bio-ucsc-api 0.3.1 → 0.4.0

data/lib/bio-ucsc/fr2/db_connection.rb

@@ -1,57 +0,0 @@
-#
-# = db_connection.rb - UCSC DB connection
-#
-# Copyright::   Cioyrught (C) 2011
-#               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 Fr2
-      DATABASE_NAME = "fr2"
-
-      # = 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
-        @@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
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection({ :adapter =>  @@db_adapter,
-                                 :host =>     @@db_host,
-                                 :database => DATABASE_NAME,
-                                 :username => @@db_username,
-                                 :password => @@db_password, })
-        end
-      end
-    end # module
-    
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/galgal3/db_connection.rb

@@ -1,57 +0,0 @@
-#
-# = db_connection.rb - UCSC DB connection
-#
-# Copyright::   Cioyrught (C) 2011
-#               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 GalGal3
-      DATABASE_NAME = "galGal3"
-
-      # = 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
-        @@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
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection({ :adapter =>  @@db_adapter,
-                                 :host =>     @@db_host,
-                                 :database => DATABASE_NAME,
-                                 :username => @@db_username,
-                                 :password => @@db_password, })
-        end
-      end
-    end # module
-    
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/gasacu1/db_connection.rb

@@ -1,57 +0,0 @@
-#
-# = db_connection.rb - UCSC DB connection
-#
-# Copyright::   Cioyrught (C) 2011
-#               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 GasAcu1
-      DATABASE_NAME = "gasAcu1"
-
-      # = 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
-        @@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
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection({ :adapter =>  @@db_adapter,
-                                 :host =>     @@db_host,
-                                 :database => DATABASE_NAME,
-                                 :username => @@db_username,
-                                 :password => @@db_password, })
-        end
-      end
-    end # module
-    
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/go/db_connection.rb

@@ -1,55 +0,0 @@
-#
-# = lib/ucsc/uniprot/db_connection.rb - UCSC GO DB connection
-#
-# Copyright::   Cioyrught (C) 2011
-#               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 Go
-      # = 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
-        @@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
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection({ :adapter =>  @@db_adapter,
-                                 :host =>     @@db_host,
-                                 :database => 'go',
-                                 :username => @@db_username,
-                                 :password => @@db_password, })
-        end
-      end
-    end # module
-    
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/hg18/db_connection.rb

@@ -1,59 +0,0 @@
-#
-# = lib/ucsc/hg18/db_connection.rb - UCSC hg18 DB connection
-#
-# Copyright::   Cioyrught (C) 2011
-#               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 Hg18
-      # = DESCRIPTION
-      # The Ucsc::Hg18::DBConnection is the actual connection established
-      # with the UCSC mysql server.
-
-      class DBConnection < ActiveRecord::Base
-        # = DESCRIPTION
-        # The Bin::Ucsc::Hg18::DBConnection#connect method makes the connection
-        # to the UCSC hg18 database.
-        #
-        # = USAGE
-        #  # Connect to the hg18
-        #  Bin::Ucsc::Hg18::DBConnection.connect
-        #
-        # ---
-        # *Arguments*: none
-        @@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
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection({ :adapter =>  @@db_adapter,
-                                 :host =>     @@db_host,
-                                 :database => 'hg18',
-                                 :username => @@db_username,
-                                 :password => @@db_password, })
-        end
-      end
-    end # module Hg18
-    
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/hg19/db_connection.rb

@@ -1,61 +0,0 @@
-#
-# = lib/ucsc/hg19/db_connection.rb - UCSC hg19 DB connection
-#
-# Copyright::   Cioyrught (C) 2011
-#               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 Hg19
-      # = DESCRIPTION
-      # The Ucsc::Hg19::DBConnection is the actual connection established
-      # with the UCSC mysql server.
-
-      class DBConnection < ActiveRecord::Base
-        # = DESCRIPTION
-        # The Bin::Ucsc::Hg19::DBConnection#connect method makes the connection
-        # to the UCSC hg19 database.
-        #
-        # = USAGE
-        #  # Connect to the hg19
-        #  Bin::Ucsc::Hg19::DBConnection.connect
-        #
-        # ---
-        # *Arguments*: none
-        @@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
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection(
-                               :adapter =>  @@db_adapter,
-                               :host =>     @@db_host,
-                               :database => 'hg19',
-                               :username => @@db_username,
-                               :password => @@db_password
-                               )
-        end
-      end
-    end # module Hg19
-    
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/hgfixed/db_connection.rb

@@ -1,55 +0,0 @@
-#
-# = db_connection.rb - UCSC DB connection
-#
-# Copyright::   Cioyrught (C) 2011
-#               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 HgFixed
-      # = 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
-        @@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
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection({ :adapter =>  @@db_adapter,
-                                 :host =>     @@db_host,
-                                 :database => 'hgFixed',
-                                 :username => @@db_username,
-                                 :password => @@db_password, })
-        end
-      end
-    end # module
-    
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/loxafr3/db_connection.rb

@@ -1,57 +0,0 @@
-#
-# = db_connection.rb
-#
-# Copyright::   Cioyrught (C) 2011
-#               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 LoxAfr3
-      DATABASE_NAME = "loxAfr3"
-
-      # = 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
-        @@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
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection({ :adapter =>  @@db_adapter,
-                                 :host =>     @@db_host,
-                                 :database => DATABASE_NAME,
-                                 :username => @@db_username,
-                                 :password => @@db_password, })
-        end
-      end
-    end # module
-    
-  end # module Ucsc
-end # module Bio