rbbt-util 5.43.0 → 5.44.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: d1bbf2cefca44eecad7465a8d4dc1b88f53f18d1e63e310353061b43ad46bed9
-  data.tar.gz: f54f659da9eca312d116430d88019f067ce5ccf519724a2a448e3b4d31dfb767
+  metadata.gz: 1c39baa8ee0c2633bea3878720d29aa0f49a057db7ec6700187685c7a07f7eae
+  data.tar.gz: ad0f8a09cb34faa3d0aa3388c26733d4849d307a02df02989656c0aced5ea72a
 SHA512:
-  metadata.gz: eaad34515129ffd123064e9af920b5f83f3897c957de45e3bef04a1101d961d419863729f21665773b81f535f3fdba45d490ce41870f9db87f0e0e5d5f987233
-  data.tar.gz: d48552f30e6434b0e27e173eb62f41a3126ecb9065cba58f2f5737f8e3aef0e2183503076a40cc6586832d90458ae5e572a55171758452f3699a4225704bc25e
+  metadata.gz: dcfcf7f6ea2b45dd4ca5e1257fb22cec0f06280be2b6c9aac3b118e1e649a8f5948db0162f62735b9c113ee9a878cb89e8f98a99fd7026a7f58f061531b93f89
+  data.tar.gz: 59e94fecbb50bf9d7635545aab508ee6b986e44f81acac59aac7e888f6c9c5748fb2d0324a0e83d784c78b249e67a50baaaba1d40b58612f194de111fd4c6579

data/lib/rbbt/association/util.rb

@@ -10,7 +10,7 @@ module Association
   end
 
   def self.parse_field_specification(spec)
-    return [2,nil,nil] if Numeric === spec
+    return [spec,nil,nil] if Numeric === spec
     spec = spec.split "=>" unless Array === spec
     field_part, final_format = spec
 

data/lib/rbbt/hpc/batch.rb

@@ -110,23 +110,25 @@ module HPC
 
       task = Symbol === job.overriden ? job.overriden : job.task_name
 
-      #override_deps = job.overriden_deps.collect do |dep| 
-      #  name = [dep.workflow.to_s, dep.task_name] * "#"
-      #  [name, dep.path] * "="  
-      #end.uniq * ","
-
-      if job.overriden?
-        #override_deps = job.rec_dependencies.
-        #  select{|dep| Symbol === dep.overriden }.
-        
-        override_deps = job.overriden_deps.
-          collect do |dep| 
-          name = [dep.workflow.to_s, dep.task_name] * "#"
-          [name, dep.path] * "="  
-        end.uniq * ","
-
-        options[:override_deps] = override_deps unless override_deps.empty?
-      end
+      override_deps = job.overriden_deps.collect do |dep| 
+        name = [dep.workflow.to_s, dep.task_name] * "#"
+        [name, dep.path] * "="  
+      end.uniq * ","
+
+      options[:override_deps] = override_deps unless override_deps.empty?
+
+      #if job.overriden?
+      #  #override_deps = job.rec_dependencies.
+      #  #  select{|dep| Symbol === dep.overriden }.
+      #  
+      #  override_deps = job.overriden_deps.
+      #    collect do |dep| 
+      #    name = [dep.workflow.to_s, dep.task_name] * "#"
+      #    [name, dep.path] * "="  
+      #  end.uniq * ","
+
+      #  options[:override_deps] = override_deps unless override_deps.empty?
+      #end
 
       # Save inputs into inputs_dir
       inputs_dir = Misc.process_options options, :inputs_dir

data/lib/rbbt/tsv/accessor.rb

@@ -567,13 +567,13 @@ module TSV
     end
   end
 
-  def dumper_stream(keys = nil, no_options = false, unmerge = false)
+  def dumper_stream(keys = nil, no_options = false, unmerge = false, stream = nil)
     unmerge = false unless type == :double
 
     options = self.options
     options[:type] = :list if unmerge
 
-    TSV::Dumper.stream options do |dumper|
+    TSV::Dumper.stream options, filename, stream do |dumper|
       case no_options
       when FalseClass, nil
         dumper.init
@@ -631,11 +631,11 @@ module TSV
             end
           end
         end
+        dumper.close
       rescue Exception
         Log.exception $!
         raise $!
       end
-      dumper.close
     end
   end
 
@@ -651,14 +651,9 @@ module TSV
       end
     end
 
-    io = dumper_stream(keys, no_options, unmerge)
-
-    str = ''
-    while block = io.read(Misc::BLOCK_SIZE)
-      str << block
-    end
-
-    str
+    io = dumper_stream(keys, no_options, unmerge, StringIO.new)
+    io.rewind
+    io.read
   end
 
   def to_unmerged_s(keys = nil, no_options = false)

data/lib/rbbt/tsv/dumper.rb

@@ -1,13 +1,24 @@
 module TSV
   class Dumper
     attr_accessor :in_stream, :stream, :options, :filename, :sep
-    def self.stream(options = {}, filename = nil, &block)
+    def self.stream(options = {}, filename = nil, stream = nil, &block)
       dumper = TSV::Dumper.new options, filename
-      Thread.new(Thread.current) do |parent|
+      if stream
+        dumper.set_stream stream if stream
         yield dumper
-        dumper.close
+        stream
+      else
+        thread = Thread.new(Thread.current) do |parent|
+          yield dumper
+        end
+        ConcurrentStream.setup(dumper.stream, threads: thread)
       end
-      dumper.stream
+    end
+
+    def set_stream(stream)
+      @stream.close
+      @in_stream.close
+      @in_stream = @stream = stream
     end
 
     def initialize(options, filename = nil)
@@ -56,16 +67,16 @@ module TSV
 
       str = TSV.header_lines(key_field, fields, options.merge(init_options || {}))
 
-      Thread.pass while IO.select(nil, [@in_stream],nil,1).nil?
+      Thread.pass while IO.select(nil, [@in_stream],nil,1).nil? if IO === @in_stream
 
-      @in_stream.puts str
+      @in_stream << str
     end
 
     def add(k,v)
       @fields ||= @options[:fields]
       @sep ||= @options[:sep]
       begin
-        Thread.pass while IO.select(nil, [@in_stream],nil,1).nil?
+        Thread.pass while IO.select(nil, [@in_stream],nil,1).nil? if IO === @in_stream
         @in_stream << k << TSV::Dumper.values_to_s(v, @fields, @sep)
       rescue IOError
       rescue Exception
@@ -74,16 +85,16 @@ module TSV
     end
 
     def close_out
-      @stream.close unless @stream.closed?
+      @stream.close unless StringIO === @stream || @stream.closed?
     end
 
     def close_in
       @in_stream.join if @in_stream.respond_to?(:join) && ! @in_stream.joined?
-      @in_stream.close unless @in_stream.closed?
+      @in_stream.close if @in_stream.respond_to?(:close) && ! @in_stream.closed? 
     end
 
     def close
-      close_in
+      close_in unless @in_stream == @stream
     end
   end
 end

data/lib/rbbt/tsv/index.rb

@@ -125,7 +125,7 @@ module TSV
   def self.index(file, options = {})
     persist_options = Misc.pull_keys options, :persist
     persist_options[:prefix] ||= "StaticIndex[#{options[:target] || :key}]"
-     
+
     Log.debug "Static Index: #{ file } - #{Misc.fingerprint options}"
     Persist.persist_tsv nil, file, options, persist_options do |data|
       data_options = Misc.pull_keys options, :data
@@ -258,6 +258,7 @@ module TSV
                else
                  file.object_id.to_s
                end
+
     persist_options = Misc.pull_keys options, :persist
     persist_options[:prefix] ||= "StaticRangeIndex[#{start_field}-#{end_field}]"
 

data/lib/rbbt/util/misc/math.rb

@@ -1,4 +1,3 @@
-
 module Misc
 
   Log2Multiplier = 1.0 / Math.log(2.0)

data/lib/rbbt/util/open.rb

@@ -729,7 +729,7 @@ module Open
       dir_sub_path.push content
       save_content_in_repo(*dir_sub_path)
     else
-      FileUtils.mkdir_p File.dirname(file)
+      FileUtils.mkdir_p File.dirname(file) unless File.directory?(file)
       case
       when block_given?
         begin

data/lib/rbbt/workflow/step/info.rb

@@ -62,6 +62,7 @@ class Step
   def load_dependencies_from_info
     relocated = nil
     @dependencies = (self.info[:dependencies] || []).collect do |task,name,dep_path|
+      dep_path = task if dep_path.nil?
       if Open.exists?(dep_path) || Open.exists?(dep_path + '.info')
         Workflow._load_step dep_path
       else

data/lib/rbbt/workflow/step.rb

@@ -303,7 +303,8 @@ class Step
 
             if result_description
               entity_info = info.dup
-              entity_info.merge! info[:inputs] if info[:inputs]
+              # Also load entity_info in rbbt6
+              entity_info.merge! info[:inputs] if Hash === info[:inputs]
               res = prepare_result res, result_description, entity_info 
             end
 

data/python/rbbt/__init__.py

@@ -67,10 +67,10 @@ def tsv_preamble(line, comment_char="#"):
     return header
 
 
-def tsv_header(filename, sep="\t", comment_char="#"):
+def tsv_header(filename, sep="\t", comment_char="#", encoding='utf8'):
     import re
 
-    f = open(filename)
+    f = open(filename, encoding=encoding)
     line = f.readline().strip()
 
     if (not line.startswith(comment_char)):

data/share/rbbt_commands/workflow/task

@@ -484,7 +484,7 @@ begin
 
   if server = options.delete(:relay)
     require 'rbbt/workflow/remote_workflow'
-    relay_dependencies = options.delete(:relay_dependencies).split(",")
+    relay_dependencies = options.delete(:relay_dependencies).split(",") if options[:relay_dependencies]
     produce_dependencies_for_relay = options.delete(:produce_dependencies_for_relay)
 
     jobs_to_relay = relay_dependencies ?  match_dependencies(relay_dependencies, job.rec_dependencies) : [job]

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.43.0
+  version: 5.44.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-02-28 00:00:00.000000000 Z
+date: 2024-05-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -457,114 +457,6 @@ 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 +476,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.6
+rubygems_version: 3.5.10
 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