taverna-t2flow 0.5.0 → 0.5.1

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Files changed (6) hide show
  1. data/CHANGES.rdoc +4 -0
  2. data/Rakefile +1 -1
  3. data/lib/t2flow/dot.rb +41 -42
  4. data/taverna-t2flow.gemspec +3 -3
  5. data/test/fixtures/component_using_workflow.t2flow +23 -23
  6. metadata +3 -3
data/CHANGES.rdoc CHANGED
@@ -1,5 +1,9 @@
1
1
  = Changes log for the T2Flow Ruby Gem
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+ == Version 0.5.1
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+
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+ * Added some missing processor colours.
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+
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  == Version 0.5.0
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  * Split out model classes into different files.
data/Rakefile CHANGED
@@ -17,7 +17,7 @@ require 'jeweler'
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  task :default => [:test]
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- T2FLOW_GEM_VERSION = "0.5.0"
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+ T2FLOW_GEM_VERSION = "0.5.1"
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  Jeweler::Tasks.new do |s|
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  s.name = "taverna-t2flow"
data/lib/t2flow/dot.rb CHANGED
@@ -20,43 +20,44 @@ module T2Flow
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  # `dot -Tpng -o"path/to/the/output/image" #{out_file.path}`
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  class Dot
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- @@processor_colours = {
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- 'apiconsumer' => '#98fb98',
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- 'beanshell' => '#deb887',
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- 'biomart' => '#d1eeee',
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- 'localworker' => '#d15fee',
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- 'biomobywsdl' => '#ffb90f',
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- 'biomoby' => '#ffb90f',
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- 'biomobyobject' => '#ffd700',
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- 'biomobyparser' => '#ffffff',
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- 'inferno' => 'violetred1',
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- 'notification' => 'mediumorchid2',
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- 'rdfgenerator' => 'purple',
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- 'rserv' => 'lightgoldenrodyellow',
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- 'seqhound' => '#836fff',
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- 'soaplabwsdl' => '#fafad2',
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- 'soaplab' => '#fafad2',
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- 'stringconstant' => '#b0c4de',
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- 'talisman' => 'plum2',
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- 'bsf' => 'burlywood2',
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- 'abstractprocessor' => 'lightgoldenrodyellow',
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- 'xmlsplitter' => '#ab92ea',
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- 'rshell' => '#648faa',
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- 'arbitrarywsdl' => 'darkolivegreen3',
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- 'wsdl' => '#a2cd5a',
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- 'workflow' => 'crimson',
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- 'rest' => '#7aafff',
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- 'xpath' => '#e6ff5e',
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- 'externaltool' => '#f28c55',
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- 'spreadsheet' => '#40e0d0',
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- 'dataflow' => '#ffc0cb',
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- 'rshell' => '#648faa',
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+ PROCESSOR_COLOURS = {
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+ :apiconsumer => "#98fb98", #palegreen
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+ :beanshell => "#deb887", #burlywood2
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+ :biomart => "#d1eeee", #lightcyan2
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+ :localworker => "#d15fee", #mediumorchid2
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+ :biomobywsdl => "#ffb90f", #darkgoldenrod1
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+ :biomoby => "#ffb90f", #darkgoldenrod1
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+ :biomobyobject => "#ffd700", #gold
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+ :biomobyparser => "#ffffff", #white
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+ :inferno => "violetred1",
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+ :notification => "mediumorchid2",
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+ :rdfgenerator => "purple",
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+ :rserv => "lightgoldenrodyellow",
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+ :seqhound => "#836fff",
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+ :soaplabwsdl => "#fafad2",
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+ :soaplab => "#fafad2",
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+ :stringconstant => "#b0c4de",
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+ :talisman => "plum2",
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+ :bsf => "burlywood2",
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+ :abstractprocessor => "lightgoldenrodyellow",
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+ :xmlsplitter => "#ab92ea",
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+ :rshell => "#648faa",
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+ :arbitrarywsdl => "darkolivegreen3",
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+ :wsdl => "#a2cd5a",
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+ :workflow => "crimson",
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+ :rest => "#7aafff",
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+ :xpath => "#e6ff5e",
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+ :externaltool => "#f28c55",
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+ :spreadsheet => "#40e0d0",
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+ :dataflow => "#ffc0cb",
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+ :interaction => "#6aeb9f",
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+ :component => "#e693d2"
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  }
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+
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+ FILL_COLOURS = %w{white aliceblue antiquewhite beige}
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- @@fill_colours = %w{white aliceblue antiquewhite beige}
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-
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- @@ranksep = '0.22'
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- @@nodesep = '0.05'
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+ RANK_SEP = '0.22'
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+ NODE_SEP = '0.05'
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  # Creates a new dot object for interaction.
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  def initialize
@@ -78,8 +79,8 @@ module T2Flow
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  stream.puts ' style=""'
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  stream.puts ' labeljust="left"'
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  stream.puts ' clusterrank="local"'
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- stream.puts " ranksep=\"#@@ranksep\""
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- stream.puts " nodesep=\"#@@nodesep\""
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+ stream.puts " ranksep=\"#RANK_SEP\""
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+ stream.puts " nodesep=\"#NODE_SEP\""
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  stream.puts ' ]'
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  stream.puts
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  stream.puts ' node ['
@@ -114,7 +115,7 @@ module T2Flow
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  stream.puts ' fontsize="10"'
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  stream.puts ' fontcolor="black"'
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  stream.puts ' clusterrank="local"'
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- stream.puts " fillcolor=\"#{@@fill_colours[depth % @@fill_colours.length]}\""
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+ stream.puts " fillcolor=\"#{FILL_COLOURS[depth % FILL_COLOURS.length]}\""
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  stream.puts ' style="filled"'
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  end
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  dataflow.processors.each {|processor| write_processor(stream, processor, prefix, depth)}
@@ -208,7 +209,6 @@ module T2Flow
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  else
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  processor = dataflow.processors.select{|p| p.name == link.source.split(':')[0]}[0]
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  if "#{processor.type}" == "workflow"
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- df = @t2flow_model.dataflow(processor.dataflow_id)
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  stream.write " \"#{prefix}#{processor.name}WORKFLOWINTERNALSINK_#{link.source.split(':')[1]}\""
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  else
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  stream.write " \"#{prefix}#{processor.name}\""
@@ -220,7 +220,6 @@ module T2Flow
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  else
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  processor = dataflow.processors.select{|p| p.name == link.sink.split(':')[0]}[0]
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  if "#{processor.type}" == "workflow"
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- df = @t2flow_model.dataflow(processor.dataflow_id)
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  stream.write "\"#{prefix}#{processor.name}WORKFLOWINTERNALSOURCE_#{link.sink.split(':')[1]}\""
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  else
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  stream.write "\"#{prefix}#{processor.name}\""
@@ -248,7 +247,7 @@ module T2Flow
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  end
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  def get_colour(processor_name) # :nodoc:
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- colour = @@processor_colours[processor_name]
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+ colour = PROCESSOR_COLOURS[processor_name.to_sym]
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  if colour
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  colour
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  else
@@ -258,7 +257,7 @@ module T2Flow
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  # Returns true if the given name is a processor; false otherwise
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  def Dot.is_processor?(processor_name)
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- true if @@processor_colours[processor_name]
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+ true if get_colour(processor_name)
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  end
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  end
data/taverna-t2flow.gemspec CHANGED
@@ -5,11 +5,11 @@
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  Gem::Specification.new do |s|
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  s.name = "taverna-t2flow"
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- s.version = "0.5.0"
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+ s.version = "0.5.1"
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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 = "2014-03-11"
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+ s.date = "2014-03-14"
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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 = ["support@mygrid.org.uk"]
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  s.extra_rdoc_files = [
@@ -58,7 +58,7 @@ 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 = "1.8.29"
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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/component_using_workflow.t2flow CHANGED
@@ -1,24 +1,24 @@
1
- <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="fa8eeaf3-5816-4e19-afb4-468c318c9832" role="top"><name>Workflow1</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Extract_PNG_dimensions</name><inputPorts><port><name>fromFilename</name><depth>0</depth></port></inputPorts><outputPorts><port><name>dimensions</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.component</group><artifact>component-activity</artifact><version>1.1.2</version></raven><class>net.sf.taverna.t2.component.ComponentActivity</class><inputMap><map from="fromFilename" to="fromFilename" /></inputMap><outputMap><map from="dimensions" to="dimensions" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.component.ComponentActivityConfigurationBean xmlns="">
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- <registryBase>http://www.myexperiment.org</registryBase>
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- <familyName>SCAPE Image Characterisation Component</familyName>
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- <componentName>Extract PNG dimensions</componentName>
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- <componentVersion>2</componentVersion>
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- </net.sf.taverna.t2.component.ComponentActivityConfigurationBean></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="fromFilename" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Extract_PNG_dimensions</processor><port>fromFilename</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Extract_PNG_dimensions</processor><port>dimensions</port></source></datalink></datalinks><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.IdentificationAssertion">
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- <identification>fa8eeaf3-5816-4e19-afb4-468c318c9832</identification>
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- </annotationBean>
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- <date>2014-03-11 09:20:07.794 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>
1
+ <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="fa8eeaf3-5816-4e19-afb4-468c318c9832" role="top"><name>Workflow1</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Extract_PNG_dimensions</name><inputPorts><port><name>fromFilename</name><depth>0</depth></port></inputPorts><outputPorts><port><name>dimensions</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.component</group><artifact>component-activity</artifact><version>1.1.2</version></raven><class>net.sf.taverna.t2.component.ComponentActivity</class><inputMap><map from="fromFilename" to="fromFilename" /></inputMap><outputMap><map from="dimensions" to="dimensions" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.component.ComponentActivityConfigurationBean xmlns="">
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+ <registryBase>http://www.myexperiment.org</registryBase>
3
+ <familyName>SCAPE Image Characterisation Component</familyName>
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+ <componentName>Extract PNG dimensions</componentName>
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+ <componentVersion>2</componentVersion>
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+ </net.sf.taverna.t2.component.ComponentActivityConfigurationBean></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="fromFilename" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Extract_PNG_dimensions</processor><port>fromFilename</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Extract_PNG_dimensions</processor><port>dimensions</port></source></datalink></datalinks><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.IdentificationAssertion">
17
+ <identification>fa8eeaf3-5816-4e19-afb4-468c318c9832</identification>
18
+ </annotationBean>
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+ <date>2014-03-11 09:20:07.794 UTC</date>
20
+ <creators />
21
+ <curationEventList />
22
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
23
+ </annotationAssertions>
24
24
  </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: taverna-t2flow
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.5.0
4
+ version: 0.5.1
5
5
  prerelease:
6
6
  platform: ruby
7
7
  authors:
@@ -12,7 +12,7 @@ authors:
12
12
  autorequire:
13
13
  bindir: bin
14
14
  cert_chain: []
15
- date: 2014-03-11 00:00:00.000000000 Z
15
+ date: 2014-03-14 00:00:00.000000000 Z
16
16
  dependencies:
17
17
  - !ruby/object:Gem::Dependency
18
18
  name: rake
@@ -149,7 +149,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
149
149
  version: '0'
150
150
  requirements: []
151
151
  rubyforge_project:
152
- rubygems_version: 1.8.24
152
+ rubygems_version: 1.8.29
153
153
  signing_key:
154
154
  specification_version: 3
155
155
  summary: Support for interacting with Taverna 2 workflows.