scout-gear 10.7.2 → 10.7.4

data/test/scout/knowledge_base/test_traverse.rb

@@ -0,0 +1,245 @@
+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/knowledge_base'
+class TestKnowledgeBaseTraverse < Test::Unit::TestCase
+  def test_traverse_single
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir
+      kb.entity_options = {"TestKnowledgeBaseQuery::Person" => {test: "Default"}}
+
+      kb.register :brothers, datafile_test(:person).brothers, undirected: true
+      kb.register :parents, datafile_test(:person).parents, entity_options: {"TestKnowledgeBaseQuery::Person" => {test: "Parents"}}
+
+      rules = []
+      rules << "Miki brothers ?1"
+      res =  kb.traverse rules
+      assert_include res.first["?1"], "Isa"
+
+      rules = []
+      rules << "Miki parents ?1"
+      entities, paths =  kb.traverse rules
+      assert_include paths.first.first.info, "Type of parent"
+
+      rules = []
+      rules << "?1 parents Domingo"
+      entities, paths =  kb.traverse rules
+      assert_include entities["?1"], "Clei"
+    end
+  end
+
+  def test_traverse_multiple
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir
+
+      kb.register :brothers, datafile_test(:person).brothers, undirected: true
+      kb.register :parents, datafile_test(:person).parents
+      kb.register :marriages, datafile_test(:person).marriages, source: "=>Alias", target: "=>Alias"
+
+      rules = []
+      rules << "Miki marriages ?1"
+      rules << "?1 brothers ?2"
+      res =  kb.traverse rules
+      assert_include res.first["?2"], "Guille"
+    end
+  end
+
+  def test_traverse_condition
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir
+
+      kb.register :brothers, datafile_test(:person).brothers, undirected: true
+      kb.register :parents, datafile_test(:person).parents
+      kb.register :marriages, datafile_test(:person).marriages, source: "=>Alias", target: "=>Alias"
+
+      rules = []
+      rules << "Miki parents ?1 - 'Type of parent=father'"
+      entities, paths =  kb.traverse rules
+      assert_equal entities["?1"], ["Juan"]
+    end
+  end
+
+  def test_traverse_identify
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir
+      kb.entity_options = {"TestKnowledgeBaseQuery::Person" => {test: "Default"}}
+
+      kb.register :brothers, datafile_test(:person).brothers, undirected: true
+      kb.register :parents, datafile_test(:person).parents, entity_options: {"TestKnowledgeBaseQuery::Person" => {test: "Parents"}}
+
+      rules = []
+      rules << "001 brothers ?1"
+      res =  kb.traverse rules
+      assert_include res.first["?1"], "Isa"
+    end
+  end
+
+  def test_traverse_target
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir
+
+      kb.register :brothers, datafile_test(:person).brothers, undirected: true
+      kb.register :parents, datafile_test(:person).parents
+
+      rules = []
+      rules << "?target =brothers 001"
+      rules << "?1 brothers ?target"
+      res =  kb.traverse rules
+      assert_include res.first["?1"], "Isa"
+      assert_include res.first["?target"], "Miki"
+    end
+  end
+
+  def test_traverse_translate_multiple
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir
+
+      kb.register :brothers, datafile_test(:person).brothers, undirected: true
+      kb.register :parents, datafile_test(:person).parents
+      kb.register :marriages, datafile_test(:person).marriages, undirected: true
+
+      rules = []
+      rules << "Guille brothers ?1"
+      rules << "?2 =marriages ?1"
+      rules << "?2 marriages ?3"
+      entities, paths =  kb.traverse rules
+      assert_include entities["?3"], "001"
+    end
+  end
+end
+
+
+
+#require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+#require 'rbbt/knowledge_base/traverse'
+#require 'rbbt/workflow'
+#
+#class TestKnowledgeBaseTraverse < Test::Unit::TestCase
+#  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 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
+#    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_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_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
+#
+#      rules = []
+#      rules << "?1 CollecTRI SMAD7 - '[ExTRI] Confidence'=High"
+#      low =  kb.traverse rules
+#
+#      assert low.last.length < all.last.length
+#    end
+#  end
+#
+#  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_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
+#    with_kb do |kb|
+#      rules = []
+#      rules << "SMAD4 ?db ?1"
+#      res =  kb.traverse rules
+#    end
+#  end
+#end
+#

data/test/scout/persist/test_tsv.rb

@@ -74,6 +74,7 @@ row2    a    a    id3
     assert_include tsv.keys, 'row1'
     assert_include tsv.keys, 'row2'
 
+    tsv.close
     assert_nothing_raised do
       tsv = Persist.persist("TEST Persist TSV", :HDB) do 
         raise

data/test/scout/test_association.rb

@@ -4,12 +4,21 @@ require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1
 require 'scout/tsv'
 class TestAssociation < Test::Unit::TestCase
 
-  def test_marriages_simple
-    database = Association.database(datadir_test.person.marriages, :source => "Wife", :target => "Husband")
+  def test_marriages_simple_no_persist
+    database = Association.database(datadir_test.person.marriages, :source => "Wife", :target => "Husband", persist: false)
     assert_equal "001", database["002"]["Husband"]
     assert_equal "2021", database["002"]["Date"]
+    refute database.respond_to?(:persistence_path)
   end
 
+  def test_marriages_simple_persist
+    database = Association.database(datadir_test.person.marriages, :source => "Wife", :target => "Husband", persist: true)
+    assert_equal "001", database["002"]["Husband"]
+    assert_equal "2021", database["002"]["Date"]
+    assert database.respond_to?(:persistence_path)
+  end
+
+
   def test_marriages_open
     database = Association.database(datadir_test.person.marriages, :source => "Wife (ID)=>Alias", :target => "Husband (ID)=>Name")
     assert_equal "Miguel", database["Clei"]["Husband"]
@@ -38,7 +47,7 @@ class TestAssociation < Test::Unit::TestCase
   end
 
   def test_brothers_rename
-    database = Association.database(datadir_test.person.brothers, :source => "Older=~Older (Alias)=>Name")
+    database = Association.database(datadir_test.person.brothers, source: "Older=~Older (Alias)=>Name")
     assert_equal "Older (Name)", database.key_field
   end
 
@@ -47,5 +56,25 @@ class TestAssociation < Test::Unit::TestCase
     database = Association.database(tsv)
     assert_equal database["Miki"], %w(Juan Mariluz)
   end
+
+  def test_persist
+    database = Association.database(datadir_test.person.brothers, source: "Older=~Older (Alias)=>Name", persist: true)
+    assert database.respond_to?(:persistence_path)
+  end
+
+  def test_extra_options
+    file=<<-EOF
+#: :extra_option=:test
+#Key,Value
+k,v
+    EOF
+
+    TmpFile.with_path(file.gsub(',', "\t")) do |f|
+      assert_nothing_raised do
+        Association.open(f, target: "Value", source: "Key")
+      end
+    end
+
+  end
 end
 

data/test/scout/test_entity.rb

@@ -7,21 +7,6 @@ class TestEntity < Test::Unit::TestCase
     Entity.entity_property_cache = tmpdir.property_cache
   end
 
-  module Person
-    extend Entity
-
-    annotation :language
-
-    property :salutation do
-      case language
-      when 'es'
-        "Hola #{self}"
-      else
-        "Hi #{self}"
-      end
-    end
-  end
-
   module EmptyEntity
     extend Entity
   end

data/test/scout/test_knowledge_base.rb

@@ -0,0 +1,27 @@
+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 TestKnowlegeBase < Test::Unit::TestCase
+  def test_no_namespace
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir
+      assert_nil kb.namespace
+      kb.save
+
+      kb = KnowledgeBase.load dir
+      assert_nil kb.namespace
+    end
+  end
+
+  def test_namespace
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir, "Hsa"
+      assert_equal "Hsa", kb.namespace
+      kb.save
+
+      kb = KnowledgeBase.load dir
+      assert_equal "Hsa", kb.namespace
+    end
+  end
+end
+

data/test/scout/test_tsv.rb

@@ -427,4 +427,19 @@ row2    A    B    Id3
       assert_equal %w(a aa aaa), tsv["row1"]
     end
   end
+
+  def test_number_key
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+1    a|aa|aaa    b    Id1|Id2
+2    A    B    Id3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/, field: "ValueB")
+      assert_equal "b", tsv["1"]
+    end
+
+
+  end
 end

data/test/scout/tsv/test_parser.rb

@@ -317,4 +317,8 @@ k4    a|A    b|B
       assert Open.read(tmp_logfile).include?("directly into")
     end
   end
+
+  def test_acceptable_parser_options
+    assert_include TSV.acceptable_parser_options, :namespace
+  end
 end

data/test/scout/tsv/test_transformer.rb

@@ -153,4 +153,17 @@ row2    A2    B2
     tsv = TSV.open(content)
     assert_equal %w(A1), tsv.to_double["row1"]["ValueA"]
   end
+
+  def test_head
+    content =<<-EOF
+#: :sep=" "
+#ID    ValueA    ValueB
+row1    A1    B1
+row2    A2    B2
+row3    A3    B3
+    EOF
+
+    tsv = TSV.open(content)
+    assert_equal ["row1", "row2"], tsv.head(2).keys
+  end
 end

data/test/scout/workflow/step/test_info.rb

@@ -3,6 +3,17 @@ require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1
 require 'scout/workflow'
 
 class TestStepInfo < Test::Unit::TestCase
+  def test_benchmark
+    i = {a:1, b: [1,2], c: "String"}
+    times = 100000
+    Misc.benchmark(times) do
+      Marshal.dump(i)
+    end
+    Misc.benchmark(times) do
+      i.to_json
+    end
+  end
+
   def test_dependency
     TmpFile.with_file do |tmpdir|
       Path.setup(tmpdir)

data/test/scout/workflow/task/test_info.rb

@@ -0,0 +1,22 @@
+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/workflow'
+class TestWorkflowInfo < Test::Unit::TestCase
+  def test_task_info
+    m = Module.new do
+      extend Workflow
+      self.name = "TestWF"
+
+      input :option1
+      task :step1 do end
+
+      dep :step1
+      input :option2
+      task :step2 do end
+    end
+    info = m.task_info :step2
+    assert_equal "TestWF/step2", info[:id]
+  end
+end
+

data/test/test_helper.rb

@@ -72,3 +72,20 @@ class Test::Unit::TestCase
     Test::Unit::TestCase.datafile_test(file)
   end
 end
+
+module Object::Person
+  extend Entity
+
+  annotation :language
+
+  property :salutation do
+    case language
+    when 'es'
+      "Hola #{self}"
+    else
+      "Hi #{self}"
+    end
+  end
+end
+
+Object::Person.add_identifiers Test::Unit::TestCase.datafile_test(:person).identifiers

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: scout-gear
 version: !ruby/object:Gem::Version
-  version: 10.7.2
+  version: 10.7.4
 platform: ruby
 authors:
 - Miguel Vazquez
-autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-12-10 00:00:00.000000000 Z
+date: 2025-03-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: scout-essentials
@@ -156,6 +155,13 @@ files:
 - lib/scout/entity/named_array.rb
 - lib/scout/entity/object.rb
 - lib/scout/entity/property.rb
+- lib/scout/knowledge_base.rb
+- lib/scout/knowledge_base/enrichment.rb
+- lib/scout/knowledge_base/entity.rb
+- lib/scout/knowledge_base/list.rb
+- lib/scout/knowledge_base/query.rb
+- lib/scout/knowledge_base/registry.rb
+- lib/scout/knowledge_base/traverse.rb
 - lib/scout/offsite.rb
 - lib/scout/offsite/exceptions.rb
 - lib/scout/offsite/ssh.rb
@@ -226,6 +232,7 @@ files:
 - lib/scout/workflow/step/status.rb
 - lib/scout/workflow/task.rb
 - lib/scout/workflow/task/dependencies.rb
+- lib/scout/workflow/task/info.rb
 - lib/scout/workflow/task/inputs.rb
 - lib/scout/workflow/usage.rb
 - lib/scout/workflow/util.rb
@@ -234,12 +241,16 @@ files:
 - scout_commands/alias
 - scout_commands/batch/clean
 - scout_commands/batch/list
-- scout_commands/db/query
-- scout_commands/db/register
-- scout_commands/db/show
 - scout_commands/doc
 - scout_commands/find
 - scout_commands/glob
+- scout_commands/kb/config
+- scout_commands/kb/entities
+- scout_commands/kb/list
+- scout_commands/kb/query
+- scout_commands/kb/register
+- scout_commands/kb/show
+- scout_commands/kb/traverse
 - scout_commands/log
 - scout_commands/offsite
 - scout_commands/rbbt
@@ -270,6 +281,12 @@ files:
 - test/scout/entity/test_named_array.rb
 - test/scout/entity/test_object.rb
 - test/scout/entity/test_property.rb
+- test/scout/knowledge_base/test_enrichment.rb
+- test/scout/knowledge_base/test_entity.rb
+- test/scout/knowledge_base/test_list.rb
+- test/scout/knowledge_base/test_query.rb
+- test/scout/knowledge_base/test_registry.rb
+- test/scout/knowledge_base/test_traverse.rb
 - test/scout/offsite/test_ssh.rb
 - test/scout/offsite/test_step.rb
 - test/scout/offsite/test_sync.rb
@@ -290,6 +307,7 @@ files:
 - test/scout/persist/tsv/test_serialize.rb
 - test/scout/test_association.rb
 - test/scout/test_entity.rb
+- test/scout/test_knowledge_base.rb
 - test/scout/test_offsite.rb
 - test/scout/test_semaphore.rb
 - test/scout/test_tsv.rb
@@ -329,6 +347,7 @@ files:
 - test/scout/workflow/step/test_provenance.rb
 - test/scout/workflow/step/test_status.rb
 - test/scout/workflow/task/test_dependencies.rb
+- test/scout/workflow/task/test_info.rb
 - test/scout/workflow/task/test_inputs.rb
 - test/scout/workflow/test_definition.rb
 - test/scout/workflow/test_documentation.rb
@@ -344,7 +363,6 @@ homepage: http://github.com/mikisvaz/scout-gear
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -359,8 +377,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.23
-signing_key: 
+rubygems_version: 3.6.5
 specification_version: 4
 summary: basic gear for scouts
 test_files: []