HTTPS Proxy

[Bjoernsen]

I am not able to fetch taxonomy data. Bio::NCBI::REST::EFetch.taxonomy(12345, 'xml')

The result: RuntimeError: Non-HTTP proxy

The reason is that we have to use a http and https proxy. But the method Bio::Command.start_http_uri only checks for URI::HTTP and not URI::HTTPS.

https://github.com/bioruby/bioruby/blob/master/lib/bio/command.rb#L733

With this small fix, the method works for me:

# from
raise 'Non-HTTP proxy' if proxyuri.class != URI::HTTP
# to
raise 'Non-HTTP proxy' if !(proxyuri.class == URI::HTTP || proxyuri.class == URI::HTTPS)

[ngoto]

The line rejecting non-HTTP proxy was taken from Ruby's open-uri.rb.
https://github.com/ruby/ruby/blob/trunk/lib/open-uri.rb#L258

The fact that the latest open-uri.rb in Ruby still has a code to rejects non-HTTP proxy suggests that Ruby does not support https://xxxx/ as a proxy server. (Note that ordinary http proxy servers support https protocol via CONNECT method with http.)