solvebio 1.6.1 → 1.7.0

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Files changed (119) hide show
  1. data/.bumpversion.cfg +6 -0
  2. data/.gitignore +5 -4
  3. data/.travis.yml +1 -1
  4. data/Gemfile +3 -0
  5. data/README.md +34 -34
  6. data/Rakefile +1 -18
  7. data/bin/solvebio.rb +14 -16
  8. data/installer +64 -0
  9. data/lib/solvebio.rb +50 -11
  10. data/lib/solvebio/acccount.rb +4 -0
  11. data/lib/solvebio/annotation.rb +11 -0
  12. data/lib/solvebio/api_operations.rb +147 -0
  13. data/lib/solvebio/api_resource.rb +32 -0
  14. data/lib/solvebio/cli.rb +75 -0
  15. data/lib/solvebio/cli/auth.rb +106 -0
  16. data/lib/solvebio/cli/credentials.rb +54 -0
  17. data/lib/{cli → solvebio/cli}/irb.rb +0 -23
  18. data/lib/solvebio/cli/irbrc.rb +48 -0
  19. data/lib/solvebio/cli/tutorial.rb +12 -0
  20. data/lib/solvebio/client.rb +149 -0
  21. data/lib/solvebio/dataset.rb +60 -0
  22. data/lib/solvebio/dataset_field.rb +12 -0
  23. data/lib/solvebio/depository.rb +38 -0
  24. data/lib/solvebio/depository_version.rb +40 -0
  25. data/lib/solvebio/errors.rb +64 -0
  26. data/lib/solvebio/filter.rb +315 -0
  27. data/lib/solvebio/list_object.rb +73 -0
  28. data/lib/solvebio/locale.rb +43 -0
  29. data/lib/solvebio/query.rb +341 -0
  30. data/lib/solvebio/sample.rb +54 -0
  31. data/lib/solvebio/singleton_api_resource.rb +25 -0
  32. data/lib/solvebio/solve_object.rb +164 -0
  33. data/lib/solvebio/tabulate.rb +589 -0
  34. data/lib/solvebio/user.rb +4 -0
  35. data/lib/solvebio/util.rb +59 -0
  36. data/lib/solvebio/version.rb +3 -0
  37. data/solvebio.gemspec +10 -18
  38. data/test/helper.rb +6 -2
  39. data/test/solvebio/data/.gitignore +1 -0
  40. data/test/solvebio/data/.netrc +6 -0
  41. data/test/{data → solvebio/data}/netrc-save +0 -0
  42. data/test/solvebio/data/sample.vcf.gz +0 -0
  43. data/test/solvebio/data/test_creds +3 -0
  44. data/test/solvebio/test_annotation.rb +45 -0
  45. data/test/solvebio/test_client.rb +29 -0
  46. data/test/solvebio/test_conversion.rb +14 -0
  47. data/test/solvebio/test_credentials.rb +67 -0
  48. data/test/solvebio/test_dataset.rb +52 -0
  49. data/test/solvebio/test_depository.rb +24 -0
  50. data/test/solvebio/test_depositoryversion.rb +22 -0
  51. data/test/solvebio/test_error.rb +31 -0
  52. data/test/solvebio/test_filter.rb +86 -0
  53. data/test/solvebio/test_query.rb +282 -0
  54. data/test/solvebio/test_query_batch.rb +38 -0
  55. data/test/solvebio/test_query_init.rb +30 -0
  56. data/test/solvebio/test_query_tabulate.rb +73 -0
  57. data/test/solvebio/test_ratelimit.rb +31 -0
  58. data/test/solvebio/test_resource.rb +29 -0
  59. data/test/solvebio/test_sample_access.rb +60 -0
  60. data/test/solvebio/test_sample_download.rb +20 -0
  61. data/test/solvebio/test_tabulate.rb +129 -0
  62. data/test/solvebio/test_util.rb +39 -0
  63. metadata +100 -85
  64. data/Makefile +0 -17
  65. data/demo/README.md +0 -14
  66. data/demo/cheatsheet.rb +0 -31
  67. data/demo/dataset/facets.rb +0 -13
  68. data/demo/dataset/field.rb +0 -13
  69. data/demo/depository/README.md +0 -24
  70. data/demo/depository/all.rb +0 -13
  71. data/demo/depository/retrieve.rb +0 -13
  72. data/demo/depository/versions-all.rb +0 -13
  73. data/demo/query/query-filter.rb +0 -30
  74. data/demo/query/query.rb +0 -13
  75. data/demo/query/range-filter.rb +0 -18
  76. data/demo/test-api.rb +0 -98
  77. data/lib/cli/auth.rb +0 -122
  78. data/lib/cli/help.rb +0 -13
  79. data/lib/cli/irbrc.rb +0 -54
  80. data/lib/cli/options.rb +0 -75
  81. data/lib/client.rb +0 -154
  82. data/lib/credentials.rb +0 -67
  83. data/lib/errors.rb +0 -81
  84. data/lib/filter.rb +0 -312
  85. data/lib/locale.rb +0 -47
  86. data/lib/main.rb +0 -46
  87. data/lib/query.rb +0 -414
  88. data/lib/resource/annotation.rb +0 -23
  89. data/lib/resource/apiresource.rb +0 -241
  90. data/lib/resource/dataset.rb +0 -91
  91. data/lib/resource/datasetfield.rb +0 -37
  92. data/lib/resource/depository.rb +0 -50
  93. data/lib/resource/depositoryversion.rb +0 -69
  94. data/lib/resource/main.rb +0 -123
  95. data/lib/resource/sample.rb +0 -75
  96. data/lib/resource/solveobject.rb +0 -122
  97. data/lib/resource/user.rb +0 -5
  98. data/lib/tabulate.rb +0 -706
  99. data/lib/util.rb +0 -29
  100. data/test/Makefile +0 -9
  101. data/test/data/sample.vcf.gz +0 -0
  102. data/test/test-annotation.rb +0 -46
  103. data/test/test-auth.rb +0 -58
  104. data/test/test-client.rb +0 -27
  105. data/test/test-conversion.rb +0 -13
  106. data/test/test-dataset.rb +0 -42
  107. data/test/test-depository.rb +0 -35
  108. data/test/test-error.rb +0 -36
  109. data/test/test-filter.rb +0 -70
  110. data/test/test-netrc.rb +0 -52
  111. data/test/test-query-batch.rb +0 -40
  112. data/test/test-query-init.rb +0 -29
  113. data/test/test-query-paging.rb +0 -102
  114. data/test/test-query.rb +0 -71
  115. data/test/test-resource.rb +0 -40
  116. data/test/test-sample-access.rb +0 -59
  117. data/test/test-sample-download.rb +0 -20
  118. data/test/test-tabulate.rb +0 -131
  119. data/test/test-util.rb +0 -42
data/test/test-util.rb DELETED
@@ -1,42 +0,0 @@
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- #!/usr/bin/env ruby
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- $VERBOSE = true
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- require 'test/unit'
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- require_relative '../lib/util'
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-
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- class TestSolveObject < Test::Unit::TestCase
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-
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- # Does our kind of camelCasing works?
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- def test_camelcase
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-
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- data =
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- [
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- ['abc', 'abc', 'no camelcase'],
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- ['aBcDef', 'a_bc_def', 'letters only'],
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- ['abc01Def', 'abc01_def', 'letters and numbers'],
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- ['aBcDef', 'a_bc_def', 'multiple letter match'],
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- ['a1B2C3', 'a1_b2_c3', 'multi letters and numbers'],
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- ['?Foo', '?_foo', 'weird symbols, part 1'],
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- ['Dataset', 'dataset', 'no camelcase with caps'],
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- ]
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- data.each do |triple|
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- assert_equal(triple[1],
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- SolveBio::camelcase_to_underscore(triple[0]),
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- triple[2])
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- end
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- end
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-
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- def test_pluralize
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- data =
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- [
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- ['depository', 'depositories', "ends in 'y'"],
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- ['dataset', 'datasets', "simply adds an 's'"]
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- ]
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- data.each do |triple|
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- assert_equal(triple[1],
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- SolveBio::pluralize(triple[0]),
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- triple[2])
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- end
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-
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- end
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-
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- end