mannie-taverna-scufl 0.6.0

data/lib/document/report.rb

@@ -0,0 +1,91 @@
+module Document
+  
+	class Report
+  
+		attr_reader :processors
+		attr_accessor :id, :status
+		
+		def initialize
+		  	@processors = Array.new
+		end
+		
+		def self.from_xml(xml)
+			Reader.read(xml)  
+		end
+	  
+		def self.from_document(document)
+			Reader.read(document)  
+		end
+	  
+	end
+	
+	class Processor
+		attr_accessor :name, :status, :time, :total, :number 
+	end
+    
+	class Reader
+
+		def self.read(report)
+			if report.kind_of?(REXML::Document)
+				document = report
+			else
+				document = REXML::Document.new(report)
+			end
+			root = document.root
+					  
+			return nil if not root
+								  
+			raise root.name + "Doesn't appear to be a workflow report!" if root.name != "workflowReport"
+								  
+			create_report(root)
+		end
+	  
+		def self.create_report(element)
+			report = Report.new
+			
+			id = element.attribute('workflowId')
+			report.id = id.value if id
+			
+			status = element.attribute('workflowStatus')
+			report.status = status.value if status
+			
+			element.elements['processorList'].each_element('processor') { |processor|
+			  add_processor(processor, report)
+			}
+			
+			report
+		end
+	  
+		def self.add_processor(element, report)
+			processor = Processor.new
+			
+			name = element.attribute('name')
+			processor.name = name.value if name
+				
+			if element.has_elements?
+			  	firstElement = element.elements[1]
+				case firstElement.name
+				when 'ProcessComplete'
+			   		processor.status = 'COMPLETE'
+					processor.time = firstElement.attribute('TimeStamp')
+				when 'ProcessScheduled'
+			   		processor.status = 'SCHEDULED'
+					processor.time = firstElement.attribute('TimeStamp')
+				when 'InvokingWithIteration'
+					processor.status = 'ITERATING'
+					processor.time = firstElement.attribute('TimeStamp')
+					processor.number = firstElement.attribute('IterationNumber')
+					processor.total = firstElement.attribute('IterationTotal')			 
+				when 'ServiceFailure'
+					processor.status = 'FAILED'
+					processor.time = firstElement.attribute('TimeStamp')
+				else
+					processor.status = 'UNKNOWN'
+				end
+			end
+			report.processors.push processor		
+		end
+	  	
+	end
+	
+end

data/lib/enactor/client.rb

@@ -0,0 +1,673 @@
+require 'rubygems'
+require 'builder'
+require "uri"
+require 'rexml/document'
+require 'net/http'
+require 'baclava/reader'
+require 'baclava/writer'
+require 'document/report'
+require 'document/data'
+
+module Enactor # :nodoc:
+
+	#Base class for Taverna service errors.
+	class TavernaServiceError < StandardError
+	end
+
+	#Job did not complete. 
+    #Thrown by execute_sync()
+	class NotCompleteError < TavernaServiceError
+		def initialize(job_url, status)
+			super("Job #{job_url} not complete, status: #{status}")
+    	end
+	end
+
+	#Could not create resource.
+	class CouldNotCreateError < TavernaServiceError
+    	def initialize(url)
+        	super("Expected 201 Created when uploading #url")
+    	end
+	end
+	
+	
+    #Status messages that can be returned from TavernaService.get_job_status().
+    #
+    #If finished?(status) is true, this means the job is finished, 
+    #either successfully (COMPLETE), unsuccessfully (CANCELLED, FAILED), or 
+    #that the job is no longer in the database (DESTROYED).
+    #
+    #When a job has just been created it will be in status NEW, after that 
+    #it will immediately be on a queue and in the state QUEUED. Once the 
+    #job has been picked up by a worker it will be in INITIALISING, this 
+    #state might include the startup time of the worker and while downloading 
+    #the workflow and input data to the worker. The state PAUSED is not 
+    #currently used. The FAILING state can occur if the workflow engine
+    #crashed, after clean-up or if the workflow itself failed, the state 
+    #will be FAILED.
+    #
+    #The job might at any time be set to the state CANCELLING by the user, 
+    #which will stop execution of the workflow, leading to the state 
+    #CANCELLED.
+    #
+    #If the workflow execution completed the state will be set to COMPLETE, 
+    #after which the workflow result data should be available by using
+    #get_job_outputs_doc().
+    #
+    #If data about the job has been lost (probably because it's too old 
+    #or has been deleted by the user), the state will be DESTROYED.
+	class Status
+    	NEW = "NEW"
+        QUEUED = "QUEUED"
+        INITIALISING = "INITIALISING"
+        PAUSED = "PAUSED"
+        FAILING = "FAILING"
+        CANCELLING = "CANCELLING"
+        CANCELLED = "CANCELLED"
+        COMPLETE = "COMPLETE"
+        FAILED = "FAILED"
+        DESTROYED = "DESTROYED"
+        FINISHED = [COMPLETE, CANCELLED, DESTROYED, FAILED]
+        ALL = [NEW, QUEUED, INITIALISING, FAILING, 
+                   CANCELLING, CANCELLED, COMPLETE, FAILED, DESTROYED]
+    
+        #Return True if the status is a finished status.
+        #
+        #This would normally include COMPLETE, CANCELLED, DESTROYED and FAILED.
+        def Status.finished?(status)
+            return FINISHED.include?(status)
+        end
+        
+        #Check if a string is a valid status.
+        def Status.valid?(status)
+            ALL.include?(status)
+        end
+	end
+        
+    #Client library for accessing a Taverna Remote execution service.
+    #
+    #Since the service is a rest interface, this library reflects that to 
+    #a certain degree and many of the methods return URLs to be used by 
+    #other methods.
+    # 
+    # The main methods of interest are - in order of a normal execution:
+    # 
+    #    execute_sync() -- Given a scufl document or the URL for a previously 
+    #        uploaded workflow, and data as a hash or URL for previously
+    #        uploaded data, submit job for execution, wait for completion 
+    #        (or a timeout) and retrieve results. This is a blocking 
+    #        convenience method that can be used instead of the methods below.
+    # 
+    #    upload_workflow() -- Given a scufl document as a string, upload the
+    #        workflow to the server for later execution. Return the URL for the
+    #        created workflow resource that can be used with submit_job()
+    #        
+    #    upload_data()-- Given a hash of input values to a
+    #        workflow run, upload the data to the user's collection.
+    #        Return the URL for the created data resource that can be used with 
+    #        submit_job()
+    #    
+    #    submit_job() -- Given the URL for a workflow resource and optionally
+    #        the URL for a input data resource, submit the a to the server 
+    #        to be executed. Return the URL to the created job resource.
+    #    
+    #    get_job_status() -- Get the status of the job. Return one of the values from
+    #        Status.
+    #        
+    #    finished?() -- Return True if the job is in a finished state. Note 
+    #        that this also includes failed states.
+    #
+    #    wait_for_job() -- Wait until job has finished execution, or a maximum
+    #        timeout is exceeded.
+    #                   
+    #    get_job_outputs() -- Get the outputs produced by job.  Return a  
+    #        hash which values are strings, lists of strings, 
+    #        or deeper lists.
+    #        
+    #Most or all of these methods might in addition to stated exceptions also raise
+    #Net::HTTPError or InvalidResponseError if anything goes wrong in communicating with the service.
+	class Client
+    
+    	#Name spaces used by various XML documents.
+  	    NAMESPACES = {
+			  :xscufl => 'http://org.embl.ebi.escience/xscufl/0.1alpha',
+			  :baclava => 'http://org.embl.ebi.escience/baclava/0.1alpha',
+			  :service => 'http://taverna.sf.net/service',
+			  :xlink => 'http://www.w3.org/1999/xlink',
+			  :dcterms => 'http://purl.org/dc/terms/'
+		}
+
+		#Mime types used by the rest protocol.
+		#
+		# See net.sf.taverna.service.interfaces.TavernaConstants.java
+		MIME_TYPES = {
+			:rest => 'application/vnd.taverna.rest+xml', # For most of the rest documents
+			:scufl => 'application/vnd.taverna.scufl+xml', # For Taverna workflows
+			:baclava => 'application/vnd.taverna.baclava+xml', # For Taverna's Baclava data documents
+			:report => 'application/vnd.taverna.report+xml', # For Taverna's internal progress reports
+			:console => 'text/plain' # For Taverna's console
+		}
+
+
+		DEFAULT_TIMEOUT = 5 * 60 # in seconds
+		DEFAULT_REFRESH = 0.5 # in seconds
+	
+		#Construct a Taverna remote execution service client accessing the service
+		#at the given base URL.  
+		#
+		#Note that this constructor will not attempt to verify the URL or the 
+		#credentials. To verify, call get_user_url() which requires authentication.
+		#
+		#url -- The base URL for the service, normally ending in /v1/, for example:
+		#    "http://myserver.com:8080/tavernaService/v1/"
+		#
+		#username -- The username of a user that has been previously created or 
+		#    registered in the web interface of the service.
+		#    
+		#password -- The password of the user. Note that the password will be sent
+		#   over the wire using unencrypted HTTP Basic Auth, unless the URL starts
+		#	with "https".
+		def initialize(url, username, password)
+			@url = url
+			@username = username
+			@password = password
+		end
+        
+		#private
+		
+		#Get the capabilities document as a REXML::Document 
+		#
+		#This document contains the links to the main collections of the service.
+		def get_capabilities_doc
+			url = URI.parse(@url)
+			request = Net::HTTP::Get.new(url.path)
+			request['Accept'] = MIME_TYPES[:rest]
+			request.basic_auth @username, @password
+			response = Net::HTTP.start(url.host, url.port) {|http|
+			  http.request(request)
+			}
+			response.value
+			REXML::Document.new(response.body)
+		end
+        
+		#Get the URL for the current user's home on the server.
+		def get_user_url
+			capabilities_doc = get_capabilities_doc()
+			#currentUser = capabilities_doc.root.elements["{#{NAMESPACES[:service]}}currentUser"]
+			current_user = capabilities_doc.root.elements['currentUser']
+			current_user_url = current_user.attributes.get_attribute_ns(NAMESPACES[:xlink], 'href').value
+			
+			url = URI.parse(current_user_url)
+			request = Net::HTTP::Get.new(url.path)
+			request['Accept'] = MIME_TYPES[:rest]
+			request.basic_auth @username, @password
+			response = Net::HTTP.start(url.host, url.port) {|http|
+				http.request(request)
+			}
+			response.error! unless response.kind_of?(Net::HTTPSuccess) or response.kind_of?(Net::HTTPRedirection)
+			response.header['Location']
+		end
+ 
+		#Get the user document as an REXML::Document object. 
+		#
+		#This document contains the links to the user owned collections, 
+		#such as where to upload workflows and jobs.
+		def get_user_doc
+			url = URI.parse(get_user_url())
+			request = Net::HTTP::Get.new(url.path)
+			request['Accept'] = MIME_TYPES[:rest]
+			request.basic_auth @username, @password
+			response = Net::HTTP.start(url.host, url.port) {|http|
+				http.request(request)
+			}
+			response.value
+			REXML::Document.new(response.body)
+		end
+		
+		#Get the URL to a user-owned collection. 
+		#
+		#collectionType -- The collection, either "workflows" or "datas"
+		def get_user_collection_url(collection)
+			user_doc = get_user_doc()
+
+			#collections = user_doc.root.elements["{#{NAMESPACES[:service]}}#{collection}"]
+			collections = user_doc.root.elements[collection]
+			return collections.attributes.get_attribute_ns(NAMESPACES[:xlink], 'href').value
+		end
+		
+		#Get the URL to the output document for a job.
+		#
+		#It generally only makes sense to call this function if
+		#get_job_status() == Status::COMPLETED, but no check is enforced here.
+		#
+		#Return the URL to a data document produced by the job, or None if the
+		#job has not (yet) produced any output.
+		#
+		#job_url -- The URL to a job resource previously created using
+		#	submit_job().
+		def get_job_outputs_url(job_url)
+			job_document = get_xml_doc(job_url)
+			#outputs_element = job_document.root.elements["{#{NAMESPACES[:service]}}outputs"]
+			outputs_element = job_document.root.elements['outputs']
+			return nil if not outputs_element
+			outputs_element.attributes.get_attribute_ns(NAMESPACES[:xlink], 'href').value 
+		end
+		
+		#Get the output document for a job.
+		#
+		#Return the output document as an REXML::Document object, or None
+		#if the job didn't have an output document (yet). This document can be
+		#parsed using parse_data_doc().
+		#
+		#job_url -- The URL to a job resource previously created using
+		#	submit_job().
+		def get_job_outputs_doc(job_url)
+			outputs_url = get_job_outputs_url(job_url)
+			return nil if not outputs_url
+			get_xml_doc(outputs_url, MIME_TYPES[:baclava])
+		end   
+		
+		#Retrieve an XML document from the given URL.
+		#
+		#Return the retrieved document as a REXML::Document.
+		#
+		#url -- The URL to a resource retrievable as an XML document
+		#
+		#mimeType -- The mime-type to request using the Accept header, by default
+		#	MIME_TYPES[:rest]
+		def get_xml_doc(doc_url, mimeType=MIME_TYPES[:rest])
+			url = URI.parse(doc_url)			
+			request = Net::HTTP::Get.new(url.path)
+			request['Accept'] = mimeType
+			request.basic_auth @username, @password
+			response = Net::HTTP.start(url.host, url.port) {|http|
+			  http.request(request)
+			}
+			response.value
+			REXML::Document.new(response.body)
+		end
+			
+		#Return the size of an XML document from the given URL without
+		#fetching the document.
+		#
+		#Return the size of a XML document .
+		#
+		#url -- The URL to a resource find the size of
+		#
+		#mimeType -- The mime-type to request using the Accept header, by default
+		#	MIME_TYPES[:rest]
+		def get_xml_doc_size(doc_url, mimeType=MIME_TYPES[:rest])
+			url = URI.parse(doc_url)			
+			request = Net::HTTP::Head.new(url.path)
+			request['Accept'] = mimeType
+			request.basic_auth @username, @password
+			response = Net::HTTP.start(url.host, url.port) {|http|
+			  http.request(request)
+			}
+			response.content_length
+		end
+   
+		#Parse a data document as returned from get_job_outputs_doc().
+		#
+		#Return a hash where the keys are strings, matching the names of 
+		#	ports of the workflow. The values are Document::Data objects. 
+		#	
+		#xml -- A data document as a REXML::Document. This data document can be created
+		#	using create_data_doc()
+		def parse_data_doc(xml_document)
+			Baclava::Reader.read(xml_document)
+		end
+		
+		#Upload a data document to the current user's collection.
+		#
+		#Return the URL of the created data resource.
+		#
+		#xml -- A data document as a REXML::Document. This data document can be created
+		#	using create_data_doc()
+		#
+		#Raises:
+		#	CouldNotCreateError -- If the service returned 200 OK instead of
+		#		creating the resource
+		def upload_data_doc(xml_document)
+			datas_url = get_user_collection_url("datas")
+			upload_to_collection(datas_url, xml_document.to_s, MIME_TYPES[:baclava])
+		end
+		
+		#Tests if the url is valid for this server
+		def url_valid?(url)
+		  url = URI.parse(url)
+		  req = Net::HTTP::Head.new(url.path)
+		  req.basic_auth @username, @password
+		  Net::HTTP.start(url.host, url.port) {|http|
+			http.request(req)
+		  }.kind_of?(Net::HTTPSuccess)
+		end
+					
+		#Upload data by POST-ing to given URL. 
+		#
+		#Return the URL of the created resource if the request succeeded with
+		#201 Created.
+		#
+		#Raises:
+		#	CouldNotCreateError -- If the service returned 200 OK instead of
+		#		creating the resource
+		#	Net::HTTPError -- If any other HTTP result code (including errors) 
+		#		was returned
+		#
+		#url -- The URL of the collection of where to POST, 
+		#	normally retrieved using get_user_collection_url().
+		#
+		#data -- The data to upload as a string
+		#
+		#content_type -- The MIME type of the data to upload. Typically the value
+		#	of one of the MimeTypes constants. For data uploaded to the "datas" user 
+		#	collection this would be MIME_TYPES[:baclava], and for workflow to the "
+		#	workflows" collection, MIME_TYPES[:scufl]. Any other XML documents from 
+		#	the NAMESPACES[:service] namespace has the mime type MIME_TYPES[:rest]
+		def upload_to_collection(url, data, content_type)
+			url = URI.parse(url)    	
+			request = Net::HTTP::Post.new(url.path)
+			request.body = data
+			request['Accept'] = MIME_TYPES[:rest]
+			request['Content-Type'] = content_type
+			request.basic_auth @username, @password
+			response = Net::HTTP.start(url.host, url.port) {|http|
+			  http.request(request)
+			}
+			response.value			
+			raise CouldNotCreateError(url, response) unless response.kind_of?(Net::HTTPCreated)
+			response.header['Location']
+		end
+	
+		#Create a data document to be uploaded with upload_data_doc(). 
+		#
+		#Return the data document a REXML::Document. This data document can be parsed using
+		#parse_data_doc()
+		#
+		#hash -- A hash where the keys are strings, matching the names of input
+		#	ports of the workflow to run. The values are Document::Data objects. 
+		#
+		def create_data_doc(hash)
+			Baclava::Writer.write_doc(hash)
+		end
+		
+		#Create a job document for submission with submit_job().
+		#
+		#Return the job document as XML.
+		#
+		#workflow_url -- The URL of a workflow previously uploaded using
+		#	upload_workflow()
+		#
+		#inputs_url -- The (optional) URL of a input document previously
+		#	uploaded using upload_data_doc()
+		def create_job_doc(workflow_url, inputs_url=nil)
+			xml = Builder::XmlMarkup.new
+			xml.instruct!
+			REXML::Document.new(xml.job('xmlns' => NAMESPACES[:service], 'xmlns:xlink' => NAMESPACES[:xlink]) {
+				xml.inputs('xlink:href' => inputs_url) if inputs_url
+				xml.workflow('xlink:href' => workflow_url)
+			})
+		end
+
+		#Submit a job to be queued for execution on the server.
+		#
+		#Return the URL to the job resource.
+		#
+		#job_document -- A job document created with create_job_doc() specifying
+		#	the workflow to run with which inputs.
+		#	
+		#Raises:
+		#	CouldNotCreateError -- If the service returned 200 OK instead of
+		#		creating the resource
+		def submit_job_doc(job_document)
+			jobsURL = get_user_collection_url("jobs")
+			upload_to_collection(jobsURL, job_document.to_s, MIME_TYPES[:rest])    
+		end
+		
+		public
+		
+		#Get the status of a previously submitted job.
+		#
+		#Return the status as a string, one of the values from Status.
+		#
+		#job_url -- The URL to a job resource previously created using
+		#	submit_job().
+		def get_job_status(job_url)
+			job_document = get_xml_doc(job_url)
+			#status = job_document.elements["{#{NAMESPACES[:service]}}status"]
+			status = job_document.root.elements['status']
+			# TODO: For future checks, use: 
+			#status_url = status.attributes.get_attribute_ns(NAMESPACES[:xlink], 'href').value
+			status.text
+		end
+		
+		#Get the date a previously submitted job was created.
+		#
+		#Return the date as a Datetime object.
+		#
+		#job_url -- The URL to a job resource previously created using
+		#	submit_job().
+		def get_job_created_date(job_url)
+			job_document = get_xml_doc(job_url)
+			#created = job_document.elements["{#{NAMESPACES[:dcterms]}}created"]
+			created = job_document.root.elements['dcterms:created'].text
+			DateTime.parse(created)
+		end
+		
+		#Get the date a previously submitted job was last modified.
+		#
+		#Return the date as a Datetime object.
+		#
+		#job_url -- The URL to a job resource previously created using
+		#	submit_job().
+		def get_job_modified_date(job_url)
+			job_document = get_xml_doc(job_url)
+			#modified = job_document.elements["{#{NAMESPACES[:dcterms]}}modified"]
+			modified = job_document.root.elements['dcterms:modified'].text
+			DateTime.parse(modified)
+		end
+		
+		#Get the job's internal progress report. This might be available
+		#while the job is running.
+		#
+		#Return the internal progress report as a Document::Report object.
+		#
+		#job_url -- The URL to a job resource previously created using submit_job().
+		def get_job_report(job_url)
+			job_document = get_xml_doc(job_url)
+			#report_element = job_document.elements["{#{NAMESPACES[:service]}}report"]
+			report_element = job_document.root.elements['report']
+			report_url = report_element.attributes.get_attribute_ns(NAMESPACES[:xlink], 'href').value
+			# TODO: Cache report_url per job
+			job_report_document = get_xml_doc(report_url, MIME_TYPES[:report])
+			Document::Report.from_document(job_report_document)
+		end
+			
+		#Get the outputs of a job.
+		#
+		#Return the job outputs as a hash where the keys are strings, 
+		#matching the names of output ports of the workflow. The values are
+		#Document::Data objects. If no outputs exists, nil is returned instead.
+		#
+		#job_url -- The URL to a job resource previously created using
+		#	submit_job().
+		def get_job_outputs(job_url)
+			job_outputs = get_job_outputs_doc(job_url)
+			return nil unless job_outputs
+			parse_data_doc(job_outputs)
+		end
+	
+		#Get the size of the outputs of a job.
+		#
+		#Return the size of the outputs of a job in kilobytes.
+		#If no outputs exists, nil is returned instead.
+		#
+		#job_url -- The URL to a job resource previously created using
+		#	submit_job().
+		def get_job_outputs_size(job_url)
+			outputs_url = get_job_outputs_url(job_url)
+			return nil if not outputs_url
+			get_xml_doc_size(outputs_url, MIME_TYPES[:baclava])
+		end
+	
+		#Check if a job has finished in one way or another. 
+		#
+		#Note that the job might have finished unsuccessfully. To check 
+		#if a job is actually complete, check::
+		#
+		#    get_job_status(job_url) == Status::COMPLETE.
+		#
+		#Return True if the job is in a finished state, that is that the
+		#Status.finished?(get_job_status()) is True.
+		#
+		#job_url -- The URL to a job resource previously created using
+		#    #submit_job().
+		#
+		def finished?(job_url)
+			status = get_job_status(job_url)
+			Status.finished?(status)
+		end
+		
+		#Submit a job to be queued for execution on the server.
+		#
+		#Return the URL to the created job resource.
+		# 
+		#workflow_url -- The URL of a workflow previously uploaded using
+		#    upload_workflow()
+		# 
+		#inputs_url -- The (optional) URL of a input resource previously
+		#    uploaded using upload_data()
+		#    
+		#Raises:
+		#    CouldNotCreateError -- If the service returned 200 OK instead of
+		#        creating the resource    
+		#
+		def submit_job(workflow_url, inputs_url=nil)
+			job_document = create_job_doc(workflow_url, inputs_url)
+			submit_job_doc(job_document)
+		end
+		
+		#Upload data to be used with submit_job().
+		#
+		#Return the URL to the created data resource.
+		#
+		#hash -- A hash where the keys are strings, matching the names of input
+		#	ports of the workflow to run. The values can be strings, lists of strings, or deeper
+		#	lists.
+		#	
+		#Raises:
+		#	CouldNotCreateError -- If the service returned 200 OK instead of
+		#		creating the resource    
+		def upload_data(hash)
+			inputs = create_data_doc(hash)
+			upload_data_doc(inputs)
+		end
+		
+		#Checks if the workflow exists on the server
+		#			
+		#workflow_url -- The URL to a workflow previously uploaded using 
+		#	upload_workflow().
+		def workflow_exists?(workflow_url)
+			url_valid?(workflow_url)
+		end
+		
+		#Checks if the username and password is valid for the service
+		def service_valid?
+			begin
+				get_user_url
+				true
+			rescue
+				false
+			end
+		end
+		
+		#Upload a workflow XML document to the current users' collection.
+		#
+		#Return the URL of the created workflow resource.
+		#
+		#workflow_xml -- The Taverna scufl workflow as a string
+		#
+		#Raises:
+		#	CouldNotCreateError -- If the service returned 200 OK instead of
+		#		creating the resource
+		def upload_workflow(workflow_xml)
+			workflows_url = get_user_collection_url("workflows")
+			upload_to_collection(workflows_url, workflow_xml, MIME_TYPES[:scufl])
+		end
+		
+		#Wait (blocking) for a job to finish, or until a maximum timeout 
+		#has been reached.
+		#
+		#Return the status of the job. If the 
+		#
+		#job_url -- The URL to a job resource previously created using
+		#	submit_job().
+		#
+		#timeout -- The maximum number of seconds (as a float) to wait for job.
+		#	The default value is DEFAULT_TIMEOUT.
+		#
+		#refresh -- In seconds (as a float), how often to check the job's 
+		#	status while waiting. The default value is DEFAULT_REFRESH.
+		def wait_for_job(job_url, timeout=DEFAULT_TIMEOUT, refresh=DEFAULT_REFRESH)
+			now = Time.now
+			_until = now + timeout
+			while _until > Time.now and not finished?(job_url)
+				now = Time.now # finished?() might have taken a while
+				sleep [[refresh, _until-now].min, 0].max
+				now = Time.now # after the sleep
+			end         
+			get_job_status(job_url)
+		end
+		
+		#Execute a workflow and wait until it's finished. 
+		#
+		#This will block until the workflow has been executed by the server, and
+		#return the result of the workflow run.
+		#
+		#Return the parsed output document as a hash where the keys are 
+		#strings, matching the names of output ports of the workflow. The 
+		#values are Document::Data objects. If the workflow
+		#did not produce any output, nil might be returned instead.
+		#
+		#workflow_xml -- The workflow as a Taverna scufl XML string. This *or* the 
+		#	workflow_url parameter is required.
+		#
+		#workflow_url -- The URL to a workflow previously uploaded using 
+		#	upload_workflow(). This *or* the workflow_xml parameter is required.
+		#	
+		#inputs -- The (optional) inputs to the workflow, either as a Baclava 
+		#	XML document (string), or as a hash where the keys are 
+		#	strings, matching the names of input ports of the workflow. The 
+		#	values can be strings, lists of strings, or deeper lists. 
+		#
+		#timeout -- The maximum number of seconds (as a float) to wait for job.
+		#	The default value is DEFAULT_TIMEOUT.
+		#
+		#refresh -- In seconds (as a float), how often to check the job's 
+		#	status while waiting. The default value is DEFAULT_REFRESH.
+		#
+		#Raises:
+		#	NotCompleteError -- If the job did not complete, for instance because
+		#		the timeout was reached before completion.
+		#	
+		#	urllib2.HTTPError -- If any step in submitting or requesting the status and
+		#		result of the job failed.
+		def execute_sync(workflow_xml=nil, workflow_url=nil, inputs=nil, 
+						timeout=DEFAULT_TIMEOUT, refresh=DEFAULT_REFRESH)
+			raise TypeError.new("workflow_xml or worklowURL must be given") unless workflow_xml or workflow_url 
+			raise TypeError.new("Only one of workflow_xml and workflow_url can be given") if workflow_xml and workflow_url
+	 
+			workflow_url = upload_workflow(workflow_xml) if workflow_xml
+			inputs_url = upload_data(inputs) if inputs
+			
+			job_url = submit_job(workflow_url, inputs_url)
+			status = wait_for_job(job_url, timeout, refresh)
+
+			raise NotCompleteError.new(job_url, status) if status != Status::COMPLETE
+	
+			get_job_outputs(job_url)
+		end
+		
+	end
+	
+end
+