workflow-to-galaxy 0.2.7

data/CHANGES

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+= Changes log for the Taverna-Galaxy Gem
+
+== Version 0.2.7
+
+* A Galaxy tool can now also be created by provided a t2flow file with the --t2flow flag.
+

data/LICENSE

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+== workflow-to-galaxy
+
+The MIT License
+
+Copyright (c) 2010 - Netherlands Bioinformatics Centre
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README

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+= workflow-to-galaxy tool generator
+
+
+Authors::     Konstantinos Karasavvas
+Gem Version:: 0.2.7
+Contact::     mailto:kostas.karasavvas@nbic.nl
+Licence::     MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
+Copyright::   (c) 2010 Netherlands Bioinformatics Centre, The Netherlands
+
+
+== Synopsis
+
+This script requires a Taverna2 workflow URL as input and generates a Galaxy tool
+(a UI XML definition plus a script) that will enable the execution of this
+workflow through Galaxy. The tool's description is as good as the description
+provided in the workflow itself. Currently, the myExperiment workflow repository
+is used to access workflow information via its REST API but a workflow description
+from a file is also supported.
+
+The name is workflow-to-galaxy rather than t2-workflow-to-galaxy because it is
+possible that it will support other workflow management system's in the future.
+
+
+== Installation
+
+[sudo] gem install workflow-to-galaxy
+
+
+== Usage
+
+workflow_to_galaxy [options] <myExperiement-workflow> | <t2flow-file>
+
+Generates a Galaxy tool (a UI xml definition plus a script) for the
+specified Taverna2 workflow, where <myExperiment-workflow> is
+the full URL of the workflow in the myExperiment website. Alternatively
+a t2flow file can be passed for workflows not in myExperiment. Available
+options are:
+
+-o OUTPUT, --output=OUTPUT  The file name(s) of the generated tool. If it is not specified then the workflow's name will be used.
+
+-s SERVER, --server=SERVER  The taverna server that the script will request execution from. If it is not specified then "http://localhost:8980/taverna-server" will be used.
+
+-t,        --t2flow         The workflow is a t2flow file.
+
+
+== Example
+
+Let's say we want to install the taverna2 workflow http://www.myexperiment.org/workflows/74.html
+from myExperiment repository:
+
+<tt>$ workflow_to_galaxy  -s http://localhost:8980/taverna-server  http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_781733.t2flow?version=5</tt>
+
+
+
+== References
+
+Galaxy::       http://galaxy.psu.edu
+Taverna2::     http://www.taverna.org.uk
+myExperiment:: http://www.myexperiment.org
+

data/Rakefile

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+# 
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+ 
+
+require 'rubygems'
+require 'rake'
+require 'rake/clean'
+require 'rake/gempackagetask'
+require 'rake/rdoctask'
+require 'rake/testtask'
+
+spec = Gem::Specification.new do |s|
+  s.name = 'workflow-to-galaxy'
+  s.version = '0.2.7'
+  s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
+  s.summary = 'This script acquires information for a taverna 2 workflow from myExperiment (or from a file) and generates a Galaxy tool (.xml and .rb files).'
+  s.description = s.summary
+  s.author = 'Kostas Karasavvas'
+  s.email = 'kostas.karasavvas@nbic.nl'
+  s.executables = ['workflow_to_galaxy.rb']
+  s.files = %w(LICENSE README CHANGES Rakefile) + Dir.glob("{bin,lib,doc,spec}/**/*")
+  s.require_path = "lib"
+  s.bindir = "bin"
+  s.add_dependency 'myexperiment-rest', '>= 0.2.6'
+  s.add_dependency 'taverna-t2flow', '>= 0.2.0'
+  s.add_dependency 't2-server', '>= 0.5.3'
+end
+
+Rake::GemPackageTask.new(spec) do |p|
+  p.gem_spec = spec
+  p.need_tar = true
+  p.need_zip = true
+end
+
+Rake::RDocTask.new do |rdoc|
+  files =['README', 'LICENSE', 'lib/**/*.rb']
+  rdoc.rdoc_files.add(files)
+  rdoc.main = "README" # page to start on
+  rdoc.title = "workflow-to-galaxy Docs"
+  rdoc.rdoc_dir = 'doc/rdoc' # rdoc output folder
+  rdoc.options << '--line-numbers'
+end
+
+Rake::TestTask.new do |t|
+  t.test_files = FileList['test/**/*.rb']
+end
+
+
+# copies galaxy tool's files to local galaxy installation
+task :copy_to_galaxy do
+  cp 'bin/BioAID_ProteinDiscovery.xml', '/home/kostas/local/galaxy-dist/tools/taverna_tools'
+  cp 'bin/BioAID_ProteinDiscovery.rb', '/home/kostas/local/galaxy-dist/tools/taverna_tools'
+end

data/bin/workflow_to_galaxy.rb

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+#!/usr/bin/env ruby
+
+require 'rubygems'
+require 'optparse'
+require 't2flow/model.rb'
+require 't2flow/parser.rb'
+require 'cgi'
+require 'myexperiment-rest'
+require 'workflow-to-galaxy'
+
+include MyExperimentREST
+include Generator
+
+
+# Populates and returns a _TavernaWorkflow_ object (same as in
+# myexperiment-rest) from a local t2flow file.
+def populate_taverna_workflow_from_t2flow(t2flow)
+  t2flow_file = File.new(t2flow, "r")
+  parsed_t2flow = T2Flow::Parser.new.parse(t2flow_file)
+
+  wkf_title = parsed_t2flow.name
+  wkf_descr = parsed_t2flow.main.annotations.descriptions[0]    # gets only the first
+  wkf_sources = []
+  parsed_t2flow.main.sources.each do |s|
+    wkf_sources << TavernaIOData.new(s.name, 
+                                     s.descriptions ? CGI.escapeHTML(s.descriptions.to_s) : [],
+                                     s.example_values ? s.example_values : [])
+  end
+  wkf_sinks = []
+  parsed_t2flow.main.sinks.each do |s|
+    wkf_sinks << TavernaIOData.new(s.name,
+                                   s.descriptions ? CGI.escapeHTML(s.descriptions.to_s) : [],
+                                   s.example_values ? s.example_values : [])
+  end
+
+  workflow = TavernaWorkflow.new(TavernaWorkflow::T2_FLOW, t2flow, wkf_title, wkf_descr, wkf_sources, wkf_sinks)
+
+end
+
+
+# Set up and parse arguments
+out_file = ""
+t2_server = ""
+options = {}
+opts = OptionParser.new do |opt|
+  opt.banner = "Usage: workflow_to_galaxy [options] <myExperiement-workflow> | <t2flow-file>"
+  opt.separator ""
+  opt.separator "Generates a Galaxy tool (a UI xml definition plus a script) for the "
+  opt.separator "specified Taverna2 workflow, where <myExperiment-workflow> is "
+  opt.separator "the full URL of the workflow in the myExperiment website. Alternatively "
+  opt.separator "a t2flow file can be passed for workflows not in myExperiment. Available "
+  opt.separator "options are:"
+
+  opt.on("-o OUTPUT", "--output=OUTPUT", "The file name(s) of the generated tool. " +
+    "If it is not specified then the workflow's name will be used.") do |val|
+    out_file = val if val != nil
+  end
+
+  opt.on("-s SERVER", "--server=SERVER", "The taverna server that the script will request execution from. " +
+    "If it is not specified then 'http://localhost:8980/taverna-server' will be used.") do |val|
+    t2_server = val if val != nil
+  end
+
+  opt.on("-t", "--t2flow", "The workflow is a t2flow file. ") do
+    options[:t2flow] = true
+  end
+end
+
+opts.parse!
+
+# Read and check workflow URL or file
+url = ARGV.shift
+if url == nil
+  puts opts
+  exit 1
+end
+
+# Object to store the workflow object
+wkf_data = nil
+
+if options[:t2flow]
+  # Parse local t2flow file -- a _Taverna_Workflow_ object is returned
+  wkf_data = populate_taverna_workflow_from_t2flow(url)
+else
+  # Get workflow data from myexperiment -- a _Taverna_Workflow_ object is returned
+  wkf_data = Workflows.new.read(url)
+end
+
+# Set output files
+if out_file != ""
+  xml_file = "#{out_file}.xml"
+  script_file = "#{out_file}.rb"
+else
+  xml_file = "#{wkf_data.title}".gsub(/\W/, '') + ".xml"
+  script_file = "#{wkf_data.title}".gsub(/\W/, '') + ".rb"
+end
+
+# Set taverna server if not specified
+t2_server = "http://localhost:8980/taverna-server"  if t2_server == ""
+
+
+
+# Generate Galaxy tool's files
+xml_file_ob = File.open(xml_file, "w")
+generate_xml(wkf_data, xml_file, xml_file_ob)
+xml_file_ob.close
+
+script_file_ob = File.open(script_file, "w")
+generate_script(wkf_data, t2_server, script_file_ob)
+script_file_ob.close

data/doc/rdoc/classes/Generator.html

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+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html 
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <title>Module: Generator</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+
+  function toggleCode( id ) {
+    if ( document.getElementById )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+
+    elemStyle = elem.style;
+    
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+
+    return true;
+  }
+  
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  
+  // ]]>
+  </script>
+
+</head>
+<body>
+
+
+
+    <div id="classHeader">
+        <table class="header-table">
+        <tr class="top-aligned-row">
+          <td><strong>Module</strong></td>
+          <td class="class-name-in-header">Generator</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../files/lib/workflow-to-galaxy/generator_rb.html">
+                lib/workflow-to-galaxy/generator.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+
+        </table>
+    </div>
+  <!-- banner header -->
+
+  <div id="bodyContent">
+
+
+
+  <div id="contextContent">
+
+    <div id="description">
+      <p>
+The <a href="Generator.html">Generator</a> module contains two public
+methods that generate a Galaxy&#8216;s tool XML and script files
+</p>
+
+    </div>
+
+
+   </div>
+
+    <div id="method-list">
+      <h3 class="section-bar">Methods</h3>
+
+      <div class="name-list">
+      <a href="#M000002">generate_script</a>&nbsp;&nbsp;
+      <a href="#M000001">generate_xml</a>&nbsp;&nbsp;
+      </div>
+    </div>
+
+  </div>
+
+
+    <!-- if includes -->
+
+    <div id="section">
+
+
+
+
+
+      
+
+
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Instance methods</h3>
+
+      <div id="method-M000002" class="method-detail">
+        <a name="M000002"></a>
+
+        <div class="method-heading">
+          <a href="#M000002" class="method-signature">
+          <span class="method-name">Generator.generate_script(my_exp_rest, t2_server, script_file) &rarr; nil<br />
+</span>
+          </a>
+        </div>
+      
+        <div class="method-description">
+          <p>
+Generates the Galaxy tool&#8216;s script file responsible for talking to
+the taverna server
+</p>
+<dl>
+<dt><tt>my_exp_rest</tt></dt><dd>a <em>Workflow</em> object as returned from
+<em>MyExperimentREST.ReadWorkflow.new(url)</em>
+
+</dd>
+<dt><tt>t2_server</tt></dt><dd>a string containing the URL of the taverna 2 server
+
+</dd>
+<dt><tt>script_out</tt></dt><dd>the file handler to write the generated script code
+
+</dd>
+</dl>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000002-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000002-source">
+<pre>
+     <span class="ruby-comment cmt"># File lib/workflow-to-galaxy/generator.rb, line 490</span>
+490:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">generate_script</span>(<span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">t2_server</span>, <span class="ruby-identifier">script_out</span>)
+491:     <span class="ruby-identifier">script_preample</span>(<span class="ruby-identifier">script_out</span>)
+492:     <span class="ruby-identifier">script_util_methods</span>(<span class="ruby-identifier">script_out</span>)
+493:     <span class="ruby-identifier">script_create_t2_run</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">t2_server</span>)
+494:     <span class="ruby-identifier">script_init_inputs</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>)
+495:     <span class="ruby-identifier">script_start_run</span>(<span class="ruby-identifier">script_out</span>)
+496:     <span class="ruby-identifier">script_get_outputs</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>)
+497:     <span class="ruby-identifier">script_finish_run</span>(<span class="ruby-identifier">script_out</span>)
+498:   <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+
+      <div id="method-M000001" class="method-detail">
+        <a name="M000001"></a>
+
+        <div class="method-heading">
+          <a href="#M000001" class="method-signature">
+          <span class="method-name">Generator.generate_xml(my_exp_rest, xml_file) &rarr; nil<br />
+</span>
+          </a>
+        </div>
+      
+        <div class="method-description">
+          <p>
+Generates the Galaxy tool&#8216;s xml file responsible for the UI.
+</p>
+<dl>
+<dt>+t2_workflow+</dt><dd>a <em>Workflow</em> object as returned from
+<em>MyExperimentREST::Workflows.new.read(url)</em>
+
+</dd>
+<dt><tt>xml_file</tt></dt><dd>a string containing the name of the generated XML file
+
+</dd>
+<dt><tt>xml_out</tt></dt><dd>the file handler to write the generated XML tags
+
+</dd>
+</dl>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000001-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000001-source">
+<pre>
+     <span class="ruby-comment cmt"># File lib/workflow-to-galaxy/generator.rb, line 471</span>
+471:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">generate_xml</span>(<span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">xml_file</span>, <span class="ruby-identifier">xml_out</span>)
+472:     <span class="ruby-identifier">tool_begin_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">title</span>)
+473:     <span class="ruby-identifier">command_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">xml_file</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-value str">'.xml'</span>, <span class="ruby-value str">'.rb'</span>))
+474:     <span class="ruby-identifier">inputs_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">inputs</span>)
+475:     <span class="ruby-identifier">outputs_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">outputs</span>)
+476:     <span class="ruby-identifier">help_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>)
+477:     <span class="ruby-identifier">tool_end_tag</span>(<span class="ruby-identifier">xml_out</span>)
+478:   <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+
+
+    </div>
+
+
+  </div>
+
+
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+
+</body>
+</html>