positions":{"0":["genus", 4], "5":["species", 11], "12":["author_word", 25], "27":["year", 31]}}}
+Nucula m'andrewii Hanley, 1860|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Nucula m'andrewii Hanley, 1860", "normalized":"Nucula m'andrewii Hanley 1860", "canonical":"Nucula m'andrewii", "hybrid":false, "details":[{"genus":{"string":"Nucula"}, "species":{"string":"m'andrewii", "authorship":"Hanley, 1860", "basionymAuthorTeam":{"authorTeam":"Hanley", "author":["Hanley"], "year":"1860"}}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17], "18":["author_word", 24], "26":["year", 30]}}}
+Eristalis l'herminierii Macquart|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Eristalis l'herminierii Macquart", "normalized":"Eristalis l'herminierii Macquart", "canonical":"Eristalis l'herminierii", "hybrid":false, "details":[{"genus":{"string":"Eristalis"}, "species":{"string":"l'herminierii", "authorship":"Macquart", "basionymAuthorTeam":{"authorTeam":"Macquart", "author":["Macquart"]}}}], "parser_run":1, "positions":{"0":["genus", 9], "10":["species", 23], "24":["author_word", 32]}}}
+Odynerus o'neili Cameron|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Odynerus o'neili Cameron", "normalized":"Odynerus o'neili Cameron", "canonical":"Odynerus o'neili", "hybrid":false, "details":[{"genus":{"string":"Odynerus"}, "species":{"string":"o'neili", "authorship":"Cameron", "basionymAuthorTeam":{"authorTeam":"Cameron", "author":["Cameron"]}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 16], "17":["author_word", 24]}}}
+Serjania meridionalis Cambess. var. o'donelli F.A. Barkley|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Serjania meridionalis Cambess. var. o'donelli F.A. Barkley", "normalized":"Serjania meridionalis Cambess. var. o'donelli F.A. Barkley", "canonical":"Serjania meridionalis o'donelli", "hybrid":false, "details":[{"genus":{"string":"Serjania"}, "species":{"string":"meridionalis", "authorship":"Cambess.", "basionymAuthorTeam":{"authorTeam":"Cambess.", "author":["Cambess."]}}, "infraspecies":[{"string":"o'donelli", "rank":"var.", "authorship":"F.A. Barkley", "basionymAuthorTeam":{"authorTeam":"F.A. Barkley", "author":["F.A. Barkley"]}}]}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 21], "22":["author_word", 30], "31":["infraspecific_type", 35], "36":["infraspecies", 45], "46":["author_word", 50], "51":["author_word", 58]}}}
 
 # whitespace names (rare, only ~50 cases)
 #TODO Donatia novae zelandiae Hook.f.
@@ -132,9 +138,6 @@ Pseudocercospora dendrobii(H.C.     Burnett, 1873)U. Braun & Crous     2003|{"sc
 Pseudocercospora dendrobii(H.C.     Burnett 1873)U. Braun & Crous ,    2003|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":1,"verbatim":"Pseudocercospora dendrobii(H.C.     Burnett 1873)U. Braun & Crous ,    2003","normalized":"Pseudocercospora dendrobii (H.C. Burnett 1873) U. Braun & Crous 2003","canonical":"Pseudocercospora dendrobii","hybrid":false,"details":[{"genus":{"string":"Pseudocercospora"},"species":{"string":"dendrobii","authorship":"(H.C.     Burnett 1873)U. Braun & Crous ,    2003","combinationAuthorTeam":{"authorTeam":"U. Braun & Crous","author":["U. Braun","Crous"],"year":"2003"},"basionymAuthorTeam":{"authorTeam":"H.C.     Burnett","author":["H.C. Burnett"],"year":"1873"}}}],"positions":{"0":["genus",16],"17":["species",26],"27":["author_word",31],"36":["author_word",43],"44":["year",48],"49":["author_word",51],"52":["author_word",57],"60":["author_word",65],"71":["year",75]}}}
 Sedella pumila (Benth.) Britton & Rose|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Sedella pumila (Benth.) Britton & Rose", "normalized":"Sedella pumila (Benth.) Britton & Rose", "canonical":"Sedella pumila", "hybrid":false, "details":[{"genus":{"string":"Sedella"}, "species":{"string":"pumila", "authorship":"(Benth.) Britton & Rose", "combinationAuthorTeam":{"authorTeam":"Britton & Rose", "author":["Britton", "Rose"]}, "basionymAuthorTeam":{"authorTeam":"Benth.", "author":["Benth."]}}}], "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 14], "16":["author_word", 22], "24":["author_word", 31], "34":["author_word", 38]}}}
 
-#binomials with apostrophe in species epithet
-Odynerus o'neili Cameron|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Odynerus o'neili Cameron", "normalized":"Odynerus oneili Cameron", "canonical":"Odynerus oneili", "hybrid":false, "details":[{"genus":{"string":"Odynerus"}, "species":{"string":"oneili", "authorship":"Cameron", "basionymAuthorTeam":{"authorTeam":"Cameron", "author":["Cameron"]}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 16], "17":["author_word", 24]}}}
-Serjania meridionalis Cambess. var. o'donelli F.A. Barkley|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Serjania meridionalis Cambess. var. o'donelli F.A. Barkley", "normalized":"Serjania meridionalis Cambess. var. odonelli F.A. Barkley", "canonical":"Serjania meridionalis odonelli", "hybrid":false, "details":[{"genus":{"string":"Serjania"}, "species":{"string":"meridionalis", "authorship":"Cambess.", "basionymAuthorTeam":{"authorTeam":"Cambess.", "author":["Cambess."]}}, "infraspecies":[{"string":"odonelli", "rank":"var.", "authorship":"F.A. Barkley", "basionymAuthorTeam":{"authorTeam":"F.A. Barkley", "author":["F.A. Barkley"]}}]}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 21], "22":["author_word", 30], "31":["infraspecific_type", 35], "36":["infraspecies", 45], "46":["author_word", 50], "51":["author_word", 58]}}}
 
 #infraspecies without rank
 Hydnellum scrobiculatum zonatum (Batsch) K. A. Harrison 1961|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Hydnellum scrobiculatum zonatum (Batsch) K. A. Harrison 1961", "normalized":"Hydnellum scrobiculatum zonatum (Batsch) K. A. Harrison 1961", "canonical":"Hydnellum scrobiculatum zonatum", "hybrid":false, "details":[{"genus":{"string":"Hydnellum"}, "species":{"string":"scrobiculatum"}, "infraspecies":[{"string":"zonatum", "rank":"n/a", "authorship":"(Batsch) K. A. Harrison 1961", "combinationAuthorTeam":{"authorTeam":"K. A. Harrison", "author":["K. A. Harrison"], "year":"1961"}, "basionymAuthorTeam":{"authorTeam":"Batsch", "author":["Batsch"]}}]}], "parser_run":1, "positions":{"0":["genus", 9], "10":["species", 23], "24":["infraspecies", 31], "33":["author_word", 39], "41":["author_word", 43], "44":["author_word", 46], "47":["author_word", 55], "56":["year", 60]}}}
@@ -357,6 +360,19 @@ Fungal prions|{"scientificName":{"parsed":false, "parser_version":"test_version"
 Human rhinovirus A11|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Human rhinovirus A11", "virus":true}}
 Kobuvirus korean black goat/South Korea/2010|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Kobuvirus korean black goat/South Korea/2010", "virus":true}}
 Australian bat lyssavirus human/AUS/1998|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Australian bat lyssavirus human/AUS/1998", "virus":true}}
+Gossypium mustilinum symptomless alphasatellite|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Gossypium mustilinum symptomless alphasatellite", "virus":true}}
+Okra leaf curl Mali alphasatellites-Cameroon|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Okra leaf curl Mali alphasatellites-Cameroon", "virus":true}}
+Bemisia betasatellite LW-2014|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Bemisia betasatellite LW-2014", "virus":true}}
+Tomato leaf curl Bangladesh betasatellites [India/Patna/Chilli/2008]|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Tomato leaf curl Bangladesh betasatellites [India/Patna/Chilli/2008]", "virus":true}}
+Intracisternal A-particles|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Intracisternal A-particles", "virus":true}}
+Saccharomyces cerevisiae killer particle M1|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Saccharomyces cerevisiae killer particle M1", "virus":true}}
+
+#should not parse non-virus names containing RNA
+ssRNA|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"ssRNA"}}
+Alpha proteobacterium RNA12|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Alpha proteobacterium RNA12"}}
+Ustilaginoidea virens RNA virus|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Ustilaginoidea virens RNA virus", "virus":true}}
+Candida albicans RNA_CTR0-3|{"scientificName":{"parsed":false, "parser_version":"test_version", "verbatim":"Candida albicans RNA_CTR0-3"}}
+Calathus (Lindrothius) KURNAKOV 1961|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Calathus (Lindrothius) KURNAKOV 1961", "normalized":"Calathus (Lindrothius) Kurnakov 1961", "canonical":"Calathus", "hybrid":false, "details":[{"uninomial":{"string":"Calathus", "infragenus":{"string":"Lindrothius"}, "authorship":"KURNAKOV 1961", "basionymAuthorTeam":{"authorTeam":"KURNAKOV", "author":["Kurnakov"], "year":"1961"}}}], "parser_run":1, "positions":{"0":["uninomial", 8], "10":["infragenus", 21], "23":["author_word", 31], "32":["year", 36]}}}
 
 #double parenthesis
 Eichornia crassipes ( (Martius) ) Solms-Laub.|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":2,"verbatim":"Eichornia crassipes ( (Martius) ) Solms-Laub.","normalized":"Eichornia crassipes (Martius) Solms-Laub.","canonical":"Eichornia crassipes","hybrid":false,"details":[{"genus":{"string":"Eichornia"},"species":{"string":"crassipes","authorship":"( (Martius) ) Solms-Laub.","combinationAuthorTeam":{"authorTeam":"Solms-Laub.","author":["Solms-Laub."]},"basionymAuthorTeam":{"authorTeam":"Martius","author":["Martius"]}}}],"positions":{"0":["genus",9],"10":["species",19],"23":["author_word",30],"34":["author_word",45]}}}

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: biodiversity
 version: !ruby/object:Gem::Version
-  version: 3.1.8
+  version: 3.1.9
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-04-22 00:00:00.000000000 Z
+date: 2015-05-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: treetop