dwc-archive 0.7.9 → 0.7.10

data/VERSION

@@ -1 +1 @@
-0.7.9
+0.7.10

data/features/dwca-reader.feature

@@ -71,7 +71,7 @@ Feature: Reading of a Darwing Core Archive
     And names used in classification can be accessed by "name_strings" method
     And vernacular names used in classification can be accessed by "vernacular_name_strings" method
     And nodes_ids organized in trees can be accessed by "tree" method
-  
+
   Scenario: Normalizing classification without canonical names
     Given path to a dwc file "data.tar.gz"
     When I create a new DarwinCore instance

data/lib/dwc-archive/classification_normalizer.rb

@@ -229,7 +229,7 @@ class DarwinCore
     def ingest_extensions
       @extensions.each do |e|
         ext, fields = *e
-        ingest_synonyms(e) if fields.keys.include? :scientificname
+        ingest_synonyms(e) if (File.split(e[0].file_path).last.match(/synonym/i) && fields.keys.include?(:scientificname))
         ingest_vernaculars(e) if fields.keys.include? :vernacularname
       end
     end
@@ -245,9 +245,13 @@ class DarwinCore
             r[fields[:scientificname]],
             r[fields[:canonicalname]],
             fields[:taxonomicstatus] ? r[fields[:taxonomicstatus]] : nil)
-          @normalized_data[r[fields[:id]]].synonyms << synonym
-          add_name_string(synonym.name)
-          add_name_string(synonym.canonical_name)
+          if @normalized_data[r[fields[:id]]]
+            @normalized_data[r[fields[:id]]].synonyms << synonym
+            add_name_string(synonym.name)
+            add_name_string(synonym.canonical_name)
+          else
+            @error_names << { :taxon => synonym, :error => :synonym_of_unknown_taxa }
+          end
         end
       end
     end
@@ -274,8 +278,12 @@ class DarwinCore
             language,
             locality,
             country_code)
-          @normalized_data[r[fields[:id]]].vernacular_names << vernacular
-          add_vernacular_name_string(vernacular.name)
+          if @normalized_data[r[fields[:id]]]
+            @normalized_data[r[fields[:id]]].vernacular_names << vernacular
+            add_vernacular_name_string(vernacular.name)
+          else
+            @error_names << { :vernacular_name => vernacular, :error => :vernacular_of_unknown_taxa }
+          end
         end
       end
     end

data/spec/lib/dwc-archive_spec.rb

@@ -25,7 +25,7 @@ describe DarwinCore do
     end
   end
 
-  describe ".new" do 
+  describe ".new" do
     it "should create DarwinCore instance out of archive file" do
       ['data.zip', 'data.tar.gz', 'minimal.tar.gz', 'junk_dir_inside.zip'].each do |file|
         file = File.join(@file_dir, file)
@@ -125,8 +125,15 @@ describe DarwinCore do
       norm = dwc.normalize_classification
       norm.select { |k,v| !v.synonyms.empty? }.map { |k,v| v.synonyms }.size.should > 0
     end
-    
-    it "should be able to assemble synonyms from extension" do
+
+    it "should not assemble synonyms from extension with scientificName, and file name not matching 'synonym'" do
+      file = File.join(@file_dir, 'not_synonym_in_extension.tar.gz')
+      dwc = DarwinCore.new(file)
+      norm = dwc.normalize_classification
+      norm.select { |k,v| !v.synonyms.empty? }.map { |k,v| v.synonyms }.size.should == 0
+    end
+
+    it "should be able to assemble synonyms from core" do
       file = File.join(@file_dir, 'synonyms_in_core_accepted_name_field.tar.gz')
       dwc = DarwinCore.new(file)
       norm = dwc.normalize_classification
@@ -155,7 +162,7 @@ describe DarwinCore do
       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)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: dwc-archive
 version: !ruby/object:Gem::Version
-  version: 0.7.9
+  version: 0.7.10
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-12-07 00:00:00.000000000Z
+date: 2011-12-08 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: parsley-store
-  requirement: &70152131291540 !ruby/object:Gem::Requirement
+  requirement: &70276232306380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: 0.3.0
   type: :runtime
   prerelease: false
-  version_requirements: *70152131291540
+  version_requirements: *70276232306380
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70152131290940 !ruby/object:Gem::Requirement
+  requirement: &70276232305380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 2.7.0
   type: :development
   prerelease: false
-  version_requirements: *70152131290940
+  version_requirements: *70276232305380
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &70152131290300 !ruby/object:Gem::Requirement
+  requirement: &70276232304860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.5.0
   type: :development
   prerelease: false
-  version_requirements: *70152131290300
+  version_requirements: *70276232304860
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &70152131289460 !ruby/object:Gem::Requirement
+  requirement: &70276232304380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.1.3
   type: :development
   prerelease: false
-  version_requirements: *70152131289460
+  version_requirements: *70276232304380
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &70152131288800 !ruby/object:Gem::Requirement
+  requirement: &70276232303880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: '1.0'
   type: :development
   prerelease: false
-  version_requirements: *70152131288800
+  version_requirements: *70276232303880
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &70152131288320 !ruby/object:Gem::Requirement
+  requirement: &70276232303360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +76,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *70152131288320
+  version_requirements: *70276232303360
 - !ruby/object:Gem::Dependency
   name: ruby-debug19
-  requirement: &70152131287820 !ruby/object:Gem::Requirement
+  requirement: &70276232302860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -87,10 +87,10 @@ dependencies:
         version: 0.11.6
   type: :development
   prerelease: false
-  version_requirements: *70152131287820
+  version_requirements: *70276232302860
 - !ruby/object:Gem::Dependency
   name: parsley-store
-  requirement: &70152131287300 !ruby/object:Gem::Requirement
+  requirement: &70276232302340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,10 +98,10 @@ dependencies:
         version: 0.3.0
   type: :runtime
   prerelease: false
-  version_requirements: *70152131287300
+  version_requirements: *70276232302340
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70152131286800 !ruby/object:Gem::Requirement
+  requirement: &70276232301840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -109,10 +109,10 @@ dependencies:
         version: 1.2.9
   type: :development
   prerelease: false
-  version_requirements: *70152131286800
+  version_requirements: *70276232301840
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &70152131286300 !ruby/object:Gem::Requirement
+  requirement: &70276232301300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,7 +120,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70152131286300
+  version_requirements: *70276232301300
 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.
@@ -171,6 +171,7 @@ files:
 - spec/files/language_locality.tar.gz
 - spec/files/meta.xml
 - spec/files/minimal.tar.gz
+- spec/files/not_synonym_in_extension.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