is_subsequent -> is_first; filtering intents; data attributes

app/helpers/taxon_names/catalog_helper.rb

@@ -23,8 +23,8 @@ def nomenclature_catalog_li_tag_data_attributes(nomenclature_catalog_item)
     data = {
       'history-origin' => n.origin,
       'history-object-id' => n.object.id,
-      'history-valid-name' => n.is_valid_name? && !n.is_subsequent?,
-      'history-is-subsequent' => n.is_subsequent?
+      'history-valid-name' => n.is_valid_name? && n.is_first, # is_subsequent?,
+      'history-is-subsequent' => !n.is_first # is_subsequent?
     }
     data
   end
@@ -118,7 +118,7 @@ def history_other_name(catalog_item, reference_taxon_name)
   def history_statuses(nomenclature_catalog_entry_item)
     i = nomenclature_catalog_entry_item
     s = i.base_object.taxon_name_classifications_for_statuses
-    return nil if (s.empty? || i.is_subsequent?)
+    return nil if (s.empty? || !i.is_first) # is_subsequent?
     return nil if i.from_relationship?
 
     content_tag(:span, class: [:history__statuses]) do
@@ -166,7 +166,7 @@ def history_in_taxon_name(t, c)
   end
 
   def history_type_material(entry_item)
-    return nil if entry_item.object_class != 'Protonym' || entry_item.is_subsequent?
+    return nil if entry_item.object_class != 'Protonym' || !entry_item.is_first # is_subsequent?
     content_tag(:span, ' '.html_safe + type_taxon_name_relationship_tag(entry_item.base_object.type_taxon_name_relationship), class: 'history__type_information')
   end
 

app/views/otus/timeline.json.jbuilder

@@ -16,12 +16,6 @@ json.topics do
   json.array! @catalog.topics.collect{|t| {t.to_global_id.to_s => { name: t.name, css_color: t.css_color} }}
 end
 
-json.sources do
-  json.array! @catalog.sources.collect{|s| { s.metamorphosize.to_global_id.to_s => { cached: s.cached, objects: @catalog.objects_for_source(s).collect{|o| o.object.to_global_id.to_s } }}}
-end
-
-
-
 json.items do
   json.array! @catalog.items_chronologically do |i|
     json.label_html send(i.html_helper, i)
@@ -32,3 +26,7 @@ json.items do
     end
   end
 end
+
+json.sources do
+  json.array! @catalog.sources.collect{|s| { s.metamorphosize.to_global_id.to_s => { cached: s.cached, objects: @catalog.objects_for_source(s).collect{|o| o.object.to_global_id.to_s } }}}
+end

lib/catalog/entry.rb

@@ -1,4 +1,4 @@
-# A Catalog::Entry has many entry items.  Together CatalogEntrys form a Catalog
+# A Catalog::Entry has many entry items.  Together Catalog::Entries form a Catalog
 class Catalog::Entry
 
   # The target object for this entry
@@ -52,7 +52,6 @@ def index_items
     true
   end
 
-
   # @return Boolean
   # Named "first` to avoid conflice with `citation#is_original`
   # Returns true if
@@ -69,7 +68,7 @@ def first_item?(item)
     return true if item.citation.is_original?
     return true if !original_citation_present? && o.index(item) == 0
 
-   false
+    false
   end
 
   def original_citation_present?
@@ -81,13 +80,13 @@ def original_citation_present?
 
   def items_by_object(object)
     # TODO- replace with index?
-    Catalog.chronological_item_sort( items.select{|i| i.object == object} )
+    ::Catalog.chronological_item_sort( items.select{|i| i.object == object} )
   end
 
   # @return [Array of NomenclatureCatalog::EntryItem]
   #   sorted by date, then taxon name name as rendered for this item
   def ordered_by_nomenclature_date
-    Catalog.chronological_item_sort(items)
+    ::Catalog.chronological_item_sort(items)
   end
 
   # @param [Source] source

lib/catalog/entry_item.rb

@@ -1,17 +1,13 @@
-
+# A Catalog::EntryItem corresponds to a single row in the catalog.  It can be thought of as a chronological entry typically 1:1 with some Citation.
 class Catalog::EntryItem
 
-  # The focus of this entry item
-  #   This is not an attribute of Catalog::Entry (no!)
-  #      Entry -> taxon name 
-  #         EntryItem.object -> relationship
-  #         EntryItem.base_object -> synonym 
+  # The visualized element of this entry item, e.g. the subject taxon name of a taxon name relationship
   attr_accessor :base_object
 
-  # The focus of this entry item
+  # The source of this entry item, e.g. a TaxonNameRelationship
   attr_accessor :object
 
-  # Optional
+  # Optional, should be provided explicitly 
   attr_accessor :citation
 
   # @return [Time, nil]
@@ -20,12 +16,15 @@ class Catalog::EntryItem
   # See also citation_date
   attr_accessor :nomenclature_date
 
+  # @return [Symbol]
+  #   a pointer to a method in /app/helpers 
   attr_accessor :to_html_method
 
+  #
   # Computed/cached attributes, built on `build` of Entry
-
+  #
   # @return [Boolean]
-  # See Entry#first_item?
+  #   See Catalog::Entry#first_item?
   attr_accessor :is_first
 
   # @param [Hash] args
@@ -49,11 +48,12 @@ def base_data_attributes
     }
   end
 
-  # @return [Boolean]
-  def is_subsequent?
-    # object == taxon_name && !citation.try(:is_original?)
-    references_self && !citation.nil? && !citation.is_original?
-  end
+  # Deprecated for is_first
+  # # @return [Boolean]
+  # def is_subsequent?
+  #   # object == taxon_name && !citation.try(:is_original?)
+  #   references_self && !citation.nil? && !citation.is_original?
+  # end
 
   def references_self?
     object == base_object 
@@ -83,7 +83,7 @@ def nomenclature_date
       nil
     end
   end
-  
+
   # @return [String]
   #  do not update with base_class
   def object_class

lib/catalog/nomenclature/entry.rb

@@ -1,38 +1,16 @@
-# A Catalog Entry contains the metadata the nomenclatural history of a single "reference" taxon name.
-# Mutiple CatalogEntries would make up a catalog.
+# A Catalog::Entry that contains the nomenclatural history of a single TaxonName
+# Mutiple Catalog::Entries would make up a catalog.
 
-# EntryItems for this Entry must follow:
+# EntryItems for this Entry must follow the pattern:
 # * The `base_object` is always a TaxonName
 # * The `object` may be a Protony, TaxonNameRelationship, or Combination
+#
 class Catalog::Nomenclature::Entry < Catalog::Entry
 
-  # The taxon name being referenced in this entry (think of it as the header)
-  # attr_accessor :reference_taxon_name
-
   def initialize(taxon_name)
     super(taxon_name)
   end
 
-  # @return [Array of NomenclatureCatalog::EntryItem]
-  #   sorted by date, then taxon name name as rendered for this item
-  def ordered_by_nomenclature_date
-    now = Time.now
-    items.sort{|a,b| [(a.nomenclature_date || now), a.object_class, a.base_object.cached_original_combination.to_s ] <=> [(b.nomenclature_date || now), b.object_class, b.base_object.cached_original_combination.to_s ] }
-  end
-
-  # @return [Array of EntryItems]
-  #   only those entry items that reference a TaxonNameRelationship
-  def relationship_items
-    items.select{|i| i.object_class =~ /TaxonNameRelationship/}
-  end
-
-  # @return [Scope]
-  def names
-    @names ||= all_names
-    @names
-  end
-
-  # @param [TaxonName] taxon_name
   def build
     v = object.valid_taxon_name
     base_names = v.historical_taxon_names
@@ -68,6 +46,20 @@ def build
     true
   end
 
+
+  # @return [Array of NomenclatureCatalog::EntryItem]
+  #   sorted by date, then taxon name name as rendered for this item
+  def ordered_by_nomenclature_date
+    now = Time.now
+    items.sort{|a,b| [(a.nomenclature_date || now), a.object_class, a.base_object.cached_original_combination.to_s ] <=> [(b.nomenclature_date || now), b.object_class, b.base_object.cached_original_combination.to_s ] }
+  end
+
+  # @return [Array]
+  def names
+    @names ||= all_names
+    @names
+  end
+
   protected
 
   # @param [CatalogEntry] catalog_item
@@ -111,4 +103,10 @@ def all_protonyms
     items.select{|i| i.origin == 'protonym' }
   end
 
+  # @return [Array of EntryItems]
+  #   only those entry items that reference a TaxonNameRelationship
+  def relationship_items
+    items.select{|i| i.object_class =~ /TaxonNameRelationship/}
+  end
+
 end

lib/catalog/nomenclature/entry_item.rb

@@ -1,9 +1,6 @@
-
-# Is 1:1 with a Citation
 class Catalog::Nomenclature::EntryItem < ::Catalog::EntryItem
-  # @param [Hash] args
+
   def initialize(object: nil, base_object: nil, citation: nil, nomenclature_date: nil, citation_date: nil) 
-    # raise if nomenclature_date.nil? && !%w{Protonym Combination TaxonNameRelationship}.include?(object.class.to_s)
     super
   end
 
@@ -23,30 +20,14 @@ def other_name
     end
   end
 
-# # @return [String]
-# def origin
-#   case object_class
-#   when 'Protonym'
-#     'protonym'
-#   when 'Hybrid'
-#     'hybrid'
-#   when 'Combination'
-#     'combination'
-#   when /TaxonNameRelationship/
-#     'taxon_name_relationship'
-#   else
-#     'error'
-#   end
-# end
-
   # @return [Boolean]
   def is_valid_name?
     object_class == 'Protonym' && object.is_valid?
   end
 
   def data_attributes
     base_data_attributes.merge(
-      'history-valid-name' => is_valid_name? && is_subsequent?
+      'history-valid-protonym' => is_valid_name? 
     )
   end
 

lib/catalog/timeline.rb

@@ -1,12 +1,11 @@
-
-# Filtering attributes
-#
-# data-
-#   origin: 'Original' Filter should be on 'otu' vs. everything else
-#   is_subsequent, 'Current' : if multiple citations, then true if is_original OR first in order if none is_original 
+# A Catalog::Timeline is a catalog that merges biolgological concepts (OTUs) with their nomenclature.
 #
-#   valid: true if object is a valid name, or object is otu and linked to valid_name ?
+# Filtering intent:
+#   Level 1: [Nomenclature, Protonym, OTU (biology)] - mutually exclusive
+#   Level 2 (All): [First, Valid]
 #
+# Visualizing intent:
+#   [Origin] tag
 class Catalog::Timeline < Catalog
 
   def build

spec/lib/catalog/entry_spec.rb

@@ -44,15 +44,15 @@
   end
 
   specify '#first_item?' do
-    expect(catalog_entry.first_item?(items.first)).to be_truthy
+    expect(catalog_entry.first_item?(catalog_entry.items.first)).to be_truthy
   end
 
   specify '#original_citation_present?' do
     expect(catalog_entry.original_citation_present?).to be_truthy
   end
 
   specify '#items_by_object' do
-    expect(catalog_entry.items_by_object(catalog.items.first.object)).to contain_exactly(items.first)
+    expect(catalog_entry.items_by_object(catalog_entry.items.first.object)).to contain_exactly(catalog_entry.items.first)
   end
 
 end