bio 1.4.3.0001 → 1.5.0

data/lib/bio/version.rb

@@ -10,20 +10,19 @@
 module Bio
 
   # BioRuby version (Array containing Integer)
-  BIORUBY_VERSION = [1, 4, 3].extend(Comparable).freeze
+  BIORUBY_VERSION = [1, 5, 0].extend(Comparable).freeze
 
   # Extra version specifier (String or nil).
-  # Existance of the value indicates pre-release version or modified version.
+  # Existance of the value indicates development version.
   #
   # nil                 :: Release version.
-  # ".0000"..".4999"    :: Release version with patches.
-  # ".5000"             :: Development unstable version.
-  # ".5001"..".8999"    :: Pre-alpha version.
-  # "-alphaN" (N=0..99) :: Alpha version.
-  # "-preN"   (N=0..99) :: Pre-release test version.
-  # "-rcN"    (N=0..99) :: Release candidate version.
+  # "-dev"              :: Development version (with YYYYMMDD digits).
+  # ".20150630"         :: Development version (specify the date digits).
   #
-  BIORUBY_EXTRA_VERSION = ".0001"
+  # By default, if the third digit (teeny) of BIORUBY_VERSION is 0,
+  # the version is regarded as a development version.
+  BIORUBY_EXTRA_VERSION =
+    nil #(BIORUBY_VERSION[2] == 0) ? "-dev" : nil
 
   # Version identifier, including extra version string (String)
   # Unlike BIORUBY_VERSION, it is not comparable.

data/sample/benchmark_clustalw_report.rb

@@ -0,0 +1,47 @@
+#
+# = sample/benchmark_clustalw_report.rb - Benchmark tests for Bio::ClustalW::Report
+#
+# Copyright::   Copyright (C) 2013
+#               Andrew Grimm <andrew.j.grimm@gmail.com>
+# License::     The Ruby License
+
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 1, "test",
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+require 'benchmark'
+require 'bio'
+
+class BenchmarkClustalWReport
+
+  DataDir = File.join(BioRubyTestDataPath, 'clustalw')
+  Filenames = [ 'example1.aln', 'example1-seqnos.aln' ]
+
+  def self.benchmark_clustalw_report
+    Filenames.each do |fn|
+      print "\n", fn, "\n"
+      fullpath = File.join(DataDir, fn)
+      self.new(fullpath).benchmark
+    end
+  end
+
+  def initialize(aln_filename)
+    @text = File.open(aln_filename, 'rb') { |f| f.read }
+    @text.freeze
+  end
+
+  def benchmark
+    GC.start
+    Benchmark.bmbm do |x|
+      x.report do
+        for i in 1...10_000
+          aln = Bio::ClustalW::Report.new(@text)
+          aln.alignment
+        end
+      end
+    end
+  end
+
+end #class BenchmarkClustalWReport
+
+BenchmarkClustalWReport.benchmark_clustalw_report

data/sample/biofetch.rb

@@ -1,8 +1,10 @@
-#!/usr/proj/bioruby/bin/ruby
+#!/usr/bin/env ruby
+# coding: utf-8
 #
-# biofetch.rb : BioFetch server (interface to GenomeNet/DBGET via KEGG API)
+# biofetch.rb : BioFetch server (interface to TogoWS)
 #
 #   Copyright (C) 2002-2004 KATAYAMA Toshiaki <k@bioruby.org>
+#                 2013      GOTO Naohisa <ng@bioruby.org>
 #
 #  This program is free software; you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
@@ -18,15 +20,97 @@
 #  along with this program; if not, write to the Free Software
 #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 #
-#  $Id: biofetch.rb,v 1.16 2005/08/07 10:02:41 k Exp $
 #
 
 require 'cgi'
-require 'html/template'
-require 'bio/io/keggapi'
+require 'erb'
+require 'open-uri'
+require 'fileutils'
+require 'tempfile'
 
 MAX_ID_NUM = 50
 
+# script name
+SCRIPT_NAME = File.basename(__FILE__)
+
+# full URL for this CGI
+BASE_URL = "http://bioruby.org/cgi-bin/#{SCRIPT_NAME}"
+
+# cache directory for metadata
+# Note: The cache is only for metadata (database list and format list).
+# Data entries are NOT cached.
+CACHE_DIR = '/tmp/biofetch_rb.cache'
+
+# cache lifetime
+CACHE_LIFETIME = 60 * 60 # 1 hour
+
+module TogoWS
+  TOGOWS_URL = 'http://togows.dbcls.jp/'
+
+  def togows_database_complete_list
+    result = togows_get_cached('/entry/')
+    result.to_s.split(/\n/).collect {|x| x.split(/\t/) }
+  end
+
+  def togows_database_formats(db)
+    db = CGI.escape(db)
+    result = togows_get_cached("/entry/#{db}/?formats")
+  end
+
+  def togows_get(path)
+    uristr = TOGOWS_URL + path
+    begin
+      result = OpenURI.open_uri(uristr).read
+    rescue OpenURI::HTTPError
+      result = nil
+    end
+    result
+  end
+
+  private
+
+  def togows_get_cached(path)
+    filepath = path.sub(/\A\//, '').sub(/\/\z/, '')
+    filepath = filepath.gsub(/\//, " ")
+    filepath = filepath.sub(/\?/, '_')
+    filepath = File.join(CACHE_DIR, filepath)
+    result = nil
+    begin
+      if Time.now - File.mtime(filepath) > CACHE_LIFETIME
+        # delete expired cache file
+        File.delete(filepath)
+      end
+      result = File.read(filepath)
+    rescue IOError, SystemCallError
+      result = nil
+    end
+    unless result then
+      # valid cache is not found
+      result = togows_get(path)
+      if result then
+        # create cache directory if not found
+        FileUtils.mkdir_p(CACHE_DIR, :mode => 0700)
+        # simple security check for the cache dir
+        if File.stat(CACHE_DIR).mode & 0022 != 0 then
+          raise SecurityError, "CACHE_DIR #{CACHE_DIR} is writeable by others"
+        end
+
+        # write to temporary file
+        tmp = Tempfile.open('temp', CACHE_DIR)
+        tmp.print result
+        tmp.close
+        # create a hard link from the temporary to the cache file
+        begin
+          File.link(tmp.path, filepath)
+        rescue IOError, SystemCallError
+        end
+        # the temporay file will be automatically removed at exit
+      end
+    end
+    result
+  end
+
+end #module TogoWS
 
 module BioFetchError
 
@@ -36,32 +120,50 @@ module BioFetchError
     exit
   end
 
+  def print_html_page(str)
+    print "Content-type: text/html; charset=UTF-8\n\n"
+    print "<pre>", CGI.escapeHTML(str), "</pre>\n"
+    exit
+  end
+
   def error1(db)
+    db = CGI.escapeHTML(db.to_s) # to avoid potential XSS with old IE
     str = "ERROR 1 Unknown database [#{db}]."
     print_text_page(str)
   end
 
   def error2(style)
+    style = CGI.escapeHTML(style.to_s) # to avoid potential XSS with old IE
     str = "ERROR 2 Unknown style [#{style}]."
     print_text_page(str)
   end
 
   def error3(format, db)
+    # to avoid potential XSS with old IE which ignores Content-Type
+    db = CGI.escapeHTML(db.to_s)
+    format = CGI.escapeHTML(format.to_s)
     str = "ERROR 3 Format [#{format}] not known for database [#{db}]."
     print_text_page(str)
   end
 
   def error4(entry_id, db)
+    # to avoid potential XSS with old IE which ignores Content-Type
+    entry_id = CGI.escapeHTML(entry_id.to_s)
+    db = CGI.escapeHTML(db.to_s)
     str = "ERROR 4 ID [#{entry_id}] not found in database [#{db}]."
     print_text_page(str)
   end
 
   def error5(count)
+    # to avoid potential XSS with old IE which ignores Content-Type
+    count = CGI.escapeHTML(count.to_s)
     str = "ERROR 5 Too many IDs [#{count}]. Max [#{MAX_ID_NUM}] allowed."
     print_text_page(str)
   end
 
   def error6(info)
+    # to avoid potential XSS with old IE which ignores Content-Type
+    count = CGI.escapeHTML(info.to_s)
     str = "ERROR 6 Illegal information request [#{info}]."
     print_text_page(str)
   end
@@ -70,23 +172,35 @@ end
 
 
 
-module KeggAPI
+module ApiBridge
 
   include BioFetchError
+  include TogoWS
+
+  def list_databases_with_synonyms
+    togows_database_complete_list
+  end
 
   def list_databases
-    serv = Bio::KEGG::API.new
-    results = serv.list_databases
-    results.collect {|x| x.entry_id}
+    list_databases_with_synonyms.flatten
   end
 
   def bget(db, id_list, format)
-    serv = Bio::KEGG::API.new
+    case format
+    when 'fasta'
+      format = '.fasta'
+    else
+      format = ''
+    end
+    db = CGI.escape(db)
+    
     results = ''
     id_list.each do |query_id|
-      entry_id = "#{db}:#{query_id}"
-      result = serv.get_entries([entry_id])
-      if result.empty?
+      query_id = CGI.escape(query_id)
+      path = "/entry/#{db}/#{query_id}#{format}"
+      result = togows_get(path)
+
+      if !result or result.empty? or /\AError\: / =~ result then
         error4(query_id, db)
       else
         results << result
@@ -95,78 +209,41 @@ module KeggAPI
     return results
   end
 
-end
-
-
-
-
-class BioFetch
-
-  include BioFetchError
-  include KeggAPI
-
-  def initialize(db, id_list, style, format)
-    check_style(style)
-    check_format(format, db)
-    check_number_of_id(id_list.length)
-    check_dbname(db)
+  def check_fasta_ok?(db)
+    result = togows_database_formats(db)
+    /^fasta$/ =~ result.to_s
+  end
 
-    if /html/.match(style)
-      goto_html_style_page(db, id_list, format)
-    end
+end #module ApiBridge
 
-    entries = bget(db, id_list, format)
+module BioFetchCheck
 
-    if /fasta/.match(format) and entries
-      entries = convert_to_fasta_format(entries, db)
-    end
-
-    print_text_page(entries)
-  end
+  include ApiBridge
 
   private
 
-  def convert_to_fasta_format(str, db)
-    require 'bio'
-    require 'stringio'
-
-    fasta = Array.new
-
-    entries = StringIO.new(str)
-    Bio::FlatFile.auto(entries) do |ff|
-      ff.each do |entry|
-        seq = nil
-        if entry.respond_to?(:seq)
-          seq = entry.seq
-        elsif entry.respond_to?(:aaseq)
-          seq = entry.aaseq
-        elsif entry.respond_to?(:naseq)
-          seq = entry.naseq
-        end
-        if seq
-          entry_id   = entry.respond_to?(:entry_id)   ? entry.entry_id   : ''
-          definition = entry.respond_to?(:definition) ? entry.definition : ''
-          fasta << seq.to_fasta("#{db}:#{entry_id} #{definition}", 60)
-        end
-      end
-    end
-    return fasta.join
-  end
-
-  def goto_html_style_page(db, id_list, format)
-    url = "http://www.genome.jp/dbget-bin/www_bget"
-    opt = '-f+' if /fasta/.match(format)
-    ids = id_list.join('%2B')
-    print "Location: #{url}?#{opt}#{db}+#{ids}\n\n"
-    exit
-  end
-
   def check_style(style)
-    error2(style) unless /html|raw/.match(style)
+    style = style.to_s.downcase
+    error2(style) unless /\A(html|raw)\z/.match(style)
+    style
   end
 
   def check_format(format, db)
-    error3(format, db) if format && ! /fasta|default/.match(format)
+    fmt = format ? format.to_s.downcase : nil
+    case fmt
+    when 'fasta'
+      db = check_dbname(db)
+      fmt = nil unless check_fasta_ok?(db)
+    when 'default'
+      # do nothing
+    when nil
+      fmt = 'default'
+    else
+      fmt = nil
+    end
+
+    error3(format, db) unless fmt
+    fmt
   end
 
   def check_number_of_id(num)
@@ -174,22 +251,50 @@ class BioFetch
   end
 
   def check_dbname(db)
+    db = db.to_s.downcase
     error1(db) unless list_databases.include?(db)
+    db
   end
 
-end
+end #module BioFetchCheck
+
+class BioFetch
+
+  include BioFetchCheck
+  include BioFetchError
+  include ApiBridge
+
+  def initialize(db, id_list, style, format)
+    style = check_style(style)
+    format = check_format(format, db)
+    check_number_of_id(id_list.length)
+    db = check_dbname(db)
+
+    entries = bget(db, id_list, format)
+
+    if style == 'html' then
+      print_html_page(entries)
+    else
+      print_text_page(entries)
+    end
+
+  end
+
+end #class BioFetch
 
 
 
 class BioFetchInfo
 
+  include BioFetchCheck
   include BioFetchError
-  include KeggAPI
+  include ApiBridge
 
   def initialize(info, db)
     @db = db
+
     begin
-      send(info)
+      check_info(info) ? __send__(info) : raise
     rescue
       error6(info)
     end
@@ -197,13 +302,18 @@ class BioFetchInfo
 
   private
 
+  def check_info(meth_name)
+    /\A(dbs|formats|maxids)\z/ =~ meth_name
+  end
+
   def dbs
     str = list_databases.sort.join(' ')
     print_text_page(str)
   end
 
   def formats
-    fasta = " fasta" if check_fasta_ok
+    db = check_dbname(@db)
+    fasta = " fasta" if check_fasta_ok?(db)
     str = "default#{fasta}"
     print_text_page(str)
   end
@@ -213,17 +323,14 @@ class BioFetchInfo
     print_text_page(str)
   end
 
-  def check_fasta_ok
-    # sequence databases supported by Bio::FlatFile.auto
-    /genes|gb|genbank|genpept|rs|refseq|emb|sp|swiss|pir/.match(@db)
-  end
-
-end
+end #class BioFetchInfo
 
 
 
 class BioFetchCGI
 
+  include ApiBridge
+
   def initialize(cgi)
     @cgi = cgi
     show_page
@@ -244,11 +351,14 @@ class BioFetchCGI
   end
 
   def show_query_page
-    html = HTML::Template.new
-    html.set_html(DATA.read)
-    html.param('max_id_num' => MAX_ID_NUM)
-    @cgi.out do
-      html.output
+    html = ERB.new(DATA.read)
+    max_id_num = MAX_ID_NUM
+    databases_with_synonyms = list_databases_with_synonyms
+    databases = list_databases
+    script_name = SCRIPT_NAME
+    base_url = BASE_URL
+    @cgi.out({ "type" => "text/html", "charset" => "utf-8" }) do
+      html.result(binding)
     end
   end
 
@@ -269,7 +379,7 @@ class BioFetchCGI
   end
 
   def id_list
-    @cgi['id'].split(/\W/)		# not only ','
+    @cgi['id'].strip.split(/[\,\s]+/)
   end
 
   def style
@@ -295,9 +405,8 @@ BioFetchCGI.new(CGI.new)
 This program was created during BioHackathon 2002, Tucson and updated
 in Cape Town :)
 
-Rewrited in 2004 to use KEGG API as the bioruby.org server left from Kyoto
-University (where DBGET runs) and the old version could not run without
-having internally accessible DBGET server.
+Rewrited in 2013 to use TogoWS API as the bioruby.org server left from The
+University of Tokyo and the old SOAP-based KEGG API is discontinued.
 
 =end
 
@@ -308,7 +417,7 @@ __END__
 <HEAD>
   <LINK href="http://bioruby.org/img/favicon.png" rel="icon" type="image/png">
   <LINK href="http://bioruby.org/css/bioruby.css" rel="stylesheet" type="text/css">
-  <TITLE>BioFetch interface to GenomeNet/DBGET</TITLE>
+  <TITLE>BioFetch interface to TogoWS</TITLE>
 </HEAD>
 
 <BODY bgcolor="#ffffff">
@@ -316,37 +425,26 @@ __END__
 <H1>
 <IMG src="http://bioruby.org/img/ruby.png" align="middle">
 BioFetch interface to
-<A href="http://www.genome.jp/dbget/">GenomeNet/DBGET</A>
+<A href="http://togows.dbcls.jp/">TogoWS</A>
 </H1>
 
-<P>This page allows you to retrieve up to <!var:max_id_num> entries at a time from various up-to-date biological databases.</P>
+<P>This page allows you to retrieve up to <%= max_id_num %> entries at a time from various up-to-date biological databases.</P>
 
 <HR>
 
-<FORM METHOD="post" ENCTYPE="application/x-www-form-urlencoded" action="biofetch.rb">
+<FORM METHOD="post" ENCTYPE="application/x-www-form-urlencoded" action="<%= script_name %>">
 
 <SELECT name="db">
-<OPTION value="genbank">GenBank</OPTION>
-<OPTION value="refseq">RefSeq</OPTION>
-<OPTION value="embl">EMBL</OPTION>
-<OPTION value="swissprot">Swiss-Prot</OPTION>
-<OPTION value="pir">PIR</OPTION>
-<OPTION value="prf">PRF</OPTION>
-<OPTION value="pdb">PDB</OPTION>
-<OPTION value="pdbstr">PDBSTR</OPTION>
-<OPTION value="epd">EPD</OPTION>
-<OPTION value="transfac">TRANSFAC</OPTION>
-<OPTION value="prosite">PROSITE</OPTION>
-<OPTION value="pmd">PMD</OPTION>
-<OPTION value="litdb">LITDB</OPTION>
-<OPTION value="omim">OMIM</OPTION>
-<OPTION value="ligand">KEGG/LIGAND</OPTION>
-<OPTION value="pathway">KEGG/PATHWAY</OPTION>
-<OPTION value="brite">KEGG/BRITE</OPTION>
-<OPTION value="genes">KEGG/GENES</OPTION>
-<OPTION value="genome">KEGG/GENOME</OPTION>
-<OPTION value="linkdb">LinkDB</OPTION>
-<OPTION value="aaindex">AAindex</OPTION>
+<% databases_with_synonyms.each do |dbs|
+     a = dbs[1..-1]
+     synonyms = unless a.empty? then
+                  " (abbr: " + a.join(", ") + ")"
+                else
+                  ""
+                end
+%>
+<OPTION value="<%= dbs[0] %>"><%= dbs[0] %><%= synonyms %></OPTION>
+<% end %>
 </SELECT>
 
 <INPUT name="id" size="40" type="text" maxlength="1000">
@@ -369,7 +467,7 @@ BioFetch interface to
 
 <H2>Direct access</H2>
 
-<P>http://bioruby.org/cgi-bin/biofetch.rb?format=(default|fasta|...);style=(html|raw);db=(genbank|embl|...);id=ID[,ID,ID,...]</P>
+<P><%= base_url %>?format=(default|fasta|...);style=(html|raw);db=(nuccore|embl|...);id=ID[,ID,ID,...]</P>
 <P>(NOTE: the option separator ';' can be '&')</P>
 
 <DL>
@@ -380,7 +478,7 @@ BioFetch interface to
   <DD> html|raw
 
   <DT> <U>db</U> (required)
-  <DD> genbank|refseq|embl|swissprot|pir|prf|pdb|pdbstr|epd|transfac|prosite|pmd|litdb|omim|ligand|pathway|brite|genes|genome|linkdb|aaindex|...
+  <DD> <%= databases.join('|') %>
 
   <DT> <U>id</U> (required)
   <DD> comma separated list of IDs
@@ -392,66 +490,65 @@ BioFetch interface to
 
 <DL>
   <DT> <A href="?info=dbs">What databases are available?</A>
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=dbs
+  <DD> <%= base_url %>?info=dbs
 
   <DT> <A href="?info=formats;db=embl">What formats does the database X have?</A>
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=formats;db=embl
+  <DD> <%= base_url %>?info=formats;db=embl
 
   <DT> <A href="?info=maxids">How many entries can be retrieved simultaneously?</A>
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=maxids
+  <DD> <%= base_url %>?info=maxids
 </DL>
 
 <H2>Examples</H2>
 
 <DL>
-  <DT> <A href="?format=default;style=raw;db=genbank;id=AJ617376">gb:AJ617376</A> (default/raw)
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genbank;id=AJ617376
+  <DT> <A href="?format=default;style=raw;db=nuccore;id=AJ617376">nuccore/AJ617376</A> (default/raw)
+  <DD> <%= base_url %>?format=default;style=raw;db=nuccore;id=AJ617376
 
-  <DT> <A href="?format=fasta;style=raw;db=genbank;id=AJ617376">gb:AJ617376</A> (fasta/raw)
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=fasta;style=raw;db=genbank;id=AJ617376
+  <DT> <A href="?format=fasta;style=raw;db=nuccore;id=AJ617376">nuccore/AJ617376</A> (fasta/raw)
+  <DD> <%= base_url %>?format=fasta;style=raw;db=nuccore;id=AJ617376
 
-  <DT> <A href="?format=default;style=html;db=genbank;id=AJ617376">gb:AJ617376</A> (default/html)
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=html;db=genbank;id=AJ617376
+  <DT> <A href="?format=default;style=html;db=nuccore;id=AJ617376">nuccore/AJ617376</A> (default/html)
+  <DD> <%= base_url %>?format=default;style=html;db=nuccore;id=AJ617376
 
-  <DT> <A href="?format=default;style=raw;db=genbank;id=AJ617376,AJ617377">gb:AJ617376,AJ617377</A> (default/raw, multiple)
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genbank;id=AJ617376,AJ617377
+  <DT> <A href="?format=default;style=raw;db=nuccore;id=AJ617376,AJ617377">nuccore/AJ617376,AJ617377</A> (default/raw, multiple)
+  <DD> <%= base_url %>?format=default;style=raw;db=nuccore;id=AJ617376,AJ617377
 
-  <DT> <A href="?format=default;style=raw;db=embl;id=BUM">embl:BUM</A> (default/raw)
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=embl;id=BUM
+  <DT> <A href="?format=default;style=raw;db=embl;id=J00231">embl/J00231</A> (default/raw)
+  <DD> <%= base_url %>?format=default;style=raw;db=embl;id=J00231
 
-  <DT> <A href="?format=default;style=raw;db=swissprot;id=CYC_BOVIN">sp:CYC_BOVIN</A> (default/raw)
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=swissprot;id=CYC_BOVIN
+  <DT> <A href="?format=default;style=raw;db=uniprot;id=CYC_BOVIN">uniprot/CYC_BOVIN</A> (default/raw)
+  <DD> <%= base_url %>?format=default;style=raw;db=uniprot;id=CYC_BOVIN
 
-  <DT> <A href="?format=fasta;style=raw;db=swissprot;id=CYC_BOVIN">sp:CYC_BOVIN</A> (fasta/raw)
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=fasta;style=raw;db=swissprot;id=CYC_BOVIN
+  <DT> <A href="?format=fasta;style=raw;db=uniprot;id=CYC_BOVIN">uniprot/CYC_BOVIN</A> (fasta/raw)
+  <DD> <%= base_url %>?format=fasta;style=raw;db=uniprot;id=CYC_BOVIN
 
-  <DT> <A href="?format=default;style=raw;db=genes;id=b0015">genes:b0015</A> (default/raw)
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genes;id=b0015
+  <DT> <A href="?format=default;style=raw;db=genes;id=eco%3Ab0015">genes/eco:b0015</A> (default/raw)
+  <DD> <%= base_url %>?format=default;style=raw;db=genes;id=eco%3Ab0015
+  <DD> <%= base_url %>?format=default;style=raw;db=genes;id=eco:b0015
 
-  <DT> <A href="?format=default;style=raw;db=prosite;id=PS00028">ps:PS00028</A> (default/raw)
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=prosite;id=PS00028
 </DL>
 
 <H2>Errors</H2>
 
 <DL>
   <DT> <A href="?format=default;style=raw;db=nonexistent;id=AJ617376">Error1</A> sample : DB not found
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=nonexistent;id=AJ617376"
+  <DD> <%= base_url %>?format=default;style=raw;db=nonexistent;id=AJ617376
 
-  <DT> <A href="?format=default;style=nonexistent;db=genbank;id=AJ617376">Error2</A> sample : unknown style
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=nonexistent;db=genbank;id=AJ617376"
+  <DT> <A href="?format=default;style=nonexistent;db=nuccore;id=AJ617376">Error2</A> sample : unknown style
+  <DD> <%= base_url %>?format=default;style=nonexistent;db=nuccore;id=AJ617376
 
-  <DT> <A href="?format=nonexistent;style=raw;db=genbank;id=AJ617376">Error3</A> sample : unknown format
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=nonexistent;style=raw;db=genbank;id=AJ617376"
+  <DT> <A href="?format=nonexistent;style=raw;db=nuccore;id=AJ617376">Error3</A> sample : unknown format
+  <DD> <%= base_url %>?format=nonexistent;style=raw;db=nuccore;id=AJ617376
 
-  <DT> <A href="?format=default;style=raw;db=genbank;id=nonexistent">Error4</A> sample : ID not found
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genbank;id=nonexistent"
+  <DT> <A href="?format=default;style=raw;db=nuccore;id=nonexistent">Error4</A> sample : ID not found
+  <DD> <%= base_url %>?format=default;style=raw;db=nuccore;id=nonexistent
 
   <DT> <A href="?style=raw;db=genes;id=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51">Error5</A> sample : too many IDs
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?style=raw;db=genes;id=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51
+  <DD> <%= base_url %>?style=raw;db=genes;id=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51
 
   <DT> <A href="?info=nonexistent">Error6</A> sample : unknown info
-  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=nonexistent"
+  <DD> <%= base_url %>?info=nonexistent"
 </DL>
 
 <H2>Other BioFetch implementations</H2>