scout-gear 10.4.0 → 10.6.1

data/lib/scout/workflow.rb

@@ -11,13 +11,45 @@ require 'scout/resource/scout'
 
 module Workflow
   class << self
-    attr_accessor :workflows, :main
+    attr_accessor :workflows, :main, :workflow_dir, :autoinstall, :workflow_repo
     def workflows
       @workflows ||= []
     end
+
+    def workflow_dir
+      @workflow_dir || 
+        ENV["SCOUT_WORKFLOW_DIR"] || 
+        begin 
+          workflow_dir_config = Path.setup("etc/workflow_dir")
+          if workflow_dir_config.exists?
+            Path.setup(workflow_dir_config.read.strip)
+          else
+            Path.setup('workflows').find(:user)
+          end
+        end
+    end
+
+    def workflow_repo
+      @workflow_repo || 
+        ENV["SCOUT_WORKFLOW_REPO"] || 
+        begin 
+          workflow_repo_config = Path.setup("etc/workflow_repo")
+          if workflow_repo_config.exists?
+            workflow_repo_config.read.strip
+          else
+            'https://github.com/Scout-Workflows/'
+          end
+        end
+    end
+
+    def autoinstall
+      @autoinstall || ENV["SCOUT_WORKFLOW_AUTOINSTALL"] = "true"
+    end
+
   end
 
   attr_accessor :libdir
+
   def self.extended(base)
     self.workflows << base
     libdir = Path.caller_lib_dir
@@ -25,22 +57,87 @@ module Workflow
     base.libdir = Path.setup(libdir).tap{|p| p.resource = base}
   end
 
+  def self.update_workflow_dir(workflow_dir)
+    Misc.in_dir(workflow_dir) do
+      Log.info "Updating: " + workflow_dir
+      `git pull`
+      `git submodule init`
+      `git submodule update`
+    end
+  end
+
+  def self.install_workflow(workflow, base_repo_url = nil)
+    case
+    when File.exist?(workflow)
+      update_workflow_dir(workflow)
+    else
+      Misc.in_dir(self.workflow_dir) do
+        Log.info "Installing: " + workflow
+
+        repo_base_url ||= self.workflow_repo
+
+
+        if repo_base_url.include?(workflow) or repo_base_url.include?(Misc.snake_case(workflow))
+          repo = repo_base_url
+        else
+          begin
+            repo = File.join(repo_base_url, workflow + '.git')
+            CMD.cmd("wget '#{repo}' -O /dev/null").read
+          rescue
+            Log.debug "Workflow repo does not exist, trying snake_case: #{ repo }"
+            begin
+              repo = File.join(repo_base_url, Misc.snake_case(workflow) + '.git')
+              CMD.cmd("wget '#{repo}' -O /dev/null").read
+            rescue
+              raise "Workflow repo does not exist: #{ repo }"
+            end
+          end
+        end
+
+        Log.warn "Cloning #{ repo }"
+        Misc.insist do
+          `git clone "#{repo}" #{ Misc.snake_case(workflow) }`
+          raise unless $?.success?
+        end
+        Log.warn "Initializing and updating submodules for #{repo}. You might be prompted for passwords."
+        Misc.in_dir(Misc.snake_case(workflow)) do
+          `git submodule init`
+          `git submodule update`
+        end
+      end
+    end
+  end
+
+  def self.require_workflow_file(file)
+    file = file.find if Path === file
+    $LOAD_PATH.unshift(File.join(File.dirname(file), 'lib'))
+    load file
+  end
+
   def self.require_workflow(workflow_name_orig)
     first = nil
     workflow_name_orig.split("+").each do |complete_workflow_name|
       self.main = nil
-      workflow_name, *subworkflows = complete_workflow_name.split("::")
-      workflow = workflow_name
-      workflow = Path.setup('workflows')[workflow_name]["workflow.rb"] unless Open.exists?(workflow)
-      workflow = Path.setup('workflows')[Misc.snake_case(workflow_name)]["workflow.rb"] unless Open.exists?(workflow)
-      workflow = Path.setup('workflows')[Misc.camel_case(workflow_name)]["workflow.rb"] unless Open.exists?(workflow)
-      if Open.exists?(workflow)
-        self.main = nil
-        workflow = workflow.find if Path === workflow
-        $LOAD_PATH.unshift(File.join(File.dirname(workflow), 'lib'))
-        load workflow
-      else
-        raise "Workflow #{workflow_name} not found"
+
+      Persist.memory(complete_workflow_name, prefix: "Workflow") do
+        begin
+          workflow_name, *subworkflows = complete_workflow_name.split("::")
+          workflow_file = workflow_name
+          workflow_file = Path.setup('workflows')[workflow_name]["workflow.rb"] unless Open.exists?(workflow_file)
+          workflow_file = Path.setup('workflows')[Misc.snake_case(workflow_name)]["workflow.rb"] unless Open.exists?(workflow_file)
+          workflow_file = Path.setup('workflows')[Misc.camel_case(workflow_name)]["workflow.rb"] unless Open.exists?(workflow_file)
+          if Open.exists?(workflow_file)
+            self.main = nil
+            require_workflow_file(workflow_file)
+          elsif autoinstall
+            install_workflow(workflow_name)
+            raise TryAgain
+          else
+            raise "Workflow #{workflow_name} not found"
+          end
+        rescue TryAgain
+          retry
+        end
       end
 
       current = begin

data/lib/scout-gear.rb

@@ -1,3 +1,5 @@
 require 'scout-essentials'
 require_relative 'scout/tsv'
 require_relative 'scout/offsite'
+
+Path.path_maps[:scout_gear] = File.join(Path.caller_lib_dir(__FILE__), "{TOPLEVEL}/{SUBPATH}")

data/lib/scout.rb

@@ -1,5 +1,4 @@
 require 'workflow-scout'
-require 'rbbt-scout'
 
 module Scout
   def self.version

data/scout-gear.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: scout-gear 10.4.0 ruby lib
+# stub: scout-gear 10.6.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "scout-gear".freeze
-  s.version = "10.4.0"
+  s.version = "10.6.1".freeze
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Miguel Vazquez".freeze]
-  s.date = "2023-08-09"
+  s.date = "2024-05-28"
   s.description = "Temporary files, logs, path, resources, persistence, workflows, TSV, etc.".freeze
   s.email = "mikisvaz@gmail.com".freeze
   s.executables = ["scout".freeze]
@@ -33,26 +33,50 @@ Gem::Specification.new do |s|
     "lib/rbbt-scout.rb",
     "lib/scout-gear.rb",
     "lib/scout.rb",
+    "lib/scout/association.rb",
+    "lib/scout/association/fields.rb",
+    "lib/scout/association/index.rb",
+    "lib/scout/association/item.rb",
+    "lib/scout/association/util.rb",
+    "lib/scout/entity.rb",
+    "lib/scout/entity/format.rb",
+    "lib/scout/entity/identifiers.rb",
+    "lib/scout/entity/object.rb",
+    "lib/scout/entity/property.rb",
     "lib/scout/offsite.rb",
     "lib/scout/offsite/exceptions.rb",
     "lib/scout/offsite/ssh.rb",
     "lib/scout/offsite/step.rb",
     "lib/scout/offsite/sync.rb",
+    "lib/scout/persist/engine.rb",
+    "lib/scout/persist/engine/fix_width_table.rb",
+    "lib/scout/persist/engine/packed_index.rb",
+    "lib/scout/persist/engine/sharder.rb",
+    "lib/scout/persist/engine/tkrzw.rb",
+    "lib/scout/persist/engine/tokyocabinet.rb",
+    "lib/scout/persist/tsv.rb",
+    "lib/scout/persist/tsv/adapter.rb",
+    "lib/scout/persist/tsv/adapter/base.rb",
+    "lib/scout/persist/tsv/adapter/fix_width_table.rb",
+    "lib/scout/persist/tsv/adapter/packed_index.rb",
+    "lib/scout/persist/tsv/adapter/sharder.rb",
+    "lib/scout/persist/tsv/adapter/tkrzw.rb",
+    "lib/scout/persist/tsv/adapter/tokyocabinet.rb",
+    "lib/scout/persist/tsv/serialize.rb",
     "lib/scout/semaphore.rb",
     "lib/scout/tsv.rb",
+    "lib/scout/tsv/annotation.rb",
+    "lib/scout/tsv/annotation/repo.rb",
     "lib/scout/tsv/attach.rb",
     "lib/scout/tsv/change_id.rb",
+    "lib/scout/tsv/change_id/translate.rb",
+    "lib/scout/tsv/csv.rb",
     "lib/scout/tsv/dumper.rb",
+    "lib/scout/tsv/entity.rb",
     "lib/scout/tsv/index.rb",
     "lib/scout/tsv/open.rb",
     "lib/scout/tsv/parser.rb",
     "lib/scout/tsv/path.rb",
-    "lib/scout/tsv/persist.rb",
-    "lib/scout/tsv/persist/adapter.rb",
-    "lib/scout/tsv/persist/fix_width_table.rb",
-    "lib/scout/tsv/persist/serialize.rb",
-    "lib/scout/tsv/persist/tkrzw.rb",
-    "lib/scout/tsv/persist/tokyocabinet.rb",
     "lib/scout/tsv/stream.rb",
     "lib/scout/tsv/transformer.rb",
     "lib/scout/tsv/traverse.rb",
@@ -72,8 +96,11 @@ Gem::Specification.new do |s|
     "lib/scout/workflow/definition.rb",
     "lib/scout/workflow/deployment.rb",
     "lib/scout/workflow/deployment/orchestrator.rb",
+    "lib/scout/workflow/deployment/trace.rb",
     "lib/scout/workflow/documentation.rb",
     "lib/scout/workflow/step.rb",
+    "lib/scout/workflow/step/archive.rb",
+    "lib/scout/workflow/step/children.rb",
     "lib/scout/workflow/step/config.rb",
     "lib/scout/workflow/step/dependencies.rb",
     "lib/scout/workflow/step/file.rb",
@@ -114,26 +141,53 @@ Gem::Specification.new do |s|
     "share/software/install_helpers",
     "share/templates/command",
     "share/templates/workflow.rb",
+    "test/data/person/brothers",
+    "test/data/person/identifiers",
+    "test/data/person/marriages",
+    "test/data/person/parents",
+    "test/scout/association/test_fields.rb",
+    "test/scout/association/test_index.rb",
+    "test/scout/association/test_item.rb",
+    "test/scout/entity/test_format.rb",
+    "test/scout/entity/test_identifiers.rb",
+    "test/scout/entity/test_object.rb",
+    "test/scout/entity/test_property.rb",
     "test/scout/offsite/test_ssh.rb",
     "test/scout/offsite/test_step.rb",
     "test/scout/offsite/test_sync.rb",
     "test/scout/offsite/test_task.rb",
+    "test/scout/persist/engine/test_fix_width_table.rb",
+    "test/scout/persist/engine/test_packed_index.rb",
+    "test/scout/persist/engine/test_sharder.rb",
+    "test/scout/persist/engine/test_tkrzw.rb",
+    "test/scout/persist/engine/test_tokyocabinet.rb",
+    "test/scout/persist/test_tsv.rb",
+    "test/scout/persist/tsv/adapter/test_base.rb",
+    "test/scout/persist/tsv/adapter/test_fix_width_table.rb",
+    "test/scout/persist/tsv/adapter/test_packed_index.rb",
+    "test/scout/persist/tsv/adapter/test_serialize.rb",
+    "test/scout/persist/tsv/adapter/test_sharder.rb",
+    "test/scout/persist/tsv/adapter/test_tkrzw.rb",
+    "test/scout/persist/tsv/adapter/test_tokyocabinet.rb",
+    "test/scout/persist/tsv/test_serialize.rb",
+    "test/scout/test_association.rb",
+    "test/scout/test_entity.rb",
     "test/scout/test_offsite.rb",
     "test/scout/test_semaphore.rb",
     "test/scout/test_tsv.rb",
     "test/scout/test_work_queue.rb",
     "test/scout/test_workflow.rb",
-    "test/scout/tsv/persist/test_adapter.rb",
-    "test/scout/tsv/persist/test_fix_width_table.rb",
-    "test/scout/tsv/persist/test_tkrzw.rb",
-    "test/scout/tsv/persist/test_tokyocabinet.rb",
+    "test/scout/tsv/annotation/test_repo.rb",
+    "test/scout/tsv/change_id/test_translate.rb",
+    "test/scout/tsv/test_annotation.rb",
     "test/scout/tsv/test_attach.rb",
     "test/scout/tsv/test_change_id.rb",
+    "test/scout/tsv/test_csv.rb",
     "test/scout/tsv/test_dumper.rb",
+    "test/scout/tsv/test_entity.rb",
     "test/scout/tsv/test_index.rb",
     "test/scout/tsv/test_open.rb",
     "test/scout/tsv/test_parser.rb",
-    "test/scout/tsv/test_persist.rb",
     "test/scout/tsv/test_stream.rb",
     "test/scout/tsv/test_transformer.rb",
     "test/scout/tsv/test_traverse.rb",
@@ -148,6 +202,9 @@ Gem::Specification.new do |s|
     "test/scout/work_queue/test_socket.rb",
     "test/scout/work_queue/test_worker.rb",
     "test/scout/workflow/deployment/test_orchestrator.rb",
+    "test/scout/workflow/deployment/test_trace.rb",
+    "test/scout/workflow/step/test_archive.rb",
+    "test/scout/workflow/step/test_children.rb",
     "test/scout/workflow/step/test_dependencies.rb",
     "test/scout/workflow/step/test_info.rb",
     "test/scout/workflow/step/test_load.rb",
@@ -167,18 +224,18 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/mikisvaz/scout-gear".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "3.5.0.dev".freeze
+  s.rubygems_version = "3.5.10".freeze
   s.summary = "basic gear for scouts".freeze
 
   s.specification_version = 4
 
-  s.add_runtime_dependency(%q<scout-essentials>.freeze, [">= 0"])
-  s.add_runtime_dependency(%q<net-ssh>.freeze, [">= 0"])
-  s.add_runtime_dependency(%q<matrix>.freeze, [">= 0"])
-  s.add_runtime_dependency(%q<RubyInline>.freeze, [">= 0"])
-  s.add_development_dependency(%q<rdoc>.freeze, ["~> 3.12"])
-  s.add_development_dependency(%q<bundler>.freeze, ["~> 1.0"])
-  s.add_development_dependency(%q<juwelier>.freeze, ["~> 2.1.0"])
-  s.add_development_dependency(%q<simplecov>.freeze, [">= 0"])
+  s.add_runtime_dependency(%q<scout-essentials>.freeze, [">= 0".freeze])
+  s.add_runtime_dependency(%q<net-ssh>.freeze, [">= 0".freeze])
+  s.add_runtime_dependency(%q<matrix>.freeze, [">= 0".freeze])
+  s.add_runtime_dependency(%q<RubyInline>.freeze, [">= 0".freeze])
+  s.add_development_dependency(%q<rdoc>.freeze, ["~> 3.12".freeze])
+  s.add_development_dependency(%q<bundler>.freeze, ["~> 1.0".freeze])
+  s.add_development_dependency(%q<juwelier>.freeze, ["~> 2.1.0".freeze])
+  s.add_development_dependency(%q<simplecov>.freeze, [">= 0".freeze])
 end
 

data/scout_commands/rbbt

@@ -1,5 +1,7 @@
 #!/usr/bin/env ruby
 
+require 'rbbt-scout'
+
 case
 when File.exist?(file = File.join(__dir__, '../modules/rbbt-util/bin/rbbt'))
   $LOAD_PATH.unshift(lib_dir = File.join(file, '../..', 'lib'))

data/test/data/person/brothers

@@ -0,0 +1,4 @@
+#: :sep=,#:type=:list
+#Older,Younger
+Clei,Guille
+Isa,Miki

data/test/data/person/identifiers

@@ -0,0 +1,10 @@
+#: :sep=,#:type=:list
+#Name,Alias,ID
+Miguel,Miki,001
+Cleia,Clei,002
+Isabel,Isa,003
+Guillermo,Guille,004
+Juan Luis,Juan,005
+Maria Luz,Mariluz,006
+Domingo,Domingo,007
+Gloria,Gloria,008

data/test/data/person/marriages

@@ -0,0 +1,3 @@
+#: :type=:list
+#Husband (ID)	Wife (ID)	Date
+001	002	2021

data/test/data/person/parents

@@ -0,0 +1,6 @@
+#: :sep=,#:type=:double
+#Child (Alias),Parent (Alias),Type of parent
+Miki,Juan|Mariluz,father|mother
+Isa,Juan|Mariluz,father|mother
+Guille,Domingo|Gloria,father|mother
+Clei,Domingo|Gloria,father|mother

data/test/scout/association/test_fields.rb

@@ -0,0 +1,105 @@
+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 'scout/tsv'
+class TestAssociationFields < 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/scout/association/test_index.rb

@@ -0,0 +1,70 @@
+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 'scout/tsv'
+require 'scout/association'
+class TestAssociationIndex < Test::Unit::TestCase
+  def test_parents_simple
+    database = Association.database datadir_test.person.parents
+    index = Association.index datadir_test.person.parents
+    assert_include index, "Miki~Juan"
+  end
+
+  def test_parents
+    index = Association.index datadir_test.person.parents, target: "Parent=>Name", source: "=>Name"
+    assert_include index, "Miguel~Juan Luis"
+  end
+
+  def test_brothers
+    index = Association.index datadir_test.person.brothers, undirected: true, persist: false
+    assert_include index, "Clei~Guille"
+    assert_include index, "Guille~Clei"
+  end
+
+  def test_brothers_match
+    index = Association.index datadir_test.person.brothers, undirected: true
+    assert_equal ["Clei~Guille"], index.match("Clei")
+    assert_equal ["Guille~Clei"], index.match("Guille")
+  end
+
+  def test_parents_subset
+    index = Association.index datadir_test.person.parents
+    assert_include index.subset(["Miki", "Guille"], :all), "Miki~Juan"
+    assert_include index.subset(["Miki", "Guille"], :all), "Guille~Gloria"
+  end
+
+  def test_parents_reverse
+    index = Association.index datadir_test.person.parents
+    assert_include index.reverse.source_field, "Parent"
+    assert_include index.reverse.subset(["Juan"], :all), "Juan~Miki"
+  end
+
+  def test_parents_filter
+    index = Association.index datadir_test.person.parents
+    assert_include index.filter('Type of parent', 'mother'), "Miki~Mariluz"
+    assert_include index.filter('Type of parent', 'mother'), "Clei~Gloria"
+    refute index.filter('Type of parent', 'mother').include?("Miki~Juan")
+  end
+
+  def test_parents_flat
+    tsv = datadir_test.person.parents.tsv type: :flat, fields: ["Parent"]
+    index = Association.index tsv
+    assert_include index, "Miki~Juan"
+    assert_include index, "Isa~Mariluz"
+  end
+
+  def test_list_serializer
+    TmpFile.with_file <<-EOF do |f|
+#: :sep=,#:type=:list
+#lowcase,upcase,double,triple
+a,A,aa,aaa
+b,B,bb,bbb
+      EOF
+      tsv = TSV.open(f)
+      i = Association.index tsv
+      assert_equal ['aa', 'aaa'], i["a~A"]
+    end
+  end
+
+end
+

data/test/scout/association/test_item.rb

@@ -0,0 +1,21 @@
+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 'scout/tsv'
+require 'scout/association'
+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
+
+  def test_brothers
+    incidence = TSV.incidence(datadir_test.person.brothers, undirected: true)
+    assert incidence["Clei"]["Guille"]
+    assert incidence["Guille"]["Clei"]
+    refute incidence["Clei"]["Isa"]
+  end
+end
+

data/test/scout/entity/test_format.rb

@@ -0,0 +1,19 @@
+require File.expand_path(__FILE__).sub(%r(/test/.*), '/test/test_helper.rb')
+require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1')
+
+class TestEntityFormat < Test::Unit::TestCase
+  def test_format
+    index = Entity::FormatIndex.new
+    index["Ensembl Gene ID"] = "Gene"
+    assert_equal "Gene", index["Ensembl Gene ID"]
+    assert_equal "Gene", index["Transcription Factor (Ensembl Gene ID)"]
+
+    Entity::FORMATS["Ensembl Gene ID"] = "Gene"
+    assert_equal "Ensembl Gene ID", Entity::FORMATS.find("Ensembl Gene ID")
+    assert_equal "Ensembl Gene ID", Entity::FORMATS.find("Transcription Factor (Ensembl Gene ID)")
+
+    assert_equal "Gene", Entity::FORMATS["Ensembl Gene ID"]
+    assert_equal "Gene", Entity::FORMATS["Transcription Factor (Ensembl Gene ID)"]
+  end
+end
+

data/test/scout/entity/test_identifiers.rb

@@ -0,0 +1,58 @@
+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 'scout/tsv'
+require 'scout/entity'
+
+class TestEntityIdentifiers < Test::Unit::TestCase
+  module Person
+    extend Entity
+  end
+
+  module PersonWithNoIds
+    extend Entity
+    include Entity::Identified
+  end
+
+  Person.add_identifiers datafile_test(Entity::Identified::NAMESPACE_TAG + '/identifiers'), "Name", "Alias"
+
+  teardown do
+    Entity.formats.clear
+  end
+
+  def test_alias
+    miguel = Person.setup("Miguel", namespace: :person)
+    assert_equal "Miki", miguel.to("Alias")
+  end
+
+  def test_alias_no_namespace
+    miguel = Person.setup("Miguel")
+
+    assert_raise do
+      miguel.to("Name")
+    end
+  end
+
+  def test_alias_no_ids
+    miguel = PersonWithNoIds.setup("Miguel", namespace: :person)
+    assert_raise do
+      miguel.to("Name")
+    end
+  end
+
+
+  def test_name_from_ID
+    assert_equal "Miki", Person.setup("001", :format => 'ID', namespace: :person).to("Alias")
+    assert_equal "Miguel", Person.setup("001", :format => 'ID', namespace: :person).to("Name")
+    assert_equal ["Miguel"], Person.setup(["001"], :format => 'ID', namespace: :person).to("Name")
+  end
+
+
+  def test_identifier_files
+    assert Person.identifier_files.any?
+  end
+
+  def test_Entity_identifier_files
+    assert Entity.identifier_files("Name").any?
+  end
+end