rbbt-util 3.2.1 → 4.0.0

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Files changed (85) hide show
  1. data/README.rdoc +65 -0
  2. data/bin/run_workflow.rb +142 -69
  3. data/lib/rbbt-util.rb +3 -3
  4. data/lib/rbbt.rb +12 -3
  5. data/lib/rbbt/annotations.rb +215 -0
  6. data/lib/rbbt/{util/fix_width_table.rb → fix_width_table.rb} +17 -13
  7. data/lib/rbbt/persist.rb +164 -0
  8. data/lib/rbbt/persist/tsv.rb +135 -0
  9. data/lib/rbbt/resource.rb +100 -0
  10. data/lib/rbbt/resource/path.rb +180 -0
  11. data/lib/rbbt/resource/rake.rb +48 -0
  12. data/lib/rbbt/resource/util.rb +111 -0
  13. data/lib/rbbt/resource/with_key.rb +28 -0
  14. data/lib/rbbt/tsv.rb +134 -0
  15. data/lib/rbbt/tsv/accessor.rb +345 -0
  16. data/lib/rbbt/tsv/attach.rb +183 -0
  17. data/lib/rbbt/tsv/attach/util.rb +277 -0
  18. data/lib/rbbt/{util/tsv/filters.rb → tsv/filter.rb} +76 -37
  19. data/lib/rbbt/tsv/index.rb +453 -0
  20. data/lib/rbbt/tsv/manipulate.rb +361 -0
  21. data/lib/rbbt/tsv/parser.rb +231 -0
  22. data/lib/rbbt/tsv/serializers.rb +79 -0
  23. data/lib/rbbt/tsv/util.rb +67 -0
  24. data/lib/rbbt/util/R.rb +3 -3
  25. data/lib/rbbt/util/chain_methods.rb +64 -0
  26. data/lib/rbbt/util/cmd.rb +17 -13
  27. data/lib/rbbt/util/excel2tsv.rb +4 -3
  28. data/lib/rbbt/util/log.rb +1 -0
  29. data/lib/rbbt/util/misc.rb +296 -285
  30. data/lib/rbbt/util/open.rb +9 -2
  31. data/lib/rbbt/util/persistence.rb +1 -1
  32. data/lib/rbbt/util/task/job.rb +3 -1
  33. data/lib/rbbt/workflow.rb +193 -0
  34. data/lib/rbbt/workflow/accessor.rb +249 -0
  35. data/lib/rbbt/workflow/annotate.rb +60 -0
  36. data/lib/rbbt/workflow/soap.rb +100 -0
  37. data/lib/rbbt/workflow/step.rb +102 -0
  38. data/lib/rbbt/workflow/task.rb +76 -0
  39. data/test/rbbt/resource/test_path.rb +12 -0
  40. data/test/rbbt/test_annotations.rb +106 -0
  41. data/test/rbbt/{util/test_fix_width_table.rb → test_fix_width_table.rb} +8 -9
  42. data/test/rbbt/test_resource.rb +66 -0
  43. data/test/rbbt/test_tsv.rb +332 -0
  44. data/test/rbbt/test_workflow.rb +102 -0
  45. data/test/rbbt/tsv/test_accessor.rb +163 -0
  46. data/test/rbbt/{util/tsv → tsv}/test_attach.rb +86 -43
  47. data/test/rbbt/{util/tsv/test_filters.rb → tsv/test_filter.rb} +31 -13
  48. data/test/rbbt/tsv/test_index.rb +284 -0
  49. data/test/rbbt/{util/tsv → tsv}/test_manipulate.rb +35 -105
  50. data/test/rbbt/util/test_R.rb +1 -1
  51. data/test/rbbt/util/test_chain_methods.rb +22 -0
  52. data/test/rbbt/util/test_filecache.rb +0 -1
  53. data/test/rbbt/util/test_misc.rb +97 -79
  54. data/test/rbbt/util/test_open.rb +1 -0
  55. data/test/rbbt/util/test_tmpfile.rb +1 -1
  56. data/test/rbbt/workflow/test_soap.rb +103 -0
  57. data/test/rbbt/workflow/test_step.rb +142 -0
  58. data/test/rbbt/workflow/test_task.rb +84 -0
  59. data/test/test_helper.rb +7 -7
  60. metadata +80 -54
  61. data/lib/rbbt/util/rake.rb +0 -176
  62. data/lib/rbbt/util/resource.rb +0 -355
  63. data/lib/rbbt/util/task.rb +0 -183
  64. data/lib/rbbt/util/tc_hash.rb +0 -324
  65. data/lib/rbbt/util/tsv.rb +0 -236
  66. data/lib/rbbt/util/tsv/accessor.rb +0 -312
  67. data/lib/rbbt/util/tsv/attach.rb +0 -416
  68. data/lib/rbbt/util/tsv/index.rb +0 -419
  69. data/lib/rbbt/util/tsv/manipulate.rb +0 -300
  70. data/lib/rbbt/util/tsv/misc.rb +0 -41
  71. data/lib/rbbt/util/tsv/parse.rb +0 -324
  72. data/lib/rbbt/util/tsv/resource.rb +0 -88
  73. data/lib/rbbt/util/workflow.rb +0 -135
  74. data/lib/rbbt/util/workflow/soap.rb +0 -116
  75. data/test/rbbt/util/test_persistence.rb +0 -201
  76. data/test/rbbt/util/test_rake.rb +0 -54
  77. data/test/rbbt/util/test_resource.rb +0 -77
  78. data/test/rbbt/util/test_task.rb +0 -133
  79. data/test/rbbt/util/test_tc_hash.rb +0 -144
  80. data/test/rbbt/util/test_tsv.rb +0 -221
  81. data/test/rbbt/util/test_workflow.rb +0 -135
  82. data/test/rbbt/util/tsv/test_accessor.rb +0 -150
  83. data/test/rbbt/util/tsv/test_index.rb +0 -241
  84. data/test/rbbt/util/tsv/test_parse.rb +0 -87
  85. data/test/rbbt/util/tsv/test_resource.rb +0 -9
data/test/rbbt/util/tsv/test_parse.rb DELETED
@@ -1,87 +0,0 @@
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- require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
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- require 'rbbt/util/tsv/parse'
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-
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- class TestTSVParse < Test::Unit::TestCase
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-
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- def test_keep_empty
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- content =<<-EOF
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- #Id ValueA ValueB Comment
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- row1 a|aa|aaa b c
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- row2 A B
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- EOF
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-
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- TmpFile.with_file(content) do |filename|
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- data = {}
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- data, extra = TSV.parse(File.open(filename), :sep => /\s+/, :keep_empty => true)
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- assert_equal ["ValueA", "ValueB", "Comment"], extra[:fields]
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- assert_equal ["c"], data["row1"][2]
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- assert_equal [""], data["row2"][2]
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- end
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- end
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-
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- def test_break_with_fix
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- content =<<-EOF
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- #Id ValueA ValueB OtherID
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- row1 a|aa|aaa b Id1|Id2
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- row2 A B Id3
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- row3 a C Id4
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- EOF
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-
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- TmpFile.with_file(content) do |filename|
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- tsv = TSV.parse(File.open(filename), :sep => /\s+/, :fix => proc{|l| l =~ /^row2/? nil : l})
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- assert_equal %w(row1), tsv.first.keys
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- end
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- end
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-
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- def test_hash
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- content =<<-EOF
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- #Id ValueA ValueB
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- row1 a|aa|aaa b
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- row2 A B
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- EOF
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-
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- TmpFile.with_file(content) do |filename|
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- data = {}
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- data, extra = TSV.parse(File.open(filename), :sep => /\s+/)
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- assert_equal "Id", extra[:key_field]
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- assert_equal ["ValueA", "ValueB"], extra[:fields]
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- assert_equal ["a", "aa", "aaa"], data["row1"][0]
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- end
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- end
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-
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- def test_unven_flat
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- content =<<-EOF
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- row1 a b
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- row2 A B C
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- EOF
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-
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- TmpFile.with_file(content) do |filename|
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- data = {}
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- data, extra = TSV.parse(File.open(filename), :type => :flat, :sep => /\s+/)
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- assert data["row2"].include? "C"
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- end
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- end
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-
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-
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-
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- def test_options_line
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- content =<<-EOF
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- #: :sep=/\\s+/#:case_insensitive=true
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- #Id ValueA ValueB
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- row1 a|aa|aaa b
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- row2 A B
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- EOF
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-
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- TmpFile.with_file(content) do |filename|
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- data = {}
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- data, extra = TSV.parse(File.open(filename))
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- assert_equal "Id", extra[:key_field]
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- assert_equal true, extra[:case_insensitive]
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- assert_equal ["ValueA", "ValueB"], extra[:fields]
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- assert_equal ["a", "aa", "aaa"], data["row1"][0]
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- end
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- end
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-
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-
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- end
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-
data/test/rbbt/util/tsv/test_resource.rb DELETED
@@ -1,9 +0,0 @@
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- require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
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- require 'rbbt/util/tsv/resource'
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-
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- class TestTSVResource < Test::Unit::TestCase
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- def test_true
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- assert true
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- end
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- end
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-