classification_normalizer.rb in dwc-archive-0.5.3

- old
+ new

@@ -20,17 +20,17 @@
 
   class SynonymNormalized < Struct.new(:name, :canonical_name, :status);end
   class VernacularNormalized < Struct.new(:name, :language);end
 
   class ClassificationNormalizer
-    attr_reader :error_names, :tree
+    attr_reader :error_names, :tree, :normalized_data
 
     def initialize(dwc_instance)
       @dwc = dwc_instance
       @core_fields = get_fields(@dwc.core)
       @extensions = @dwc.extensions.map { |e| [e, get_fields(e)] }
-      @res = {}
+      @normalized_data = {}
       @parser = ParsleyStore.new(1,2)
       @name_strings = {}
       @error_names = []
       @tree = {}
     end
@@ -43,28 +43,28 @@
       @name_strings.keys
     end
 
     def normalize
       DarwinCore.logger_write(@dwc.object_id, "Started normalization of the classification")
-      @res = {}
+      @normalized_data = {}
       ingest_core
       DarwinCore.logger_write(@dwc.object_id, "Calculating the classification parent/child paths")
       calculate_classification_path
       DarwinCore.logger_write(@dwc.object_id, "Ingesting data from extensions")
       ingest_extensions
-      @res
+      @normalized_data
     end
 
   private
 
     def get_canonical_name(a_scientific_name)
       if R19
         a_scientific_name.force_encoding('utf-8')
       end
       canonical_name = @parser.parse(a_scientific_name, :canonical_only => true)
       add_name_string(a_scientific_name)
-      add_name_string(canonical_name) unless canonical_name.empty?
+      add_name_string(canonical_name) unless canonical_name.to_s.empty?
       canonical_name.empty? ? a_scientific_name : canonical_name
     end
     
     def get_fields(element)
       data = element.fields.inject({}) { |res, f| res[f[:term].split('/')[-1].downcase.to_sym] = f[:index].to_i; res }
@@ -75,11 +75,11 @@
     def status_synonym?(status)
       status && !!status.match(/^syn/)
     end
     
     def add_synonym_from_core(taxon_id, row)
-      taxon = @res[row[taxon_id]] ? @res[row[taxon_id]] : @res[row[taxon_id]] = DarwinCore::TaxonNormalized.new
+      taxon = @normalized_data[row[taxon_id]] ? @normalized_data[row[taxon_id]] : @normalized_data[row[taxon_id]] = DarwinCore::TaxonNormalized.new
       taxon.synonyms << SynonymNormalized.new(
         row[@core_fields[:scientificname]], 
         row[@core_fields[:canonicalname]], 
         @core_fields[:taxonomicstatus] ? row[@core_fields[:taxonomicstatus]] : nil)
     end
@@ -101,11 +101,11 @@
           if @core_fields[:acceptednameusageid] && r[@core_fields[:acceptednameusageid]] && r[@core_fields[:acceptednameusageid]] != r[@core_fields[:id]]
             add_synonym_from_core(@core_fields[:acceptednameusageid], r)
           elsif !@core_fields[:acceptednameusageid] && status_synonym?(r[@core_fields[:taxonomicstatus]])
             add_synonym_from_core(parent_id, r)
           else
-            taxon = @res[r[@core_fields[:id]]] ? @res[r[@core_fields[:id]]] : @res[r[@core_fields[:id]]] = DarwinCore::TaxonNormalized.new
+            taxon = @normalized_data[r[@core_fields[:id]]] ? @normalized_data[r[@core_fields[:id]]] : @normalized_data[r[@core_fields[:id]]] = DarwinCore::TaxonNormalized.new
             taxon.id = r[@core_fields[:id]]
             taxon.current_name = r[@core_fields[:scientificname]]
             taxon.current_name_canonical = r[@core_fields[:canonicalname]]
             taxon.parent_id = r[parent_id] 
             taxon.rank = r[@core_fields[:taxonrank]] if @core_fields[:taxonrank]
@@ -118,11 +118,11 @@
     def parent_id
       parent_id_field = @core_fields[:highertaxonid] || @core_fields[:parentnameusageid]
     end
 
     def calculate_classification_path
-      @res.each do |taxon_id, taxon|
+      @normalized_data.each do |taxon_id, taxon|
         next if !taxon.classification_path.empty?
         begin
           get_classification_path(taxon)
         rescue DarwinCore::ParentNotCurrentError
           next
@@ -137,26 +137,26 @@
         taxon.classification_path << taxon.current_name_canonical
         taxon.classification_path_id << taxon.id
         @tree.merge!(current_node)
       else
         begin
-          parent_cp = @res[taxon.parent_id].classification_path
+          parent_cp = @normalized_data[taxon.parent_id].classification_path
         rescue NoMethodError #name has a parent which is not a current name
           error = "The parent of the taxon \'#{taxon.current_name}\' is deprecated"
           @error_names << {:name => taxon, :error => error}
           raise DarwinCore::ParentNotCurrentError, error
         end
         if parent_cp.empty?
-          get_classification_path(@res[taxon.parent_id]) 
-          taxon.classification_path += @res[taxon.parent_id].classification_path + [taxon.current_name_canonical]
-          taxon.classification_path_id += @res[taxon.parent_id].classification_path_id + [taxon.id]
-          parent_node = @res[taxon.parent_id].classification_path_id.inject(@tree) {|node, id| node[id]}
+          get_classification_path(@normalized_data[taxon.parent_id]) 
+          taxon.classification_path += @normalized_data[taxon.parent_id].classification_path + [taxon.current_name_canonical]
+          taxon.classification_path_id += @normalized_data[taxon.parent_id].classification_path_id + [taxon.id]
+          parent_node = @normalized_data[taxon.parent_id].classification_path_id.inject(@tree) {|node, id| node[id]}
           parent_node.merge!(current_node)
         else
           taxon.classification_path += parent_cp + [taxon.current_name_canonical]
-          taxon.classification_path_id += @res[taxon.parent_id].classification_path_id + [taxon.id]
-          parent_node = @res[taxon.parent_id].classification_path_id.inject(@tree) {|node, id| node[id]}
+          taxon.classification_path_id += @normalized_data[taxon.parent_id].classification_path_id + [taxon.id]
+          parent_node = @normalized_data[taxon.parent_id].classification_path_id.inject(@tree) {|node, id| node[id]}
           parent_node.merge!(current_node)
         end
       end
     end
 
@@ -172,11 +172,11 @@
       DarwinCore.logger_write(@dwc.object_id, "Ingesting synonyms extension")
       ext, fields = *extension
       ext.read do |rows|
         rows[0].each do |r|
           set_scientific_name(r, fields)
-          @res[r[fields[:id]]].synonyms << SynonymNormalized.new(
+          @normalized_data[r[fields[:id]]].synonyms << SynonymNormalized.new(
             r[fields[:scientificname]], 
             r[fields[:canonicalname]], 
             fields[:taxonomicstatus] ? r[fields[:taxonomicstatus]] : nil)
         end
       end
@@ -185,10 +185,10 @@
     def ingest_vernaculars(extension)
       DarwinCore.logger_write(@dwc.object_id, "Ingesting vernacular names extension")
       ext, fields = *extension
       ext.read do |rows|
         rows[0].each do |r|
-          @res[r[fields[:id]]].vernacular_names << VernacularNormalized.new(
+          @normalized_data[r[fields[:id]]].vernacular_names << VernacularNormalized.new(
             r[fields[:vernacularname]],
             fields[:languagecode] ? r[fields[:languagecode]] : nil)
           add_name_string(r[fields[:vernacularname]])
         end
       end