Re: Status of BioRuby
On Mon, Oct 05, 2009 at 01:56:13PM -0400, John M Miller wrote:
> Ruby is unusual in that it comes with unit-testing built in. If BioRuby
> used that feature you probably would not have asked for help in the
> first place.
The build log says:
ruby setup.rb test
Running tests...
Loaded suite test
Started
...
Finished in 222.790163 seconds.
This is the good news. The may be bad thing is:
1) Error:
test_log(Bio::FuncTestSOAPWSDL):
EOFError: end of file reached
/usr/lib/ruby/1.8/net/protocol.rb:135:in `sysread'
/usr/lib/ruby/1.8/net/protocol.rb:135:in `rbuf_fill'
/usr/lib/ruby/1.8/timeout.rb:62:in `timeout'
/usr/lib/ruby/1.8/timeout.rb:93:in `timeout'
/usr/lib/ruby/1.8/net/protocol.rb:134:in `rbuf_fill'
/usr/lib/ruby/1.8/net/protocol.rb:116:in `readuntil'
/usr/lib/ruby/1.8/net/protocol.rb:126:in `readline'
/usr/lib/ruby/1.8/net/http.rb:2020:in `read_status_line'
/usr/lib/ruby/1.8/net/http.rb:2009:in `read_new'
/usr/lib/ruby/1.8/net/http.rb:1050:in `request'
/usr/lib/ruby/1.8/net/http.rb:772:in `get'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:105:in `get_content'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:116:in `start'
/usr/lib/ruby/1.8/net/http.rb:543:in `start'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:115:in `start'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:104:in `get_content'
/usr/lib/ruby/1.8/wsdl/xmlSchema/importer.rb:64:in `fetch'
/usr/lib/ruby/1.8/wsdl/xmlSchema/importer.rb:30:in `import'
/usr/lib/ruby/1.8/wsdl/importer.rb:18:in `import'
/usr/lib/ruby/1.8/soap/wsdlDriver.rb:124:in `import'
/usr/lib/ruby/1.8/soap/wsdlDriver.rb:28:in `initialize'
./lib/bio/io/soapwsdl.rb:63:in `new'
./lib/bio/io/soapwsdl.rb:63:in `create_driver'
./lib/bio/io/soapwsdl.rb:57:in `initialize'
./test/functional/bio/io/test_soapwsdl.rb:25:in `new'
./test/functional/bio/io/test_soapwsdl.rb:25:in `setup'
2) Error:
test_set_log(Bio::FuncTestSOAPWSDL):
EOFError: end of file reached
/usr/lib/ruby/1.8/net/protocol.rb:135:in `sysread'
/usr/lib/ruby/1.8/net/protocol.rb:135:in `rbuf_fill'
/usr/lib/ruby/1.8/timeout.rb:62:in `timeout'
/usr/lib/ruby/1.8/timeout.rb:93:in `timeout'
/usr/lib/ruby/1.8/net/protocol.rb:134:in `rbuf_fill'
/usr/lib/ruby/1.8/net/protocol.rb:116:in `readuntil'
/usr/lib/ruby/1.8/net/protocol.rb:126:in `readline'
/usr/lib/ruby/1.8/net/http.rb:2020:in `read_status_line'
/usr/lib/ruby/1.8/net/http.rb:2009:in `read_new'
/usr/lib/ruby/1.8/net/http.rb:1050:in `request'
/usr/lib/ruby/1.8/net/http.rb:772:in `get'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:105:in `get_content'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:116:in `start'
/usr/lib/ruby/1.8/net/http.rb:543:in `start'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:115:in `start'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:104:in `get_content'
/usr/lib/ruby/1.8/wsdl/xmlSchema/importer.rb:64:in `fetch'
/usr/lib/ruby/1.8/wsdl/xmlSchema/importer.rb:30:in `import'
/usr/lib/ruby/1.8/wsdl/importer.rb:18:in `import'
/usr/lib/ruby/1.8/soap/wsdlDriver.rb:124:in `import'
/usr/lib/ruby/1.8/soap/wsdlDriver.rb:28:in `initialize'
./lib/bio/io/soapwsdl.rb:63:in `new'
./lib/bio/io/soapwsdl.rb:63:in `create_driver'
./lib/bio/io/soapwsdl.rb:57:in `initialize'
./test/functional/bio/io/test_soapwsdl.rb:25:in `new'
./test/functional/bio/io/test_soapwsdl.rb:25:in `setup'
3) Error:
test_set_wsdl(Bio::FuncTestSOAPWSDL):
EOFError: end of file reached
/usr/lib/ruby/1.8/net/protocol.rb:135:in `sysread'
/usr/lib/ruby/1.8/net/protocol.rb:135:in `rbuf_fill'
/usr/lib/ruby/1.8/timeout.rb:62:in `timeout'
/usr/lib/ruby/1.8/timeout.rb:93:in `timeout'
/usr/lib/ruby/1.8/net/protocol.rb:134:in `rbuf_fill'
/usr/lib/ruby/1.8/net/protocol.rb:116:in `readuntil'
/usr/lib/ruby/1.8/net/protocol.rb:126:in `readline'
/usr/lib/ruby/1.8/net/http.rb:2020:in `read_status_line'
/usr/lib/ruby/1.8/net/http.rb:2009:in `read_new'
/usr/lib/ruby/1.8/net/http.rb:1050:in `request'
/usr/lib/ruby/1.8/net/http.rb:772:in `get'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:105:in `get_content'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:116:in `start'
/usr/lib/ruby/1.8/net/http.rb:543:in `start'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:115:in `start'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:104:in `get_content'
/usr/lib/ruby/1.8/wsdl/xmlSchema/importer.rb:64:in `fetch'
/usr/lib/ruby/1.8/wsdl/xmlSchema/importer.rb:30:in `import'
/usr/lib/ruby/1.8/wsdl/importer.rb:18:in `import'
/usr/lib/ruby/1.8/soap/wsdlDriver.rb:124:in `import'
/usr/lib/ruby/1.8/soap/wsdlDriver.rb:28:in `initialize'
./lib/bio/io/soapwsdl.rb:63:in `new'
./lib/bio/io/soapwsdl.rb:63:in `create_driver'
./lib/bio/io/soapwsdl.rb:57:in `initialize'
./test/functional/bio/io/test_soapwsdl.rb:25:in `new'
./test/functional/bio/io/test_soapwsdl.rb:25:in `setup'
4) Error:
test_wsdl(Bio::FuncTestSOAPWSDL):
EOFError: end of file reached
/usr/lib/ruby/1.8/net/protocol.rb:135:in `sysread'
/usr/lib/ruby/1.8/net/protocol.rb:135:in `rbuf_fill'
/usr/lib/ruby/1.8/timeout.rb:62:in `timeout'
/usr/lib/ruby/1.8/timeout.rb:93:in `timeout'
/usr/lib/ruby/1.8/net/protocol.rb:134:in `rbuf_fill'
/usr/lib/ruby/1.8/net/protocol.rb:116:in `readuntil'
/usr/lib/ruby/1.8/net/protocol.rb:126:in `readline'
/usr/lib/ruby/1.8/net/http.rb:2020:in `read_status_line'
/usr/lib/ruby/1.8/net/http.rb:2009:in `read_new'
/usr/lib/ruby/1.8/net/http.rb:1050:in `request'
/usr/lib/ruby/1.8/net/http.rb:772:in `get'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:105:in `get_content'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:116:in `start'
/usr/lib/ruby/1.8/net/http.rb:543:in `start'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:115:in `start'
/usr/lib/ruby/1.8/soap/netHttpClient.rb:104:in `get_content'
/usr/lib/ruby/1.8/wsdl/xmlSchema/importer.rb:64:in `fetch'
/usr/lib/ruby/1.8/wsdl/xmlSchema/importer.rb:30:in `import'
/usr/lib/ruby/1.8/wsdl/importer.rb:18:in `import'
/usr/lib/ruby/1.8/soap/wsdlDriver.rb:124:in `import'
/usr/lib/ruby/1.8/soap/wsdlDriver.rb:28:in `initialize'
./lib/bio/io/soapwsdl.rb:63:in `new'
./lib/bio/io/soapwsdl.rb:63:in `create_driver'
./lib/bio/io/soapwsdl.rb:57:in `initialize'
./test/functional/bio/io/test_soapwsdl.rb:25:in `new'
./test/functional/bio/io/test_soapwsdl.rb:25:in `setup'
2328 tests, 5625 assertions, 0 failures, 4 errors
I have no idea in how far this 4 of 2328 tests will influence the
package. The former maintainer / upstream did not cased an exit on test
failures. It might be that the problem is caused because of building
in pbuilder with no network access that calls containing things like
soap/netHttpClient.rb
just have to fail and the package is perfectly right.
> Maybe it would be best to upload the package as-is and take the time
> to build testing into the package in an ordered way. After the unit-
> testing
> is written, and any interim user complaints have been addressed, and
> feedback from some of the original authors has been solicited, then
> the better version could be uploaded?
Your reasoning sounds convincing to me to upload even if there were
these 4 errors. As I said it sounds probable to me that the tests can
not succeed without network connection.
> An earlier comment about extending BioRuby in the direction of
> the Rails framework does not seem really manageable to me without
> using unit-testing.
IMHO we do not have any man power to implement any extensions.
So I will wait for further comments and if nobody insists I might
upload tomorrow.
Kind regards
Andreas.
--
http://fam-tille.de
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