[BioRuby-cvs] bioruby/lib/bio/io dbget.rb, 1.11, 1.12 ddbjxml.rb, 1.10, 1.11 fetch.rb, 1.7, 1.8 registry.rb, 1.16, 1.17 soapwsdl.rb, 1.3, 1.4
Katayama Toshiaki
k at dev.open-bio.org
Mon May 8 14:30:00 UTC 2006
Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv16979/io
Modified Files:
dbget.rb ddbjxml.rb fetch.rb registry.rb soapwsdl.rb
Log Message:
* license is changed to Ruby's
Index: soapwsdl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/soapwsdl.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** soapwsdl.rb 18 Dec 2005 16:51:18 -0000 1.3
--- soapwsdl.rb 8 May 2006 14:29:58 -0000 1.4
***************
*** 4,14 ****
# Copyright:: Copyright (C) 2004
# KATAYAMA Toshiaki <k at bioruby.org>
! # License:: LGPL
#
# $Id$
#
- # SOAP/WSDL
- #
- #
# == Examples
#
--- 4,11 ----
# Copyright:: Copyright (C) 2004
# KATAYAMA Toshiaki <k at bioruby.org>
! # License:: Ruby's
#
# $Id$
#
# == Examples
#
***************
*** 37,58 ****
# % export http_proxy=http://localhost:8080
#
- #--
- #
- # This library is free software; you can redistribute it and/or
- # modify it under the terms of the GNU Lesser General Public
- # License as published by the Free Software Foundation; either
- # version 2 of the License, or (at your option) any later version.
- #
- # This library 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
- # Lesser General Public License for more details.
- #
- # You should have received a copy of the GNU Lesser General Public
- # License along with this library; if not, write to the Free Software
- # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
- #
- #++
- #
begin
--- 34,37 ----
Index: ddbjxml.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ddbjxml.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** ddbjxml.rb 2 Feb 2006 16:30:29 -0000 1.10
--- ddbjxml.rb 8 May 2006 14:29:58 -0000 1.11
***************
*** 4,29 ****
# Copyright:: Copyright (C) 2003, 2004
# KATAYAMA Toshiaki <k at bioruby.org>
! # License:: LGPL
#
# $Id$
#
- #--
- #
- # This library is free software; you can redistribute it and/or
- # modify it under the terms of the GNU Lesser General Public
- # License as published by the Free Software Foundation; either
- # version 2 of the License, or (at your option) any later version.
- #
- # This library 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
- # Lesser General Public License for more details.
- #
- # You should have received a copy of the GNU Lesser General Public
- # License along with this library; if not, write to the Free Software
- # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
- #
- #++
- #
require 'bio/io/soapwsdl'
--- 4,11 ----
# Copyright:: Copyright (C) 2003, 2004
# KATAYAMA Toshiaki <k at bioruby.org>
! # License:: Ruby's
#
# $Id$
#
require 'bio/io/soapwsdl'
Index: registry.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/registry.rb,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** registry.rb 18 Dec 2005 15:58:42 -0000 1.16
--- registry.rb 8 May 2006 14:29:58 -0000 1.17
***************
*** 4,8 ****
# Copyright:: Copyright (C) 2002, 2003, 2004, 2005
# Toshiaki Katayama <k at bioruby.org>
! # License:: LGPL
#
# $Id$
--- 4,8 ----
# Copyright:: Copyright (C) 2002, 2003, 2004, 2005
# Toshiaki Katayama <k at bioruby.org>
! # License:: Ruby's
#
# $Id$
***************
*** 82,102 ****
# * http://www.open-bio.org/registry/seqdatabase.ini
#
- #--
- # This library is free software; you can redistribute it and/or
- # modify it under the terms of the GNU Lesser General Public
- # License as published by the Free Software Foundation; either
- # version 2 of the License, or (at your option) any later version.
- #
- # This library 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
- # Lesser General Public License for more details.
- #
- # You should have received a copy of the GNU Lesser General Public
- # License along with this library; if not, write to the Free Software
- # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
- #
- #++
- #
require 'uri'
--- 82,85 ----
Index: dbget.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/dbget.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** dbget.rb 5 Nov 2005 08:32:26 -0000 1.11
--- dbget.rb 8 May 2006 14:29:58 -0000 1.12
***************
*** 5,9 ****
# Mitsuteru C. Nakao <n at bioruby.org>,
# Toshiaki Katayama <k at bioruby.org>
! # License:: LGPL
#
# $Id$
--- 5,9 ----
# Mitsuteru C. Nakao <n at bioruby.org>,
# Toshiaki Katayama <k at bioruby.org>
! # License:: Ruby's
#
# $Id$
***************
*** 14,35 ****
# http://www.genome.jp/dbget/ within the intranet.
#
- #--
- #
- # This library is free software; you can redistribute it and/or
- # modify it under the terms of the GNU Lesser General Public
- # License as published by the Free Software Foundation; either
- # version 2 of the License, or (at your option) any later version.
- #
- # This library 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
- # Lesser General Public License for more details.
- #
- # You should have received a copy of the GNU Lesser General Public
- # License along with this library; if not, write to the Free Software
- # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
- #
- #++
- #
require 'socket'
--- 14,17 ----
Index: fetch.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/fetch.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** fetch.rb 27 Mar 2006 18:34:35 -0000 1.7
--- fetch.rb 8 May 2006 14:29:58 -0000 1.8
***************
*** 1,27 ****
#
! # bio/io/biofetch.rb - BioFetch access module
#
! # Copyright (C) 2002, 2005 Toshiaki Katayama <k at bioruby.org>
! # 2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
!
! # License: LGPL
#
#
! # This library is free software; you can redistribute it and/or
! # modify it under the terms of the GNU Lesser General Public
! # License as published by the Free Software Foundation; either
! # version 2 of the License, or (at your option) any later version.
#
! # This library 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
! # Lesser General Public License for more details.
#
! # You should have received a copy of the GNU Lesser General Public
! # License along with this library; if not, write to the Free Software
! # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! # $Id$
#
require 'uri'
--- 1,28 ----
#
! # = bio/io/biofetch.rb - BioFetch access module
#
! # Copyright:: Copyright (C) 2002, 2005 Toshiaki Katayama <k at bioruby.org>,
! # Copyright (C) 2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License:: Ruby's
#
+ # $Id$
#
! # == DESCRIPTION
#
! # Using BioRuby BioFetch server
#
! # br_server = Bio::Fetch.new()
! # puts br_server.databases
! # puts br_server.formats('embl')
! # puts br_server.maxids
#
! # Using EBI BioFetch server
#
+ # ebi_server = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch')
+ # puts ebi_server.fetch('embl', 'J00231', 'raw')
+ # puts ebi_server.fetch('embl', 'J00231', 'html')
+ # puts Bio::Fetch.query('genbank', 'J00231')
+ # puts Bio::Fetch.query('genbank', 'J00231', 'raw', 'fasta')
+ #
require 'uri'
***************
*** 179,202 ****
end # module Bio
-
-
- if __FILE__ == $0
-
- puts "# test 1"
- br_server = Bio::Fetch.new()
- puts br_server.databases
- puts br_server.formats('embl')
- puts br_server.maxids
- ebi_server = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch')
- puts "# test 2"
- puts ebi_server.fetch('embl', 'J00231', 'raw')
- puts "# test 3"
- puts ebi_server.fetch('embl', 'J00231', 'html')
- puts "# test 4"
- puts Bio::Fetch.query('genbank', 'J00231')
- puts "# test 5"
- puts Bio::Fetch.query('genbank', 'J00231', 'raw', 'fasta')
-
- end
-
-
--- 180,181 ----
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