#!/usr/proj/bioruby/bin/ruby
#
# biofetch.rb : BioFetch server (interface to GenomeNet/DBGET via KEGG API)
#
#   Copyright (C) 2002-2004 KATAYAMA Toshiaki <k@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
#  the Free Software Foundation; either version 2 of the License, or
#  (at your option) any later version.
#
#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  You should have received a copy of the GNU General Public License
#  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'

MAX_ID_NUM = 50


module BioFetchError

  def print_text_page(str)
    print "Content-type: text/plain; charset=UTF-8\n\n"
    puts str
    exit
  end

  def error1(db)
    str = "ERROR 1 Unknown database [#{db}]."
    print_text_page(str)
  end

  def error2(style)
    str = "ERROR 2 Unknown style [#{style}]."
    print_text_page(str)
  end

  def error3(format, db)
    str = "ERROR 3 Format [#{format}] not known for database [#{db}]."
    print_text_page(str)
  end

  def error4(entry_id, db)
    str = "ERROR 4 ID [#{entry_id}] not found in database [#{db}]."
    print_text_page(str)
  end

  def error5(count)
    str = "ERROR 5 Too many IDs [#{count}]. Max [#{MAX_ID_NUM}] allowed."
    print_text_page(str)
  end

  def error6(info)
    str = "ERROR 6 Illegal information request [#{info}]."
    print_text_page(str)
  end

end



module KeggAPI

  include BioFetchError

  def list_databases
    serv = Bio::KEGG::API.new
    results = serv.list_databases
    results.collect {|x| x.entry_id}
  end

  def bget(db, id_list, format)
    serv = Bio::KEGG::API.new
    results = ''
    id_list.each do |query_id|
      entry_id = "#{db}:#{query_id}"
      result = serv.get_entries([entry_id])
      if result.empty?
        error4(query_id, db)
      else
        results << result
      end
    end
    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)

    if /html/.match(style)
      goto_html_style_page(db, id_list, format)
    end

    entries = bget(db, id_list, format)

    if /fasta/.match(format) and entries
      entries = convert_to_fasta_format(entries, db)
    end

    print_text_page(entries)
  end

  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)
  end

  def check_format(format, db)
    error3(format, db) if format && ! /fasta|default/.match(format)
  end

  def check_number_of_id(num)
    error5(num) if num > MAX_ID_NUM
  end

  def check_dbname(db)
    error1(db) unless list_databases.include?(db)
  end

end



class BioFetchInfo

  include BioFetchError
  include KeggAPI

  def initialize(info, db)
    @db = db
    begin
      send(info)
    rescue
      error6(info)
    end
  end

  private

  def dbs
    str = list_databases.sort.join(' ')
    print_text_page(str)
  end

  def formats
    fasta = " fasta" if check_fasta_ok
    str = "default#{fasta}"
    print_text_page(str)
  end

  def maxids
    str = MAX_ID_NUM.to_s
    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



class BioFetchCGI

  def initialize(cgi)
    @cgi = cgi
    show_page
  end

  private

  def show_page
    if info.empty?
      if id_list.empty?
        show_query_page
      else
        show_result_page(db, id_list, style, format)
      end
    else
      show_info_page(info, db)
    end
  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
    end
  end

  def show_result_page(db, id_list, style, format)
    BioFetch.new(db, id_list, style, format)
  end

  def show_info_page(info, db)
    BioFetchInfo.new(info, db)
  end

  def info
    @cgi['info'].downcase
  end

  def db
    @cgi['db'].downcase
  end

  def id_list
    @cgi['id'].split(/\W/)		# not only ','
  end

  def style
    s = @cgi['style'].downcase
    return s.empty? ? "html" : s
  end

  def format
    f = @cgi['format'].downcase
    return f.empty? ? "default" : f
  end

end



BioFetchCGI.new(CGI.new)



=begin

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.

=end


__END__

<HTML>
<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>
</HEAD>

<BODY bgcolor="#ffffff">

<H1>
<IMG src="http://bioruby.org/img/ruby.png" align="middle">
BioFetch interface to
<A href="http://www.genome.jp/dbget/">GenomeNet/DBGET</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>

<HR>

<FORM METHOD="post" ENCTYPE="application/x-www-form-urlencoded" action="biofetch.rb">

<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>
</SELECT>

<INPUT name="id" size="40" type="text" maxlength="1000">

<SELECT name="format">
<OPTION value="default">Default</OPTION>
<OPTION value="fasta">Fasta</OPTION>
</SELECT>

<SELECT name="style">
<OPTION value="raw">Raw</OPTION>
<OPTION value="html">HTML</OPTION>
</SELECT>

<INPUT type="submit">

</FORM>

<HR>

<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>(NOTE: the option separator ';' can be '&')</P>

<DL>
  <DT> <U>format</U> (optional)
  <DD> default|fasta|...

  <DT> <U>style</U> (required)
  <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|...

  <DT> <U>id</U> (required)
  <DD> comma separated list of IDs
</DL>

<P>See the <A href="http://obda.open-bio.org/">BioFetch specification</A> for more details.</P>

<H2>Server informations</H2>

<DL>
  <DT> <A href="?info=dbs">What databases are available?</A>
  <DD> http://bioruby.org/cgi-bin/biofetch.rb?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

  <DT> <A href="?info=maxids">How many entries can be retrieved simultaneously?</A>
  <DD> http://bioruby.org/cgi-bin/biofetch.rb?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=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=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=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=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=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=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=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=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"

  <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=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=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="?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

  <DT> <A href="?info=nonexistent">Error6</A> sample : unknown info
  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=nonexistent"
</DL>

<H2>Other BioFetch implementations</H2>

<UL>
  <LI> <A href="http://www.ebi.ac.uk/cgi-bin/dbfetch">dbfetch at EBI</A>
</UL>

<HR>

<DIV align=right>
<I>
staff@Bio<span class="ruby">Ruby</span>.org
</I>
<BR>
<BR>
<A href="http://bioruby.org/"><IMG border=0 src="/img/banner.gif"></A>
</DIV>

</BODY>
</HTML>