dwc-archive 0.5.18 → 0.6.0

data/VERSION

@@ -1 +1 @@
-0.5.18
+0.6.0

data/lib/dwc-archive/classification_normalizer.rb

@@ -89,13 +89,29 @@ class DarwinCore
 
     def set_scientific_name(row, fields)
       row[fields[:scientificname]] = 'N/A' unless row[fields[:scientificname]]
-      canonical_name = get_canonical_name(row[fields[:scientificname]])
+      canonical_name = ''
+      scientific_name = row[fields[:scientificname]].strip
+      if separate_canonical_and_authorship?(row, fields)
+        canonical_name = row[fields[:scientificname]].strip
+        scientific_name += " #{row[fields[:scientificnameauthorship]].strip}"
+      else
+        canonical_name = get_canonical_name(row[fields[:scientificname]])
+      end
       fields[:canonicalname] = row.size
       row << canonical_name
-      scientific_name = row[fields[:scientificname]].strip
       row[fields[:scientificname]] = scientific_name
     end
 
+    def separate_canonical_and_authorship?(row, fields)
+      authorship = ''
+      if fields[:scientificnameauthorship]
+        authorship = row[fields[:scientificnameauthorship]].to_s.strip
+      end
+      !(authorship.empty? || row[fields[:scientificname]].index(authorship))
+    end
+
+
+
     def ingest_core
       raise RuntimeError, "Darwin Core core fields must contain taxon id and scientific name" unless (@core_fields[:id] && @core_fields[:scientificname])
       @dwc.core.read do |rows|

data/spec/lib/dwc-archive_spec.rb

@@ -101,16 +101,28 @@ describe DarwinCore do
       nodes_with_syn.first[1].synonyms.first.status.should == 'synonym'
     end
 
-    # it "should be able work with files which have scientificNameAuthorship" do
-    #   file = File.join(@file_dir, 'sci_name_authorship.tar.gz')
-    #   dwc = DarwinCore.new(file)
-    #   $lala = 1
-    #   norm = dwc.normalize_classification
-    #   taxa = norm.select{|k,v| v.current_name_canonical.match " "}.select{|k,v| [v.current_name.split(" ").size >  v.current_name_canonical.split(" ").size]}
-    #   taxa.size.should == 507
-    #   syn = norm.select{|k,v| v.synonyms.size > 0}.map {|k,v| v.synonyms}.flatten.select {|s| s.name.split(" ").size  > s.canonical_name.split(" ").size}
-    #   syn.size.should == 50
-    # end
+    it "should be able work with files which have scientificNameAuthorship" do
+      file = File.join(@file_dir, 'sci_name_authorship.tar.gz')
+      dwc = DarwinCore.new(file)
+      $lala = 1
+      norm = dwc.normalize_classification
+      require 'ruby-debug'; debugger
+      taxa = norm.select{|k,v| v.current_name_canonical.match " "}.select{|k,v| [v.current_name.split(" ").size >  v.current_name_canonical.split(" ").size]}
+      taxa.size.should == 507
+      syn = norm.select{|k,v| v.synonyms.size > 0}.map {|k,v| v.synonyms}.flatten.select {|s| s.name.split(" ").size  > s.canonical_name.split(" ").size}
+      syn.size.should == 50
+    end
+    
+    it "should be able work with files which repeat scientificNameAuthorship value in scientificName field" do
+      file = File.join(@file_dir, 'sci_name_authorship_dup.tar.gz')
+      dwc = DarwinCore.new(file)
+      $lala = 1
+      norm = dwc.normalize_classification
+      taxa = norm.select{|k,v| v.current_name_canonical.match " "}.select{|k,v| [v.current_name.split(" ").size >  v.current_name_canonical.split(" ").size]}
+      taxa.size.should == 507
+      syn = norm.select{|k,v| v.synonyms.size > 0}.map {|k,v| v.synonyms}.flatten.select {|s| s.name.split(" ").size  > s.canonical_name.split(" ").size}
+      syn.size.should == 50
+    end
 
     it "should be able to get language and locality fields for vernacular names" do
       file = File.join(@file_dir, 'language_locality.tar.gz')

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: dwc-archive
 version: !ruby/object:Gem::Version
-  version: 0.5.18
+  version: 0.6.0
   prerelease: 
 platform: ruby
 authors:
@@ -13,7 +13,7 @@ date: 2011-11-04 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: parsley-store
-  requirement: &70273545347720 !ruby/object:Gem::Requirement
+  requirement: &70322001068080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70273545347720
+  version_requirements: *70322001068080
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70273545347240 !ruby/object:Gem::Requirement
+  requirement: &70322001067600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *70273545347240
+  version_requirements: *70322001067600
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &70273545345720 !ruby/object:Gem::Requirement
+  requirement: &70322001067120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70273545345720
+  version_requirements: *70322001067120
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &70273545345120 !ruby/object:Gem::Requirement
+  requirement: &70322001066640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70273545345120
+  version_requirements: *70322001066640
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &70273545344540 !ruby/object:Gem::Requirement
+  requirement: &70322001066140 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *70273545344540
+  version_requirements: *70322001066140
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &70273545344060 !ruby/object:Gem::Requirement
+  requirement: &70322001065660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +76,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *70273545344060
+  version_requirements: *70322001065660
 - !ruby/object:Gem::Dependency
   name: ruby-debug19
-  requirement: &70273545343580 !ruby/object:Gem::Requirement
+  requirement: &70322001065180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70273545343580
+  version_requirements: *70322001065180
 - !ruby/object:Gem::Dependency
   name: parsley-store
-  requirement: &70273545343100 !ruby/object:Gem::Requirement
+  requirement: &70322001064700 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,10 +98,10 @@ dependencies:
         version: 0.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *70273545343100
+  version_requirements: *70322001064700
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70273545342620 !ruby/object:Gem::Requirement
+  requirement: &70322001064220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -109,10 +109,10 @@ dependencies:
         version: 1.2.9
   type: :development
   prerelease: false
-  version_requirements: *70273545342620
+  version_requirements: *70322001064220
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &70273545328540 !ruby/object:Gem::Requirement
+  requirement: &70322001063720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,7 +120,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70273545328540
+  version_requirements: *70322001063720
 description: Darwin Core Archive is the current standard exchange format for GLobal
   Names Architecture modules. This gem makes it easy to incorporate files in Darwin
   Core Archive format into a ruby project.
@@ -172,6 +172,7 @@ files:
 - spec/files/meta.xml
 - spec/files/minimal.tar.gz
 - spec/files/sci_name_authorship.tar.gz
+- spec/files/sci_name_authorship_dup.tar.gz
 - spec/files/synonyms_in_core_accepted_name_field.tar.gz
 - spec/files/synonyms_in_extension.tar.gz
 - spec/files/uncompressed