rbbt-util 5.43.0 → 5.44.0

data/test/rbbt/test_knowledge_base.rb

@@ -1,226 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/../test_helper')
-require 'rbbt/util/tmpfile'
-require 'test/unit'
-
-require 'rbbt/workflow'
-require 'rbbt/entity'
-require 'rbbt/entity/identifiers'
-
-require 'rbbt/association'
-require 'rbbt/knowledge_base'
-
-module Gene
-  extend Entity
-  property :follow => :single do |kb,name,annotate=nil|
-    if annotate.nil? or annotate
-      l = kb.children(name, self).target_entity
-      self.annotate l if annotate and kb.source(name) == format
-      l
-    else
-      kb._children(name, self).collect{|v| v.partition("~").last }
-    end
-  end
-
-  property :backtrack => :single do |kb,name,annotate=nil|
-    if annotate.nil? or annotate
-      l = kb.parents(name, self).target_entity
-      self.annotate l if annotate and kb.target(name) == format
-      l
-    else
-      kb._parents(name, self).collect{|v| v.partition("~").last }
-    end
-  end
-
-  property :expand => :single do |kb,name,annotate=nil|
-    if annotate.nil? or annotate
-      n = kb.neighbours(name, self)
-      if kb.source(name) == kb.target(name) 
-        self.annotate n.collect{|k,v| v.target}.flatten
-      else
-        n.collect{|k,v| v.target_entity.to_a}.flatten
-      end
-    else
-      n = kb._neighbours(name, self)
-      n.values.flatten.collect{|v| v.partition("~").last}
-    end
-  end
-end
-
-
-class TestKnowledgeBase < Test::Unit::TestCase
-  def setup
-    require 'rbbt/sources/organism'
-
-    Gene.add_identifiers Organism.identifiers("NAMESPACE"), "Ensembl Gene ID", "Associated Gene Name"
-  end
-
-  def test_knowledge_base_simple
-    organism = Organism.default_code("Hsa")
-    TmpFile.with_file do |tmpdir|
-      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
-      kb.format = {"Gene" => "Ensembl Gene ID"}
-
-      kb.register :gene_ages, datadir_test.gene_ages
-
-      i = kb.get_index(:gene_ages)
-
-      assert_include i.match("ENSG00000000003"), "ENSG00000000003~Bilateria"
-    end
-  end
-
-  def test_knowledge_base_translate
-    organism = Organism.default_code("Hsa")
-    TmpFile.with_file do |tmpdir|
-      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
-      kb.format = {"Gene" => "Ensembl Gene ID"}
-
-      kb.register :gene_ages, datadir_test.gene_ages, :source => "FamilyAge", :target => "=>Associated Gene Name"
-
-      i = kb.get_index(:gene_ages)
-
-      assert_include i.match("Bilateria"), "Bilateria~SMAD4"
-    end
-  end
-
-
-  def test_knowledge_base_reverse
-    organism = Organism.default_code("Hsa")
-    TmpFile.with_file do |tmpdir|
-      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
-      kb.format = {"Gene" => "Ensembl Gene ID"}
-
-      kb.register :gene_ages, datadir_test.gene_ages
-
-      ri = kb.get_index(:gene_ages).reverse
-
-      assert_include ri.match("Bilateria"), "Bilateria~ENSG00000000003"
-    end
-  end
-
-  def test_entity
-    organism = Organism.default_code("Hsa")
-    TmpFile.with_file do |tmpdir|
-      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
-      kb.format = {"Gene" => "Ensembl Gene ID"}
-
-      kb.register :gene_ages, datadir_test.gene_ages, :source => "=>Associated Gene Name"
-
-      kb.register :CollecTRI, datadir_test.CollecTRI, 
-        :source => "Transcription Factor", :target => "Target Gene",
-        :fields => ["[ExTRI] Confidence", "[ExTRI] PMID"]
-
-      smad4 = Gene.setup("SMAD4", "Associated Gene Name", kb.namespace)
-      smad7 = Gene.setup("SMAD7", "Associated Gene Name", kb.namespace)
-
-
-      assert_include smad4.follow(kb, :CollecTRI), smad7
-      assert_include smad7.backtrack(kb, :CollecTRI), smad4
-      refute smad7.follow(kb, :CollecTRI).include?(smad4)
-      assert_include smad7.expand(kb, :CollecTRI), smad4
-      assert_include smad4.expand(kb, :CollecTRI), smad7
-
-    end
-  end
-
-  def __test_benchmark
-    organism = Organism.default_code("Hsa")
-    TmpFile.with_file do |tmpdir|
-      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
-      kb.format = {"Gene" => "Ensembl Gene ID"}
-
-      kb.register :gene_ages, datadir_test.gene_ages, :source => "=>Associated Gene Name"
-
-      kb.register :CollecTRI, datadir_test.CollecTRI, 
-        :source => "Transcription Factor", :target => "Target Gene (Associated Gene Name)",
-        :fields => ["[ExTRI] Confidence", "[ExTRI] PMID"]
-
-
-      smad4 = Gene.setup("SMAD4", "Associated Gene Name", kb.namespace)
-      downstream = smad4.follow(kb, :CollecTRI, true)
-      Gene.setup(downstream)
-
-      downstream.follow(kb, :CollecTRI)
-      downstream.backtrack(kb, :CollecTRI)
-      downstream.expand(kb, :CollecTRI)
-
-      Misc.benchmark(50) do
-        downstream.follow(kb, :CollecTRI)
-        downstream.backtrack(kb, :CollecTRI)
-        downstream.expand(kb, :CollecTRI)
-      end
-      
-      Misc.benchmark(50) do
-        downstream.follow(kb, :CollecTRI, true)
-        downstream.backtrack(kb, :CollecTRI, true)
-        downstream.expand(kb, :CollecTRI, true)
-      end
-    end
-  end
-
-  def test_identifier_files
-    organism = Organism.default_code("Hsa")
-    TmpFile.with_file do |tmpdir|
-      Path.setup(tmpdir)
-      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
-
-      kb.register :gene_ages, datadir_test.gene_ages
-
-      assert_include kb.get_database(:gene_ages).identifier_files.first, "test/data"
-      assert_include kb.get_index(:gene_ages).identifier_files.first, "test/data"
-
-    end
-  end
-
-  def test_knowledge_base_reuse
-    organism = Organism.default_code("Hsa")
-    TmpFile.with_file do |tmpdir|
-      Path.setup(tmpdir)
-      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
-      kb.register :CollecTRI, datadir_test.CollecTRI,
-        :source => "Transcription Factor=~Associated Gene Name=>Ensembl Gene ID", :target => "Target Gene",
-        :fields => ["[ExTRI] Confidence", "[ExTRI] PMID"]
-
-      assert kb.get_database(:CollecTRI).identifier_files.any?
-
-      i = Association.index(datadir_test.CollecTRI, :persist_file => tmpdir.CollecTRI, 
-                        :source => "Transcription Factor=~Associated Gene Name=>Ensembl Gene ID", :target => "Target Gene",
-                        :fields => ["[ExTRI] Confidence", "[ExTRI] PMID"],
-                        :format => {"Gene" => "Ensembl Gene ID"},
-                        :namespace => Organism.default_code("Hsa"))
-
-      assert i.identifier_files.any?
-
-      kb = KnowledgeBase.load(tmpdir)
-
-      assert kb.get_database(:CollecTRI).identifier_files.any?
-
-      i =  kb.get_index(:CollecTRI)
-
-      assert i.identifier_files.any?
-      assert kb.identify_source('CollecTRI', "SMAD4") =~ /ENSG/
-    end
-  end
-
-
-  def test_flat
-    organism = Organism.default_code("Hsa")
-    TmpFile.with_file do |tmpdir|
-      kbfile = File.join(tmpdir, 'kb')
-      file = File.join(tmpdir, 'file')
-      kb = KnowledgeBase.new kbfile
-      kb.register :test_flat do
-        str =<<-EOF
-#: :type=:flat#:sep=' '
-#Key Value
-a b c d e
-A B C D E
-        EOF
-        Open.write(file, str)
-        file
-      end
-      db = kb.get_database(:test_flat)
-      assert db["a"].first.length > 1
-    end
-  end
-end
-

data/test/rbbt/test_monitor.rb

@@ -1,11 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '..', 'test_helper.rb')
-require 'rbbt/monitor'
-
-class TestMonitor < Test::Unit::TestCase
-end
-
-if __FILE__ == $0
-  iii Rbbt.lock_info.select{|k,v| k =~ /.file_repo/}
-
-end
-

data/test/rbbt/test_packed_index.rb

@@ -1,68 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '..', 'test_helper.rb')
-require 'rbbt/packed_index'
-
-class TestPackedIndex < Test::Unit::TestCase
-  def test_packed_index
-
-    TmpFile.with_file do |tmpfile|
-      pi = PackedIndex.new tmpfile, true, %w(i i 23s f f f f f)
-      100.times do |i|
-        pi << [i, i+2, i.to_s * 10, rand, rand, rand, rand, rand]
-      end
-      pi << nil
-      pi << nil
-      pi.close
-      pi = PackedIndex.new(tmpfile, false)
-      Misc.benchmark(1000) do
-        100.times do |i|
-          assert_equal i, pi[i][0] 
-          assert_equal i+2, pi[i][1] 
-        end
-      end
-      assert_equal nil, pi[100]
-      assert_equal nil, pi[101]
-    end
-  end
-
-  def test_bgzip
-
-    size = 1000000
-    density = 0.1
-
-    access = []
-    (size * density).to_i.times do
-      access << rand(size-1) + 1
-    end
-    access.sort!
-    access.uniq!
-
-    TmpFile.with_file do |tmpfile|
-      pi = PackedIndex.new tmpfile, true, %w(i i 23s f f f f f)
-      size.times do |i|
-        pi << [i, i+2, i.to_s * 10, rand, rand, rand, rand, rand]
-      end
-      pi << nil
-      pi << nil
-      pi.close
-
-      pi = PackedIndex.new(tmpfile, false)
-      Misc.benchmark do
-        access.each do |point|
-          assert_equal point+2, pi[point][1]
-        end
-      end
-
-      `bgzip #{tmpfile} `
-      `mv #{tmpfile}.gz #{tmpfile}.bgz`
-
-      pi = PackedIndex.new(tmpfile + '.bgz', false)
-      pi[0]
-      Misc.benchmark do
-        access.each do |point|
-          assert_equal point+2, pi[point][1]
-        end
-      end
-    end
-  end
-end
-

data/test/rbbt/test_persist.rb

@@ -1,85 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/../test_helper')
-require 'rbbt/persist'
-require 'rbbt/annotations'
-require 'rbbt/util/tmpfile'
-require 'test/unit'
-
-class TestPersist < Test::Unit::TestCase
-
-  def test_array_persist
-    TmpFile.with_file do |tmp|
-      10.times do
-        assert_equal ["1", "2"],(Persist.persist("Test", :array, :file => tmp) do
-          ["1", "2"]
-        end)
-      end
-    end
-
-    TmpFile.with_file do |tmp|
-      10.times do
-        assert_equal [],(Persist.persist("Test", :array, :file => tmp) do
-          []
-        end)
-      end
-    end
-
-    TmpFile.with_file do |tmp|
-      10.times do
-        assert_equal ["1"],(Persist.persist("Test", :array, :file => tmp) do
-          ["1"]
-        end)
-      end
-    end
-  end
-
-  def test_tsv_dumper
-    TmpFile.with_file do |tmpdir|
-      tsv = Persist.persist("Dumper", :tsv, :dir => tmpdir) do
-        dumper = TSV::Dumper.new :key_field => "Field 1", :fields => ["Field 2"], :type => :single
-
-        dumper.init
-        Thread.new do
-          10.times do |i|
-            key = i.to_s
-            dumper.add key, key + " - 2"
-          end
-          dumper.close
-        end
-        dumper
-      end
-
-      assert_equal 10, tsv.size
-    end
-  end
-
-  def test_tsv_dumper_stream
-    TmpFile.with_file do |tmpdir|
-      stream = Persist.persist("Dumper", :tsv, :dir => tmpdir, :no_load => :stream) do
-        dumper = TSV::Dumper.new :key_field => "Field 1", :fields => ["Field 2"], :type => :single
-
-        Thread.new do
-          10.times do |i|
-            key = i.to_s
-            dumper.add key, key + " - 2"
-          end
-          dumper.close
-        end
-
-        dumper
-      end
-
-      assert_equal 10, stream.read.split("\n").length
-      stream.join
-    end
-  end
-
-  def test_newer
-    TmpFile.with_file("Test1") do |tmp1|
-      sleep 1
-      TmpFile.with_file("Test1") do |tmp2|
-        assert Persist.newer?(tmp1, tmp2)
-        assert ! Persist.newer?(tmp2, tmp1)
-      end
-    end
-  end
-end

data/test/rbbt/test_resource.rb

@@ -1,110 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/../test_helper')
-require 'rbbt'
-require 'rbbt/resource'
-require 'rbbt/util/tmpfile'
-require 'test/unit'
-
-module TestResource
-  extend Resource
-
-  self.subdir = 'tmp/tmp-share/resource/TestResource/'
-
-  claim tmp.test.google, :url, "http://google.com"
-  claim tmp.test.string, :string, "TEST"
-  claim tmp.test.proc, :proc do
-    "PROC TEST"
-  end
-
-  claim tmp.test.rakefiles.foo , :string , <<-EOF
-file 'foo' do |t|
-  Open.write(t.name, "TEST")
-end
-
-rule /.*/ do |t|
-  Open.write(t.name, "bar")
-end
-  EOF
-
-  claim tmp.test.work.footest, :rake, TestResource.tmp.test.rakefiles.foo
-
-  claim tmp.test.work.file_proc, :file_proc do |file,filename|
-    Open.write(filename, file)
-    nil
-  end
-end
-
-class TestTSV < Test::Unit::TestCase
-
-  def test_tsv
-    require 'rbbt/tsv'
-    TestResource.claim TestResource.tmp.test.test_tsv, :proc do 
-      tsv = {"a" => 1, "b" => 2}
-      TSV.setup(tsv, :key_field => "Letter", :fields => ["Value"], :type => :single)
-    end
-    assert TSV === TestResource.tmp.test.test_tsv.tsv
-  end
-
-  def test_rake
-    assert_equal TestResource.tmp.test.work.footest.foo.read, "TEST"
-    assert_equal TestResource.tmp.test.work.footest.bar.read, "bar"
-  end
-
-
-  def test_proc
-    assert TestResource.tmp.test.proc.read == "PROC TEST"
-  end
-
-  def test_string
-    assert TestResource.tmp.test.string.read == "TEST"
-  end
-
-  def test_url
-    assert TestResource[].tmp.test.google.read =~ /google/
-  end
-
-
-  def __test_resolve
-    assert_equal File.join(ENV['HOME'], '.rbbt/etc/foo'), Path.setup('etc/foo').find(:user)
-    assert_equal File.join(ENV['HOME'], '.phgx/etc/foo'), Path.setup('etc/foo', 'phgx').find(:user)
-
-    assert_equal File.join('/', 'etc/rbbt/foo'), Path.setup('etc/foo').find(:global)
-    assert_equal File.join('/', 'etc/phgx/foo'), Path.setup('etc/foo', 'phgx').find(:global)
-
-    assert_equal File.join('/usr/local', 'etc/rbbt/foo'), Path.setup('etc/foo').find(:local)
-    assert_equal File.join('/usr/local', 'etc/phgx/foo'), Path.setup('etc/foo', 'phgx').find(:local)
-
-    assert_equal File.expand_path(File.join(File.dirname(File.expand_path(__FILE__)), '../../', 'etc/foo')), Path.setup('etc/foo').find(:lib)
-    assert_equal File.expand_path(File.join(File.dirname(File.expand_path(__FILE__)), '../../', 'etc/foo')), Path.setup('etc/foo').find(:lib)
-
-    assert_equal File.join(ENV['HOME'], '.rbbt/etc/foo'), Path.setup('etc/foo').find()
-    assert_equal File.join(ENV['HOME'], '.phgx/etc/foo'), Path.setup('etc/foo', 'phgx').find()
-  end
-
-  def test_libdir
-    assert File.exist?(Rbbt.share.Rlib["util.R"].find(:lib))
-    assert File.exist?(Rbbt.share.Rlib["util.R"].find)
-  end
-
-  def __test_server
-    require 'rbbt/sources/organism'
-    TmpFile.with_file :extension => 'gz' do |tmp|
-      Organism.get_from_server("Hsa/b37/known_sites/dbsnp_138.vcf.gz", tmp, 'http://rbbt.bsc.es')
-      Open.open(tmp) do |f|
-        assert f.gets =~  /^#/
-      end
-    end
-  end
-
-  def test_identify
-    assert_equal 'etc/', Rbbt.identify(File.join(ENV["HOME"], '.rbbt/etc/'))
-    assert_equal 'share/databases/', Rbbt.identify('/usr/local/share/rbbt/databases/')
-    assert_equal 'share/databases/DATABASE', Rbbt.identify('/usr/local/share/rbbt/databases/DATABASE')
-    assert_equal 'share/databases/DATABASE/FILE', Rbbt.identify('/usr/local/share/rbbt/databases/DATABASE/FILE')
-    assert_equal 'share/databases/DATABASE/FILE', Rbbt.identify(File.join(ENV["HOME"], '.rbbt/share/databases/DATABASE/FILE'))
-    assert_equal 'share/databases/DATABASE/FILE', Rbbt.identify('/usr/local/share/rbbt/databases/DATABASE/FILE')
-
-    assert_equal 'etc/somefile', TestResource.identify(TestResource.etc.somefile.find(:user))
-    assert_equal 'etc/somefile', TestResource.identify(TestResource.etc.somefile.find(:local))
-  end
-
-end