lib/bio/io/fetch.rb in bio-1.2.1 vs lib/bio/io/fetch.rb in bio-1.3.0

@@ -3,11 +3,11 @@
 #
 # Copyright::	Copyright (C) 2002, 2005 Toshiaki Katayama <[e-mail]>,
 #               Copyright (C) 2006 Jan Aerts <[e-mail]>
 # License::     The Ruby License
 #
-#  $Id: fetch.rb,v 1.10 2007/04/05 23:35:41 trevor Exp $
+#  $Id:$
 #
 # == DESCRIPTION
 #
 # Using BioRuby BioFetch server
 #
@@ -24,10 +24,11 @@
 #   puts Bio::Fetch.query('genbank', 'J00231')
 #   puts Bio::Fetch.query('genbank', 'J00231', 'raw', 'fasta')
 # 
 
 require 'uri'
+require 'cgi'
 require 'bio/command'
 
 module Bio
   # = DESCRIPTION
   # The Bio::Fetch class provides an interface to dbfetch servers. Given
@@ -100,15 +101,16 @@
     # * _database_: name of database to query (see Bio::Fetch#databases to get list of supported databases)
     # * _id_: single ID or ID list separated by commas or white space
     # * _style_: [raw|html] (default = 'raw')
     # * _format_: name of output format (see Bio::Fetch#formats)
     def fetch(db, id, style = 'raw', format = nil)
-      query = [ "db=#{db}", "id=#{id}", "style=#{style}" ]
-      query.push("format=#{format}") if format
-      query = query.join('&')
+      query = [ [ 'db',    db ],
+                [ 'id',    id ],
+                [ 'style', style ] ]
+      query.push([ 'format', format ]) if format
   
-      Bio::Command.read_uri(@url + '?' + URI.escape(query))
+      _get(query)
     end
   
     # Shortcut for using BioRuby's BioFetch server. You can fetch an entry
     # without creating an instance of BioFetch server. This method uses the 
     # default dbfetch server, which is http://bioruby.org/cgi-bin/biofetch.rb
@@ -137,13 +139,11 @@
     # of databases available from the EBI, see the EBI website at 
     # http://www.ebi.ac.uk/cgi-bin/dbfetch/
     # ---
     # *Returns*:: array of database names
     def databases
-      query = "info=dbs"
-
-      Bio::Command.read_uri(@url + '?' + URI.escape(query)).strip.split(/\s+/)
+      _get_single('info', 'dbs').strip.split(/\s+/)
     end
   
     # Lists the formats that are available for a given database. Like the
     # Bio::Fetch#databases method, this method is only available on 
     # the bioruby dbfetch server.
@@ -154,13 +154,13 @@
     # *Arguments*:
     # * _database_:: name of database you want the supported formats for
     # *Returns*:: array of formats
     def formats(database = @database)
       if database
-        query = "info=formats;db=#{database}"
-
-        Bio::Command.read_uri(@url + '?' + URI.escape(query)).strip.split(/\s+/)
+        query = [ [ 'info', 'formats' ],
+                  [ 'db',   database  ] ]
+        _get(query).strip.split(/\s+/)
       end
     end
   
     # A dbfetch server will only return entries up to a given maximum number.
     # This method retrieves that number from the server. As for the databases
@@ -168,14 +168,28 @@
     # dbfetch server.
     # ---
     # *Arguments*: none
     # *Returns*:: number
     def maxids
-      query = "info=maxids"
+      _get_single('info', 'maxids').to_i
+    end
 
-      Bio::Command.read_uri(@url + '?' + URI.escape(query)).to_i
+    private
+    # (private) query to the server.
+    # ary must be nested array, e.g. [ [ key0, val0 ], [ key1, val1 ], ... ]
+    def _get(ary)
+      query = ary.collect do |a|
+        "#{CGI.escape(a[0])}=#{CGI.escape(a[1])}"
+      end.join('&')
+      Bio::Command.read_uri(@url + '?' + query)
     end
-  
+
+    # (private) query with single parameter
+    def _get_single(key, val)
+      query = "#{CGI.escape(key)}=#{CGI.escape(val)}"
+      Bio::Command.read_uri(@url + '?' + query)
+    end
+
   end
 
 end # module Bio