bio-phyloxml 0.9.0

data/test/unit/bio/test_phyloxml_writer.rb

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+#
+# = test/unit/bio/test_phyloxml_writer.rb - Unit test for Bio::PhyloXML::Writer
+#
+# Copyright::   Copyright (C) 2009
+#               Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
+# License::     The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
+                            'helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'singleton'
+require 'bio/command'
+
+begin
+  require 'libxml'
+rescue LoadError
+end
+
+if defined?(LibXML) then
+  require 'bio/phyloxml'
+end
+
+module Bio
+  class TestPhyloXMLWriter_Check_LibXML < Test::Unit::TestCase
+    def test_libxml
+      assert(defined?(LibXML),
+             "Error: libxml-ruby library is not present. Please install libxml-ruby library. It is needed for Bio::PhyloXML module. Unit test for PhyloXML will not be performed.")
+    end
+  end #class TestPhyloXMLWriter_Check_LibXML
+end #module Bio
+
+module Bio
+
+  module TestPhyloXMLWriterData
+
+  PHYLOXML_WRITER_TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'phyloxml')).cleanpath.to_s
+
+  def self.example_xml
+    File.join PHYLOXML_WRITER_TEST_DATA, 'phyloxml_examples.xml'
+  end
+
+  def self.mollusca_short_xml
+    File.join PHYLOXML_WRITER_TEST_DATA, 'ncbi_taxonomy_mollusca_short.xml'
+  end
+
+  def self.made_up_xml
+    File.join PHYLOXML_WRITER_TEST_DATA, 'made_up.xml'
+  end
+
+  end #end module TestPhyloXMLWriterData
+
+  class TestPhyloXMLWriter < Test::Unit::TestCase
+
+    # helper class to write files using temporary directory
+    class WriteTo
+      include Singleton
+
+      def initialize
+        @leave_tmpdir = ENV['BIORUBY_TEST_DEBUG'].to_s.empty? ? false : true
+        @tests = nil
+        @tests_passed = 0
+        @tmpdir = nil
+      end
+
+      attr_accessor :tests
+
+      def test_passed
+        @tests_passed += 1
+        if !@leave_tmpdir and @tmpdir and @tests and
+            @tests_passed >= @tests then
+          #$stderr.print "Removing #{@tmpdir.path}\n"
+          @tmpdir.close!
+          @tmpdir = nil
+          @tests_passed = 0
+        end
+      end
+
+      def tmpdir
+        @tmpdir ||= Bio::Command::Tmpdir.new('PhyloXML')
+        @tmpdir
+      end
+
+      def file(f)
+        File.join(self.tmpdir.path, f)
+      end
+    
+      def example_xml_test
+        self.file('phyloxml_examples_written.xml')
+      end
+    end #class WriteTo
+
+    def setup
+      @writeto = WriteTo.instance
+      @writeto.tests ||= self.methods.collect { |x|
+        x.to_s }.find_all { |y|
+        /\Atest\_/ =~ y }.size
+    end
+
+    def teardown
+      @writeto.test_passed
+    end
+
+#    def test_write
+#       # @todo this is test for Tree.write
+#      tree = Bio::PhyloXML::Tree.new
+#      filename = @writeto.file('test.xml')
+#      tree.write(filename)
+#    end
+
+    def test_init
+      filename = @writeto.file("test2.xml")
+      writer = Bio::PhyloXML::Writer.new(filename)
+      
+      tree = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.mollusca_short_xml) { |px| px.next_tree }
+      
+      writer.write(tree)
+
+      assert_nothing_thrown do
+        Bio::PhyloXML::Parser.open(filename) { |px| true }
+      end
+
+      #File.delete(filename)
+    end
+
+    def test_simple_xml
+      filename = @writeto.file("sample.xml")
+      writer = Bio::PhyloXML::Writer.new(filename)
+      tree = Bio::PhyloXML::Tree.new
+      tree.rooted = true
+      tree.name = "Test tree"
+      root_node = Bio::PhyloXML::Node.new
+      tree.root = root_node
+      root_node.name = "A"
+      #root_node.taxonomies[0] = Bio::PhyloXML::Taxonomy.new
+      root_node.taxonomies << Bio::PhyloXML::Taxonomy.new
+      root_node.taxonomies[0].scientific_name = "Animal animal"
+      node2 = Bio::PhyloXML::Node.new
+      node2.name = "B"
+      tree.add_node(node2)
+      tree.add_edge(root_node, node2)
+      writer.write(tree)
+      
+      lines = File.readlines(filename)
+      assert_equal("<phyloxml xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd\" xmlns=\"http://www.phyloxml.org\">",
+                    lines[1].chomp)
+      assert_equal("  <phylogeny rooted=\"true\">", lines[2].chomp)
+      assert_equal("    <name>Test tree</name>", lines[3].chomp)
+      assert_equal("    <clade>", lines[4].chomp)
+      assert_equal("      <name>A</name>", lines[5].chomp)
+      assert_equal("      <taxonomy>", lines[6].chomp)
+      assert_equal("        <scientific_name>Animal animal</scientific_name>", lines[7].chomp)
+      assert_equal("      </taxonomy>", lines[8].chomp)
+      assert_equal("        <name>B</name>", lines[10].chomp)
+      assert_equal("    </clade>", lines[12].chomp)
+      assert_equal("  </phylogeny>", lines[13].chomp)
+      assert_equal("</phyloxml>", lines[14].chomp)
+
+      #File.delete(filename)
+    end
+
+    def test_phyloxml_examples_tree1
+      tree = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml) { |px| px.next_tree }
+
+      filename = @writeto.file('example_tree1.xml')
+      writer = Bio::PhyloXML::Writer.new(filename)
+      writer.write_branch_length_as_subelement = false
+      writer.write(tree)
+
+      assert_nothing_thrown do
+        tree2  = Bio::PhyloXML::Parser.open(filename) { |px| true }
+      end
+
+      #File.delete(filename)
+
+      #@todo check if branch length is written correctly
+    end
+
+    def test_phyloxml_examples_tree2
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml)
+      2.times do
+        @tree = phyloxml.next_tree
+      end
+      phyloxml.close
+      
+      filename = @writeto.file('example_tree2.xml')
+      writer = Bio::PhyloXML::Writer.new(filename)
+      writer.write(@tree)
+
+      assert_nothing_thrown do
+        tree2  = Bio::PhyloXML::Parser.open(filename) { |px| true }
+      end
+      
+      #File.delete(filename)
+    end
+
+    def test_phyloxml_examples_tree4
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml)
+      4.times do
+        @tree = phyloxml.next_tree
+      end
+      phyloxml.close
+      #@todo tree = phyloxml[4]
+      filename = @writeto.file('example_tree4.xml')
+      writer = Bio::PhyloXML::Writer.new(filename)
+      writer.write(@tree)
+      assert_nothing_thrown do
+        @tree2 = Bio::PhyloXML::Parser.open(filename) { |px| px.next_tree }
+      end
+      assert_equal(@tree.name, @tree2.name)
+      assert_equal(@tree.get_node_by_name('A').taxonomies[0].scientific_name, @tree2.get_node_by_name('A').taxonomies[0].scientific_name)
+      assert_equal(@tree.get_node_by_name('B').sequences[0].annotations[0].desc,
+        @tree2.get_node_by_name('B').sequences[0].annotations[0].desc)
+     # assert_equal(@tree.get_node_by_name('B').sequences[0].annotations[0].confidence.value,@tree2.get_node_by_name('B').sequences[0].annotations[0].confidence.value)
+     #File.delete(filename)
+    end
+
+    def test_phyloxml_examples_sequence_relation
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml)
+      filename = @writeto.example_xml_test
+      writer = Bio::PhyloXML::Writer.new(filename)
+      phyloxml.each do |tree|
+        writer.write(tree)
+      end
+      phyloxml.close
+
+      assert_nothing_thrown do
+        @phyloxml_test = Bio::PhyloXML::Parser.open(filename)
+      end
+
+      5.times do
+        @tree = @phyloxml_test.next_tree
+      end
+
+      @phyloxml_test.close
+
+      assert_equal("x", @tree.sequence_relations[0].id_ref_0)
+      assert_equal("z", @tree.sequence_relations[1].id_ref_1)
+      assert_equal(nil, @tree.sequence_relations[2].distance)
+      assert_equal("orthology", @tree.sequence_relations[2].type)
+
+      #File.delete(filename)
+    end
+
+    def test_generate_xml_with_sequence
+      tree = Bio::PhyloXML::Tree.new
+      r = Bio::PhyloXML::Node.new
+      tree.add_node(r)
+      tree.root = r
+      n = Bio::PhyloXML::Node.new
+      tree.add_node(n)
+      tree.add_edge(tree.root, n)
+      tree.rooted = true
+
+      n.name = "A"
+      seq = PhyloXML::Sequence.new
+      n.sequences[0] = seq
+      seq.annotations[0] = PhyloXML::Annotation.new
+      seq.annotations[0].desc = "Sample annotation"
+      seq.name = "sequence name"
+      seq.location = "somewhere"
+      seq.accession = PhyloXML::Accession.new
+      seq.accession.source = "ncbi"
+      seq.accession.value = "AAB80874"
+      seq.symbol = "adhB"
+      seq.mol_seq = "TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD"
+      seq.uri = PhyloXML::Uri.new
+      seq.uri.desc = "EMBL REPTILE DATABASE"
+      seq.uri.uri = "http://www.embl-heidelberg.de/~uetz/families/Varanidae.html"
+      seq.domain_architecture = PhyloXML::DomainArchitecture.new
+      seq.domain_architecture.length = 1249
+      domain1 = PhyloXML::ProteinDomain.new
+      seq.domain_architecture.domains << domain1
+      domain1.from = 6
+      domain1.to = 90
+      domain1.confidence = "7.0E-26"
+      domain1.value = "CARD"
+      domain2 = PhyloXML::ProteinDomain.new
+      seq.domain_architecture.domains << domain2
+      domain2.from = 109
+      domain2.to = 414
+      domain2.confidence = "7.2E-117"
+      domain2.value = "NB-ARC"
+
+      filename = @writeto.file('sequence.xml')
+      Bio::PhyloXML::Writer.new(filename).write(tree)
+
+      assert_nothing_thrown do
+        Bio::PhyloXML::Parser.open(filename) { |px| px.next_tree }
+      end
+
+      #File.delete(filename)
+    end
+
+    def test_phyloxml_examples_file
+      outputfn = "phyloxml_examples_generated_in_test.xml"
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml)
+      filename = @writeto.file(outputfn)
+      writer = Bio::PhyloXML::Writer.new(filename)
+      phyloxml.each do |tree|
+        writer.write(tree)
+      end
+      writer.write_other(phyloxml.other)
+
+      assert_nothing_thrown do
+        Bio::PhyloXML::Parser.open(filename) { |px| true }
+      end
+      # The output file is not deleted since it might be used in the phyloxml
+      # parser test. But since the order of tests can't be assumed, I can't
+      # hard code it in.
+    end
+
+    def test_made_up_xml_file
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.made_up_xml)
+      filename = @writeto.file("made_up_generated_in_test.xml")
+      writer = Bio::PhyloXML::Writer.new(filename)
+      # The output file is not deleted since it might be used in the phyloxml
+      # parser test. But since the order of tests can't be assumed, I can't
+      # hard code it in.
+      phyloxml.each do |tree|
+        writer.write(tree)
+      end      
+      phyloxml.close
+    end
+
+  end
+
+
+end if defined?(LibXML) #end module Bio
+

metadata

@@ -0,0 +1,155 @@
+--- !ruby/object:Gem::Specification
+name: bio-phyloxml
+version: !ruby/object:Gem::Version
+  version: 0.9.0
+  prerelease: 
+platform: ruby
+authors:
+- Diana Jaunzeikare
+- Clayton Wheeler
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-05-24 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: libxml-ruby
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.3.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.3.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+description: Provides PhyloXML support for BioRuby.
+email: cswh@umich.edu
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/bio-phyloxml.rb
+- lib/bio/phyloxml.rb
+- lib/bio/phyloxml/elements.rb
+- lib/bio/phyloxml/parser.rb
+- lib/bio/phyloxml/phyloxml.xsd
+- lib/bio/phyloxml/writer.rb
+- sample/test_phyloxml_big.rb
+- test/data/phyloxml/apaf.xml
+- test/data/phyloxml/bcl_2.xml
+- test/data/phyloxml/made_up.xml
+- test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml
+- test/data/phyloxml/phyloxml_examples.xml
+- test/helper.rb
+- test/unit/bio/test_phyloxml.rb
+- test/unit/bio/test_phyloxml_writer.rb
+homepage: http://github.com/csw/bioruby-phyloxml
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 1827548371593570525
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: PhyloXML plugin for BioRuby
+test_files: []