biodiversity 3.1.0 → 3.1.1

data/CHANGELOG

@@ -1,3 +1,5 @@
+3.1.1 -- fixed problem with names ending on sp 
+
 3.1.0 -- added surrogates: Genbank, Barcode of life names. 
 Also cf., sp. spp are flagged as surrogates
 

data/VERSION

@@ -1 +1 @@
-3.1.0
+3.1.1

data/lib/biodiversity/parser.rb

@@ -256,7 +256,7 @@ class ScientificNameParser
     name = parsed_data[:verbatim]
     pos = parsed_data[:positions].to_a.flatten
     surrogate1 = /BOLD:|[\d]{5,}/i
-    surrogate2 = /(spp|sp|nr|cf)[\.]?[\s]*$/i
+    surrogate2 = /\b(spp|sp|nr|cf)[\.]?[\s]*$/i
     is_surrogate = false
       
     ai_index = pos.index('annotation_identification')

data/spec/parser/test_data.txt

@@ -175,8 +175,8 @@ Abturia cf. alabamensis (Morton )|{"scientificName":{"parsed":true, "parser_vers
 Abturia cf alabamensis (Morton )|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Abturia cf alabamensis (Morton )", "normalized":"Abturia cf alabamensis (Morton)", "canonical":"Abturia alabamensis", "hybrid":false, "details":[{"genus":{"string":"Abturia"}, "annotation_identification":"cf", "species":{"species":{"string":"alabamensis", "authorship":"(Morton )", "basionymAuthorTeam":{"authorTeam":"Morton", "author":["Morton"]}}}}], "parser_run":1, "positions":{"0":["genus", 7], "8":["annotation_identification", 11], "11":["species", 22], "24":["author_word", 30]}, "surrogate": true}}
 Alyxia reinwardti var|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alyxia reinwardti var", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
 Alyxia reinwardti var.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alyxia reinwardti var.", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
-Alyxia reinwardti ssp|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alyxia reinwardti ssp", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}, "surrogate": true}}
-Alyxia reinwardti ssp.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alyxia reinwardti ssp.", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}, "surrogate": true}}
+Alyxia reinwardti ssp|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alyxia reinwardti ssp", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
+Alyxia reinwardti ssp.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alyxia reinwardti ssp.", "normalized":"Alyxia reinwardti", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 17]}}}
 Alaria spp|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alaria spp", "normalized":"Alaria", "canonical":"Alaria", "hybrid":false, "details":[{"uninomial":{"string":"Alaria"}}], "parser_run":1, "positions":{"0":["uninomial", 6]}, "surrogate": true}}
 Alaria spp.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alaria spp.", "normalized":"Alaria", "canonical":"Alaria", "hybrid":false, "details":[{"uninomial":{"string":"Alaria"}}], "parser_run":1, "positions":{"0":["uninomial", 6]}, "surrogate": true}}
 Xenodon sp|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Xenodon sp", "normalized":"Xenodon", "canonical":"Xenodon", "hybrid":false, "details":[{"uninomial":{"string":"Xenodon"}}], "parser_run":1, "positions":{"0":["uninomial", 7]}, "surrogate": true}}
@@ -421,3 +421,4 @@ Coleoptera Bold:AAV0432|{"scientificName":{"parsed":true, "parser_version":"test
 
 #should not flag as surrogates similar to surrogates names
 Dryopteris X separabilis Small (pro sp.)|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Dryopteris X separabilis Small (pro sp.)", "normalized":"Dryopteris × separabilis Small", "canonical":"Dryopteris separabilis", "hybrid":false, "details":[{"genus":{"string":"Dryopteris"}, "species":{"string":"separabilis", "authorship":"Small", "basionymAuthorTeam":{"authorTeam":"Small", "author":["Small"]}}}], "parser_run":2, "positions":{"0":["genus", 10], "13":["species", 24], "25":["author_word", 30]}}}
+Nemcia epacridoides (Meissner)Crisp|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Nemcia epacridoides (Meissner)Crisp", "normalized":"Nemcia epacridoides (Meissner) Crisp", "canonical":"Nemcia epacridoides", "hybrid":false, "details":[{"genus":{"string":"Nemcia"}, "species":{"string":"epacridoides", "authorship":"(Meissner)Crisp", "combinationAuthorTeam":{"authorTeam":"Crisp", "author":["Crisp"]}, "basionymAuthorTeam":{"authorTeam":"Meissner", "author":["Meissner"]}}}], "parser_run":1, "positions":{"0":["genus", 6], "7":["species", 19], "21":["author_word", 29], "30":["author_word", 35]}}}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: biodiversity
 version: !ruby/object:Gem::Version
-  version: 3.1.0
+  version: 3.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-17 00:00:00.000000000 Z
+date: 2013-06-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake