[BioRuby] esoap.rb

david wheeler wheeler at ncbi.nlm.nih.gov
Fri Dec 10 11:17:07 EST 2004 

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
>

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