rbbt-util 5.28.9 → 5.28.10

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Files changed (54) hide show
  1. checksums.yaml +4 -4
  2. data/lib/rbbt/entity.rb +1 -1
  3. data/lib/rbbt/fix_width_table.rb +5 -4
  4. data/lib/rbbt/persist.rb +1 -1
  5. data/lib/rbbt/persist/tsv/adapter.rb +0 -1
  6. data/lib/rbbt/persist/tsv/fix_width_table.rb +5 -3
  7. data/lib/rbbt/tsv/dumper.rb +6 -2
  8. data/lib/rbbt/util/cmd.rb +1 -0
  9. data/lib/rbbt/util/misc/bgzf.rb +1 -1
  10. data/lib/rbbt/util/named_array.rb +1 -1
  11. data/lib/rbbt/util/open.rb +17 -16
  12. data/lib/rbbt/workflow/definition.rb +2 -1
  13. data/lib/rbbt/workflow/integration/ansible.rb +53 -0
  14. data/lib/rbbt/workflow/integration/ansible/workflow.rb +60 -0
  15. data/lib/rbbt/workflow/step.rb +5 -0
  16. data/lib/rbbt/workflow/step/accessor.rb +1 -1
  17. data/lib/rbbt/workflow/util/archive.rb +2 -0
  18. data/lib/rbbt/workflow/util/orchestrator.rb +22 -9
  19. data/share/rbbt_commands/ansible +55 -0
  20. data/share/rbbt_commands/purge_job +0 -1
  21. data/share/rbbt_commands/workflow/forget_deps +9 -0
  22. data/test/rbbt/association/test_index.rb +6 -6
  23. data/test/rbbt/knowledge_base/test_query.rb +3 -3
  24. data/test/rbbt/knowledge_base/test_registry.rb +1 -1
  25. data/test/rbbt/persist/tsv/test_cdb.rb +0 -7
  26. data/test/rbbt/persist/tsv/test_kyotocabinet.rb +2 -8
  27. data/test/rbbt/persist/tsv/test_leveldb.rb +0 -6
  28. data/test/rbbt/persist/tsv/test_lmdb.rb +0 -6
  29. data/test/rbbt/persist/tsv/test_tokyocabinet.rb +15 -14
  30. data/test/rbbt/test_entity.rb +0 -1
  31. data/test/rbbt/test_knowledge_base.rb +3 -4
  32. data/test/rbbt/test_persist.rb +10 -6
  33. data/test/rbbt/test_workflow.rb +17 -16
  34. data/test/rbbt/tsv/test_accessor.rb +11 -0
  35. data/test/rbbt/tsv/test_attach.rb +0 -2
  36. data/test/rbbt/tsv/test_index.rb +6 -7
  37. data/test/rbbt/tsv/test_manipulate.rb +2 -3
  38. data/test/rbbt/util/R/test_model.rb +2 -1
  39. data/test/rbbt/util/R/test_plot.rb +0 -2
  40. data/test/rbbt/util/concurrency/test_processes.rb +1 -1
  41. data/test/rbbt/util/misc/test_bgzf.rb +11 -7
  42. data/test/rbbt/util/misc/test_lock.rb +0 -1
  43. data/test/rbbt/util/misc/test_multipart_payload.rb +1 -1
  44. data/test/rbbt/util/misc/test_pipes.rb +0 -5
  45. data/test/rbbt/util/test_R.rb +1 -0
  46. data/test/rbbt/util/test_log.rb +4 -6
  47. data/test/rbbt/util/test_misc.rb +0 -2
  48. data/test/rbbt/util/test_open.rb +0 -1
  49. data/test/rbbt/util/test_python.rb +17 -1
  50. data/test/rbbt/workflow/test_remote_workflow.rb +1 -1
  51. data/test/rbbt/workflow/test_step.rb +8 -3
  52. data/test/rbbt/workflow/util/test_orchestrator.rb +50 -0
  53. metadata +5 -4
  54. data/test/rbbt/workflow/remote/test_client.rb +0 -56
data/test/rbbt/workflow/remote/test_client.rb DELETED
@@ -1,56 +0,0 @@
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- require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
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- require 'rbbt/workflow'
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- require 'rbbt/workflow/remote/client'
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-
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- class TestWFRest
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- extend Workflow
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-
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- input :name, :string, "Name to greet", "World"
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- task :hi => :string do |name|
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- "Hello #{name}"
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- end
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-
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- dep :hi
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- task :intro => :string do
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- step(:hi).load + ", nice to meet you"
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- end
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- end
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-
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- class TestRemote < Test::Unit::TestCase
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-
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- def test_ssh
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- Log.severity = 0
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- client = WorkflowRemoteClient.new "ssh://turbo:Translation", "Translation"
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- job = client.job("translate", "SSH-TEST", :genes => ["TP53","KRAS"])
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- assert_equal 2, job.run.select{|l| l =~ /ENSG/}.length
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- end
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-
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- def test_rest
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- Log.with_severity 0 do
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-
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- workflow_server(TestWFRest) do |client|
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- assert_equal "Hello World", client.job(:hi, nil, {}).run.chomp
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- assert_equal "Hello Miguel", client.job(:hi, nil, {:name => :Miguel}).run.chomp
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- assert_equal "Hello Miguel, nice to meet you", client.job(:intro, nil, {:name => :Miguel}).run.chomp
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- end
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-
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- workflow_server(TestWFRest, :Port => 1902) do |client|
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- assert_equal "Hello World", client.job(:hi, nil, {}).run.chomp
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- assert_equal "Hello Miguel", client.job(:hi, nil, {:name => :Miguel}).run.chomp
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- assert_equal "Hello Miguel, nice to meet you", client.job(:intro, nil, {:name => :Miguel}).run.chomp
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- end
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- end
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- end
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-
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- def test_rest_clean
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- real_job = TestWFRest.job(:hi)
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- real_job.run
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- first_time = File.ctime(real_job.path)
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- workflow_server(TestWFRest) do |client|
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- assert File.ctime(real_job.path) == first_time
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- assert_equal "Hello World", client.job(:hi, nil, {}).clean.run
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- assert File.ctime(real_job.path) > first_time
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- end
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- end
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- end
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-