taverna-t2flow 0.4.4 → 0.4.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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 @@
1
1
  = 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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8
 
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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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13
 
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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="">
66
- <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>
73
- <usecaseid />
74
- <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 />
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>
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>
157
+ <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 />
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+ <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 />
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+ <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 />
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="">
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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="">
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+ <annotationAssertions>
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+ <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