workflow-to-galaxy 0.2.9 → 0.3.0

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: workflow-to-galaxy
 version: !ruby/object:Gem::Version 
-  hash: 5
+  hash: 19
   prerelease: 
   segments: 
   - 0
-  - 2
-  - 9
-  version: 0.2.9
+  - 3
+  - 0
+  version: 0.3.0
 platform: ruby
 authors: 
 - Kostas Karasavvas
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-07-26 00:00:00 Z
+date: 2011-10-13 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: myexperiment-rest
@@ -23,14 +23,14 @@ dependencies:
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
-        hash: 27
+        hash: 19
         segments: 
         - 0
-        - 2
-        - 6
-        version: 0.2.6
+        - 3
+        - 0
+        version: 0.3.0
   type: :runtime
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
@@ -39,7 +39,7 @@ dependencies:
   requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
         hash: 23
         segments: 
@@ -55,14 +55,14 @@ dependencies:
   requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
-        hash: 13
+        hash: 5
         segments: 
         - 0
-        - 5
-        - 3
-        version: 0.5.3
+        - 6
+        - 1
+        version: 0.6.1
   type: :runtime
   version_requirements: *id003
 - !ruby/object:Gem::Dependency 
@@ -71,7 +71,7 @@ dependencies:
   requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
         hash: 51
         segments: 
@@ -97,14 +97,15 @@ files:
 - CHANGES
 - Rakefile
 - bin/workflow_to_galaxy.rb
-- lib/workflow_to_galaxy.rb
-- lib/generator.rb
-- lib/workflow-to-galaxy/generator.rb
+- lib/workflow-to-galaxy/galaxy.rb
+- lib/workflow-to-galaxy/constants.rb
 - lib/workflow-to-galaxy.rb
 - doc/rdoc/WorkflowToGalaxy.html
 - doc/rdoc/rdoc.css
 - doc/rdoc/Generator.html
 - doc/rdoc/LICENSE.html
+- doc/rdoc/WorkflowToGalaxy/Workflows.html
+- doc/rdoc/WorkflowToGalaxy/GalaxyTool.html
 - doc/rdoc/index.html
 - doc/rdoc/js/jquery.js
 - doc/rdoc/js/thickbox-compressed.js
@@ -116,6 +117,7 @@ files:
 - doc/rdoc/lib/workflow-to-galaxy_rb.html
 - doc/rdoc/lib/generator_rb.html
 - doc/rdoc/lib/workflow-to-galaxy/generator_rb.html
+- doc/rdoc/lib/workflow-to-galaxy/constants_rb.html
 - doc/rdoc/created.rid
 - doc/rdoc/CHANGES.html
 - doc/rdoc/images/find.png

data/lib/generator.rb

@@ -1,265 +0,0 @@
-
-# Contains code to generate the Galaxy's tool xml and script files
-module Generator
-
-  INDENT = "  "
-
-
-  # private methods
-  private
-
-  def tool_b(out, name)
-    out.write("<tool id=\"#{name}_id\" name=\"#{name}\">\n")
-  end
-
-  def command_be(out, me_rest, script)
-    out.write "#{INDENT}<command interpreter=\"ruby\">"
-    out.write script + " "
-    me_rest.workflow.inputs.each do |i|
-      out.write "\"$#{i.name}\" "
-    end
-    me_rest.workflow.outputs.each do |o|
-      out.write "$#{o.name} "
-    end
-    out.write "</command>\n"
-  end
-
-  def inputs_be(out, inputs)
-    out.write "#{INDENT}<inputs>\n"
-    if inputs.size >= 1
-      inputs.each do |i|
-        2.times { out.write "#{INDENT}" }
-        out.write "<param name=\"#{i.name}\" type=\"text\" size=\"30\" "
-        if i.examples.size >= 1
-          # escape double quotes characters for galaxy's xml file
-          ex = i.examples[0].to_s.gsub('"', '&quot;')
-          out.write "value=\"#{ex}\" "
-        end
-        out.write "label=\"Enter #{i.name}\"/>\n"
-      end
-    else
-      2.times { out.write "#{INDENT}" }
-      out.write "<param name=\"input\" type=\"select\" display=\"radio\" size=\"250\" label=\"This workflow has no inputs\" />\n"
-    end  
-    out.write "#{INDENT}</inputs>\n"
-  end
-
-  def outputs_be(out, outputs)
-    out.write "#{INDENT}<outputs>\n"
-    outputs.each do |o|
-      2.times { out.write "#{INDENT}" }
-      out.write "<data format=\"tabular\" name=\"#{o.name}\" label=\"#{o.name}\"/>\n"
-    end
-    out.write "#{INDENT}</outputs>\n"
-  end
-
-  def help_be(out, me_rest)
-    out.write "#{INDENT}<help>\n"
-    out.write "**What it does**\n\n"
-
-    # Sometimes the workflow description contains HTML tags that are not allowed
-    # in Galaxy's xml interface specification and thus are removed! Same for
-    # HTML entities!
-    out.write me_rest.workflow.description.gsub(/<.*?>|&.*?;/, '') + "\n\n"
-
-    if me_rest.workflow.inputs.size >= 1
-      out.write "-----\n\n"
-      out.write "**Inputs**\n\n"
-      me_rest.workflow.inputs.each do |i|
-        out.write "- **#{i.name}** "
-        if i.descriptions.size >= 1
-          i.descriptions.each do |desc|
-            out.write desc.to_s + " "
-          end
-        end
-        if i.examples.size >= 1
-          out.write "Examples include:\n\n"
-          i.examples.each do |ex|
-            out.write "  - " + ex.to_s + "\n"
-          end
-        end
-        out.write "\n"
-      end
-      out.write "\n"
-    end
-
-    # TODO this code is identical to the inputs code above -- method?
-    if me_rest.workflow.outputs.size >= 1
-      out.write "-----\n\n"
-      out.write "**Outputs**\n\n"
-      me_rest.workflow.outputs.each do |o|
-        out.write "- **#{o.name}** "
-        if o.descriptions.size >= 1
-          o.descriptions.each do |desc|
-            out.write desc.to_s + " "
-          end
-        end
-        if o.examples.size >= 1
-          out.write "Examples include:\n\n"
-          o.examples.each do |ex|
-            out.write "  - " + ex.to_s + "\n"
-          end
-        end
-        out.write "\n"
-      end
-      out.write "\n"
-    end
-
-
-    out.write "-----\n\n"
-    out.write "For more information on that workflow please visit #{me_rest.uri.gsub(/(.*workflows\/\d+)[\/.].*/, '\1')}.\n"
-
-    out.write "#{INDENT}</help>\n"
-  end
-
-  def tool_e(out)
-    out.write("</tool>\n")
-  end
-
-
-
-
-  def script_preample(out)
-    out.write("#!/usr/bin/env ruby\n\n")
-    out.write("require 'rubygems'\n")
-    out.write("require 't2-server'\n")
-    out.write("require 'open-uri'\n\n")
-  end
-
-  def script_util_methods(out)
-
-    out.write <<UTIL_METHODS
-    
-  # method that flattens the list of list of list ... result of get_output
-  def print_flattened_result(out, data_lists)
-    data_lists.each do |l|
-      if l.instance_of? Array
-        print_flattened_result(out, l)
-      else
-        out.puts l
-      end
-    end
-  end
-
-
-  # method that acquires all the results of the specified output
-  def get_outputs(run, refs, outfile, dir)
-    data_lists = run.get_output(dir, refs)
-    print_flattened_result(outfile, data_lists)
-  end
-
-
-  #
-  # Sanitize single and double quotes in str. E.g. galaxy substitures them to
-  # __sq__ and __dq__ respectively. This methods turns them back to their
-  # original values before using them
-  #
-  def sanitize(string)
-    string.gsub(/(__sq__|__dq__|__at__)/) do
-      if $1 == '__sq__'
-        "'"
-      elsif $1 == '__dq__'
-        '\\\"'
-      else
-        '@'
-      end
-    end
-  end
-
-UTIL_METHODS
-
-  end
-
-
-  def script_create_t2_run(out, wkf_uri, t2_uri)
-    out.write <<CREATE_T2_RUN
-
-# use the uri reference to download the workflow locally
-wkf_file = URI.parse('#{wkf_uri}')
-in_wkf = open(wkf_file)
-wkf = in_wkf.read()
-
-# create run
-begin
-  run = T2Server::Run.create('#{t2_uri}', wkf)
-rescue T2Server::T2ServerError => e
-  exit 1
-end
-
-CREATE_T2_RUN
-
-  end
-
-
-  def script_init_inputs(out, me_rest)
-    out.write "# get input arguments\n"
-    0.upto(me_rest.workflow.inputs.size-1) do |i|
-      out.write "input#{i}_arg = ARGV[#{i}].chomp\n"
-      out.write "run.set_input('" + me_rest.workflow.inputs[i].name.to_s + "', sanitize(input#{i}_arg))\n"
-    end
-
-  end
-
-
-  def script_start_run(out)
-    out.write <<START_RUN
-
-# start run and wait until it is finished
-run.start
-run.wait(:progress => true)
-
-START_RUN
-  end
-
-
-  def script_get_outputs(out, me_rest)
-    outputs_start_index = me_rest.workflow.inputs.size
-    outputs_end_index = outputs_start_index + me_rest.workflow.outputs.size - 1
-    out.write "# get output arguments and associated them with a file\n"
-    outputs_start_index.upto(outputs_end_index) do |o|
-      out.write "output#{o} = File.open(ARGV[#{o}], \"w\")\n"
-      out.write "get_outputs(run, false, output#{o}, '" + me_rest.workflow.outputs[o - outputs_start_index].name.to_s + "')\n"
-    end
-
-  end
-
-
-  def script_finish_run(out)
-    out.write "\n# delete run\n"
-    out.write "run.delete\n"
-  end
-
-
-
-  # public methods from here onwards
-  public
-
-  # Generates the Galaxy tool's xml file responsible for the UI.
-  def generate_xml(me_rest, xml_file)
-    out = File.open(xml_file, "w")
-    tool_b(out, me_rest.workflow.title)
-    command_be(out, me_rest, xml_file.gsub('.xml', '.rb'))
-    inputs_be(out, me_rest.workflow.inputs)
-    outputs_be(out, me_rest.workflow.outputs)
-    help_be(out, me_rest)
-    tool_e(out)
-    out.close
-  end
-
-  #
-  # Generates the Galaxy tool's script file responsible for talking to the
-  # taverna server
-  #
-  def generate_script(me_rest, t2_server, script_file)
-    out = File.open(script_file, "w")
-    script_preample(out)
-    script_util_methods(out)
-    script_create_t2_run(out, me_rest.uri, t2_server)
-    script_init_inputs(out, me_rest)
-    script_start_run(out)
-    script_get_outputs(out, me_rest)
-    script_finish_run(out)
-    out.close
-  end
-
-end

data/lib/workflow-to-galaxy/generator.rb

@@ -1,511 +0,0 @@
-#
-# The Generator module contains two public methods that generate a Galaxy's tool
-# XML and script files
-#--
-# Add appropriate requires here. Currently they are all in the executable!
-module Generator
-
-  # private methods
-  private
-
-  # Used to create indentation when generating code
-  def indent(n)
-    ind = ""
-    n.times { ind += "  "  }
-    ind
-  end
-
-  # Galaxy's XML tool tag
-  def tool_begin_tag(out, name)
-    out.write("<tool id=\"#{name}_id\" name=\"#{name}\">\n")
-  end
-
-  # Galaxy's XML command tag
-  def command_tag(out, t2_workflow, script)
-    out.write indent(1) + "<command interpreter=\"ruby\">\n"
-    out.write indent(2) + script + "\n"
-
-    # inputs
-    t2_workflow.inputs.each do |i|
-      out.write indent(2) + "#if $#{i.name}_source.history_or_textfield == \"textfield\":\n"
-      out.write indent(3) + "false \"$#{i.name}_source.textfield_#{i.name}\"\n"
-      out.write indent(2) + "#else:\n"
-      out.write indent(3) + "true  \"$#{i.name}_source.history_#{i.name}\"\n"
-      out.write indent(2) + "#end if\n"
-    end
-
-    # results as zip input
-    out.write indent(2) + "$results_as_zip\n"
-
-    # outputs
-    out.write indent(2)
-    t2_workflow.outputs.each do |o|
-      out.write "$#{o.name} "
-    end
-
-    # result zip output
-    out.write "$result_zip\n"
-    
-    out.write indent(1) + "</command>\n"
-  end
-
-
-  # Galaxy's XML inputs tag
-  def inputs_tag(out, inputs)
-    out.write indent(1) + "<inputs>\n"
-    if inputs.size >= 1
-      inputs.each do |i|
-        out.write indent(2) + "<conditional name=\"#{i.name}_source\">\n"
-        out.write indent(3) + "<param name=\"history_or_textfield\" type=\"select\" label=\"Select source for #{i.name}\">\n"
-        out.write indent(4) + "<option value=\"history\">From history</option>\n"
-        out.write indent(4) + "<option value=\"textfield\" selected=\"true\">Type manually</option>\n"
-        out.write indent(3) + "</param>\n"
-        out.write indent(3) + "<when value=\"history\">\n"
-        out.write indent(4) + "<param name=\"history_#{i.name}\" type=\"data\" label=\"Select #{i.name}\"/>\n"
-        out.write indent(3) + "</when>\n"
-        out.write indent(3) + "<when value=\"textfield\">\n"
-        out.write indent(4) + "<param name=\"textfield_#{i.name}\" type=\"text\" area=\"True\" size=\"2x50\" "
-        if i.examples.size >= 1 
-          # escape double quotes characters for galaxy's xml file
-          ex = i.examples[0].to_s.gsub('"', '&quot;')
-          # convert newlines to HTML newlines to display in textareas inputs
-          ex = ex.gsub(/[\n]/, '&#xA;')
-          out.write "value=\"#{ex}\" "          
-        end
-        out.write "label=\"Enter #{i.name}\"/>\n"
-        out.write indent(3) + "</when>\n"
-        out.write indent(2) + "</conditional>\n"
-      end
-    else
-      out.write indent(2) + "<param name=\"input\" type=\"select\" display=\"radio\" size=\"250\" label=\"This workflow has no inputs\" />\n"
-    end
-
-    # result as zip input
-    out.write indent(2) + "<param name=\"results_as_zip\" type=\"select\" label=\"Would you also like the raw results as a zip file\">\n"
-    out.write indent(3) + "<option value=\"yes\">Yes</option>\n"
-    out.write indent(3) + "<option value=\"no\" selected=\"true\">No</option>\n"
-    out.write indent(2) + "</param>\n"
-
-    out.write indent(1) + "</inputs>\n"
-  end
-
-  # Galaxy's XML outputs tag
-  def outputs_tag(out, outputs)
-    out.write indent(1) + "<outputs>\n"
-    outputs.each do |o|
-      out.write indent(2) + "<data format=\"tabular\" name=\"#{o.name}\" label=\"#{o.name}\"/>\n"
-    end
-
-    # result zip output
-    out.write indent(2) + "<data format=\"zip\" name=\"result_zip\" label=\"Compressed Results (zip)\">\n"
-    out.write indent(3) + "<filter>results_as_zip == \"yes\"</filter>\n"
-    out.write indent(2) + "</data>\n"
-
-    out.write indent(1) + "</outputs>\n"
-  end
-
-  # Galaxy's XML help tag
-  def help_tag(out, t2_workflow)
-    out.write indent(1) + "<help>\n"
-
-    if t2_workflow.description
-      out.write "**What it does**\n\n"
-
-      description = t2_workflow.description + "\n\n"
-
-      # Sometimes the workflow description contains HTML tags that are not allowed
-      # in Galaxy's xml interface specification and thus are removed! Same for
-      # HTML entities!
-      # TODO go through tags and find Galaxy's equivalent to include
-      description.gsub!(/<.*?>|&.*?;/, '')
-
-      # To remove ^M (cntl-v + cntl-m) characters that DOS files might have
-      description.gsub!(/\r/, '')
-
-      # TODO that works as a literal too but font changes to courier!
-      #out.write "::\n\n"   # Start Galaxy's literal block to ignore indendation
-
-      # remove indendation from all description lines since Galaxy is confused by it
-      description.split(/[\n]/).each { |l| out.write "#{l.gsub(/^\s+/, '')}\n" }
-
-      # endline makes the following be parsed as a Galaxy GUI construct
-      out.write "\n"
-    end
-
-    # if at least one input add it to tool's UI help description
-    if t2_workflow.inputs.size >= 1
-      out.write "-----\n\n"
-      out.write "**Inputs**\n\n"
-      t2_workflow.inputs.each do |i|
-        out.write "- **#{i.name}** "
-        if i.descriptions.size >= 1
-          i.descriptions.each do |desc|
-            out.write desc.to_s + " "
-          end
-        end
-        if i.examples.size >= 1
-          out.write "Examples include:\n\n"
-          i.examples.each do |ex|
-            # some examples have a newline between them that breaks Galaxy's GUI
-            # so we substitute it with ' '
-            #out.write "  - " + ex.to_s.gsub(/[\n]/, ' ') + "\n"
-
-            # We could substitute them with with &#xA; that works for HTML (e.g. wkf 1180)
-            # But if an example input is truly multiline then input descr. will
-            # display them all as separate inputs...
-            out.write "  - " + ex.to_s.gsub(/[\n]/, '&#xA;  - ') + "\n"
- 
-            # display example inputs as verbatim/literal so it is not our responsibility!!
-            # add indendation after each newline to specify the literal block
-            # TODO this looks ugly if we don't remove all the bullet points!
-            #out.write "::\n\n  " + ex.to_s.gsub(/\n/, '&#xA;  ') + "\n"
-          end
-        end
-        out.write "\n"
-      end
-      out.write "\n"
-    end
-
-    # if at least one output add it to tool's UI help description
-    if t2_workflow.outputs.size >= 1
-      out.write "-----\n\n"
-      out.write "**Outputs**\n\n"
-      t2_workflow.outputs.each do |o|
-        out.write "- **#{o.name}** "
-        if o.descriptions.size >= 1
-          o.descriptions.each do |desc|
-            out.write desc.to_s + " "
-          end
-        end
-        if o.examples.size >= 1
-          out.write "Examples include:\n\n"
-          o.examples.each do |ex|
-            out.write "  - " + ex.to_s + "\n"
-          end
-        end
-        out.write "\n"
-      end
-      out.write "\n"
-    end
-
-    out.write "-----\n\n"
-    out.write ".. class:: warningmark\n\n"
-    out.write "**Please note that some workflows are not up-to-date or have dependencies** " <<
-              "that cannot be met by the specific Taverna server that you specified during " <<
-              "generation of this tool. You can make sure that the workflow is valid " <<
-              "by running it in the Taverna Workbench first to confirm that it works " <<
-              "before running it via Galaxy.\n\n"
-
-    if t2_workflow.input_type == TavernaWorkflow::MY_EXPERIMENT
-      out.write "-----\n\n"
-      out.write ".. class:: warningmark\n\n"
-      out.write "**Please note that there might be some repetitions in the workflow description** " <<
-                "in some of the generated workflows. This is due to a backwards compatibility " <<
-                "issue on the myExperiment repository which keeps the old descriptions to make " <<
-                "sure that no information is lost.\n\n"
-
-      out.write "-----\n\n"
-      out.write ".. class:: infomark\n\n"
-      out.write "**For more information on that workflow please visit** #{t2_workflow.xml_uri.gsub(/(.*workflows\/\d+)[\/.].*/, '\1')}.\n\n"
-    end
-
-    out.write indent(1) + "</help>\n"
-  end
-
-  # Galaxy's XML tool tag close
-  def tool_end_tag(out)
-    out.write("</tool>\n")
-  end
-
-
-
-  # Galaxy's script preample
-  def script_preample(out)
-    out.write("#!/usr/bin/env ruby\n\n")
-
-    out.write("# This script can be tested without Galaxy. You can run from the shell as follows:\n#\n")
-    out.write("#   $ script_name.rb <input1> true|false <input2> true|false  yes|no  <output1> <output2>\n#\n")
-    out.write("# After each input value a boolean specifies if the value is literal (false) or if\n")
-    out.write("# it specifies a file name to read as input.\n#\n")
-    out.write("# After all workflow inputs a yes or no input specifies if we also want our results zipped.\n#\n")
-    out.write("# Finally, all the output files follow. Note that if you selected to also get a zip\n")
-    out.write("# then you need to specify an additional output in the end after the normal workflow\n")
-    out.write("# outputs.\n\n")
-
-    out.write("require 'rubygems'\n")
-    out.write("require 't2-server'\n")
-    out.write("require 'open-uri'\n")
-    out.write("require 'zip/zipfilesystem'\n\n")
-  end
-
-
-  # Galaxy's script utility methods
-  # TODO: use ruby's flatten instead of our own !!!
-  def script_util_methods(out)
-
-    out.write <<'UTIL_METHODS'
-
-# sends the zip file to specified output
-def output_zip_file(uuid, zip_out)
-  File.open("/tmp/#{uuid}.zip") do |zip|
-    while data = zip.read(4096)
-      zip_out.write data
-    end
-  end
-  File.delete("/tmp/#{uuid}.zip")
-end
-
-
-#
-# replicates the directory result structure as constructed by the
-# taverna server and recreates it in a zip File
-#
-def add_to_zip_file(output_dir, data_lists, zip_out) 
-  zip_out.dir.mkdir("#{output_dir}")
-  data_lists.each_with_index do |item, index|
-    if item.instance_of? Array
-      add_to_zip_file("#{output_dir}/#{index+1}", item, zip_out)
-    else
-      zip_out.file.open("#{output_dir}/#{index+1}", "w") { |f| f.puts item }
-    end
-  end
-end
-
-    
-# method that flattens the list of list of list ... result of get_output
-def print_flattened_result(out, data_lists)
-  data_lists.each do |l|
-    if l.instance_of? Array
-      print_flattened_result(out, l)
-    else
-      out.puts l
-    end
-  end
-end
-
-
-#
-# Method that acquires all the results of the specified output directory.
-# If valid zip File is passed it also accumulates results as a zip file.
-#
-def get_outputs(run, refs, outfile, dir, zip_out=nil) 
-  data_lists = run.get_output(dir, refs)
-  print_flattened_result(outfile, data_lists)
-  if zip_out
-    add_to_zip_file(dir, data_lists, zip_out)
-  end
-end
-
-
-#
-# Sanitize all special characters in UI inputs that Galaxy substitutes for
-# security reasons. This methods turns them back to their original values before
-# using them (i.e. sending them to the taverna server
-# NB: note that double quote is sanitized to "'" that is because the double code
-#     confuses the Taverna server ruby library. Apparently, this is not trivial
-#     to fix.
-#
-def sanitize(string)
-  string.gsub(/(__sq__|__dq__|__at__|__cr__|__cn__|__tc__|__gt__|__lt__|__ob__|__cb__|__oc__|__cc__)/) do
-    if $1 == '__sq__'
-      "'"
-    elsif $1 == '__dq__'
-      "'"
-    elsif $1 == '__cr__'
-      "\r"
-    elsif $1 == '__cn__'
-      "\n"
-    elsif $1 == '__tc__'
-      "\t"
-    elsif $1 == '__gt__'
-      '>'
-    elsif $1 == '__lt__'
-      '<'
-    elsif $1 == '__ob__'
-      '['
-    elsif $1 == '__cb__'
-      ']'
-    elsif $1 == '__oc__'
-      '{'
-    elsif $1 == '__cc__'
-      '}'
-    else
-      '@'
-    end
-  end
-end
-
-#
-# Deletes last new line of file if it exists! It is needed for t2 workflows that
-# do not sanitize properly, i.e. via a user-provided beanshell script
-#
-def chomp_last_newline(file)
-
-  if File.file?(file) and File.size(file) > 1
-    f = open(file, "rb+")
-    f.seek(-1, File::SEEK_END)
-    f.truncate(File.size(file) - 1) if f.read(1) == "\n"
-    f.close
-  end
-
-end
-
-
-UTIL_METHODS
-
-  end
-
-  # Galaxy's script taverna 2 run
-  def script_create_t2_run(out, wkf, t2_uri)
-    if wkf.input_type == TavernaWorkflow::MY_EXPERIMENT
-      out.write "# use the uri reference to download the workflow locally\n"
-      out.write "wkf_file = URI.parse('#{wkf.xml_uri}')\n"
-      out.write "in_wkf = open(wkf_file)\n"
-    else     # TavernaWorkflow::T2_FLOW
-      out.write "# uri contains local t2flow file\n"
-      out.write "in_wkf = open('#{wkf.xml_uri}')\n"
-    end
-
-    out.write <<CREATE_T2_RUN
-
-wkf = in_wkf.read()
-
-# create run
-begin
-  run = T2Server::Run.create('#{t2_uri}', wkf)
-rescue T2Server::T2ServerError => e
-  exit 1
-end
-
-CREATE_T2_RUN
-
-  end
-
-
-  # Galaxy's script input handling
-  def script_init_inputs(out, t2_workflow)
-    out.write "#\n"
-    out.write "# Get input arguments -- for each input a boolean specifies if it's from history\n"
-    out.write "# thus, for each t2_workflow input we have two arguments in the script!\n"
-    out.write "#\n"
-    t2_workflow.inputs.each_with_index do |input, i|
-      i_name = input.name.to_s
-      out.write "#{i_name}_from_history = ARGV[#{i*2}].chomp\n"
-      out.write "#{i_name}_tmp = ARGV[#{i*2+1}].chomp\n"
-      out.write "if #{i_name}_from_history == \"true\"\n"
-      out.write "  chomp_last_newline(#{i_name}_tmp)\n"
-      out.write "  run.upload_input_file('#{i_name}', #{i_name}_tmp)\n"
-      out.write "else\n"
-      out.write "  run.set_input('#{i_name}', sanitize(#{i_name}_tmp))\n"
-      out.write "end\n"
-    end
-
-    # add code to handle results_as_zip input, i.e. create zip file
-    out.write "\n# get results_as_zip input and open zip file if appropriate\n"
-    # get argument index after workflow inputs
-    zip_index = t2_workflow.inputs.size * 2
-    out.write "zipped = ARGV[#{zip_index}].chomp == \"yes\"\n"
-    out.write 'zip_out = Zip::ZipFile.open("/tmp/#{run.uuid}.zip", Zip::ZipFile::CREATE) if zipped' + "\n"
-    
-  end
-
-
-  # Galaxy's script starting taverna run
-  def script_start_run(out)
-    out.write <<START_RUN
-
-
-# start run and wait until it is finished
-run.start
-run.wait(:progress => true)
-
-START_RUN
-  end
-
-
-  # Galaxy's script output handling
-  def script_get_outputs(out, t2_workflow)
-    # outputs start after all inputs plus the results_as_zip input
-    outputs_start_index = t2_workflow.inputs.size * 2 + 1
-    outputs_end_index = outputs_start_index + t2_workflow.outputs.size - 1
-    out.write "# get output arguments and associated them with a file\n"
-    outputs_start_index.upto(outputs_end_index) do |o|
-      out.write "output#{o} = File.open(ARGV[#{o}], \"w\")\n"
-      out.write "begin\n"
-      out.write "  get_outputs(run, false, output#{o}, '" + t2_workflow.outputs[o - outputs_start_index].name.to_s + "', zip_out)\n"
-      out.write "rescue Exception => err\n"
-      out.write "  get_outputs(run, false, output#{o}, '" + t2_workflow.outputs[o - outputs_start_index].name.to_s + ".error', zip_out)\n"
-      out.write "ensure\n"
-      out.write "  output#{o}.close\n"
-      out.write "end\n"
-    end
-
-    # close zip file if created when dealing with the inputs
-    #--
-    # ideally that would semantically belong to a separate method
-    out.write "\n# close zip_out (the newly created zip file) if opened\n"
-    out.write "zip_out.close if zip_out\n"
-
-    # dealing with zip output here -- zip arg index is outputs_end_index (last
-    # output) plus 1
-    out.write "\n# open galaxy zip output and write zip file\n"
-    out.write "if zipped\n"
-    out.write "  galaxy_zip_out = File.open(ARGV[#{outputs_end_index+1}], \"w\")\n"
-    out.write "  output_zip_file(run.uuid, galaxy_zip_out)\n"
-    out.write "  galaxy_zip_out.close\n"
-    out.write "end\n"
-    
-  end
-
-
-  # Galaxy's script cleaning taverna run
-  def script_finish_run(out)
-    out.write "\n# delete run\n"
-    out.write "run.delete\n"
-  end
-
-
-  
-
-
-  # public methods from here onwards
-  public
-
-  # Generates the Galaxy tool's xml file responsible for the UI.
-  #
-  # :call-seq:
-  #   Generator.generate_xml(my_exp_rest, xml_file) -> nil
-  #
-  # [+t2_workflow+] a _Workflow_ object as returned from <em>MyExperimentREST::Workflows.new.read(url)</em>
-  # [+xml_file+]    a string containing the name of the generated XML file
-  # [+xml_out+]     the file handler to write the generated XML tags
-  def generate_xml(t2_workflow, xml_file, xml_out)
-    tool_begin_tag(xml_out, t2_workflow.title)
-    command_tag(xml_out, t2_workflow, xml_file.gsub('.xml', '.rb'))
-    inputs_tag(xml_out, t2_workflow.inputs)
-    outputs_tag(xml_out, t2_workflow.outputs)
-    help_tag(xml_out, t2_workflow)
-    tool_end_tag(xml_out)
-  end
-
-
-  # Generates the Galaxy tool's script file responsible for talking to the
-  # taverna server
-  #
-  # :call-seq:
-  #   Generator.generate_script(my_exp_rest, t2_server, script_file) -> nil
-  #
-  # [+my_exp_rest+]      a _Workflow_ object as returned from <em>MyExperimentREST.ReadWorkflow.new(url)</em>
-  # [<tt>t2_server</tt>] a string containing the URL of the taverna 2 server
-  # [+script_out+]       the file handler to write the generated script code
-  def generate_script(t2_workflow, t2_server, script_out)
-    script_preample(script_out)
-    script_util_methods(script_out)
-    script_create_t2_run(script_out, t2_workflow, t2_server)
-    script_init_inputs(script_out, t2_workflow)
-    script_start_run(script_out)
-    script_get_outputs(script_out, t2_workflow)
-    script_finish_run(script_out)
-  end
-
-end