taverna-t2flow 0.4.4 → 0.4.5

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Files changed (15) hide show
  1. data/CHANGES.rdoc +4 -0
  2. data/README.rdoc +7 -8
  3. data/Rakefile +7 -4
  4. data/lib/t2flow/dot.rb +9 -0
  5. data/lib/t2flow/model.rb +11 -1
  6. data/lib/t2flow/parser.rb +12 -2
  7. data/lib/taverna-t2flow.rb +12 -0
  8. data/taverna-t2flow.gemspec +5 -4
  9. data/test/fixtures/image_to_tiff_migration_action.t2flow +277 -277
  10. data/test/run_tests.rb +5 -6
  11. data/test/test_bogus_workflows.rb +8 -7
  12. data/test/test_component_workflows.rb +8 -7
  13. data/test/test_helper.rb +9 -0
  14. data/test/test_starter_pack_workflows.rb +8 -7
  15. metadata +75 -89
data/CHANGES.rdoc CHANGED
@@ -1,5 +1,9 @@
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  = Changes log for the T2Flow Ruby Gem
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+ == Version 0.4.5
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+
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+ * Add a top-level include file that matches the gem name.
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+
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  == Version 0.4.4
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  * Fixed issue with flow control in nested workflows with no input ports.
data/README.rdoc CHANGED
@@ -4,7 +4,7 @@ Authors:: Finn Bacall, Robert Haines, Mannie Tagarira, David Withers
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  Contact:: mailto:support@mygrid.org.uk
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  URL:: http://www.taverna.org.uk/
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  Licence:: LGPL 3 (See LICENCE or http://www.gnu.org/licenses/lgpl.html)
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- Copyright:: (c) 2008-2012, University of Manchester, UK
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+ Copyright:: (c) 2008-2013, University of Manchester, UK
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  == Synopsis
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@@ -34,10 +34,10 @@ To install the Taverna 2 gem, type into your command prompt:
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  == Usage
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- To be able to generate at least a T2Flow model using the gem, you need to
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- include in your ruby code the following lines:
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- require "t2flow/model.rb"
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- require "t2flow/parser.rb"
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+ To be able to use this gem, you need to require the library:
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+ require 'taverna-t2flow'
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+
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+ === t2flow models
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  To generate the model you can then use the gem as follows:
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  foo = File.new("path/to/workflow/file", "r")
@@ -58,10 +58,9 @@ You can also interact with remote workflows.
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  foo = Uri.parse("xxxx://uri_to_workflow").read
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  bar = T2Flow::Parser.new.parse(foo)
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- To be enable you to draw images of the T2Flow, you need to include:
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- require "t2flow/dot.rb"
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+ === t2flow diagrams
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- To be able to use any functionality included in "t2flow/dot.rb", you need to
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+ To be able to use any diagram functionality included in thsi gem you need to
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  have GraphViz[http://www.graphviz.org/Download.php] installed on your system.
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  Once this package has been installed, you may use the gem to draw an image
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  showing the structure of the T2Flow as follows.
data/Rakefile CHANGED
@@ -1,8 +1,11 @@
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- # Copyright (c) 2012 The University of Manchester, UK.
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+ # Copyright (c) 2009-2013 The University of Manchester, UK.
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  #
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  # See LICENCE file for details.
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  #
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- # Author: Robert Haines
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+ # Authors: Finn Bacall
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+ # Robert Haines
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+ # David Withers
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+ # Mannie Tagarira
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  require 'rubygems'
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  require 'rake'
@@ -14,13 +17,13 @@ require 'jeweler'
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  task :default => [:test]
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- T2FLOW_GEM_VERSION = "0.4.4"
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+ T2FLOW_GEM_VERSION = "0.4.5"
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  Jeweler::Tasks.new do |s|
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  s.name = "taverna-t2flow"
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  s.version = T2FLOW_GEM_VERSION
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  s.authors = ["Finn Bacall", "Robert Haines", "David Withers", "Mannie Tagarira"]
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- s.email = ["finn.bacall@cs.man.ac.uk", "rhaines@manchester.ac.uk"]
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+ s.email = ["support@mygrid.org.uk"]
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  s.homepage = "http://www.taverna.org.uk/"
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  s.platform = Gem::Platform::RUBY
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  s.summary = "Support for interacting with Taverna 2 workflows."
data/lib/t2flow/dot.rb CHANGED
@@ -1,3 +1,12 @@
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+ # Copyright (c) 2009-2013 The University of Manchester, UK.
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+ #
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+ # See LICENCE file for details.
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+ #
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+ # Authors: Finn Bacall
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+ # Robert Haines
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+ # David Withers
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+ # Mannie Tagarira
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+
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  module T2Flow
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  # This class enables you to write the script will will be used by dot
data/lib/t2flow/model.rb CHANGED
@@ -1,4 +1,14 @@
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- # This is the module containing the T2Flow model implementation i.e. the model structure/definition and all its internals.
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+ # Copyright (c) 2009-2013 The University of Manchester, UK.
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+ #
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+ # See LICENCE file for details.
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+ #
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+ # Authors: Finn Bacall
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+ # Robert Haines
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+ # David Withers
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+ # Mannie Tagarira
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+ #
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+ # This is the module containing the T2Flow model implementation i.e. the
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+ # model structure/definition and all its internals.
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  module T2Flow # :nodoc:
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data/lib/t2flow/parser.rb CHANGED
@@ -1,5 +1,15 @@
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- require "libxml"
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- require "cgi"
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+ # Copyright (c) 2009-2013 The University of Manchester, UK.
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+ #
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+ # See LICENCE file for details.
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+ #
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+ # Authors: Finn Bacall
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+ # Robert Haines
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+ # David Withers
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+ # Mannie Tagarira
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+
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+ require 'rubygems'
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+ require 'libxml'
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+ require 'cgi'
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  module T2Flow
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data/lib/taverna-t2flow.rb ADDED
@@ -0,0 +1,12 @@
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+ # Copyright (c) 2009-2013 The University of Manchester, UK.
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+ #
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+ # See LICENCE file for details.
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+ #
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+ # Authors: Finn Bacall
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+ # Robert Haines
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+ # David Withers
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+ # Mannie Tagarira
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+
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+ require 't2flow/model'
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+ require 't2flow/parser'
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+ require 't2flow/dot'
data/taverna-t2flow.gemspec CHANGED
@@ -5,13 +5,13 @@
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  Gem::Specification.new do |s|
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  s.name = "taverna-t2flow"
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- s.version = "0.4.4"
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+ s.version = "0.4.5"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Finn Bacall", "Robert Haines", "David Withers", "Mannie Tagarira"]
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- s.date = "2013-02-06"
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+ s.date = "2013-03-14"
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  s.description = "This a gem developed by myGrid for the purpose of interacting with Taverna 2 workflows. An example use would be the image genaration for the model representing Taverna 2 workflows as used in myExperiment."
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- s.email = ["finn.bacall@cs.man.ac.uk", "rhaines@manchester.ac.uk"]
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+ s.email = ["support@mygrid.org.uk"]
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  s.extra_rdoc_files = [
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  "CHANGES.rdoc",
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  "LICENCE",
@@ -26,6 +26,7 @@ Gem::Specification.new do |s|
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  "lib/t2flow/dot.rb",
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  "lib/t2flow/model.rb",
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  "lib/t2flow/parser.rb",
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+ "lib/taverna-t2flow.rb",
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  "taverna-t2flow.gemspec",
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  "test/fixtures/1000.t2flow",
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  "test/fixtures/1001.t2flow",
@@ -51,7 +52,7 @@ Gem::Specification.new do |s|
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  s.homepage = "http://www.taverna.org.uk/"
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  s.rdoc_options = ["-N", "--tab-width=2", "--main=README.rdoc"]
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  s.require_paths = ["lib"]
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- s.rubygems_version = "1.8.24"
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+ s.rubygems_version = "1.8.21"
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  s.summary = "Support for interacting with Taverna 2 workflows."
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  s.test_files = ["test/run_tests.rb"]
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data/test/fixtures/image_to_tiff_migration_action.t2flow CHANGED
@@ -1,278 +1,278 @@
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- <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="16841f82-e1fe-4527-b7ef-411c4c59493b" role="top"><name>Image_to_tiff_migrat</name><inputPorts><port><name>from_uri</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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- <annotationAssertions>
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- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
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- <text>description</text>
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- </annotationBean>
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- <date>2012-11-16 16:22:56.977 UTC</date>
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- <creators />
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- <curationEventList />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- </annotationAssertions>
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- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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- <annotationAssertions>
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- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
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- <text>example</text>
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- </annotationBean>
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- <date>2012-11-16 16:22:43.712 UTC</date>
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- <creators />
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- <curationEventList />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- </annotationAssertions>
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- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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- <annotationAssertions>
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- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
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- <mimeType>text/rdf+n3</mimeType>
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- <content>[] &lt;http://scape-project.eu/pc/vocab/profiles#hasPortType&gt;
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- &lt;http://scape-project.eu/pc/vocab/profiles#FromURIPort&gt; .
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- </content>
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- </annotationBean>
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- <date>2012-11-19 15:53:49.250 UTC</date>
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- <creators />
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- <curationEventList />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- </annotationAssertions>
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- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></port><port><name>to_uri</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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- <annotationAssertions>
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- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
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- <mimeType>text/rdf+n3</mimeType>
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- <content>[] &lt;http://scape-project.eu/pc/vocab/profiles#hasPortType&gt;
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- &lt;http://scape-project.eu/pc/vocab/profiles#ToURIPort&gt; .
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- </content>
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- </annotationBean>
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- <date>2012-11-20 12:09:41.928 UTC</date>
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- <creators />
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- <curationEventList />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- </annotationAssertions>
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- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></port></inputPorts><outputPorts /><processors><processor><name>Tool</name><inputPorts><port><name>to_uri</name><depth>0</depth></port><port><name>from_uri</name><depth>0</depth></port></inputPorts><outputPorts /><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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- <annotationAssertions>
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- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
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- <mimeType>text/rdf+n3</mimeType>
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- <content>[] &lt;http://scape-project.eu/pc/vocab/profiles#hasDependency&gt;
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- &lt;http://scape-project.eu/pc/vocab/profiles#imagemagick-image2tiff&gt; .
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- </content>
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- </annotationBean>
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- <date>2012-11-20 12:17:37.420 UTC</date>
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- <creators />
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- <curationEventList />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- </annotationAssertions>
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- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap><map from="to_uri" to="to_uri" /><map from="from_uri" to="from_uri" /></inputMap><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
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- <mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
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- <mechanismName>default local</mechanismName>
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- <mechanismXML>&lt;?xml version="1.0" encoding="UTF-8"?&gt;&#xD;
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- &lt;localInvocation&gt;&lt;shellPrefix&gt;/bin/sh -c&lt;/shellPrefix&gt;&lt;linkCommand&gt;/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%&lt;/linkCommand&gt;&lt;/localInvocation&gt;&#xD;
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- </mechanismXML>
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- <externaltoolid>1c6b3cec-667d-4364-8a77-315a3b3c71f8</externaltoolid>
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- <useCaseDescription>
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- <usecaseid />
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- <description />
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- <command>convert %%from_uri%% tiff:%%to_uri%%</command>
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- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
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- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
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- <tags>
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- <string>from_uri</string>
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- <string>to_uri</string>
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- </tags>
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- <REs />
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- <queue__preferred />
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- <queue__deny />
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- <static__inputs />
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- <inputs>
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- <entry>
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- <string>to_uri</string>
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- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
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- <tag>to_uri</tag>
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- <file>false</file>
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- <tempFile>false</tempFile>
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- <binary>false</binary>
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- <charsetName>MacRoman</charsetName>
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- <forceCopy>false</forceCopy>
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- <list>false</list>
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- <concatenate>false</concatenate>
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- <mime />
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- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
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- </entry>
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- <entry>
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- <string>from_uri</string>
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- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
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- <tag>from_uri</tag>
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- <file>false</file>
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- <tempFile>false</tempFile>
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- <binary>false</binary>
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- <charsetName>MacRoman</charsetName>
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- <forceCopy>false</forceCopy>
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- <list>false</list>
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- <concatenate>false</concatenate>
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- <mime />
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- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
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- </entry>
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- </inputs>
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- <outputs />
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- <includeStdIn>false</includeStdIn>
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- <includeStdOut>true</includeStdOut>
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- <includeStdErr>true</includeStdErr>
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- <validReturnCodes>
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- <int>0</int>
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- </validReturnCodes>
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- </useCaseDescription>
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- <edited>false</edited>
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- </net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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- <maxJobs>1</maxJobs>
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- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
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- <backoffFactor>1.0</backoffFactor>
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- <initialDelay>1000</initialDelay>
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- <maxDelay>5000</maxDelay>
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- <maxRetries>0</maxRetries>
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- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="to_uri" depth="0" /><port name="from_uri" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Tool</processor><port>to_uri</port></sink><source type="dataflow"><port>to_uri</port></source></datalink><datalink><sink type="processor"><processor>Tool</processor><port>from_uri</port></sink><source type="dataflow"><port>from_uri</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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- <annotationAssertions>
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- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
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- <text>SCAPE Migration Components that converts any ImageMagick supported image format to TIFF</text>
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- </annotationBean>
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- <date>2012-11-15 13:07:59.763 UTC</date>
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- <creators />
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- <curationEventList />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- </annotationAssertions>
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- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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- <annotationAssertions>
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- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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- <identification>fd401dac-c521-4d94-8014-8efeba355d7a</identification>
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- </annotationBean>
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- <date>2012-11-19 15:55:14.145 UTC</date>
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- <creators />
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- <curationEventList />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- </annotationAssertions>
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- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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- <annotationAssertions>
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- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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- <identification>22bc577f-9a74-4981-8725-c3b4ac28d88b</identification>
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- </annotationBean>
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- <date>2012-11-20 12:10:07.110 UTC</date>
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- <creators />
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- <curationEventList />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- </annotationAssertions>
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- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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- <annotationAssertions>
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- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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- <identification>052219d1-09ed-4c6b-a5a4-2bad004a10ed</identification>
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- </annotationBean>
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- <date>2012-11-19 16:17:25.295 UTC</date>
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- <creators />
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- <curationEventList />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- </annotationAssertions>
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- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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- <annotationAssertions>
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- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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- <identification>5abab48b-a3f0-4f14-9894-e824a2fa5966</identification>
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- </annotationBean>
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- <date>2012-11-16 16:39:00.691 UTC</date>
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- <creators />
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- <curationEventList />
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- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
186
- </annotationAssertions>
187
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
188
- <annotationAssertions>
189
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
190
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
191
- <text>David Withers</text>
192
- </annotationBean>
193
- <date>2012-11-15 12:25:42.359 UTC</date>
194
- <creators />
195
- <curationEventList />
196
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
197
- </annotationAssertions>
198
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
199
- <annotationAssertions>
200
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
201
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
202
- <identification>b5361a0e-6abd-4070-8655-5dd7b4237576</identification>
203
- </annotationBean>
204
- <date>2012-11-15 13:36:38.115 UTC</date>
205
- <creators />
206
- <curationEventList />
207
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
208
- </annotationAssertions>
209
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
210
- <annotationAssertions>
211
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
212
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
213
- <identification>2bec9695-c132-4728-988c-c3a03ddcc78d</identification>
214
- </annotationBean>
215
- <date>2012-11-15 13:08:31.374 UTC</date>
216
- <creators />
217
- <curationEventList />
218
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
219
- </annotationAssertions>
220
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
221
- <annotationAssertions>
222
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
223
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
224
- <identification>0d60174b-0d75-481d-8b4d-194c6109bc96</identification>
225
- </annotationBean>
226
- <date>2012-11-20 12:17:54.280 UTC</date>
227
- <creators />
228
- <curationEventList />
229
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
230
- </annotationAssertions>
231
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
232
- <annotationAssertions>
233
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
234
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
235
- <mimeType>text/rdf+n3</mimeType>
236
- <content>[] &lt;http://scape-project.eu/pc/vocab/profiles#hasMigrationPath&gt;
237
- &lt;http://scape-project.eu/pc/vocab/profiles#jpegToTiff&gt; .
238
- </content>
239
- </annotationBean>
240
- <date>2012-11-20 12:17:49.904 UTC</date>
241
- <creators />
242
- <curationEventList />
243
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
244
- </annotationAssertions>
245
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
246
- <annotationAssertions>
247
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
248
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
249
- <identification>16841f82-e1fe-4527-b7ef-411c4c59493b</identification>
250
- </annotationBean>
251
- <date>2012-11-21 11:00:56.248 UTC</date>
252
- <creators />
253
- <curationEventList />
254
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
255
- </annotationAssertions>
256
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
257
- <annotationAssertions>
258
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
259
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
260
- <identification>a5aee4f0-01d8-4ae3-96f0-c992b8d40af2</identification>
261
- </annotationBean>
262
- <date>2012-11-15 13:14:14.243 UTC</date>
263
- <creators />
264
- <curationEventList />
265
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
266
- </annotationAssertions>
267
- </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
268
- <annotationAssertions>
269
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
270
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
271
- <text>Image to tiff migration action</text>
272
- </annotationBean>
273
- <date>2012-11-21 11:00:54.84 UTC</date>
274
- <creators />
275
- <curationEventList />
276
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
277
- </annotationAssertions>
1
+ <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="16841f82-e1fe-4527-b7ef-411c4c59493b" role="top"><name>Image_to_tiff_migrat</name><inputPorts><port><name>from_uri</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
2
+ <annotationAssertions>
3
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
4
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
5
+ <text>description</text>
6
+ </annotationBean>
7
+ <date>2012-11-16 16:22:56.977 UTC</date>
8
+ <creators />
9
+ <curationEventList />
10
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
11
+ </annotationAssertions>
12
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
13
+ <annotationAssertions>
14
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
15
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
16
+ <text>example</text>
17
+ </annotationBean>
18
+ <date>2012-11-16 16:22:43.712 UTC</date>
19
+ <creators />
20
+ <curationEventList />
21
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
22
+ </annotationAssertions>
23
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
24
+ <annotationAssertions>
25
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
26
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
27
+ <mimeType>text/rdf+n3</mimeType>
28
+ <content>[] &lt;http://scape-project.eu/pc/vocab/profiles#hasPortType&gt;
29
+ &lt;http://scape-project.eu/pc/vocab/profiles#FromURIPort&gt; .
30
+ </content>
31
+ </annotationBean>
32
+ <date>2012-11-19 15:53:49.250 UTC</date>
33
+ <creators />
34
+ <curationEventList />
35
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
36
+ </annotationAssertions>
37
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></port><port><name>to_uri</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
38
+ <annotationAssertions>
39
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
40
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
41
+ <mimeType>text/rdf+n3</mimeType>
42
+ <content>[] &lt;http://scape-project.eu/pc/vocab/profiles#hasPortType&gt;
43
+ &lt;http://scape-project.eu/pc/vocab/profiles#ToURIPort&gt; .
44
+ </content>
45
+ </annotationBean>
46
+ <date>2012-11-20 12:09:41.928 UTC</date>
47
+ <creators />
48
+ <curationEventList />
49
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
50
+ </annotationAssertions>
51
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></port></inputPorts><outputPorts /><processors><processor><name>Tool</name><inputPorts><port><name>to_uri</name><depth>0</depth></port><port><name>from_uri</name><depth>0</depth></port></inputPorts><outputPorts /><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
52
+ <annotationAssertions>
53
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
54
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
55
+ <mimeType>text/rdf+n3</mimeType>
56
+ <content>[] &lt;http://scape-project.eu/pc/vocab/profiles#hasDependency&gt;
57
+ &lt;http://scape-project.eu/pc/vocab/profiles#imagemagick-image2tiff&gt; .
58
+ </content>
59
+ </annotationBean>
60
+ <date>2012-11-20 12:17:37.420 UTC</date>
61
+ <creators />
62
+ <curationEventList />
63
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
64
+ </annotationAssertions>
65
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap><map from="to_uri" to="to_uri" /><map from="from_uri" to="from_uri" /></inputMap><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
66
+ <mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
67
+ <mechanismName>default local</mechanismName>
68
+ <mechanismXML>&lt;?xml version="1.0" encoding="UTF-8"?&gt;&#xD;
69
+ &lt;localInvocation&gt;&lt;shellPrefix&gt;/bin/sh -c&lt;/shellPrefix&gt;&lt;linkCommand&gt;/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%&lt;/linkCommand&gt;&lt;/localInvocation&gt;&#xD;
70
+ </mechanismXML>
71
+ <externaltoolid>1c6b3cec-667d-4364-8a77-315a3b3c71f8</externaltoolid>
72
+ <useCaseDescription>
73
+ <usecaseid />
74
+ <description />
75
+ <command>convert %%from_uri%% tiff:%%to_uri%%</command>
76
+ <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
77
+ <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
78
+ <tags>
79
+ <string>from_uri</string>
80
+ <string>to_uri</string>
81
+ </tags>
82
+ <REs />
83
+ <queue__preferred />
84
+ <queue__deny />
85
+ <static__inputs />
86
+ <inputs>
87
+ <entry>
88
+ <string>to_uri</string>
89
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
90
+ <tag>to_uri</tag>
91
+ <file>false</file>
92
+ <tempFile>false</tempFile>
93
+ <binary>false</binary>
94
+ <charsetName>MacRoman</charsetName>
95
+ <forceCopy>false</forceCopy>
96
+ <list>false</list>
97
+ <concatenate>false</concatenate>
98
+ <mime />
99
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
100
+ </entry>
101
+ <entry>
102
+ <string>from_uri</string>
103
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
104
+ <tag>from_uri</tag>
105
+ <file>false</file>
106
+ <tempFile>false</tempFile>
107
+ <binary>false</binary>
108
+ <charsetName>MacRoman</charsetName>
109
+ <forceCopy>false</forceCopy>
110
+ <list>false</list>
111
+ <concatenate>false</concatenate>
112
+ <mime />
113
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
114
+ </entry>
115
+ </inputs>
116
+ <outputs />
117
+ <includeStdIn>false</includeStdIn>
118
+ <includeStdOut>true</includeStdOut>
119
+ <includeStdErr>true</includeStdErr>
120
+ <validReturnCodes>
121
+ <int>0</int>
122
+ </validReturnCodes>
123
+ </useCaseDescription>
124
+ <edited>false</edited>
125
+ </net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
126
+ <maxJobs>1</maxJobs>
127
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
128
+ <backoffFactor>1.0</backoffFactor>
129
+ <initialDelay>1000</initialDelay>
130
+ <maxDelay>5000</maxDelay>
131
+ <maxRetries>0</maxRetries>
132
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="to_uri" depth="0" /><port name="from_uri" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Tool</processor><port>to_uri</port></sink><source type="dataflow"><port>to_uri</port></source></datalink><datalink><sink type="processor"><processor>Tool</processor><port>from_uri</port></sink><source type="dataflow"><port>from_uri</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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+ <annotationAssertions>
134
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
135
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
136
+ <text>SCAPE Migration Components that converts any ImageMagick supported image format to TIFF</text>
137
+ </annotationBean>
138
+ <date>2012-11-15 13:07:59.763 UTC</date>
139
+ <creators />
140
+ <curationEventList />
141
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
142
+ </annotationAssertions>
143
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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+ <annotationAssertions>
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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+ <identification>fd401dac-c521-4d94-8014-8efeba355d7a</identification>
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+ </annotationBean>
149
+ <date>2012-11-19 15:55:14.145 UTC</date>
150
+ <creators />
151
+ <curationEventList />
152
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
153
+ </annotationAssertions>
154
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
155
+ <annotationAssertions>
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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+ <identification>22bc577f-9a74-4981-8725-c3b4ac28d88b</identification>
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+ </annotationBean>
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+ <date>2012-11-20 12:10:07.110 UTC</date>
161
+ <creators />
162
+ <curationEventList />
163
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
164
+ </annotationAssertions>
165
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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+ <annotationAssertions>
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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+ <identification>052219d1-09ed-4c6b-a5a4-2bad004a10ed</identification>
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+ </annotationBean>
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+ <date>2012-11-19 16:17:25.295 UTC</date>
172
+ <creators />
173
+ <curationEventList />
174
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
175
+ </annotationAssertions>
176
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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+ <annotationAssertions>
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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+ <identification>5abab48b-a3f0-4f14-9894-e824a2fa5966</identification>
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+ </annotationBean>
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+ <date>2012-11-16 16:39:00.691 UTC</date>
183
+ <creators />
184
+ <curationEventList />
185
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
186
+ </annotationAssertions>
187
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
188
+ <annotationAssertions>
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
190
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
191
+ <text>David Withers</text>
192
+ </annotationBean>
193
+ <date>2012-11-15 12:25:42.359 UTC</date>
194
+ <creators />
195
+ <curationEventList />
196
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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+ </annotationAssertions>
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+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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+ <annotationAssertions>
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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+ <identification>b5361a0e-6abd-4070-8655-5dd7b4237576</identification>
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+ </annotationBean>
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+ <date>2012-11-15 13:36:38.115 UTC</date>
205
+ <creators />
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+ <curationEventList />
207
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
208
+ </annotationAssertions>
209
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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+ <annotationAssertions>
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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+ <identification>2bec9695-c132-4728-988c-c3a03ddcc78d</identification>
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+ </annotationBean>
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+ <date>2012-11-15 13:08:31.374 UTC</date>
216
+ <creators />
217
+ <curationEventList />
218
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
219
+ </annotationAssertions>
220
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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+ <annotationAssertions>
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
223
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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+ <identification>0d60174b-0d75-481d-8b4d-194c6109bc96</identification>
225
+ </annotationBean>
226
+ <date>2012-11-20 12:17:54.280 UTC</date>
227
+ <creators />
228
+ <curationEventList />
229
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
230
+ </annotationAssertions>
231
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
232
+ <annotationAssertions>
233
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
234
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
235
+ <mimeType>text/rdf+n3</mimeType>
236
+ <content>[] &lt;http://scape-project.eu/pc/vocab/profiles#hasMigrationPath&gt;
237
+ &lt;http://scape-project.eu/pc/vocab/profiles#jpegToTiff&gt; .
238
+ </content>
239
+ </annotationBean>
240
+ <date>2012-11-20 12:17:49.904 UTC</date>
241
+ <creators />
242
+ <curationEventList />
243
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
244
+ </annotationAssertions>
245
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
246
+ <annotationAssertions>
247
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
248
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
249
+ <identification>16841f82-e1fe-4527-b7ef-411c4c59493b</identification>
250
+ </annotationBean>
251
+ <date>2012-11-21 11:00:56.248 UTC</date>
252
+ <creators />
253
+ <curationEventList />
254
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
255
+ </annotationAssertions>
256
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
257
+ <annotationAssertions>
258
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
259
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
260
+ <identification>a5aee4f0-01d8-4ae3-96f0-c992b8d40af2</identification>
261
+ </annotationBean>
262
+ <date>2012-11-15 13:14:14.243 UTC</date>
263
+ <creators />
264
+ <curationEventList />
265
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
266
+ </annotationAssertions>
267
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
268
+ <annotationAssertions>
269
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
270
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
271
+ <text>Image to tiff migration action</text>
272
+ </annotationBean>
273
+ <date>2012-11-21 11:00:54.84 UTC</date>
274
+ <creators />
275
+ <curationEventList />
276
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
277
+ </annotationAssertions>
278
278
  </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
data/test/run_tests.rb CHANGED
@@ -1,8 +1,7 @@
1
- require 'rubygems'
2
1
  require 'test/unit'
2
+ require 'taverna-t2flow'
3
3
 
4
- require File.expand_path(File.join(__FILE__, "..", "test_helper.rb"))
5
-
6
- require File.expand_path(File.join(__FILE__, "..", "test_bogus_workflows.rb"))
7
- require File.expand_path(File.join(__FILE__, "..", "test_starter_pack_workflows.rb"))
8
- require File.expand_path(File.join(__FILE__, "..", "test_component_workflows.rb"))
4
+ require 'test_helper.rb'
5
+ require 'test_bogus_workflows.rb'
6
+ require 'test_starter_pack_workflows.rb'
7
+ require 'test_component_workflows.rb'
data/test/test_bogus_workflows.rb CHANGED
@@ -1,10 +1,11 @@
1
- require 'rubygems'
2
- require 'test/unit'
3
-
4
- require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "model.rb"))
5
- require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "parser.rb"))
6
-
7
- require File.expand_path(File.join(__FILE__, "..", "test_helper.rb"))
1
+ # Copyright (c) 2009-2013 The University of Manchester, UK.
2
+ #
3
+ # See LICENCE file for details.
4
+ #
5
+ # Authors: Finn Bacall
6
+ # Robert Haines
7
+ # David Withers
8
+ # Mannie Tagarira
8
9
 
9
10
  class BogusWorkflowTest < Test::Unit::TestCase
10
11
 
data/test/test_component_workflows.rb CHANGED
@@ -1,10 +1,11 @@
1
- require 'rubygems'
2
- require 'test/unit'
3
-
4
- require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "model.rb"))
5
- require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "parser.rb"))
6
-
7
- require File.expand_path(File.join(__FILE__, "..", "test_helper.rb"))
1
+ # Copyright (c) 2009-2013 The University of Manchester, UK.
2
+ #
3
+ # See LICENCE file for details.
4
+ #
5
+ # Authors: Finn Bacall
6
+ # Robert Haines
7
+ # David Withers
8
+ # Mannie Tagarira
8
9
 
9
10
  class ComponentWorkflowTest < Test::Unit::TestCase
10
11
 
data/test/test_helper.rb CHANGED
@@ -1,3 +1,12 @@
1
+ # Copyright (c) 2009-2013 The University of Manchester, UK.
2
+ #
3
+ # See LICENCE file for details.
4
+ #
5
+ # Authors: Finn Bacall
6
+ # Robert Haines
7
+ # David Withers
8
+ # Mannie Tagarira
9
+
1
10
  module TestHelper
2
11
 
3
12
  def generic_model_test(model)
data/test/test_starter_pack_workflows.rb CHANGED
@@ -1,10 +1,11 @@
1
- require 'rubygems'
2
- require 'test/unit'
3
-
4
- require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "model.rb"))
5
- require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "parser.rb"))
6
-
7
- require File.expand_path(File.join(__FILE__, "..", "test_helper.rb"))
1
+ # Copyright (c) 2009-2013 The University of Manchester, UK.
2
+ #
3
+ # See LICENCE file for details.
4
+ #
5
+ # Authors: Finn Bacall
6
+ # Robert Haines
7
+ # David Withers
8
+ # Mannie Tagarira
8
9
 
9
10
  class StarterPackWorkflowsTest < Test::Unit::TestCase
10
11
 
metadata CHANGED
@@ -1,15 +1,10 @@
1
- --- !ruby/object:Gem::Specification
1
+ --- !ruby/object:Gem::Specification
2
2
  name: taverna-t2flow
3
- version: !ruby/object:Gem::Version
4
- hash: 7
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.4.5
5
5
  prerelease:
6
- segments:
7
- - 0
8
- - 4
9
- - 4
10
- version: 0.4.4
11
6
  platform: ruby
12
- authors:
7
+ authors:
13
8
  - Finn Bacall
14
9
  - Robert Haines
15
10
  - David Withers
@@ -17,86 +12,84 @@ authors:
17
12
  autorequire:
18
13
  bindir: bin
19
14
  cert_chain: []
20
-
21
- date: 2013-02-06 00:00:00 Z
22
- dependencies:
23
- - !ruby/object:Gem::Dependency
24
- prerelease: false
25
- requirement: &id001 !ruby/object:Gem::Requirement
15
+ date: 2013-03-14 00:00:00.000000000 Z
16
+ dependencies:
17
+ - !ruby/object:Gem::Dependency
18
+ name: rake
19
+ requirement: !ruby/object:Gem::Requirement
26
20
  none: false
27
- requirements:
21
+ requirements:
28
22
  - - ~>
29
- - !ruby/object:Gem::Version
30
- hash: 63
31
- segments:
32
- - 0
33
- - 9
34
- - 2
23
+ - !ruby/object:Gem::Version
35
24
  version: 0.9.2
36
25
  type: :development
37
- name: rake
38
- version_requirements: *id001
39
- - !ruby/object:Gem::Dependency
40
26
  prerelease: false
41
- requirement: &id002 !ruby/object:Gem::Requirement
27
+ version_requirements: !ruby/object:Gem::Requirement
28
+ none: false
29
+ requirements:
30
+ - - ~>
31
+ - !ruby/object:Gem::Version
32
+ version: 0.9.2
33
+ - !ruby/object:Gem::Dependency
34
+ name: rdoc
35
+ requirement: !ruby/object:Gem::Requirement
42
36
  none: false
43
- requirements:
44
- - - ">="
45
- - !ruby/object:Gem::Version
46
- hash: 43
47
- segments:
48
- - 3
49
- - 9
50
- - 4
37
+ requirements:
38
+ - - ! '>='
39
+ - !ruby/object:Gem::Version
51
40
  version: 3.9.4
52
41
  type: :development
53
- name: rdoc
54
- version_requirements: *id002
55
- - !ruby/object:Gem::Dependency
56
42
  prerelease: false
57
- requirement: &id003 !ruby/object:Gem::Requirement
43
+ version_requirements: !ruby/object:Gem::Requirement
44
+ none: false
45
+ requirements:
46
+ - - ! '>='
47
+ - !ruby/object:Gem::Version
48
+ version: 3.9.4
49
+ - !ruby/object:Gem::Dependency
50
+ name: jeweler
51
+ requirement: !ruby/object:Gem::Requirement
58
52
  none: false
59
- requirements:
53
+ requirements:
60
54
  - - ~>
61
- - !ruby/object:Gem::Version
62
- hash: 49
63
- segments:
64
- - 1
65
- - 8
66
- - 3
55
+ - !ruby/object:Gem::Version
67
56
  version: 1.8.3
68
57
  type: :development
69
- name: jeweler
70
- version_requirements: *id003
71
- - !ruby/object:Gem::Dependency
72
58
  prerelease: false
73
- requirement: &id004 !ruby/object:Gem::Requirement
59
+ version_requirements: !ruby/object:Gem::Requirement
60
+ none: false
61
+ requirements:
62
+ - - ~>
63
+ - !ruby/object:Gem::Version
64
+ version: 1.8.3
65
+ - !ruby/object:Gem::Dependency
66
+ name: libxml-ruby
67
+ requirement: !ruby/object:Gem::Requirement
74
68
  none: false
75
- requirements:
76
- - - ">="
77
- - !ruby/object:Gem::Version
78
- hash: 27
79
- segments:
80
- - 1
81
- - 1
82
- - 4
69
+ requirements:
70
+ - - ! '>='
71
+ - !ruby/object:Gem::Version
83
72
  version: 1.1.4
84
73
  type: :runtime
85
- name: libxml-ruby
86
- version_requirements: *id004
87
- description: This a gem developed by myGrid for the purpose of interacting with Taverna 2 workflows. An example use would be the image genaration for the model representing Taverna 2 workflows as used in myExperiment.
88
- email:
89
- - finn.bacall@cs.man.ac.uk
90
- - rhaines@manchester.ac.uk
74
+ prerelease: false
75
+ version_requirements: !ruby/object:Gem::Requirement
76
+ none: false
77
+ requirements:
78
+ - - ! '>='
79
+ - !ruby/object:Gem::Version
80
+ version: 1.1.4
81
+ description: This a gem developed by myGrid for the purpose of interacting with Taverna
82
+ 2 workflows. An example use would be the image genaration for the model representing
83
+ Taverna 2 workflows as used in myExperiment.
84
+ email:
85
+ - support@mygrid.org.uk
91
86
  executables: []
92
-
93
87
  extensions: []
94
-
95
- extra_rdoc_files:
88
+ extra_rdoc_files:
96
89
  - CHANGES.rdoc
97
90
  - LICENCE
98
91
  - README.rdoc
99
- files:
92
+ files:
100
93
  - .rvmrc
101
94
  - CHANGES.rdoc
102
95
  - LICENCE
@@ -105,6 +98,7 @@ files:
105
98
  - lib/t2flow/dot.rb
106
99
  - lib/t2flow/model.rb
107
100
  - lib/t2flow/parser.rb
101
+ - lib/taverna-t2flow.rb
108
102
  - taverna-t2flow.gemspec
109
103
  - test/fixtures/1000.t2flow
110
104
  - test/fixtures/1001.t2flow
@@ -128,38 +122,30 @@ files:
128
122
  - test/test_starter_pack_workflows.rb
129
123
  homepage: http://www.taverna.org.uk/
130
124
  licenses: []
131
-
132
125
  post_install_message:
133
- rdoc_options:
126
+ rdoc_options:
134
127
  - -N
135
128
  - --tab-width=2
136
129
  - --main=README.rdoc
137
- require_paths:
130
+ require_paths:
138
131
  - lib
139
- required_ruby_version: !ruby/object:Gem::Requirement
132
+ required_ruby_version: !ruby/object:Gem::Requirement
140
133
  none: false
141
- requirements:
142
- - - ">="
143
- - !ruby/object:Gem::Version
144
- hash: 3
145
- segments:
146
- - 0
147
- version: "0"
148
- required_rubygems_version: !ruby/object:Gem::Requirement
134
+ requirements:
135
+ - - ! '>='
136
+ - !ruby/object:Gem::Version
137
+ version: '0'
138
+ required_rubygems_version: !ruby/object:Gem::Requirement
149
139
  none: false
150
- requirements:
151
- - - ">="
152
- - !ruby/object:Gem::Version
153
- hash: 3
154
- segments:
155
- - 0
156
- version: "0"
140
+ requirements:
141
+ - - ! '>='
142
+ - !ruby/object:Gem::Version
143
+ version: '0'
157
144
  requirements: []
158
-
159
145
  rubyforge_project:
160
- rubygems_version: 1.8.24
146
+ rubygems_version: 1.8.21
161
147
  signing_key:
162
148
  specification_version: 3
163
149
  summary: Support for interacting with Taverna 2 workflows.
164
- test_files:
150
+ test_files:
165
151
  - test/run_tests.rb