mannie-taverna-scufl 0.6.0

data/LICENCE

@@ -0,0 +1,165 @@
+		   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions. 
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version. 
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

data/README

@@ -0,0 +1,133 @@
+= Taverna[http://taverna.sourceforge.net] 1 Interaction Gem
+
+Authors::       Stian Soiland, David Withers, Emmanuel Tagarira
+Version::       0.6.0
+Contact::       taverna-hackers@lists.sourceforge.net
+URL::           http://taverna.sourceforge.net/
+Licence::       LGPL 3 (See LICENCE or http://www.gnu.org/licenses/lgpl.html)
+Copyright::     (c)2006-2008 University of Manchester, UK
+
+
+
+== Synopsis
+
+This is a Ruby library to support the interaction with Taverna[http://taverna.sourceforge.net] version 1 workflows (Scufls).  This relies on the functionality provided by a graph visualization package called GraphViz[http://www.graphviz.org/Download.php].
+
+
+
+== Installation
+To install the gems required by the Taverna 1 gem library, type into your command prompt:
+  [sudo] gem install libxml-ruby
+  [sudo] gem install rdoc
+  [sudo] gem install darkfish-rdoc
+
+When you have the required gems on your system, you may install this gem using the following commands:
+  gem sources -a http://gems.github.com
+  [sudo] gem install mannie-taverna-scufl
+
+
+
+== Usage
+
+To be able to generate at least a Scufl model using the gem, you can use the code following code:
+  require "scufl/model.rb"
+  require "scufl/parser.rb"
+  
+  foo = File.new("path/to/workflow/file", "r")
+  bar = Scufl::Parser.new.parse(foo)
+
+Alternatively:
+  foo = File.new("path/to/workflow/file", "r").read
+  bar = Scufl::Parser.new.parse(foo)
+
+You will then be able to use your Scufl model to retrieve information about the workflow by invoking the different methods and attributes.
+  bar.INVOKED
+... where INVOKED is the method or attribute required.
+
+You can also interact with remote workflows.
+  require "open-uri"
+  
+  foo = Uri.parse("xxxx://uri_to_workflow").read
+  bar = Scufl::Parser.new.parse(foo)
+
+To be enable you to draw images of the Scufl, you need to include:
+  require "scufl/dot.rb"
+
+To be able to use any functionality included in "scufl/dot.rb", you need to have GraphViz[http://www.graphviz.org/Download.php] installed on your system.  Once this package has been installed, you may use the gem to draw an image showing the structure of the Scufl as follows.
+  out_file = File.new("path/to/file/you/want/the/dot/script/to/be/written", "w+")
+  Scufl::Dot.new.write_dot(out_file, bar)
+  `dot -Tpng -o"path/to/the/output/image" #{out_file.path}`
+The last line draws a PNG image using +out_file+.  To learn more about dot, try typing into your command prompt:
+  % man dot
+or
+  % dot -h
+
+
+
+== Taverna Remote Execution Service Client
+
+The library also includes support for submitting Taverna[http://taverna.sourceforge.net] workflows to the Taverna
+Remote Execution service[2]. This requires the Remote Execution service that
+has already been installed and configured, and with a client username and
+password already registered by the administrator of the service. We 
+recommend first testing the service using the Remote Execution service
+from the Taverna workbench[3].
+
+
+
+== Usage
+
+Here's the simplest usecase. Given a Taverna workflow in "workflow.xml" (that produces
+a value at the port "myOutput") and a Taverna Remote Execution service [2] running 
+at http://localhost:8080/tavernaservice/v1/ you can try:
+
+	SERVICE = "http://localhost:8080/tavernaservice/v1/"
+	workflow = IO.read("workflow.xml")
+	require 'rubygems'
+	require 'enactor/client'
+	enactor = Enactor::Client(SERVICE, "johndoe", "s3cret")
+	results = enactor.execute_sync(workflow)
+	print results["myOutput"]
+
+
+Note that the call to execute_sync() will block until the workflow has been executed
+on the server. If you want to do this asynchronously, try:
+	
+	workflow_url = enactor.upload_workflow(workflow)
+	job_url = enactor.submit_job(workflow_url)
+	sleep 1 while not enactor.finished?(job_url)
+	if enactor.get_job_status(job_url) == Enactor::Status.COMPLETE
+	  results = enactor.get_job_outputs(job_url)
+	  print results["myOutput"]
+	end
+
+
+You can also supply inputs as a hash:
+
+	inputs = {}
+	inputs['gene'] = ["MY_GENE", "HIS_GENE"]
+	inputs['database'] = "kegg"
+	results = enactor.execute_sync(workflow, inputs)
+
+or
+
+	inputs_url = enactor.upload_data(inputs)
+	job_url = enactor.submitJob(workflow_url, inputsURL)
+
+
+See the rdoc documentation of Enactor::Client for more information, try:
+
+	help Enactor::Client
+
+Included are also lower level modules Baclava for parsing 
+and creating Baclava data documents, and Scufl for extracting basic 
+information about a workflow, such as which input and output ports it defines.
+
+
+
+== References
+
+[1] http://taverna.sourceforge.net
+[2] http://www.mygrid.org.uk/usermanual1.7/remote_execution_server.html
+[3] http://www.mygrid.org.uk/usermanual1.7/remote_execution.html
+

data/lib/baclava/reader.rb

@@ -0,0 +1,61 @@
+require "rexml/document"
+require "document/data"
+
+module Baclava
+  
+  class Reader
+    
+    #Reads a baclava document amd returns a hash of Document::Data objects
+    def self.read(xml)
+      if xml.kind_of?(REXML::Document)
+      	document = xml
+      else
+        document = REXML::Document.new(xml)
+      end
+      root = document.root
+      raise "'#{root.name}' doesn't appear to be a data thing!" if root.name != "dataThingMap"
+      
+      create_data_map(root)
+    end
+    
+    def self.create_data_map(element)
+      data_map = {}
+      
+      element.each_element('b:dataThing') { |datathing|
+        key = datathing.attribute('key').value
+        data = Document::Data.new
+        data_map[key] = data
+        datathing.each_element('b:myGridDataDocument')  { |dataDocument|
+          dataDocument.each_element('s:metadata')  { |metadata| data.annotation = get_metadata(metadata) }
+          dataDocument.each_element('b:partialOrder') { |partialOrder| data.value = get_list(partialOrder) }
+          dataDocument.each_element('b:dataElement')  { |dataElement| data.value = get_element(dataElement) }
+        }
+      }
+      
+      data_map   
+    end
+    
+    def self.get_list(element)
+      list = []
+      element.each_element('b:itemList') { |itemList|  
+        itemList.each_element('b:dataElement')  { |dataElement| list << get_element(dataElement) }
+        itemList.each_element('b:partialOrder') { |partialOrder| list << get_list(partialOrder) }
+      }
+      list
+    end
+    
+    def self.get_metadata(element)
+      list = []
+      element.each_element('s:mimeTypes') { |mimeTypes|
+        mimeTypes.each_element('s:mimeType')  { |mimeType| list << mimeType.text }
+      }
+      list
+    end
+    
+    def self.get_element(element)
+      element.each_element('b:dataElementData') { |data| return Base64.decode64(data.text) }
+    end
+    
+  end
+  
+end

data/lib/baclava/writer.rb

@@ -0,0 +1,82 @@
+require 'base64'
+require 'rubygems'
+require 'builder'
+
+module Baclava # :nodoc:
+  
+  class Writer
+    
+	def self.write_doc(data_map)
+		REXML::Document.new(write(data_map))
+	end  	
+
+    def self.write(data_map)
+      xml = Builder::XmlMarkup.new :indent => 2
+      xml.instruct!
+      xml.b :dataThingMap, 'xmlns:b' => 'http://org.embl.ebi.escience/baclava/0.1alpha' do
+        for key in data_map.keys do
+          data = data_map[key]
+          xml.b :dataThing, 'key' => key do
+            xml.b :myGridDataDocument, 'lsid' => '', 'syntactictype' => '' do
+              #write_metadata xml, data.annotation
+              write_data xml, data.value
+            end
+          end
+        end
+      end
+    end
+    
+    #def self.write_metadata(xml, metadata)
+    #  xml.s :metadata, 'xmlns:s' => 'http://org.embl.ebi.escience/xscufl/0.1alpha' do
+    #    xml.s :mimeTypes do
+    #      for mimetype in metadata do
+    #        xml.s :mimetype, mimetype
+    #      end
+    #    end
+    #  end    
+    #end
+    
+    def self.write_data(xml, data, index = nil)
+      if data.is_a? Array
+        write_list xml, data, index
+      else
+        if index
+          xml.b :dataElement, 'lsid' => '', 'index' => index do
+            xml.b :dataElementData, Base64.encode64(data)
+          end
+        else
+          xml.b :dataElement, 'lsid' => '' do
+            xml.b :dataElementData, Base64.encode64(data)
+          end
+        end
+      end
+      
+    end
+    
+    def self.write_list(xml, list, index)
+      if index
+        xml.b :partialOrder, 'lsid' => '', 'type' => 'list', 'index' => index do
+          write_item_list xml, list
+        end
+      else
+        xml.b :partialOrder, 'lsid' => '', 'type' => 'list' do
+          write_item_list xml, list
+        end
+      end
+    end
+    
+    def self.write_item_list(xml, list)
+      xml.b :relationList
+      for i in 0..list.length - 1 do
+        xml.b :relation, 'parent' => i, 'child' => i + 1
+      end
+      xml.b :itemList do
+        for i in 0..list.length - 1 do
+          write_data xml, list[i], i
+        end
+      end
+    end
+    
+  end
+  
+end

data/lib/document/data.rb

@@ -0,0 +1,24 @@
+module Document # :nodoc:
+	
+	#Input or output data
+	#
+	#value - the data value or a (possibly nested) list of data values
+	class Data
+		attr_accessor :value, :annotation
+		
+		def initialize(value=nil, annotation=nil)
+			@value = value
+			@annotation = annotation
+		end
+				
+		def eql?(other)
+			@value.eql?(other.value) and @annotation.eql?(other.annotation)
+		end
+		
+		def ==(other)
+			@value == other.value and @annotation == other.annotation
+		end
+		
+	end
+	
+end