sequencescape-client-api 0.3.10 → 0.4.0.pre.rc1

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Files changed (96) hide show
  1. checksums.yaml +4 -4
  2. data/.rubocop.yml +44 -0
  3. data/.rubocop_todo.yml +338 -0
  4. data/.ruby-version +1 -0
  5. data/Gemfile +1 -1
  6. data/README.markdown +13 -0
  7. data/lib/sequencescape-api.rb +1 -1
  8. data/lib/sequencescape-api/actions.rb +9 -8
  9. data/lib/sequencescape-api/associations.rb +8 -6
  10. data/lib/sequencescape-api/associations/base.rb +1 -1
  11. data/lib/sequencescape-api/associations/base/instance_methods.rb +10 -8
  12. data/lib/sequencescape-api/associations/belongs_to.rb +4 -4
  13. data/lib/sequencescape-api/associations/has_many.rb +14 -13
  14. data/lib/sequencescape-api/associations/has_many/json.rb +1 -1
  15. data/lib/sequencescape-api/associations/has_many/validation.rb +1 -1
  16. data/lib/sequencescape-api/composition.rb +11 -7
  17. data/lib/sequencescape-api/connection_factory.rb +6 -5
  18. data/lib/sequencescape-api/connection_factory/actions.rb +17 -12
  19. data/lib/sequencescape-api/core.rb +12 -7
  20. data/lib/sequencescape-api/core_ext/array.rb +1 -1
  21. data/lib/sequencescape-api/core_ext/hash.rb +3 -3
  22. data/lib/sequencescape-api/errors.rb +2 -2
  23. data/lib/sequencescape-api/finder_methods.rb +16 -11
  24. data/lib/sequencescape-api/rails.rb +8 -7
  25. data/lib/sequencescape-api/resource/active_model.rb +1 -1
  26. data/lib/sequencescape-api/resource/attribute_groups.rb +11 -7
  27. data/lib/sequencescape-api/resource/attributes.rb +8 -8
  28. data/lib/sequencescape-api/resource/instance_methods.rb +17 -9
  29. data/lib/sequencescape-api/resource/json.rb +18 -15
  30. data/lib/sequencescape-api/resource/modifications.rb +20 -11
  31. data/lib/sequencescape-api/resource_model_proxy.rb +7 -5
  32. data/lib/sequencescape-api/version.rb +1 -1
  33. data/lib/sequencescape.rb +1 -2
  34. data/lib/sequencescape/bait_library.rb +1 -1
  35. data/lib/sequencescape/bait_library_layout.rb +2 -2
  36. data/lib/sequencescape/barcoded_asset.rb +1 -1
  37. data/lib/sequencescape/batch.rb +6 -6
  38. data/lib/sequencescape/behaviour/qced.rb +3 -4
  39. data/lib/sequencescape/behaviour/receptacle.rb +3 -3
  40. data/lib/sequencescape/behaviour/state_driven.rb +4 -4
  41. data/lib/sequencescape/bulk_transfer.rb +1 -1
  42. data/lib/sequencescape/comment.rb +0 -2
  43. data/lib/sequencescape/extraction_attribute.rb +1 -1
  44. data/lib/sequencescape/library_event.rb +1 -1
  45. data/lib/sequencescape/library_tube.rb +1 -1
  46. data/lib/sequencescape/lot.rb +0 -1
  47. data/lib/sequencescape/lot_type.rb +1 -2
  48. data/lib/sequencescape/order_template.rb +1 -2
  49. data/lib/sequencescape/pipeline.rb +1 -1
  50. data/lib/sequencescape/plate.rb +19 -15
  51. data/lib/sequencescape/plate/pooling.rb +9 -3
  52. data/lib/sequencescape/plate/well_structure.rb +6 -6
  53. data/lib/sequencescape/plate_conversion.rb +3 -3
  54. data/lib/sequencescape/plate_creation.rb +3 -3
  55. data/lib/sequencescape/plate_purpose.rb +3 -3
  56. data/lib/sequencescape/plate_template.rb +0 -2
  57. data/lib/sequencescape/pooled_plate_creation.rb +3 -3
  58. data/lib/sequencescape/project.rb +2 -1
  59. data/lib/sequencescape/qc_decision.rb +0 -1
  60. data/lib/sequencescape/qc_file.rb +0 -3
  61. data/lib/sequencescape/qcable.rb +0 -3
  62. data/lib/sequencescape/qcable_creator.rb +0 -3
  63. data/lib/sequencescape/request.rb +3 -3
  64. data/lib/sequencescape/search.rb +10 -8
  65. data/lib/sequencescape/specific_tube_creation.rb +2 -2
  66. data/lib/sequencescape/stamp.rb +0 -1
  67. data/lib/sequencescape/state_change.rb +2 -2
  68. data/lib/sequencescape/study.rb +1 -1
  69. data/lib/sequencescape/submission.rb +1 -2
  70. data/lib/sequencescape/tag2_layout.rb +3 -3
  71. data/lib/sequencescape/tag2_layout_template.rb +2 -2
  72. data/lib/sequencescape/tag_group.rb +0 -1
  73. data/lib/sequencescape/tag_layout.rb +3 -3
  74. data/lib/sequencescape/tag_layout_template.rb +4 -4
  75. data/lib/sequencescape/transfer.rb +2 -2
  76. data/lib/sequencescape/transfer_request.rb +4 -5
  77. data/lib/sequencescape/transfer_template.rb +2 -2
  78. data/lib/sequencescape/tube.rb +3 -3
  79. data/lib/sequencescape/tube_creation.rb +3 -3
  80. data/lib/sequencescape/tube_from_tube_creation.rb +3 -3
  81. data/lib/sequencescape/tube_purpose.rb +3 -3
  82. data/lib/sequencescape/user.rb +2 -2
  83. data/lib/sequencescape/volume_update.rb +1 -1
  84. data/lib/sequencescape/well.rb +0 -2
  85. data/lib/sequencescape/work_completion.rb +1 -1
  86. data/sequencescape-api.gemspec +18 -17
  87. data/spec/sequencescape-api/associations_spec.rb +4 -2
  88. data/spec/sequencescape-api/finding_methods_spec.rb +3 -1
  89. data/spec/sequencescape-api/modifications_spec.rb +17 -16
  90. data/spec/sequencescape-api/root_spec.rb +11 -6
  91. data/spec/spec_helper.rb +3 -1
  92. data/spec/support/contract_helper.rb +18 -10
  93. data/spec/support/namespaces.rb +9 -9
  94. data/spec/support/shared_examples.rb +2 -0
  95. metadata +53 -35
  96. data/.rvmrc +0 -52
data/.rvmrc DELETED
@@ -1,52 +0,0 @@
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- #!/usr/bin/env bash
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-
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- # This is an RVM Project .rvmrc file, used to automatically load the ruby
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- # development environment upon cd'ing into the directory
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-
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- # First we specify our desired <ruby>[@<gemset>], the @gemset name is optional,
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- # Only full ruby name is supported here, for short names use:
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- # echo "rvm use 1.9.3" > .rvmrc
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- environment_id="ruby-2.3.7@sequencescape-api"
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-
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- # Uncomment the following lines if you want to verify rvm version per project
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- # rvmrc_rvm_version="1.15.3 (master)" # 1.10.1 seams as a safe start
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- # eval "$(echo ${rvm_version}.${rvmrc_rvm_version} | awk -F. '{print "[[ "$1*65536+$2*256+$3" -ge "$4*65536+$5*256+$6" ]]"}' )" || {
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- # echo "This .rvmrc file requires at least RVM ${rvmrc_rvm_version}, aborting loading."
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- # return 1
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- # }
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-
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- # First we attempt to load the desired environment directly from the environment
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- # file. This is very fast and efficient compared to running through the entire
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- # CLI and selector. If you want feedback on which environment was used then
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- # insert the word 'use' after --create as this triggers verbose mode.
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- if [[ -d "${rvm_path:-$HOME/.rvm}/environments"
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- && -s "${rvm_path:-$HOME/.rvm}/environments/$environment_id" ]]
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- then
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- \. "${rvm_path:-$HOME/.rvm}/environments/$environment_id"
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- [[ -s "${rvm_path:-$HOME/.rvm}/hooks/after_use" ]] &&
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- \. "${rvm_path:-$HOME/.rvm}/hooks/after_use" || true
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- if [[ $- == *i* ]] # check for interactive shells
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- then echo "Using: $(tput setaf 2)$GEM_HOME$(tput sgr0)" # show the user the ruby and gemset they are using in green
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- else echo "Using: $GEM_HOME" # don't use colors in non-interactive shells
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- fi
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- else
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- # If the environment file has not yet been created, use the RVM CLI to select.
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- rvm --create use "$environment_id" || {
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- echo "Failed to create RVM environment '${environment_id}'."
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- return 1
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- }
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- fi
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-
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- # If you use bundler, this might be useful to you:
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- # if [[ -s Gemfile ]] && {
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- # ! builtin command -v bundle >/dev/null ||
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- # builtin command -v bundle | GREP_OPTIONS= \grep $rvm_path/bin/bundle >/dev/null
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- # }
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- # then
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- # printf "%b" "The rubygem 'bundler' is not installed. Installing it now.\n"
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- # gem install bundler
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- # fi
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- # if [[ -s Gemfile ]] && builtin command -v bundle >/dev/null
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- # then
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- # bundle install | GREP_OPTIONS= \grep -vE '^Using|Your bundle is complete'
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- # fi