[BioRuby-cvs] bioruby/lib/bio/io fetch.rb,1.2,1.3

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv8180/bio/io

Modified Files:
	fetch.rb 
Log Message:
* converted to RDoc format
* databases, formats, maxids methods are added


Index: fetch.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/fetch.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** fetch.rb	21 Feb 2004 19:40:34 -0000	1.2
--- fetch.rb	28 Nov 2005 02:02:38 -0000	1.3
***************
*** 1,6 ****
  #
! # bio/io/biofetch.rb - BioFetch access module
  #
! #   Copyright (C) 2002 KATAYAMA Toshiaki <k at bioruby.org>
  #
  #  This library is free software; you can redistribute it and/or
--- 1,12 ----
  #
! # = bio/io/biofetch.rb - BioFetch access module
  #
! # Copyright::   Copyright (C) 2002, 2005
! #               Toshiaki Katayama <k at bioruby.org>
! # Licence::     LGPL
! #
! # $Id$
! #
! #--
  #
  #  This library is free software; you can redistribute it and/or
***************
*** 18,22 ****
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #  $Id$
  #
  
--- 24,28 ----
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #++
  #
  
***************
*** 26,57 ****
  module Bio
  
!   class Fetch
  
!     def initialize(url = 'http://bioruby.org/cgi-bin/biofetch.rb')
!       schema, user, @host, @port, reg, @path, = URI.split(url)
!     end
!     attr_accessor :database
  
!     def get_by_id(id)
!       fetch(@database, id)
!     end
  
!     def fetch(db, id, style = 'raw', format = nil)
!       data = [ "db=#{db}", "id=#{id}", "style=#{style}" ]
!       data.push("format=#{format}") if format
!       data = data.join('&')
  
!       responce, result = Net::HTTP.new(@host, @port).post(@path, data)
!       return result
!     end
  
!     def self.query(*args)
!       self.new.fetch(*args)
      end
  
    end
  
  end
  
  
  
--- 32,97 ----
  module Bio
  
! class Fetch
  
!   # Create a new Bio::Fetch server object.
!   # Use Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch') to connect
!   # to EBI BioFetch server.
!   def initialize(url = 'http://bioruby.org/cgi-bin/biofetch.rb')
!     schema, user, @host, @port, reg, @path, = URI.split(url)
!   end
  
!   # Set default database to dbname (prepare for get_by_id).
!   attr_accessor :database
  
!   # Get raw database entry by id (mainly used by Bio::Registry).
!   def get_by_id(id)
!     fetch(@database, id)
!   end
  
!   # Fetch a database entry as specified by database (db), entry id (id),
!   # 'raw' text or 'html' (style), and format.  When using BioRuby's
!   # BioFetch server, value for the format should not be set.
!   def fetch(db, id, style = 'raw', format = nil)
!     data = [ "db=#{db}", "id=#{id}", "style=#{style}" ]
!     data.push("format=#{format}") if format
!     data = data.join('&')
  
!     responce, result = Net::HTTP.new(@host, @port).post(@path, data)
!     return result
!   end
! 
!   # Short cut for using BioRuby's BioFetch server.  You can fetch an entry
!   # without creating instance of BioFetch server.
!   def self.query(*args)
!     self.new.fetch(*args)
!   end
! 
!   # What databases are available?
!   def databases
!     query = "info=dbs"
!     responce, result = Net::HTTP.new(@host, @port).post(@path, query)
!     return result
!   end
! 
!   # What formats does the database X have?
!   def formats(database = @database)
!     if database
!       query = "info=formats;db=#{database}"
!       responce, result = Net::HTTP.new(@host, @port).post(@path, query)
!       return result
      end
+   end
  
+   # How many entries can be retrieved simultaneously?
+   def maxids
+     query = "info=maxids"
+     responce, result = Net::HTTP.new(@host, @port).post(@path, query)
+     return result
    end
  
  end
  
+ end # module Bio
+ 
  
  
***************
*** 72,104 ****
  end
  
- 
- =begin
- 
- = Bio::Fetch
- 
- --- Bio::Fetch.new(url = 'http://bioruby.org/cgi-bin/biofetch.rb')
- 
-       Use Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch') to connect
-       to EBI BioFetch server.
- 
- --- Bio::Fetch#fetch(db, id, style = 'raw', format = nil)
- 
-       Fetch a database entry as specified by database (db), entry id (id),
-       'raw' text or 'html' (style), and format.  When using BioRuby's
-       BioFetch server, value for the format should not be set.
- 
- --- Bio::Fetch#database=(dbname)
- 
-       Set default database to dbname (prepare for get_by_id).
- 
- --- Bio::Fetch#get_by_id(id)
- 
-       Get raw database entry by id (mainly used by Bio::Registry).
- 
- --- Bio::Fetch.query(db, id, style = 'raw', format = nil)
- 
-       Short cut for using BioRuby's BioFetch server.  You can fetch an entry
-       without creating instance of BioFetch server.
- 
- =end
  
--- 112,114 ----