dwc-archive 0.7.16 → 0.7.17

data/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2010 Dmitry Mozzherin
+Copyright (c) 2010-2012 Marine Biological Laboratoryj
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.rdoc

@@ -62,6 +62,9 @@ Update to latest rubygems (v >= 1.3.6) which adds gemcutter sources by default.
     # if you don't want to generate path consisting of canonical forms of ancestors to a taxon
     cn.normalize(:with_canonical_names => false)
 
+    # if you don't want to ingest information from extensions 
+    cn.normalize(:with_extensions => false)
+
     # to get a flat hash of nodes with attached vernacular names and synonyms
     normalized_data = cn.normalized_data
 
@@ -148,4 +151,4 @@ Update to latest rubygems (v >= 1.3.6) which adds gemcutter sources by default.
 
 == Copyright
 
-Copyright (c) 2010 Dmitry Mozzherin. See LICENSE for details.
+Copyright (c) 2010-2012 Marine Biological Laboratory. See LICENSE for details.

data/VERSION

@@ -1 +1 @@
-0.7.16
+0.7.17

data/features/dwca-reader.feature

@@ -79,3 +79,9 @@ Feature: Reading of a Darwing Core Archive
     Then I am able to use normalize method without canonical names path
     And get normalized classification in expected format
     And there are id paths, no canonical names paths in normalized classification
+  
+  Scenario: Normalizing classification skipping extensions data
+    Given path to a dwc file "synonyms_in_extension.tar.gz"
+    When I create a new DarwinCore instance
+    Then I am able to use normalize method without ingesting extensions
+    And extension information is not ingested

data/features/step_definitions/dwc-reader_steps.rb

@@ -253,3 +253,13 @@ Then /^I am able to use normalize method without canonical names path$/ do
   @cn = DarwinCore::ClassificationNormalizer.new(@dwc)
   @cn.normalize(:with_canonical_names => false)
 end
+
+Then /^I am able to use normalize method without ingesting extensions$/ do
+  @cn = DarwinCore::ClassificationNormalizer.new(@dwc)
+  @cn.normalize(:with_extensions => false)
+end
+
+Then /^extension information is not ingested$/ do
+  @cn.normalized_data.keys.size.should > 0;
+  @cn.normalized_data.values.select { |d| d.synonyms.size > 0 }.size.should == 0
+end

data/lib/dwc-archive/classification_normalizer.rb

@@ -46,30 +46,35 @@ class DarwinCore
       @vernacular_name_strings[name_string] = 1 unless @vernacular_name_strings[name_string]
     end
 
-    def name_strings(opts = {with_hash: false})
-      if opts[:with_hash]
+    def name_strings(opts = {})
+      opts = { with_hash: false }.merge(opts)
+      if !!opts[:with_hash]
         @name_strings
       else
         @name_strings.keys
       end
     end
 
-    def vernacular_name_strings(opts = {with_hash: false})
-      if opts[:with_hash]
+    def vernacular_name_strings(opts = {})
+      opts = { with_hash: false }.merge(opts)
+      if !!opts[:with_hash]
         @vernacular_name_strings
       else
         @vernacular_name_strings.keys
       end
     end
 
-    def normalize(opts = {:with_canoical_names => true})
-      @with_canonical_names = opts[:with_canonical_names] != nil ? opts[:with_canonical_names] : true
+    def normalize(opts = {})
+      opts = { :with_canonical_names => true, :with_extensions => true }.merge(opts)
+      @with_canonical_names = !!opts[:with_canonical_names]
       DarwinCore.logger_write(@dwc.object_id, "Started normalization of the classification")
       ingest_core
       DarwinCore.logger_write(@dwc.object_id, "Calculating the classification parent/child paths")
       has_parent_id? ? calculate_classification_path : @normalized_data.keys.each { |id| @tree[id] = {} }
       DarwinCore.logger_write(@dwc.object_id, "Ingesting data from extensions")
-      ingest_extensions
+      if !!opts[:with_extensions]
+        ingest_extensions
+      end
       @normalized_data
     end
 

data/spec/lib/dwc-archive_spec.rb

@@ -135,6 +135,23 @@ describe DarwinCore do
       norm.select { |k,v| !v.synonyms.empty? }.map { |k,v| v.synonyms }.size.should == 0
     end
 
+    it "should not attempt to assemble extensions with with_extensions opts set to false" do
+      file = File.join(@file_dir, 'data.tar.gz')
+      dwc = DarwinCore.new(file)
+      cn = DarwinCore::ClassificationNormalizer.new(dwc)
+      norm = cn.normalize(:with_extensions => false)
+      norm.select { |k,v| !v.vernacular_names.empty? }.size.should == 0
+      norm = cn.normalize()
+      norm.select { |k,v| !v.vernacular_names.empty? }.size.should > 0
+      file = File.join(@file_dir, 'synonyms_in_extension.tar.gz')
+      dwc = DarwinCore.new(file)
+      cn = DarwinCore::ClassificationNormalizer.new(dwc)
+      norm = cn.normalize(:with_extensions => false)
+      norm.select { |k,v| !v.synonyms.empty? }.size.should == 0
+      norm = cn.normalize()
+      norm.select { |k,v| !v.synonyms.empty? }.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)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: dwc-archive
 version: !ruby/object:Gem::Version
-  version: 0.7.16
+  version: 0.7.17
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-12-30 00:00:00.000000000Z
+date: 2012-02-15 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &70206375224560 !ruby/object:Gem::Requirement
+  requirement: &70271462144240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *70206375224560
+  version_requirements: *70271462144240
 - !ruby/object:Gem::Dependency
   name: parsley-store
-  requirement: &70206375222800 !ruby/object:Gem::Requirement
+  requirement: &70271462143620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 0.3.0
   type: :runtime
   prerelease: false
-  version_requirements: *70206375222800
+  version_requirements: *70271462143620
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70206375220540 !ruby/object:Gem::Requirement
+  requirement: &70271462142960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 2.7.0
   type: :development
   prerelease: false
-  version_requirements: *70206375220540
+  version_requirements: *70271462142960
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &70206375218040 !ruby/object:Gem::Requirement
+  requirement: &70271462133960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.1.3
   type: :development
   prerelease: false
-  version_requirements: *70206375218040
+  version_requirements: *70271462133960
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &70206375167640 !ruby/object:Gem::Requirement
+  requirement: &70271462133200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: '1.0'
   type: :development
   prerelease: false
-  version_requirements: *70206375167640
+  version_requirements: *70271462133200
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &70206375163980 !ruby/object:Gem::Requirement
+  requirement: &70271462132480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +76,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *70206375163980
+  version_requirements: *70271462132480
 - !ruby/object:Gem::Dependency
   name: ruby-debug19
-  requirement: &70206375153100 !ruby/object:Gem::Requirement
+  requirement: &70271462131580 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -87,10 +87,10 @@ dependencies:
         version: 0.11.6
   type: :development
   prerelease: false
-  version_requirements: *70206375153100
+  version_requirements: *70271462131580
 - !ruby/object:Gem::Dependency
   name: parsley-store
-  requirement: &70206375149880 !ruby/object:Gem::Requirement
+  requirement: &70271462130840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,10 +98,10 @@ dependencies:
         version: 0.3.0
   type: :runtime
   prerelease: false
-  version_requirements: *70206375149880
+  version_requirements: *70271462130840
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70206375138240 !ruby/object:Gem::Requirement
+  requirement: &70271462130180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -109,10 +109,10 @@ dependencies:
         version: 1.2.9
   type: :development
   prerelease: false
-  version_requirements: *70206375138240
+  version_requirements: *70271462130180
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &70206375130880 !ruby/object:Gem::Requirement
+  requirement: &70271462129460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,7 +120,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70206375130880
+  version_requirements: *70271462129460
 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.
@@ -201,7 +201,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.6
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: Handler of Darwin Core Archive files