biodiversity19 3.0.1 → 3.1.0

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data/CHANGELOG CHANGED
@@ -1,3 +1,6 @@
1
+ 3.1.0 -- added surrogates: Genbank, Barcode of life names.
2
+ Also cf., sp. spp are flagged as surrogates
3
+
1
4
  3.0.1 -- updated gems
2
5
 
3
6
  3.0.0 -- removing support for ruby 1.8.7, making biodiversity gem be the same
data/LICENSE CHANGED
@@ -1,4 +1,6 @@
1
- Copyright (c) 2009-2012 Marine Biological Laboratory
1
+ The MIT License (MIT)
2
+
3
+ Copyright (c) 2008-2013 Marine Biological Laboratory
2
4
 
3
5
  Permission is hereby granted, free of charge, to any person obtaining
4
6
  a copy of this software and associated documentation files (the
data/README.md CHANGED
@@ -46,7 +46,8 @@ you can use a socket server
46
46
  parserver -h
47
47
  Usage: parserver [options]
48
48
 
49
- -r, --canonical_with_rank Adds infraspecies rank to canonical forms
49
+ -r, --canonical_with_rank Adds infraspecies rank
50
+ to canonical forms
50
51
 
51
52
  -o, --output=output Specifies the type of the output:
52
53
  json - parsed results in json
@@ -116,15 +117,18 @@ You can use it as a library in Ruby, JRuby etc.
116
117
  parser.parse(" Plantago major ")[:scientificName][:normalized]
117
118
 
118
119
  # to get only cleaned up latin part of the name
119
- parser.parse("Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003")[:scientificName][:canonical]
120
+ parser.parse("Pseudocercospora dendrobii (H.C. Burnett) U. \
121
+ Braun & Crous 2003")[:scientificName][:canonical]
120
122
 
121
123
  # to get detailed information about elements of the name
122
- parser.parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003")[:scientificName][:details]
124
+ parser.parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. \
125
+ Braun & Crous 2003")[:scientificName][:details]
123
126
 
124
127
  Returned result is not always linear, if name is complex. To get simple linear
125
128
  representation of the name you can use:
126
129
 
127
- parser.parse("Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003")[:scientificName][:position]
130
+ parser.parse("Pseudocercospora dendrobii (H.C. Burnett) \
131
+ U. Braun & Crous 2003")[:scientificName][:position]
128
132
  # returns {0=>["genus", 16], 17=>["species", 26],
129
133
  # 28=>["author_word", 32], 33=>["author_word", 40],
130
134
  # 42=>["author_word", 44], 45=>["author_word", 50],
@@ -134,34 +138,64 @@ representation of the name you can use:
134
138
  # of the word, second element of the value is the character index
135
139
  # of end of the word
136
140
 
141
+ 'Surrogate' is a broad group which includes 'Barcode of Life' names, and various
142
+ undetermined names with cf. sp. spp. nr. in them:
143
+
144
+ parser.parse("Coleoptera BOLD:1234567")[:scientificName][:surrogate]
145
+
137
146
  To parse using several CPUs (4 seem to be optimal)
138
147
 
139
148
  parser = ParallelParser.new
140
149
  # ParallelParser.new(4) will try to run 4 processes if hardware allows
141
150
  array_of_names = ["Betula alba", "Homo sapiens"....]
142
151
  parser.parse(array_of_names)
143
- # Output: {"Betula alba" => {:scientificName...}, "Homo sapiens" => {:scientificName...}, ...}
152
+ # Output: {"Betula alba" => {:scientificName...},
153
+ # "Homo sapiens" => {:scientificName...}, ...}
144
154
 
145
- parallel parser takes list of names and returns back a hash with names as keys and parsed data as values
155
+ parallel parser takes list of names and returns back a hash with names as
156
+ keys and parsed data as values
146
157
 
147
158
  To get canonicals with ranks for infraspecific epithets:
148
159
 
149
160
  parser = ScientificNameParser.new(canonical_with_rank: true)
150
- parser.parse('Cola cordifolia var. puberula A. Chev.')[:scientificName][:canonical]
161
+ parser.parse('Cola cordifolia var. puberula \
162
+ A. Chev.')[:scientificName][:canonical]
151
163
  # Output: Cola cordifolia var. puberula
152
164
 
153
165
  To resolve lsid and get back RDF file
154
166
 
155
167
  LsidResolver.resolve("urn:lsid:ubio.org:classificationbank:2232671")
156
168
 
169
+ Troubleshooting
170
+ ---------------
171
+
172
+ If nnparse or parserver do not start -- try to run
173
+
174
+ gem uninstall biodiversity
175
+ gem uninstall biodiversity19
176
+
177
+ and make sure you remove all versions and all nnparse and parserver scripts.
178
+ Then install biodiversity again
179
+
180
+ gem install biodiversity
181
+
182
+ It should fix the problem.
183
+
184
+ Copyright
185
+ ---------
186
+
187
+ Authors: [Dmitry Mozzherin][10],
157
188
 
189
+ Copyright (c) 2008-2013 Marine Biological Laboratory. See LICENSE for
190
+ further details.
158
191
 
159
- [1]: https://badge.fury.io/rb/biodiversity19.png
160
- [2]: http://badge.fury.io/rb/biodiversity19
192
+ [1]: https://badge.fury.io/rb/biodiversity.png
193
+ [2]: http://badge.fury.io/rb/biodiversity
161
194
  [3]: https://secure.travis-ci.org/GlobalNamesArchitecture/biodiversity.png
162
195
  [4]: http://travis-ci.org/GlobalNamesArchitecture/biodiversity
163
196
  [5]: https://codeclimate.com/github/GlobalNamesArchitecture/biodiversity.png
164
197
  [6]: https://codeclimate.com/github/GlobalNamesArchitecture/biodiversity
165
198
  [7]: https://gemnasium.com/GlobalNamesArchitecture/biodiversity.png
166
199
  [8]: https://gemnasium.com/GlobalNamesArchitecture/biodiversity
167
- [9]: https://github.com/GlobalNamesArchitecture/biodiversity/blob/master/examples/socket_client.rb
200
+ [9]: http://bit.ly/149iLm5
201
+ [10]: https://github.com/dimus
data/VERSION CHANGED
@@ -1 +1 @@
1
- 3.0.1
1
+ 3.1.0
@@ -233,6 +233,7 @@ class ScientificNameParser
233
233
  res[:details][0][:infraspecies])
234
234
  ScientificNameParser.add_rank_to_canonical(res)
235
235
  end
236
+ res[:surrogate] = true if ScientificNameParser.surrogate?(res)
236
237
  res = {:scientificName => res}
237
238
  end
238
239
 
@@ -250,6 +251,24 @@ class ScientificNameParser
250
251
 
251
252
  private
252
253
 
254
+ def self.surrogate?(parsed_data)
255
+ return false unless parsed_data[:parsed]
256
+ name = parsed_data[:verbatim]
257
+ pos = parsed_data[:positions].to_a.flatten
258
+ surrogate1 = /BOLD:|[\d]{5,}/i
259
+ surrogate2 = /(spp|sp|nr|cf)[\.]?[\s]*$/i
260
+ is_surrogate = false
261
+
262
+ ai_index = pos.index('annotation_identification')
263
+ if ai_index
264
+ ai = name[pos[ai_index - 1]..pos[ai_index + 1]]
265
+ is_surrogate = true if ai.match(/^(spp|cf|sp|nr)/)
266
+ end
267
+ is_surrogate = true if !is_surrogate && (name.match(surrogate1) ||
268
+ name.match(surrogate2))
269
+ is_surrogate
270
+ end
271
+
253
272
  def self.add_rank_to_canonical(parsed)
254
273
  parts = parsed[:canonical].split(' ')
255
274
  name_ary = parts[0..1]
@@ -171,27 +171,27 @@ Euastrum divergens var. rhodesiense f. coronulum A.M. Scott & Prescott|{"scienti
171
171
  #species and infraspecies without epithets, comparisons
172
172
  Acarinina aff. pentacamerata|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Acarinina aff. pentacamerata", "normalized":"Acarinina", "canonical":"Acarinina", "hybrid":false, "details":[{"genus":{"string":"Acarinina"}, "annotation_identification":"aff.", "ignored":{"species":{"string":"pentacamerata"}}}], "parser_run":1, "positions":{"0":["genus", 9], "10":["annotation_identification", 14]}}}
173
173
  Acarinina aff pentacamerata|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Acarinina aff pentacamerata", "normalized":"Acarinina", "canonical":"Acarinina", "hybrid":false, "details":[{"genus":{"string":"Acarinina"}, "annotation_identification":"aff", "ignored":{"species":{"string":"pentacamerata"}}}], "parser_run":1, "positions":{"0":["genus", 9], "10":["annotation_identification", 14]}}}
174
- Abturia cf. alabamensis (Morton )|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Abturia cf. alabamensis (Morton )", "normalized":"Abturia cf. alabamensis (Morton)", "canonical":"Abturia alabamensis", "hybrid":false, "details":[{"genus":{"string":"Abturia"}, "annotation_identification":"cf.", "species":{"species":{"string":"alabamensis", "authorship":"(Morton )", "basionymAuthorTeam":{"authorTeam":"Morton", "author":["Morton"]}}}}], "parser_run":1, "positions":{"0":["genus", 7], "8":["annotation_identification", 11], "12":["species", 23], "25":["author_word", 31]}}}
175
- 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]}}}
174
+ Abturia cf. alabamensis (Morton )|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Abturia cf. alabamensis (Morton )", "normalized":"Abturia cf. alabamensis (Morton)", "canonical":"Abturia alabamensis", "hybrid":false, "details":[{"genus":{"string":"Abturia"}, "annotation_identification":"cf.", "species":{"species":{"string":"alabamensis", "authorship":"(Morton )", "basionymAuthorTeam":{"authorTeam":"Morton", "author":["Morton"]}}}}], "parser_run":1, "positions":{"0":["genus", 7], "8":["annotation_identification", 11], "12":["species", 23], "25":["author_word", 31]}, "surrogate": true}}
175
+ 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}}
176
176
  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]}}}
177
177
  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]}}}
178
- 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]}}}
179
- 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]}}}
180
- 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]}}}
181
- 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]}}}
182
- 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]}}}
183
- 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]}}}
184
- Formicidae cf.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Formicidae cf.", "normalized":"Formicidae", "canonical":"Formicidae", "hybrid":false, "details":[{"uninomial":{"string":"Formicidae"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}}}
185
- Formicidae cf|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Formicidae cf", "normalized":"Formicidae", "canonical":"Formicidae", "hybrid":false, "details":[{"uninomial":{"string":"Formicidae"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}}}
186
- Acastoides spp.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Acastoides spp.", "normalized":"Acastoides", "canonical":"Acastoides", "hybrid":false, "details":[{"uninomial":{"string":"Acastoides"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}}}
187
- Sphingomonas sp. 37|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Sphingomonas sp. 37", "normalized":"Sphingomonas", "canonical":"Sphingomonas", "hybrid":false, "details":[{"genus":{"string":"Sphingomonas"}, "annotation_identification":"sp.", "ignored":{"unparsed":"37"}}], "parser_run":1, "positions":{"0":["genus", 12], "13":["annotation_identification", 16]}}}
188
- Thryothorus leucotis spp. bogotensis|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Thryothorus leucotis spp. bogotensis", "normalized":"Thryothorus leucotis", "canonical":"Thryothorus leucotis", "hybrid":false, "details":[{"genus":{"string":"Thryothorus"}, "species":{"string":"leucotis"}, "infraspecies":[{"annotation_identification":"spp.", "ignored":{"infraspecies":{"string":"bogotensis", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 20], "21":["annotation_identification", 25]}}}
189
- Endoxyla sp. GM-, 2003|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Endoxyla sp. GM-, 2003", "normalized":"Endoxyla", "canonical":"Endoxyla", "hybrid":false, "details":[{"genus":{"string":"Endoxyla"}, "annotation_identification":"sp.", "ignored":{"unparsed":"GM-, 2003"}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["annotation_identification", 12]}}}
190
- Liopropoma sp.2 Not applicable|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Liopropoma sp.2 Not applicable", "normalized":"Liopropoma", "canonical":"Liopropoma", "hybrid":false, "details":[{"genus":{"string":"Liopropoma"}, "annotation_identification":"sp.", "ignored":{"unparsed":"2 Not applicable"}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["annotation_identification", 14]}}}
191
- Lacanobia nr. subjuncta Bold:Aab, 0925|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Lacanobia nr. subjuncta Bold:Aab, 0925", "normalized":"Lacanobia", "canonical":"Lacanobia", "hybrid":false, "details":[{"genus":{"string":"Lacanobia"}, "annotation_identification":"nr.", "ignored":{"species":{"string":"subjuncta", "authorship":"Bold:Aab", "basionymAuthorTeam":{"authorTeam":"Bold:Aab", "author":["Bold:Aab"]}}}}], "parser_run":2, "positions":{"0":["genus", 9], "10":["annotation_identification", 13]}}}
192
- Lacanobia sp. nr. subjuncta Bold:Aab, 0925|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Lacanobia sp. nr. subjuncta Bold:Aab, 0925", "normalized":"Lacanobia", "canonical":"Lacanobia", "hybrid":false, "details":[{"genus":{"string":"Lacanobia"}, "annotation_identification":"sp. nr.", "ignored":{"species":{"string":"subjuncta", "authorship":"Bold:Aab", "basionymAuthorTeam":{"authorTeam":"Bold:Aab", "author":["Bold:Aab"]}}}}], "parser_run":2, "positions":{"0":["genus", 9], "10":["annotation_identification", 17]}}}
178
+ 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}}
179
+ 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}}
180
+ 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}}
181
+ 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}}
182
+ 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}}
183
+ Xenodon sp.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Xenodon sp.", "normalized":"Xenodon", "canonical":"Xenodon", "hybrid":false, "details":[{"uninomial":{"string":"Xenodon"}}], "parser_run":1, "positions":{"0":["uninomial", 7]}, "surrogate": true}}
184
+ Formicidae cf.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Formicidae cf.", "normalized":"Formicidae", "canonical":"Formicidae", "hybrid":false, "details":[{"uninomial":{"string":"Formicidae"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}, "surrogate": true}}
185
+ Formicidae cf|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Formicidae cf", "normalized":"Formicidae", "canonical":"Formicidae", "hybrid":false, "details":[{"uninomial":{"string":"Formicidae"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}, "surrogate": true}}
186
+ Acastoides spp.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Acastoides spp.", "normalized":"Acastoides", "canonical":"Acastoides", "hybrid":false, "details":[{"uninomial":{"string":"Acastoides"}}], "parser_run":1, "positions":{"0":["uninomial", 10]}, "surrogate": true}}
187
+ Sphingomonas sp. 37|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Sphingomonas sp. 37", "normalized":"Sphingomonas", "canonical":"Sphingomonas", "hybrid":false, "details":[{"genus":{"string":"Sphingomonas"}, "annotation_identification":"sp.", "ignored":{"unparsed":"37"}}], "parser_run":1, "positions":{"0":["genus", 12], "13":["annotation_identification", 16]}, "surrogate": true}}
188
+ Thryothorus leucotis spp. bogotensis|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Thryothorus leucotis spp. bogotensis", "normalized":"Thryothorus leucotis", "canonical":"Thryothorus leucotis", "hybrid":false, "details":[{"genus":{"string":"Thryothorus"}, "species":{"string":"leucotis"}, "infraspecies":[{"annotation_identification":"spp.", "ignored":{"infraspecies":{"string":"bogotensis", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 20], "21":["annotation_identification", 25]}, "surrogate": true}}
189
+ Endoxyla sp. GM-, 2003|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Endoxyla sp. GM-, 2003", "normalized":"Endoxyla", "canonical":"Endoxyla", "hybrid":false, "details":[{"genus":{"string":"Endoxyla"}, "annotation_identification":"sp.", "ignored":{"unparsed":"GM-, 2003"}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["annotation_identification", 12]}, "surrogate": true}}
190
+ Liopropoma sp.2 Not applicable|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Liopropoma sp.2 Not applicable", "normalized":"Liopropoma", "canonical":"Liopropoma", "hybrid":false, "details":[{"genus":{"string":"Liopropoma"}, "annotation_identification":"sp.", "ignored":{"unparsed":"2 Not applicable"}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["annotation_identification", 14]}, "surrogate": true}}
191
+ Lacanobia nr. subjuncta Bold:Aab, 0925|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Lacanobia nr. subjuncta Bold:Aab, 0925", "normalized":"Lacanobia", "canonical":"Lacanobia", "hybrid":false, "details":[{"genus":{"string":"Lacanobia"}, "annotation_identification":"nr.", "ignored":{"species":{"string":"subjuncta", "authorship":"Bold:Aab", "basionymAuthorTeam":{"authorTeam":"Bold:Aab", "author":["Bold:Aab"]}}}}], "parser_run":2, "positions":{"0":["genus", 9], "10":["annotation_identification", 13]}, "surrogate": true}}
192
+ Lacanobia sp. nr. subjuncta Bold:Aab, 0925|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Lacanobia sp. nr. subjuncta Bold:Aab, 0925", "normalized":"Lacanobia", "canonical":"Lacanobia", "hybrid":false, "details":[{"genus":{"string":"Lacanobia"}, "annotation_identification":"sp. nr.", "ignored":{"species":{"string":"subjuncta", "authorship":"Bold:Aab", "basionymAuthorTeam":{"authorTeam":"Bold:Aab", "author":["Bold:Aab"]}}}}], "parser_run":2, "positions":{"0":["genus", 9], "10":["annotation_identification", 17]}, "surrogate": true}}
193
193
  #Larus occidentalis cf. wymani|{}
194
- Calidris cf. cooperi|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Calidris cf. cooperi", "normalized":"Calidris cf. cooperi", "canonical":"Calidris cooperi", "hybrid":false, "details":[{"genus":{"string":"Calidris"}, "annotation_identification":"cf.", "species":{"species":{"string":"cooperi"}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["annotation_identification", 12], "13":["species", 20]}}}
194
+ Calidris cf. cooperi|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Calidris cf. cooperi", "normalized":"Calidris cf. cooperi", "canonical":"Calidris cooperi", "hybrid":false, "details":[{"genus":{"string":"Calidris"}, "annotation_identification":"cf.", "species":{"species":{"string":"cooperi"}}}], "parser_run":1, "positions":{"0":["genus", 8], "9":["annotation_identification", 12], "13":["species", 20]}, "surrogate": true}}
195
195
  #TODO:Gemmula cf. cosmoi NP-2008 -- generates wrong authorship
196
196
 
197
197
  #unknown authorship
@@ -393,12 +393,12 @@ Zygaena witti Wiegel [1973]|{"scientificName":{"parsed":true, "parser_version":"
393
393
  Deyeuxia coarctata Kunth, 1815 [1816]|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":2,"verbatim":"Deyeuxia coarctata Kunth, 1815 [1816]","normalized":"Deyeuxia coarctata Kunth 1815 (1816)","canonical":"Deyeuxia coarctata","hybrid":false,"details":[{"genus":{"string":"Deyeuxia"},"species":{"string":"coarctata","authorship":"Kunth, 1815 [1816]","basionymAuthorTeam":{"authorTeam":"Kunth","author":["Kunth"],"year":"1815","approximate_year":"(1816)"}}}],"positions":{"0":["genus",8],"9":["species",18],"19":["author_word",24],"26":["year",30],"32":["year",36]}}}
394
394
 
395
395
  #names with garbage at the end
396
- Morea (Morea) Burt 2342343242 23424322342 23424234|{"scientificName":{"parsed":true, "verbatim":"Morea (Morea) Burt 2342343242 23424322342 23424234", "normalized":"Morea (Morea) Burt", "canonical":"Morea", "hybrid":false, "details":[{"uninomial":{"string":"Morea", "infragenus":{"string":"Morea"}, "authorship":"Burt", "basionymAuthorTeam":{"authorTeam":"Burt", "author":["Burt"]}}}], "parser_version":"test_version", "parser_run":2, "positions":{"0":["uninomial", 5], "7":["infragenus", 12], "14":["author_word", 18]}}}
396
+ Morea (Morea) Burt 2342343242 23424322342 23424234|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Morea (Morea) Burt 2342343242 23424322342 23424234", "normalized":"Morea (Morea) Burt", "canonical":"Morea", "hybrid":false, "details":[{"uninomial":{"string":"Morea", "infragenus":{"string":"Morea"}, "authorship":"Burt", "basionymAuthorTeam":{"authorTeam":"Burt", "author":["Burt"]}}}], "parser_run":2, "positions":{"0":["uninomial", 5], "7":["infragenus", 12], "14":["author_word", 18]}, "surrogate":true}}
397
397
  Nautilus asterizans von|{"scientificName":{"parsed":true, "verbatim":"Nautilus asterizans von", "normalized":"Nautilus asterizans", "canonical":"Nautilus asterizans", "hybrid":false, "details":[{"genus":{"string":"Nautilus"}, "species":{"string":"asterizans"}}], "parser_version":"test_version", "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 19]}}}
398
398
 
399
399
  #salvage canonical
400
- Morea ssjjlajajaj324$33 234243242|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Morea ssjjlajajaj324$33 234243242", "normalized":"Morea", "canonical":"Morea", "hybrid":false, "details":[{"uninomial":{"string":"Morea"}}], "parser_run":2, "positions":{"0":["uninomial", 5]}}}
401
- Morea (Morea) burtius 2342343242 23424322342 23424234|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":2,"verbatim":"Morea (Morea) burtius 2342343242 23424322342 23424234","normalized":"Morea (Morea) burtius","canonical":"Morea burtius","hybrid":false,"details":[{"genus":{"string":"Morea"},"infragenus":{"string":"Morea"},"species":{"string":"burtius"}}],"positions":{"0":["genus",5],"7":["infragenus",12],"14":["species",21]}}}
400
+ Morea ssjjlajajaj324$33 234243242|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Morea ssjjlajajaj324$33 234243242", "normalized":"Morea", "canonical":"Morea", "hybrid":false, "details":[{"uninomial":{"string":"Morea"}}], "parser_run":2, "positions":{"0":["uninomial", 5]}, "surrogate":true}}
401
+ Morea (Morea) burtius 2342343242 23424322342 23424234|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Morea (Morea) burtius 2342343242 23424322342 23424234", "normalized":"Morea (Morea) burtius", "canonical":"Morea burtius", "hybrid":false, "details":[{"genus":{"string":"Morea"}, "infragenus":{"string":"Morea"}, "species":{"string":"burtius"}}], "parser_run":2, "positions":{"0":["genus", 5], "7":["infragenus", 12], "14":["species", 21]}, "surrogate":true}}
402
402
  Verpericola megasoma ""Dall" Pils.|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":2,"verbatim":"Verpericola megasoma \"\"Dall\" Pils.","normalized":"Verpericola megasoma","canonical":"Verpericola megasoma","hybrid":false,"details":[{"genus":{"string":"Verpericola"},"species":{"string":"megasoma"}}],"positions":{"0":["genus",11],"12":["species",20]}}}
403
403
  Verpericola megasoma "Dall" Pils.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Verpericola megasoma \"Dall\" Pils.", "normalized":"Verpericola megasoma", "canonical":"Verpericola megasoma", "hybrid":false, "details":[{"genus":{"string":"Verpericola"}, "species":{"string":"megasoma"}}], "parser_run":2, "positions":{"0":["genus", 11], "12":["species", 20]}}}
404
404
  Moraea spathulata ( (L. f. Klatt|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":2,"verbatim":"Moraea spathulata ( (L. f. Klatt","normalized":"Moraea spathulata","canonical":"Moraea spathulata","hybrid":false,"details":[{"genus":{"string":"Moraea"},"species":{"string":"spathulata"}}],"positions":{"0":["genus",6],"7":["species",17]}}}
@@ -412,5 +412,12 @@ Kerana var. cameroni|{"scientificName":{"parsed":true, "parser_version":"test_ve
412
412
  #should parse names which previously caused prolems:
413
413
  Buteo borealis ? ventralis|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Buteo borealis ? ventralis", "normalized":"Buteo borealis", "canonical":"Buteo borealis", "hybrid":false, "details":[{"genus":{"string":"Buteo"}, "species":{"string":"borealis"}, "infraspecies":[{"annotation_identification":"?", "ignored":{"infraspecies":{"string":"ventralis", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 14], "15":["annotation_identification", 17]}}}
414
414
  Cetraria islandica ? islandica|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Cetraria islandica ? islandica", "normalized":"Cetraria islandica", "canonical":"Cetraria islandica", "hybrid":false, "details":[{"genus":{"string":"Cetraria"}, "species":{"string":"islandica"}, "infraspecies":[{"annotation_identification":"?", "ignored":{"infraspecies":{"string":"islandica", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 18], "19":["annotation_identification", 21]}}}
415
- Euxoa nr. idahoensis sp. 1clay|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Euxoa nr. idahoensis sp. 1clay", "normalized":"Euxoa idahoensis", "canonical":"Euxoa idahoensis", "hybrid":false, "details":[{"genus":{"string":"Euxoa"}, "species":{"string":"idahoensis"}, "infraspecies":[{"annotation_identification":"sp.", "ignored":{"infraspecies":{"string":"uniclay", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 5], "10":["species", 20], "21":["annotation_identification", 24]}}}
415
+ Euxoa nr. idahoensis sp. 1clay|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Euxoa nr. idahoensis sp. 1clay", "normalized":"Euxoa idahoensis", "canonical":"Euxoa idahoensis", "hybrid":false, "details":[{"genus":{"string":"Euxoa"}, "species":{"string":"idahoensis"}, "infraspecies":[{"annotation_identification":"sp.", "ignored":{"infraspecies":{"string":"uniclay", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 5], "10":["species", 20], "21":["annotation_identification", 24]}, "surrogate": true}}
416
416
  Parus caeruleus species complex|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Parus caeruleus species complex", "normalized":"Parus caeruleus", "canonical":"Parus caeruleus", "hybrid":false, "details":[{"genus":{"string":"Parus"}, "species":{"string":"caeruleus"}}], "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 15]}}}
417
+
418
+ #should flag surrogate names
419
+ Coleoptera sp. BOLD:AAV0432|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Coleoptera sp. BOLD:AAV0432", "normalized":"Coleoptera", "canonical":"Coleoptera", "hybrid":false, "details":[{"genus":{"string":"Coleoptera"}, "annotation_identification":"sp.", "ignored":{"unparsed":"BOLD:AAV0432"}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["annotation_identification", 14]}, "surrogate":true}}
420
+ Coleoptera Bold:AAV0432|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Coleoptera Bold:AAV0432", "normalized":"Coleoptera", "canonical":"Coleoptera", "hybrid":false, "details":[{"uninomial":{"string":"Coleoptera"}}], "parser_run":2, "positions":{"0":["uninomial", 10]}, "surrogate":true}}
421
+
422
+ #should not flag as surrogates similar to surrogates names
423
+ Dryopteris X separabilis Small (pro sp.)|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Dryopteris X separabilis Small (pro sp.)", "normalized":"Dryopteris × separabilis Small", "canonical":"Dryopteris separabilis", "hybrid":false, "details":[{"genus":{"string":"Dryopteris"}, "species":{"string":"separabilis", "authorship":"Small", "basionymAuthorTeam":{"authorTeam":"Small", "author":["Small"]}}}], "parser_run":2, "positions":{"0":["genus", 10], "13":["species", 24], "25":["author_word", 30]}}}
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: biodiversity19
3
3
  version: !ruby/object:Gem::Version
4
- version: 3.0.1
4
+ version: 3.1.0
5
5
  prerelease:
6
6
  platform: ruby
7
7
  authors:
@@ -9,7 +9,7 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2013-05-08 00:00:00.000000000 Z
12
+ date: 2013-06-17 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: rake
@@ -209,9 +209,6 @@ required_ruby_version: !ruby/object:Gem::Requirement
209
209
  - - ! '>='
210
210
  - !ruby/object:Gem::Version
211
211
  version: '0'
212
- segments:
213
- - 0
214
- hash: 3385796249642264380
215
212
  required_rubygems_version: !ruby/object:Gem::Requirement
216
213
  none: false
217
214
  requirements: