ensembl 0.0.7 → 0.0.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 16d2860f71a33c2c465b0fccf217377d71d583d9
-  data.tar.gz: bb8022c713d11e6fcc6c5baed00676bb3d9edd93
+  metadata.gz: 9184473a4f510dc3c745429272faf91ece792c13
+  data.tar.gz: b2cf56a525faae69a4ef6d1555e1fcdd193738af
 SHA512:
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+  metadata.gz: 116db18ee8d13e996dbe637dbfee8e50a3a0bc6fa8774c5097bc9b4543650e87dcd0d31df25355323e15698760bdc337f7841da1b945e23cc4fa09ea2ff364e2
+  data.tar.gz: 9e6f98c89c2c3018b930478144b2e17207ae166fed90b0425aab18b0ddec924c2153177e26880e9efdba67ebe5acd6df16607193c1e6b93e996f8ade840d45e6

data/lib/ensembl/core/activerecord.rb

@@ -7,12 +7,16 @@ module Ensembl
       end
     end
 
+    # ConnectionPool implemented from:
+    # http://www.lucasallan.com/2014/05/26/fixing-concurrency-issues-with-active-record-in-a-rack-application.html
     class Connection < ActiveRecord::Base
-      self.extend TableNameOverrides
+      self.extend Ensembl::TableNameOverrides
+      self.extend Ensembl::ConnectionPool
 
       self.abstract_class = true
 
       self.establish_connection :core
+
     end
 
     class ModelBase < Connection

data/lib/ensembl/variation/activerecord.rb

@@ -2,8 +2,13 @@ require 'active_record'
 
 module Ensembl
   module Variation
+
+    # ConnectionPool implemented from:
+    # http://www.lucasallan.com/2014/05/26/fixing-concurrency-issues-with-active-record-in-a-rack-application.html
     class Connection < ActiveRecord::Base
-      self.extend TableNameOverrides
+
+      self.extend Ensembl::TableNameOverrides
+      self.extend Ensembl::ConnectionPool
 
       self.abstract_class = true
 
@@ -234,15 +239,17 @@ module Ensembl
       belongs_to :study
       belongs_to :seq_region, class_name: 'Ensembl::Core::SeqRegion'
 
+      has_one :variation, primary_key: 'object_id', foreign_key: 'name'
+
       has_many :phenotype_feature_attribs
       has_many :attrib_types, through: :phenotype_feature_attribs
 
       scope :significant, -> { where(is_significant: true )}
       scope :with_studies, -> { where.not(study_id:nil)}
 
-      def variation
-        Variation.find_by name: object_id
-      end
+      # def variation
+      #   Variation.find_by name: object_id
+      # end
 
       def risk_allele
         pf=phenotype_feature_attribs.risk_alleles.first
@@ -489,7 +496,7 @@ module Ensembl
       end
 
       def all_phenotype_features
-        object_ids = synonyms
+        object_ids = synonym_names
         object_ids<<name
         PhenotypeFeature.eager_load(:phenotype).where(object_id: object_ids, type: 'Variation')
       end

data/lib/ensembl/version.rb

@@ -1,3 +1,3 @@
 module Ensembl
-  VERSION = '0.0.7'
+  VERSION = '0.0.9'
 end

data/lib/ensembl.rb

@@ -19,18 +19,17 @@ module Ensembl
     end
   end
 
-  # module AttributeLike
-  #   def a_like(attribute, string, search_type=:between)
-  #     at=self.arel_table
-  #     if search_type == :ends_with
-  #       where(at[attribute].matches("%#{string}"))
-  #     elsif search_type == :starts_with
-  #       where(at[attribute].matches("#{string}%"))
-  #     else
-  #       where(at[attribute].matches("%#{string}%"))
-  #     end
-  #   end
-  # end
+  # ConnectionPool implemented from:
+  # http://www.lucasallan.com/2014/05/26/fixing-concurrency-issues-with-active-record-in-a-rack-application.html
+  module ConnectionPool
+    singleton_class.send(:alias_method, :original_connection, :connection)
+
+    def self.connection
+      ActiveRecord::Base.connection_pool.with_connection do |conn|
+        conn
+      end
+    end
+  end
 end
 
 require File.dirname(__FILE__) + '/ensembl/helpers/like_search.rb'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ensembl
 version: !ruby/object:Gem::Version
-  version: 0.0.7
+  version: 0.0.9
 platform: ruby
 authors:
 - Kristjan Metsalu
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-12 00:00:00.000000000 Z
+date: 2014-09-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: mysql2