dwc-archive 0.7.18 → 0.8.0

data/CHANGELOG

@@ -0,0 +1 @@
+0.8.0 Added linnean classification path to normalized data from DwCA. It consists of data associated with clades like 'kingdom', 'order' etc.

data/VERSION

@@ -1 +1 @@
-0.7.18
+0.8.0

data/lib/dwc-archive/classification_normalizer.rb

@@ -4,7 +4,7 @@ require 'parsley-store'
 class DarwinCore
 
   class TaxonNormalized
-    attr_accessor :id, :local_id, :global_id, :source, :parent_id, :classification_path_id, :classification_path, :current_name, :current_name_canonical, :synonyms, :vernacular_names, :rank, :status
+    attr_accessor :id, :local_id, :global_id, :source, :parent_id, :classification_path_id, :classification_path, :linnean_classification_path, :current_name, :current_name_canonical, :synonyms, :vernacular_names, :rank, :status
 
     def initialize
       @id = @parent_id = @rank = @status = nil
@@ -17,6 +17,7 @@ class DarwinCore
       @classification_path_id = []
       @synonyms = []
       @vernacular_names = []
+      @linnean_classification_path = []
     end
 
   end
@@ -165,6 +166,7 @@ class DarwinCore
             taxon.status = r[@core_fields[:taxonomicstatus]] if @core_fields[:taxonomicstatus]
             taxon.source = r[@core_fields[:source]] if @core_fields[:source]
             taxon.local_id = r[@core_fields[:localid]] if @core_fields[:localid]
+            taxon.linnean_classification_path = get_linnean_classification_path(r)
             taxon.global_id = r[@core_fields[:globalid]] if @core_fields[:globalid]
             add_name_string(taxon.current_name)
             add_name_string(taxon.current_name_canonical) if taxon.current_name_canonical && !taxon.current_name_canonical.empty?
@@ -312,5 +314,13 @@ class DarwinCore
       end
     end
 
+    def get_linnean_classification_path(row)
+      res = []
+      [:kingdom, :phylum, :class, :order, :family, :genus, :subgenus].each do |clade|
+        res << [row[@core_fields[clade]], clade] if @core_fields[clade] 
+      end
+      res
+    end
+
   end
 end

data/spec/lib/dwc-archive_spec.rb

@@ -152,6 +152,22 @@ describe DarwinCore do
       norm.select { |k,v| !v.synonyms.empty? }.size.should > 0
     end
 
+    it "should assemble linnean classification if terms for it exists" do
+      file = File.join(@file_dir, 'linnean.tar.gz')
+      dwc = DarwinCore.new(file)
+      cn = DarwinCore::ClassificationNormalizer.new(dwc)
+      norm = cn.normalize
+      cn.normalized_data.first.last.linnean_classification_path.should == [["Animalia", :kingdom], ["Arthropoda", :phylum], ["Insecta", :class], ["Diptera", :order], ["Cecidomyiidae", :family], ["Resseliella", :genus]]
+    end
+
+    it "should keep linnean classification empty if terms are not there" do
+      file = File.join(@file_dir, 'data.tar.gz')
+      dwc = DarwinCore.new(file)
+      cn = DarwinCore::ClassificationNormalizer.new(dwc)
+      norm = cn.normalize
+      cn.normalized_data.first.last.linnean_classification_path.should == []
+    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)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: dwc-archive
 version: !ruby/object:Gem::Version
-  version: 0.7.18
+  version: 0.8.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-04 00:00:00.000000000Z
+date: 2012-07-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &70360456842240 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,15 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *70360456842240
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.5.0
 - !ruby/object:Gem::Dependency
   name: parsley-store
-  requirement: &70360456841320 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +37,15 @@ dependencies:
         version: 0.3.0
   type: :runtime
   prerelease: false
-  version_requirements: *70360456841320
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.3.0
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70360456840500 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +53,15 @@ dependencies:
         version: 2.7.0
   type: :development
   prerelease: false
-  version_requirements: *70360456840500
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.7.0
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &70360456839540 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +69,15 @@ dependencies:
         version: 1.1.3
   type: :development
   prerelease: false
-  version_requirements: *70360456839540
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.3
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &70360456831940 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +85,15 @@ dependencies:
         version: '1.0'
   type: :development
   prerelease: false
-  version_requirements: *70360456831940
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &70360456831120 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +101,15 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *70360456831120
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.4
 - !ruby/object:Gem::Dependency
   name: ruby-debug19
-  requirement: &70360456830180 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -87,10 +117,15 @@ dependencies:
         version: 0.11.6
   type: :development
   prerelease: false
-  version_requirements: *70360456830180
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.11.6
 - !ruby/object:Gem::Dependency
   name: parsley-store
-  requirement: &70360456829120 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,10 +133,15 @@ dependencies:
         version: 0.3.0
   type: :runtime
   prerelease: false
-  version_requirements: *70360456829120
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.3.0
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70360456828380 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -109,10 +149,15 @@ dependencies:
         version: 1.2.9
   type: :development
   prerelease: false
-  version_requirements: *70360456828380
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.9
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &70360456827580 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,7 +165,12 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70360456827580
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 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.
@@ -133,6 +183,7 @@ extra_rdoc_files:
 files:
 - .document
 - .rvmrc
+- CHANGELOG
 - Gemfile
 - Gemfile.lock
 - LICENSE
@@ -169,6 +220,7 @@ files:
 - spec/files/invalid.tar.gz
 - spec/files/junk_dir_inside.zip
 - spec/files/language_locality.tar.gz
+- spec/files/linnean.tar.gz
 - spec/files/meta.xml
 - spec/files/minimal.tar.gz
 - spec/files/not_synonym_in_extension.tar.gz
@@ -206,7 +258,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: Handler of Darwin Core Archive files