added citation and citation_topic linkages, added string utility to t…

…rim and set to nil if empty

app/models/biological_association.rb

@@ -1,4 +1,7 @@
 class BiologicalAssociation < ActiveRecord::Base
+
+  include Shared::Citable
+
   belongs_to :biological_relationship
 
   # TODO Must rename object

app/models/biological_associations_graph.rb

@@ -1,5 +1,7 @@
 class BiologicalAssociationsGraph < ActiveRecord::Base
 
+  include Shared::Citable
+
   has_many :biological_associations
 
 

app/models/citation.rb

@@ -1,6 +1,12 @@
+# Citation is like Roles in that it is also a linking table between a data object & a source.
+# (Assertion that the subject was referenced in a source)
 class Citation < ActiveRecord::Base
 
   belongs_to :citation_object, polymorphic: :true
-  belongs_to :source
+  belongs_to :source, inverse_of: :citations
 
+  has_many :citation_topics, inverse_of: :citation
+
+  validates_presence_of :citation_object_id, :citation_object_type, :source_id
+  validates_uniqueness_of :citation_object_id, :citation_object_type, :source_id
 end

app/models/citation_topic.rb

@@ -1,15 +1,13 @@
 class CitationTopic < ActiveRecord::Base
-  belongs_to :topic
-  belongs_to :citation
+  belongs_to :topic, inverse_of: :citation_topics
+  belongs_to :citation, inverse_of: :citation_topics
 
   validates_presence_of :topic_id, :citation_id
   validates_uniqueness_of :topic_id, :citation_id
 
-  before_save :trim_pages
+  nil_trim_attributes(:pages)
+
 
   protected
 
-  def trim_pages # pages should have content or be empty
-    self.pages = self.pages.to_str.strip
-  end
-end
+ end

app/models/collecting_event.rb

@@ -1,4 +1,7 @@
 class CollectingEvent < ActiveRecord::Base
+
+  include Shared::Citable  # ?
+
   # several lines commented out per Matt ('old stuff')
   # belongs_to :geographic_area
   # belongs_to :confidence

app/models/collection_object.rb

@@ -2,6 +2,7 @@ class CollectionObject < ActiveRecord::Base
 
   include Shared::Identifiable
   include Shared::Containable
+  include Shared::Citable
 
   belongs_to :preparation_type
 

app/models/controlled_vocabulary_term/topic.rb

@@ -1,2 +1,3 @@
-class ControlledVocabularyTerm::Topic < ControlledVocabularyTerm 
+class ControlledVocabularyTerm::Topic < ControlledVocabularyTerm
+  has_many :citation_topics, inverse_of: :topic
 end

app/models/otu.rb

@@ -1,6 +1,8 @@
 class Otu < ActiveRecord::Base
 
   include Shared::Identifiable
+  include Shared::Citable        # ?
+
   has_many :taxon_determinations
 
   has_many :contents

app/models/source.rb

@@ -1,6 +1,9 @@
 class Source < ActiveRecord::Base
   include Shared::Identifiable 
-  include Shared::HasRoles 
+  include Shared::HasRoles
+
+  has_many :citations, inverse_of: :source
+  has_many :cited_objects, through: :citations, source: :citation_object # not ordered
 
   #validate :not_empty
 

app/models/taxon_determination.rb

@@ -19,6 +19,7 @@
 class TaxonDetermination < ActiveRecord::Base
 
   include Shared::HasRoles
+  include Shared::Citable
 
   belongs_to :otu
   belongs_to :biological_collection_object

app/models/type_specimen.rb

@@ -1,4 +1,7 @@
 class TypeSpecimen < ActiveRecord::Base
+
+  include Shared::Citable
+
   belongs_to :biological_object
   belongs_to :taxon_name
 

lib/activerecord_utilities.rb

@@ -0,0 +1,36 @@
+module ActiverecordUtilities
+# this is for shared utilies, like string manipulation methods.
+
+  extend ActiveSupport::Concern
+
+  included do
+    # these are the extensions (like has_many)
+    before_validation :trim_attributes
+    class_attribute :attributes_to_trim
+
+  end
+
+  module ClassMethods
+    # any def inside here is a class method
+    def nil_trim_attributes(*attributes) # this assigns the attributes to be trimmed
+      self.attributes_to_trim = attributes
+    end
+  end
+
+  protected
+# any def below this is an instance method
+  def trim_attributes
+    if !self.attributes_to_trim.nil?
+      self.attributes_to_trim.each do |a|
+        self.send("#{a}=".to_sym, Utilities::Strings.nil_strip(self.send(a)))
+      end
+    end
+  end
+
+end
+
+class ActiveRecord::Base
+  include ActiverecordUtilities
+end
+
+

lib/taxonworks.rb

@@ -7,4 +7,5 @@
 
 
 module TaxonWorks
+  require 'activerecord_utilities'
 end

lib/utilities/strings.rb

@@ -0,0 +1,10 @@
+module Utilities::Strings
+
+  def self.nil_strip(string) # string should have content or be empty
+    if !string.nil?
+      string.strip!
+      string = nil if string == ''
+    end
+    string
+  end
+end

spec/lib/activerecord_utilities_spec.rb

@@ -0,0 +1,10 @@
+require 'spec_helper'
+require 'activerecord_utilities'
+
+#include dummy class to test the activerecord_utilities
+
+class TestStringsManipulations
+#     include ActiverecordUtilities
+
+
+end

spec/models/citation_spec.rb

@@ -4,6 +4,7 @@
   let(:citation) {Citation.new}
 
   context 'associations' do
+
     context 'belongs_to' do
       specify 'citation_object' do
         expect(citation).to respond_to(:citation_object)
@@ -15,6 +16,10 @@
     end
   end
 
+  context 'validations' do
+    # check for all required fields.
+  end
+
   context 'concerns' do
     specify 'isolate and create concern citable (see identifiable concern)' 
   end

spec/models/source/bibtex_spec.rb

@@ -359,8 +359,44 @@
       end
     end
   end
-
 
+
+  context 'class methods' do
+    # create_with_roles(bibtex_entry, opts = {})
+    #    opts = {
+    #      use_vetted_people: false
+    #    }.merge!(opts)
+    context 'create_with_roles(BibTeX::Entry instance)' do
+
+      specify 'creates author/editor roles with Person::Unvetted by default' do
+        pending
+      end
+
+      context 'parameters' do
+        specify '{use_vetted_people: true} - uses exactly matching Person::Vetted found, otherwise creates new editors/authors' do
+          pending
+        end
+      end
+    end
+  end
+
+  context 'supporting libs' do
+    context 'if I have a zotero bibliography' do
+      context 'and I import it to TW' do
+        context 'when I update a record in zotero' do
+          specify 'then TW should be aware and notify me of discrepancies' do
+            pending 'not implemented yet'
+          end
+        end
+      end
+    end
+
+    context 'Hackathon requirements' do
+      # TODO: code lib/bibtex
+      pending 'Should be able to round trip data a whole file '
+      #(e.g. import a BibTex file, then output a BibTex file and have them be the same.)
+    end
+  end
   context('Beth') do
 =begin
     notes/things to do:
@@ -389,42 +425,6 @@
     #  bs3.save
     #end
 
-    context 'class methods' do
-      # create_with_roles(bibtex_entry, opts = {})
-      #    opts = {
-      #      use_vetted_people: false
-      #    }.merge!(opts)
-      context 'create_with_roles(BibTeX::Entry instance)' do
-
-        specify 'creates author/editor roles with Person::Unvetted by default' do
-          pending
-        end
-
-        context 'parameters' do
-          specify '{use_vetted_people: true} - uses exactly matching Person::Vetted found, otherwise creates new editors/authors' do
-            pending
-          end
-        end
-      end
-    end
-
-    context 'supporting libs' do
-      context 'if I have a zotero bibliography' do
-        context 'and I import it to TW' do
-          context 'when I update a record in zotero' do
-            specify 'then TW should be aware and notify me of discrepancies' do
-              pending 'not implemented yet'
-            end
-          end
-        end
-      end
-
-      context 'Hackathon requirements' do
-        # TODO: code lib/bibtex
-        pending 'Should be able to round trip data a whole file '
-        #(e.g. import a BibTex file, then output a BibTex file and have them be the same.)
-      end
-    end
   end
 
   context 'concerns' do

spec/models/source_spec.rb

@@ -4,6 +4,14 @@
   let(:source) { Source.new }
 
 
+  context 'associtations' do
+    specify 'sources have citations' do
+      expect(source).to respond_to(:citations)
+    end
+    specify 'sources have cited_objects' do
+      expect(source).to respond_to(:cited_objects)
+    end
+  end
 
   context "concerns" do
     it_behaves_like 'identifiable'