[BioRuby] Running BioRuby tests offline

[Peter Cock]

Hi all,

I recently tried running the BioRuby test suite while offline (on a train),


$ ruby runner.rb
Loaded suite .
Started
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Finished in 100.74387 seconds.

  1) Failure:
test_read_uri(Bio::FuncTestCommandNet) [./functional/bio/test_command.rb:337]:
Exception raised:
Class: <SocketError>
Message: <"getaddrinfo: nodename nor servname provided, or not known">
---Backtrace---
...
 73) Failure:
test_libxml(Bio::TestPhyloXML_Check_LibXML) [./unit/bio/db/test_phyloxml.rb:29]:
Error: libxml-ruby library is not present. Please install libxml-ruby
library. It is needed for Bio::PhyloXML module. Unit test for PhyloXML
will not be performed.
<nil> is not true.

3640 tests, 20824 assertions, 26 failures, 47 errors

By eye, all 73 failures or errors were down to missing the XML
library, or lacking network access.

Is there a way to run the test suite skipping the tests requiring
network access?

If BioRuby starts running nightly tests (I was talking to Raoul about
this at the BioHackathon last month), an offline switch would seem a
good idea. We do this in Biopython to avoid hitting any online servers
too hard, and because network issues would otherwise get flagged as
potential regressions (false positives).

Regards,

Peter