rbbt-util 5.42.0 → 5.44.0

data/test/rbbt/hpc/test_orchestrate.rb

@@ -1,144 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
-require 'rbbt/workflow'
-require 'rbbt/hpc/orchestrate'
-
-module TestWFA
-  extend Workflow
-
-  task :a1 => :string do self.task_name.to_s end
-
-  dep :a1
-  task :a2 => :string do self.task_name.to_s end
-
-  dep :a2
-  task :a3 => :string do self.task_name.to_s end
-end
-
-module TestWFB
-  extend Workflow
-
-  dep TestWFA, :a2
-  task :b1 => :string do self.task_name.to_s end
-
-  dep :b1
-  task :b2 => :string do self.task_name.to_s end
-end
-
-module TestWFC
-  extend Workflow
-
-  dep TestWFA, :a1
-  dep_task :c1, TestWFB, :b2
-
-  task :c2 => :string do self.task_name.to_s end
-
-  dep :c1
-  dep :c2
-  task :c3 => :string do self.task_name.to_s end
-end
-
-class TestOrchestrate < Test::Unit::TestCase
-
-  RULES = IndiferentHash.setup(YAML.load(<<-EOF))
----
-defaults:
-  queue: first_queue
-  time: 1h
-  log: 2
-  config_keys: key1 value1 token1
-chains:
-  chain_a:
-    workflow: TestWFA
-    tasks: a1, a2, a3
-    config_keys: key2 value2 token2, key3 value3 token3.1 token3.2
-  chain_b:
-    workflow: TestWFB
-    tasks: b1, b2
-  chain_b2:
-    comment: This chain is not valid, it is missing a2
-    tasks: TestWFA#a1, TestWFA#a3, TestWFB#b1, TestWFB#b2
-TestWFA:
-  defaults:
-    log: 4
-    config_keys: key4 value4 token4
-  a1:
-    cpus: 10
-    config_keys: key5 value5 token5
-TestWFC:
-  defaults:
-    skip: true
-    log: 4
-  EOF
-
-  def test_parse_chains
-    chains = HPC::Orchestration.parse_chains RULES
-    assert chains[:chain_a][:tasks]["TestWFA"].include?("a1")
-  end
-
-  def test_task_options
-    rules = HPC::Orchestration.task_specific_rules RULES, "TestWFA", :a1
-    assert_equal 10, rules[:cpus]
-    assert_equal 4, rules[:log]
-  end
-
-  def test_job_workload
-    job = TestWFB.job(:b2, nil)
-    job.recursive_clean
-
-    workload = HPC::Orchestration.job_workload(job)
-
-    assert workload.include? job
-  end
-
-  def test_job_chains
-    job = TestWFB.job(:b2, nil)
-
-    job.recursive_clean
-    job_chains = HPC::Orchestration.job_chains(RULES, job)
-    assert_equal 3, job_chains.length
-
-    TestWFB.job(:b1).run
-    job_chains = HPC::Orchestration.job_chains(RULES, job)
-    assert_equal 0, job_chains.length
-
-    job.recursive_clean
-    TestWFA.job(:a1).run
-    job_chains = HPC::Orchestration.job_chains(RULES, job)
-    assert_equal 2, job_chains.length
-  end
-
-  def test_job_batches
-    job = TestWFB.job(:b2, nil)
-
-    job.recursive_clean
-    batches = HPC::Orchestration.job_batches(RULES, job)
-    assert_equal 2, batches.length
-
-    assert_equal job.rec_dependencies.length + 1, batches.inject(0){|acc,e| acc += e[:jobs].length }
-  end
-
-  def test_job_batches_skip
-    job = TestWFC.job(:c1, nil)
-
-    job.recursive_clean
-    batches = HPC::Orchestration.job_batches(RULES, job)
-    assert_equal 2, batches.length
-
-    assert_equal job.rec_dependencies.length + 1, batches.inject(0){|acc,e| acc += e[:jobs].length }
-  end
-
-  def test_job_batches_skip_2
-    job = TestWFC.job(:c3, nil)
-
-    job.recursive_clean
-    batches = HPC::Orchestration.job_batches(RULES, job)
-    assert_equal 4, batches.length
-
-    assert_equal job.rec_dependencies.length + 1, batches.inject(0){|acc,e| acc += e[:jobs].length }
-
-    batches
-  end
-
-
-end
-

data/test/rbbt/hpc/test_pbs.rb

@@ -1,43 +0,0 @@
-require File.expand_path(__FILE__).sub(%r(/test/.*), '/test/test_helper.rb')
-require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1')
-
-require 'rbbt/workflow'
-
-class TestPBS < Test::Unit::TestCase
-  def workflow
-    @workflow ||= Module.new do
-      extend Workflow
-
-      def self.to_s
-        "TestWorkflow"
-      end
-
-      input :name, :string
-      task :hello => :string do |name|
-        "hello #{name}"
-      end
-    end
-  end
-
-  def test_template
-    job = workflow.job(:hello, "TEST", :name => "world")
-
-    TmpFile.with_file do |batch_dir|
-
-      template = HPC::PBS.job_template(job, :batch_dir => batch_dir, :lua_modules => 'java')
-      ppp template
-
-    end
-  end
-
-  def __test_run_job
-    job = Sample.job(:mutect2, "small", :reference => "hg38")
-
-    job.clean
-
-    jobid = HPC::SLURM.run_job(job, :workflows => "HTS", :batch_modules => 'java', :env_cmd => '_JAVA_OPTIONS="-Xms1g -Xmx${MAX_MEMORY}m"', :queue => :debug, :time => '01:00:00', :config_keys => "HTS_light", :task_cpus => '10', :tail => true, :clean_task => "HTS#mutect2")
-    assert jobid.to_s =~ /^\d+$/
-  end
-
-end
-

data/test/rbbt/hpc/test_slurm.rb

@@ -1,32 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
-require 'rbbt/hpc/slurm'
-require 'rbbt/workflow'
-
-class TestSLURM < Test::Unit::TestCase
-  def setup
-    Workflow.require_workflow "Sample"
-    Workflow.require_workflow "HTS"
-  end
-
-  def __test_template
-    job = Sample.job(:mutect2, "small", :reference => "hg38")
-
-    TmpFile.with_file do |batch_dir|
-
-      template = HPC::SLURM.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java')
-      ppp template
-
-    end
-  end
-
-  def __test_run_job
-    job = Sample.job(:mutect2, "small", :reference => "hg38")
-
-    job.clean
-
-    jobid = HPC::SLURM.run_job(job, :workflows => "HTS", :batch_modules => 'java', :env_cmd => '_JAVA_OPTIONS="-Xms1g -Xmx${MAX_MEMORY}m"', :queue => :debug, :time => '01:00:00', :config_keys => "HTS_light", :task_cpus => '10', :tail => true, :clean_task => "HTS#mutect2")
-    assert jobid.to_s =~ /^\d+$/
-  end
-
-end
-

data/test/rbbt/knowledge_base/test_enrichment.rb

@@ -1,48 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '../../../test_helper')
-require 'rbbt/util/tmpfile'
-require 'test/unit'
-require 'rbbt/knowledge_base'
-require 'rbbt/knowledge_base/enrichment'
-
-
-class TestKnowledgeBaseEnrichment < Test::Unit::TestCase
-  def knowledge_base(file)
-
-    effect =StringIO.new <<-END
-#: :sep=" "#:type=:double
-#SG TG Effect
-MDM2 TP53 inhibition
-TP53 NFKB1|GLI1 activation|activation true|true
-    END
-
-    effect_options = {
-      :source => "SG=~Associated Gene Name",
-      :target => "TG=~Associated Gene Name=>Ensembl Gene ID",
-      :persist => false,
-      :identifiers => datafile_test('identifiers'),
-      :undirected => true,
-      :namespace => "Hsa"
-    }
-
-    effect_tsv = TSV.open effect, effect_options.dup 
-
-    knowledge_base = KnowledgeBase.new file, "Hsa/feb2014"
-    knowledge_base.format = {"Gene" => "Ensembl Gene ID"}
-
-    knowledge_base.register :effects, effect_tsv, effect_options.dup
-    knowledge_base.register :gene_ages, datafile_test('gene_ages')
-    knowledge_base.register :nature, datafile_test('nature'), :source => "UniProt/SwissProt Accession", :target => "NCI Nature Pathway ID"
-
-    knowledge_base
-  end
-
-  def test_enrichment
-    TmpFile.with_file do |tmp_kb|
-      genes = %w(P17706-2 LMAN1 P17706-1 P29353-2 JAK3 Q8NFM1 EIF2AK2 JAK1 SRC PIAS1 KPNB1 KPNA2 STAT3 PTPN1 ATR CREBBP PTPRA SGK1 P46108-1 NCK2 O00145 PTPN1 CBL SORBS1 IRS1 SHC1 AKT2 GRB2 SOS1 RPS6KB1 AKT1 DOK1 RASA1 NCK1 FOXO3 RAPGEF1 TRIP10 EIF4EBP1 PDPK1 GRB14 PTPN11 INS GRB10 CAV1 EIF4B RPS6KB1 EEF2 EEF2K AKT1 TSC1 TSC2 CLIP1 DDIT4 SGK1 PDPK1 DEPTOR SREBF1 CYCS IRS1 RPS6KA1 BNIP3 RRN3 RICTOR IKBKB AKT1S1 PXN PML EIF4A1 PPARGC1A YY1 PRKCA RPTOR PDCD4 SIK1 P10636-8 BRSK1 MYC SMARCD3 STK11 ETV4 MARK4 MAP2 MARK2 CRTC2 PSEN2 MST4 CTSD BRSK2 SIK2 ESR1 CAB39 STK11IP SMAD4 CREB1 PRKACA EZR TP53 GSK3B SIK3 CDC37 HSP90AA1 )
-      assert knowledge_base(tmp_kb).enrichment(:nature, genes).any?
-    end
-  end
-
-end
-
-

data/test/rbbt/knowledge_base/test_entity.rb

@@ -1,42 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '../../../test_helper')
-require 'rbbt-util'
-require 'rbbt/util/tmpfile'
-require 'test/unit'
-require 'rbbt/knowledge_base'
-require 'rbbt/knowledge_base/entity'
-
-module Gene
-  extend Entity
-end
-
-class TestKnowledgeEnity < Test::Unit::TestCase
-
-  EFFECT =StringIO.new <<-END
-#: :sep=" "#:type=:double
-#SG TG Effect
-MDM2 TP53 inhibition
-TP53 NFKB1|GLI1 activation|activation true|true
-  END
-
-  EFFECT_OPTIONS = {
-    :source => "SG=~Associated Gene Name",
-    :target => "TG=~Associated Gene Name=>Ensembl Gene ID",
-    :undirected => true,
-    :persist => true,
-    :namespace => "Hsa"
-  }
-  Gene.add_identifiers datafile_test('identifiers')
-
-  EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup 
-
-  KNOWLEDGE_BASE = KnowledgeBase.new '/tmp/kb.foo3', "Hsa"
-  KNOWLEDGE_BASE.format = {"Gene" => "Associated Gene Name"}
-
-  KNOWLEDGE_BASE.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup
-
-  def test_entity_options
-    KNOWLEDGE_BASE.entity_options = {"Gene" => {:organism => "Mmu"}}
-    assert_equal "Mmu", KNOWLEDGE_BASE.children(:effects, "TP53").target_entity.organism
-  end
-end
-

data/test/rbbt/knowledge_base/test_query.rb

@@ -1,46 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '../../../test_helper')
-require 'rbbt/util/tmpfile'
-require 'test/unit'
-require 'rbbt/knowledge_base'
-require 'rbbt/knowledge_base/query'
-
-class TestKnowledgeBaseQuery < Test::Unit::TestCase
-
-  EFFECT =StringIO.new <<-END
-#: :sep=" "#:type=:double
-#SG TG Effect
-MDM2 TP53 inhibition
-TP53 NFKB1|GLI1 activation|activation true|true
-  END
-
-  EFFECT_OPTIONS = {
-    :source => "SG=~Associated Gene Name=>Ensembl Gene ID",
-    :target => "TG=~Associated Gene Name=>Ensembl Gene ID",
-    :persist => false,
-    :identifiers => datafile_test('identifiers'),
-    :undirected => true,
-    :namespace => "Hsa"
-  }
-
-  EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup
-
-  KNOWLEDGE_BASE = KnowledgeBase.new Rbbt.tmp.test.kb_foo2, "Hsa"
-  KNOWLEDGE_BASE.format = {"Gene" => "Ensembl Gene ID"}
-
-  KNOWLEDGE_BASE.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup
-
-  def test_subset_all_persist
-    Misc.benchmark(1000) do
-      assert_equal 6, KNOWLEDGE_BASE.subset(:effects, :all).length
-
-      assert_equal 4, KNOWLEDGE_BASE.subset(:effects, :all).target_entity.uniq.length
-      assert_equal %w(Effect), KNOWLEDGE_BASE.subset(:effects, :all).info.first.keys
-    end
-  end
-
-  def _test_subset_all_persist_format
-    assert KNOWLEDGE_BASE.subset(:effects, :all).target_entity.reject{|e| e =~ /^ENS/}.empty?
-  end
-
-end
-

data/test/rbbt/knowledge_base/test_registry.rb

@@ -1,81 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '../../../test_helper')
-require 'rbbt/util/tmpfile'
-require 'test/unit'
-require 'rbbt/knowledge_base'
-require 'rbbt/knowledge_base/registry'
-
-
-class TestKnowledgeBaseRegistry < Test::Unit::TestCase
-
-  EFFECT =StringIO.new <<-END
-#: :sep=" "#:type=:double
-#SG TG Effect
-MDM2 TP53 inhibition
-TP53 NFKB1|GLI1 activation|activation true|true
-  END
-
-  EFFECT_OPTIONS = {
-    :source => "SG=~Associated Gene Name",
-    :target => "TG=~Associated Gene Name=>Ensembl Gene ID",
-    :persist => false,
-    :identifiers => datafile_test('identifiers'),
-    :undirected => true,
-    :namespace => "Hsa"
-  }
-
-  EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup 
-
-  KNOWLEDGE_BASE = KnowledgeBase.new '/tmp/kb.foo2'
-
-  KNOWLEDGE_BASE.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup
-
-  KNOWLEDGE_BASE.register :pina, datafile_test('pina'), :source => "UniProt/SwissProt Accession", :target => "Interactor UniProt/SwissProt Accession=~UniProt/SwissProt Accession", :undirected => true
-
-  def test_database
-    assert_equal "Associated Gene Name", KNOWLEDGE_BASE.get_database(:effects, :source_format => "Associated Gene Name").key_field
-  end
-
-  def test_index
-    assert KNOWLEDGE_BASE.get_index(:effects, :source_format => "Associated Gene Name", :target_format => "Ensembl Gene ID", :persist => false).include? "MDM2~ENSG00000141510"
-  end
-
-  def test_index_persist
-    assert KNOWLEDGE_BASE.get_index(:effects, :source_format => "Associated Gene Name", :target_format => "Ensembl Gene ID", :persist => true).include? "MDM2~ENSG00000141510"
-  end
-
-  def test_index_flat
-    require 'rbbt/sources/tfacts'
-    file = TFactS.regulators
-    KNOWLEDGE_BASE.register :tfacts, file,  :type => :flat, :source => "Transcription Factor Associated Gene Name=~Associated Gene Name", :merge => true
-    assert KNOWLEDGE_BASE.subset(:tfacts, :source => ["TP53"], :target => :all).length > 10
-  end
-
-  def test_pina
-    index = KNOWLEDGE_BASE.get_index(:pina, :persist => false, :source_format => "Associated Gene Name", :target_format => "Associated Gene Name")
-    assert index["TP53~ARID1A"]
-    assert index["ARID1A~TP53"]
-    assert_equal index["ARID1A~TP53"], index["TP53~ARID1A"]
-
-    index = KNOWLEDGE_BASE.get_index(:pina, :persist => false, :source_format => "Associated Gene Name", :target_format => "Associated Gene Name", :undirected => false)
-    count = 0
-    index.through do |k,values|
-      split_values = values.collect{|v| v.split ";;" }
-      count += 1 if Misc.zip_fields(split_values).uniq != Misc.zip_fields(split_values)
-    end
-
-    index = KNOWLEDGE_BASE.get_index(:pina, :persist => false, :source_format => "Associated Gene Name", :target_format => "Associated Gene Name", :undirected => true)
-    count2 = 0
-    index.through do |k,values|
-      split_values = values.collect{|v| v.split ";;" }
-      count2 += 1 if Misc.zip_fields(split_values).uniq != Misc.zip_fields(split_values)
-    end
-
-  end
-
-  def test_pina2
-    KNOWLEDGE_BASE.entity_options["Gene"] = {:organism => "Mmu"}
-    index = KNOWLEDGE_BASE.get_index(:pina, :persist => true, :source_format => "Ensembl Gene ID", :target_format => "Ensembl Gene ID", :undirected => true)
-    assert_equal "Mmu", index.entity_options["Gene"][:organism]
-  end
-end
-

data/test/rbbt/knowledge_base/test_syndicate.rb

@@ -1,48 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '../../../test_helper')
-require 'rbbt/util/tmpfile'
-require 'test/unit'
-require 'rbbt/knowledge_base'
-require 'rbbt/knowledge_base/query'
-
-module Gene
-  extend Entity
-end
-class TestKnowledgeBaseSyndicate < Test::Unit::TestCase
-
-  EFFECT =StringIO.new <<-END
-#: :sep=" "#:type=:double
-#SG TG Effect
-MDM2 TP53 inhibition
-TP53 NFKB1|GLI1 activation|activation true|true
-  END
-
-  EFFECT_OPTIONS = {
-    :source => "SG=~Associated Gene Name",
-    :target => "TG=~Associated Gene Name=>Ensembl Gene ID",
-    :persist => false,
-    :identifiers => datafile_test('identifiers'),
-    :undirected => true,
-    :namespace => "Hsa"
-  }
-
-  EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup 
-
-  KNOWLEDGE_BASE = KnowledgeBase.new '/tmp/kb.foo2', "Hsa"
-  KNOWLEDGE_BASE.format = {"Gene" => "Ensembl Gene ID"}
-  KNOWLEDGE_BASE.entity_options["Gene"] = {:organism => "Mmu", :test_option => "TEST"}
-
-  KNOWLEDGE_BASE.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup
-
-  def test_syndicate_entity_options
-    Gene.add_identifiers datafile_test('identifiers')
-    kb = KnowledgeBase.new "/tmp/kb.foo3", "Hsa"
-    kb.format = {"Gene" => "Associated Gene Name"} 
-    kb.syndicate :orig, KNOWLEDGE_BASE
-    assert_equal "Mmu", KNOWLEDGE_BASE.entity_options_for("Gene", "effects")[:organism]
-    assert_equal "Mmu", kb.get_index("effects@orig").entity_options["Gene"][:organism]
-    assert_equal "Mmu", kb.get_database("effects@orig").entity_options["Gene"][:organism]
-    assert_equal "Mmu", kb.entity_options_for("Gene", "effects@orig")[:organism]
-    assert_equal "Mmu", kb.children("effects@orig", "TP53").source_entity.organism
-  end
-end
-

data/test/rbbt/knowledge_base/test_traverse.rb

@@ -1,85 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
-require 'rbbt/knowledge_base/traverse'
-require 'rbbt/workflow'
-
-class TestKnowledgeBaseTraverse < Test::Unit::TestCase
-  def setup
-    Workflow.require_workflow "Genomics"
-  end
-
-  def kb
-    Genomics.knowledge_base
-  end
-
-  def test_traverse
-    rules = []
-    rules << "?1 pina SF3B1 - Method=MI:0006"
-    rules << "TP53 pina ?2"
-    rules << "?2 pina ?1"
-    res =  kb.traverse rules
-    assert res.first.include? "?1"
-  end
-
-  def test_traverse2
-    rules = []
-    rules << "?target =pina SF3B1"
-    rules << "?1 pina ?target - Method=MI:0006"
-    rules << "TP53 pina ?2"
-    rules << "?2 pina ?1"
-    res =  kb.traverse rules
-    assert res.first.include? "?1"
-  end
-
-  def test_traverse3
-    rules = []
-    rules << "?target = ENSG00000115524"
-    rules << "?1 pina ?target - Method=MI:0006"
-    rules << "TP53 pina ?2"
-    rules << "?2 pina ?1"
-    res =  kb.traverse rules
-    assert res.first.include? "?1"
-  end
-
-
-  def test_traverse_acc
-    Log.severity = 0
-    rules_str=<<-EOF
-?target{
-  ?target pina SF3B1
-}
-?1 pina TP53
-?1 pina ?target
-    EOF
-    rules = rules_str.split "\n"
-    res =  kb.traverse rules
-    iii res
-    assert res.first.include? "?1"
-  end
-
-
-  def test_path
-    rules = []
-    rules << "?1 pina ARPC2"
-    rules << "ARPC3 pina ?2"
-    rules << "?2 pina ?1"
-    res =  kb.traverse rules
-    assert res.first.include? "?1"
-  end
-
-  def test_path2
-    rules = []
-    rules << "?1 pina SF3B1"
-    rules << "?2 pina SF3B1"
-    rules << "?1 pina ?2"
-    res =  kb.traverse rules
-    assert res.first.include? "?1"
-  end
-
-  def test_wildcard_db
-    rules = []
-    rules << "?1 ?db SF3B1 - Method=MI:0006"
-    res =  kb.traverse rules
-    assert res.first.include? "?1"
-  end
-end
-

data/test/rbbt/persist/test_tsv.rb

@@ -1,88 +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 TestPersistTSV < Test::Unit::TestCase
-  MAX = 100_002
-
-  def tsv_path
-    Random.new
-    require 'rbbt/workflow'
-    Workflow.require_workflow "Genomes1000"
-    require 'rbbt/sources/genomes1000'
-    CMD.cmd("grep -v '^\\.\t' | head -n #{MAX}", :in => Genomes1000.mutations.open, :pipe => true)
-  end
-
-  def run_bechmark(file, engine)
-    Log.info "Testing #{ Term::ANSIColor.red(engine) }"
-    TmpFile.with_file nil, false do |tmp_file|
-      db= nil
-
-      Misc.benchmark(1, "Build database with #{MAX - 2} entries") do
-        db = TSV.open(file, :fields => [1], :persist => true, :persist_engine => engine, :persist_dir => tmp_file, :type => :single, :unnamed => true)
-      end
-
-      _test = db.keys.sort{rand}[1..100000]
-      Misc.benchmark(5, "Access #{test.length} random entries") do
-        _test.each do |k| db[k] end
-      end
-      Log.info "Profiling access to #{test.length} random entries"
-      Misc.profile :min_percent => 0.1 do
-        _test.each do |k| db[k] end
-      end
-      assert_equal "1:10611:G", db["rs189107123"]
-    end
-  end
-
-  def __test_benchmark_tch
-    engine = "HDB"
-    run_bechmark(tsv_path, engine)
-  end
-
-  def __test_benchmark_tcb
-    engine = "BDB"
-    run_bechmark(tsv_path, engine)
-  end
-
-  def __test_benchmark_kch
-    engine = "kch"
-    run_bechmark(tsv_path, engine)
-  end
-
-  def __test_benchmark_kcb
-    engine = "kct"
-    run_bechmark(tsv_path, engine)
-  end
-
-  def __test_benchmark_cdb
-    engine = "CDB"
-    run_bechmark(tsv_path, engine)
-  end
-
-  def __test_benchmark_leveldb
-    engine = "LevelDB"
-    run_bechmark(tsv_path, engine)
-  end
-
-  def __test_benchmark_lmdb
-    engine = "LMDB"
-    run_bechmark(tsv_path, engine)
-  end
-
-  def test_tsv_persist
-    content =<<-EOF
-#: :cast=:to_f
-#Key Value1 Value2
-k1 1.1 2.1
-k2 1.2 2.2
-    EOF
-    TmpFile.with_file(content) do |tsv_file|
-      tsv = TSV.open(tsv_file, :sep => " ", :persist => true, :type => :double, :merge => true)
-      iii tsv["k1"]
-    end
-  end
-end

data/test/rbbt/persist/tsv/test_cdb.rb

@@ -1,18 +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 TestPersistTSVCDB < Test::Unit::TestCase
-
-  if Persist.respond_to? :open_cbd
-    def test_organism
-      require 'rbbt/sources/organism'
-      TmpFile.with_file nil do |tmp_file|
-        tsv = Organism.identifiers("Hsa").tsv(:key_field => "Associated Gene Name", :fields => ["Ensembl Gene ID"], :type => :single, :persist => true, :persist_engine => "CDB", :persist_dir => tmp_file)
-        assert_equal "ENSG00000141510", tsv["TP53"]
-      end
-    end
-  end
-end