rbbt-util 5.42.0 → 5.43.0

data/test/rbbt/hpc/orchestrate/test_batches.rb

@@ -2,52 +2,9 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_he
 require 'rbbt/workflow'
 require 'rbbt/hpc/orchestrate/batches'
 
-module TestWFA
-  extend Workflow
+require_relative '../hpc_test_workflows'
 
-  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
-
-  dep_task :c4, TestWFC, :c3
-end
-
-module TestWFD
-  extend Workflow
-
-  dep TestWFC, :c3, :jobname => "First c3"
-  dep TestWFC, :c3, :jobname => "Second c3"
-  task :d1 => :string do self.task_name.to_s end
-end
-
-class TestOrchestrate < Test::Unit::TestCase
+class TestOrchestrateBatches < Test::Unit::TestCase
 
   RULES = IndiferentHash.setup(YAML.load(<<-EOF))
 ---

data/test/rbbt/hpc/orchestrate/test_chains.rb

@@ -1,51 +1,9 @@
 require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/workflow'
 require 'rbbt/hpc/orchestrate/chains'
 
-module TestWFA
-  extend Workflow
+require_relative '../hpc_test_workflows'
 
-  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
-
-module TestWFD
-  extend Workflow
-
-  dep TestWFC, :c3, :jobname => "First c3"
-  dep TestWFC, :c3, :jobname => "Second c3"
-  task :d1 => :string do self.task_name.to_s end
-end
-
-class TestOrchestrate < Test::Unit::TestCase
+class TestOrchestrateChains < Test::Unit::TestCase
 
   RULES = IndiferentHash.setup(YAML.load(<<-EOF))
 ---
@@ -135,5 +93,16 @@ TestWFC:
 
     assert_equal 1, job_chains.select{|n,i| n == 'chain_d' }.length
   end
+
+  def __test_benchmark
+
+    job = TestDeepWF.job(:suite, :size => 100)
+    job.recursive_clean
+
+    Misc.benchmark(10) do
+      HPC::Orchestration.job_chains(RULES, job)
+    end
+
+  end
 end
 

data/test/rbbt/hpc/orchestrate/test_rules.rb

@@ -2,42 +2,9 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_he
 require 'rbbt/workflow'
 require 'rbbt/hpc/orchestrate/rules'
 
-module TestWFA
-  extend Workflow
+require_relative '../hpc_test_workflows'
 
-  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
+class TestOrchestrateRules < Test::Unit::TestCase
 
   RULES = IndiferentHash.setup(YAML.load(<<-EOF))
 ---

data/test/rbbt/hpc/test_batch.rb

@@ -2,64 +2,60 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helpe
 require 'rbbt/hpc/batch'
 require 'rbbt/workflow'
 
-class TestSLURM < Test::Unit::TestCase
+require_relative 'hpc_test_workflows'
 
-  def setup
-    Workflow.require_workflow "Sample"
-    Workflow.require_workflow "HTS"
-  end
+class TestBatch < Test::Unit::TestCase
 
   def test_batch_options
-    job = Sample.job(:mutect2, "small", :reference => "hg38")
+    job = TestWFB.job(:b1, "TEST")
 
     TmpFile.with_file do |batch_dir|
 
       options = HPC::BATCH.batch_options(job, :batch_dir => batch_dir, :batch_modules => 'java')
-
-      iii options
+      assert_equal options[:step_path], job.path
     end
   end
 
   def test_template
-    job = Sample.job(:mutect2, "small", :reference => "hg38")
+    job = TestWFB.job(:b1, "TEST")
 
     TmpFile.with_file do |batch_dir|
 
-      template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java')
-      ppp template
-
+      template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :lua_modules => 'java')
+      assert_include template, 'module load java'
     end
   end
 
   def test_template_singularity
-    job = Sample.job(:mutect2, "small", :reference => "hg38")
+    job = TestWFB.job(:b1, "TEST")
 
     TmpFile.with_file do |batch_dir|
 
-      template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java', :singularity => true)
-      ppp template
-
+      template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :lua_modules => 'java', :singularity => true)
+      assert_include template, "singularity exec"
     end
   end
 
   def test_template_contain
-    job = Sample.job(:mutect2, "small", :reference => "hg38")
+    job = TestWFB.job(:b1, "TEST")
 
     TmpFile.with_file do |batch_dir|
 
-      template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java', :contain_and_sync => true, :wipe_container => 'force')
-      ppp template
+      template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :lua_modules => 'java', :contain_and_sync => true, :wipe_container => 'force')
+      assert_include template, "batch_erase_contain_dir"
 
     end
   end
   
   def test_template_singularity_contain
-    job = Sample.job(:mutect2, "small", :reference => "hg38")
+    job = TestWFB.job(:b1, "TEST")
 
     TmpFile.with_file do |batch_dir|
 
-      template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java', :contain_and_sync => true, :wipe_container => 'force', :singularity => true)
-      ppp template
+      template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :lua_modules => 'java', :contain_and_sync => true, :wipe_container => 'force', :singularity => true)
+      assert_include template, "--workdir_all"
+      assert_include template, "batch_erase_contain_dir"
+      assert_include template, "singularity exec"
 
     end
   end

data/test/rbbt/hpc/test_pbs.rb

@@ -25,7 +25,7 @@ class TestPBS < Test::Unit::TestCase
     TmpFile.with_file do |batch_dir|
 
       template = HPC::PBS.job_template(job, :batch_dir => batch_dir, :lua_modules => 'java')
-      ppp template
+      assert_include template, "rbbt workflow task TestWorkflow hello"
 
     end
   end

data/test/rbbt/hpc/test_slurm.rb

@@ -2,20 +2,16 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helpe
 require 'rbbt/hpc/slurm'
 require 'rbbt/workflow'
 
+require_relative 'hpc_test_workflows'
 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")
+  def test_template
+    job = TestWFA.job(:a2, "TEST")
 
     TmpFile.with_file do |batch_dir|
 
-      template = HPC::SLURM.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java')
-      ppp template
-
+      template = HPC::SLURM.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java', :time => '10min')
+      assert_include template, "rbbt workflow task TestWFA a2"
+      assert_include template, "00:10:00"
     end
   end
 

data/test/rbbt/knowledge_base/test_enrichment.rb

@@ -37,9 +37,11 @@ TP53 NFKB1|GLI1 activation|activation true|true
   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?
+    keyword_test :R do
+      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

@@ -29,14 +29,34 @@ TP53 NFKB1|GLI1 activation|activation true|true
 
   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 with_kb(&block)
+    keyword_test :organism do
+      require 'rbbt/sources/organism'
+      organism = Organism.default_code("Hsa")
+      TmpFile.with_file do |tmpdir|
+        kb = KnowledgeBase.new tmpdir, "Hsa"
+        kb.format = {"Gene" => "Associated Gene Name"}
+
+        kb.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup
+
+        yield kb
+      end
+    end
+  end
 
   def test_entity_options
-    KNOWLEDGE_BASE.entity_options = {"Gene" => {:organism => "Mmu"}}
-    assert_equal "Mmu", KNOWLEDGE_BASE.children(:effects, "TP53").target_entity.organism
+    with_kb do |kb|
+      kb.entity_options = {"Gene" => {:organism => "Mmu"}}
+      assert_include kb.children(:effects, "TP53").target_entity.to("Associated Gene Name"), "GLI1"
+      assert_equal "Mmu", kb.children(:effects, "TP53").target_entity.organism
+    end
   end
+
+  def test_source_type
+    with_kb do |kb|
+      assert_match "Gene", kb.source_type(:effects).to_s
+    end
+  end
+
 end
 

data/test/rbbt/knowledge_base/test_query.rb

@@ -38,7 +38,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
     end
   end
 
-  def _test_subset_all_persist_format
+  def test_subset_all_persist_format
     assert KNOWLEDGE_BASE.subset(:effects, :all).target_entity.reject{|e| e =~ /^ENS/}.empty?
   end
 

data/test/rbbt/knowledge_base/test_registry.rb

@@ -25,57 +25,50 @@ TP53 NFKB1|GLI1 activation|activation true|true
 
   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 with_kb(&block)
+    keyword_test :organism do
+      require 'rbbt/sources/organism'
+      organism = Organism.default_code("Hsa")
+      TmpFile.with_file do |tmpdir|
+        kb = KnowledgeBase.new tmpdir
+        kb.namespace = organism
+        kb.format = {"Gene" => "Associated Gene Name"}
+
+        kb.register :effects, EFFECT_TSV, EFFECT_OPTIONS
+        kb.register :pina, datafile_test('pina'), 
+          :source => "UniProt/SwissProt Accession", 
+          :target => "Interactor UniProt/SwissProt Accession=~UniProt/SwissProt Accession", 
+          :undirected => true
+
+        kb.register :gene_ages, datadir_test.gene_ages, :source => "=>Associated Gene Name"
+
+        kb.register :CollecTRI, datadir_test.CollecTRI, 
+          :source => "Transcription Factor=~Associated Gene Name", 
+          :target => "Target Gene=~Associated Gene Name",
+          :fields => ["[ExTRI] Confidence", "[ExTRI] PMID"]
+
+        yield kb
+      end
+    end
+  end
 
   def test_database
-    assert_equal "Associated Gene Name", KNOWLEDGE_BASE.get_database(:effects, :source_format => "Associated Gene Name").key_field
+    with_kb do |kb|
+      assert_equal "Associated Gene Name", kb.get_database(:effects, :source_format => "Associated Gene Name").key_field
+    end
   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"
+    with_kb do |kb|
+      assert kb.get_index(:effects, :source_format => "Associated Gene Name", :target_format => "Ensembl Gene ID", :persist => false).include? "MDM2~ENSG00000141510"
+    end
   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)
+    with_kb do |kb|
+      assert kb.get_index(:effects, :source_format => "Associated Gene Name", :target_format => "Ensembl Gene ID", :persist => true).include? "MDM2~ENSG00000141510"
     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_traverse.rb

@@ -3,83 +3,131 @@ require 'rbbt/knowledge_base/traverse'
 require 'rbbt/workflow'
 
 class TestKnowledgeBaseTraverse < Test::Unit::TestCase
-  def setup
-    Workflow.require_workflow "Genomics"
+  def with_kb(&block)
+    keyword_test :organism do
+      require 'rbbt/sources/organism'
+      organism = Organism.default_code("Hsa")
+      TmpFile.with_file do |tmpdir|
+        kb = KnowledgeBase.new tmpdir
+        kb.namespace = organism
+        kb.format = {"Gene" => "Associated Gene Name"}
+
+        kb.register :gene_ages, datadir_test.gene_ages, :source => "=>Associated Gene Name"
+
+        kb.register :CollecTRI, datadir_test.CollecTRI, 
+          :source => "Transcription Factor=~Associated Gene Name", 
+          :target => "Target Gene=~Associated Gene Name",
+          :fields => ["[ExTRI] Confidence", "[ExTRI] PMID"]
+
+        yield kb
+      end
+    end
+  end
+
+  def test_traverse_simple
+    with_kb do |kb|
+      rules = []
+      rules << "SMAD4 gene_ages ?1"
+      res =  kb.traverse rules
+      assert_include res.first["?1"], "Bilateria"
+    end
   end
 
-  def kb
-    Genomics.knowledge_base
+  def test_traverse_CollecTRI
+    with_kb do |kb|
+      rules = []
+      rules << "SMAD4 CollecTRI ?1 - '[ExTRI] Confidence=High'"
+      res =  kb.traverse rules
+      assert res.last.any?
+    end
   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"
+    with_kb do |kb|
+      rules = []
+      rules << "?1 CollecTRI SMAD7"
+      rules << "?1 gene_ages ?2"
+      rules << "SMAD4 gene_ages ?2"
+      res =  kb.traverse rules
+      assert res.first["?1"].include? "MYC"
+    end
   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"
+  def test_target
+    with_kb do |kb|
+      rules = []
+      rules << "?target =CollecTRI SMAD7"
+      rules << "?1 CollecTRI ?target"
+      rules << "?1 gene_ages ?2"
+      rules << "SMAD4 gene_ages ?2"
+      res =  kb.traverse rules
+      assert res.first["?1"].include? "MYC"
+    end
   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"
+  def test_target_translate
+    with_kb do |kb|
+      rules = []
+      rules << "?target =CollecTRI ENSG00000101665"
+      rules << "?1 CollecTRI ?target"
+      res =  kb.traverse rules
+      assert res.first["?1"].include? "MYC"
+    end
   end
 
+  def test_target_attribute
+    with_kb do |kb|
+      rules = []
+      rules << "?1 CollecTRI SMAD7"
+      all =  kb.traverse rules
 
-  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
+      rules = []
+      rules << "?1 CollecTRI SMAD7 - '[ExTRI] Confidence'=High"
+      low =  kb.traverse rules
 
+      assert low.last.length < all.last.length
+    end
+  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"
+  def test_traverse_same_age
+    with_kb do |kb|
+      rules_str=<<-EOF
+?target1 =gene_ages SMAD7
+?target2 =gene_ages SMAD4
+?target1 gene_ages ?age
+?target2 gene_ages ?age
+?1 gene_ages ?age
+      EOF
+      rules = rules_str.split "\n"
+      res =  kb.traverse rules
+      assert_include res.first["?1"], "MET"
+    end
   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"
+  def test_traverse_same_age_acc
+    with_kb do |kb|
+      rules_str=<<-EOF
+?target1 =gene_ages SMAD7
+?target2 =gene_ages SMAD4
+?age{
+  ?target1 gene_ages ?age
+  ?target2 gene_ages ?age
+}
+?1 gene_ages ?age
+      EOF
+      rules = rules_str.split "\n"
+      res =  kb.traverse rules
+      assert_include res.first["?1"], "MET"
+    end
   end
 
   def test_wildcard_db
-    rules = []
-    rules << "?1 ?db SF3B1 - Method=MI:0006"
-    res =  kb.traverse rules
-    assert res.first.include? "?1"
+    with_kb do |kb|
+      rules = []
+      rules << "SMAD4 ?db ?1"
+      res =  kb.traverse rules
+    end
   end
 end
 

data/test/rbbt/persist/test_tsv.rb

@@ -26,13 +26,13 @@ class TestPersistTSV < Test::Unit::TestCase
         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]
+      test = db.keys.sort{rand}[1..100000]
       Misc.benchmark(5, "Access #{test.length} random entries") do
-        _test.each do |k| db[k] end
+        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
+        test.each do |k| db[k] end
       end
       assert_equal "1:10611:G", db["rs189107123"]
     end
@@ -82,7 +82,7 @@ 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"]
+      assert_equal [[1.1], [2.1]], tsv["k1"]
     end
   end
 end