New method Bio::Command#start_http_uri(uri) with tests

 * lib/bio/command.rb: New method Bio::Command#start_http_uri(uri)
   that supports HTTPS. Note that this method is intended to be
   called only from BioRuby internals.
 * lib/bio/command.rb: Bio::Command#post and #post_form are changed
   to use the start_http_uri().
 * test/network/bio/test_command.rb: tests for start_http_uri().

lib/bio/command.rb

@@ -13,6 +13,7 @@
 require 'open-uri'
 require 'cgi'
 require 'net/http'
+require 'net/https'
 require 'tmpdir'
 require 'fileutils'
 
@@ -706,6 +707,43 @@ def read_uri(uri)
     OpenURI.open_uri(uri).read
   end
 
+  # Same as:
+  #   Net::HTTP.start(uri.address, uri.port)
+  # and
+  # it uses proxy if an environment variable (same as OpenURI.open_uri)
+  # is set.
+  # It supports https.
+  #
+  # Note: This method ignores uri.path.
+  # It only uses uri.address and uri.port.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _uri_: URI object or String containing URI
+  # *Returns*:: (same as Net::HTTP::start except for proxy and https support)
+  def start_http_uri(uri, &block)
+    unless uri.is_a?(URI)
+      uri = URI.parse(uri)
+    end
+
+    # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
+    # If the spec of open-uri.rb would be changed, we should change below.
+    if proxyuri = uri.find_proxy then
+      raise 'Non-HTTP proxy' if proxyuri.class != URI::HTTP
+      klass = Net::HTTP.Proxy(proxyuri.host, proxyuri.port)
+    else
+      klass = Net::HTTP
+    end
+
+    http = klass.new(uri.host, uri.port)
+    case uri.scheme
+    when 'https'
+      http.use_ssl = true
+    end
+
+    http.start(&block)
+  end
+
   # Same as:
   #   Net::HTTP.start(address, port)
   # and 
@@ -813,7 +851,7 @@ def post_form(uri, params = nil, header = {})
     }
     hash.update(header)
 
-    start_http(uri.host, uri.port) do |http|
+    start_http_uri(uri) do |http|
       http.post(uri.path, data, hash)
     end
   end
@@ -937,7 +975,7 @@ def post(uri, data, header = {})
     }
     hash.update(header)
 
-    start_http(uri.host, uri.port) do |http|
+    start_http_uri(uri) do |http|
       http.post(uri.path, data, hash)
     end
   end

test/network/bio/test_command.rb

@@ -13,6 +13,7 @@
 
 # libraries needed for the tests
 require 'test/unit'
+require 'uri'
 require 'bio/command'
 
 module Bio
@@ -22,6 +23,7 @@ def setup
       @port = 80 
       @path = "/"
       @url = "http://bioruby.open-bio.org:80/"
+      @uri = URI.parse(@url)
     end
 
     def test_read_uri
@@ -32,6 +34,21 @@ def test_read_uri
       assert(!str.to_s.empty?)
     end
 
+    def test_start_http_uri
+      ht = Bio::Command.start_http_uri(@uri)
+      assert_kind_of(Net::HTTP, ht)
+      res = ht.get(@path)
+      assert_kind_of(Net::HTTPResponse, res)
+    end
+
+    def test_start_http_uri_with_block
+      res = Bio::Command.start_http_uri(@uri) do |ht|
+        assert_kind_of(Net::HTTP, ht)
+        ht.get(@path)
+      end
+      assert_kind_of(Net::HTTPResponse, res)
+    end
+
     def test_start_http
       ht = Bio::Command.start_http(@host, @port)
       assert_kind_of(Net::HTTP, ht)