workflow-to-galaxy 0.3.1 → 0.3.3
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- data/CHANGES +16 -2
- data/README +1 -1
- data/Rakefile +1 -1
- data/bin/workflow_to_galaxy.rb +7 -7
- data/doc/rdoc/CHANGES.html +30 -2
- data/doc/rdoc/LICENSE.html +2 -0
- data/doc/rdoc/README.html +3 -1
- data/doc/rdoc/String.html +203 -0
- data/doc/rdoc/WorkflowToGalaxy.html +2 -0
- data/doc/rdoc/WorkflowToGalaxy/GalaxyTool.html +33 -24
- data/doc/rdoc/WorkflowToGalaxy/Workflows.html +2 -0
- data/doc/rdoc/created.rid +5 -5
- data/doc/rdoc/index.html +5 -1
- data/doc/rdoc/lib/workflow-to-galaxy/galaxy_rb.html +1 -1
- data/doc/rdoc/lib/workflow-to-galaxy_rb.html +1 -1
- data/lib/workflow-to-galaxy.rb +14 -0
- data/lib/workflow-to-galaxy/galaxy.rb +37 -23
- metadata +5 -5
- data/bin/Fetch_PDB_flatfile_from_RCSB_server.xml +0 -0
data/CHANGES
CHANGED
@@ -1,8 +1,22 @@
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= Changes log for the Taverna-Galaxy Gem
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== Version 0.3.3
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* Multiline output examples are now displayed better in HTML/Galaxy (similar to inputs)
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* Updated wkf 74 test
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* Fixed default values for output files and taverna server
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* Added an optional parameter (:response) to the config in case we already have the myExp wkf
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- was needed by myExperiment in order to call the myExp REST API beforehand for auth
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== Version 0.3.2
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* Automatic filename creation is more robust (all special chars are removed)
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* More workflow tests
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== Version 0.3.1
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-
*
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-
* For safety default
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* Used semver formally (taged: v0.3.1 semver)
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* For safety default wkf title substitutes ' ' with '_'
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* Extended workflow tests
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== Version 0.3.0
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data/README
CHANGED
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Authors:: Konstantinos Karasavvas
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-
Gem Version:: 0.3.
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Gem Version:: 0.3.3
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Contact:: mailto:kostas.karasavvas@nbic.nl
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Licence:: MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
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Copyright:: (c) 2010 Netherlands Bioinformatics Centre, The Netherlands
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data/Rakefile
CHANGED
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spec = Gem::Specification.new do |s|
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s.name = 'workflow-to-galaxy'
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-
s.version = '0.3.
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s.version = '0.3.3'
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s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
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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).'
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s.description = s.summary
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data/bin/workflow_to_galaxy.rb
CHANGED
@@ -9,8 +9,8 @@ include WorkflowToGalaxy
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# Set up and parse arguments
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-
out_file =
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-
t2_server =
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out_file = nil
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t2_server = nil
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options = {}
|
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opts = OptionParser.new do |opt|
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opt.banner = "Usage: workflow_to_galaxy [options] <myExperiment-workflow> | <t2flow-file>"
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@@ -49,7 +49,7 @@ if url == nil
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end
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# Set taverna server if not specified
|
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-
t2_server ||=
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t2_server ||= 'http://localhost:8080/taverna-server'
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#if options[:t2flow]
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@@ -59,7 +59,7 @@ t2_server ||= "http://localhost:8080/taverna-server"
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#end
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# create file handlers
|
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-
if out_file !=
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if out_file != nil
|
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xml_out = open("#{out_file}.xml", "w")
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rb_out = open("#{out_file}.rb", "w")
|
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end
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@@ -68,7 +68,7 @@ end
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# create generator or wrapper (could have used url for t2flow key to avoid
|
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# if/else but future sources would still need them)
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if options[:t2flow]
|
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-
if out_file !=
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if out_file != nil
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wkf = GalaxyTool.new(:wkf_source => Workflows::T2FLOW,
|
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:params => {:t2_server => t2_server,
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:t2flow => url,
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:t2flow => url } )
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end
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else
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-
if out_file !=
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if out_file != nil
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wkf = GalaxyTool.new(:wkf_source => Workflows::MYEXPERIMENT_TAVERNA2,
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:params => {:t2_server => t2_server,
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:url => url,
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end
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# close file handlers
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-
if out_file !=
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if out_file != nil
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xml_out.close
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rb_out.close
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end
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data/doc/rdoc/CHANGES.html
CHANGED
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<li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
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<li><a href="./String.html">String</a></li>
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</ul>
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<div id="no-class-search-results" style="display: none;">No matching classes.</div>
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</div>
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<h1>Changes log for the Taverna-Galaxy Gem</h1>
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<h2>Version 0.3.3</h2>
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<ul><li>
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<p>Multiline output examples are now displayed better in HTML/Galaxy (similar
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+
to inputs)</p>
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</li><li>
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<p>Updated wkf 74 test</p>
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</li><li>
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<p>Fixed default values for output files and taverna server</p>
|
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</li><li>
|
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<p>Added an optional parameter (:response) to the config in case we already
|
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have the myExp wkf</p>
|
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<ul><li>
|
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<p>was needed by myExperiment in order to call the myExp REST API beforehand
|
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for auth</p>
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</li></ul>
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</li></ul>
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<h2>Version 0.3.2</h2>
|
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<ul><li>
|
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<p>Automatic filename creation is more robust (all special chars are removed)</p>
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</li><li>
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<p>More workflow tests</p>
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</li></ul>
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<h2>Version 0.3.1</h2>
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<ul><li>
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-
<p>
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<p>Used semver formally (taged: v0.3.1 semver)</p>
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</li><li>
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<p>For safety default wkf title substitutes ‘ ’ with ‘_’</p>
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</li><li>
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-
<p>
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<p>Extended workflow tests</p>
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</li></ul>
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<h2>Version 0.3.0</h2>
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data/doc/rdoc/LICENSE.html
CHANGED
data/doc/rdoc/README.html
CHANGED
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<li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
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<li><a href="./String.html">String</a></li>
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</ul>
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<div id="no-class-search-results" style="display: none;">No matching classes.</div>
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</div>
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<p>Konstantinos Karasavvas</p>
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</td></tr><tr><td class="rdoc-term"><p>Gem Version</p></td>
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<td>
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-
<p>0.3.
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<p>0.3.3</p>
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</td></tr><tr><td class="rdoc-term"><p>Contact</p></td>
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<td>
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<p><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a></p>
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
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<title>Class: String</title>
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<link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
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<script src="./js/jquery.js" type="text/javascript" charset="utf-8"></script>
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<script src="./js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
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<script src="./js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
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<script src="./js/darkfish.js" type="text/javascript" charset="utf-8"></script>
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</head>
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<body id="top" class="class">
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<div id="metadata">
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<div id="home-metadata">
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<div id="home-section" class="section">
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<h3 class="section-header">
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<a href="./index.html">Home</a>
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<a href="./index.html#classes">Classes</a>
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<a href="./index.html#methods">Methods</a>
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</h3>
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</div>
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</div>
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<div id="file-metadata">
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<div id="file-list-section" class="section">
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<h3 class="section-header">In Files</h3>
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<div class="section-body">
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<ul>
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<li><a href="./lib/workflow-to-galaxy_rb.html?TB_iframe=true&height=550&width=785"
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class="thickbox" title="lib/workflow-to-galaxy.rb">lib/workflow-to-galaxy.rb</a></li>
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</ul>
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</div>
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</div>
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</div>
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<div id="class-metadata">
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<!-- Parent Class -->
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<div id="parent-class-section" class="section">
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<h3 class="section-header">Parent</h3>
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<p class="link">Object</p>
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</div>
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<!-- Method Quickref -->
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<div id="method-list-section" class="section">
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<h3 class="section-header">Methods</h3>
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<ul class="link-list">
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<li><a href="#method-i-to_filename">#to_filename</a></li>
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</ul>
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</div>
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</div>
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<div id="project-metadata">
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<div id="fileindex-section" class="section project-section">
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<h3 class="section-header">Files</h3>
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<ul>
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<li class="file"><a href="./CHANGES.html">CHANGES</a></li>
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<li class="file"><a href="./LICENSE.html">LICENSE</a></li>
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<li class="file"><a href="./README.html">README</a></li>
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</ul>
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</div>
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<div id="classindex-section" class="section project-section">
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<h3 class="section-header">Class/Module Index
|
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<span class="search-toggle"><img src="./images/find.png"
|
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height="16" width="16" alt="[+]"
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title="show/hide quicksearch" /></span></h3>
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<form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
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<fieldset>
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<legend>Quicksearch</legend>
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<input type="text" name="quicksearch" value=""
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class="quicksearch-field" />
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</fieldset>
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</form>
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<ul class="link-list">
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<li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
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<li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
|
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|
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<li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
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|
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<li><a href="./String.html">String</a></li>
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|
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</ul>
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<div id="no-class-search-results" style="display: none;">No matching classes.</div>
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</div>
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</div>
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</div>
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<div id="documentation">
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<h1 class="class">String</h1>
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<div id="description" class="description">
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<p>Add methods to the <a href="String.html">String</a> class to operate on
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file paths.</p>
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</div><!-- description -->
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<div id="5Buntitled-5D" class="documentation-section">
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<!-- Methods -->
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<div id="public-instance-method-details" class="method-section section">
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<h3 class="section-header">Public Instance Methods</h3>
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|
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|
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<div id="to_filename-method" class="method-detail ">
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<a name="method-i-to_filename"></a>
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|
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<div class="method-heading">
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<span class="method-callseq">to_filename → string</span>
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|
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<div class="method-description">
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<p>Returns a new <a href="String.html">String</a> with spaces substituted by
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underscores and removes all special characters.</p>
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<div class="method-source-code" id="to_filename-source">
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<pre>
|
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<span class="ruby-comment"># File lib/workflow-to-galaxy.rb, line 17</span>
|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">to_filename</span>
|
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<span class="ruby-keyword">self</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-regexp">/ /</span>, <span class="ruby-string">'_'</span>).<span class="ruby-identifier">gsub</span>(<span class="ruby-regexp">/[^A-Za-z0-9_]/</span>, <span class="ruby-string">''</span>)
|
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<span class="ruby-keyword">end</span></pre>
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</div><!-- to_filename-source -->
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</div>
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</div><!-- to_filename-method -->
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</div><!-- public-instance-method-details -->
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<span class="ruby-keyword">if</span>(<span class="ruby-identifier">config</span>[<span class="ruby-value">:wkf_source</span>] <span class="ruby-operator">==</span> <span class="ruby-constant">Workflows</span><span class="ruby-operator">::</span><span class="ruby-constant">MYEXPERIMENT_TAVERNA2</span>)
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<span class="ruby-comment"># for all to see...</span>
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<span class="ruby-ivar">@wkf_object</span> = <span class="ruby-identifier">config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:response</span>]
|
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<span class="ruby-comment"># Get workflow data from myexperiment -- a _MyExperimentWorkflow_ object is returned</span>
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<span class="ruby-ivar">@wkf_object</span> = <span class="ruby-constant">MyExperimentREST</span><span class="ruby-operator">::</span><span class="ruby-constant">Workflow</span>.<span class="ruby-identifier">from_uri</span>(<span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:url</span>])
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<span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">e</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-string">"Problem acquiring workflow data from myExperiment!\n"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">e</span>
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<span class="ruby-comment">#
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<span class="ruby-
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<span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">e</span>
|
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<span class="ruby-identifier">raise</span> <span class="ruby-string">"Problem acquiring workflow data from t2flow file!\n"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">e</span>
|
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|
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<span class="ruby-keyword">end</span>
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<span class="ruby-comment"># TODO: check and add auth stuff -- even more unsafe with session cookies</span>
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<span class="ruby-comment"># since the myexp username/passwd will be saved in the galaxy ruby script</span>
|
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<span class="ruby-comment"># for all to see...</span>
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<span class="ruby-keyword">begin</span>
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<span class="ruby-comment"># Get workflow data from myexperiment -- a _MyExperimentWorkflow_ object is returned</span>
|
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|
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<span class="ruby-ivar">@wkf_object</span> = <span class="ruby-constant">MyExperimentREST</span><span class="ruby-operator">::</span><span class="ruby-constant">Workflow</span>.<span class="ruby-identifier">from_uri</span>(<span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:url</span>])
|
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<span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">e</span>
|
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|
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<span class="ruby-identifier">raise</span> <span class="ruby-string">"Problem acquiring workflow data from myExperiment!\n"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">e</span>
|
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|
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<span class="ruby-keyword">end</span>
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|
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|
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<span class="ruby-keyword">elsif</span>(<span class="ruby-identifier">config</span>[<span class="ruby-value">:wkf_source</span>] <span class="ruby-operator">==</span> <span class="ruby-constant">Workflows</span><span class="ruby-operator">::</span><span class="ruby-constant">T2FLOW</span>)
|
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|
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|
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|
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<span class="ruby-keyword">begin</span>
|
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|
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<span class="ruby-comment"># Get workflow data from t2flow file -- a _MyExperimentWorkflow_ object is returned</span>
|
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|
+
<span class="ruby-ivar">@wkf_object</span> = <span class="ruby-identifier">populate_taverna_workflow_from_t2flow</span>(<span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:t2flow</span>])
|
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<span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">e</span>
|
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|
+
<span class="ruby-identifier">raise</span> <span class="ruby-string">"Problem acquiring workflow data from t2flow file!\n"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">e</span>
|
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|
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<span class="ruby-keyword">end</span>
|
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|
+
|
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|
+
<span class="ruby-keyword">else</span>
|
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|
+
<span class="ruby-identifier">raise</span> <span class="ruby-string">"No such workflow source supported!"</span>
|
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|
+
<span class="ruby-keyword">end</span>
|
291
300
|
<span class="ruby-keyword">end</span>
|
292
301
|
|
293
302
|
<span class="ruby-comment"># if an xml_out file handler was not given provide one with the title as the value</span>
|
294
303
|
<span class="ruby-keyword">if</span> <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:xml_out</span>]
|
295
304
|
<span class="ruby-identifier">generate_xml</span>(<span class="ruby-ivar">@wkf_object</span>, <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:xml_out</span>])
|
296
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|
<span class="ruby-keyword">else</span>
|
297
|
-
<span class="ruby-identifier">xml_out</span> = <span class="ruby-identifier">open</span>(<span class="ruby-ivar">@wkf_object</span>.<span class="ruby-identifier">title</span>.<span class="ruby-identifier">
|
306
|
+
<span class="ruby-identifier">xml_out</span> = <span class="ruby-identifier">open</span>(<span class="ruby-ivar">@wkf_object</span>.<span class="ruby-identifier">title</span>.<span class="ruby-identifier">to_filename</span> <span class="ruby-operator">+</span> <span class="ruby-string">".xml"</span>, <span class="ruby-string">"w"</span>)
|
298
307
|
<span class="ruby-identifier">generate_xml</span>(<span class="ruby-ivar">@wkf_object</span>, <span class="ruby-identifier">xml_out</span>)
|
299
308
|
<span class="ruby-identifier">xml_out</span>.<span class="ruby-identifier">close</span>
|
300
309
|
<span class="ruby-keyword">end</span>
|
@@ -303,7 +312,7 @@ the workflow object that will be used to generate the galaxy tool</p>
|
|
303
312
|
<span class="ruby-keyword">if</span> <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:rb_out</span>]
|
304
313
|
<span class="ruby-identifier">generate_rb</span>(<span class="ruby-ivar">@wkf_object</span>, <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:rb_out</span>], <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:t2_server</span>])
|
305
314
|
<span class="ruby-keyword">else</span>
|
306
|
-
<span class="ruby-identifier">rb_out</span> = <span class="ruby-identifier">open</span>(<span class="ruby-ivar">@wkf_object</span>.<span class="ruby-identifier">title</span>.<span class="ruby-identifier">
|
315
|
+
<span class="ruby-identifier">rb_out</span> = <span class="ruby-identifier">open</span>(<span class="ruby-ivar">@wkf_object</span>.<span class="ruby-identifier">title</span>.<span class="ruby-identifier">to_filename</span> <span class="ruby-operator">+</span> <span class="ruby-string">".rb"</span>, <span class="ruby-string">"w"</span>)
|
307
316
|
<span class="ruby-identifier">generate_rb</span>(<span class="ruby-ivar">@wkf_object</span>, <span class="ruby-identifier">rb_out</span>, <span class="ruby-ivar">@config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:t2_server</span>])
|
308
317
|
<span class="ruby-identifier">rb_out</span>.<span class="ruby-identifier">close</span>
|
309
318
|
<span class="ruby-keyword">end</span>
|
data/doc/rdoc/created.rid
CHANGED
@@ -1,7 +1,7 @@
|
|
1
|
-
|
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|
-
lib/workflow-to-galaxy.rb
|
1
|
+
Mon, 16 Jan 2012 16:21:48 +0100
|
2
|
+
lib/workflow-to-galaxy.rb Tue, 15 Nov 2011 15:48:17 +0100
|
3
3
|
lib/workflow-to-galaxy/constants.rb Mon, 10 Oct 2011 14:10:32 +0200
|
4
|
-
lib/workflow-to-galaxy/galaxy.rb
|
4
|
+
lib/workflow-to-galaxy/galaxy.rb Mon, 16 Jan 2012 14:03:11 +0100
|
5
5
|
LICENSE Tue, 26 Jul 2011 16:35:55 +0200
|
6
|
-
README Thu,
|
7
|
-
CHANGES
|
6
|
+
README Thu, 12 Jan 2012 14:58:21 +0100
|
7
|
+
CHANGES Mon, 16 Jan 2012 16:21:32 +0100
|
data/doc/rdoc/index.html
CHANGED
@@ -29,7 +29,7 @@
|
|
29
29
|
<p>Konstantinos Karasavvas</p>
|
30
30
|
</td></tr><tr><td class="rdoc-term"><p>Gem Version</p></td>
|
31
31
|
<td>
|
32
|
-
<p>0.3.
|
32
|
+
<p>0.3.3</p>
|
33
33
|
</td></tr><tr><td class="rdoc-term"><p>Contact</p></td>
|
34
34
|
<td>
|
35
35
|
<p><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a></p>
|
@@ -131,6 +131,8 @@ href="http://semver.org/.">semver.org/.</a></p>
|
|
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|
|
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|
<li class="module"><a href="WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
|
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|
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|
+
<li class="class"><a href="String.html">String</a></li>
|
135
|
+
|
134
136
|
</ul>
|
135
137
|
|
136
138
|
<h2 id="methods">Methods</h2>
|
@@ -140,6 +142,8 @@ href="http://semver.org/.">semver.org/.</a></p>
|
|
140
142
|
|
141
143
|
<li><a href="WorkflowToGalaxy/GalaxyTool.html#method-i-generate">#generate — WorkflowToGalaxy::GalaxyTool</a></li>
|
142
144
|
|
145
|
+
<li><a href="String.html#method-i-to_filename">#to_filename — String</a></li>
|
146
|
+
|
143
147
|
</ul>
|
144
148
|
|
145
149
|
<div id="validator-badges">
|
data/lib/workflow-to-galaxy.rb
CHANGED
@@ -5,3 +5,17 @@ require 'workflow-to-galaxy/constants'
|
|
5
5
|
module WorkflowToGalaxy # TODO rename to WorkflowWrappers?
|
6
6
|
|
7
7
|
end
|
8
|
+
|
9
|
+
# Add methods to the String class to operate on file paths.
|
10
|
+
class String
|
11
|
+
|
12
|
+
# :call-seq:
|
13
|
+
# str.to_filename -> string
|
14
|
+
#
|
15
|
+
# Returns a new String with spaces substituted by underscores and
|
16
|
+
# removes all special characters.
|
17
|
+
def to_filename
|
18
|
+
self.gsub(/ /, '_').gsub(/[^A-Za-z0-9_]/, '')
|
19
|
+
end
|
20
|
+
|
21
|
+
end
|
@@ -28,6 +28,7 @@ module WorkflowToGalaxy
|
|
28
28
|
# :url (the myexperiment workflow URL)
|
29
29
|
# :xml_out (the file handle for the generated xml -- optional)
|
30
30
|
# :rb_out (the file handle for the generated rb -- optional)
|
31
|
+
# :response (the response from myExperiment if already obtained -- optional)
|
31
32
|
#
|
32
33
|
# :params (a hash with the following parameters -- T2FLOW)
|
33
34
|
# :t2flow (the file name and path)
|
@@ -54,6 +55,8 @@ module WorkflowToGalaxy
|
|
54
55
|
|
55
56
|
# Galaxy's XML tool tag
|
56
57
|
def tool_begin_tag(out, name)
|
58
|
+
# wkf title is used for id but spaces are changed to underscores
|
59
|
+
# TODO: delete other special characters!!
|
57
60
|
out.write("<tool id=\"#{name.gsub(/ /, '_')}_id\" name=\"#{name}\">\n")
|
58
61
|
end
|
59
62
|
|
@@ -217,7 +220,10 @@ module WorkflowToGalaxy
|
|
217
220
|
if o.examples.size >= 1
|
218
221
|
out.write "Examples include:\n\n"
|
219
222
|
o.examples.each do |ex|
|
220
|
-
|
223
|
+
# We could substitute them with with 
 that works for HTML (e.g. wkf 1180)
|
224
|
+
# But if an example input is truly multiline then input descr. will
|
225
|
+
# display them all as separate inputs...
|
226
|
+
out.write " - " + ex.to_s.gsub(/[\n]/, '
 - ') + "\n"
|
221
227
|
end
|
222
228
|
end
|
223
229
|
out.write "\n"
|
@@ -278,6 +284,7 @@ module WorkflowToGalaxy
|
|
278
284
|
|
279
285
|
# Galaxy's script utility methods
|
280
286
|
# TODO: use ruby's flatten instead of our own !!!
|
287
|
+
# TODO: add_to_zip_file does not work for multiple files -- with new API??
|
281
288
|
def script_util_methods(out)
|
282
289
|
|
283
290
|
out.write <<'UTIL_METHODS'
|
@@ -574,38 +581,45 @@ START_RUN
|
|
574
581
|
#
|
575
582
|
def generate
|
576
583
|
|
577
|
-
|
578
|
-
if(config[:wkf_source] == Workflows::MYEXPERIMENT_TAVERNA2)
|
584
|
+
if(config[:params][:response])
|
579
585
|
|
580
|
-
|
581
|
-
# since the myexp username/passwd will be saved in the galaxy ruby script
|
582
|
-
# for all to see...
|
586
|
+
@wkf_object = config[:params][:response]
|
583
587
|
|
584
|
-
|
585
|
-
# Get workflow data from myexperiment -- a _MyExperimentWorkflow_ object is returned
|
586
|
-
@wkf_object = MyExperimentREST::Workflow.from_uri(@config[:params][:url])
|
587
|
-
rescue Exception => e
|
588
|
-
raise "Problem acquiring workflow data from myExperiment!\n" + e
|
589
|
-
end
|
588
|
+
else
|
590
589
|
|
591
|
-
|
590
|
+
# check the type of workflow source and acquire the appropriate data
|
591
|
+
if(config[:wkf_source] == Workflows::MYEXPERIMENT_TAVERNA2)
|
592
592
|
|
593
|
-
|
594
|
-
#
|
595
|
-
|
596
|
-
rescue Exception => e
|
597
|
-
raise "Problem acquiring workflow data from t2flow file!\n" + e
|
598
|
-
end
|
593
|
+
# TODO: check and add auth stuff -- even more unsafe with session cookies
|
594
|
+
# since the myexp username/passwd will be saved in the galaxy ruby script
|
595
|
+
# for all to see...
|
599
596
|
|
600
|
-
|
601
|
-
|
597
|
+
begin
|
598
|
+
# Get workflow data from myexperiment -- a _MyExperimentWorkflow_ object is returned
|
599
|
+
@wkf_object = MyExperimentREST::Workflow.from_uri(@config[:params][:url])
|
600
|
+
rescue Exception => e
|
601
|
+
raise "Problem acquiring workflow data from myExperiment!\n" + e
|
602
|
+
end
|
603
|
+
|
604
|
+
elsif(config[:wkf_source] == Workflows::T2FLOW)
|
605
|
+
|
606
|
+
begin
|
607
|
+
# Get workflow data from t2flow file -- a _MyExperimentWorkflow_ object is returned
|
608
|
+
@wkf_object = populate_taverna_workflow_from_t2flow(@config[:params][:t2flow])
|
609
|
+
rescue Exception => e
|
610
|
+
raise "Problem acquiring workflow data from t2flow file!\n" + e
|
611
|
+
end
|
612
|
+
|
613
|
+
else
|
614
|
+
raise "No such workflow source supported!"
|
615
|
+
end
|
602
616
|
end
|
603
617
|
|
604
618
|
# if an xml_out file handler was not given provide one with the title as the value
|
605
619
|
if @config[:params][:xml_out]
|
606
620
|
generate_xml(@wkf_object, @config[:params][:xml_out])
|
607
621
|
else
|
608
|
-
xml_out = open(@wkf_object.title.
|
622
|
+
xml_out = open(@wkf_object.title.to_filename + ".xml", "w")
|
609
623
|
generate_xml(@wkf_object, xml_out)
|
610
624
|
xml_out.close
|
611
625
|
end
|
@@ -614,7 +628,7 @@ START_RUN
|
|
614
628
|
if @config[:params][:rb_out]
|
615
629
|
generate_rb(@wkf_object, @config[:params][:rb_out], @config[:params][:t2_server])
|
616
630
|
else
|
617
|
-
rb_out = open(@wkf_object.title.
|
631
|
+
rb_out = open(@wkf_object.title.to_filename + ".rb", "w")
|
618
632
|
generate_rb(@wkf_object, rb_out, @config[:params][:t2_server])
|
619
633
|
rb_out.close
|
620
634
|
end
|
metadata
CHANGED
@@ -1,13 +1,13 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: workflow-to-galaxy
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
hash:
|
4
|
+
hash: 21
|
5
5
|
prerelease:
|
6
6
|
segments:
|
7
7
|
- 0
|
8
8
|
- 3
|
9
|
-
-
|
10
|
-
version: 0.3.
|
9
|
+
- 3
|
10
|
+
version: 0.3.3
|
11
11
|
platform: ruby
|
12
12
|
authors:
|
13
13
|
- Kostas Karasavvas
|
@@ -15,7 +15,7 @@ autorequire:
|
|
15
15
|
bindir: bin
|
16
16
|
cert_chain: []
|
17
17
|
|
18
|
-
date:
|
18
|
+
date: 2012-01-16 00:00:00 Z
|
19
19
|
dependencies:
|
20
20
|
- !ruby/object:Gem::Dependency
|
21
21
|
name: myexperiment-rest
|
@@ -97,7 +97,6 @@ files:
|
|
97
97
|
- CHANGES
|
98
98
|
- Rakefile
|
99
99
|
- bin/workflow_to_galaxy.rb
|
100
|
-
- bin/Fetch_PDB_flatfile_from_RCSB_server.xml
|
101
100
|
- lib/workflow-to-galaxy/galaxy.rb
|
102
101
|
- lib/workflow-to-galaxy/constants.rb
|
103
102
|
- lib/workflow-to-galaxy.rb
|
@@ -122,6 +121,7 @@ files:
|
|
122
121
|
- doc/rdoc/lib/workflow-to-galaxy/constants_rb.html
|
123
122
|
- doc/rdoc/created.rid
|
124
123
|
- doc/rdoc/CHANGES.html
|
124
|
+
- doc/rdoc/String.html
|
125
125
|
- doc/rdoc/images/find.png
|
126
126
|
- doc/rdoc/images/bug.png
|
127
127
|
- doc/rdoc/images/bullet_toggle_minus.png
|
File without changes
|