rbbt-util 5.43.0 → 5.44.0

data/test/rbbt/association/test_index.rb

@@ -1,127 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
-require 'rbbt/util/misc'
-require 'rbbt/association'
-require 'rbbt/association/index'
-
-class TestAssociationIndex < Test::Unit::TestCase
-   
-  EFFECT =<<-END
-#: :sep=" "#:type=:double
-#SG TG Effect directed?
-MDM2 TP53 inhibition false
-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'),
-    :namespace => "Hsa"
-  }
-
-  EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup
-
-  def test_index_no_persist_string
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:source => "TG", :target => "SG=~Associated Gene Name"), :persist => false)
-    tsv.unnamed = false
-    assert_equal "inhibition", tsv["TP53~MDM2"]["Effect"]
-  end
-
-  def test_index_no_persist_string_undirected
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => true, :source => "TG", :target => "SG=~Associated Gene Name"), :persist => false)
-    tsv.unnamed = false
-    assert_equal "inhibition", tsv["TP53~MDM2"]["Effect"]
-  end
-
-  def test_index_persist_string
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:source => "SG", :target => "TG=~Associated Gene Name"), :persist => true, :update => true)
-    tsv.unnamed = false
-    assert_equal "inhibition", tsv["MDM2~TP53"]["Effect"]
-    assert_equal %w(TP53~NFKB1 TP53~GLI1).sort, tsv.match("TP53").sort
-  end
-
-  def test_index_persist_reverse
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:source => "TG", :target => "SG=~Associated Gene Name"), :persist => true, :update => true).reverse
-    tsv.unnamed = false
-    assert_equal "inhibition", tsv["MDM2~TP53"]["Effect"]
-    assert_equal %w(MDM2~TP53), tsv.match("MDM2")
-  end
-
-  def test_index_persist_undirected
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => true, :source => "TG=~Associated Gene Name", :target => "SG=~Associated Gene Name"), :persist => true)
-    tsv.unnamed = false
-    assert_equal "inhibition", tsv["MDM2~TP53"]["Effect"]
-    assert_equal "inhibition", tsv["TP53~MDM2"]["Effect"]
-    assert_equal %w(MDM2~TP53), tsv.match("MDM2")
-  end
-
-  def test_index_persist_directed_subset
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => true, :source => "TG=~Associated Gene Name", :target => "SG=~Associated Gene Name"), :persist => true)
-    tsv.unnamed = false
-    assert_equal %w(TP53~GLI1 TP53~MDM2).sort, tsv.subset(["TP53"], ["GLI1","MDM2"]).sort
-    assert_equal %w(MDM2~TP53).sort, tsv.subset(["MDM2"], :all).sort
-    assert_equal %w(GLI1~TP53).sort, tsv.subset(["GLI1"], :all).sort
-    assert_equal %w(TP53~GLI1).sort, tsv.subset(:all, ["GLI1"]).sort
-  end
-
-  def test_index_persist_undirected_subset
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
-    tsv.unnamed = false
-    assert_equal %w(TP53~GLI1 TP53~NFKB1).sort, tsv.subset(["TP53"], ["GLI1","MDM2", "NFKB1"]).sort
-  end
-
-  def test_index_flat
-    require 'rbbt/sources/tfacts'
-    file = TFactS.regulators
-    tsv = Association.index(file,  :type => :flat, :source => "Transcription Factor Associated Gene Name=~Associated Gene Name", :merge => true)
-    assert tsv.match("TP53").length > 10
-  end
-
-  def test_index_flat_to_matrix
-    require 'rbbt/sources/tfacts'
-    file = TFactS.regulators
-    tsv = Association.index(file,  :type => :flat, :source => "Transcription Factor Associated Gene Name=~Associated Gene Name", :merge => true)
-    assert(tsv.to_matrix(false))
-  end
-
-  def test_filter_no_block
-    require 'rbbt/sources/tfacts'
-    file = TFactS.regulators
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
-    tsv.unnamed = false
-    matches = tsv.filter :directed?
-    assert_equal 2, matches.length
-  end
-
-  def test_filter_no_block_value
-    require 'rbbt/sources/tfacts'
-    file = TFactS.regulators
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
-    tsv.unnamed = false
-    matches = tsv.filter :Effect, "inhibition"
-    assert_equal ["MDM2~TP53"], matches
-  end
-
-  def test_filter_block_value_field
-    require 'rbbt/sources/tfacts'
-    file = TFactS.regulators
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
-    tsv.unnamed = false
-    matches = tsv.filter :Effect do |value|
-      return value.include? "inhibition"
-    end
-    assert_equal ["MDM2~TP53"], matches
-  end
-
-  def test_filter_block_no_value_field
-    require 'rbbt/sources/tfacts'
-    file = TFactS.regulators
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
-    tsv.unnamed = false
-    matches = tsv.filter do |key,values|
-      return values.flatten.include? "inhibition"
-    end
-    assert_equal ["MDM2~TP53"], matches
-  end
-end

data/test/rbbt/association/test_item.rb

@@ -1,15 +0,0 @@
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '../../..', 'lib'))
-$LOAD_PATH.unshift(File.dirname(__FILE__))
-require 'test/unit'
-require 'rbbt/tsv'
-require 'rbbt/association/item'
-
-class TestAssociationItem < Test::Unit::TestCase
-  def test_incidence
-    pairs = [[:A, :a], [:B, :b]].collect{|p| "#{p.first.to_s}~#{p.last.to_s}"}
-    assert TSV === AssociationItem.incidence(pairs)
-    assert_equal 2, AssociationItem.incidence(pairs).length
-    assert_equal 2, AssociationItem.incidence(pairs).fields.length
-  end
-end
-

data/test/rbbt/association/test_open.rb

@@ -1,63 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
-require 'rbbt/util/misc'
-require 'rbbt/association'
-require 'rbbt/association/open'
-
-class TestAssociationOpen < Test::Unit::TestCase
-   
-  EFFECT =<<-END
-#: :sep=" "#:type=:double
-#SG TG Effect directed?
-MDM2 TP53 inhibition false
-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'),
-    :namespace => "Hsa"
-  }
-
-  EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup
-
-  def test_open_no_persist
-    tsv = Association.open(EFFECT_TSV, EFFECT_OPTIONS, :persist => false)
-    assert_equal "ENSG00000141510", tsv["MDM2"]["Ensembl Gene ID"].first
-    assert_equal ["false"], tsv["MDM2"]["directed?"]
-  end
-
-
-  def test_open_persist
-    tsv = Association.open(EFFECT, EFFECT_OPTIONS, :persist => true, :update => true)
-    assert_equal "ENSG00000141510", tsv["MDM2"]["Ensembl Gene ID"].first
-    assert_equal ["false"], tsv["MDM2"]["directed?"]
-  end
-
-  def test_open_no_persist_string
-    tsv = Association.open(EFFECT, EFFECT_OPTIONS.merge(:source => "TG", :target => "SG=~Associated Gene Name"), :persist => false)
-    tsv.include? "TP53"
-    assert_equal ["MDM2"], tsv["TP53"]["Associated Gene Name"]
-  end
-
-  def test_index_no_persist_string
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:source => "TG", :target => "SG=~Associated Gene Name"), :persist => false)
-    tsv.unnamed = false
-    assert_equal "inhibition", tsv["TP53~MDM2"]["Effect"]
-  end
-
-  def test_index_persist_string
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:source => "SG", :target => "TG=~Associated Gene Name"), :persist => true)
-    tsv.unnamed = false
-    assert_equal "inhibition", tsv["MDM2~TP53"]["Effect"]
-    assert_equal %w(TP53~GLI1 TP53~NFKB1), tsv.match("TP53").sort
-  end
-
-  def test_index_persist_reverse
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge( :source => "TG", :target => "SG=~Associated Gene Name"), :persist => true).reverse
-    tsv.unnamed = false
-    assert_equal "inhibition", tsv["MDM2~TP53"]["Effect"]
-    assert_equal %w(MDM2~TP53), tsv.match("MDM2")
-  end
-end

data/test/rbbt/association/test_util.rb

@@ -1,108 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
-require 'rbbt/util/misc'
-require 'rbbt/association'
-require 'rbbt/association'
-require 'rbbt/association/util'
-
-class TestAssociationUtil < Test::Unit::TestCase
-
-  def test_specs
-    spec = Association.parse_field_specification "=~Associated Gene Name=>Ensembl Gene ID"
-    assert_equal [nil, "Associated Gene Name", "Ensembl Gene ID"], spec
-
-    spec = Association.parse_field_specification "TG=~Associated Gene Name=>Ensembl Gene ID"
-    assert_equal ["TG", "Associated Gene Name", "Ensembl Gene ID"], spec
-
-    spec = Association.parse_field_specification "TG=~Associated Gene Name"
-    assert_equal ["TG", "Associated Gene Name", nil], spec
-
-    spec = Association.parse_field_specification "Associated Gene Name=>Ensembl Gene ID"
-    assert_equal ["Associated Gene Name", nil, "Ensembl Gene ID"], spec
-  end
-
-  def test_normalize_specs
-    spec = Association.normalize_specs "TG=~Associated Gene Name=>Ensembl Gene ID", %w(SG TG Effect directed?)
-    assert_equal ["TG", "Associated Gene Name", "Ensembl Gene ID"], spec
-
-    spec = Association.normalize_specs "Ensembl Gene ID", %w(SG TG Effect directed?)
-    assert_equal ["Ensembl Gene ID", nil, nil], spec
-
-    spec = Association.normalize_specs "Ensembl Gene ID"
-    assert_equal ["Ensembl Gene ID", nil, nil], spec
-  end
-
-  def test_process_specs
-    spec = Association.extract_specs %w(SG TG Effect directed?), :target => "TG=~Associated Gene Name=>Ensembl Gene ID"
-    assert_equal ["TG", "Associated Gene Name", "Ensembl Gene ID"], spec[:target]
-    assert_equal ["SG", nil, nil], spec[:source]
-
-    spec = Association.extract_specs %w(SG TG Effect directed?)
-    assert_equal ["SG", nil, nil], spec[:source]
-    assert_equal ["TG", nil,nil], spec[:target]
-
-    spec = Association.extract_specs %w(SG TG Effect directed?), :source => "TG"
-    assert_equal ["TG", nil, nil], spec[:source]
-    assert_equal ["SG", nil,nil], spec[:target]
-
-    spec = Association.extract_specs %w(SG TG Effect directed?), :source => "SG"
-    assert_equal ["SG", nil, nil], spec[:source]
-    assert_equal ["TG", nil,nil], spec[:target]
-
-    spec = Association.extract_specs %w(SG TG Effect directed?), :target => "SG"
-    assert_equal ["TG", nil, nil], spec[:source]
-    assert_equal ["SG", nil,nil], spec[:target]
-  end
-
-  def test_headers
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect)
-    assert_equal 0, spec[0]
-    assert_equal 1, spec[1][0]
-
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect), :source => "SG"
-    assert_equal 0, spec[0]
-    assert_equal 1, spec[1][0]
-
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect), :target => "TG"
-    assert_equal 0, spec[0]
-    assert_equal 1, spec[1][0]
-
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect), :target => "TG", :source => "SG"
-    assert_equal 0, spec[0]
-    assert_equal 1, spec[1][0]
-
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect), :source => "TG"
-    assert_equal 1, spec[0]
-    assert_equal 0, spec[1][0]
-
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect), :target => "SG"
-    assert_equal 1, spec[0]
-    assert_equal 0, spec[1][0]
-
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect), :target => "SG", :source => "TG"
-    assert_equal 1, spec[0]
-    assert_equal 0, spec[1][0]
-
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect), :target => "SG", :source => "TG=~Associated Gene Name=>Ensembl Gene ID"
-    assert_equal 1, spec[0]
-    assert_equal 0, spec[1][0]
-
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect), :target => "SG=~Associated Gene Name=>Ensembl Gene ID", :source => "TG=~Associated Gene Name=>Ensembl Gene ID"
-    assert_equal 1, spec[0]
-    assert_equal 0, spec[1][0]
-
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect), :target => "SG=~Associated Gene Name", :source => "TG=~Associated Gene Name=>Ensembl Gene ID"
-    assert_equal 1, spec[0]
-    assert_equal 0, spec[1][0]
-
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect), :target => "TG=~Associated Gene Name", :source => "SG=~Associated Gene Name", :target_format => "Ensembl Gene ID"
-    assert_equal 0, spec[0]
-    assert_equal "Ensembl Gene ID", spec[5]
-    assert_equal nil, spec[4]
-
-
-    spec = Association.headers  %w(SG TG Effect directed?), %w(Effect), :target => "TG=~Associated Gene Name", :source => "SG=~Associated Gene Name", :source_format => "Ensembl Gene ID"
-    assert_equal 0, spec[0]
-    assert_equal "Ensembl Gene ID", spec[4]
-    assert_equal nil, spec[5]
-  end
-end

data/test/rbbt/entity/test_identifiers.rb

@@ -1,34 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
-require 'rbbt-util'
-require 'rbbt/entity'
-require 'rbbt/entity/identifiers'
-
-module Gene
-  extend Entity
-end
-
-class TestEntityIdentifiers < Test::Unit::TestCase
-
-  def test_name
-    Gene.add_identifiers datafile_test('identifiers'), "Ensembl Gene ID", "Associated Gene Name"
-    assert_equal "TP53", Gene.setup("ENSG00000141510").name
-  end
-
-  def test_name_organism
-    keyword_test :organism do
-      require 'rbbt/sources/organism'
-      Gene.add_identifiers Organism.identifiers("NAMESPACE"), "Ensembl Gene ID", "Associated Gene Name"
-      assert_equal "TP53", Gene.setup("ENSG00000141510", "Ensembl Gene ID", "Hsa/feb2014").name
-    end
-  end
-
-  def test_identifier_files
-    Gene.add_identifiers datafile_test('identifiers'), "Ensembl Gene ID", "Associated Gene Name"
-    assert Gene.identifier_files.any?
-  end
-
-  def test_Entity_identifier_files
-    Gene.add_identifiers datafile_test('identifiers'), "Ensembl Gene ID", "Associated Gene Name"
-    assert Entity.identifier_files("Ensembl Gene ID").any?
-  end
-end

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

@@ -1,70 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/workflow'
-require 'rbbt/hpc/orchestrate/batches'
-
-require_relative '../hpc_test_workflows'
-
-class TestOrchestrateBatches < 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_b:
-    tasks: TestWFB#b1, TestWFB#b2, TestWFA#a1, TestWFA#a2
-    config_keys: key2 value2 token2, key3 value3 token3.1 token3.2
-  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:
-    tasks: TestWFB#b1, TestWFB#b2, TestWFA#a1
-  chain_d:
-    tasks: TestWFD#d1, TestWFC#c1, TestWFC#c2, TestWFC#c3
-TestWFA:
-  defaults:
-    log: 4
-    config_keys: key4 value4 token4
-    time: 10min
-  a1:
-    cpus: 10
-    config_keys: key5 value5 token5
-TestWFC:
-  defaults:
-    skip: true
-    log: 4
-    time: 10s
-  EOF
-
-
-  def test_job_batches_d
-    job = TestWFD.job(:d1, nil)
-    job.recursive_clean
-
-    batches = HPC::Orchestration.job_batches(RULES, job)
-    assert_equal 3, batches.length
-  end
-
-  def test_job_batches_c3
-    job = TestWFC.job(:c3, nil)
-    job.recursive_clean
-
-    batches = HPC::Orchestration.job_batches(RULES, job)
-  end
-
-  def test_job_batches_c4
-    job = TestWFC.job(:c4, nil)
-    job.recursive_clean
-
-    batches = HPC::Orchestration.job_batches(RULES, job)
-    assert_equal 3, batches.length
-  end
-
-end

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

@@ -1,108 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/hpc/orchestrate/chains'
-
-require_relative '../hpc_test_workflows'
-
-class TestOrchestrateChains < 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_b:
-    tasks: TestWFB#b1, TestWFB#b2, TestWFA#a1, TestWFA#a2
-    comment: Should not include TestWFA#a1
-  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:
-    tasks: TestWFB#b1, TestWFB#b2, TestWFA#a1
-  chain_d:
-    tasks: TestWFD#d1, TestWFC#c1, TestWFC#c2, TestWFC#c3
-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_job_chain_a
-    job = TestWFA.job(:a3, nil)
-    job.recursive_clean
-
-    job_chains = HPC::Orchestration.job_chains(RULES, job)
-    job_chains = NamedArray.setup(job_chains, job_chains.collect{|n,i| n })
-
-    assert_equal %w(chain_a_b chain_a), job_chains.fields
-    assert_equal 3, job_chains["chain_a"].last[:jobs].length
-    assert_equal job, job_chains["chain_a"].last[:top_level]
-  end
-
-  def test_job_chain_b
-    job = TestWFB.job(:b2, nil)
-    job.recursive_clean
-
-    job_chains = HPC::Orchestration.job_chains(RULES, job)
-    job_chains = NamedArray.setup(job_chains, job_chains.collect{|n,i| n })
-
-    assert_equal %w(chain_a chain_b chain_b2 chain_a_b).sort, job_chains.fields.sort
-
-    assert_equal 2, job_chains["chain_a"].last[:jobs].length
-    assert_equal job.step("a2"), job_chains["chain_a"].last[:top_level]
-
-    assert_equal 2, job_chains["chain_b"].last[:jobs].length
-    assert_equal job, job_chains["chain_b"].last[:top_level]
-
-    assert_equal 2, job_chains["chain_b2"].last[:jobs].length
-    assert_equal job, job_chains["chain_b2"].last[:top_level]
-
-    assert_equal 4, job_chains["chain_a_b"].last[:jobs].length
-    assert_equal job, job_chains["chain_a_b"].last[:top_level]
-  end
-  
-  def test_job_chains_double
-    job = TestWFD.job(:d1, nil)
-    job.recursive_clean
-
-    job_chains = HPC::Orchestration.job_chains(RULES, job)
-    job_chains = NamedArray.setup(job_chains, job_chains.collect{|n,i| n })
-
-    assert_equal 2, job_chains.select{|n,i| n == 'chain_a' }.length
-    assert_equal ["First c3", "Second c3"].sort, job_chains.
-      select{|n,i| n == 'chain_a' }.
-      collect{|n,i| i[:top_level].name }.sort
-
-    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

@@ -1,59 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/workflow'
-require 'rbbt/hpc/orchestrate/rules'
-
-require_relative '../hpc_test_workflows'
-
-class TestOrchestrateRules < 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_defaults
-    rules = HPC::Orchestration.task_specific_rules RULES, "TestWFA", :a1
-    assert_equal "first_queue" , rules[:queue]
-  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_skip
-    rules = HPC::Orchestration.task_specific_rules RULES, "TestWFC", :c1
-    assert rules[:skip]
-  end
-
-
-end
-

data/test/rbbt/hpc/test_batch.rb

@@ -1,64 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
-require 'rbbt/hpc/batch'
-require 'rbbt/workflow'
-
-require_relative 'hpc_test_workflows'
-
-class TestBatch < Test::Unit::TestCase
-
-  def test_batch_options
-    job = TestWFB.job(:b1, "TEST")
-
-    TmpFile.with_file do |batch_dir|
-
-      options = HPC::BATCH.batch_options(job, :batch_dir => batch_dir, :batch_modules => 'java')
-      assert_equal options[:step_path], job.path
-    end
-  end
-
-  def test_template
-    job = TestWFB.job(:b1, "TEST")
-
-    TmpFile.with_file do |batch_dir|
-
-      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 = TestWFB.job(:b1, "TEST")
-
-    TmpFile.with_file do |batch_dir|
-
-      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 = TestWFB.job(:b1, "TEST")
-
-    TmpFile.with_file do |batch_dir|
-
-      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 = TestWFB.job(:b1, "TEST")
-
-    TmpFile.with_file do |batch_dir|
-
-      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
-  
-end
-