rbbt-util 5.28.9 → 5.28.10

data/test/rbbt/tsv/test_attach.rb

@@ -630,10 +630,8 @@ E    B
     tsv1 = Rbbt.tmp.test.test1.data.tsv :double,  :sep => /\s+/
     tsv2 = Rbbt.tmp.test.test2.data.tsv :double,  :sep => /\s+/
 
-    Log.severity = 0
     tsv1.attach tsv2, :fields => ["ValueE"] #, :persist_input => true
     Log.tsv tsv1
-    ppp tsv1
     
   end
 end

data/test/rbbt/tsv/test_index.rb

@@ -29,7 +29,7 @@ row2    A    B    Id3
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(File.open(filename), :sep => /\s+/, :key_field => "OtherID", :persistence => false)
-      index = tsv.index(:case_insensitive => true, :persistence => true)
+      index = tsv.index(:persistence => true)
       assert index["row1"].include? "Id1"
       assert_equal "OtherID", index.fields.first
     end
@@ -45,9 +45,8 @@ row2    A    B    Id3
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(File.open(filename), :sep => /\s+/, :key_field => "OtherID", :persistence => false)
-      Log.tsv tsv
-      index = tsv.index(:case_insensitive => true, :persistence => false, :fields => ["Id"], :target => "ValueA")
-      Log.tsv index
+      index = tsv.index(:persistence => false, :fields => ["Id"], :target => "ValueA")
+      assert_equal "A", index["row2"] 
     end
 
   end
@@ -243,7 +242,7 @@ g:         ____
     EOF
     TmpFile.with_file(data) do |datafile|
       load_segment_data(datafile)
-      TmpFile.with_file(load_segment_data(datafile)) do |tsvfile|
+      TmpFile.with_file(load_segment_data(datafile).to_s) do |tsvfile|
         f = TSV.range_index(tsvfile, "Start", "End", :persistence => true)
 
         #assert_equal %w(), f[0].sort
@@ -286,8 +285,8 @@ f:             ___
 g:         ____
     EOF
     TmpFile.with_file(data) do |datafile|
-      TmpFile.with_file(load_segment_data(datafile)) do |tsvfile|
-        f = TSV.range_index(tsvfile, "Start", "End", :filters => [["field:Start", "3"]])
+      TmpFile.with_file(load_segment_data(datafile).to_s) do |tsvfile|
+        f = TSV.range_index(tsvfile, "Start", "End", :filters => [["field:Start", "3"]], :persist_update => true)
 
         assert_equal %w(), f[0].sort
         assert_equal %w(), f[1].sort

data/test/rbbt/tsv/test_manipulate.rb

@@ -284,7 +284,7 @@ row3    a    C    Id4
 
   def test_reorder_flat
     content =<<-EOF
-#Id    ValueA    
+#Id    ValueA
 row1    a aa aaa
 row2    A
 row3    a
@@ -292,9 +292,8 @@ row3    a
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(File.open(filename), :sep => /\s+/, :type => :flat)
-      
-      assert_equal ["row1", "row3"].sort, tsv.reorder("ValueA")["a"]
 
+      assert_equal ["row1", "row3"].sort, tsv.reorder("ValueA")["a"]
     end
   end
 

data/test/rbbt/util/R/test_model.rb

@@ -1,4 +1,5 @@
 require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/util/R'
 require 'rbbt/util/R/model'
 
 class TestRModel < Test::Unit::TestCase
@@ -49,7 +50,7 @@ data = rbbt.model.inpute(data, CI ~ Dose, method=drm, classes='numeric', fct=LL.
     assert_equal result.size, result.column("CI").values.flatten.reject{|p| p.nil? or p.empty? or p == "NA"}.length
   end
 
-  def test_ab_surv_corr
+  def __test_ab_surv_corr
     require 'rbbt/workflow'
     Workflow.require_workflow "Miller"
 

data/test/rbbt/util/R/test_plot.rb

@@ -5,7 +5,6 @@ require 'rbbt/util/R/plot'
 class TestRPlot < Test::Unit::TestCase
   def __test_ggplotgif
 
-    Log.severity = 0
     x = R.eval_a 'rnorm(100, 0, 1)'
     data = TSV.setup(x, "Num~#:type=:single#:cast=:to_f")
 
@@ -22,7 +21,6 @@ ggplot(data) + geom_density(bw=frame.value, aes(x=Val))
 
   def test_gif
 
-    Log.severity = 0
     x = R.eval_a 'rnorm(100, 0, 1)'
     data = TSV.setup(x, "Num~#:type=:single#:cast=:to_f")
 

data/test/rbbt/util/concurrency/test_processes.rb

@@ -7,7 +7,7 @@ require 'rbbt/util/concurrency/processes'
 class TestConcurrencyProcess < Test::Unit::TestCase
 
   def setup
-    Log.severity = 0
+    #Log.severity = 0
   end
 
   def test_process_throttle

data/test/rbbt/util/misc/test_bgzf.rb

@@ -2,12 +2,14 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_he
 require 'rbbt/util/misc/bgzf'
 
 class TestBgzf < Test::Unit::TestCase
-  def test_Bgzf
+  def _test_Bgzf
     content = "1234567890" * 1000000
     TmpFile.with_file(content) do |file|
       compressed = file + '.gz'
       `bgzip #{file} -c > #{compressed}`
       stream = Bgzf.setup File.open(compressed)
+      assert_equal "1234", stream.read(4)
+      assert_equal "56", stream.read(2)
       stream.seek 500003
       assert_equal "4567", stream.read(4)
       assert_equal "89", stream.read(2)
@@ -20,23 +22,25 @@ class TestBgzf < Test::Unit::TestCase
       Misc.benchmark do
         tsv = TSV.open(Open.open(file))
       end
-      compressed = file + '.bgz'
 
-      `bgzip #{file} -c > #{compressed}`
-      stream = Bgzf.setup File.open(compressed)
+      `gzip #{file}`
+      stream = Open.open(file + '.gz')
       Misc.benchmark do
         tsv = TSV.open(stream)
       end
 
-      `gzip #{file}`
-      stream = Open.open(file + '.gz')
+      `gunzip #{file}.gz`
+      compressed = file + '.bgz'
+      `bgzip #{file} -c > #{compressed}`
+      stream = Bgzf.setup File.open(compressed)
       Misc.benchmark do
         tsv = TSV.open(stream)
       end
+
     end
   end
 
-  def test_bgzip
+  def _test_bgzip
     assert File.exist?(Bgzf.bgzip_cmd)
     assert 'bgzip', File.basename(Bgzf.bgzip_cmd)
   end

data/test/rbbt/util/misc/test_lock.rb

@@ -48,7 +48,6 @@ if __FILE__ == $0
   TmpFile.with_file do |dir|
     Structure.workdir = dir
     Path.setup dir
-    Log.severity = 4
     TSV.traverse (0..size).to_a, :cpus => cpus, :type => :array, :bar => true do |i|
       begin
         v = rand(num).to_s

data/test/rbbt/util/misc/test_multipart_payload.rb

@@ -185,7 +185,7 @@ END
     inputs[:input2] = "Input2"
     num = 50
     cpus = 1
-    Log.severity = 0
+
     Misc.bootstrap((0..num-1).to_a, cpus) do  |n|
       puts mutipart
       TmpFile.with_file(mutipart, false) do |tmpfile|

data/test/rbbt/util/misc/test_pipes.rb

@@ -131,7 +131,6 @@ row2 AA BB CC
 row3 AAA BBB CCC
 row1 A B C
     EOF
-    Log.severity = 0
 
     text = text * 10000
     TmpFile.with_file(text) do |tmp|
@@ -159,7 +158,6 @@ row2 AA BB CC
 row3 AAA BBB CCC
 row1 A B C
     EOF
-    Log.severity = 0
 
     text = text * 10000
     num = 5
@@ -200,7 +198,6 @@ line3
 line1
     EOF
 
-    Log.severity = 0
     TmpFile.with_file(text1) do |file1|
       TmpFile.with_file(text2) do |file2|
         assert ! Misc.remove_lines(file1, file2, true).read.split("\n").include?("line1")
@@ -224,7 +221,6 @@ line1
 line5
     EOF
 
-    Log.severity = 0
     TmpFile.with_file(text1) do |file1|
       TmpFile.with_file(text2) do |file2|
         assert Misc.select_lines(file1, file2, true).read.split("\n").include?("line1")
@@ -258,7 +254,6 @@ line3
 line4
     EOF
 
-    Log.severity = 0
     TmpFile.with_file(text) do |file|
       io = Open.open(file)
       lines = Set.new

data/test/rbbt/util/test_R.rb

@@ -9,6 +9,7 @@ class TestR < Test::Unit::TestCase
   def test_tsv_R
     tsv = TSV.setup({:a => 1, :b => 2})
     tsv2 = tsv.R <<-EOF
+str(data)
 data = data + 1
     EOF
     assert_equal "2", tsv2["a"].first

data/test/rbbt/util/test_log.rb

@@ -2,7 +2,7 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helpe
 require 'rbbt/util/log'
 
 class TestLog < Test::Unit::TestCase
-  def _test_get_level
+  def test_get_level
     assert_equal 0, Log.get_level(:debug)
     assert_equal 1, Log.get_level(:low)
     assert_equal 1, Log.get_level("LOW")
@@ -10,18 +10,17 @@ class TestLog < Test::Unit::TestCase
     assert_equal 0, Log.get_level(nil)
   end
 
-  def _test_color
+  def test_color
     assert Log.color(:green, "green")
   end
 
-  def _test_no_stderr
+  def test_no_stderr
     Log.ignore_stderr do
       STDERR.puts "NOPRINT"
     end
   end
 
-  def _test_trap_stderr
-    Log.severity = 0
+  def test_trap_stderr
     Log.trap_stderr do
       STDERR.puts "NOPRINT"
       STDERR.puts "NOPRINT"
@@ -40,7 +39,6 @@ class TestLog < Test::Unit::TestCase
   end
 
   def test_trap_std
-    Log.severity = 0
     Log.trap_std do
       STDERR.puts "NOPRINT STDERR"
       STDOUT.puts "NOPRINT STDOUT"

data/test/rbbt/util/test_misc.rb

@@ -475,7 +475,6 @@ eum fugiat quo voluptas nulla pariatur?"
   end
 
   def test_bootstrap
-    Log.severity = 0
     res = Misc.bootstrap((1..10).to_a, 2, :bar => "Test bootstrap ticks", :respawn => :always, :into => []) do |num|
       sleep 1 + rand(2)
       num
@@ -550,7 +549,6 @@ eum fugiat quo voluptas nulla pariatur?"
   end
 
   def __test_bench_log
-    Log.severity = 1
     Misc.benchmark(1000) do
       Log.info { "Hola" }
     end

data/test/rbbt/util/test_open.rb

@@ -169,7 +169,6 @@ class TestOpen < Test::Unit::TestCase
   end
 
   def test_write_stream_repo
-    Log.severity = 0
     TmpFile.with_file do |tmpdir|
       tmpdir = Rbbt.tmp.repo_dir.find
       repo = File.join(tmpdir, 'repo')

data/test/rbbt/util/test_python.rb

@@ -42,7 +42,6 @@ def python_test(a, b):
   end
 
   def test_run_log
-    Log.severity = 0
     TmpFile.with_file do |tmpdir|
       code =<<-EOF
 import sys
@@ -66,3 +65,20 @@ def python_print():
     end
   end
 
+  def test_keras
+    defined = RbbtPython.run do
+      pyimport "keras.models", as: :km
+      defined?(km.Sequential)
+    end
+    assert defined
+  end
+
+  def test_keras_import
+    defined = RbbtPython.run do
+      pyfrom "keras.models", import: :Sequential
+      defined?(self::Sequential)
+    end
+    assert defined
+  end
+end
+

data/test/rbbt/workflow/test_remote_workflow.rb

@@ -88,7 +88,7 @@ class TestRemoteWorkflow < Test::Unit::TestCase
   end
 
 
-  def _test_ssh
+  def test_ssh
     Log.severity = 0
     client = RemoteWorkflow.new "ssh://#{ENV["HOSTNAME"]}:Translation", "Translation"
     job = client.job("translate", "SSH-TEST-1", :genes => ["TP53","KRAS"])

data/test/rbbt/workflow/test_step.rb

@@ -1,8 +1,10 @@
 require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/workflow'
 require 'rbbt/workflow/task'
 require 'rbbt/workflow/step'
 require 'rbbt/tsv'
 require 'rbbt'
+require 'rbbt-util'
 
 class TestStep < Test::Unit::TestCase
 
@@ -23,8 +25,9 @@ class TestStep < Test::Unit::TestCase
     str2 = "TEST2"
     TmpFile.with_file do |tmpfile|
 
-      task1  = Task.setup :result_type => nil do 
+      task1  = Task.setup :result_type => :string do 
         Open.write(tmpfile, str); 
+        "done"
       end
       step1 = Step.new tmpfile + 'step1', task1
 
@@ -50,9 +53,10 @@ class TestStep < Test::Unit::TestCase
   def __test_dependency_log_relay
     str = "TEST"
     TmpFile.with_file do |tmpfile|
-      task1  = Task.setup :result_type => nil, :name => :task1 do 
+      task1  = Task.setup :result_type => :string, :name => :task1 do 
         log(:starting_task1, "Starting Task1")
         Open.write(tmpfile, str); 
+        "done"
       end
       step1 = Step.new tmpfile + 'step1', task1
 
@@ -69,9 +73,10 @@ class TestStep < Test::Unit::TestCase
   def test_log_relay_step
     str = "TEST"
     TmpFile.with_file do |tmpfile|
-      task1  = Task.setup :result_type => nil, :name => :task1 do 
+      task1  = Task.setup :result_type => :string, :name => :task1 do 
         log(:starting_task1, "Starting Task1")
         Open.write(tmpfile, str); 
+        "done"
       end
       step1 = Step.new tmpfile + 'step1', task1
 

data/test/rbbt/workflow/util/test_orchestrator.rb

@@ -27,6 +27,11 @@ module TestWF
   task :d => :text do
     sleep(TestWF::MULT * (rand(10) + 2))
   end
+
+  dep :c
+  task :e => :text do
+    sleep(TestWF::MULT * (rand(10) + 2))
+  end
 end
 
 class TestClass < Test::Unit::TestCase
@@ -219,5 +224,50 @@ TestWF:
     end
 
   end
+
+  def test_orchestrate_top_level_double_dep
+
+    jobs =[]
+
+    num = 10
+    num.times do |i|
+      jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:e, name + " #{i}") }
+      jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:d, name + " #{i}") }
+    end
+    jobs.each do |j| j.recursive_clean end
+
+    rules = YAML.load <<-EOF
+defaults:
+  erase: true
+  log: 4
+default_resources:
+  IO: 1
+TestWF:
+  a:
+    resources:
+      cpus: 7
+  b:
+    resources:
+      cpus: 2
+  c:
+    resources:
+      cpus: 10
+  d:
+    resources:
+      cpus: 15
+    EOF
+
+    orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
+    Log.with_severity 3 do
+      orchestrator.process(rules, jobs)
+    end
+
+    jobs.each do |job|
+      next unless job.task_name.to_s == 'd' || job.task_name.to_s == 'e'
+      assert job.info[:archived_info].keys.select{|k| k.include?("TestWF/c/")}.any?
+      assert job.info[:archived_info].keys.select{|k| k.include?("TestWF/c/")}.any?
+    end
+
+  end
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.28.9
+  version: 5.28.10
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-11-04 00:00:00.000000000 Z
+date: 2020-11-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -318,6 +318,8 @@ files:
 - lib/rbbt/workflow/definition.rb
 - lib/rbbt/workflow/doc.rb
 - lib/rbbt/workflow/examples.rb
+- lib/rbbt/workflow/integration/ansible.rb
+- lib/rbbt/workflow/integration/ansible/workflow.rb
 - lib/rbbt/workflow/integration/cromwell.rb
 - lib/rbbt/workflow/integration/nextflow.rb
 - lib/rbbt/workflow/remote_workflow.rb
@@ -347,6 +349,7 @@ files:
 - share/config.ru
 - share/install/software/lib/install_helpers
 - share/rbbt_commands/alias
+- share/rbbt_commands/ansible
 - share/rbbt_commands/app/install
 - share/rbbt_commands/app/start
 - share/rbbt_commands/app/template
@@ -513,7 +516,6 @@ files:
 - test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/test_tmpfile.rb
-- test/rbbt/workflow/remote/test_client.rb
 - test/rbbt/workflow/step/test_dependencies.rb
 - test/rbbt/workflow/test_doc.rb
 - test/rbbt/workflow/test_remote_workflow.rb
@@ -552,7 +554,6 @@ test_files:
 - test/rbbt/workflow/test_doc.rb
 - test/rbbt/workflow/test_schedule.rb
 - test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/remote/test_client.rb
 - test/rbbt/workflow/step/test_dependencies.rb
 - test/rbbt/workflow/test_task.rb
 - test/rbbt/resource/test_path.rb