miga-base 0.2.0.6 → 0.2.0.7

data/scripts/haai_distances.bash

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+set -e
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1

data/scripts/init.bash

@@ -206,6 +206,8 @@ echo "{
 
 # Confirm configuration
 echo "
+MIGA_CONFIG_VERSION='$("$MIGA/bin/miga" -v)'
+MIGA_CONFIG_LONGVERSION='$("$MIGA/bin/miga" -V)'
 MIGA_CONFIG_DATE='$(date "+%Y-%m-%d %H:%M:%S %z")'
 " >> "$HOME/.miga_rc"
 

data/scripts/mytaxa.bash

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+set -e
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1

data/scripts/mytaxa_scan.bash

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+set -e
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1

data/scripts/ogs.bash

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+set -e
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1

data/scripts/read_quality.bash

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+set -e
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1

data/scripts/ssu.bash

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+set -e
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1

data/scripts/subclades.bash

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+set -e
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1

data/scripts/trimmed_fasta.bash

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+set -e
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1

data/scripts/trimmed_reads.bash

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+set -e
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1

data/test/common_test.rb

@@ -0,0 +1,82 @@
+require "test_helper"
+
+class CommonTest < Test::Unit::TestCase
+  
+  def setup
+    $gui_tests = !ENV["GUI_TESTS"].nil?
+  end
+
+  def test_debug
+    assert_respond_to(MiGA::MiGA, :DEBUG)
+    assert_respond_to(MiGA::MiGA, :DEBUG_ON)
+    assert_respond_to(MiGA::MiGA, :DEBUG_OFF)
+    MiGA::MiGA.DEBUG_ON
+    err = capture_stderr do
+      MiGA::MiGA.DEBUG "Tralari"
+    end
+    assert_equal("Tralari\n", err.string)
+    MiGA::MiGA.DEBUG_OFF
+    err = capture_stderr do
+      MiGA::MiGA.DEBUG "Tralara"
+    end
+    assert_equal("", err.string)
+  ensure
+    MiGA::MiGA.DEBUG_OFF
+  end
+
+  def test_debug_trace
+    assert_respond_to(MiGA::MiGA, :DEBUG)
+    assert_respond_to(MiGA::MiGA, :DEBUG_ON)
+    assert_respond_to(MiGA::MiGA, :DEBUG_OFF)
+    omit_if($gui_tests, "JRuby doesn't like interceptions.")
+    MiGA::MiGA.DEBUG_TRACE_ON
+    err = capture_stderr do
+      MiGA::MiGA.DEBUG "Dandadi"
+    end
+    assert(err.string =~ /Dandadi\n    .*block in test_debug_trace/)
+    MiGA::MiGA.DEBUG_TRACE_OFF
+    err = capture_stderr do
+      MiGA::MiGA.DEBUG "Dandada"
+    end
+    assert_equal("Dandada\n", err.string)
+  ensure
+    MiGA::MiGA.DEBUG_TRACE_OFF
+    MiGA::MiGA.DEBUG_OFF
+  end
+
+  def test_generic_transfer
+    $tmp = Dir.mktmpdir
+    hello = File.expand_path("Hello", $tmp)
+    world = File.expand_path("World", $tmp)
+    assert_respond_to(File, :generic_transfer)
+    FileUtils.touch(hello)
+    File.generic_transfer(hello, world, :symlink)
+    assert_equal("link", File.ftype(world), "World should be a link.")
+    File.generic_transfer(hello, world, :copy)
+    assert_equal("link", File.ftype(world), "World should still be a link.")
+    File.unlink world
+    File.generic_transfer(hello, world, :hardlink)
+    assert_equal("file", File.ftype(world), "A hardlink should be a file.")
+    File.open(hello, "w"){ |fh| fh.print "!" }
+    File.open(world, "r"){ |fh| assert_equal("!", fh.gets) }
+    File.unlink world
+    File.generic_transfer(hello, world, :copy)
+    assert_equal("file", File.ftype(world), "A copy should be a file.")
+    File.unlink world
+    assert_raise do
+      File.generic_transfer(hello, world, :monkey)
+    end
+    assert(!File.exist?(world), "A monkey shouldn't create files.")
+  ensure
+    FileUtils.rm_rf $tmp
+  end
+
+  def test_tabulate
+    tab = MiGA::MiGA.tabulate(%w[a b], [%w[123 45], %w[678 90]])
+    assert_equal("  a  b ", tab[0])
+    assert_equal("  -  - ", tab[1])
+    assert_equal("123  45", tab[2])
+    assert_equal("678  90", tab[3])
+  end
+
+end

data/test/daemon_test.rb

@@ -0,0 +1,53 @@
+require "test_helper"
+require "miga/daemon"
+
+class DaemonTest < Test::Unit::TestCase
+  
+  def setup
+    $tmp = Dir.mktmpdir
+    ENV["MIGA_HOME"] = $tmp
+    FileUtils.touch("#{ENV["MIGA_HOME"]}/.miga_rc")
+    File.open("#{ENV["MIGA_HOME"]}/.miga_daemon.json", "w") do |fh|
+      fh.puts '{"maxjobs":1,"ppn":1,"latency":2}'
+    end
+    $p1 = MiGA::Project.new(File.expand_path("project1", $tmp))
+    $d1 = MiGA::Daemon.new($p1)
+  end
+
+  def teardown
+    FileUtils.rm_rf $tmp
+    ENV["MIGA_HOME"] = nil
+  end
+  
+  def test_last_alive
+    p = MiGA::Project.new(File.expand_path("last_alive", $tmp))
+    d = MiGA::Daemon.new(p)
+    assert_nil(d.last_alive)
+    d.declare_alive
+    assert(d.last_alive - DateTime.now < 1)
+  end
+
+  def test_options
+    assert_respond_to($d1, :default_options)
+    assert_equal(:normal, $d1.default_options[:dir_mode])
+    assert_equal(2, $d1.runopts(:latency))
+    assert_equal(1, $d1.maxjobs)
+    assert_equal(2, $d1.latency)
+    assert_equal(1, $d1.ppn)
+    $d1.runopts(:alo, :ha)
+    assert_equal(:ha, $d1.runopts(:alo))
+    $d1.runopts(:maxjobs, "1")
+    assert_equal(1, $d1.maxjobs)
+    assert_raise do
+      $d1.runopts(:latency, "!")
+    end
+  end
+
+  def test_say
+    out = capture_stdout do
+      $d1.say "Olm"
+    end
+    assert(out.string =~ /^\[.*\] Olm/)
+  end
+
+end

data/test/dataset_test.rb

@@ -0,0 +1,156 @@
+require "test_helper"
+require "miga/project"
+
+class DatasetTest < Test::Unit::TestCase
+  
+  def setup
+    $tmp = Dir.mktmpdir
+    ENV["MIGA_HOME"] = $tmp
+    FileUtils.touch("#{ENV["MIGA_HOME"]}/.miga_rc")
+    FileUtils.touch("#{ENV["MIGA_HOME"]}/.miga_daemon.json")
+    $p1 = MiGA::Project.new(File.expand_path("project1", $tmp))
+    $d1 = $p1.add_dataset("dataset1")
+  end
+
+  def teardown
+    FileUtils.rm_rf $tmp
+    ENV["MIGA_HOME"] = nil
+  end
+  
+  def test_known_types
+    assert_respond_to(MiGA::Dataset, :KNOWN_TYPES)
+    assert(MiGA::Dataset.KNOWN_TYPES.has_key?(:genome))
+  end
+
+  def test_exist
+    assert_respond_to(MiGA::Dataset, :exist?)
+    assert(MiGA::Dataset.exist?($p1, "dataset1"))
+    assert(! MiGA::Dataset.exist?($p1, "Nope"))
+  end
+
+  def test_info_fields
+    assert_respond_to(MiGA::Dataset, :INFO_FIELDS)
+    assert(MiGA::Dataset.INFO_FIELDS.include?("name"))
+  end
+
+  def test_initialize
+    assert_raise do
+      MiGA::Dataset.new($p1, "dataset-1")
+    end
+    assert_equal($p1, $d1.project)
+    assert_equal("dataset1", $d1.name)
+    assert($d1.is_ref?)
+    assert_equal(MiGA::Metadata, $d1.metadata.class)
+  end
+
+  def test_save
+    d2 = $p1.add_dataset("ds_save")
+    assert_respond_to(d2, :save)
+    d2.save
+    assert(!d2.is_multi?)
+    assert(!d2.is_nonmulti?)
+    assert_nil(d2.metadata[:type])
+    d2.metadata[:tax] = {:ns=>"COMMUNITY"}
+    d2.save
+    assert_equal(:metagenome, d2.metadata[:type])
+    assert(d2.is_multi?)
+    assert(!d2.is_nonmulti?)
+  end
+
+  def test_remove
+    d2 = $p1.add_dataset("ds_remove")
+    assert(File.exist?(d2.metadata.path))
+    d2.remove!
+    assert(! File.exist?(d2.metadata.path))
+  end
+
+  def test_info
+    assert_equal($d1.name, $d1.info.first)
+  end
+
+  def test_add_result
+    d2 = $p1.add_dataset("ds_add_result")
+    assert_nil(d2.add_result(:koop))
+    assert_nil(d2.add_result(:raw_reads))
+    FileUtils.touch(
+      File.expand_path("data/01.raw_reads/#{d2.name}.1.fastq",$p1.path))
+    assert_nil(d2.add_result(:raw_reads))
+    FileUtils.touch(
+      File.expand_path("data/01.raw_reads/#{d2.name}.done",$p1.path))
+    assert_equal(MiGA::Result, d2.add_result(:raw_reads).class)
+  end
+
+  def test_preprocessing
+    d2 = $p1.add_dataset("ds_preprocessing")
+    assert_nil(d2.first_preprocessing)
+    assert_nil(d2.next_preprocessing)
+    assert(! d2.done_preprocessing?)
+    FileUtils.touch(File.expand_path(
+      "data/02.trimmed_reads/#{d2.name}.1.clipped.fastq",$p1.path))
+    FileUtils.touch(File.expand_path(
+      "data/02.trimmed_reads/#{d2.name}.done",$p1.path))
+    assert_equal(:trimmed_reads, d2.first_preprocessing(true))
+    assert_equal(:read_quality, d2.next_preprocessing(true))
+    assert(! d2.done_preprocessing?(true))
+    assert(d2.ignore_task?(:mytaxa))
+    assert(d2.ignore_task?(:distances))
+    d2.metadata[:type] = :metagenome
+    assert(! d2.ignore_task?(:mytaxa))
+    assert(d2.ignore_task?(:distances))
+    d2.metadata[:type] = :genome
+    assert(d2.ignore_task?(:mytaxa))
+    assert(! d2.ignore_task?(:distances))
+  end
+
+  def test_profile_advance
+    d2 = $p1.add_dataset("ds_profile_advance")
+    assert_equal(0, d2.profile_advance(true).first)
+    assert_equal(0, d2.profile_advance(true).last)
+    assert_equal(0, d2.profile_advance(true).inject(:+))
+    Dir.mkdir(File.expand_path(
+      "data/03.read_quality/#{d2.name}.solexaqa",$p1.path))
+    Dir.mkdir(File.expand_path(
+      "data/03.read_quality/#{d2.name}.fastqc",$p1.path))
+    FileUtils.touch(File.expand_path(
+      "data/03.read_quality/#{d2.name}.done",$p1.path))
+    assert_equal([0,0,1,2], d2.profile_advance(true)[0..3])
+    assert_equal(2, d2.profile_advance(true).last)
+  end
+
+  def test_add_result_other
+    d2 = $p1.add_dataset("ds_add_result_other")
+    Dir.mkdir(File.expand_path(
+      "data/07.annotation/01.function/01.essential/#{d2.name}.ess", $p1.path))
+    to_test = {
+      :trimmed_fasta => [
+        "data/04.trimmed_fasta/#{d2.name}.SingleReads.fa",
+        "data/04.trimmed_fasta/#{d2.name}.done"],
+      :assembly => [
+        "data/05.assembly/#{d2.name}.LargeContigs.fna",
+        "data/05.assembly/#{d2.name}.done"],
+      :cds => [
+        "data/06.cds/#{d2.name}.faa",
+        "data/06.cds/#{d2.name}.fna",
+        "data/06.cds/#{d2.name}.done"],
+      :essential_genes => %w[ess.faa ess/log done].map { |x|
+          "data/07.annotation/01.function/01.essential/#{d2.name}.#{x}" },
+      :ssu => [
+        "data/07.annotation/01.function/02.ssu/#{d2.name}.ssu.fa",
+        "data/07.annotation/01.function/02.ssu/#{d2.name}.done"],
+      :mytaxa_scan => %w[pdf wintax mytaxa reg done].map { |x|
+          "data/07.annotation/03.qa/02.mytaxa_scan/#{d2.name}.#{x}" },
+      :distances => [
+        "data/09.distances/01.haai/#{d2.name}.db",
+        "data/09.distances/#{d2.name}.done"]
+    }
+    to_test.each do |k,v|
+      assert_nil(d2.add_result(k), "Result for #{k} should be nil.")
+      v.each { |i| FileUtils.touch(File.expand_path(i, $p1.path)) }
+      FileUtils.touch(File.expand_path(
+        "data/04.trimmed_fasta/#{d2.name}.done",$p1.path))
+      assert_equal(MiGA::Result, d2.add_result(k).class,
+        "Result for #{k} should be MiGA::Result.")
+    end
+  end
+
+end

data/test/jruby_gui_test.rb

@@ -0,0 +1,20 @@
+require "test_helper"
+require "miga/gui"
+
+class GUITest < Test::Unit::TestCase
+  
+  def setup
+    $app = MiGA::GUI.new
+  end
+
+  def test_status
+    assert_respond_to(MiGA::GUI, :status)
+    assert_equal("Initializing MiGA...", MiGA::GUI.status)
+    assert_equal(MiGA::GUI, $app.class)
+    MiGA::GUI.status = "Well well well..."
+    assert_equal("Well well well...", MiGA::GUI.status)
+    MiGA::GUI.reset_status
+    assert_equal("MiGA is ready to go!", MiGA::GUI.status)
+  end
+
+end

data/test/metadata_test.rb

@@ -0,0 +1,48 @@
+require "test_helper"
+require "miga/metadata"
+
+class MetadataTest < Test::Unit::TestCase
+  
+  def setup
+    $tmp = Dir.mktmpdir
+    $gui_tests = !ENV["GUI_TESTS"].nil?
+  end
+
+  def teardown
+    FileUtils.rm_rf $tmp
+  end
+  
+  def test_save
+    omit_if($gui_tests, "JRuby doesn't implement fork.")
+    md1 = MiGA::Metadata.new(File.expand_path("md_save.json", $tmp))
+    FileUtils.touch(md1.lock_file)
+    fork do
+      sleep(1)
+      File.unlink(md1.lock_file)
+    end
+    t1 = Time.new
+    md1.save
+    t2 = Time.new
+    assert(! File.exist?(md1.lock_file))
+    assert(t2-t1 >= 1.0)
+  end
+
+  def test_load
+    md1 = MiGA::Metadata.new(File.expand_path("md_load.json", $tmp), {:t=>1})
+    assert_equal(1, md1[:t])
+    omit_if($gui_tests, "JRuby doesn't implement fork.")
+    FileUtils.touch(md1.lock_file)
+    fork do
+      sleep(1)
+      File.open(md1.path, "w"){ |fh| fh.print '{"t": 2}' }
+      File.unlink(md1.lock_file)
+    end
+    t1 = Time.new
+    md1.load
+    t2 = Time.new
+    assert_equal(2, md1[:t])
+    assert(! File.exist?(md1.lock_file))
+    assert(t2-t1 >= 1.0)
+  end
+
+end

data/test/project_test.rb

@@ -0,0 +1,54 @@
+require "test_helper"
+require "miga/project"
+
+class ProjectTest < Test::Unit::TestCase
+  
+  def setup
+    $tmp = Dir.mktmpdir
+    ENV["MIGA_HOME"] = $tmp
+    FileUtils.touch("#{ENV["MIGA_HOME"]}/.miga_rc")
+    FileUtils.touch("#{ENV["MIGA_HOME"]}/.miga_daemon.json")
+    $p1 = MiGA::Project.new(File.expand_path("project1", $tmp))
+  end
+
+  def teardown
+    FileUtils.rm_rf $tmp
+    ENV["MIGA_HOME"] = nil
+  end
+  
+  def test_class_load
+    assert_nil(MiGA::Project.load($tmp + "/O_o"))
+    assert_equal(MiGA::Project, MiGA::Project.load($p1.path).class)
+  end
+
+  def test_create
+    assert_equal($tmp + "create", MiGA::Project.new($tmp + "create").path)
+    assert_raise do
+      ENV["MIGA_HOME"] = $tmp + "/chez-moi"
+      MiGA::Project.new($tmp + "/cuckoo")
+    end
+  ensure
+    ENV["MIGA_HOME"] = $tmp
+  end
+
+  def test_load
+    p = MiGA::Project.new($tmp + "/load")
+    assert_equal(MiGA::Project, p.class)
+    File.unlink p.metadata.path
+    assert_raise do
+      p.load
+    end
+  end
+
+  def test_datasets
+    p = MiGA::Project.new(File.expand_path("datasets", $tmp))
+    d = p.add_dataset("d1")
+    assert_equal(MiGA::Dataset, d.class)
+    assert_equal([d], p.datasets)
+    p.each_dataset{ |ds| assert_equal(d, ds) }
+    dr = p.unlink_dataset("d1")
+    assert_equal(d, dr)
+    assert_equal([], p.datasets)
+  end
+
+end

data/test/remote_dataset_test.rb

@@ -0,0 +1,41 @@
+require "test_helper"
+require "miga/project"
+require "miga/remote_dataset"
+
+class RemoteDatasetTest < Test::Unit::TestCase
+  
+  def setup
+    $tmp = Dir.mktmpdir
+    ENV["MIGA_HOME"] = $tmp
+    FileUtils.touch("#{ENV["MIGA_HOME"]}/.miga_rc")
+    FileUtils.touch("#{ENV["MIGA_HOME"]}/.miga_daemon.json")
+    $p1 = MiGA::Project.new(File.expand_path("project1", $tmp))
+    $remote_tests = !ENV["REMOTE_TESTS"].nil?
+  end
+
+  def teardown
+    FileUtils.rm_rf $tmp
+    ENV["MIGA_HOME"] = nil
+  end
+  
+  def test_class_universe
+    assert_respond_to(MiGA::RemoteDataset, :UNIVERSE)
+    assert(MiGA::RemoteDataset.UNIVERSE.keys.include? :ebi)
+  end
+
+  def test_bad_remote_dataset
+    assert_raise { MiGA::RemoteDataset.new("ids", :embl, :marvel) }
+    assert_raise { MiGA::RemoteDataset.new("ids", :google, :ebi) }
+  end
+
+  def test_ebi
+    hiv2 = "M30502.1"
+    rd = MiGA::RemoteDataset.new(hiv2, :embl, :ebi)
+    assert_equal([hiv2], rd.ids)
+    omit_if(!$remote_tests, "Remote access is error-prone.")
+    tx = rd.get_ncbi_taxonomy
+    assert_equal(MiGA::Taxonomy, tx.class)
+    assert_equal("Lentivirus", tx[:g])
+  end
+
+end

data/test/tax_index_test.rb

@@ -0,0 +1,44 @@
+require "test_helper"
+require "miga/tax_index"
+
+class TaxIndexTest < Test::Unit::TestCase
+  
+  def test_initialization
+    ti = MiGA::TaxIndex.new
+    assert_equal(:root, ti.root.rank)
+  end
+
+  def test_dataset
+    $tmp = Dir.mktmpdir
+    ENV["MIGA_HOME"] = $tmp
+    FileUtils.touch("#{ENV["MIGA_HOME"]}/.miga_rc")
+    FileUtils.touch("#{ENV["MIGA_HOME"]}/.miga_daemon.json")
+    p = MiGA::Project.new(File.expand_path("project1", $tmp))
+    d = p.add_dataset("dataset1")
+    
+    ti = MiGA::TaxIndex.new
+    assert(ti.datasets.empty?)
+    ti << d
+    assert(ti.datasets.empty?, "Index should ignore datasets without tax.")
+    d.metadata[:tax] = MiGA::Taxonomy.new("k:Fantasia g:Unicornia")
+    ti << d
+    assert_equal(1, ti.datasets.size, "Index should have one dataset.")
+    assert_equal(1, ti.root.datasets_count)
+  ensure
+    FileUtils.rm_rf $tmp
+    ENV["MIGA_HOME"] = nil
+  end
+
+  def test_to_json
+    js = JSON.parse(MiGA::TaxIndex.new.to_json)
+    assert(js.keys.include? "datasets")
+    assert_equal(2, js.keys.size)
+    assert(js["datasets"].empty?)
+  end
+
+  def test_to_tab
+    ti = MiGA::TaxIndex.new
+    assert_equal("root:biota: 0\n", ti.to_tab)
+  end
+
+end

data/test/taxonomy_test.rb

@@ -0,0 +1,36 @@
+require "test_helper"
+require "miga/taxonomy"
+
+class TaxonomyTest < Test::Unit::TestCase
+  
+  def test_ranks
+    assert_respond_to(MiGA::Taxonomy, :KNOWN_RANKS)
+    assert(MiGA::Taxonomy.KNOWN_RANKS.include? :s)
+    assert_nil(MiGA::Taxonomy.normalize_rank "No Rank")
+    assert_nil(MiGA::Taxonomy.normalize_rank "Captain")
+    assert_equal(:f, MiGA::Taxonomy.normalize_rank(:Family))
+  end
+
+  def test_json
+    js = '{"json_class":"MiGA::Taxonomy",' +
+      '"str":"k:Fantasia f:Dragonaceae s:Dragonia_azura"}'
+    tx = JSON.parse(js, {:symbolize_names=>false, :create_additions=>true})
+    assert_equal(MiGA::Taxonomy, tx.class)
+    assert_equal("Dragonaceae", tx[:f])
+    assert_equal(js, tx.to_json)
+  end
+
+  def test_append
+    tx = MiGA::Taxonomy.new ""
+    assert_equal("", "#{tx}")
+    tx << ["domain:Public","family:GNU"]
+    assert_equal("GNU", tx[:f])
+    tx << "class:ShareAlike"
+    assert_equal("ShareAlike", tx[:c])
+    tx << { :genus => "v3" }
+    assert_equal("v3", tx[:g])
+    tx << "s:v3_0"
+    assert(tx.is_in? MiGA::Taxonomy.new("species:v3_0"))
+  end
+
+end

data/test/test_helper.rb

@@ -0,0 +1,32 @@
+require "codeclimate-test-reporter"
+CodeClimate::TestReporter.start
+
+require "rubygems"
+require "test/unit"
+require "miga/common"
+require "stringio"
+
+##
+# Kernel extensions tp capture +$stdout+ and +$stderr+ based on
+# http://thinkingdigitally.com/archive/capturing-output-from-puts-in-ruby/
+module Kernel
+  
+  def capture_stdout
+    out = StringIO.new
+    $stdout = out
+    yield
+    return out
+  ensure
+    $stdout = STDOUT
+  end
+
+  def capture_stderr
+    err = StringIO.new
+    $stderr = err
+    yield
+    return err
+  ensure
+    $stderr = STDERR
+  end
+
+end