dwc-archive 0.4.6 → 0.4.7

data/VERSION

@@ -1 +1 @@
-0.4.6
+0.4.7

data/features/dwca-reader.feature

@@ -60,3 +60,4 @@ Feature: Reading of a Darwing Core Archive
     When I create a new DarwinCore instance
     Then I am able to use DarwinCore#normalize_classification method
     And get normalized classification in expected format
+    And there are paths, synonyms and vernacular names in normalized classification

data/features/step_definitions/dwc-reader_steps.rb

@@ -170,3 +170,24 @@ Then /^get normalized classification in expected format$/ do
   key = @normalized_classification.keys[0]
   @normalized_classification[key].class.should == DarwinCore::TaxonNormalized
 end
+
+Then /^there are paths, synonyms and vernacular names in normalized classification$/ do
+  @paths_are_generated = false
+  @synonyms_are_generated = false
+  @vernaculars_are_generated = false
+  @normalized_classification.each do |k, v|
+    if v.classification_path.size > 0
+      @paths_are_generated = true
+    end
+    if v.synonyms.size > 0
+      @synonyms_are_generated = true
+    end
+    if v.vernacular_names.size > 0
+      @vernaculars_are_generated = true
+    end
+    break if (@vernaculars_are_generated && @paths_are_generated && @synonyms_are_generated)
+  end
+  @paths_are_generated.should be_true
+  @vernaculars_are_generated.should be_true
+  @synonyms_are_generated.should be_true
+end

data/lib/dwc-archive/classification_normalizer.rb

@@ -37,9 +37,9 @@ class DarwinCore
 
     def normalize
       @res = {}
-      injest_core
+      ingest_core
       calculate_classification_path
-      injest_extensions
+      ingest_extensions
       @res
     end
 
@@ -76,14 +76,14 @@ class DarwinCore
         @core[:taxonomicstatus] ? row[@core[:taxonomicstatus]] : nil)
     end
 
-    def injest_core
+    def ingest_core
       raise RuntimeError, "Darwin Core core fields must contain taxon id and scientific name" unless (@core[:id] && @core[:scientificname])
       puts "Reading core information" if @verbose
       rows = @dwc.core.read[0]
-      puts "Injesting information from the core" if @verbose
+      puts "Ingesting information from the core" if @verbose
       rows.each_with_index do |r, i|
         count = i + 1
-        puts "Injesting %s'th record" % count if @verbose and count % @verbose_count == 0
+        puts "Ingesting %s'th record" % count if @verbose and count % @verbose_count == 0
         #core has AcceptedNameUsageId
         if @core[:acceptednameusageid] && r[@core[:acceptednameusageid]] && r[@core[:acceptednameusageid]] != r[@core[:id]]
           add_synonym_from_core(@core[:acceptednameusageid], r)
@@ -107,7 +107,7 @@ class DarwinCore
 
     def calculate_classification_path
       @res.each do |taxon_id, taxon|
-        next if taxon.classification_path 
+        next if !taxon.classification_path.empty?
         begin
           get_classification_path(taxon)
         rescue DarwinCore::ParentNotCurrentError
@@ -117,7 +117,7 @@ class DarwinCore
     end
 
     def get_classification_path(taxon)
-      return if taxon.classification_path
+      return if !taxon.classification_path.empty?
       if DarwinCore.nil_field?(taxon.parent_id)
         taxon.classification_path << taxon.current_name_canonical
       else
@@ -129,28 +129,28 @@ class DarwinCore
           raise DarwinCore::ParentNotCurrentError, error
         end
         if parent_cp
-          taxon.classification_path = parent_cp + [taxon.current_name_canonical]
+          taxon.classification_path << parent_cp + [taxon.current_name_canonical]
         else
           get_classification_path(@res[taxon.parent_id]) 
-          taxon.classification_path = @res[taxon.parent_id].classification_path + [taxon.current_name_canonical]
+          taxon.classification_path << @res[taxon.parent_id].classification_path + [taxon.current_name_canonical]
         end
       end
     end
 
-    def injest_extensions
+    def ingest_extensions
       @extensions.each do |e|
         ext, fields = *e
-        injest_synonyms(e) if fields.keys.include? :scientificname
-        injest_vernaculars(e) if fields.keys.include? :vernacularname
+        ingest_synonyms(e) if fields.keys.include? :scientificname
+        ingest_vernaculars(e) if fields.keys.include? :vernacularname
       end
     end
     
-    def injest_synonyms(extension)
-      puts "Injesting synonyms extension" if @verbose
+    def ingest_synonyms(extension)
+      puts "Ingesting synonyms extension" if @verbose
       ext, fields = *extension
       ext.read[0].each_with_index do |r, i|
         count = i + 1
-        puts "Injesting %s'th record" % count if @verbose && count % @verbose_count == 0
+        puts "Ingesting %s'th record" % count if @verbose && count % @verbose_count == 0
         @res[r[fields[:id]]].synonyms << SynonymNormalized.new(
           r[fields[:scientificname]], 
           canonical_name(r[fields[:scientificname]]), 
@@ -158,12 +158,12 @@ class DarwinCore
       end
     end
 
-    def injest_vernaculars(extension)
-      puts "Injesting vernacular names" if @verbose
+    def ingest_vernaculars(extension)
+      puts "Ingesting vernacular names" if @verbose
       ext, fields = *extension
       ext.read[0].each_with_index do |r, i|
         count = i + 1
-        puts "Injesting %s'th record" % count if @verbose && count % @verbose_count == 0
+        puts "Ingesting %s'th record" % count if @verbose && count % @verbose_count == 0
         @res[r[fields[:id]]].vernacular_names << VernacularNormalized.new(
           r[fields[:vernacularname]],
           fields[:languagecode] ? r[fields[:languagecode]] : nil)

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: dwc-archive
 version: !ruby/object:Gem::Version 
-  hash: 3
+  hash: 1
   prerelease: false
   segments: 
   - 0
   - 4
-  - 6
-  version: 0.4.6
+  - 7
+  version: 0.4.7
 platform: ruby
 authors: 
 - Dmitry Mozzherin
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-09-17 00:00:00 -04:00
+date: 2010-09-18 00:00:00 -04:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency