bio-ucsc-api 0.3.1 → 0.4.0

data/lib/bio-ucsc/ce6/gap.rb

@@ -12,16 +12,19 @@ module Bio
     module Ce6
 
       class Gap
+        include DBConnector
+        DBConnection.database "ce6"
+
         KLASS = "Gap"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)
@@ -30,19 +33,19 @@ module Bio
         Bio::Ucsc::Ce6::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true

data/lib/bio-ucsc/ce6/gold.rb

@@ -12,16 +12,19 @@ module Bio
     module Ce6
 
       class Gold
+        include DBConnector
+        DBConnection.database "ce6"
+
         KLASS = "Gold"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)
@@ -30,19 +33,19 @@ module Bio
         Bio::Ucsc::Ce6::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true

data/lib/bio-ucsc/ce6/intronest.rb

@@ -12,16 +12,19 @@ module Bio
     module Ce6
 
       class IntronEst
+        include DBConnector
+        DBConnection.database "ce6"
+
         KLASS = "IntronEst"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)
@@ -30,19 +33,19 @@ module Bio
         Bio::Ucsc::Ce6::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true

data/lib/bio-ucsc/ce6/mrna.rb

@@ -12,16 +12,19 @@ module Bio
     module Ce6
 
       class Mrna
+        include DBConnector
+        DBConnection.database "ce6"
+
         KLASS = "Mrna"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)
@@ -30,19 +33,19 @@ module Bio
         Bio::Ucsc::Ce6::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true

data/lib/bio-ucsc/ce6/rmsk.rb

@@ -12,16 +12,19 @@ module Bio
     module Ce6
 
       class Rmsk
+        include DBConnector
+        DBConnection.database "ce6"
+
         KLASS = "Rmsk"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)
@@ -30,19 +33,19 @@ module Bio
         Bio::Ucsc::Ce6::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true

data/lib/bio-ucsc/ce6/t25mersrepeats.rb

@@ -7,16 +7,19 @@ module Bio
     module Ce6
 
       class T25mersRepeats < DBConnection
-        set_table_name "25mersRepeats"
-        def self.find_by_interval(interval, opt = {:partial => true})
+        include DBConnector
+        DBConnection.database "ce6"
+
+        self.table_name = "25mersRepeats"
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           find_first_or_all_by_interval(interval, :first, opt)
         end
         
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           find_first_or_all_by_interval(interval, :all, opt)
         end
             
-        def self.find_first_or_all_by_interval(interval, first_all, opt)
+        def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
           zstart = interval.zero_start
           zend   = interval.zero_end
 

data/lib/bio-ucsc/ci2.rb

@@ -6,8 +6,8 @@
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{File.dirname(__FILE__)}/ci2/db_connection"
-require "#{File.dirname(__FILE__)}/table_class_detector"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -15,9 +15,12 @@ module Bio
       CHROMS = 
 %w(chr01p chr01q chr02q chr03p chr03q chr04q chr05q chr06q chr07q chr08q
 chr09p chr09q chr10p chr10q chr12p chr12q chr13q chr14p chr14q)
+
       extend TableClassDetector
+      include DBConnector
+      DBConnection.database "ci2"
 
-      base = "#{File.dirname(__FILE__)}/ci2"
+      base = "#{::File.dirname(__FILE__)}/ci2"
     end
   end
 end

data/lib/bio-ucsc/danrer7.rb

@@ -6,8 +6,8 @@
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{File.dirname(__FILE__)}/danrer7/db_connection"
-require "#{File.dirname(__FILE__)}/table_class_detector"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -16,9 +16,12 @@ module Bio
 %w(Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10
 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 
 Chr20 Chr21 Chr22 Chr23 Chr24 Chr25)
+
       extend TableClassDetector
+      include DBConnector
+      DBConnection.database "danRer7"
 
-      base = "#{File.dirname(__FILE__)}/danrer7"
+      base = "#{::File.dirname(__FILE__)}/danrer7"
     end
   end
 end

data/lib/bio-ucsc/{apimel2/db_connection.rb → db_connector.rb}

@@ -1,39 +1,44 @@
 #
-# = db_connection.rb - UCSC DB connection
+# = db_connector.rb
 #
-# Copyright::   Cioyrught (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
 # Copyright::   Copyright (C) 2010
 #               Jan Aerts <jan.aerts@gmail.com>
 # License::     Ruby licence (Ryby's / GPLv2 dual)
 
-require 'rubygems'
-require 'active_record'
-
 module Bio
   module Ucsc
 
-    module ApiMel2
-      DATABASE_NAME = "apiMel2"
+    module DBConnector
+      def self.included(base)
+        base.extend(ClassMethods)
+      end
+
+      module ClassMethods
+        def default
+          DBConnection.default
+        end
+
+        def connect(param = Hash.new)
+          DBConnection.db_adapter = param[:db_adapter] if param[:db_adapter]
+          DBConnection.db_host = param[:db_host] if param[:db_host]
+          DBConnection.db_username = param[:db_username] if param[:db_username]
+          DBConnection.password = param[:password] if param[:password]
+          DBConnection.connect
+        end
+      end
 
-      # = DESCRIPTION
-      # Actual connection established to the UCSC mysql server.
       class DBConnection < ActiveRecord::Base
-        # = DESCRIPTION
-        # The #connect method make the connection
-        #
-        # = USAGE
-        # Bin::Ucsc::DB_NAME::DBConnection.connect
-        #
-        # ---
-        # *Arguments*: none
+        include SafeAttributes
+
         @@db_adapter  ||= 'mysql'
         @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
         @@db_username ||= 'genome'
         @@db_password ||= ''
 
         cattr_accessor :db_adapter, :db_host, :db_username, :db_password
-
+        
         self.abstract_class = true
 
         def self.default
@@ -42,16 +47,21 @@ module Bio
           @@db_username = 'genome'
           @@db_password = ''
         end
+        
+        def self.database(dbname)
+          @@db_name = dbname
+        end
 
         def self.connect
           establish_connection({ :adapter =>  @@db_adapter,
                                  :host =>     @@db_host,
-                                 :database => DATABASE_NAME,
+                                 :database => @@db_name,
                                  :username => @@db_username,
                                  :password => @@db_password, })
         end
-      end
-    end # module
-    
-  end # module Ucsc
+        
+      end # class DBConnection
+    end # module DBConnector
+
+  end # module Ucsc 
 end # module Bio

data/lib/bio-ucsc/dm3.rb

@@ -1,13 +1,13 @@
 #
 # = AUTOMATIC Table Definition of D. melanogaster Apr. 2006 (BDGP R5/dm3)
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               MISHIMA, Hiroyuki
 #               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{File.dirname(__FILE__)}/dm3/db_connection"
-require "#{File.dirname(__FILE__)}/table_class_detector"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -16,8 +16,10 @@ module Bio
 %w(chr2L chr2LHet chr2R chr2RHet chr3L chr3LHet chr3R chr3RHet
 chr4 chrX chrXHet chrYHet chrU chrUextra chrM)
       extend TableClassDetector
+      include DBConnector
+      DBConnection.database "dm3"
 
-      base = "#{File.dirname(__FILE__)}/dm3"
+      base = "#{::File.dirname(__FILE__)}/dm3"
       autoload :ChainAnoGam1, "#{base}/chainanogam1"
       autoload :ChainAnoGam1Link, "#{base}/chainanogam1link"
       autoload :ChainApiMel3, "#{base}/chainapimel3"

data/lib/bio-ucsc/dm3/chainanogam1.rb

@@ -12,16 +12,19 @@ module Bio
     module Dm3
 
       class ChainAnoGam1
+        include DBConnector
+        DBConnection.database "dm3"
+
         KLASS = "ChainAnoGam1"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)
@@ -30,19 +33,19 @@ module Bio
         Bio::Ucsc::Dm3::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true