scout-gear 10.7.0 → 10.7.2

data/scout_commands/db/show

@@ -0,0 +1,47 @@
+#!/usr/bin/env ruby
+
+require 'scout'
+require 'scout/association'
+
+$0 = "scout #{$previous_commands.any? ? $previous_commands*" " + " " : "" }#{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+Show a database
+
+$ #{$0} [<options>] <name>
+
+-h--help Print this help
+EOF
+if options[:help]
+  if defined? scout_usage
+    scout_usage 
+  else
+    puts SOPT.doc
+  end
+  exit 0
+end
+
+
+registry = begin
+             Scout.var.databases.registry.yaml
+           rescue
+             {}
+           end
+
+name = ARGV.first
+
+if name.nil?
+  puts registry.keys * "\n"
+
+else
+
+  raise ParameterException "Database #{name} not found Options: #{Log.fingerprint registry.keys}" unless registry.include? name
+
+  file, options = registry[name]
+
+  IndiferentHash.setup(options)
+  options.keys_to_sym!
+
+  Log.tsv Association.database(file, **options)
+end

data/test/scout/entity/test_named_array.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')
+
+class TestNamedArrayEntity < Test::Unit::TestCase
+  def setup
+    m = Module.new do
+      extend Entity
+      self.format = "SomeEntity"
+
+      property :prop do
+        "PROP: #{self}"
+      end
+    end
+  end
+
+  def test_true
+    a = NamedArray.setup(["a", "b"], %w(SomeEntity Other))
+    assert a["SomeEntity"].respond_to?(:prop)
+  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_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
+

data/test/scout/tsv/test_stream.rb

@@ -218,5 +218,98 @@ row2\tBB
     assert_equal ["AAA"], tsv["row3"][0]
   end
 
+  def test_concat_4_streams
+
+    text1=<<-EOF
+#Key\tValueA
+row1\tA
+row2\tAA
+    EOF
+
+    text2=<<-EOF
+#Key\tValueA
+row3\tAAA
+row2\tBB
+    EOF
+
+    text3=<<-EOF
+#Key\tValueA
+row4\tAAA
+row5\tBB
+    EOF
+
+    text4=<<-EOF
+#Key\tValueA
+row6\tAAA
+row7\tBB
+    EOF
+
+    s1 = StringIO.new text1
+    s2 = StringIO.new text2
+    s3 = StringIO.new text3
+    s4 = StringIO.new text4
+    tsv = TSV.open TSV.concat_streams([s1,s2,s3,s4]), :merge => true
+    assert_equal ["A"], tsv["row1"][0]
+    assert_equal ["AA","BB"], tsv["row2"][0]
+    assert_equal ["AAA"], tsv["row3"][0]
+    assert_equal ["BB"], tsv["row7"][0]
+  end
+
+
+  def test_paste_streams_repeat
+    text1=<<-EOF
+YHR055C	856452|856450	YHR055C|YHR055C
+YPR161C	856290	YPR161C
+YOL138C	853982	YOL138C
+YDR395W	852004	YDR395W
+YGR129W	853030	YGR129W
+YPR165W	856294	YPR165W
+YPR098C	856213	YPR098C
+YPL015C	856092	YPL015C
+YCL050C	850307	YCL050C
+YAL069W		YAL069W
+    EOF
+
+    text2=<<-EOF
+YHR055C	CUP1-2	AAA34541
+YHR055C	CUP1-2	AAB68382
+YHR055C	CUP1-2	AAS56843
+YHR055C	CUP1-2	DAA06748
+YHR055C	CUP1-2	AAB68384
+YHR055C	CUP1-2	AAT93096
+YHR055C	CUP1-2	DAA06746
+YPR161C	SGV1	BAA14347
+YPR161C	SGV1	AAB59314
+YPR161C	SGV1	AAB68058
+    EOF
+
+    s1 = StringIO.new text1
+    s2 = StringIO.new text2
+    tsv = TSV.open(TSV.paste_streams([s1,s2], sort:true, one2one: false), merge: true, one2one: false)
+    assert_equal 2, tsv["YHR055C"][0].length
+    assert_equal %w(SGV1) * 3, tsv["YPR161C"][2]
+  end
+
+  def test_paste_stream_flat
+    text1=<<-EOF
+#: :sep=" "
+#Row LabelA LabelB LabelC
+row1 A B C
+row2 AA BB CC
+row3 AAA BBB CCC
+    EOF
+
+    text2=<<-EOF
+#: :sep=" "#:type=:flat
+#Row Flat
+row1 f1 f2 f3
+    EOF
+
+
+    s1 = StringIO.new text1
+    s2 = StringIO.new text2
+    tsv = TSV.open TSV.paste_streams([s1,s2], :sep => " ", :type => :double)
+    assert_include tsv["row1"], %w(f1 f2 f3)
+  end
 end
 

data/test/scout/tsv/test_traverse.rb

@@ -275,5 +275,104 @@ row3    a
       assert_equal %w(a aa aaa), data["row1"]
     end
   end
+
+  def test_traverse_entity_list
+    m = Module.new do
+      extend Entity
+      self.format = "ValueA"
+    end
+
+    content =<<-EOF
+#Id    ValueA
+row1    a
+row2    A
+row3    a
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(File.open(filename), :sep => /\s+/, :type => :list)
+      data = {}
+      k, f = tsv.traverse "Id", ["ValueA"] do |k,v|
+        data[k] = v
+      end
+      assert_equal %w(a), data["row1"]
+      assert Annotation::AnnotatedObject === data["row1"]
+    end
+  end
+
+  def test_traverse_entity_double
+    m = Module.new do
+      extend Entity
+      self.format = "ValueA"
+    end
+
+    content =<<-EOF
+#Id    ValueA
+row1    a|aa|aaa
+row2    A
+row3    a
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(File.open(filename), :sep => /\s+/)
+      data = {}
+      k, f = tsv.traverse "Id", ["ValueA"] do |k,v|
+        data[k] = v
+      end
+      assert_equal %w(a aa aaa), data["row1"][0]
+      assert NamedArray === data["row1"]
+      assert AnnotatedArray === data["row1"]["ValueA"]
+    end
+  end
+
+
+  def test_traverse_entity_flat
+    m = Module.new do
+      extend Entity
+      self.format = "ValueA"
+    end
+
+    content =<<-EOF
+#Id    ValueA
+row1    a aa aaa
+row2    A
+row3    a
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(File.open(filename), :sep => /\s+/, :type => :flat)
+      data = {}
+      k, f = tsv.traverse "Id", ["ValueA"] do |k,v|
+        data[k] = v
+      end
+      assert_equal %w(a aa aaa), data["row1"]
+      assert AnnotatedArray === data["row1"]
+      assert Annotation::AnnotatedObject === data["row1"][0]
+    end
+  end
+
+  def test_traverse_entity_single
+    m = Module.new do
+      extend Entity
+      self.format = "ValueA"
+    end
+
+    content =<<-EOF
+#Id    ValueA
+row1    a
+row2    A
+row3    a
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(File.open(filename), :sep => /\s+/, :type => :single)
+      data = {}
+      k, f = tsv.traverse "Id", ["ValueA"] do |k,v|
+        data[k] = v
+      end
+      assert_equal "a", data["row1"]
+      assert Annotation::AnnotatedObject === data["row1"]
+    end
+  end
 end
 

data/test/scout/tsv/test_util.rb

@@ -16,6 +16,8 @@ row2    a    a    id3
       TSV.open(filename, :sep => " " )
     end
     assert_equal %w(row1 row2), tsv.collect{|k,v| k }
+    refute NamedArray === tsv.collect{|k,v| v }.first
+    tsv.unnamed = false
     assert NamedArray === tsv.collect{|k,v| v }.first
     assert "row1", tsv["row1"].key
   end

data/test/scout/tsv/util/test_select.rb

@@ -23,6 +23,28 @@ row2    AA    BB    Id33
     assert_equal ['row2'], s.keys
   end
 
+  def test_select_invert
+    content =<<-'EOF'
+#: :sep=/\s+/#:type=:double
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row2    AA    BB    Id33
+    EOF
+
+    tsv = TmpFile.with_file(content) do |filename|
+      TSV.open(filename, :persist => true)
+    end
+
+    s = tsv.select("ValueA" => 'a')
+
+    assert_equal ['row1'], s.keys
+
+    s = tsv.select({"ValueA" => 'a'}, true)
+
+    assert_equal ['row2'], s.keys
+  end
+
   def test_select_values
     content =<<-'EOF'
 #: :sep=" "

data/test/scout/tsv/util/test_sort.rb

@@ -46,5 +46,29 @@ row2 A b C
       assert_equal %w(row1 row2), tsv.sort("ValueB"){|a,b| a[1] <=> b[1] }.collect{|k,v| k}
     end
   end
+
+  def test_sort_entity
+    content =<<-EOF
+#ID ValueA ValueB Comment NumericValue
+row1 a B c 20
+row2 A b C 100
+row3 A b C 3
+    EOF
+
+    m = Module.new do
+      extend Entity
+      self.format = "NumericValue"
+
+      def <=>(b)
+        self.to_f <=> b.to_f
+      end
+    end
+
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(File.open(filename), :type => :list, :sep => /\s/)
+      assert_equal %w(row3 row1 row2), tsv.sort("NumericValue", true)
+    end
+  end
 end
 

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

@@ -89,5 +89,31 @@ class TestStepDependencies < Test::Unit::TestCase
       end
     end
   end
+
+  def test_recursive_inputs_priority
+    tmpfile = tmpdir.test_step
+    step1 = Step.new tmpfile.step1, NamedArray.setup(["1"], %w(input1)) do |s|
+      s.length
+    end
+
+    step2 = Step.new tmpfile.step2, NamedArray.setup(["2"], %w(input1)) do |times|
+      step1 = dependencies.first
+      (step1.inputs.first + " has " + step1.load.to_s + " characters") * times
+    end
+
+    step3 = Step.new tmpfile.step2, NamedArray.setup([], %w()) do |times|
+      step1 = dependencies.first
+      (step1.inputs.first + " has " + step1.load.to_s + " characters") * times
+    end
+
+
+    step2.dependencies = [step1]
+
+    step3.dependencies = [step1, step2]
+
+    assert_equal "2", step2.inputs["input1"]
+    assert_equal "2", step2.recursive_inputs["input1"]
+    assert_equal "1", step3.recursive_inputs["input1"]
+  end
 end
 

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

@@ -58,4 +58,39 @@ class TestStepInfo < Test::Unit::TestCase
       assert_equal %w(Message1 Message2), step1.messages
     end
   end
+
+  def test_overriden_fixed
+    TmpFile.with_file("HELLO") do |file|
+      wf = Module.new do
+        extend Workflow
+
+        self.name = "TestWF"
+
+        task :message => :string do
+          "HI"
+        end
+
+        dep :message
+        task :say => :string do
+          "I say #{step(:message).load}"
+        end
+
+        task_alias :say_hello, self, :say, "TestWF#message" => file, :not_overriden => true
+      end
+
+      assert_equal "I say HI", wf.job(:say).run
+
+      job1 = wf.job(:say, "TestWF#message" => file)
+      assert_equal "I say HELLO", job1.run
+
+      job2 = wf.job(:say_hello)
+      assert_equal "I say HELLO", job2.run
+
+      assert job1.overriden?
+      refute job2.overriden?
+
+      assert job1.overriden_deps.any?
+      refute job2.overriden_deps.any?
+    end
+  end
 end

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

@@ -353,5 +353,71 @@ class TestTaskDependencies < Test::Unit::TestCase
     assert_equal "0", wf.job(:step2, :input1 => "-2").run
   end
 
-end
+  def test_jobname_input
+    wf = Workflow.annonymous_workflow "JobnameInput" do
+      input :input1, :string, "", nil, jobname: true
+      task :step1 => :string do |i1| 
+        i1
+      end
+
+      input :input2, :string, "", "Hi"
+      dep :step1 do |jobname,options|
+        {jobname: options[:input2]}
+      end
+      task :step2 do
+        step(:step1).load
+      end
+    end
+
+    assert_equal "Hi", wf.job(:step2).run.strip
+    assert_equal "Hello", wf.job(:step2, input2: "Hello").run.strip
 
+    job = wf.job(:step2, input1: "Hello")
+    assert_equal "Hello", job.run
+    assert_equal "Default", job.clean_name
+    assert_equal "Hi", job.step(:step1).clean_name
+  end
+
+  def test_jobname_input_reset
+    wf = Workflow.annonymous_workflow "JobnameInput" do
+      input :input1, :string, "", nil, jobname: true
+      task :step1 => :string do |i1| 
+        i1
+      end
+
+      input :input2, :string, "", "Hi", jobname: true
+      dep :step1, input1: "Name1", jobname: nil do |jobname,options|
+        {inputs: options}
+      end
+      task :step2 do
+        step(:step1).load
+      end
+
+    end
+
+    job = wf.job(:step2, input2: "Name2")
+    assert_equal "Name2", job.clean_name
+    assert_equal "Name1", job.step(:step1).clean_name
+    assert_equal "Name", wf.job(:step1, input1: "Name").clean_name
+  end
+
+  def test_non_default_inputs_ignore_hidden
+    wf = Workflow.annonymous_workflow "JobnameInput" do
+      input :input1, :string, "", nil, jobname: true
+      task :step1 => :string do |i1| 
+        i1
+      end
+
+      dep :step1, jobname: nil, input1: :placeholder do |jobname,options|
+        {inputs: options.merge(input1: "TEST") }
+      end
+      task :step2 do
+        step(:step1).load
+      end
+
+    end
+
+    job = wf.job(:step2, input2: "Name2")
+    assert job.non_default_inputs.empty?
+  end
+end