miga-base 0.6.0.0 → 0.6.1.0

data/test/dataset_test.rb

@@ -1,22 +1,22 @@
-require "test_helper"
-require "miga/project"
+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")
+    ENV['MIGA_HOME'] = $tmp
+    FileUtils.touch(File.expand_path('.miga_rc', ENV['MIGA_HOME']))
+    FileUtils.touch(File.expand_path('.miga_daemon.json', ENV['MIGA_HOME']))
+    $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
+    ENV['MIGA_HOME'] = nil
   end
-  
+
   def test_known_types
     assert_respond_to(MiGA::Dataset, :KNOWN_TYPES)
     assert(MiGA::Dataset.KNOWN_TYPES.has_key?(:genome))
@@ -24,27 +24,25 @@ class DatasetTest < Test::Unit::TestCase
 
   def test_exist
     assert_respond_to(MiGA::Dataset, :exist?)
-    assert(MiGA::Dataset.exist?($p1, "dataset1"))
-    assert(! MiGA::Dataset.exist?($p1, "Nope"))
+    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"))
+    assert(MiGA::Dataset.INFO_FIELDS.include?('name'))
   end
 
   def test_initialize
-    assert_raise do
-      MiGA::Dataset.new($p1, "dataset-1")
-    end
+    assert_raise { MiGA::Dataset.new($p1, 'dataset-1') }
     assert_equal($p1, $d1.project)
-    assert_equal("dataset1", $d1.name)
+    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")
+    d2 = $p1.add_dataset('ds_save')
     assert_respond_to(d2, :save)
     d2.save
     assert(!d2.is_multi?)
@@ -58,7 +56,7 @@ class DatasetTest < Test::Unit::TestCase
   end
 
   def test_remove
-    d2 = $p1.add_dataset("ds_remove")
+    d2 = $p1.add_dataset('ds_remove')
     assert(File.exist?(d2.metadata.path))
     d2.remove!
     assert(! File.exist?(d2.metadata.path))
@@ -69,7 +67,7 @@ class DatasetTest < Test::Unit::TestCase
   end
 
   def test_add_result
-    d2 = $p1.add_dataset("ds_add_result")
+    d2 = $p1.add_dataset('ds_add_result')
     assert_nil(d2.add_result(:koop))
     assert_nil(d2.add_result(:raw_reads))
     FileUtils.touch(
@@ -81,14 +79,16 @@ class DatasetTest < Test::Unit::TestCase
   end
 
   def test_preprocessing
-    d2 = $p1.add_dataset("ds_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))
+      "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))
+      "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))
@@ -114,53 +114,70 @@ class DatasetTest < Test::Unit::TestCase
   end
 
   def test_profile_advance
-    d2 = $p1.add_dataset("ds_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))
+      "data/03.read_quality/#{d2.name}.solexaqa", $p1.path
+    ))
     Dir.mkdir(File.expand_path(
-      "data/03.read_quality/#{d2.name}.fastqc",$p1.path))
+      "data/03.read_quality/#{d2.name}.fastqc", $p1.path
+    ))
     FileUtils.touch(File.expand_path(
-      "data/03.read_quality/#{d2.name}.done",$p1.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")
+    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))
+      "data/07.annotation/01.function/01.essential/#{d2.name}.ess", $p1.path
+    ))
     to_test = {
-      :trimmed_fasta => [
+      trimmed_fasta: [
         "data/04.trimmed_fasta/#{d2.name}.SingleReads.fa",
-        "data/04.trimmed_fasta/#{d2.name}.done"],
-      :assembly => [
+        "data/04.trimmed_fasta/#{d2.name}.done"
+      ],
+      assembly: [
         "data/05.assembly/#{d2.name}.LargeContigs.fna",
-        "data/05.assembly/#{d2.name}.done"],
-      :cds => [
+        "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/06.cds/#{d2.name}.done"
+      ],
+      essential_genes: %w[ess.faa ess/log done]
+        .map do |x|
+          "data/07.annotation/01.function/01.essential/#{d2.name}.#{x}"
+        end,
+      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/07.annotation/01.function/02.ssu/#{d2.name}.done"
+      ],
+      mytaxa_scan: %w[pdf wintax mytaxa reg done]
+        .map do |x|
+          "data/07.annotation/03.qa/02.mytaxa_scan/#{d2.name}.#{x}"
+        end,
+      distances: [
         "data/09.distances/01.haai/#{d2.name}.db",
-        "data/09.distances/#{d2.name}.done"]
+        "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.")
+        "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
 

data/test/hook_test.rb

@@ -2,12 +2,12 @@ require 'test_helper'
 require 'miga/project'
 
 class HookTest < 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")
+    FileUtils.touch(File.expand_path('.miga_rc', ENV['MIGA_HOME']))
+    FileUtils.touch(File.expand_path('.miga_daemon.json', ENV['MIGA_HOME']))
     $p1 = MiGA::Project.new(File.expand_path('project1', $tmp))
     $d1 = $p1.add_dataset('dataset1')
   end
@@ -33,6 +33,8 @@ class HookTest < Test::Unit::TestCase
     end
   end
 
+  ##
+  # Dummy class with hooks
   class MyHanger
     include MiGA::Common::Hooks
   end
@@ -61,12 +63,15 @@ class HookTest < Test::Unit::TestCase
 
   def test_dataset_clear_run_counts
     $d1.metadata[:_try_something] = 1
+    $d1.metadata[:_step] = 'Boop'
     $d1.metadata[:_not_a_counter] = 1
     $d1.save
     assert_equal(1, $d1.metadata[:_try_something])
+    assert_equal('Boop', $d1.metadata[:_step])
     $d1.add_hook(:on_remove, :clear_run_counts)
     $d1.remove!
     assert_nil($d1.metadata[:_try_something])
+    assert_nil($d1.metadata[:_step])
     assert_equal(1, $d1.metadata[:_not_a_counter])
   end
 
@@ -91,13 +96,20 @@ class HookTest < Test::Unit::TestCase
   def test_project_result_hooks
     $res = :test
     $counter = 1
-    $p1.add_hook(:on_result_ready,
-      :run_lambda, Proc.new { |r| $res = r })
-    $p1.add_hook(:on_result_ready_project_stats,
-      :run_lambda, Proc.new { $counter += 1 })
+    $p1.add_hook(
+      :on_result_ready,
+      :run_lambda,
+      Proc.new { |r| $res = r }
+    )
+    $p1.add_hook(
+      :on_result_ready_project_stats,
+      :run_lambda,
+      Proc.new { $counter += 1 }
+    )
     %w[taxonomy.json metadata.db done].each do |ext|
       FileUtils.touch(File.expand_path(
-        "data/90.stats/miga-project.#{ext}", $p1.path))
+        "data/90.stats/miga-project.#{ext}", $p1.path
+      ))
     end
     assert_equal(:project_stats, $p1.next_task(nil, false))
     assert_equal(:test, $res)

data/test/json_test.rb

@@ -1,12 +1,16 @@
 require 'test_helper'
 
 class JsonTest < Test::Unit::TestCase
-  
+
   def test_parse
-    assert_equal({a: 1, b: 2},
-      MiGA::Json.parse('{"a": 1, "b": 2}', contents: true))
-    assert_equal({'a' => 1, 'b' => 2},
-      MiGA::Json.parse('{"a": 1, "b": 2}', contents: true, symbolize: false))
+    assert_equal(
+      {a: 1, b: 2},
+      MiGA::Json.parse('{"a": 1, "b": 2}', contents: true)
+    )
+    assert_equal(
+      {'a' => 1, 'b' => 2},
+      MiGA::Json.parse('{"a": 1, "b": 2}', contents: true, symbolize: false)
+    )
     assert_equal(1.0, MiGA::Json.parse('1.0', contents: true))
   end
 
@@ -23,15 +27,18 @@ class JsonTest < Test::Unit::TestCase
 
     assert_equal(
       {a: 123, k: false, kb: false, t: nil},
-      MiGA::Json.parse(tmp1.path, default: tmp2.path))
+      MiGA::Json.parse(tmp1.path, default: tmp2.path)
+    )
     assert_equal(
       {a: 456, k: false, kb: false, t: 10.0},
-      MiGA::Json.parse(tmp2.path, default: tmp1.path))
+      MiGA::Json.parse(tmp2.path, default: tmp1.path)
+    )
   end
 
   def test_generate
     assert_equal("{\n  \"a\": 1,\n  \"b\": 2\n}",
-      MiGA::Json.generate({a: 1, b: 2}))
+      MiGA::Json.generate({a: 1, b: 2})
+    )
   end
 
 end

data/test/metadata_test.rb

@@ -1,20 +1,20 @@
-require "test_helper"
-require "miga/metadata"
+require 'test_helper'
+require 'miga/metadata'
 
 class MetadataTest < Test::Unit::TestCase
-  
+
   def setup
     $tmp = Dir.mktmpdir
-    $jruby_tests = !ENV["JRUBY_TESTS"].nil?
+    $jruby_tests = !ENV['JRUBY_TESTS'].nil?
   end
 
   def teardown
     FileUtils.rm_rf $tmp
   end
-  
+
   def test_save
-    omit_if($jruby_tests, "JRuby doesn't implement fork.")
-    md1 = MiGA::Metadata.new(File.expand_path("md_save.json", $tmp))
+    omit_if($jruby_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)
@@ -28,13 +28,13 @@ class MetadataTest < Test::Unit::TestCase
   end
 
   def test_load
-    md1 = MiGA::Metadata.new(File.expand_path("md_load.json", $tmp), {:t=>1})
+    md1 = MiGA::Metadata.new(File.expand_path('md_load.json', $tmp), {t: 1})
     assert_equal(1, md1[:t])
-    omit_if($jruby_tests, "JRuby doesn't implement fork.")
+    omit_if($jruby_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.open(md1.path, 'w') { |fh| fh.print '{"t": 2}' }
       File.unlink(md1.lock_file)
     end
     t1 = Time.new

data/test/project_test.rb

@@ -1,23 +1,23 @@
-require "test_helper"
-require "miga/project"
+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))
+    ENV['MIGA_HOME'] = $tmp
+    FileUtils.touch(File.expand_path('.miga_rc', ENV['MIGA_HOME']))
+    FileUtils.touch(File.expand_path('.miga_daemon.json', ENV['MIGA_HOME']))
+    $p1 = MiGA::Project.new(File.expand_path('project1', $tmp))
   end
 
   def teardown
     FileUtils.rm_rf $tmp
-    ENV["MIGA_HOME"] = nil
+    ENV['MIGA_HOME'] = nil
   end
-  
+
   def test_class_load
-    assert_nil(MiGA::Project.load($tmp + "/O_o"))
+    assert_nil(MiGA::Project.load($tmp + '/O_o'))
     assert_equal(MiGA::Project, MiGA::Project.load($p1.path).class)
   end
 
@@ -25,15 +25,15 @@ class ProjectTest < Test::Unit::TestCase
     assert_equal("#{$tmp}/create", MiGA::Project.new("#{$tmp}/create").path)
     assert(Dir.exist?("#{$tmp}/create"))
     assert_raise do
-      ENV["MIGA_HOME"] = $tmp + "/chez-moi"
-      MiGA::Project.new($tmp + "/cuckoo")
+      ENV['MIGA_HOME'] = $tmp + '/chez-moi'
+      MiGA::Project.new($tmp + '/cuckoo')
     end
   ensure
-    ENV["MIGA_HOME"] = $tmp
+    ENV['MIGA_HOME'] = $tmp
   end
 
   def test_load
-    p = MiGA::Project.new($tmp + "/load")
+    p = MiGA::Project.new($tmp + '/load')
     assert_equal(MiGA::Project, p.class)
     File.unlink p.metadata.path
     assert_raise do
@@ -43,12 +43,12 @@ class ProjectTest < Test::Unit::TestCase
 
   def test_datasets
     p = $p1
-    d = p.add_dataset("d1")
+    d = p.add_dataset('d1')
     assert_equal(MiGA::Dataset, d.class)
     assert_equal([d], p.datasets)
-    assert_equal(["d1"], p.dataset_names)
+    assert_equal(['d1'], p.dataset_names)
     p.each_dataset{ |ds| assert_equal(d, ds) }
-    dr = p.unlink_dataset("d1")
+    dr = p.unlink_dataset('d1')
     assert_equal(d, dr)
     assert_equal([], p.datasets)
     assert_equal([], p.dataset_names)
@@ -56,23 +56,27 @@ class ProjectTest < Test::Unit::TestCase
 
   def test_import_dataset
     p1 = $p1
-    d1 = p1.add_dataset("d1")
-    File.open("#{p1.path}/data/01.raw_reads/#{d1.name}.1.fastq",
-      "w") { |f| f.puts ":-)" }
-    File.open("#{p1.path}/data/01.raw_reads/#{d1.name}.done",
-      "w") { |f| f.puts ":-)" }
+    d1 = p1.add_dataset('d1')
+    File.open(
+      "#{p1.path}/data/01.raw_reads/#{d1.name}.1.fastq", 'w'
+    ) { |f| f.puts ':-)' }
+    File.open(
+      "#{p1.path}/data/01.raw_reads/#{d1.name}.done", 'w'
+    ) { |f| f.puts ':-)' }
     d1.next_preprocessing(true)
-    p2 = MiGA::Project.new(File.expand_path("import_dataset", $tmp))
+    p2 = MiGA::Project.new(File.expand_path('import_dataset', $tmp))
     assert(p2.datasets.empty?)
-    assert_nil(p2.dataset("d1"))
+    assert_nil(p2.dataset('d1'))
     p2.import_dataset(d1)
     assert_equal(1, p2.datasets.size)
-    assert_equal(MiGA::Dataset, p2.dataset("d1").class)
-    assert_equal(1, p2.dataset("d1").results.size)
+    assert_equal(MiGA::Dataset, p2.dataset('d1').class)
+    assert_equal(1, p2.dataset('d1').results.size)
     assert(File.exist?(
-      File.expand_path("data/01.raw_reads/#{d1.name}.1.fastq", p2.path)))
+      File.expand_path("data/01.raw_reads/#{d1.name}.1.fastq", p2.path)
+    ))
     assert(File.exist?(
-      File.expand_path("metadata/#{d1.name}.json", p2.path)))
+      File.expand_path("metadata/#{d1.name}.json", p2.path)
+    ))
   end
 
   def test_add_result
@@ -81,7 +85,8 @@ class ProjectTest < Test::Unit::TestCase
     %w[.Rdata .log .txt .done].each do |x|
       assert_nil(p1.add_result(:haai_distances))
       FileUtils.touch(
-        File.expand_path("data/09.distances/01.haai/miga-project#{x}",p1.path))
+        File.expand_path("data/09.distances/01.haai/miga-project#{x}",p1.path)
+      )
     end
     assert_equal(MiGA::Result, p1.add_result(:haai_distances).class)
   end
@@ -90,8 +95,9 @@ class ProjectTest < Test::Unit::TestCase
     p1 = $p1
     assert_nil(p1.result :n00b)
     assert_nil(p1.result :project_stats)
-    File.open(File.expand_path("data/90.stats/miga-project.json",p1.path),
-      "w"){ |fh| fh.puts "{}" }
+    File.open(
+      File.expand_path('data/90.stats/miga-project.json', p1.path), 'w'
+    ) { |fh| fh.puts '{}' }
     assert_not_nil(p1.result :project_stats)
     assert_equal(1, p1.results.size)
   end
@@ -99,8 +105,8 @@ class ProjectTest < Test::Unit::TestCase
   def test_preprocessing
     p1 = $p1
     assert(p1.done_preprocessing?)
-    d1 = p1.add_dataset("BAH")
-    assert(! p1.done_preprocessing?)
+    d1 = p1.add_dataset('BAH')
+    assert(!p1.done_preprocessing?)
     FileUtils.touch(File.expand_path("data/90.stats/#{d1.name}.done", p1.path))
     assert(p1.done_preprocessing?)
 
@@ -108,12 +114,14 @@ class ProjectTest < Test::Unit::TestCase
     assert_equal(:project_stats, p1.next_distances)
     d = MiGA::Project.RESULT_DIRS[:project_stats]
     %w[.done .taxonomy.json .metadata.db].each do |x|
-      assert_nil(p1.add_result(:project_stats),
-        "Premature registration of result project_stats at extension #{x}.")
+      assert_nil(
+        p1.add_result(:project_stats),
+        "Premature registration of result project_stats at extension #{x}."
+      )
       FileUtils.touch(File.expand_path("data/#{d}/miga-project#{x}", p1.path))
     end
     assert_equal(MiGA::Result, p1.add_result(:project_stats).class,
-      "Imposible to add project_stats result.")
+      'Imposible to add project_stats result.')
 
     # Distances
     [:haai_distances, :aai_distances, :ani_distances].each do |r|
@@ -121,15 +129,17 @@ class ProjectTest < Test::Unit::TestCase
       assert_equal(Symbol, p1.next_distances.class)
       d = MiGA::Project.RESULT_DIRS[r]
       %w[.done .Rdata .log .txt].each do |x|
-        assert_nil(p1.add_result(r),
-          "Premature registration of result #{r} at extension #{x}.")
+        assert_nil(
+          p1.add_result(r),
+          "Premature registration of result #{r} at extension #{x}."
+        )
         FileUtils.touch(File.expand_path("data/#{d}/miga-project#{x}", p1.path))
       end
       assert_equal(MiGA::Result, p1.add_result(r).class,
         "Imposible to add #{r} result.")
     end
     assert_equal(:clade_finding, p1.next_distances)
-    
+
     # Clades
     assert_nil(p1.next_inclade)
     p1.metadata[:type] = :clade
@@ -144,15 +154,19 @@ class ProjectTest < Test::Unit::TestCase
       d = MiGA::Project.RESULT_DIRS[r]
       assert_equal(Symbol, p1.next_inclade.class)
       ([".done"] + xs).each do |x|
-        assert_nil(p1.add_result(r),
-          "Premature registration of result #{r} at extension #{x}.")
+        assert_nil(
+          p1.add_result(r),
+          "Premature registration of result #{r} at extension #{x}."
+        )
         FileUtils.touch(File.expand_path("data/#{d}/miga-project#{x}", p1.path))
       end
-      assert_equal(MiGA::Result, p1.add_result(r).class,
-        "Impossible to add #{r} result.")
+      assert_equal(
+        MiGA::Result,
+        p1.add_result(r).class,
+        "Impossible to add #{r} result."
+      )
     end
     assert_nil(p1.next_inclade)
-
   end
 
 end

data/test/remote_dataset_test.rb

@@ -1,23 +1,23 @@
-require "test_helper"
-require "miga/project"
-require "miga/remote_dataset"
+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?
+    ENV['MIGA_HOME'] = $tmp
+    FileUtils.touch(File.expand_path('.miga_rc', ENV["MIGA_HOME"]))
+    FileUtils.touch(File.expand_path('.miga_daemon.json', ENV["MIGA_HOME"]))
+    $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
+    ENV['MIGA_HOME'] = nil
   end
-  
+
   def test_class_universe
     assert_respond_to(MiGA::RemoteDataset, :UNIVERSE)
     assert(MiGA::RemoteDataset.UNIVERSE.keys.include? :ebi)
@@ -38,11 +38,16 @@ class RemoteDatasetTest < Test::Unit::TestCase
       msg = "Failed on #{universe}:#{db}"
       assert_equal(MiGA::Taxonomy, tx.class, msg)
       assert_equal('Lentivirus', tx[:g], msg)
-      assert_equal('ns:ncbi o:Ortervirales f:Retroviridae ' \
-        'g:Lentivirus s:Human_immunodeficiency_virus_2', tx.to_s, msg)
-      assert_equal('ns:ncbi d: k: p: c: o:Ortervirales f:Retroviridae ' \
-        'g:Lentivirus s:Human_immunodeficiency_virus_2 ssp: str: ds:',
-        tx.to_s(true), msg)
+      assert_equal(
+        'ns:ncbi o:Ortervirales f:Retroviridae ' \
+          'g:Lentivirus s:Human_immunodeficiency_virus_2',
+        tx.to_s, msg
+      )
+      assert_equal(
+        'ns:ncbi d: k: p: c: o:Ortervirales f:Retroviridae ' \
+          'g:Lentivirus s:Human_immunodeficiency_virus_2 ssp: str: ds:',
+        tx.to_s(true), msg
+      )
       assert_equal('ncbi', tx.namespace, msg)
     end
   end

data/test/result_test.rb

@@ -0,0 +1,49 @@
+require 'test_helper'
+require 'miga/project'
+
+class ResultTest < Test::Unit::TestCase
+
+  def setup
+    $tmp = Dir.mktmpdir
+    ENV['MIGA_HOME'] = $tmp
+    FileUtils.touch(File.expand_path('.miga_rc', ENV['MIGA_HOME']))
+    FileUtils.touch(File.expand_path('.miga_daemon.json', ENV['MIGA_HOME']))
+    $p1 = MiGA::Project.new(File.expand_path('project1', $tmp))
+    $d1 = $p1.add_dataset('dataset1')
+    FileUtils.touch(File.expand_path(
+      "data/02.trimmed_reads/#{$d1.name}.1.clipped.fastq", $p1.path))
+    FileUtils.touch(File.expand_path(
+      "data/02.trimmed_reads/#{$d1.name}.done", $p1.path))
+    FileUtils.touch(File.expand_path(
+      'data/10.clades/01.find/miga-project.empty', $p1.path))
+    FileUtils.touch(File.expand_path(
+      'data/10.clades/01.find/miga-project.done', $p1.path))
+  end
+
+  def teardown
+    FileUtils.rm_rf $tmp
+    ENV['MIGA_HOME'] = nil
+  end
+
+  def test_add_result
+    r = $d1.add_result(:trimmed_reads)
+    assert_equal(MiGA::Result, r.class)
+    r = $d1.add_result(:asssembly)
+    assert_nil(r)
+    r = $p1.add_result(:clade_finding)
+    assert_equal(MiGA::Result, r.class)
+  end
+
+  def test_result_source
+    r = $d1.add_result(:trimmed_reads)
+    assert_equal($d1.name, r.source.name)
+    assert_equal(:trimmed_reads, r.key)
+    assert_equal('data/02.trimmed_reads', r.relative_dir)
+    assert_equal('data/02.trimmed_reads/dataset1.json', r.relative_path)
+    assert_equal($p1.path, r.project.path)
+    assert_equal($p1.path, r.project_path)
+    r = $p1.add_result(:clade_finding)
+    assert_equal($p1.path, r.source.path)
+  end
+
+end