t2-server 0.0.1

data/LICENCE

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+Copyright (c) 2010, The University of Manchester, UK.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+ * Neither the names of The University of Manchester nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission. 
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

data/README.rdoc

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+= Taverna[http://www.taverna.org.uk/] 2 Server Interaction Gem
+
+Authors::    Robert Haines
+Version::    0.1
+Contact::    mailto:rhaines@manchester.ac.uk
+URL::        http://taverna.sourceforge.net/
+Licence::    BSD (See LICENCE or http://www.opensource.org/licenses/bsd-license.php)
+Copyright::  (c) 2010 The University of Manchester, UK
+
+
+== Synopsis
+
+This is a Ruby library to interface with the Taverna 2 Server REST interface.
+
+== Installation
+
+[sudo] gem install t2-server
+
+== Usage
+
+TBC

data/bin/delete_all_runs

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+#!/usr/bin/env ruby
+# Copyright (c) 2010, The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission. 
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+require 't2server'
+require 'optparse'
+
+# set up options
+opts = OptionParser.new do |opt|
+  opt.banner = "Usage: delete_all_runs [options] server-address"
+  opt.separator ""
+  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_tail("-h", "-?", "--help", "Show this message") do
+    puts opt
+    exit
+  end
+  opt.on_tail("-v", "--version", "Show the version") do
+    puts "Taverna 2 Server Ruby Gem version: #{T2Server::GEM_VERSION}"
+    puts "Taverna 2 Server REST API version: #{T2Server::API_VERSION}"
+    exit
+  end
+end
+
+# parse options
+opts.parse!
+
+# check for server address
+if ARGV[0] == nil
+  puts opts
+  exit 1
+end
+
+# connect and delete them all!
+T2Server::Server.connect(ARGV[0]).delete_all_runs

data/bin/run_workflow

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+#!/usr/bin/env ruby
+# Copyright (c) 2010, The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission. 
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+require 't2server'
+require 'optparse'
+
+# go through the outputs and either print the contents
+# out or save them to a file.
+# if the output is a list, it appears as a directory so
+# all the individual entries must be grabbed from there.
+# server seems to be rather sensitive to slashes, hence
+# all the [...] mucking about.
+def get_outputs(run, pout, dir="")
+  outputs = run.ls("out#{dir}")
+  outputs.each do |out|
+    if out.include? "/"
+      get_outputs(run, pout, "#{dir}/#{out[0...-1]}")
+    else
+      print "          #{dir}/#{out} -> "
+      data = run.get_output("#{dir[1..-1]}/#{out}")
+      if pout
+        p data
+      else
+        filename = "#{dir[1..-1]}/#{out}".gsub('/','-')
+        File.open(filename, "w") do |file|
+          file.syswrite(data)
+        end
+        puts "written to file: #{filename}"
+      end
+    end
+  end
+end
+
+# set up options
+inputs  = {}
+wkf_file = ""
+print_output = true
+opts = OptionParser.new do |opt|
+  opt.banner = "Usage: run_workflow [options] server-address"
+  opt.separator ""
+  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("-w WORKFLOW", "--workflow=WORKFLOW", "The workflow to run. If this is not " +
+    "specified then the workflow is read from standard input") do |val|
+    wkf_file = val
+  end
+  opt.on("-i INPUT:VALUE", "--input=INPUT:VALUE", "Set input port INPUT to VALUE") do |val|
+    input, value = val.chomp.split(':')
+    inputs[input] = value
+  end
+  opt.on("-p", "--[no-]print", "Print outputs to the console. On by default") do |val|
+    print_output = val
+  end
+  opt.on_tail("-h", "-?", "--help", "Show this message") do
+    puts opt
+    exit
+  end
+  opt.on_tail("-v", "--version", "Show the version") do
+    puts "Taverna 2 Server Ruby Gem version: #{T2Server::GEM_VERSION}"
+    puts "Taverna 2 Server REST API version: #{T2Server::API_VERSION}"
+    exit
+  end
+end
+
+# parse options
+opts.parse!
+
+# read and check server address
+uri = ARGV.shift
+if uri == nil
+  puts opts
+  exit 1
+end
+
+# read workflow
+if wkf_file == ""
+  wkf = ARGF.read
+else
+  wkf = IO.read(wkf_file)
+end
+
+# create run and set inputs
+run = T2Server::Run.create(uri, wkf)
+puts "Created run with uuid: #{run.uuid}"
+
+inputs.each do |input, value|
+  puts "Set input '#{input}' to #{value}"
+  run.set_input(input, value)
+end
+
+# start run and wait until it is finished
+print "Running"
+run.start_and_wait(:progress => true)
+
+# get outputs
+stdout = run.stdout
+stderr = run.stderr
+puts "Exitcode: #{run.exitcode}"
+if stdout != "" then puts "Stdout:\n          #{stdout}" end
+if stderr != "" then puts "Stderr:\n          #{stderr}" end
+
+puts "Outputs:"
+get_outputs(run, print_output)
+
+# delete run
+run.delete
+puts "Finished and deleted run"

data/lib/t2server.rb

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+# Copyright (c) 2010, The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission. 
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+require 't2server/xml'
+require 't2server/server'
+require 't2server/run'
+
+module T2Server
+  GEM_VERSION = "0.0.1"
+  API_VERSION = "2.2.0a1"
+end

data/lib/t2server/run.rb

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+# Copyright (c) 2010, The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission. 
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+require 'rexml/document'
+include REXML
+
+module T2Server
+  
+  class Run
+    
+    STATE = {
+      :initialized => "Initialized",
+      :running     => "Operating",
+      :finished    => "Finished",
+      :stopped     => "Stopped"
+    }
+    
+    private_class_method :new
+    attr_reader :uuid
+    
+    def initialize(server, uuid)
+      @server = server
+      @uuid = uuid
+      @workflow = ""
+      @baclava = false
+      
+      @links = get_attributes(@server.get_run_attribute(uuid, ""))
+      #@links.each {|key, val| puts "#{key}: #{val}"}
+    end
+
+    def Run.create(server, workflow, uuid="")
+      if server.class == String
+        server = Server.connect(server)
+      end
+      if uuid == ""
+        new(server, server.initialize_run(workflow))
+      else
+        new(server, uuid)
+      end
+    end
+    
+    def delete
+      @server.delete_run uuid
+    end
+    
+    def inputs
+      @links[:inputs]
+    end
+    
+    def set_input(input, value)
+      @server.set_run_input(self, input, value)
+    end
+    
+    def set_input_file(input, filename)
+      @server.set_run_input_file(self, input, filename)
+    end
+    
+    def get_output(output, type="text/plain")
+      return unless finished?   ### raise exception?
+      doc = @server.get_run_attribute(@uuid, "#{@links[:wdir]}/out/#{output}")
+      doc
+    end
+    
+    def expiry
+      @server.get_run_attribute(@uuid, @links[:expiry])
+    end
+    
+    def expiry=(date)
+      @server.set_run_attribute(@uuid, @links[:expiry], date)
+    end
+
+    def workflow
+      if @workflow == ""
+        @workflow = @server.get_run_attribute(@uuid, @links[:workflow])
+      end
+      @workflow
+    end
+    
+    def status
+      @server.get_run_attribute(@uuid, @links[:status])
+    end
+    
+    def start
+      @server.set_run_attribute(@uuid, @links[:status], STATE[:running])
+    end
+    
+    def start_and_wait(params={})
+      interval = params[:interval] || 1
+      progress = params[:progress] || false
+      keepalive = params[:keepalive] || false ### TODO maybe move out of params
+      
+      # start run and wait
+      start
+      until finished?
+        sleep(interval)
+        if progress
+          print "."
+          STDOUT.flush
+        end
+      end
+      
+      # tidy up output if there is any
+      puts if progress
+    end
+    
+    def exitcode
+      @server.get_run_attribute(@uuid, @links[:exitcode]).to_i
+    end
+    
+    def stdout
+      @server.get_run_attribute(@uuid, @links[:stdout])
+    end
+    
+    def stderr
+      @server.get_run_attribute(@uuid, @links[:stderr])
+    end
+    
+    def mkdir(dir)
+      @server.make_run_dir(@uuid, @links[:wdir], dir)
+    end
+    
+    def upload_file(filename, params={})
+      location = params[:dir] || ""
+      location = "#{@links[:wdir]}/#{location}"
+      rename = params[:rename] || ""
+      @server.upload_run_file(@uuid, filename, location, rename)
+    end
+    
+    def upload_input_file(input, filename, params={})
+      file = upload_file(filename, params)
+      set_input_file(input, file)
+    end
+    
+    def upload_baclava_file(filename)
+      @baclava = true
+      rename = upload_file(filename)
+      @server.set_run_attribute(@uuid, @links[:baclava], rename)
+    end
+
+    def ls(dir="")
+      dir_list = @server.get_run_attribute(@uuid, "#{@links[:wdir]}/#{dir}")
+      doc = Document.new(dir_list)
+
+      # compile a list of directory entries stripping the
+      # directory name from the front of each filename
+      entries = []
+      XPath.each(doc, "//nss:dir", Namespaces::MAP) {|e| entries << "#{e.text.split('/')[-1]}/"}
+      XPath.each(doc, "//nss:file", Namespaces::MAP) {|e| entries << e.text.split('/')[-1]}
+      entries
+    end
+
+    def initialized?
+      status == STATE[:initialized]
+    end
+    
+    def running?
+      status == STATE[:running]
+    end
+    
+    def finished?
+      status == STATE[:finished]
+    end
+
+    private
+    def get_attributes(desc)
+      # first parse out the basic stuff
+      links = parse_description(desc)
+      
+      # get inputs
+      inputs = @server.get_run_attribute(@uuid, links[:inputs])
+      doc = Document.new(inputs)
+      nsmap = Namespaces::MAP
+      links[:baclava] = "#{links[:inputs]}/" + XPath.first(doc, "//nsr:baclava", nsmap).attributes["href"].split('/')[-1]
+
+      # set io properties
+      links[:io]       = "#{links[:listeners]}/io"
+      links[:stdout]   = "#{links[:io]}/properties/stdout"
+      links[:stderr]   = "#{links[:io]}/properties/stderr"
+      links[:exitcode] = "#{links[:io]}/properties/exitcode"
+      
+      links
+    end
+
+    def parse_description(desc)
+      doc = Document.new(desc)
+      nsmap = Namespaces::MAP
+      {
+        :expiry    => XPath.first(doc, "//nsr:expiry", nsmap).attributes["href"].split('/')[-1],
+        :workflow  => XPath.first(doc, "//nsr:creationWorkflow", nsmap).attributes["href"].split('/')[-1],
+        :status    => XPath.first(doc, "//nsr:status", nsmap).attributes["href"].split('/')[-1],
+        :wdir      => XPath.first(doc, "//nsr:workingDirectory", nsmap).attributes["href"].split('/')[-1],
+        :inputs    => XPath.first(doc, "//nsr:inputs", nsmap).attributes["href"].split('/')[-1],
+        :output    => XPath.first(doc, "//nsr:output", nsmap).attributes["href"].split('/')[-1],
+        :securectx => XPath.first(doc, "//nsr:securityContext", nsmap).attributes["href"].split('/')[-1],
+        :listeners => XPath.first(doc, "//nsr:listeners", nsmap).attributes["href"].split('/')[-1]
+      }
+    end
+  end
+end

data/lib/t2server/server.rb

@@ -0,0 +1,324 @@
+# Copyright (c) 2010, The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission. 
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+require 'base64'
+require 'uri'
+require 'net/http'
+require 'rexml/document'
+include REXML
+
+module T2Server
+  class Server
+    private_class_method :new
+    attr_reader :uri, :run_limit
+    
+    # list of servers we know about
+    @@servers = []
+    
+    def initialize(uri)
+      @uri = uri
+      uri = URI.parse(uri)
+      @host = uri.host
+      @port = uri.port
+      @base_path = uri.path
+      @rest_path = uri.path + "/rest"
+      @links = get_server_description
+      #@links.each {|key, val| puts "#{key}: #{val}"}
+      
+      # get max runs
+      @run_limit = get_attribute(@links[:runlimit]).to_i
+      
+      # initialise run list
+      @runs = {}
+      @runs = runs
+    end
+
+    def Server.connect(uri)
+      # see if we've already got this server
+      server = @@servers.find {|s| s.uri == uri}
+
+      if !server
+        # no, so create new one and return it
+        server = new(uri)
+        @@servers << server
+      end
+      
+      server
+    end
+    
+    def create_run(workflow)
+      uuid = initialize_run(workflow)
+      @runs[uuid] = Run.create(self, "", uuid)
+    end
+    
+    def initialize_run(workflow)
+      request = Net::HTTP::Post.new("#{@links[:runs]}")
+      request.content_type = "application/xml"
+      response = Net::HTTP.new(@host, @port).start do |http|
+        http.request(request, Fragments::WORKFLOW % workflow)
+      end
+      
+      case response
+      when Net::HTTPCreated
+        # return the uuid of the newly created run
+        epr = URI.parse(response['location'])
+        epr.path[-36..-1]
+      when Net::HTTPForbidden
+        puts "Sorry, but the server is already running its configured limit of concurrent workflows."
+        puts "Please try again later."
+        ""
+      else
+        response_error(response)
+        ""
+      end
+    end
+      
+    def runs
+      request = Net::HTTP::Get.new("#{@links[:runs]}")
+      response = Net::HTTP.new(@host, @port).start {|http| http.request(request)}
+      
+      case response
+      when Net::HTTPOK  
+        doc = Document.new(response.body)
+        
+        # get list of run uuids
+        uuids = []
+        XPath.each(doc, "//nsr:run", Namespaces::MAP) do |run|
+          uuids << run.attributes["href"].split('/')[-1]
+        end
+                
+        # add new runs
+        uuids.each do |uuid|
+          if !@runs.has_key? uuid
+            description = get_run_description(uuid)
+            @runs[uuid] = Run.create(self, "", uuid)
+          end
+        end
+        
+        # clear out the expired runs
+        if @runs.length > @run_limit
+          @runs.delete_if {|key, val| !uuids.member? key}
+        end
+
+        @runs
+      else
+        response_error(response)
+      end
+    end
+
+    def delete_run(uuid)
+      request = Net::HTTP::Delete.new("#{@links[:runs]}/#{uuid}")
+      response = Net::HTTP.new(@host, @port).start {|http| http.request(request)}
+      
+      case response
+      when Net::HTTPNoContent
+        # Success, carry on...
+        @runs.delete(uuid)
+        true
+      when Net::HTTPNotFound
+        puts "Cannot find run #{run.uuid}."
+        false
+      else
+        response_error(response)
+      end
+    end
+    
+    def delete_all_runs
+      # first refresh run list
+      runs.each_value {|run| run.delete}
+    end
+    
+    def set_run_input(run, input, value)
+      request = Net::HTTP::Put.new("#{@links[:runs]}/#{run.uuid}/#{run.inputs}/input/#{input}")
+      request.content_type = "application/xml"
+      response = Net::HTTP.new(@host, @port).start do |http|
+        http.request(request, Fragments::RUNINPUTVALUE % value)
+      end
+      
+      case response
+      when Net::HTTPOK
+        # Yay!
+        true
+      else
+        response_error(response)
+      end
+    end
+
+    def set_run_input_file(run, input, filename)
+      request = Net::HTTP::Put.new("#{@links[:runs]}/#{run.uuid}/#{run.inputs}/input/#{input}")
+      request.content_type = "application/xml"
+      response = Net::HTTP.new(@host, @port).start do |http|
+        http.request(request, Fragments::RUNINPUTFILE % filename)
+      end
+      
+      case response
+      when Net::HTTPOK
+        # Yay!
+        true
+      else
+        response_error(response)
+      end
+    end
+
+    def make_run_dir(uuid, root, dir)
+      request = Net::HTTP::Post.new("#{@links[:runs]}/#{uuid}/#{root}")
+      request.content_type = "application/xml"
+      response = Net::HTTP.new(@host, @port).start do |http|
+        http.request(request,  Fragments::MKDIR % dir)
+      end
+      
+      case response
+      when Net::HTTPCreated
+        # OK, carry on...
+        true
+      when Net::HTTPForbidden
+        puts "Error!", response.body
+        false
+      when Net::HTTPNotFound
+        puts "Cannot find run #{uuid}."
+        false
+      else
+        response_error(response)
+      end
+    end
+    
+    def upload_run_file(uuid, filename, location, rename)
+      contents = Base64.encode64(IO.read(filename))
+      rename = filename.split('/')[-1] if rename == ""
+      request = Net::HTTP::Post.new("#{@links[:runs]}/#{uuid}/#{location}")
+      request.content_type = "application/xml"
+      response = Net::HTTP.new(@host, @port).start do |http|
+        http.request(request,  Fragments::UPLOAD % [rename, contents])
+      end
+      
+      case response
+      when Net::HTTPCreated
+        # Success, return remote name of uploaded file
+        rename
+      when Net::HTTPForbidden
+        puts "Error!", response.body
+      else
+        response_error(response)
+      end
+    end
+
+    def get_run_attribute(uuid, path)
+      get_attribute("#{@links[:runs]}/#{uuid}/#{path}")
+    end
+
+    def set_run_attribute(uuid, path, value)
+      request = Net::HTTP::Put.new("#{@links[:runs]}/#{uuid}/#{path}")
+      request.content_type = "text/plain"
+      response = Net::HTTP.new(@host, @port).start {|http| http.request(request, value)}
+      
+      case response
+      when Net::HTTPOK
+        # OK, so carry on
+        true
+      when Net::HTTPForbidden
+        puts "Error!"
+        puts response.body
+        false
+      when Net::HTTPNotFound
+        puts "Cannot find run #{uuid}."
+        false
+      else
+        response_error(response)
+      end
+    end
+    
+    protected
+    def get_attribute(path)
+      request = Net::HTTP::Get.new(path)
+      response = Net::HTTP.new(@host, @port).start {|http| http.request(request)}
+      
+      case response
+      when Net::HTTPOK
+        return response.body
+      when Net::HTTPNotFound
+        puts "Cannot find attribute #{path}."
+      else
+        response_error(response)
+      end
+    end
+    
+    private
+    def get_server_description
+      request = Net::HTTP::Get.new(@rest_path)
+      response = Net::HTTP.new(@host, @port).start {|http| http.request(request)}
+      
+      case response
+      when Net::HTTPOK
+        parse_description(response.body)
+      else
+        response_error(response)
+      end
+    end
+
+    def parse_description(desc)
+      doc = Document.new(desc)
+      nsmap = Namespaces::MAP
+      {
+        :runs          => URI.parse(XPath.first(doc, "//nsr:runs", nsmap).attributes["href"]).path,
+        :runlimit      => URI.parse(XPath.first(doc, "//nsr:runLimit", nsmap).attributes["href"]).path,
+        :permworkflows => URI.parse(XPath.first(doc, "//nsr:permittedWorkflows", nsmap).attributes["href"]).path,
+        :permlisteners => URI.parse(XPath.first(doc, "//nsr:permittedListeners", nsmap).attributes["href"]).path
+      }
+    end
+
+    def get_run_description(uuid)
+      request = Net::HTTP::Get.new("#{@links[:runs]}/#{uuid}")
+      response = Net::HTTP.new(@host, @port).start {|http| http.request(request)}
+      
+      case response
+      when Net::HTTPOK
+        return response.body
+      when Net::HTTPNotFound
+        puts "Cannot find run #{uuid}."
+      else
+        response_error(response)
+      end
+    end
+    
+    def response_error(response)
+      puts "Unnexpected response from Taverna Server!"
+      puts "Server is: #{@host}:#{@port}#{@base_path}"
+      puts "Response code is: #{response.code}"
+      if response.body
+        puts "Response body is: \n#{response.body}"
+      end
+      puts "\nRaw error is: \n#{response.error!}"
+      false
+    end
+    
+  end  
+end

data/lib/t2server/xml.rb

@@ -0,0 +1,51 @@
+# Copyright (c) 2010, The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission. 
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+module T2Server
+  module Namespaces
+    SERVER = "http://ns.taverna.org.uk/2010/xml/server/"
+    REST   = SERVER + "rest/"
+    MAP    = {
+      "nss" => Namespaces::SERVER,
+      "nsr" => Namespaces::REST
+    }
+  end
+  
+  module Fragments
+    WORKFLOW      = "<t2s:scufl xmlns:t2s=\"#{Namespaces::SERVER}\">\n  %s\n</t2s:scufl>"
+    RUNINPUT      = "<t2sr:runInput xmlns:t2sr=\"#{Namespaces::REST}\">\n  %s\n</t2sr:runInput>"
+    RUNINPUTVALUE = RUNINPUT % "<t2sr:value>%s</t2sr:value>"
+    RUNINPUTFILE  = RUNINPUT % "<t2sr:file>%s</t2sr:file>"
+    UPLOAD        = "<t2sr:upload xmlns:t2sr=\"#{Namespaces::REST}\" t2sr:name=\"%s\">\n  %s\n</t2sr:upload>"
+    MKDIR         = "<t2sr:mkdir xmlns:t2sr=\"#{Namespaces::REST}\" t2sr:name=\"%s\" />"
+  end
+end

metadata

@@ -0,0 +1,75 @@
+--- !ruby/object:Gem::Specification 
+name: t2-server
+version: !ruby/object:Gem::Version 
+  hash: 29
+  prerelease: false
+  segments: 
+  - 0
+  - 0
+  - 1
+  version: 0.0.1
+platform: ruby
+authors: 
+- Robert Haines
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-07-21 00:00:00 +01:00
+default_executable: 
+dependencies: []
+
+description: This gem provides access to the Taverna 2 Server REST interface from Ruby.
+email: rhaines@manchester.ac.uk
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README.rdoc
+- LICENCE
+files: 
+- bin/run_workflow
+- bin/delete_all_runs
+- lib/t2server.rb
+- lib/t2server/server.rb
+- lib/t2server/xml.rb
+- lib/t2server/run.rb
+- README.rdoc
+- LICENCE
+has_rdoc: true
+homepage: http://www.taverna.org.uk/
+licenses: []
+
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+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 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: Support for interacting with Taverna 2 Server.
+test_files: []
+