taverna-baclava 1.0.0

data/Changes.rdoc

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+= Changes log for the Taverna Baclava Ruby Gem
+
+
+== About this Changes file
+
+This file is, at least in part, generated by the following command:
+
+ $ git log --pretty=format:"* %s" --reverse --no-merges <commit-hash>..

data/Licence.rdoc

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+Copyright (c) 2006-2012 The University of Manchester, UK.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the names of The University of Manchester nor the names of its
+  contributors may be used to endorse or promote products derived from this
+  software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

data/ReadMe.rdoc

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+= Taverna[http://www.taverna.org.uk/] Baclava Gem
+
+Authors:: Robert Haines, Stian Soiland-Reyes, David Withers, Emmanuel Tagarira
+Contact:: mailto:support@mygrid.org.uk
+URL::     http://www.taverna.org.uk/
+Licence:: BSD (See Licence or http://www.opensource.org/licenses/bsd-license.php)
+Copyright::   (c) 2006-2012 The University of Manchester, UK
+
+== Synopsis
+
+This is a Ruby library to support the reading and writing of the
+Baclava data format.
+
+== Support
+
+Please email mailto:support@mygrid.org.uk for any questions relating to
+this Ruby gem.

data/lib/baclava/node.rb

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+# Copyright (c) 2006-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Authors: Robert Haines, Stian Soiland-Reyes, David Withers, Emmanuel Tagarira
+
+module Taverna
+  module Baclava
+
+    # An annotated data value.
+    class Node
+
+      # The value of this Node.
+      attr_reader :value
+
+      # A list of annotations on this Node.
+      attr_accessor :annotation
+
+      # The syntactic type of this node.
+      attr_reader :syntactic_type
+
+      # Create a new Node. If a list is passed in as the value then it is
+      # recursively processed into a list of Nodes.
+      def initialize(value = nil, annotation = [])
+        @syntactic_type = ""
+        @value = value.nil? ? nil : _set_value(value)
+        @annotation = annotation
+      end
+
+      # Set the value of this Node. If a list is passed in then it is
+      # recursively processed into a list of Nodes.
+      def value=(value)
+        @value = value.nil? ? nil : _set_value(value)
+      end
+
+      # Test for equality between this and another Node.
+      def ==(other)
+        @value == other.value and @annotation == other.annotation
+      end
+
+      # Extract the data value(s) from this Node and return them in the same
+      # structure as the given Node.
+      def Node.extract_node_data(node)
+        case node
+        when Hash
+          hash = {}
+          node.each { |k, v| hash[k] = Node.extract_node_data(v.value) }
+          hash
+        when Array
+          list = []
+          node.each { |n| list << Node.extract_node_data(n.value) }
+          list
+        when Taverna::Baclava::Node
+          Node.extract_node_data(node.value)
+        else
+          node
+        end
+      end
+
+      private
+
+      # Recursively set the value of this node, creating the underlying lists
+      # if necessary.
+      def _set_value(value)
+        if value.is_a? Array
+          value.map do |v|
+            v.is_a?(Taverna::Baclava::Node) ? v : Node.new(v)
+          end
+        else
+          value.to_s
+        end
+      end
+
+    end
+  end
+end

data/lib/baclava/reader.rb

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+# Copyright (c) 2006-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Authors: Robert Haines, Stian Soiland-Reyes, David Withers, Emmanuel Tagarira
+
+require 'baclava/node'
+require 'rexml/document'
+
+module Taverna
+  module Baclava
+
+    class Reader
+
+      # Reads a baclava document and returns a hash of Baclava::Node objects.
+      def self.read(xml)
+        if xml.kind_of?(REXML::Document)
+          document = xml
+        else
+          document = REXML::Document.new(xml)
+        end
+        root = document.root
+        raise "'#{root.name}' doesn't appear to be a data thing!" if root.name != "dataThingMap"
+
+        create_data_map(root)
+      end
+
+      # :stopdoc:
+
+      def self.create_data_map(element)
+        data_map = {}
+
+        element.each_element('b:dataThing') do |datathing|
+          key = datathing.attribute('key').value
+          data = Node.new
+          data_map[key] = data
+          datathing.each_element('b:myGridDataDocument')  do |dataDocument|
+            dataDocument.each_element('s:metadata') do |metadata|
+              data.annotation = get_metadata(metadata)
+            end
+            dataDocument.each_element('b:partialOrder') do |partialOrder|
+              data.value = get_list(partialOrder)
+            end
+            dataDocument.each_element('b:dataElement') do |dataElement|
+              data.value = get_element(dataElement)
+            end
+          end
+        end
+
+        data_map
+      end
+
+      def self.get_list(element)
+        list = []
+        element.each_element('b:itemList') do |itemList|
+          itemList.each_element('b:dataElement') do |dataElement|
+            list << get_element(dataElement)
+          end
+          itemList.each_element('b:partialOrder') do |partialOrder|
+            list << get_list(partialOrder)
+          end
+        end
+        list
+      end
+
+      def self.get_metadata(element)
+        list = []
+        element.each_element('s:mimeTypes') do |mimeTypes|
+          mimeTypes.each_element('s:mimeType') do |mimeType|
+            list << mimeType.text
+          end
+        end
+        list
+      end
+
+      def self.get_element(element)
+        element.each_element('b:dataElementData') do |data|
+          text = data.text
+          return text.nil? ? "" : Base64.decode64(text)
+        end
+      end
+    end
+  end
+end

data/lib/baclava/writer.rb

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+# Copyright (c) 2006-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Authors: Robert Haines, Stian Soiland-Reyes, David Withers, Emmanuel Tagarira
+
+
+require 'baclava/node'
+require 'base64'
+require 'rexml/document'
+require 'rubygems'
+require 'builder'
+
+module Taverna
+  module Baclava
+
+    class Writer
+
+      # Write a hash of Baclava::Node objects into a REXML::Document.
+      def self.write_doc(data_map)
+        REXML::Document.new(write(data_map))
+      end
+
+      # Write a hash of Baclava::Node objects into a XML String.
+      def self.write(data_map)
+        xml = Builder::XmlMarkup.new :indent => 2
+        xml.instruct!
+        xml.b :dataThingMap, 'xmlns:b' => 'http://org.embl.ebi.escience/baclava/0.1alpha' do
+          data_map.each_key do |key|
+            data = data_map[key]
+            xml.b :dataThing, 'key' => key do
+              xml.b :myGridDataDocument, 'lsid' => '', 'syntactictype' => data.syntactic_type do
+                write_metadata xml, data.annotation unless data.annotation.nil?
+                write_data xml, data.value
+              end
+            end
+          end
+        end
+      end
+
+      # :stopdoc:
+
+      def self.write_metadata(xml, metadata)
+        xml.s :metadata, 'xmlns:s' => 'http://org.embl.ebi.escience/xscufl/0.1alpha' do
+          return if metadata.empty?
+          xml.s :mimeTypes do
+            metadata.each do |mimetype|
+              xml.s :mimetype, mimetype.chomp
+            end
+          end
+        end
+      end
+
+      def self.write_data(xml, data, index = nil)
+        if data.is_a? Array
+          write_list xml, data, index
+        else
+          if index
+            xml.b :dataElement, 'lsid' => '', 'index' => index do |x|
+              x.b :dataElementData, Base64.encode64(data).chomp
+            end
+          else
+            xml.b :dataElement, 'lsid' => '' do |x|
+              x.b :dataElementData, Base64.encode64(data).chomp
+            end
+          end
+        end
+      end
+
+      def self.write_list(xml, list, index)
+        if index
+          xml.b :partialOrder, 'lsid' => '', 'type' => 'list', 'index' => index do
+            write_item_list xml, list
+          end
+        else
+          xml.b :partialOrder, 'lsid' => '', 'type' => 'list' do
+            write_item_list xml, list
+          end
+        end
+      end
+
+      def self.write_item_list(xml, list)
+        xml.b :relationList do
+          (1...list.length).each do |i|
+            xml.b :relation, 'parent' => (i - 1), 'child' => i
+          end
+        end
+        xml.b :itemList do
+          (0...list.length).each do |i|
+            write_data xml, list[i].value, i
+          end
+        end
+      end
+    end
+  end
+end

data/lib/taverna-baclava.rb

@@ -0,0 +1,34 @@
+# Copyright (c) 2006-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Authors: Robert Haines, Stian Soiland-Reyes, David Withers, Emmanuel Tagarira
+
+require 'baclava/reader'
+require 'baclava/writer'

data/test/tc_baclava.rb

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+# Copyright (c) 2006-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+class TestBaclava < Test::Unit::TestCase
+  SINGLE_IN = []
+  MANY_IN =   [[["boo"]], [["", "Hello"]], [], [[], ["test"], []]]
+  MAP =       {
+    "SINGLE_IN" => Taverna::Baclava::Node.new(SINGLE_IN),
+    "MANY_IN" => Taverna::Baclava::Node.new(MANY_IN)
+  }
+
+  def test_reader
+    input = Taverna::Baclava::Reader.read(File.read("test/test.baclava"))
+    assert_equal(input, MAP)
+    map = Taverna::Baclava::Node.extract_node_data(input)
+    assert_equal(map["SINGLE_IN"], SINGLE_IN)
+    assert_equal(map["MANY_IN"], MANY_IN)
+  end
+
+  def test_writer
+    input = Taverna::Baclava::Reader.read(Taverna::Baclava::Writer.write(MAP))
+    assert_equal(input, MAP)
+    map = Taverna::Baclava::Node.extract_node_data(input)
+    assert_equal(map["SINGLE_IN"], SINGLE_IN)
+    assert_equal(map["MANY_IN"], MANY_IN)
+  end
+end

data/test/tc_node.rb

@@ -0,0 +1,75 @@
+# Copyright (c) 2006-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+class TestNode < Test::Unit::TestCase
+  TEST_VALUE = "Hello"
+  TEST_LIST = ["Hello", "World!"]
+  TEST_NUMBER = 1337
+
+  def test_singleton
+    node = Taverna::Baclava::Node.new(TEST_VALUE)
+    assert_equal(node.value, TEST_VALUE)
+    assert_equal(node.annotation, [])
+  end
+
+  def test_lists
+    node = Taverna::Baclava::Node.new(TEST_LIST)
+    assert_equal(node.value[0].value, TEST_LIST[0])
+    assert_equal(node.value[1].value, TEST_LIST[1])
+    assert_equal(node.annotation, [])
+  end
+
+  def test_non_strings
+    node = Taverna::Baclava::Node.new(TEST_NUMBER)
+    assert_equal(node.value, TEST_NUMBER.to_s)
+    assert_equal(node.annotation, [])
+  end
+
+  def test_extract
+    n1 = Taverna::Baclava::Node.new(TEST_VALUE)
+    n2 = Taverna::Baclava::Node.new(TEST_LIST)
+    n3 = Taverna::Baclava::Node.new(TEST_NUMBER)
+    map = {
+      "value"  => n1,
+      "list"   => n2,
+      "number" => n3
+    }
+
+    assert_equal(Taverna::Baclava::Node.extract_node_data(n1), TEST_VALUE)
+    assert_equal(Taverna::Baclava::Node.extract_node_data(n2), TEST_LIST)
+    assert_equal(Taverna::Baclava::Node.extract_node_data(n3),
+      TEST_NUMBER.to_s)
+
+    map_x = Taverna::Baclava::Node.extract_node_data(map)
+    assert_equal(map_x["list"], TEST_LIST)
+  end
+end

data/test/test.baclava

@@ -0,0 +1,86 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<b:dataThingMap xmlns:b="http://org.embl.ebi.escience/baclava/0.1alpha">
+  <b:dataThing key="MANY_IN">
+    <b:myGridDataDocument lsid="" syntactictype="l(l(l('null')))">
+      <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" />
+      <b:partialOrder lsid="" type="list">
+        <b:relationList>
+          <b:relation parent="0" child="1" />
+          <b:relation parent="1" child="2" />
+          <b:relation parent="2" child="3" />
+        </b:relationList>
+        <b:itemList>
+          <b:partialOrder lsid="" type="list" index="0">
+            <b:relationList />
+            <b:itemList>
+              <b:partialOrder lsid="" type="list" index="0">
+                <b:relationList />
+                <b:itemList>
+                  <b:dataElement lsid="" index="0">
+                    <b:dataElementData>Ym9v</b:dataElementData>
+                  </b:dataElement>
+                </b:itemList>
+              </b:partialOrder>
+            </b:itemList>
+          </b:partialOrder>
+          <b:partialOrder lsid="" type="list" index="1">
+            <b:relationList />
+            <b:itemList>
+              <b:partialOrder lsid="" type="list" index="0">
+                <b:relationList>
+                  <b:relation parent="0" child="1" />
+                </b:relationList>
+                <b:itemList>
+                  <b:dataElement lsid="" index="0">
+                    <b:dataElementData />
+                  </b:dataElement>
+                  <b:dataElement lsid="" index="1">
+                    <b:dataElementData>SGVsbG8=</b:dataElementData>
+                  </b:dataElement>
+                </b:itemList>
+              </b:partialOrder>
+            </b:itemList>
+          </b:partialOrder>
+          <b:partialOrder lsid="" type="list" index="2">
+            <b:relationList />
+            <b:itemList />
+          </b:partialOrder>
+          <b:partialOrder lsid="" type="list" index="3">
+            <b:relationList>
+              <b:relation parent="0" child="1" />
+              <b:relation parent="1" child="2" />
+            </b:relationList>
+            <b:itemList>
+              <b:partialOrder lsid="" type="list" index="0">
+                <b:relationList />
+                <b:itemList />
+              </b:partialOrder>
+              <b:partialOrder lsid="" type="list" index="1">
+                <b:relationList />
+                <b:itemList>
+                  <b:dataElement lsid="" index="0">
+                    <b:dataElementData>dGVzdA==</b:dataElementData>
+                  </b:dataElement>
+                </b:itemList>
+              </b:partialOrder>
+              <b:partialOrder lsid="" type="list" index="2">
+                <b:relationList />
+                <b:itemList />
+              </b:partialOrder>
+            </b:itemList>
+          </b:partialOrder>
+        </b:itemList>
+      </b:partialOrder>
+    </b:myGridDataDocument>
+  </b:dataThing>
+  <b:dataThing key="SINGLE_IN">
+    <b:myGridDataDocument lsid="" syntactictype="l('null')">
+      <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" />
+      <b:partialOrder lsid="" type="list">
+        <b:relationList />
+        <b:itemList />
+      </b:partialOrder>
+    </b:myGridDataDocument>
+  </b:dataThing>
+</b:dataThingMap>
+

data/test/ts_baclava.rb

@@ -0,0 +1,38 @@
+# Copyright (c) 2006-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+require 'test/unit'
+require 'taverna-baclava'
+
+# tests
+require 'tc_node'
+require 'tc_baclava'

metadata

@@ -0,0 +1,126 @@
+--- !ruby/object:Gem::Specification 
+name: taverna-baclava
+version: !ruby/object:Gem::Version 
+  hash: 23
+  prerelease: 
+  segments: 
+  - 1
+  - 0
+  - 0
+  version: 1.0.0
+platform: ruby
+authors: 
+- Robert Haines
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2012-03-13 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rake
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 63
+        segments: 
+        - 0
+        - 9
+        - 2
+        version: 0.9.2
+  type: :development
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: rdoc
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 43
+        segments: 
+        - 3
+        - 9
+        - 4
+        version: 3.9.4
+  type: :development
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: builder
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 3
+        - 0
+        - 0
+        version: 3.0.0
+  type: :runtime
+  version_requirements: *id003
+description: A Ruby library to support the reading and writing of the Baclava data format.
+email: rhaines@manchester.ac.uk
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- ReadMe.rdoc
+- Licence.rdoc
+- Changes.rdoc
+files: 
+- lib/baclava/node.rb
+- lib/baclava/writer.rb
+- lib/baclava/reader.rb
+- lib/taverna-baclava.rb
+- test/tc_baclava.rb
+- test/ts_baclava.rb
+- test/tc_node.rb
+- test/test.baclava
+- ReadMe.rdoc
+- Licence.rdoc
+- Changes.rdoc
+homepage: http://www.taverna.org.uk/
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- -N
+- --tab-width=2
+- --main=ReadMe.rdoc
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.10
+signing_key: 
+specification_version: 3
+summary: Ruby support for the Baclava file format.
+test_files: 
+- test/ts_baclava.rb