Reverts some geo stuff. Adds some gems.

Gemfile

@@ -8,13 +8,14 @@ gem 'pg', '~> 0.17.0'
 
 # Postgis
 gem 'activerecord-postgis-adapter'
+# gem 'rgeo-activerecord'
+# gem 'activerecord-spatial'
+gem 'squeel'
 
 # rgeo support
 gem 'ffi-geos'
 gem 'rgeo-shapefile'
 gem 'rgeo-geojson'
-gem 'rgeo-activerecord'
-# gem 'activerecord-spatial'
 
 # Use SCSS for stylesheets
 gem 'sass-rails', '~> 4.0'
@@ -69,6 +70,7 @@ gem 'rabl'
 
 group :test, :development do
   gem 'rspec-rails'
+  gem 'byebug'
   gem 'debugger', {}.merge(ENV['RM_INFO'] ? {require: false} : {})
   gem 'awesome_print'
 end

app/models/biocuration_classification.rb

@@ -2,7 +2,7 @@ class BiocurationClassification < ActiveRecord::Base
   include Housekeeping
 
   belongs_to :biocuration_class
-  belongs_to :biological_collection_object
+  belongs_to :biological_collection_object, class_name: 'CollectionObject::BiologicalCollectionObject'
 
   validates_presence_of :biocuration_class, :biological_collection_object
 

app/models/geographic_item.rb

@@ -3,6 +3,8 @@ class GeographicItem < ActiveRecord::Base
   # RGeo::Geos.preferred_native_interface = :ffi
   # RGeo::ActiveRecord::GeometryMixin.set_json_generator(:geojson)
 
+  include RGeo::ActiveRecord
+
   include Housekeeping::Users
  #  include ActiveRecordSpatial::SpatialColumns
  #  include ActiveRecordSpatial::SpatialScopes
@@ -17,13 +19,11 @@ class GeographicItem < ActiveRecord::Base
                 :multi_polygon,
                 :geometry_collection]
 
-
-  column_factory = RGeo::Geos.factory(
-    native_interface: :ffi,
-    srid:             4326,
-    has_z_coordinate: true,
-    has_m_coordinate: false)
-
+# column_factory = RGeo::Geos.factory(
+#   native_interface: :ffi,
+#   srid:             4326,
+#   has_z_coordinate: true,
+#   has_m_coordinate: false)
 
   column_factory = Georeference::FACTORY
 
@@ -38,6 +38,16 @@ class GeographicItem < ActiveRecord::Base
 
   validate :proper_data_is_provided
 
+
+  # FactoryGirl.create(:valid_geographic_item)
+  # FactoryGirl.create(:valid_geographic_item)
+  # FactoryGirl.create(:valid_geographic_item)
+  # p = GeographicItem.first.geo_object
+  #
+  # GeographicItem.where{st_intersects(point, p)}.count
+
+  # The last {} bit comes from Squeel and see bottom of https://github.com/neighborland/activerecord-postgis-adapter/blob/master/Documentation.rdoc
+
   scope :intersecting_boxes, -> (geographic_item) {
     select("ST_Contains(geographic_items.polygon, #{geographic_item.geo_object})",
           ) }

db/migrate/20140303225547_drop_biocuration_class.rb

@@ -0,0 +1,5 @@
+class DropBiocurationClass < ActiveRecord::Migration
+  def change
+    drop_table :biocuration_classes
+  end
+end

lib/material.rb

@@ -20,15 +20,11 @@ def self.create_quick_verbatim(options  = {})
       object = stub_object.clone
       object.total = opts[:collection_objects][o][:total]
 
-        foo = 2
-
       if opts[:collection_objects][o][:biocuration_classes] 
-
         object.biocuration_classes << BiocurationClass.find(opts[:collection_objects][o][:biocuration_classes]) 
       end
 
-      i += 1
-
+      # byebug 
       object.notes << note.clone if note
       object.container = container if container
       response.collection_objects.push object

lib/taxonworks.rb

@@ -5,4 +5,5 @@ module TaxonWorks
   Dir[Rails.root.to_s + '/app/models/container/**/*.rb'].sort.each {|file| require file }
   require 'soft_validation'
   require 'activerecord_utilities'
+  require 'squeel'  
 end

spec/factories/collection_object/biological_collection_object_factory.rb

@@ -0,0 +1,8 @@
+FactoryGirl.define do
+  factory :collection_object_biological_collection_object, class: 'CollectionObject::BiologicalCollectionObject', traits: [:housekeeping] do
+    factory :valid_collection_object_biological_collection_object do
+      type 'Specimen'
+      total 1
+    end
+  end
+end

spec/lib/material_spec.rb

@@ -91,8 +91,8 @@
       @two_objects_stub[:collection_objects][:object2][:biocuration_classes] = [attribute1.id, attribute4.id]
 
       response = Material.create_quick_verbatim(@two_objects_stub)
-      expect(response.collection_objects.first.biocuration_classifications).to have(4).things
-      expect(response.collection_objects.last.biocuration_classifications).to have(2).things
+      expect(response.collection_objects.first.biocuration_classes).to have(4).things
+      expect(response.collection_objects.last.biocuration_classes).to have(2).things
     end
 
   end