From mmhohman at northwestern.edu Fri Dec 3 02:20:46 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Fri Dec 3 02:18:32 2004 Subject: [BioRuby] added page to wiki describing how to use CVS branches Message-ID: As promised a few weeks ago, I have finally completed a page describing how to use CVS branches (in preparation for the upcoming fork of BioRuby, allowing for the development of a Ruby 1.8-only version of BioRuby). http://wiki.bioruby.org/English/?Using+CVS+branches Please edit it as you see fit, or ask me to clarify anything that isn't clear (which is probably plenty). Moses From wheeler at ncbi.nlm.nih.gov Thu Dec 9 17:35:43 2004 From: wheeler at ncbi.nlm.nih.gov (david wheeler) Date: Thu Dec 9 17:34:26 2004 Subject: [BioRuby] esoap.rb Message-ID: <200412092235.iB9MZd8C026271@mail-blade7.ncbi.nlm.nih.gov> 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 From mmhohman at northwestern.edu Thu Dec 9 17:51:02 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Thu Dec 9 17:48:32 2004 Subject: [BioRuby] esoap.rb In-Reply-To: <200412092235.iB9MZd8C026271@mail-blade7.ncbi.nlm.nih.gov> References: <200412092235.iB9MZd8C026271@mail-blade7.ncbi.nlm.nih.gov> Message-ID: 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@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From mmhohman at northwestern.edu Thu Dec 9 17:51:02 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Thu Dec 9 17:48:35 2004 Subject: [BioRuby] esoap.rb In-Reply-To: <200412092235.iB9MZd8C026271@mail-blade7.ncbi.nlm.nih.gov> References: <200412092235.iB9MZd8C026271@mail-blade7.ncbi.nlm.nih.gov> Message-ID: 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@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Thu Dec 9 23:53:43 2004 From: ktym at hgc.jp (Toshiaki Katayama) Date: Thu Dec 9 23:51:00 2004 Subject: [BioRuby] esoap.rb In-Reply-To: References: <200412092235.iB9MZd8C026271@mail-blade7.ncbi.nlm.nih.gov> Message-ID: <77A816E7-4A67-11D9-9C8F-000D93347CEA@hgc.jp> 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@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby >> > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby From ktym at hgc.jp Thu Dec 9 23:57:41 2004 From: ktym at hgc.jp (Toshiaki Katayama) Date: Thu Dec 9 23:54:58 2004 Subject: [BioRuby] added page to wiki describing how to use CVS branches In-Reply-To: References: Message-ID: <05E21288-4A68-11D9-9C8F-000D93347CEA@hgc.jp> Hi Moses, Thank you for your great job and sorry for the delay in responding. I'm considering to translate your page into Japanese. Regards, Toshiaki Katayama On 2004/12/03, at 16:20, Moses Hohman wrote: > As promised a few weeks ago, I have finally completed a page > describing how to use CVS branches (in preparation for the upcoming > fork of BioRuby, allowing for the development of a Ruby 1.8-only > version of BioRuby). > > http://wiki.bioruby.org/English/?Using+CVS+branches > > Please edit it as you see fit, or ask me to clarify anything that > isn't clear (which is probably plenty). > > Moses > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby From mmhohman at northwestern.edu Fri Dec 10 02:20:57 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Fri Dec 10 02:18:31 2004 Subject: [BioRuby] esoap.rb In-Reply-To: <77A816E7-4A67-11D9-9C8F-000D93347CEA@hgc.jp> References: <200412092235.iB9MZd8C026271@mail-blade7.ncbi.nlm.nih.gov> <77A816E7-4A67-11D9-9C8F-000D93347CEA@hgc.jp> Message-ID: <09651CB5-4A7C-11D9-AACF-000393DB7722@northwestern.edu> 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 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@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From mmhohman at northwestern.edu Fri Dec 10 02:20:57 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Fri Dec 10 02:18:35 2004 Subject: [BioRuby] esoap.rb In-Reply-To: <77A816E7-4A67-11D9-9C8F-000D93347CEA@hgc.jp> References: <200412092235.iB9MZd8C026271@mail-blade7.ncbi.nlm.nih.gov> <77A816E7-4A67-11D9-9C8F-000D93347CEA@hgc.jp> Message-ID: <09651CB5-4A7C-11D9-AACF-000393DB7722@northwestern.edu> 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 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@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From wheeler at ncbi.nlm.nih.gov Fri Dec 10 09:48:06 2004 From: wheeler at ncbi.nlm.nih.gov (David Wheeler) Date: Fri Dec 10 09:46:27 2004 Subject: [BioRuby] esoap.rb In-Reply-To: <77A816E7-4A67-11D9-9C8F-000D93347CEA@hgc.jp> References: <200412092235.iB9MZd8C026271@mail-blade7.ncbi.nlm.nih.gov> <77A816E7-4A67-11D9-9C8F-000D93347CEA@hgc.jp> Message-ID: Toshiaki: No ideas yet but the error is not unfamiliar to me....I got stopped by this one also. I'll run it past our SOAP expert; perhaps we need to change a server setting. David On Fri, 10 Dec 2004, 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@open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/bioruby > >> > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby@open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From wheeler at ncbi.nlm.nih.gov Fri Dec 10 09:48:06 2004 From: wheeler at ncbi.nlm.nih.gov (David Wheeler) Date: Fri Dec 10 09:46:40 2004 Subject: [BioRuby] esoap.rb In-Reply-To: <77A816E7-4A67-11D9-9C8F-000D93347CEA@hgc.jp> References: <200412092235.iB9MZd8C026271@mail-blade7.ncbi.nlm.nih.gov> <77A816E7-4A67-11D9-9C8F-000D93347CEA@hgc.jp> Message-ID: Toshiaki: No ideas yet but the error is not unfamiliar to me....I got stopped by this one also. I'll run it past our SOAP expert; perhaps we need to change a server setting. David On Fri, 10 Dec 2004, 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@open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/bioruby > >> > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby@open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From wheeler at ncbi.nlm.nih.gov Fri Dec 10 11:17:07 2004 From: wheeler at ncbi.nlm.nih.gov (david wheeler) Date: Fri Dec 10 11:16:09 2004 Subject: [BioRuby] esoap.rb In-Reply-To: <09651CB5-4A7C-11D9-AACF-000393DB7722@northwestern.edu> Message-ID: <200412101617.iBAGH6C0011043@mail-blade8.ncbi.nlm.nih.gov> 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@portal.open-bio.org [mailto:bioruby-bounces@portal.open-bio.org] On Behalf Of Moses Hohman Sent: Friday, December 10, 2004 2:21 AM To: bioruby@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 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@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > _______________________________________________ BioRuby mailing list BioRuby@open-bio.org http://portal.open-bio.org/mailman/listinfo/bioruby From ktym at hgc.jp Sat Dec 11 01:03:01 2004 From: ktym at hgc.jp (Toshiaki Katayama) Date: Sat Dec 11 01:00:18 2004 Subject: [BioRuby] esoap.rb In-Reply-To: <200412101617.iBAGH6C0011043@mail-blade8.ncbi.nlm.nih.gov> References: <200412101617.iBAGH6C0011043@mail-blade8.ncbi.nlm.nih.gov> Message-ID: <5047B543-4B3A-11D9-9842-000D93347CEA@hgc.jp> 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@portal.open-bio.org > [mailto:bioruby-bounces@portal.open-bio.org] On Behalf Of Moses Hohman > Sent: Friday, December 10, 2004 2:21 AM > To: bioruby@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 > 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@open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>> >>> >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby >> > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby From wheeler at ncbi.nlm.nih.gov Sat Dec 11 09:37:53 2004 From: wheeler at ncbi.nlm.nih.gov (David Wheeler) Date: Sat Dec 11 09:36:23 2004 Subject: [BioRuby] esoap.rb In-Reply-To: <5047B543-4B3A-11D9-9842-000D93347CEA@hgc.jp> References: <200412101617.iBAGH6C0011043@mail-blade8.ncbi.nlm.nih.gov> <5047B543-4B3A-11D9-9842-000D93347CEA@hgc.jp> Message-ID: 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 #old import block that is giving parse errors 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@portal.open-bio.org > > [mailto:bioruby-bounces@portal.open-bio.org] On Behalf Of Moses Hohman > > Sent: Friday, December 10, 2004 2:21 AM > > To: bioruby@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 > > 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@open-bio.org > >>>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>>> > >>> > >>> _______________________________________________ > >>> BioRuby mailing list > >>> BioRuby@open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/bioruby > >> > >> _______________________________________________ > >> BioRuby mailing list > >> BioRuby@open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/bioruby > >> > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby@open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioruby > > > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby@open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From mmhohman at northwestern.edu Sat Dec 11 15:49:57 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Sat Dec 11 15:47:20 2004 Subject: [BioRuby] esoap.rb In-Reply-To: References: <200412101617.iBAGH6C0011043@mail-blade8.ncbi.nlm.nih.gov> <5047B543-4B3A-11D9-9842-000D93347CEA@hgc.jp> Message-ID: <37A1585E-4BB6-11D9-9C25-000393DB7722@northwestern.edu> 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 > > > targetNamespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/"> > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > schemaLocation="egquery.xsd"/> > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > schemaLocation="einfo.xsd"/> > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > schemaLocation="elink.xsd"/> > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > schemaLocation="esearch.xsd"/> > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > schemaLocation="efetch.xsd"/> > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > schemaLocation="esummary.xsd"/> > > > > > > #old import block that is giving parse errors > > > > 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@portal.open-bio.org >>> [mailto:bioruby-bounces@portal.open-bio.org] On Behalf Of Moses >>> Hohman >>> Sent: Friday, December 10, 2004 2:21 AM >>> To: bioruby@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 >>> 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@open-bio.org >>>>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>>>> >>>>> >>>>> _______________________________________________ >>>>> BioRuby mailing list >>>>> BioRuby@open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>> >>>> _______________________________________________ >>>> BioRuby mailing list >>>> BioRuby@open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>> >>> >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >>> >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From wheeler at ncbi.nlm.nih.gov Sat Dec 11 16:38:21 2004 From: wheeler at ncbi.nlm.nih.gov (David Wheeler) Date: Sat Dec 11 16:36:30 2004 Subject: [BioRuby] esoap.rb In-Reply-To: <37A1585E-4BB6-11D9-9C25-000393DB7722@northwestern.edu> References: <200412101617.iBAGH6C0011043@mail-blade8.ncbi.nlm.nih.gov> <5047B543-4B3A-11D9-9842-000D93347CEA@hgc.jp> <37A1585E-4BB6-11D9-9C25-000393DB7722@northwestern.edu> Message-ID: 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 > > > > > > > targetNamespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/"> > > > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > > schemaLocation="egquery.xsd"/> > > > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > > schemaLocation="einfo.xsd"/> > > > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > > schemaLocation="elink.xsd"/> > > > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > > schemaLocation="esearch.xsd"/> > > > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > > schemaLocation="efetch.xsd"/> > > > namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > > schemaLocation="esummary.xsd"/> > > > > > > > > > > > > #old import block that is giving parse errors > > > > > > > > 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@portal.open-bio.org > >>> [mailto:bioruby-bounces@portal.open-bio.org] On Behalf Of Moses > >>> Hohman > >>> Sent: Friday, December 10, 2004 2:21 AM > >>> To: bioruby@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 > >>> 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@open-bio.org > >>>>>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> BioRuby mailing list > >>>>> BioRuby@open-bio.org > >>>>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>>> > >>>> _______________________________________________ > >>>> BioRuby mailing list > >>>> BioRuby@open-bio.org > >>>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>>> > >>> > >>> _______________________________________________ > >>> BioRuby mailing list > >>> BioRuby@open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>> > >>> > >>> _______________________________________________ > >>> BioRuby mailing list > >>> BioRuby@open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/bioruby > >> > >> _______________________________________________ > >> BioRuby mailing list > >> BioRuby@open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby mailing list > > BioRuby@open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioruby > > > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From mmhohman at northwestern.edu Sun Dec 12 03:52:10 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Sun Dec 12 03:49:25 2004 Subject: [BioRuby] esoap.rb In-Reply-To: References: <200412101617.iBAGH6C0011043@mail-blade8.ncbi.nlm.nih.gov> <5047B543-4B3A-11D9-9842-000D93347CEA@hgc.jp> <37A1585E-4BB6-11D9-9C25-000393DB7722@northwestern.edu> Message-ID: <1BEECA74-4C1B-11D9-B2EC-000393DB7722@northwestern.edu> 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 >>> >>> >>> >> targetNamespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/"> >>> >> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" >>> schemaLocation="egquery.xsd"/> >>> >> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" >>> schemaLocation="einfo.xsd"/> >>> >> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" >>> schemaLocation="elink.xsd"/> >>> >> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" >>> schemaLocation="esearch.xsd"/> >>> >> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" >>> schemaLocation="efetch.xsd"/> >>> >> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" >>> schemaLocation="esummary.xsd"/> >>> >>> >>> >>> >>> >>> #old import block that is giving parse errors >>> >>> >>> >>> 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@portal.open-bio.org >>>>> [mailto:bioruby-bounces@portal.open-bio.org] On Behalf Of Moses >>>>> Hohman >>>>> Sent: Friday, December 10, 2004 2:21 AM >>>>> To: bioruby@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 >>>>> 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@open-bio.org >>>>>>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> BioRuby mailing list >>>>>>> BioRuby@open-bio.org >>>>>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>>>> >>>>>> _______________________________________________ >>>>>> BioRuby mailing list >>>>>> BioRuby@open-bio.org >>>>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>>>> >>>>> >>>>> _______________________________________________ >>>>> BioRuby mailing list >>>>> BioRuby@open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>>> >>>>> >>>>> _______________________________________________ >>>>> BioRuby mailing list >>>>> BioRuby@open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>> >>>> _______________________________________________ >>>> BioRuby mailing list >>>> BioRuby@open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>> >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From wheeler at ncbi.nlm.nih.gov Sun Dec 12 11:28:45 2004 From: wheeler at ncbi.nlm.nih.gov (David Wheeler) Date: Sun Dec 12 11:26:26 2004 Subject: [BioRuby] esoap.rb In-Reply-To: <1BEECA74-4C1B-11D9-B2EC-000393DB7722@northwestern.edu> References: <200412101617.iBAGH6C0011043@mail-blade8.ncbi.nlm.nih.gov> <5047B543-4B3A-11D9-9842-000D93347CEA@hgc.jp> <37A1585E-4BB6-11D9-9C25-000393DB7722@northwestern.edu> <1BEECA74-4C1B-11D9-B2EC-000393DB7722@northwestern.edu> Message-ID: 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 > >>> > >>> > >>> >>> targetNamespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/"> > >>> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > >>> schemaLocation="egquery.xsd"/> > >>> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > >>> schemaLocation="einfo.xsd"/> > >>> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > >>> schemaLocation="elink.xsd"/> > >>> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > >>> schemaLocation="esearch.xsd"/> > >>> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > >>> schemaLocation="efetch.xsd"/> > >>> >>> namespace="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/" > >>> schemaLocation="esummary.xsd"/> > >>> > >>> > >>> > >>> > >>> > >>> #old import block that is giving parse errors > >>> > >>> > >>> > >>> 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@portal.open-bio.org > >>>>> [mailto:bioruby-bounces@portal.open-bio.org] On Behalf Of Moses > >>>>> Hohman > >>>>> Sent: Friday, December 10, 2004 2:21 AM > >>>>> To: bioruby@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 > >>>>> 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@open-bio.org > >>>>>>>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> BioRuby mailing list > >>>>>>> BioRuby@open-bio.org > >>>>>>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>>>>> > >>>>>> _______________________________________________ > >>>>>> BioRuby mailing list > >>>>>> BioRuby@open-bio.org > >>>>>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> BioRuby mailing list > >>>>> BioRuby@open-bio.org > >>>>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> BioRuby mailing list > >>>>> BioRuby@open-bio.org > >>>>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>>> > >>>> _______________________________________________ > >>>> BioRuby mailing list > >>>> BioRuby@open-bio.org > >>>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>>> > >>> _______________________________________________ > >>> BioRuby mailing list > >>> BioRuby@open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/bioruby > >>> > >> > >> _______________________________________________ > >> BioRuby mailing list > >> BioRuby@open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby mailing list > > BioRuby@open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioruby > > > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Mon Dec 13 00:30:57 2004 From: ktym at hgc.jp (Toshiaki Katayama) Date: Mon Dec 13 00:28:08 2004 Subject: [BioRuby] BioRuby 0.6.2 released Message-ID: <2A8FCAC7-4CC8-11D9-9842-000D93347CEA@hgc.jp> Hi, I have just released BioRuby 0.6.2 at: http://bioruby.org/archive/bioruby-0.6.2.tar.gz This release includes Unit Tests contributed by Moses Hohman, support for Sim4, Spidey and BLAT by Naohisa Goto, many other improvements and bug fixes. See ChangeLog for more details. Regards, Toshiaki Katayama -- Human Genome Center, Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan tel://+81-3-5449-5614, fax://+81-3-5449-5434 BioRuby project http://bioruby.org/~k/ GenomeNet/KEGG http://www.genome.jp/ Human Genome Center http://www.hgc.jp/