bel_parser 1.0.8 → 1.1.1

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Files changed (112) hide show
  1. checksums.yaml +4 -4
  2. data/.gemspec +12 -2
  3. data/VERSION +1 -1
  4. data/bin/bel2_compatibility +12 -9
  5. data/bin/bel2_upgrade +18 -6
  6. data/bin/bel2_validator +6 -3
  7. data/bin/bel_script_reader +1 -0
  8. data/lib/bel_parser/completion.rb +984 -0
  9. data/lib/bel_parser/language/apply_namespace_encoding.rb +14 -3
  10. data/lib/bel_parser/language/expression_validator.rb +1 -2
  11. data/lib/bel_parser/language/function.rb +4 -0
  12. data/lib/bel_parser/language/relationship.rb +4 -0
  13. data/lib/bel_parser/language/semantics/function_deprecation.rb +1 -0
  14. data/lib/bel_parser/language/semantics/list_function_subject.rb +2 -0
  15. data/lib/bel_parser/language/semantics/multiple_subject_object.rb +4 -1
  16. data/lib/bel_parser/language/semantics/nested_statement_without_object.rb +43 -0
  17. data/lib/bel_parser/language/semantics/non_object_list.rb +3 -0
  18. data/lib/bel_parser/language/semantics/relationship_not_listable.rb +2 -0
  19. data/lib/bel_parser/language/semantics/signature_mapping.rb +2 -0
  20. data/lib/bel_parser/language/semantics_ast.rb +0 -7
  21. data/lib/bel_parser/language/syntax/invalid_function.rb +6 -1
  22. data/lib/bel_parser/language/syntax/invalid_relationship.rb +1 -0
  23. data/lib/bel_parser/language/version1_0/relationships/acts_in.rb +9 -9
  24. data/lib/bel_parser/language/version1_0/relationships/analogous.rb +6 -4
  25. data/lib/bel_parser/language/version1_0/relationships/association.rb +8 -7
  26. data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb +6 -5
  27. data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb +8 -7
  28. data/lib/bel_parser/language/version1_0/relationships/decreases.rb +13 -12
  29. data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb +8 -6
  30. data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb +8 -6
  31. data/lib/bel_parser/language/version1_0/relationships/has_component.rb +14 -14
  32. data/lib/bel_parser/language/version1_0/relationships/has_components.rb +12 -11
  33. data/lib/bel_parser/language/version1_0/relationships/has_member.rb +10 -8
  34. data/lib/bel_parser/language/version1_0/relationships/has_members.rb +12 -11
  35. data/lib/bel_parser/language/version1_0/relationships/has_modification.rb +9 -7
  36. data/lib/bel_parser/language/version1_0/relationships/has_product.rb +10 -8
  37. data/lib/bel_parser/language/version1_0/relationships/has_variant.rb +9 -7
  38. data/lib/bel_parser/language/version1_0/relationships/includes.rb +11 -10
  39. data/lib/bel_parser/language/version1_0/relationships/increases.rb +12 -13
  40. data/lib/bel_parser/language/version1_0/relationships/is_a.rb +10 -8
  41. data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb +9 -7
  42. data/lib/bel_parser/language/version1_0/relationships/orthologous.rb +9 -8
  43. data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb +8 -5
  44. data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb +8 -6
  45. data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb +10 -9
  46. data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb +10 -8
  47. data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb +13 -12
  48. data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb +8 -7
  49. data/lib/bel_parser/language/version1_0/relationships/translated_to.rb +9 -7
  50. data/lib/bel_parser/language/version1_0/relationships/translocates.rb +10 -9
  51. data/lib/bel_parser/language/version2_0/functions/protein_modification.rb +1 -2
  52. data/lib/bel_parser/language/version2_0/functions/translocation.rb +1 -2
  53. data/lib/bel_parser/language/version2_0/functions/variant.rb +1 -2
  54. data/lib/bel_parser/language/version2_0/relationships/acts_in.rb +10 -9
  55. data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb +7 -5
  56. data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb +9 -7
  57. data/lib/bel_parser/language/version2_0/relationships/decreases.rb +13 -12
  58. data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb +8 -6
  59. data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb +8 -6
  60. data/lib/bel_parser/language/version2_0/relationships/has_component.rb +15 -14
  61. data/lib/bel_parser/language/version2_0/relationships/has_components.rb +12 -11
  62. data/lib/bel_parser/language/version2_0/relationships/has_member.rb +9 -8
  63. data/lib/bel_parser/language/version2_0/relationships/has_members.rb +12 -11
  64. data/lib/bel_parser/language/version2_0/relationships/has_modification.rb +9 -7
  65. data/lib/bel_parser/language/version2_0/relationships/has_product.rb +10 -8
  66. data/lib/bel_parser/language/version2_0/relationships/has_variant.rb +9 -7
  67. data/lib/bel_parser/language/version2_0/relationships/includes.rb +11 -10
  68. data/lib/bel_parser/language/version2_0/relationships/increases.rb +13 -12
  69. data/lib/bel_parser/language/version2_0/relationships/is_a.rb +10 -8
  70. data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb +9 -7
  71. data/lib/bel_parser/language/version2_0/relationships/orthologous.rb +10 -8
  72. data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb +7 -5
  73. data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb +8 -6
  74. data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb +10 -9
  75. data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb +10 -8
  76. data/lib/bel_parser/language/version2_0/relationships/regulates.rb +9 -8
  77. data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb +13 -12
  78. data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb +8 -7
  79. data/lib/bel_parser/language/version2_0/relationships/translated_to.rb +9 -7
  80. data/lib/bel_parser/language/version2_0/relationships/translocates.rb +10 -9
  81. data/lib/bel_parser/mixin/levenshtein.rb +20 -0
  82. data/lib/bel_parser/parsers/ast/node.rb +49 -2
  83. data/lib/bel_parser/parsers/bel_script/define_annotation.rb +156 -156
  84. data/lib/bel_parser/parsers/bel_script/define_namespace.rb +60 -60
  85. data/lib/bel_parser/parsers/bel_script/set.rb +200 -200
  86. data/lib/bel_parser/parsers/bel_script/set_document.rb +188 -188
  87. data/lib/bel_parser/parsers/bel_script/unset.rb +14 -14
  88. data/lib/bel_parser/parsers/common/common.rl +1 -0
  89. data/lib/bel_parser/parsers/common/function.rb +8 -8
  90. data/lib/bel_parser/parsers/common/function.rl +6 -6
  91. data/lib/bel_parser/parsers/common/identifier.rb +3 -3
  92. data/lib/bel_parser/parsers/common/identifier.rl +4 -4
  93. data/lib/bel_parser/parsers/common/list.rb +78 -78
  94. data/lib/bel_parser/parsers/common/multi_identifier.rb +275 -0
  95. data/lib/bel_parser/parsers/common/multi_identifier.rl +141 -0
  96. data/lib/bel_parser/parsers/common/string.rb +6 -6
  97. data/lib/bel_parser/parsers/common/string.rl +4 -4
  98. data/lib/bel_parser/parsers/common.rb +1 -0
  99. data/lib/bel_parser/parsers/expression/nested_statement.rb +30180 -29055
  100. data/lib/bel_parser/parsers/expression/observed_term.rb +1456 -1099
  101. data/lib/bel_parser/parsers/expression/parameter.rb +192 -111
  102. data/lib/bel_parser/parsers/expression/parameter.rl +6 -3
  103. data/lib/bel_parser/parsers/expression/relationship.rb +43 -19
  104. data/lib/bel_parser/parsers/expression/relationship.rl +1 -0
  105. data/lib/bel_parser/parsers/expression/simple_statement.rb +17805 -17093
  106. data/lib/bel_parser/parsers/expression/statement_autocomplete.rb +1035 -0
  107. data/lib/bel_parser/parsers/expression/statement_autocomplete.rl +736 -0
  108. data/lib/bel_parser/parsers/expression/term.rb +960 -705
  109. data/lib/bel_parser/parsers/serializer.rb +8 -4
  110. data/lib/bel_parser/version.rb +33 -0
  111. data/lib/bel_parser.rb +3 -0
  112. metadata +25 -3
@@ -61,7 +61,7 @@ module BELParser
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  # Get the character range enclosing this AST node. It is defined
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  # as the close interval containing all the characters of this
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  # AST node.
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- attr_reader :character_range
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+ attr_accessor :character_range
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  # Get/Set the complete property.
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  attr_accessor :complete
@@ -445,7 +445,7 @@ module BELParser
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  end
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  end
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- # AST node representing the definition of a namespace.
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+ # AST node representing an identifier (e.g. non-quoted value).
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  class Identifier < Node
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  # AST node type
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  @ast_type = :identifier
@@ -465,6 +465,26 @@ module BELParser
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  end
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  end
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+ # AST node representing a multi-valued identifier without needing quotes (e.g. greedy).
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+ class MultiIdentifier < Node
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+ # AST node type
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+ @ast_type = :multi_identifier
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+ # MultiIdentifier have no semantics
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+ @has_semantics = false
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+
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+ # New MultiIdentifier AST node.
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+ #
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+ # @see Node#initialize Node class for basic properties
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+ def initialize(children = [], properties = {})
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+ super(MultiIdentifier.ast_type, children, properties)
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+ end
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+
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+ # Get the string literal.
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+ def string_literal
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+ children[0]
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+ end
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+ end
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+
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  # AST node representing a list.
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  class List < Node
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  # AST node type
@@ -825,6 +845,15 @@ module BELParser
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  def string_literal
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  children[0]
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  end
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+
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+ def string_value
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+ return nil if children[0].nil?
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+
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+ value = children[0].dup
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+ value.slice!(0) if value[0] == '"'
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+ value.slice!(-1) if value[-1] == '"'
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+ value
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+ end
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  end
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  # AST node representing a term.
@@ -944,6 +973,20 @@ module BELParser
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  #
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  # @see https://en.wikipedia.org/wiki/S-expression S-expression
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  module Sexp
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+ def self.build(&block)
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+ raise ArgumentError, 'expecting block' unless block_given?
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+
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+ builder = _builder_class.new
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+ builder.instance_eval(&block)
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+ end
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+
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+ def self._builder_class
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+ Class.new do
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+ include Sexp
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+ end
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+ end
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+ private_class_method :_builder_class
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+
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  def nested_statement(*children, **props)
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  NestedStatement.new(children, props)
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  end
@@ -1004,6 +1047,10 @@ module BELParser
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  Identifier.new(children, props)
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  end
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+ def multi_identifier(*children, **props)
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+ MultiIdentifier.new(children, props)
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+ end
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+
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  def string(*children, **props)
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  String.new(children, props)
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  end