miga-base 0.7.4.0 → 0.7.9.0

data/test/result_test.rb

@@ -2,62 +2,69 @@ require 'test_helper'
 require 'miga/project'
 
 class ResultTest < Test::Unit::TestCase
+  include TestHelper
 
   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 = $p1.add_dataset('dataset1')
+    initialize_miga_home
     FileUtils.touch(
-      File.join($p1.path, "data/02.trimmed_reads/#{$d1.name}.1.clipped.fastq"))
+      File.join(
+        project.path, 'data', '02.trimmed_reads',
+        "#{dataset.name}.1.clipped.fastq"
+      )
+    )
     FileUtils.touch(
-      File.join($p1.path, "data/02.trimmed_reads/#{$d1.name}.done"))
+      File.join(
+        project.path, 'data', '02.trimmed_reads', "#{dataset.name}.done"
+      )
+    )
     FileUtils.touch(
-      File.join($p1.path, 'data/10.clades/01.find/miga-project.empty'))
+      File.join(
+        project.path, 'data', '10.clades', '01.find', 'miga-project.empty'
+      )
+    )
     FileUtils.touch(
-      File.join($p1.path, 'data/10.clades/01.find/miga-project.done'))
-  end
-
-  def teardown
-    FileUtils.rm_rf $tmp
-    ENV['MIGA_HOME'] = nil
+      File.join(
+        project.path, 'data', '10.clades', '01.find', 'miga-project.done'
+      )
+    )
   end
 
   def test_add_result
-    r = $d1.add_result(:trimmed_reads)
-    assert_equal(MiGA::Result, r.class)
-    r = $d1.add_result(:asssembly)
+    r = dataset.add_result(:trimmed_reads)
+    assert_instance_of(MiGA::Result, r)
+    r = dataset.add_result(:asssembly)
     assert_nil(r)
-    r = $p1.add_result(:clade_finding)
-    assert_equal(MiGA::Result, r.class)
+    r = project.add_result(:clade_finding)
+    assert_instance_of(MiGA::Result, r)
   end
 
   def test_result_source
-    r = $d1.add_result(:trimmed_reads)
-    assert_equal($d1.name, r.source.name)
+    r = dataset.add_result(:trimmed_reads)
+    assert_equal(dataset.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)
+    assert_equal('data/02.trimmed_reads/dataset0.json', r.relative_path)
+    assert_equal(project.path, r.project.path)
+    assert_equal(project.path, r.project_path)
+    r = project.add_result(:clade_finding)
+    assert_equal(project.path, r.source.path)
   end
 
   def test_dates
-    r = $d1.add_result(:trimmed_reads)
+    r = dataset.add_result(:trimmed_reads)
     assert_nil(r.done_at)
     assert_nil(r.started_at)
-    tf = File.join($p1.path, "data/02.trimmed_reads/#{$d1.name}.done")
-    File.open(tf, 'w') { |fh| fh.puts Time.new(1,2,3,4,5) }
+    tf = File.join(
+      project.path, 'data', '02.trimmed_reads', "#{dataset.name}.done"
+    )
+    File.open(tf, 'w') { |fh| fh.puts Time.new(1, 2, 3, 4, 5) }
     assert_equal(Time, r.done_at.class)
     assert_nil(r.running_time)
-    tf = File.join($p1.path, "data/02.trimmed_reads/#{$d1.name}.start")
-    File.open(tf, 'w') { |fh| fh.puts Time.new(1,2,3,4,0) }
-    r = $d1.add_result(:trimmed_reads)
+    tf = File.join(
+      project.path, 'data', '02.trimmed_reads', "#{dataset.name}.start"
+    )
+    File.open(tf, 'w') { |fh| fh.puts Time.new(1, 2, 3, 4, 0) }
+    r = dataset.add_result(:trimmed_reads)
     assert_equal(5.0, r.running_time)
   end
-
 end

data/test/tax_dist_test.rb

@@ -2,7 +2,6 @@ require 'test_helper'
 require 'miga/tax_dist'
 
 class TaxDistTest < Test::Unit::TestCase
-
   def test_aai_path
     assert_path_exist(MiGA::TaxDist.aai_path(:intax))
     assert_path_exist(MiGA::TaxDist.aai_path(:novel))
@@ -54,5 +53,4 @@ class TaxDistTest < Test::Unit::TestCase
     close_intax = MiGA::TaxDist.aai_taxtest(99.0, :intax, engine: :blast)
     assert_equal(:s, close_intax[:probably][0])
   end
-
 end

data/test/tax_index_test.rb

@@ -1,7 +1,9 @@
 require 'test_helper'
+require 'miga'
 require 'miga/tax_index'
 
 class TaxIndexTest < Test::Unit::TestCase
+  include TestHelper
 
   def test_initialization
     ti = MiGA::TaxIndex.new
@@ -9,12 +11,8 @@ class TaxIndexTest < Test::Unit::TestCase
   end
 
   def test_dataset
-    $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"]))
-    p = MiGA::Project.new(File.expand_path('project1', $tmp))
-    d = p.add_dataset('dataset1')
+    initialize_miga_home
+    d = dataset
 
     ti = MiGA::TaxIndex.new
     assert_empty(ti.datasets)
@@ -24,9 +22,6 @@ class TaxIndexTest < Test::Unit::TestCase
     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
@@ -40,5 +35,4 @@ class TaxIndexTest < Test::Unit::TestCase
     ti = MiGA::TaxIndex.new
     assert_equal("root:biota: 0\n", ti.to_tab)
   end
-
 end

data/test/taxonomy_test.rb

@@ -2,7 +2,6 @@ require 'test_helper'
 require 'miga/taxonomy'
 
 class TaxonomyTest < Test::Unit::TestCase
-
   def test_ranks
     assert_respond_to(MiGA::Taxonomy, :KNOWN_RANKS)
     assert_include(MiGA::Taxonomy.KNOWN_RANKS, :s)
@@ -14,7 +13,7 @@ class TaxonomyTest < Test::Unit::TestCase
   def test_json
     txt = 'k:Fantasia f:Dragonaceae s:Dragonia_azura'
     js = '{"json_class":"MiGA::Taxonomy","str":"' + txt + '"}'
-    tx = JSON.parse(js, {symbolize_names: false, create_additions: true})
+    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)
@@ -25,7 +24,7 @@ class TaxonomyTest < Test::Unit::TestCase
     tx = MiGA::Taxonomy.new(txt)
     assert_equal(txt, tx.to_s)
     assert_equal(
-      [[:k, 'Fantasia'],[:f, 'Dragonaceae'],[:s, 'Dragonia azura']],
+      [[:k, 'Fantasia'], [:f, 'Dragonaceae'], [:s, 'Dragonia azura']],
       tx.sorted_ranks
     )
     assert_equal('Irrealis', tx.namespace)
@@ -46,7 +45,7 @@ class TaxonomyTest < Test::Unit::TestCase
   end
 
   def test_init_methods
-    tx = MiGA::Taxonomy.new({k: 'Mascot', c: 'Cereal', s: 'Melvin'})
+    tx = MiGA::Taxonomy.new({ k: 'Mascot', c: 'Cereal', s: 'Melvin' })
     assert_equal('k:Mascot c:Cereal s:Melvin', tx.to_s)
     tx = MiGA::Taxonomy.new('Mascot College Buzz', 'k c s')
     assert_equal('k:Mascot c:College s:Buzz', tx.to_s)
@@ -56,7 +55,7 @@ class TaxonomyTest < Test::Unit::TestCase
   end
 
   def test_rank_order
-    tx = MiGA::Taxonomy.new({k: 'Mascot', s: 'Melvin', c: 'Cereal'})
+    tx = MiGA::Taxonomy.new({ k: 'Mascot', s: 'Melvin', c: 'Cereal' })
     assert_equal([:d, nil], tx.highest(true))
     assert_equal([:k, 'Mascot'], tx.highest)
     assert_equal([:ds, nil], tx.lowest(true))
@@ -65,7 +64,7 @@ class TaxonomyTest < Test::Unit::TestCase
 
   def test_alternative
     tx = MiGA::Taxonomy.new('ns:a s:Arnie', nil,
-      ['ns:b s:Bernie','ns:c s:Cornie','s:Darnie'])
+                            ['ns:b s:Bernie', 'ns:c s:Cornie', 's:Darnie'])
     # Fields
     assert_equal('ns:a s:Arnie', tx.to_s)
     assert_equal([[:s, 'Arnie']], tx.sorted_ranks)
@@ -77,7 +76,7 @@ class TaxonomyTest < Test::Unit::TestCase
     assert_equal(3, tx.alternative.size)
     # JSON
     js = tx.to_json
-    tx_js = JSON.parse(js, {symbolize_names: false, create_additions: true})
+    tx_js = JSON.parse(js, { symbolize_names: false, create_additions: true })
     assert_equal(tx.to_s, tx_js.to_s)
     assert_equal(tx.alternative(2).to_s, tx_js.alternative(2).to_s)
     assert_equal(tx.alternative.size, tx_js.alternative.size)
@@ -94,7 +93,7 @@ class TaxonomyTest < Test::Unit::TestCase
 
   def test_reset
     tx = MiGA::Taxonomy.new('ns:Letters d:Latin s:A', nil,
-      ['ns:Words d:English s:A', 'ns:Music d:Tone s:A'])
+                            ['ns:Words d:English s:A', 'ns:Music d:Tone s:A'])
     # Reset
     assert_equal(2, tx.alternative.size)
     assert_equal('Letters', tx.namespace)
@@ -112,5 +111,4 @@ class TaxonomyTest < Test::Unit::TestCase
     tx.add_alternative(MiGA::Taxonomy.new('ns:Letters d:Unicode s:A'))
     assert_equal('ns:Letters d:Unicode s:A', tx.to_s)
   end
-
 end

data/test/test_helper.rb

@@ -11,7 +11,6 @@ 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
@@ -29,5 +28,47 @@ module Kernel
   ensure
     $stderr = STDERR
   end
+end
 
+module TestHelper
+  def teardown
+    @tmpdir ||= nil
+    FileUtils.rm_rf tmpdir unless @tmpdir.nil?
+    ENV['MIGA_HOME'] = nil
+  end
+
+  def declare_remote_access
+    omit_if(ENV['REMOTE_TESTS'].nil?, 'Remote access is error-prone')
+  end
+
+  def declare_forks
+    omit_if(!ENV['JRUBY_TESTS'].nil?, 'JRuby doesn\'t implement fork')
+  end
+
+  def tmpdir
+    @tmpdir ||= Dir.mktmpdir
+  end
+
+  def tmpfile(name)
+    File.join(tmpdir, name)
+  end
+
+  def initialize_miga_home(daemon = '{}')
+    ENV['MIGA_HOME'] = tmpdir
+    FileUtils.touch(File.join(ENV['MIGA_HOME'], '.miga_rc'))
+    File.open(File.join(ENV['MIGA_HOME'], '.miga_daemon.json'), 'w') do |fh|
+      fh.puts daemon
+    end
+  end
+
+  def project(i = 0)
+    @project ||= {}
+    i = "project#{i}" unless i.is_a? String
+    @project[i] ||= MiGA::Project.new(tmpfile(i))
+  end
+
+  def dataset(project_i = 0, n = 0)
+    n = "dataset#{n}" unless n.is_a? String
+    project(project_i).dataset(n) || project(project_i).add_dataset(n)
+  end
 end

data/test/with_daemon_test.rb

@@ -2,15 +2,7 @@ require 'test_helper'
 require 'miga/common/with_daemon'
 
 class WithDaemonTest < Test::Unit::TestCase
-
-  def setup
-    $jruby_tests = !ENV['JRUBY_TESTS'].nil?
-    $tmp = Dir.mktmpdir
-  end
-
-  def teardown
-    FileUtils.rm_rf $tmp
-  end
+  include TestHelper
 
   class TestWithDaemon < MiGA::MiGA
     include MiGA::Common::WithDaemon
@@ -40,7 +32,7 @@ class WithDaemonTest < Test::Unit::TestCase
       puts(*o)
     end
   end
-  
+
   class TestWithDaemon2 < TestWithDaemon
     def daemon_loop
       puts 'I am 2.0!'
@@ -54,20 +46,20 @@ class WithDaemonTest < Test::Unit::TestCase
   end
 
   def test_with_daemon
-    d = TestWithDaemon.new($tmp)
+    d = TestWithDaemon.new(tmpdir)
     assert_respond_to(d, :pid_file)
     assert_respond_to(d.class, :daemon_home)
     assert_nil(d.loop_i)
   end
 
   def test_daemon_run
-    d = TestWithDaemon2.new($tmp)
+    d = TestWithDaemon2.new(tmpdir)
     capture_stdout { d.run }
     assert_path_not_exist(d.pid_file)
   end
 
   def test_daemmon_status
-    d = TestWithDaemon.new($tmp)
+    d = TestWithDaemon.new(tmpdir)
     out = capture_stdout { d.status }.string
     assert_match(/Not running/, out)
 
@@ -84,11 +76,11 @@ class WithDaemonTest < Test::Unit::TestCase
   end
 
   def test_daemon_operations
-    d = TestWithDaemon.new($tmp)
+    d = TestWithDaemon.new(tmpdir)
     FileUtils.touch(d.output_file)
     assert_not_predicate(d, :active?)
 
-    omit_if($jruby_tests, 'JRuby doesn\'t implement fork.')
+    declare_forks
     capture_stdout do
       pid = d.start
       assert_gt(pid, 0)
@@ -112,7 +104,7 @@ class WithDaemonTest < Test::Unit::TestCase
   end
 
   def test_termination_file
-    d = TestWithDaemon2.new($tmp)
+    d = TestWithDaemon2.new(tmpdir)
     assert { !d.termination_file?(nil) }
     FileUtils.touch(d.terminate_file)
     err = capture_stdout do
@@ -124,19 +116,19 @@ class WithDaemonTest < Test::Unit::TestCase
   end
 
   def test_process_alive
-    d = TestWithDaemon2.new($tmp)
+    d = TestWithDaemon2.new(tmpdir)
     assert { d.process_alive?(Process.pid) }
     assert { !d.process_alive?(1e9) }
   end
 
   def test_declare_alive_loop
-    d = TestWithDaemon.new(File.join($tmp, 'nope'))
+    d = TestWithDaemon.new(tmpfile('nope'))
     assert_equal(:no_home, d.declare_alive_loop)
 
-    d = TestWithDaemon.new($tmp)
+    d = TestWithDaemon.new(tmpdir)
     assert_equal(:no_process_alive, d.declare_alive_loop(1e9))
 
-    omit_if($jruby_tests, 'JRuby doesn\'t implement fork.')
+    declare_forks
     FileUtils.touch(d.terminate_file)
     child = fork { sleep(3) }
     capture_stdout do
@@ -145,12 +137,12 @@ class WithDaemonTest < Test::Unit::TestCase
   end
 
   def test_write_alive_file
-    d = TestWithDaemon.new(File.join($tmp, 'nope'))
+    d = TestWithDaemon.new(tmpfile('nope'))
     assert_not_predicate(d, :active?)
     assert_raise { d.write_alive_file }
     assert_not_predicate(d, :active?)
 
-    d = TestWithDaemon.new($tmp)
+    d = TestWithDaemon.new(tmpdir)
     assert_not_predicate(d, :active?)
     d.write_alive_file
     assert_predicate(d, :active?)

data/utils/adapters.fa

@@ -300,3 +300,16 @@ AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
 >TruSeq3_UniversalAdapter
 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
+
+>Nextera_PE_PrefixNX/1
+AGATGTGTATAAGAGACAG
+>Nextera_PE_PrefixNX/2
+AGATGTGTATAAGAGACAG
+>Nextera_PE_Trans1
+TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
+>Nextera_PE_Trans1_rc
+CTGTCTCTTATACACATCTGACGCTGCCGACGA
+>Nextera_PE_Trans2
+GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
+>Nextera_PE_Trans2_rc
+CTGTCTCTTATACACATCTCCGAGCCCACGAGAC

data/utils/cleanup-databases.rb

@@ -10,23 +10,24 @@ p = MiGA::Project.load(ARGV[0])
 ds_names = p.dataset_names
 thr = ARGV[1].to_i
 
-pc = [0] + (1 .. 100).map{ |i| ds_names.size * i / 100 }
-$stderr.puts (('.'*9 + '|')*10) + ' 100%'
+pc = [0] + (1..100).map { |i| ds_names.size * i / 100 }
+$stderr.puts (('.' * 9 + '|') * 10) + ' 100%'
 
-(0 .. thr-1).each do |t|
+(0..thr - 1).each do |t|
   fork do
     ds_names.each_with_index do |i, idx|
-      while t == 0 and idx+1 > pc.first
+      while t == 0 and idx + 1 > pc.first
         $stderr.print '#'
         pc.shift
       end
       next unless (idx % thr) == t
+
       d = p.dataset(i)
       next unless d.is_ref? and d.is_active?
+
       d.cleanup_distances!
     end
   end
 end
 Process.waitall
 $stderr.puts ' Done'
-

data/utils/distance/base.rb

@@ -1,4 +1,3 @@
-
 require 'miga'
 require 'miga/tax_dist'