rbbt-util 5.43.0 → 5.44.1

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.43.0
+  version: 5.44.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-02-28 00:00:00.000000000 Z
+date: 2024-12-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -283,6 +283,7 @@ files:
 - lib/rbbt/util/misc/options.rb
 - lib/rbbt/util/misc/pipes.rb
 - lib/rbbt/util/misc/serialize.rb
+- lib/rbbt/util/misc/ssw.rb
 - lib/rbbt/util/misc/system.rb
 - lib/rbbt/util/named_array.rb
 - lib/rbbt/util/open.rb
@@ -457,114 +458,6 @@ files:
 - share/rbbt_commands/workflow/write_info
 - share/unicorn.rb
 - share/workflow_config.ru
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/hpc/orchestrate/test_batches.rb
-- test/rbbt/hpc/orchestrate/test_chains.rb
-- test/rbbt/hpc/orchestrate/test_rules.rb
-- test/rbbt/hpc/test_batch.rb
-- test/rbbt/hpc/test_hpc_test_workflows.rb
-- test/rbbt/hpc/test_orchestrate.rb
-- test/rbbt/hpc/test_pbs.rb
-- test/rbbt/hpc/test_slurm.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/test_association.rb
-- test/rbbt/test_entity.rb
-- test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_csv.rb
-- test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_marshal.rb
-- test/rbbt/tsv/test_matrix.rb
-- test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/R/test_plot.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/misc/test_bgzf.rb
-- test/rbbt/util/misc/test_communication.rb
-- test/rbbt/util/misc/test_development.rb
-- test/rbbt/util/misc/test_format.rb
-- test/rbbt/util/misc/test_indiferent_hash.rb
-- test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
-- test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/misc/test_pipes.rb
-- test/rbbt/util/misc/test_serialize.rb
-- test/rbbt/util/python/test_util.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_config.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/test_log.rb
-- test/rbbt/util/test_migrate.rb
-- test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_procpath.rb
-- test/rbbt/util/test_python.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/test_ssh.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/step/test_save_load_inputs.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_remote_workflow.rb
-- test/rbbt/workflow/test_schedule.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/workflow/util/test_archive.rb
-- test/rbbt/workflow/util/test_data.rb
-- test/rbbt/workflow/util/test_orchestrator.rb
-- test/test_helper.rb
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses:
 - MIT
@@ -584,116 +477,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.6
+rubygems_version: 3.5.23
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
-test_files:
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/hpc/orchestrate/test_batches.rb
-- test/rbbt/hpc/orchestrate/test_chains.rb
-- test/rbbt/hpc/orchestrate/test_rules.rb
-- test/rbbt/hpc/test_batch.rb
-- test/rbbt/hpc/test_hpc_test_workflows.rb
-- test/rbbt/hpc/test_orchestrate.rb
-- test/rbbt/hpc/test_pbs.rb
-- test/rbbt/hpc/test_slurm.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/test_association.rb
-- test/rbbt/test_entity.rb
-- test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_csv.rb
-- test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_marshal.rb
-- test/rbbt/tsv/test_matrix.rb
-- test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/R/test_plot.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/misc/test_bgzf.rb
-- test/rbbt/util/misc/test_communication.rb
-- test/rbbt/util/misc/test_development.rb
-- test/rbbt/util/misc/test_format.rb
-- test/rbbt/util/misc/test_indiferent_hash.rb
-- test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
-- test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/misc/test_pipes.rb
-- test/rbbt/util/misc/test_serialize.rb
-- test/rbbt/util/python/test_util.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_config.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/test_log.rb
-- test/rbbt/util/test_migrate.rb
-- test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_procpath.rb
-- test/rbbt/util/test_python.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/test_ssh.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/step/test_save_load_inputs.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_remote_workflow.rb
-- test/rbbt/workflow/test_schedule.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/workflow/util/test_archive.rb
-- test/rbbt/workflow/util/test_data.rb
-- test/rbbt/workflow/util/test_orchestrator.rb
-- test/test_helper.rb
+test_files: []

data/test/rbbt/annotations/test_util.rb

@@ -1,43 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
-require 'rbbt/annotations'
-
-module TestEntityString
-  extend Entity
-  self.annotation :code
-end
-
-class TestAnnotation < Test::Unit::TestCase
-  def test_marshal
-    a = "STRING"
-    a = TestEntityString.setup(a)
-
-    #assert !(Annotated === Marshal.load(Marshal.dump(a)))
-    assert_equal a, Marshal.load(Marshal.dump(a))
-  end
-
-  def test_marshal_array
-    a = ["STRING"]
-    TestEntityString.setup(a)
-
-    #assert !(Annotated === Marshal.load(Marshal.dump(a)))
-    assert Annotated === a
-    assert Annotated === a.first
-    assert_equal a, Marshal.load(Marshal.dump(a))
-  end
-
-  def test_hash
-    e = TestEntityString.setup("TEST", :code => 10)
-    assert_equal "TEST", Annotated.to_hash(e)[:literal]
-    assert_equal 10, Annotated.to_hash(e)[:info][:code]
-  end
-
-  def test_traverse_cpus
-    strings = (1..10).to_a.collect{|n| n.to_s }
-    res = TSV.traverse strings, :cpus => 2, :into => [] do |s|
-      TestEntityString.setup(s, :code => s.to_i)
-    end
-
-    assert TestEntityString === res.first
-  end
-end
-

data/test/rbbt/association/test_database.rb

@@ -1,87 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
-require 'rbbt-util'
-require 'rbbt/association'
-require 'rbbt/association'
-require 'rbbt/association/database'
-
-class TestAssociationDatabase < Test::Unit::TestCase
-   
-  def effect_options
-    effect_options = {
-      :source => "SG=~Associated Gene Name",
-      :target => "TG=~Associated Gene Name=>Ensembl Gene ID",
-      :persist => false,
-    :identifiers => datafile_test('identifiers'),
-    }
-  end
-
-  def effect_tsv
-    effect =<<-END
-#: :sep=" "#:type=:double
-#SG TG Effect directed?
-MDM2 TP53 inhibition false
-TP53 NFKB1|GLI1 activation|activation true|true
-    END
-
-    effect_tsv = TSV.open effect, effect_options.dup
-  end
-
-  def effect_database
-    effect_database = Association.database(effect_tsv)
-  end
-
-  def test_tsv
-    assert_equal %w(NFKB1 GLI1), effect_tsv["TP53"]["TG"]
-  end
-
-  def test_open_new_tsv
-    tsv = Association.database effect_tsv, :fields => ["Effect"], :target => "TG=~Associated Gene Name=>Ensembl Gene ID"
-    assert_equal ["Ensembl Gene ID", "Effect"], tsv.fields
-    assert_equal "SG", tsv.key_field
-    assert tsv.include? "MDM2"
-  end
-
-  def test_open_new_tsv_reverse
-    tsv = Association.database effect_tsv, :fields => ["Effect"], :target => "SG=~Associated Gene Name=>Ensembl Gene ID", :zipped => true
-    assert_equal ["Ensembl Gene ID", "Effect"], tsv.fields
-    assert_equal "TG", tsv.key_field
-    assert tsv.include? "NFKB1"
-  end
-
-  def test_database_translate
-    database = Association.database(effect_tsv, effect_options.merge({:source => "SG=~Associated Gene Name=>Ensembl Gene ID", :target => "TG"}))
-    assert_equal %w(inhibition), database["ENSG00000135679"]["Effect"]
-    assert_equal %w(activation activation), database["ENSG00000141510"]["Effect"]
-  end
-
-  def test_database
-    assert_equal %w(inhibition), effect_database["MDM2"]["Effect"]
-    assert_equal %w(activation activation), effect_database["TP53"]["Effect"]
-  end
-
-  def test_index_list
-    file = datafile_test('gene_ages')
-    tsv = Association.database(file)
-    assert_equal [["Bilateria"], ["Euteleostomi"], ["Duplicate"]], tsv["ENSG00000000003"]
-  end
-
-  def test_gene_ages
-    file = datafile_test('gene_ages')
-    assert Association.database(file, :source => "FamilyAge", :merge => true, :target => "Ensembl Gene ID", :persist => false).values.first.length > 1
-  end
-
-  def __test_reorder_multiple_mismatch
-
-    text =<<-EOF
-#: :filename=BLADDER_11_and_12#:namespace=Hsa/feb2014#:type=:double
-#Genomic Mutation	Ensembl Gene ID	affected	damaged	splicing	broken	Sample
-12:54423561:A	ENSG00000273049|ENSG00000197757|ENSG00000198353|ENSG00000273046	false|true|false|false	false|true|false|false	false|false|false|false	false|true|false|false	51106212
-    EOF
-
-    tsv = TSV.open(StringIO.new(text))
-  
-    index =  Association.index(tsv, :source => "Sample", :target => "Genomic Mutation", :merge => true, :persist_update => true)
-    assert_equal 4, index["51106212~12:54423561:A"][0].split(";;").length
-
-  end
-end

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