Newly added sample script to test big PhyloXML data

* Newly added a sample script to test big PhyloXML data based on Diana Jaunzeikare's work. (http://github.com/latvianlinuxgirl/bioruby/blob/ 20627fc5a443d6c2e3dc73ed50e9c578ffcbc330/ test/unit/bio/db/test_phyloxml_big.rb).
csw · Nov 18, 2009 · b6d2f1e · b6d2f1e
1 parent d5ef954
commit b6d2f1e
Showing 1 changed file with 205 additions and 0 deletions.
diff --git a/sample/test_phyloxml_big.rb b/sample/test_phyloxml_big.rb
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+#
+# = sample/test_phyloxml_big.rb - Tests for Bio::PhyloXML. Testing very big files.
+#
+# Copyright::   Copyright (C) 2009
+#               Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+
+# libraries needed for the tests
+require 'libxml'
+require 'pathname'
+require 'test/unit'
+require 'digest/sha1'
+
+require 'bio/command'
+require 'bio/db/phyloxml/phyloxml_parser'
+require 'bio/db/phyloxml/phyloxml_writer'
+
+PhyloXMLBigDataPath = ARGV.shift
+
+if !PhyloXMLBigDataPath then
+  exit_code = 0
+elsif !File.directory?(PhyloXMLBigDataPath) then
+  exit_code = 1
+else
+  exit_code = false
+end
+
+if exit_code then
+  puts "Usage: #{$0} path_to_data (test options...)"
+  puts ""
+  puts "Requirements:"
+  puts " - Write permission to the path_to_data"
+  puts " - Internet connection for downloading test data"
+  puts " - unzip command to extract downloaded test data"
+  puts ""
+  puts "You may want to run Ruby with -rubygems and -I<path_to_bioruby_lib>."
+  puts ""
+  puts "Example of usage using /tmp:"
+  puts "    $ mkdir /tmp/phyloxml"
+  puts "    $ ruby -rubygems -I lib #{$0} /tmp/phyloxml -v"
+  puts ""
+  exit(exit_code)
+end
+
+module TestPhyloXMLBigData
+
+  module_function
+
+  def metazoa_xml
+    #puts "Metazoa 30MB"
+    filename = 'ncbi_taxonomy_metazoa.xml'
+    uri = "http://www.phylosoft.org/archaeopteryx/examples/data/ncbi_taxonomy_metazoa.xml.zip"
+    download_and_unzip_if_not_found(filename, uri, "1M", "33M")
+  end
+
+  def metazoa_test_xml
+    #puts "writing Metazoa 30MB"
+    File.join PhyloXMLBigDataPath, 'writer_test_ncbi_taxonomy_metazoa.xml'
+  end
+
+  def metazoa_roundtrip_xml
+    #puts "writing Metazoa 30MB roundtrip"
+    File.join PhyloXMLBigDataPath, 'roundtrip_test_ncbi_taxonomy_metazoa.xml'
+  end
+
+  def mollusca_xml
+    #puts "Mollusca 1.5MB"
+    filename = 'ncbi_taxonomy_mollusca.xml'
+    uri = "http://www.phylosoft.org/archaeopteryx/examples/data/ncbi_taxonomy_mollusca.xml.zip"
+    download_and_unzip_if_not_found(filename, uri, "67K", "1.5M")
+  end
+
+  def mollusca_test_xml
+    #puts "Writing Mollusca 1.5MB"
+    File.join PhyloXMLBigDataPath, 'writer_test_ncbi_taxonomy_mollusca.xml'
+  end
+
+  def mollusca_roundtrip_xml
+    #puts "Writing Mollusca 1.5MB roundtrip"
+    File.join PhyloXMLBigDataPath, 'roundtrip_test_ncbi_taxonomy_mollusca.xml'
+  end
+
+  def life_xml
+    #Right now this file is not compatible with xsd 1.10
+    filename = 'tol_life_on_earth_1.xml'
+    uri = "http://www.phylosoft.org/archaeopteryx/examples/data/tol_life_on_earth_1.xml.zip"
+
+    download_and_unzip_if_not_found(filename, uri, '10M', '45M')
+  end
+
+  def life_test_xml
+    File.join PhyloXMLBigDataPath, 'writer_test_tol_life_on_earth_1.xml'
+  end
+
+  def life_roundtrip_xml
+    File.join PhyloXMLBigDataPath, 'roundtrip_test_tol_life_on_earth_1.xml'
+  end
+
+  def unzip_file(file, target_dir)
+    flag = system('unzip', "#{file}.zip", "-d", target_dir)
+    unless flag then
+      raise "Failed to unzip #{file}.zip"
+    end
+    file
+  end
+
+  def download_and_unzip_if_not_found(basename, uri, zipsize, origsize)
+    file = File.join PhyloXMLBigDataPath, basename
+    return file if File.exists?(file)
+
+    if File.exists?("#{file}.zip")
+      unzip_file(file, PhyloXMLBigDataPath)
+      return file
+    end
+
+    puts "File #{basename} does not exist. Do you want to download it? (If yes, ~#{zipsize}B zip file will be downloaded and extracted (to #{origsize}B), if no, the test will be skipped.) y/n?"
+    res = gets
+    if res.to_s.chomp.downcase == "y"
+      File.open("#{file}.zip", "wb") do |f|
+        f.write(Bio::Command.read_uri(uri))
+      end
+      puts "File downloaded."
+      self.unzip_file(file, PhyloXMLBigDataPath)
+      return file
+    else
+      return nil
+      #return File.join PHYLOXML_TEST_DATA, "#{basename}.stub"
+    end
+  end
+
+end #end module TestPhyloXMLBigData
+
+module Bio
+
+  class TestPhyloXMLBig < Test::Unit::TestCase
+
+    def do_test_next_tree(readfilename)
+      raise "the test is skipped" unless readfilename
+      filesizeMB = File.size(readfilename) / 1048576.0
+      printf "Reading %s (%2.1f MB)\n", readfilename, filesizeMB
+
+      begin
+        phyloxml = Bio::PhyloXML::Parser.open(readfilename)
+      rescue NoMethodError
+        phyloxml = Bio::PhyloXML::Parser.new(readfilename)
+      end
+      tree = nil
+      assert_nothing_raised {
+        tree = phyloxml.next_tree
+      }
+      tree
+    end
+    private :do_test_next_tree
+
+    def do_test_write(tree, writefilename)
+      printf "Writing to %s\n", writefilename
+      writer = Bio::PhyloXML::Writer.new(writefilename)
+      assert_nothing_raised {
+        writer.write(tree)
+      }
+
+      # checks file size and sha1sum
+      str = File.open(writefilename, 'rb') { |f| f.read }
+      sha1 = Digest::SHA1.hexdigest(str)
+      puts "Wrote #{str.length} bytes."
+      puts "sha1: #{sha1}"
+    end
+    private :do_test_write
+
+    def test_mollusca
+      tree = do_test_next_tree(TestPhyloXMLBigData.mollusca_xml)
+      do_test_write(tree, TestPhyloXMLBigData.mollusca_test_xml)
+
+      tree2 = do_test_next_tree(TestPhyloXMLBigData.mollusca_test_xml)
+      do_test_write(tree2, TestPhyloXMLBigData.mollusca_roundtrip_xml)
+    end
+
+    def test_metazoa
+      tree = do_test_next_tree(TestPhyloXMLBigData.metazoa_xml)
+      do_test_write(tree, TestPhyloXMLBigData.metazoa_test_xml)
+
+      tree2 = do_test_next_tree(TestPhyloXMLBigData.metazoa_test_xml)
+      do_test_write(tree2, TestPhyloXMLBigData.metazoa_roundtrip_xml)
+    end
+
+    if false
+      # Disabled because of the error.
+      # LibXML::XML::Error: Fatal error: Input is not proper UTF-8,
+      # indicate encoding !
+      # Bytes: 0xE9 0x6B 0x65 0x73 at tol_life_on_earth_1.xml:132170.
+      #
+      def test_life
+        tree = do_test_next_tree(TestPhyloXMLBigData.life_xml)
+        do_test_write(tree, TestPhyloXMLBigData.life_test_xml)
+
+        tree2 = do_test_next_tree(TestPhyloXMLBigData.life_test_xml)
+        do_test_write(tree2, TestPhyloXMLBigData.life_roundtrip_xml)
+      end
+    end #if false
+
+  end
+
+end