scout-gear 10.7.1 → 10.7.3

data/test/scout/knowledge_base/test_entity.rb

@@ -0,0 +1,38 @@
+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 TestKnowledgeBaseQuery < Test::Unit::TestCase
+  def test_types
+    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
+
+      assert_include kb.all_databases, :brothers
+
+      assert_equal Person, kb.target_type(:parents)
+    end
+  end
+
+  def test_options
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir
+      kb.register :brothers, datafile_test(:person).brothers, undirected: true
+      kb.entity_options = { "Person" => {language: "es"} }
+
+      assert_include kb.entity_options_for("Person"), :language
+    end
+  end
+
+  def test_identify
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir
+      kb.register :brothers, datafile_test(:person).brothers, undirected: true
+
+      assert_equal "Miki", kb.identify(:brothers, "001")
+    end
+  end
+end

data/test/scout/knowledge_base/test_list.rb

@@ -0,0 +1,40 @@
+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 TestKnowledgeBaseQuery < Test::Unit::TestCase
+  def test_entity_list
+    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
+
+      list = kb.subset(:brothers, :all).target_entity
+
+      kb.save_list("bro_and_sis", list)
+      assert_equal list, kb.load_list("bro_and_sis")
+
+      assert_include kb.list_files["Person"], "bro_and_sis"
+      kb.delete_list("bro_and_sis")
+
+      refute kb.list_files["simple"]
+    end
+  end
+
+  def test_simple_list
+    list = ["Miki", "Isa"]
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir
+
+      kb.save_list("bro_and_sis", list)
+
+      assert_equal list, kb.load_list("bro_and_sis")
+
+      assert_include kb.list_files["simple"], "bro_and_sis"
+
+      kb.delete_list("bro_and_sis")
+
+      refute kb.list_files["simple"]
+    end
+  end
+end

data/test/scout/knowledge_base/test_query.rb

@@ -0,0 +1,39 @@
+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 TestKnowledgeBaseQuery < Test::Unit::TestCase
+  def test_query
+    TmpFile.with_dir do |dir|
+      kb = KnowledgeBase.new dir
+      kb.entity_options = {"Person" => {language: "es"}}
+
+      kb.register :brothers, datafile_test(:person).brothers, undirected: true
+      kb.register :parents, datafile_test(:person).parents, entity_options: {"Person" => {language: "en"}}
+
+      assert_include kb.all_databases, :brothers
+
+      matches = kb.subset(:parents, :all)
+      assert_include matches, "Clei~Domingo"
+
+      matches = kb.subset(:parents, target: :all, source: ["Miki"])
+      assert_include matches, "Miki~Juan"
+
+
+      assert_include kb.children(:parents, "Miki").target, "Juan"
+      assert_include kb.children(:brothers, "Miki").target, "Isa"
+
+      parents = matches.target_entity
+
+      assert_include parents, "Juan"
+      assert Person === parents.first
+      assert_equal "en", parents.first.language
+
+
+      matches = kb.subset(:brothers, target: :all, source: ["Miki"])
+      assert_equal "es", matches.first.source_entity.language
+    end
+  end
+end

data/test/scout/knowledge_base/test_registry.rb

@@ -0,0 +1,16 @@
+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 TestKnowlegeBase < Test::Unit::TestCase
+  def test_registry
+    TmpFile.with_dir do |dir|
+      brothers = datafile_test(:person).brothers
+      kb = KnowledgeBase.new dir
+      kb.register :brothers, brothers
+      assert_include kb.all_databases, :brothers
+    end
+  end
+end
+

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

@@ -40,6 +40,7 @@ row2    a    a    id3
       end
     end
 
+    assert_include tsv.fields, "ValueA"
     assert_include tsv.keys, 'row1'
     assert_include tsv.keys, 'row2'
   end
@@ -67,6 +68,7 @@ row2    a    a    id3
       end
       refute Open.exists?(tk)
       assert Open.exists?(data.persistence_path)
+      refute tsv.fields.nil?
     end
 
     assert_include tsv.keys, 'row1'
@@ -142,5 +144,23 @@ row2    a    a    id3
     assert_include tsv.keys, 'row1'
     assert_include tsv.keys, 'row2'
   end
+
+  def test_tsv_open_persist
+    content =<<-'EOF'
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row2    a    a    id3
+    EOF
+
+
+    tsv = nil
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, sep: /\s+/, type: :double, persist: true, merge: true)
+      assert Array === tsv.fields
+      tsv = TSV.open(filename, sep: /\s+/, type: :double, persist: true, merge: true)
+      assert Array === tsv.fields
+    end
+  end
 end
 

data/test/scout/persist/tsv/adapter/test_base.rb

@@ -39,5 +39,25 @@ class TestTSVAdapter < Test::Unit::TestCase
     assert_equal [1, 2, 3], tsv["a"]
     assert_equal [1, 2, 3], Marshal.load(tsv.orig_get("a"))
   end
+
+  def test_persist_annotations
+    content =<<-'EOF'
+#: :sep=/\s+/#:type=:double#:merge=:concat
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row2    a    a    id3
+    EOF
+
+    TmpFile.with_file(content) do |tsv_file|
+      pid = Process.fork do
+        tsv = TSV.open tsv_file, persist: true
+      end
+      Process.waitpid pid
+      tsv = TSV.open tsv_file, persist: true
+      refute tsv.fields.nil?
+    end
+  end
+
 end
 

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 +56,10 @@ 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
 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

@@ -387,4 +387,44 @@ row2    A    B    Id3
       tsv = TSV.open(filename, :sep => /\s+/, :identifiers => Scout.share.identifiers)
     end
   end
+
+  def test_identifier_file_auto
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+    EOF
+
+    ids =<<-EOF
+#Id    Alias
+row1    r1
+row2    r2
+    EOF
+
+    TmpFile.with_dir do |dir|
+      Path.setup(dir)
+      Open.write(dir.tsv_file, content)
+      Open.write(dir.identifiers, ids)
+      tsv = TSV.open(dir.tsv_file)
+      assert_equal dir.identifiers, tsv.identifiers
+    end
+  end
+
+  def test_single_field
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/, field: "ValueB")
+      assert_equal "b", tsv["row1"]
+    end
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/, field: "ValueA", type: :flat)
+      assert_equal %w(a aa aaa), tsv["row1"]
+    end
+  end
 end

data/test/scout/tsv/test_dumper.rb

@@ -78,5 +78,29 @@ b\t2|22\t3|33
     assert tsv2.filename
   end
 
+  def test_compact
+    dumper = TSV::Dumper.new :key_field => "Key", :fields => %w(Field1 Field2), :type => :double, compact: true
+    dumper.init
+    t = Thread.new do
+      dumper.add "a", [["1", "11"], ["2", "22"]]
+      dumper.add "b", [[nil, nil], ["3", "33"]]
+      dumper.close
+    end
+
+    tsv = TSV.open(dumper.stream)
+    assert_equal [], tsv["b"]["Field1"]
+
+    dumper = TSV::Dumper.new :key_field => "Key", :fields => %w(Field1 Field2), :type => :double, compact: false
+    dumper.init
+    t = Thread.new do
+      dumper.add "a", [["1", "11"], ["2", "22"]]
+      dumper.add "b", [[nil, nil], ["3", "33"]]
+      dumper.close
+    end
+
+    tsv = TSV.open(dumper.stream)
+    assert_equal ["", ""], tsv["b"]["Field1"]
+  end
+
 end
 

data/test/scout/tsv/test_path.rb

@@ -0,0 +1,24 @@
+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 TestTsvPath < Test::Unit::TestCase
+  def test_tsv_open_persist
+    content =<<-'EOF'
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row2    a    a    id3
+    EOF
+
+
+    tsv = nil
+    TmpFile.with_file(content) do |filename|
+      Path.setup(filename)
+      tsv = filename.tsv persist: true, merge: true, type: :list, sep: /\s+/
+      assert_equal %w(ValueA ValueB OtherID), tsv.fields
+      tsv = filename.tsv persist: true, merge: true, type: :list, sep: /\s+/
+      assert_equal %w(ValueA ValueB OtherID), tsv.fields
+    end
+  end
+end
+