t2-server 0.9.0 → 0.9.1

data/CHANGES.rdoc

@@ -1,5 +1,13 @@
 = Changes log for the T2 Ruby Gem
 
+== Version 0.9.1
+
+* Update unit test code for Ruby 1.9 compatibility.
+* Major reductions in the time taken to instantiate a Run object.
+* t2-server-info: Don't list runs by default.
+* Move to persistent HTTP connections.
+* SSL certificate store changes.
+
 == Version 0.9.0
 
 * t2-run-workflow: Add a switch to set the expiry date/time.

data/README.rdoc

@@ -40,6 +40,17 @@ on your console output. Anything marked as deprecated will be removed in
 version 1.0.0 so you are advised to update your code at your earliest
 convenience.
 
+== Compatibility with Ruby versions
+
+This library is known to work with the following versions of Ruby:
+* 1.8.7 *
+* 1.9.2
+* 1.9.3 *
+* jruby 1.6.4 (in Ruby 1.8 mode)
+
+Those marked with an asterisk (*) are supported and bugs found against them
+will be fixed. Other versions may work but are not supported.
+
 == Usage
 
 There are two entry points for the T2Server API:
@@ -70,10 +81,12 @@ And can be set like this for a standard https connection:
 
   conn_params = ConnectionParameters.new
   conn_params[:verify_peer] = true
-  conn_params[:ca_path] = "/etc/ssl/certs"
 
 This will ensure that the identity of the Taverna Server you are connecting to
 will be verified using the set of certificates in <tt>/etc/ssl/certs</tt>.
+<tt>:ca_path</tt> can also be set to a list of paths if required. You do not
+need to include your platform's default certificate paths as these are included
+automatically.
 
 For convenience a number of standard sets of parameters have been defined. The
 above example is available as +DefaultConnectionParameters+. Others available

data/Rakefile

@@ -66,6 +66,7 @@ Jeweler::Tasks.new do |s|
   s.add_development_dependency('nokogiri', '>= 1.5.0')
   s.add_development_dependency('rdoc', '>= 3.9.4')
   s.add_development_dependency('jeweler', '~> 1.8.3')
+  s.add_runtime_dependency('net-http-persistent', '~> 2.6')
   s.add_runtime_dependency('taverna-baclava', '~> 1.0.0')
   s.add_runtime_dependency('hirb', '>= 0.4.0')
 end
@@ -80,14 +81,14 @@ end
 #    t.test_files = FileList['test/ts_t2server.rb']
 #    t.verbose = true
 #  end
-task :test, :server, :user1, :user2 do |t, args|
+task :test, [:server, :user1, :user2] do |t, args|
   args.with_defaults(:server => "", :user1 => "", :user2 => "")
   RakeFileUtils.verbose(true) do
     server_arg = ""
     if args[:server] != ""
-      server_arg = " -- #{args[:server]} #{args[:user1]} #{args[:user2]}"
+      server_arg = "#{args[:server]} #{args[:user1]} #{args[:user2]}"
     end
-    ruby "-I\"lib:test\" -S testrb test/ts_t2server.rb" + server_arg
+    ruby "-I\"lib:test\" test/ts_t2server.rb " + server_arg
   end
 end
 

data/bin/t2-server-info

@@ -37,11 +37,17 @@ require 'hirb'
 
 include T2Server::CLI
 
+# set up options
+options = {}
 conn_params, creds = register_options("Usage: t2-server-info [options] " +
   "server-address") do |opt|
   opt.separator "  Where server-address is the full URI of the server to"
   opt.separator "  connect to, e.g.: http://example.com:8080/taverna"
   opt.separator "  and [options] can be:"
+
+  opt.on("-l", "--list", "List details for the runs on this server.") do
+    options[:list] = true
+  end
 end
 
 # read and check server address and credentials
@@ -55,7 +61,7 @@ begin
     print "  Run limit: #{server.run_limit(creds)}\n"
     runs = server.runs(creds)
     print "No. of runs: #{runs.length}\n"
-    if runs.length > 0
+    if options[:list] && runs.length > 0
       puts (Hirb::Helpers::ObjectTable.render runs,
         :fields=>[:identifier, :status, :expiry],
         :headers=>{:identifier=>'Run ID', :status=>'Status',

data/lib/t2-server.rb

@@ -34,9 +34,9 @@ require 'yaml'
 require 't2-server/util'
 require 't2-server/xml/xml'
 require 't2-server/exceptions'
-require 't2-server/credentials'
-require 't2-server/connection'
-require 't2-server/connection-parameters'
+require 't2-server/net/credentials'
+require 't2-server/net/connection'
+require 't2-server/net/parameters'
 require 't2-server/port'
 require 't2-server/server'
 require 't2-server/run'

data/lib/t2-server/{connection.rb → net/connection.rb}

@@ -31,7 +31,7 @@
 # Author: Robert Haines
 
 require 'uri'
-require 'net/https'
+require 'net/http/persistent'
 
 module T2Server
 
@@ -93,8 +93,8 @@ module T2Server
       @uri = uri
       @params = params || DefaultConnectionParameters.new
 
-      # set up http connection
-      @http = Net::HTTP.new(@uri.host, @uri.port)
+      # set up persistent http connection
+      @http = Net::HTTP::Persistent.new("Taverna_Server_Ruby_Client")
     end
 
     # :call-seq:
@@ -174,7 +174,8 @@ module T2Server
       get = Net::HTTP::Get.new(path)
       get["Accept"] = type
       get["Range"] = "bytes=#{range.min}-#{range.max}" unless range.nil?
-      response = submit(get, nil, credentials)
+
+      response = submit(get, path, credentials)
 
       case response
       when Net::HTTPOK, Net::HTTPPartialContent
@@ -203,7 +204,9 @@ module T2Server
     def PUT(path, value, type, credentials)
       put = Net::HTTP::Put.new(path)
       put.content_type = type
-      response = submit(put, value, credentials)
+      put.body = value
+
+      response = submit(put, path, credentials)
 
       case response
       when Net::HTTPOK
@@ -251,7 +254,8 @@ module T2Server
     def DELETE(path, credentials)
       run = path.split("/")[-1]
       delete = Net::HTTP::Delete.new(path)
-      response = submit(delete, nil, credentials)
+
+      response = submit(delete, path, credentials)
 
       case response
       when Net::HTTPNoContent
@@ -275,7 +279,8 @@ module T2Server
     # of the headers returned.
     def OPTIONS(path, credentials)
       options = Net::HTTP::Options.new(path)
-      response = submit(options, nil, credentials)
+
+      response = submit(options, path, credentials)
 
       case response
       when Net::HTTPOK
@@ -293,18 +298,23 @@ module T2Server
     def _POST(path, value, type, credentials)
       post = Net::HTTP::Post.new(path)
       post.content_type = type
-      submit(post, value, credentials)
+      post.body = value
+
+      submit(post, path, credentials)
     end
 
     def path_leaf_from_uri(uri)
       URI.parse(uri).path.split('/')[-1]
     end
 
-    def submit(request, value, credentials)
+    def submit(request, path, credentials)
+      full_uri = @uri.clone
+      full_uri.path = path
+
       credentials.authenticate(request) unless credentials.nil?
 
       begin
-        @http.request(request, value)
+        @http.request(full_uri, request)
       rescue InternalHTTPError => e
         raise ConnectionError.new(e)
       end
@@ -326,16 +336,24 @@ module T2Server
     def initialize(uri, params = nil)
       super(uri, params)
 
-      # Configure connection options using params
-      @http.use_ssl = true
-
       # Peer verification
       if @params[:verify_peer]
         if @params[:ca_file]
           @http.ca_file = @params[:ca_file]
-        else
-          @http.ca_path = @params[:ca_path]
         end
+
+        if @params[:ca_path]
+          store = OpenSSL::X509::Store.new
+          store.set_default_paths
+          if @params[:ca_path].is_a? Array
+            @params[:ca_path].each { |path| store.add_path(path) }
+          else
+            store.add_path(@params[:ca_path])
+          end
+
+          @http.cert_store = store
+        end
+
         @http.verify_mode = OpenSSL::SSL::VERIFY_PEER
       else
         @http.verify_mode = OpenSSL::SSL::VERIFY_NONE
@@ -344,8 +362,9 @@ module T2Server
       # Client authentication
       if @params[:client_certificate]
         pem = File.read(@params[:client_certificate])
-        @http.cert = OpenSSL::X509::Certificate.new(pem)
-        @http.key = OpenSSL::PKey::RSA.new(pem, @params[:client_password])
+        @http.certificate = OpenSSL::X509::Certificate.new(pem)
+        @http.private_key = OpenSSL::PKey::RSA.new(pem,
+          @params[:client_password])
       end
     end
   end

data/lib/t2-server/{connection-parameters.rb → net/parameters.rb}

@@ -82,7 +82,6 @@ module T2Server
     def initialize
       super
       self[:verify_peer] = true
-      self[:ca_path] = "/etc/ssl/certs" # need to get good defaults for Win/OSX
     end
   end
 

data/lib/t2-server/run.rb

@@ -58,9 +58,6 @@ module T2Server
     # The server instance that this run is hosted on.
     attr_reader :server
 
-    # The owner (username) of this run
-    attr_reader :owner
-
     # :stopdoc:
     XPaths = {
       # Run XPath queries
@@ -112,10 +109,11 @@ module T2Server
 
       @credentials = credentials
 
-      run_desc = xml_document(@server.get_run_attribute(@identifier, "",
-        "application/xml", @credentials))
-      @owner = xpath_attr(run_desc, XPaths[:run_desc], "owner")
-      @links = get_attributes(run_desc)
+      # The following three fields hold cached data about the run that is only
+      # downloaded the first time it is requested.
+      @run_doc = nil
+      @owner = nil
+      @links = nil
 
       # initialize ports lists to nil as an empty list means no inputs/outputs
       @input_ports = nil
@@ -176,6 +174,17 @@ module T2Server
     end
     # :startdoc:
 
+    # :call-seq:
+    #   owner -> String
+    #
+    # Get the username of the owner of this run. The owner is the user who
+    # created the run on the server.
+    def owner
+      @owner = _get_run_owner if @owner.nil?
+
+      @owner
+    end
+
     # :call-seq:
     #   delete
     #
@@ -187,7 +196,7 @@ module T2Server
     # :stopdoc:
     def inputs
       warn "[DEPRECATION] 'inputs' is deprecated and will be removed in 1.0."
-      @links[:inputs]
+      links[:inputs]
     end
 
     def set_input(input, value)
@@ -273,7 +282,7 @@ module T2Server
     #
     # Return the expiry time of this run as an instance of class Time.
     def expiry
-      Time.parse(@server.get_run_attribute(@identifier, @links[:expiry],
+      Time.parse(@server.get_run_attribute(@identifier, links[:expiry],
         "text/plain", @credentials))
     end
 
@@ -293,7 +302,7 @@ module T2Server
       # parse timezone offsets with a colon (eg +00:00)
       date_str = time.xmlschema(2)
       date_str = date_str[0..-4] + date_str[-2..-1]
-      @server.set_run_attribute(@identifier, @links[:expiry], date_str,
+      @server.set_run_attribute(@identifier, links[:expiry], date_str,
         "text/plain", @credentials)
     end
 
@@ -303,7 +312,7 @@ module T2Server
     # Get the workflow that this run represents.
     def workflow
       if @workflow == ""
-        @workflow = @server.get_run_attribute(@identifier, @links[:workflow],
+        @workflow = @server.get_run_attribute(@identifier, links[:workflow],
           "application/xml", @credentials)
       end
       @workflow
@@ -315,7 +324,7 @@ module T2Server
     # Get the status of this run. Status can be one of :initialized,
     # :running or :finished.
     def status
-      text_to_state(@server.get_run_attribute(@identifier, @links[:status],
+      text_to_state(@server.get_run_attribute(@identifier, links[:status],
         "text/plain", @credentials))
     end
 
@@ -332,7 +341,7 @@ module T2Server
       # set all the inputs
       _check_and_set_inputs unless baclava_input?
 
-      @server.set_run_attribute(@identifier, @links[:status],
+      @server.set_run_attribute(@identifier, links[:status],
         state_to_text(:running), "text/plain", @credentials)
     end
 
@@ -370,7 +379,7 @@ module T2Server
     #
     # Get the return code of the run. Zero indicates success.
     def exitcode
-      @server.get_run_attribute(@identifier, @links[:exitcode], "text/plain",
+      @server.get_run_attribute(@identifier, links[:exitcode], "text/plain",
         @credentials).to_i
     end
 
@@ -379,7 +388,7 @@ module T2Server
     #
     # Get anything that the run printed to the standard out stream.
     def stdout
-      @server.get_run_attribute(@identifier, @links[:stdout], "text/plain",
+      @server.get_run_attribute(@identifier, links[:stdout], "text/plain",
         @credentials)
     end
 
@@ -388,7 +397,7 @@ module T2Server
     #
     # Get anything that the run printed to the standard error stream.
     def stderr
-      @server.get_run_attribute(@identifier, @links[:stderr], "text/plain",
+      @server.get_run_attribute(@identifier, links[:stderr], "text/plain",
         @credentials)
     end
 
@@ -404,10 +413,10 @@ module T2Server
         # end and add the rest of the path to the wdir link
         leaf = dir.split("/")[-1]
         path = dir[0...-(leaf.length + 1)]
-        @server.create_dir(@identifier, "#{@links[:wdir]}/#{path}", leaf,
+        @server.create_dir(@identifier, "#{links[:wdir]}/#{path}", leaf,
           @credentials)
       else
-        @server.create_dir(@identifier, @links[:wdir], dir, @credentials)
+        @server.create_dir(@identifier, links[:wdir], dir, @credentials)
       end
     end
 
@@ -423,7 +432,7 @@ module T2Server
     # The name of the file on the server is returned.
     def upload_file(filename, params={})
       location = params[:dir] || ""
-      location = "#{@links[:wdir]}/#{location}"
+      location = "#{links[:wdir]}/#{location}"
       rename = params[:rename] || ""
       @server.upload_file(@identifier, filename, location, rename,
         @credentials)
@@ -436,7 +445,7 @@ module T2Server
     # remote directory to put this file in can also be specified, but if it is
     # it must first have been created by a call to Run#mkdir.
     def upload_data(data, remote_name, remote_directory = "")
-      location = "#{@links[:wdir]}/#{remote_directory}"
+      location = "#{links[:wdir]}/#{remote_directory}"
       @server.upload_data(@identifier, data, remote_name, location,
         @credentials)
     end
@@ -461,7 +470,7 @@ module T2Server
       raise RunStateError.new(state, :initialized) if state != :initialized
 
       rename = upload_file(filename)
-      result = @server.set_run_attribute(@identifier, @links[:baclava], rename,
+      result = @server.set_run_attribute(@identifier, links[:baclava], rename,
         "text/plain", @credentials)
 
       @baclava_in = true if result
@@ -493,7 +502,7 @@ module T2Server
       state = status
       raise RunStateError.new(state, :initialized) if state != :initialized
 
-      @baclava_out = @server.set_run_attribute(@identifier, @links[:output],
+      @baclava_out = @server.set_run_attribute(@identifier, links[:output],
         BACLAVA_FILE, "text/plain", @credentials)
     end
 
@@ -533,7 +542,7 @@ module T2Server
 
       raise AccessForbiddenError.new("baclava output") if !@baclava_out
       @server.get_run_attribute(@identifier,
-        "#{@links[:wdir]}/#{BACLAVA_FILE}", "*/*", @credentials)
+        "#{links[:wdir]}/#{BACLAVA_FILE}", "*/*", @credentials)
     end
 
     # :stopdoc:
@@ -553,7 +562,7 @@ module T2Server
       state = status
       raise RunStateError.new(state, :finished) if state != :finished
 
-      @server.get_run_attribute(@identifier, "#{@links[:wdir]}/out",
+      @server.get_run_attribute(@identifier, "#{links[:wdir]}/out",
         "application/zip", @credentials)
     end
 
@@ -586,7 +595,7 @@ module T2Server
     #
     # Get the creation time of this run as an instance of class Time.
     def create_time
-      Time.parse(@server.get_run_attribute(@identifier, @links[:createtime],
+      Time.parse(@server.get_run_attribute(@identifier, links[:createtime],
         "text/plain", @credentials))
     end
 
@@ -595,7 +604,7 @@ module T2Server
     #
     # Get the start time of this run as an instance of class Time.
     def start_time
-      Time.parse(@server.get_run_attribute(@identifier, @links[:starttime],
+      Time.parse(@server.get_run_attribute(@identifier, links[:starttime],
         "text/plain", @credentials))
     end
 
@@ -604,7 +613,7 @@ module T2Server
     #
     # Get the finish time of this run as an instance of class Time.
     def finish_time
-      Time.parse(@server.get_run_attribute(@identifier, @links[:finishtime],
+      Time.parse(@server.get_run_attribute(@identifier, links[:finishtime],
         "text/plain", @credentials))
     end
 
@@ -617,7 +626,7 @@ module T2Server
     # are. Sometimes it is useful to know if the user accessing the run is
     # actually the owner of it or not.
     def owner?
-      @credentials.username == @owner
+      @credentials.username == owner
     end
 
     # :call-seq:
@@ -631,7 +640,7 @@ module T2Server
       return unless owner?
 
       value = XML::Fragments::PERM_UPDATE % [username, permission.to_s]
-      @server.create_run_attribute(@identifier, @links[:sec_perms], value,
+      @server.create_run_attribute(@identifier, links[:sec_perms], value,
         "application/xml", @credentials)
     end
 
@@ -646,7 +655,7 @@ module T2Server
 
       perms = {}
       doc = xml_document(@server.get_run_attribute(@identifier,
-        @links[:sec_perms], "application/xml", @credentials))
+        links[:sec_perms], "application/xml", @credentials))
 
       xpath_find(doc, XPaths[:sec_perm]).each do |p|
         user = xml_node_content(xpath_first(p, XPaths[:sec_uname]))
@@ -678,7 +687,7 @@ module T2Server
     def revoke_permission(username)
       return unless owner?
 
-      path = "#{@links[:sec_perms]}/#{username}"
+      path = "#{links[:sec_perms]}/#{username}"
       @server.delete_run_attribute(@identifier, path, @credentials)
     end
 
@@ -702,10 +711,10 @@ module T2Server
       value = XML::Fragments::CREDENTIAL % cred
 
       if id.nil?
-        @server.create_run_attribute(@identifier, @links[:sec_creds], value,
+        @server.create_run_attribute(@identifier, links[:sec_creds], value,
           "application/xml", @credentials)
       else
-        path = "#{@links[:sec_creds]}/#{id}"
+        path = "#{links[:sec_creds]}/#{id}"
         @server.set_run_attribute(@identifier, path, value, "application/xml",
           @credentials)
       end
@@ -736,7 +745,7 @@ module T2Server
         type, password]
       value = XML::Fragments::CREDENTIAL % cred
 
-      @server.create_run_attribute(@identifier, @links[:sec_creds], value,
+      @server.create_run_attribute(@identifier, links[:sec_creds], value,
         "application/xml", @credentials)
     end
 
@@ -751,7 +760,7 @@ module T2Server
 
       creds = {}
       doc = xml_document(@server.get_run_attribute(@identifier,
-        @links[:sec_creds], "application/xml", @credentials))
+        links[:sec_creds], "application/xml", @credentials))
 
       xpath_find(doc, XPaths[:sec_cred]).each do |c|
         uri = xml_node_content(xpath_first(c, XPaths[:sec_suri]))
@@ -783,7 +792,7 @@ module T2Server
     def delete_credential(uri)
       return unless owner?
 
-      path = "#{@links[:sec_creds]}/#{credentials[uri]}"
+      path = "#{links[:sec_creds]}/#{credentials[uri]}"
       @server.delete_run_attribute(@identifier, path, @credentials)
     end
 
@@ -796,7 +805,7 @@ module T2Server
     def delete_all_credentials
       return unless owner?
 
-      @server.delete_run_attribute(@identifier, @links[:sec_creds],
+      @server.delete_run_attribute(@identifier, links[:sec_creds],
         @credentials)
     end
 
@@ -815,7 +824,7 @@ module T2Server
       contents = Base64.encode64(IO.read(filename))
 
       value = XML::Fragments::TRUST % [contents, type]
-      @server.create_run_attribute(@identifier, @links[:sec_trusts], value,
+      @server.create_run_attribute(@identifier, links[:sec_trusts], value,
         "application/xml", @credentials)
     end
 
@@ -832,7 +841,7 @@ module T2Server
 
       t_ids = []
       doc = xml_document(@server.get_run_attribute(@identifier,
-        @links[:sec_trusts], "application/xml", @credentials))
+        links[:sec_trusts], "application/xml", @credentials))
 
       xpath_find(doc, XPaths[:sec_trust]). each do |t|
         t_ids << xml_node_attribute(t, "href").split('/')[-1]
@@ -850,7 +859,7 @@ module T2Server
     def delete_trust(id)
       return unless owner?
 
-      path = "#{@links[:sec_trusts]}/#{id}"
+      path = "#{links[:sec_trusts]}/#{id}"
       @server.delete_run_attribute(@identifier, path, @credentials)
     end
 
@@ -863,7 +872,7 @@ module T2Server
     def delete_all_trusts
       return unless owner?
 
-      @server.delete_run_attribute(@identifier, @links[:sec_trusts],
+      @server.delete_run_attribute(@identifier, links[:sec_trusts],
         @credentials)
     end
 
@@ -872,13 +881,19 @@ module T2Server
     # items (leaves) as files. This method (not part of the public API)
     # downloads a file from the run's working directory.
     def download_output_data(path, range = nil)
-      @server.download_run_file(@identifier, "#{@links[:wdir]}/out/#{path}",
+      @server.download_run_file(@identifier, "#{links[:wdir]}/out/#{path}",
         range, @credentials)
     end
     # :startdoc:
 
     private
 
+    def links
+      @links = _get_run_links if @links.nil?
+
+      @links
+    end
+
     # Check each input to see if it requires a list input and call the
     # requisite upload method for the entire set of inputs.
     def _check_and_set_inputs
@@ -908,13 +923,13 @@ module T2Server
           end
 
           xml_value = xml_text_node(port.file)
-          path = "#{@links[:inputs]}/input/#{port.name}"
+          path = "#{links[:inputs]}/input/#{port.name}"
           @server.set_run_attribute(self, path,
             XML::Fragments::RUNINPUTFILE % xml_value, "application/xml",
             @credentials)
         else
           xml_value = xml_text_node(port.value)
-          path = "#{@links[:inputs]}/input/#{port.name}"
+          path = "#{links[:inputs]}/input/#{port.name}"
           @server.set_run_attribute(self, path,
             XML::Fragments::RUNINPUTVALUE % xml_value, "application/xml",
             @credentials)
@@ -945,7 +960,7 @@ module T2Server
       # Create and upload the baclava data.
       baclava = Taverna::Baclava::Writer.write(data_map)
       upload_data(baclava, "in.baclava")
-      @server.set_run_attribute(@identifier, @links[:baclava], "in.baclava",
+      @server.set_run_attribute(@identifier, links[:baclava], "in.baclava",
         "text/plain", @credentials)
     end
 
@@ -973,7 +988,7 @@ module T2Server
     def _ls_ports(dir="", top=true)
       dir = Util.strip_path_slashes(dir)
       dir_list = @server.get_run_attribute(@identifier,
-        "#{@links[:wdir]}/#{dir}", "*/*", @credentials)
+        "#{links[:wdir]}/#{dir}", "*/*", @credentials)
 
       # compile a list of directory entries stripping the
       # directory name from the front of each filename
@@ -1013,10 +1028,10 @@ module T2Server
         if items.include? output
           if refs
             return "#{@server.uri}/rest/runs/#{@identifier}/" +
-              "#{@links[:wdir]}/out/#{output}"
+              "#{links[:wdir]}/out/#{output}"
           else
             return @server.get_run_attribute(@identifier,
-              "#{@links[:wdir]}/out/#{output}", "application/octet-stream",
+              "#{links[:wdir]}/out/#{output}", "application/octet-stream",
               @credentials)
           end
         end
@@ -1037,10 +1052,10 @@ module T2Server
       items.each do |item|
         if refs
           result << "#{@server.uri}/rest/runs/#{@identifier}/" +
-            "#{@links[:wdir]}/out/#{output}/#{item}"
+            "#{links[:wdir]}/out/#{output}/#{item}"
         else
           result << @server.get_run_attribute(@identifier,
-            "#{@links[:wdir]}/out/#{output}/#{item}",
+            "#{links[:wdir]}/out/#{output}/#{item}",
             "application/octet-stream", @credentials)
         end
       end
@@ -1050,7 +1065,7 @@ module T2Server
 
     def _get_input_port_info
       ports = {}
-      port_desc = @server.get_run_attribute(@identifier, @links[:inputexp],
+      port_desc = @server.get_run_attribute(@identifier, links[:inputexp],
         "application/xml", @credentials)
 
       doc = xml_document(port_desc)
@@ -1065,7 +1080,7 @@ module T2Server
 
     def _get_output_port_info
       ports = {}
-      port_desc = @server.get_run_attribute(@identifier, @links[:output],
+      port_desc = @server.get_run_attribute(@identifier, links[:output],
         "application/xml", @credentials)
 
       doc = xml_document(port_desc)
@@ -1078,7 +1093,24 @@ module T2Server
       ports
     end
 
-    def get_attributes(doc)
+    def _get_run_description
+      if @run_doc.nil?
+        @run_doc = xml_document(@server.get_run_attribute(@identifier, "",
+          "application/xml", @credentials))
+      end
+
+      @run_doc
+    end
+
+    def _get_run_owner
+      doc = _get_run_description
+
+      xpath_attr(doc, XPaths[:run_desc], "owner")
+    end
+
+    def _get_run_links
+      doc = _get_run_description
+
       # first parse out the basic stuff
       links = {}
 

data/t2-server.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "t2-server"
-  s.version = "0.9.0"
+  s.version = "0.9.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Robert Haines"]
-  s.date = "2012-03-26"
+  s.date = "2012-04-30"
   s.description = "This gem provides access to the Taverna 2 Server REST interface from Ruby."
   s.email = ["rhaines@manchester.ac.uk"]
   s.executables = ["t2-delete-runs", "t2-run-workflow", "t2-server-info", "t2-get-output", "t2-server-admin"]
@@ -31,10 +31,10 @@ Gem::Specification.new do |s|
     "lib/t2-server-cli.rb",
     "lib/t2-server.rb",
     "lib/t2-server/admin.rb",
-    "lib/t2-server/connection-parameters.rb",
-    "lib/t2-server/connection.rb",
-    "lib/t2-server/credentials.rb",
     "lib/t2-server/exceptions.rb",
+    "lib/t2-server/net/connection.rb",
+    "lib/t2-server/net/credentials.rb",
+    "lib/t2-server/net/parameters.rb",
     "lib/t2-server/port.rb",
     "lib/t2-server/run.rb",
     "lib/t2-server/server.rb",
@@ -44,6 +44,7 @@ Gem::Specification.new do |s|
     "lib/t2-server/xml/rexml.rb",
     "lib/t2-server/xml/xml.rb",
     "lib/t2server.rb",
+    "t2-server.gemspec",
     "test/tc_admin.rb",
     "test/tc_params.rb",
     "test/tc_perms.rb",
@@ -75,7 +76,7 @@ Gem::Specification.new do |s|
   s.homepage = "http://www.taverna.org.uk/"
   s.rdoc_options = ["-N", "--tab-width=2", "--main=README.rdoc"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.10"
+  s.rubygems_version = "1.8.21"
   s.summary = "Support for interacting with Taverna 2 Server."
   s.test_files = ["test/ts_t2server.rb"]
 
@@ -88,6 +89,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<nokogiri>, [">= 1.5.0"])
       s.add_development_dependency(%q<rdoc>, [">= 3.9.4"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_runtime_dependency(%q<net-http-persistent>, ["~> 2.6"])
       s.add_runtime_dependency(%q<taverna-baclava>, ["~> 1.0.0"])
       s.add_runtime_dependency(%q<hirb>, [">= 0.4.0"])
     else
@@ -96,6 +98,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<nokogiri>, [">= 1.5.0"])
       s.add_dependency(%q<rdoc>, [">= 3.9.4"])
       s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_dependency(%q<net-http-persistent>, ["~> 2.6"])
       s.add_dependency(%q<taverna-baclava>, ["~> 1.0.0"])
       s.add_dependency(%q<hirb>, [">= 0.4.0"])
     end
@@ -105,6 +108,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<nokogiri>, [">= 1.5.0"])
     s.add_dependency(%q<rdoc>, [">= 3.9.4"])
     s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+    s.add_dependency(%q<net-http-persistent>, ["~> 2.6"])
     s.add_dependency(%q<taverna-baclava>, ["~> 1.0.0"])
     s.add_dependency(%q<hirb>, [">= 0.4.0"])
   end

data/test/ts_t2server.rb

@@ -50,6 +50,9 @@ if ARGV.size != 0
 
   puts "Using server at: #{address}"
   puts "   With user(s): #{user1} #{user2}" if user1
+
+  # Clear the commandline arguments so that we don't confuse runit.
+  ARGV.clear
 else
   # get a server address to test - 30 second timeout
   print "\nPlease supply a valid Taverna 2 Server address.\n\nNOTE that " +

data/version.yml

@@ -1,4 +1,4 @@
 ---
   :major: 0
   :minor: 9
-  :patch: 0
+  :patch: 1

metadata

@@ -1,151 +1,160 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: t2-server
-version: !ruby/object:Gem::Version 
-  hash: 59
+version: !ruby/object:Gem::Version
+  version: 0.9.1
   prerelease: 
-  segments: 
-  - 0
-  - 9
-  - 0
-  version: 0.9.0
 platform: ruby
-authors: 
+authors:
 - Robert Haines
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-04-10 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2012-04-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: rake
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 63
-        segments: 
-        - 0
-        - 9
-        - 2
+      - !ruby/object:Gem::Version
         version: 0.9.2
   type: :development
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: libxml-ruby
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 27
-        segments: 
-        - 1
-        - 1
-        - 4
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.9.2
+- !ruby/object:Gem::Dependency
+  name: libxml-ruby
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.1.4
   type: :development
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: nokogiri
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 1
-        - 5
-        - 0
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.4
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.5.0
   type: :development
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: rdoc
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 43
-        segments: 
-        - 3
-        - 9
-        - 4
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.0
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 3.9.4
   type: :development
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: jeweler
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.9.4
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 49
-        segments: 
-        - 1
-        - 8
-        - 3
+      - !ruby/object:Gem::Version
         version: 1.8.3
   type: :development
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  name: taverna-baclava
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+- !ruby/object:Gem::Dependency
+  name: net-http-persistent
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.6'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.6'
+- !ruby/object:Gem::Dependency
+  name: taverna-baclava
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 23
-        segments: 
-        - 1
-        - 0
-        - 0
+      - !ruby/object:Gem::Version
         version: 1.0.0
   type: :runtime
-  version_requirements: *id006
-- !ruby/object:Gem::Dependency 
-  name: hirb
   prerelease: false
-  requirement: &id007 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 15
-        segments: 
-        - 0
-        - 4
-        - 0
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+- !ruby/object:Gem::Dependency
+  name: hirb
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.4.0
   type: :runtime
-  version_requirements: *id007
-description: This gem provides access to the Taverna 2 Server REST interface from Ruby.
-email: 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+description: This gem provides access to the Taverna 2 Server REST interface from
+  Ruby.
+email:
 - rhaines@manchester.ac.uk
-executables: 
+executables:
 - t2-delete-runs
 - t2-run-workflow
 - t2-server-info
 - t2-get-output
 - t2-server-admin
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - CHANGES.rdoc
 - LICENCE.rdoc
 - README.rdoc
-files: 
-- .rvmrc
+files:
 - CHANGES.rdoc
 - LICENCE.rdoc
 - README.rdoc
@@ -158,10 +167,10 @@ files:
 - lib/t2-server-cli.rb
 - lib/t2-server.rb
 - lib/t2-server/admin.rb
-- lib/t2-server/connection-parameters.rb
-- lib/t2-server/connection.rb
-- lib/t2-server/credentials.rb
 - lib/t2-server/exceptions.rb
+- lib/t2-server/net/connection.rb
+- lib/t2-server/net/credentials.rb
+- lib/t2-server/net/parameters.rb
 - lib/t2-server/port.rb
 - lib/t2-server/run.rb
 - lib/t2-server/server.rb
@@ -201,38 +210,30 @@ files:
 - version.yml
 homepage: http://www.taverna.org.uk/
 licenses: []
-
 post_install_message: 
-rdoc_options: 
+rdoc_options:
 - -N
 - --tab-width=2
 - --main=README.rdoc
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 1.8.21
 signing_key: 
 specification_version: 3
 summary: Support for interacting with Taverna 2 Server.
-test_files: 
+test_files:
 - test/ts_t2server.rb

data/.rvmrc

@@ -1 +0,0 @@
-rvm use ruby-1.8.7@t2server --create