biodiversity19 1.0.12 → 1.0.13

data/CHANGELOG

@@ -0,0 +1,7 @@
+1.0.13 -- canonical forms for cf. aff. qualifiers are modified: canonical for 
+'Aus cf. bus' is now 'Aus bus'; canonical for 'Aus aff. bus' is now 'Aus'.
+Ranks at the end of the name like 'var', 'ssp', 'spp' are considered junk and
+are ignored
+
+1.0.12 -- bug is fixed which prevented 'Cucurbita pepo' be parsed correctly, 
+f., forma, fr. are now treated as any other ranks.

data/Gemfile

@@ -8,6 +8,8 @@ group :development do
 end
 
 group :test do
-  gem "ruby-debug19", :require => "ruby-debug"
+  if RUBY_VERSION =~ /^1\.9/
+    gem "ruby-debug19", :require => "ruby-debug"
+  end
   gem "rspec"
 end

data/Gemfile.lock

@@ -1,16 +1,12 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    archive-tar-minitar (0.5.2)
-    columnize (0.3.4)
     diff-lcs (1.1.3)
     git (1.2.5)
     jeweler (1.6.4)
       bundler (~> 1.0)
       git (>= 1.2.5)
       rake
-    linecache19 (0.5.12)
-      ruby_core_source (>= 0.1.4)
     parallel (0.5.9)
     polyglot (0.3.3)
     rake (0.9.2.2)
@@ -22,16 +18,6 @@ GEM
     rspec-expectations (2.7.0)
       diff-lcs (~> 1.1.2)
     rspec-mocks (2.7.0)
-    ruby-debug-base19 (0.11.25)
-      columnize (>= 0.3.1)
-      linecache19 (>= 0.5.11)
-      ruby_core_source (>= 0.1.4)
-    ruby-debug19 (0.11.6)
-      columnize (>= 0.3.1)
-      linecache19 (>= 0.5.11)
-      ruby-debug-base19 (>= 0.11.19)
-    ruby_core_source (0.1.5)
-      archive-tar-minitar (>= 0.5.2)
     treetop (1.4.10)
       polyglot
       polyglot (>= 0.3.1)
@@ -43,5 +29,4 @@ DEPENDENCIES
   jeweler
   parallel
   rspec
-  ruby-debug19
   treetop

data/VERSION

@@ -1 +1 @@
-1.0.12
+1.0.13

data/lib/biodiversity/parser.rb

@@ -12,12 +12,17 @@ module PreProcessor
   TAXON_CONCEPTS2 = /\s+(\(?s\.\s?s\.|\(?s\.\s?l\.|\(?s\.\s?str\.|\(?s\.\s?lat\.|sec\.|sec|near)\b.*$/
   TAXON_CONCEPTS3 = /(,\s*|\s+)(pro parte|p\.\s?p\.)\s*$/i  
   NOMEN_CONCEPTS  = /(,\s*|\s+)(\(?nomen|\(?nom\.|\(?comb\.).*$/i
-  LAST_WORD_JUNK  = /(,\s*|\s+)(von|van|sensu|new|non|nec|cf|ssp|subsp|subgen|hybrid|hort.|hort)\s*$/i
+  COMPARATORS     = /\s+(aff\.|aff)\b.*$/i
+  CF_COMPARATOR   = /\s+(cf\.|cf)\s+/i
+  LAST_WORD_JUNK  = /(,\s*|\s+)(spp\.|spp|var\.|var|von|van|sensu|new|non|nec|cf|ssp|subsp|subgen|hybrid|hort\.|hort)\s*$/i
   
   def self.clean(a_string)
-    [NOTES, TAXON_CONCEPTS1, TAXON_CONCEPTS2, TAXON_CONCEPTS3, NOMEN_CONCEPTS, LAST_WORD_JUNK].each do |i|
+    [NOTES, TAXON_CONCEPTS1, TAXON_CONCEPTS2, TAXON_CONCEPTS3, NOMEN_CONCEPTS, COMPARATORS, LAST_WORD_JUNK].each do |i|
       a_string = a_string.gsub(i, '')
     end
+    [CF_COMPARATOR].each do |i|
+      a_string = a_string.gsub(i, ' ')
+    end
     a_string = a_string.tr('ſ','s') #old 's'
     a_string
   end   

data/lib/biodiversity/parser/scientific_name_clean.treetop

@@ -401,7 +401,7 @@ grammar ScientificNameClean
       end    
     }
   end
-  
+
   rule rank
     ("morph."/"f.sp."/"B"/"ssp."/"ssp"/"mut."/"nat"/"nothosubsp."/"convar."/"pseudovar."/"sect."/"ser."/"var."/"subvar."/ "[var.]" /"var"/"subsp."/"subsp"/"subf."/"race"/"forma"/"form."/"form"/"fo."/"f."/"α"/"ββ"/"β"/"γ"/"δ"/"ε"/"φ"/"θ"/"μ"/"a."/"b."/"c."/"d."/"e."/"g."/"k."/"****"/"**"/"*")
     {

data/spec/parser/test_data.txt

@@ -125,6 +125,19 @@ Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 19
 Senecio fuchsii C.C.Gmel. subsp. fuchsii var. expansus (Boiss. & Heldr.) Hayek|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Senecio fuchsii C.C.Gmel. subsp. fuchsii var. expansus (Boiss. & Heldr.) Hayek", "normalized":"Senecio fuchsii C.C.Gmel. subsp. fuchsii var. expansus (Boiss. et Heldr.) Hayek", "canonical":"Senecio fuchsii fuchsii expansus", "hybrid":false, "details":[{"genus":{"string":"Senecio"}, "species":{"string":"fuchsii", "authorship":"C.C.Gmel.", "basionymAuthorTeam":{"authorTeam":"C.C.Gmel.", "author":["C.C.Gmel."]}}, "infraspecies":[{"string":"fuchsii", "rank":"subsp."}, {"string":"expansus", "rank":"var.", "authorship":"(Boiss. & Heldr.) Hayek", "combinationAuthorTeam":{"authorTeam":"Hayek", "author":["Hayek"]}, "basionymAuthorTeam":{"authorTeam":"Boiss. & Heldr.", "author":["Boiss.", "Heldr."]}}]}], "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 15], "16":["author_word", 25], "26":["infraspecific_type", 32], "33":["infraspecies", 40], "41":["infraspecific_type", 45], "46":["infraspecies", 54], "56":["author_word", 62], "65":["author_word", 71], "73":["author_word", 78]}}}
 Senecio fuchsii C.C.Gmel. subsp. fuchsii var. fuchsii|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Senecio fuchsii C.C.Gmel. subsp. fuchsii var. fuchsii", "normalized":"Senecio fuchsii C.C.Gmel. subsp. fuchsii var. fuchsii", "canonical":"Senecio fuchsii fuchsii fuchsii", "hybrid":false, "details":[{"genus":{"string":"Senecio"}, "species":{"string":"fuchsii", "authorship":"C.C.Gmel.", "basionymAuthorTeam":{"authorTeam":"C.C.Gmel.", "author":["C.C.Gmel."]}}, "infraspecies":[{"string":"fuchsii", "rank":"subsp."}, {"string":"fuchsii", "rank":"var."}]}], "parser_run":1, "positions":{"0":["genus", 7], "8":["species", 15], "16":["author_word", 25], "26":["infraspecific_type", 32], "33":["infraspecies", 40], "41":["infraspecific_type", 45], "46":["infraspecies", 53]}}}
 
+
+#species and infraspecies without epithets, comparisons
+Alviniconcha aff alba|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alviniconcha aff alba", "normalized":"Alviniconcha", "canonical":"Alviniconcha", "hybrid":false, "details":[{"uninomial":{"string":"Alviniconcha"}}], "parser_run":1, "positions":{"0":["uninomial", 12]}}}
+Alviniconcha aff. alba|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alviniconcha aff. alba", "normalized":"Alviniconcha", "canonical":"Alviniconcha", "hybrid":false, "details":[{"uninomial":{"string":"Alviniconcha"}}], "parser_run":1, "positions":{"0":["uninomial", 12]}}}
+Alviniconcha cf. alba|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alviniconcha cf. alba", "normalized":"Alviniconcha alba", "canonical":"Alviniconcha alba", "hybrid":false, "details":[{"genus":{"string":"Alviniconcha"}, "species":{"string":"alba"}}], "parser_run":1, "positions":{"0":["genus", 12], "13":["species", 17]}}}
+Alviniconcha cf alba|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alviniconcha cf alba", "normalized":"Alviniconcha alba", "canonical":"Alviniconcha alba", "hybrid":false, "details":[{"genus":{"string":"Alviniconcha"}, "species":{"string":"alba"}}], "parser_run":1, "positions":{"0":["genus", 12], "13":["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 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]}}}
+Alyxia reinwardti ssp.|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Alyxia reinwardti ssp.", "normalized":"Alyxia reinwardti ssp.", "canonical":"Alyxia reinwardti", "hybrid":false, "details":[{"genus":{"string":"Alyxia"}, "species":{"string":"reinwardti"}, "status":"ssp."}], "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]}}}
+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]}}}
+
 #unknown authorship
 Tragacantha leporina (?) Kuntze|{"scientificName":{"parsed":true, "parser_version":"test_version", "parser_run":1,"verbatim":"Tragacantha leporina (?) Kuntze","normalized":"Tragacantha leporina (?) Kuntze","canonical":"Tragacantha leporina","hybrid":false,"details":[{"genus":{"string":"Tragacantha"},"species":{"string":"leporina","authorship":"(?) Kuntze","combinationAuthorTeam":{"authorTeam":"Kuntze","author":["Kuntze"]},"basionymAuthorTeam":{"authorTeam":"(?)","author":["?"]}}}],"positions":{"0":["genus",11],"12":["species",20],"22":["unknown_author",23],"25":["author_word",31]}}}
 Lachenalia tricolor var. nelsonii (auct.) Baker|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Lachenalia tricolor var. nelsonii (auct.) Baker", "normalized":"Lachenalia tricolor var. nelsonii (auct.) Baker", "canonical":"Lachenalia tricolor nelsonii", "hybrid":false, "details":[{"genus":{"string":"Lachenalia"}, "species":{"string":"tricolor"}, "infraspecies":[{"string":"nelsonii", "rank":"var.", "authorship":"(auct.) Baker", "combinationAuthorTeam":{"authorTeam":"Baker", "author":["Baker"]}, "basionymAuthorTeam":{"authorTeam":"auct.", "author":["unknown"]}}]}], "parser_run":1, "positions":{"0":["genus", 10], "11":["species", 19], "20":["infraspecific_type", 24], "25":["infraspecies", 33], "35":["unknown_author", 40], "42":["author_word", 47]}}}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: biodiversity19
 version: !ruby/object:Gem::Version
-  version: 1.0.12
+  version: 1.0.13
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-15 00:00:00.000000000 Z
+date: 2012-06-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: treetop
@@ -119,6 +119,7 @@ extra_rdoc_files:
 files:
 - .document
 - .rvmrc
+- CHANGELOG
 - Gemfile
 - Gemfile.lock
 - LICENSE