[BioRuby] esoap.rb

David Wheeler wheeler at ncbi.nlm.nih.gov
Sun Dec 12 11:28:45 EST 2004 

Moses:

Wow, this is great!  It is much cleaner than the example we have posted on
our website using Java and Axis and it works like a charm!

David


On Sun, 12 Dec 2004, Moses Hohman wrote:

> Agreed, sounds good.
>
> I'm a bit of a SOAP and soap4r neophyte, so it took me way too long,
> but I was able to make a successful efetch round-trip using a local
> copy of the eUtils WSDL modified as David suggested. It also required a
> modification of soap4r's soap/mapping/mapping.rb, because some of the
> XML tags in the efetch response have names with -s in them, and
> mapping.rb was calling Module#const_defined? on those names, which
> results in a NameError, since they're not legal Ruby constant names,
> even though they are legal XML element names. A patch to mapping.rb is
> to change line 152 (the second line below:
>
>    def self.class_from_name(name)
>      if /^[A-Z]/ !~ name
>        return nil
>      end
>      .
>      .
>      .
>
> to
>
>    def self.class_from_name(name)
>      if /^[A-Z]/ !~ name or /[^A-Za-z0-9_]/ =~ name
>        return nil
>      end
>      .
>      .
>      .
>
> That patch allows you to perform a successful call, although I think
> it's not quite the right patch, because the "offending" element
> (GBSeq_other-seqids) should be a property on the resulting Ruby
> SOAP::Mapping::Object response, but it isn't there (though it *is* in
> the SOAP XML response).
>
> With the mapping.rb patch, the following code will perform a successful
> call on eUtils' eFetch:
>
> #
> # bio/io/eutils.rb - NCBI eUtils access class
> #
>
> require 'bio/io/soapwsdl'
> require 'soap/element'
> require 'xsd/datatypes'
>
> module Bio
> class NCBI
>
> class EUtils < Bio::SOAPWSDL
>
>    SERVER_URI =
> 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl'
>
>    EFETCH_NAMESPACE = 'http://eutils.ncbi.nlm.nih.gov/soap/eutils/efetch'
>    EFETCH_REQUEST_QNAME = XSD::QName.new(EFETCH_NAMESPACE,
> 'eFetchRequest')
>
>    def initialize(wsdl = nil, log = nil)
>      @wsdl = wsdl || SERVER_URI
>      @log = log
>      create_driver
>    end
>
>    def efetch(db, identifier)
>      request_body=SOAP::SOAPElement.new(EFETCH_REQUEST_QNAME)
>      request_body.add(SOAP::SOAPElement.new('db', db))
>      request_body.add(SOAP::SOAPElement.new('id', identifier))
>      request_header = nil
>      @driver.run_eFetch(request_header, request_body)
>    end
> end # EUtils
> end # NCBI
> end # Bio
>
> if __FILE__ == $0
>    serv = Bio::NCBI::EUtils.new("eutils.wsdl", STDOUT)
>
>    response_header, response_body = serv.efetch('nucleotide',
> 'NM_000027')
>    puts response_body.GBSeq.GBSeq_locus
>    puts response_body.GBSeq.GBSeq_definition
>    puts response_body.GBSeq.GBSeq_sequence
> end
>
> On Dec 11, 2004, at 3:38 PM, David Wheeler wrote:
>
> > Moses:
> >
> > Yes, I think we're using non-standard syntax but I need to check with
> > our
> > developers to see if they agree.  If so, they we'll change it and that
> > should fix the eutils problem. But, if the author of SOAP4R feels that
> > the
> > syntax we're using now is common enough to be worth accommodating, I
> > don't
> > want to discourage that.
> >
> > David
> >
> > On Sat, 11 Dec 2004, Moses Hohman wrote:
> >
> >> So, David, you think it's actually a server-side WSDL problem? Just
> >> confirming that I understand your email.
> >>
> >> That would be good news.
> >>
> >> Moses
> >>
> >> On Dec 11, 2004, at 8:37 AM, David Wheeler wrote:
> >>
> >>> Toshiaki:
> >>>
> >>> Great!  In case it helps, I've been exploring the wsdl we're using in
> >>> eutils_a.wsdl and I can eliminate most of the problems by replacing
> >>> the
> >>> wsdl:import statements with xsd:import statements and including the
> >>> xsd
> >>> namespace. Hence, if I replace the original import block, commented
> >>> out
> >>> below, with the wsdl:types block that follows, problem Number Two
> >>> goes
> >>> away.  From what I read on the web, the syntax of the second block is
> >>> not
> >>> considered to be correct.
> >>>
> >>> David
> >>>
> >>> #need to add this to use xsd:schema tag
> >>> xmlns:xsd="http://www.w3.org/2001/XMLSchema"
> >>>
> >>> #new import block that seems to work
> >>>
> >>>  <wsdl:types>
> >>>     <xsd:schema
> >>> targetNamespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/">
> >>>     <xsd:import
> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>>       schemaLocation="egquery.xsd"/>
> >>>       <xsd:import
> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>>       schemaLocation="einfo.xsd"/>
> >>>       <xsd:import
> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>>       schemaLocation="elink.xsd"/>
> >>>       <xsd:import
> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>>       schemaLocation="esearch.xsd"/>
> >>>       <xsd:import
> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>>       schemaLocation="efetch.xsd"/>
> >>>       <xsd:import
> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>>       schemaLocation="esummary.xsd"/>
> >>>
> >>>     </xsd:schema>
> >>>   </wsdl:types>
> >>>
> >>>
> >>> #old import block that is giving parse errors
> >>>
> >>> <!--
> >>>   <wsdl:import
> >>> namespace="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>> location="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/egquery.xsd"
> >>> />
> >>>   <wsdl:import
> >>> namespace="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>> location="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/einfo.xsd"
> >>> />
> >>>   <wsdl:import
> >>> namespace="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>> location="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/elink.xsd"
> >>> />
> >>>   <wsdl:import
> >>> namespace="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>> location="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/esearch.xsd"
> >>> />
> >>>   <wsdl:import
> >>> namespace="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>> location="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/
> >>> esummary.xsd"
> >>> />
> >>>   <wsdl:import
> >>> namespace="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/"
> >>> location="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/efetch.xsd"
> >>> />
> >>>
> >>> -->
> >>>
> >>> On Sat, 11 Dec 2004, Toshiaki Katayama wrote:
> >>>
> >>>> Hi David,
> >>>>
> >>>> I have contacted the author of SOAP4R.
> >>>> He will implement this function soon so that we can use
> >>>> eutils_a.wsdl
> >>>> without any modification on server side, hopefully. :)
> >>>>
> >>>> Regards,
> >>>> Toshiaki Katayama
> >>>>
> >>>> On 2004/12/11, at 1:17, david wheeler wrote:
> >>>>
> >>>>> Moses, Toshiaki:
> >>>>>
> >>>>> Looks like the relative urls you saw in the wsdl were one
> >>>>> problem...
> >>>>> Our
> >>>>> SOAP specialist has created a new wsdl for testing with absolute
> >>>>> urls
> >>>>> at:
> >>>>>
> >>>>> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils_a.wsdl
> >>>>>
> >>>>> Using this one, gets me to the new error that you also see when you
> >>>>> curl the
> >>>>> XSD files:
> >>>>>
> >>>>> /usr/lib/ruby/1.8/wsdl/xmlSchema/element.rb:76:in `parse_attr':
> >>>>> NotImplementedError (NotImplementedError)
> >>>>>         from /usr/lib/ruby/1.8/wsdl/xmlSchema/parser.rb:141:in
> >>>>> `decode_tag'
> >>>>>         from /usr/lib/ruby/1.8/wsdl/xmlSchema/parser.rb:121:in
> >>>>> `each'
> >>>>>         from /usr/lib/ruby/1.8/wsdl/xmlSchema/parser.rb:121:in
> >>>>> `decode_tag'
> >>>>>         from /usr/lib/ruby/1.8/wsdl/xmlSchema/parser.rb:79:in
> >>>>> `start_element'
> >>>>>         from /usr/lib/ruby/1.8/xsd/xmlparser/parser.rb:67:in
> >>>>> `start_element'
> >>>>>         from /usr/lib/ruby/1.8/xsd/xmlparser/rexmlparser.rb:34:in
> >>>>> `tag_start'
> >>>>>         from /usr/lib/ruby/1.8/rexml/parsers/streamparser.rb:17:in
> >>>>> `parse'
> >>>>>         from /usr/lib/ruby/1.8/rexml/document.rb:166:in
> >>>>> `parse_stream'
> >>>>>          ... 18 levels...
> >>>>>         from /usr/lib/ruby/1.8/soap/wsdlDriver.rb:70:in `import'
> >>>>>         from /usr/lib/ruby/1.8/soap/wsdlDriver.rb:34:in
> >>>>> `initialize'
> >>>>>         from ./ncbi_soap.rb:8:in `new'
> >>>>>         from ./ncbi_soap.rb:8
> >>>>>
> >>>>> I'll pursue this on our end but if you have any ideas, let me know.
> >>>>>
> >>>>>
> >>>>> David
> >>>>>
> >>>>>
> >>>>> -----Original Message-----
> >>>>> From: bioruby-bounces at portal.open-bio.org
> >>>>> [mailto:bioruby-bounces at portal.open-bio.org] On Behalf Of Moses
> >>>>> Hohman
> >>>>> Sent: Friday, December 10, 2004 2:21 AM
> >>>>> To: bioruby at portal.open-bio.org
> >>>>> Cc: BioRuby Project Discussion List
> >>>>> Subject: Re: [BioRuby] esoap.rb
> >>>>>
> >>>>> I get a different error:
> >>>>>
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1283:in
> >>>>> `initialize':
> >>>>> Can't assign requested address - connect(2) (Errno::EADDRNOTAVAIL)
> >>>>>          from
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1283:in
> >>>>> `new'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1283:in
> >>>>> `create_socket'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1252:in
> >>>>> `connect'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1251:in
> >>>>> `timeout'
> >>>>>          from /usr/local/lib/ruby/1.8/timeout.rb:55:in `timeout'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1251:in
> >>>>> `connect'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1111:in
> >>>>> `query'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:833:in
> >>>>> `query'
> >>>>>           ... 26 levels...
> >>>>>          from /usr/local/lib/ruby/1.8/soap/wsdlDriver.rb:71:in
> >>>>> `import'
> >>>>>          from /usr/local/lib/ruby/1.8/soap/wsdlDriver.rb:35:in
> >>>>> `initialize'
> >>>>>          from test_eruby.rb:12:in `new'
> >>>>>
> >>>>> The full backtrace is after the rest of my message.
> >>>>>
> >>>>> This seems to have something to do with the fact that eutils.wsdl
> >>>>> has
> >>>>> <wsdl:import> tags with locations that don't specify a base URL or
> >>>>> something
> >>>>> (I'm not very familiar with WSDL). soap4r apparently can't handle
> >>>>> this, or
> >>>>> maybe there's an option one has to set that I don't know. If you
> >>>>> curl
> >>>>> the
> >>>>> various imported XSD files, the error goes away and a new error
> >>>>> occurs:
> >>>>>
> >>>>> /usr/local/lib/ruby/1.8/wsdl/xmlSchema/element.rb:76:in
> >>>>> `parse_attr':
> >>>>> NotImplementedError (NotImplementedError)
> >>>>>          from
> >>>>> /usr/local/lib/ruby/1.8/wsdl/xmlSchema/parser.rb:142:in
> >>>>> `decode_tag'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/1.8/wsdl/xmlSchema/parser.rb:122:in
> >>>>> `each'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/1.8/wsdl/xmlSchema/parser.rb:122:in
> >>>>> `decode_tag'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/1.8/wsdl/xmlSchema/parser.rb:79:in
> >>>>> `start_element'
> >>>>>          from /usr/local/lib/ruby/1.8/xsd/xmlparser/parser.rb:67:in
> >>>>> `start_element'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/1.8/xsd/xmlparser/xmlscanner.rb:139:in
> >>>>> `on_stag_end'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/1.8/xsd/xmlparser/xmlscanner.rb:134:in
> >>>>> `on_stag_end_empty'
> >>>>>          from
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/xmlscan/scanner.rb:470:in
> >>>>> `on_stag_end_empty'
> >>>>>           ... 28 levels...
> >>>>>          from /usr/local/lib/ruby/1.8/soap/wsdlDriver.rb:71:in
> >>>>> `import'
> >>>>>          from /usr/local/lib/ruby/1.8/soap/wsdlDriver.rb:35:in
> >>>>> `initialize'
> >>>>>          from test_eruby.rb:12:in `new'
> >>>>>          from test_eruby.rb:12
> >>>>>
> >>>>>
> >>>>> I'm running 1.8.2 preview 3 on OS X 10.3.6. I've also installed a
> >>>>> ton
> >>>>> of
> >>>>> ruby stuff, so it's possible my setup's errors will be unique : )
> >>>>>
> >>>>> Moses
> >>>>>
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1283:in
> >>>>> `initialize'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1283:in `new'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1283:in
> >>>>> `create_socket'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1252:in `connect'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1251:in `timeout'
> >>>>> /usr/local/lib/ruby/1.8/timeout.rb:55:in `timeout'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1251:in `connect'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:1111:in `query'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:833:in `query'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:383:in
> >>>>> `do_get_block'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:327:in
> >>>>> `conn_request'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:259:in `request'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:234:in `get'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/http-access2.rb:209:in
> >>>>> `get_content'
> >>>>> /usr/local/lib/ruby/1.8/wsdl/importer.rb:39:in `import'
> >>>>> /usr/local/lib/ruby/1.8/wsdl/importer.rb:20:in `import'
> >>>>> /usr/local/lib/ruby/1.8/wsdl/import.rb:65:in `import'
> >>>>> /usr/local/lib/ruby/1.8/wsdl/import.rb:49:in `parse_attr'
> >>>>> /usr/local/lib/ruby/1.8/wsdl/parser.rb:143:in `decode_tag'
> >>>>> /usr/local/lib/ruby/1.8/wsdl/parser.rb:126:in `each'
> >>>>> /usr/local/lib/ruby/1.8/wsdl/parser.rb:126:in `decode_tag'
> >>>>> /usr/local/lib/ruby/1.8/wsdl/parser.rb:81:in `start_element'
> >>>>> /usr/local/lib/ruby/1.8/xsd/xmlparser/parser.rb:67:in
> >>>>> `start_element'
> >>>>> /usr/local/lib/ruby/1.8/xsd/xmlparser/xmlscanner.rb:139:in
> >>>>> `on_stag_end'
> >>>>> /usr/local/lib/ruby/1.8/xsd/xmlparser/xmlscanner.rb:134:in
> >>>>> `on_stag_end_empty'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/xmlscan/scanner.rb:470:in
> >>>>> `on_stag_end_empty'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/xmlscan/scanner.rb:794:in
> >>>>> `scan_stag'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/xmlscan/scanner.rb:826:in
> >>>>> `scan_content'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/xmlscan/scanner.rb:1051:in
> >>>>> `scan_prolog'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/xmlscan/scanner.rb:1058:in
> >>>>> `scan_document'
> >>>>> /usr/local/lib/ruby/site_ruby/1.8/xmlscan/scanner.rb:1073:in
> >>>>> `parse'
> >>>>> /usr/local/lib/ruby/1.8/xsd/xmlparser/xmlscanner.rb:25:in
> >>>>> `do_parse'
> >>>>> /usr/local/lib/ruby/1.8/wsdl/parser.rb:62:in `parse'
> >>>>> /usr/local/lib/ruby/1.8/wsdl/importer.rb:43:in `import'
> >>>>> /usr/local/lib/ruby/1.8/wsdl/importer.rb:20:in `import'
> >>>>> /usr/local/lib/ruby/1.8/soap/wsdlDriver.rb:71:in `import'
> >>>>> /usr/local/lib/ruby/1.8/soap/wsdlDriver.rb:35:in `initialize'
> >>>>> test_eruby.rb:12:in `new'
> >>>>>
> >>>>>
> >>>>> On Dec 9, 2004, at 10:53 PM, Toshiaki Katayama wrote:
> >>>>>
> >>>>>> Hi,
> >>>>>>
> >>>>>> I have not completed esoap.rb yet. :)
> >>>>>>
> >>>>>> It seems that wsdl:import fails when loading eutils.wsdl in Ruby
> >>>>>> 1.8.1
> >>>>>> (comes with SOAP4R).  Any ideas?
> >>>>>>
> >>>>>> Regards,
> >>>>>> Toshiaki Katayama
> >>>>>>
> >>>>>> esoap_test.rb:
> >>>>>> -------------------------
> >>>>>> #!/usr/bin/env ruby
> >>>>>>
> >>>>>> require 'soap/wsdlDriver'
> >>>>>>
> >>>>>> wsdl =
> >>>>>> "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl"
> >>>>>>
> >>>>>> driver = SOAP::WSDLDriverFactory.new(wsdl).create_driver
> >>>>>> -------------------------
> >>>>>>
> >>>>>> % ruby esoap.rb
> >>>>>> /usr/local/lib/ruby/1.8/soap/netHttpClient.rb:121:in
> >>>>>> `create_connection': Cannot connect to egquery.xsd (Not HTTP.)
> >>>>>> (RuntimeError)
> >>>>>>         from /usr/local/lib/ruby/1.8/soap/netHttpClient.rb:91:in
> >>>>>> `start'
> >>>>>>         from /usr/local/lib/ruby/1.8/soap/netHttpClient.rb:82:in
> >>>>>> `get_content'
> >>>>>>         from /usr/local/lib/ruby/1.8/wsdl/importer.rb:39:in
> >>>>>> `import'
> >>>>>>         from /usr/local/lib/ruby/1.8/wsdl/importer.rb:20:in
> >>>>>> `import'
> >>>>>>         from /usr/local/lib/ruby/1.8/wsdl/import.rb:65:in `import'
> >>>>>>         from /usr/local/lib/ruby/1.8/wsdl/import.rb:49:in
> >>>>>> `parse_attr'
> >>>>>>         from /usr/local/lib/ruby/1.8/wsdl/parser.rb:141:in
> >>>>>> `decode_tag'
> >>>>>>         from /usr/local/lib/ruby/1.8/wsdl/parser.rb:124:in `each'
> >>>>>>          ... 9 levels...
> >>>>>>         from /usr/local/lib/ruby/1.8/soap/wsdlDriver.rb:69:in
> >>>>>> `import'
> >>>>>>         from /usr/local/lib/ruby/1.8/soap/wsdlDriver.rb:33:in
> >>>>>> `initialize'
> >>>>>>         from esoap_test.rb:5:in `new'
> >>>>>>         from esoap_test.rb:5
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> On 2004/12/10, at 7:51, Moses Hohman wrote:
> >>>>>>
> >>>>>>> It would be great if you could help out. esoap.rb is not in CVS,
> >>>>>>> so
> >>>>>>> Toshiaki will have to email it : )
> >>>>>>>
> >>>>>>> Moses
> >>>>>>>
> >>>>>>> On Dec 9, 2004, at 4:35 PM, david wheeler wrote:
> >>>>>>>
> >>>>>>>> Hi:
> >>>>>>>>
> >>>>>>>> Is it still true that esoap.rb is not working? Is the current
> >>>>>>>> version available?  If so, I'd be happy to help if I could get a
> >>>>>>>> copy.
> >>>>>>>>
> >>>>>>>> David Wheeler, NCBI
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> BioRuby mailing list
> >>>>>>>> BioRuby at open-bio.org
> >>>>>>>> http://portal.open-bio.org/mailman/listinfo/bioruby
> >>>>>>>>
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> BioRuby mailing list
> >>>>>>> BioRuby at open-bio.org
> >>>>>>> http://portal.open-bio.org/mailman/listinfo/bioruby
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> BioRuby mailing list
> >>>>>> BioRuby at open-bio.org
> >>>>>> http://portal.open-bio.org/mailman/listinfo/bioruby
> >>>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> BioRuby mailing list
> >>>>> BioRuby at open-bio.org
> >>>>> http://portal.open-bio.org/mailman/listinfo/bioruby
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> BioRuby mailing list
> >>>>> BioRuby at open-bio.org
> >>>>> http://portal.open-bio.org/mailman/listinfo/bioruby
> >>>>
> >>>> _______________________________________________
> >>>> BioRuby mailing list
> >>>> BioRuby at open-bio.org
> >>>> http://portal.open-bio.org/mailman/listinfo/bioruby
> >>>>
> >>> _______________________________________________
> >>> BioRuby mailing list
> >>> BioRuby at open-bio.org
> >>> http://portal.open-bio.org/mailman/listinfo/bioruby
> >>>
> >>
> >> _______________________________________________
> >> BioRuby mailing list
> >> BioRuby at open-bio.org
> >> http://portal.open-bio.org/mailman/listinfo/bioruby
> >>
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioruby
> >
>
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