bel_parser 1.0.0.alpha.1

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  1. checksums.yaml +7 -0
  2. data/.gemspec +28 -0
  3. data/CHANGELOG.md +10 -0
  4. data/LICENSE +191 -0
  5. data/README.md +9 -0
  6. data/VERSION +1 -0
  7. data/bin/bel2_termcheck +39 -0
  8. data/lib/bel_parser.rb +17 -0
  9. data/lib/bel_parser/ast_filter.rb +27 -0
  10. data/lib/bel_parser/ast_generator.rb +86 -0
  11. data/lib/bel_parser/ast_validator.rb +40 -0
  12. data/lib/bel_parser/expression/parser.rb +42 -0
  13. data/lib/bel_parser/expression/term_semantics.rb +36 -0
  14. data/lib/bel_parser/language.rb +7 -0
  15. data/lib/bel_parser/language/function.rb +59 -0
  16. data/lib/bel_parser/language/quoting.rb +236 -0
  17. data/lib/bel_parser/language/semantic_ast.rb +604 -0
  18. data/lib/bel_parser/language/semantics/analyzer.rb +59 -0
  19. data/lib/bel_parser/language/signature.rb +39 -0
  20. data/lib/bel_parser/language/specification.rb +49 -0
  21. data/lib/bel_parser/language/syntax/expression/incomplete_node.rb +14 -0
  22. data/lib/bel_parser/language/syntax/expression/invalid_term_function.rb +22 -0
  23. data/lib/bel_parser/language/version1.rb +50 -0
  24. data/lib/bel_parser/language/version1/functions/abundance.rb +85 -0
  25. data/lib/bel_parser/language/version1/functions/biological_process.rb +85 -0
  26. data/lib/bel_parser/language/version1/functions/catalytic_activity.rb +110 -0
  27. data/lib/bel_parser/language/version1/functions/cell_secretion.rb +80 -0
  28. data/lib/bel_parser/language/version1/functions/cell_surface_expression.rb +80 -0
  29. data/lib/bel_parser/language/version1/functions/chaperone_activity.rb +110 -0
  30. data/lib/bel_parser/language/version1/functions/complex_abundance.rb +115 -0
  31. data/lib/bel_parser/language/version1/functions/composite_abundance.rb +80 -0
  32. data/lib/bel_parser/language/version1/functions/degradation.rb +80 -0
  33. data/lib/bel_parser/language/version1/functions/fusion.rb +302 -0
  34. data/lib/bel_parser/language/version1/functions/gene_abundance.rb +125 -0
  35. data/lib/bel_parser/language/version1/functions/gtp_bound_activity.rb +110 -0
  36. data/lib/bel_parser/language/version1/functions/kinase_activity.rb +110 -0
  37. data/lib/bel_parser/language/version1/functions/list.rb +115 -0
  38. data/lib/bel_parser/language/version1/functions/micro_rna_abundance.rb +85 -0
  39. data/lib/bel_parser/language/version1/functions/molecular_activity.rb +80 -0
  40. data/lib/bel_parser/language/version1/functions/pathology.rb +85 -0
  41. data/lib/bel_parser/language/version1/functions/peptidase_activity.rb +110 -0
  42. data/lib/bel_parser/language/version1/functions/phosphatase_activity.rb +110 -0
  43. data/lib/bel_parser/language/version1/functions/products.rb +80 -0
  44. data/lib/bel_parser/language/version1/functions/protein_abundance.rb +245 -0
  45. data/lib/bel_parser/language/version1/functions/protein_modification.rb +167 -0
  46. data/lib/bel_parser/language/version1/functions/reactants.rb +80 -0
  47. data/lib/bel_parser/language/version1/functions/reaction.rb +85 -0
  48. data/lib/bel_parser/language/version1/functions/ribosylation_activity.rb +110 -0
  49. data/lib/bel_parser/language/version1/functions/rna_abundance.rb +125 -0
  50. data/lib/bel_parser/language/version1/functions/substitution.rb +96 -0
  51. data/lib/bel_parser/language/version1/functions/transcriptional_activity.rb +110 -0
  52. data/lib/bel_parser/language/version1/functions/translocation.rb +100 -0
  53. data/lib/bel_parser/language/version1/functions/transport_activity.rb +110 -0
  54. data/lib/bel_parser/language/version1/functions/truncation.rb +82 -0
  55. data/lib/bel_parser/language/version1/return_types/abundance.rb +20 -0
  56. data/lib/bel_parser/language/version1/return_types/any.rb +74 -0
  57. data/lib/bel_parser/language/version1/return_types/biological_process.rb +17 -0
  58. data/lib/bel_parser/language/version1/return_types/catalytic_activity.rb +20 -0
  59. data/lib/bel_parser/language/version1/return_types/chaperone_activity.rb +20 -0
  60. data/lib/bel_parser/language/version1/return_types/complex_abundance.rb +17 -0
  61. data/lib/bel_parser/language/version1/return_types/fusion.rb +17 -0
  62. data/lib/bel_parser/language/version1/return_types/gene_abundance.rb +17 -0
  63. data/lib/bel_parser/language/version1/return_types/gtp_bound_activity.rb +20 -0
  64. data/lib/bel_parser/language/version1/return_types/kinase_activity.rb +20 -0
  65. data/lib/bel_parser/language/version1/return_types/list.rb +17 -0
  66. data/lib/bel_parser/language/version1/return_types/micro_rna_abundance.rb +17 -0
  67. data/lib/bel_parser/language/version1/return_types/molecular_activity.rb +20 -0
  68. data/lib/bel_parser/language/version1/return_types/pathology.rb +17 -0
  69. data/lib/bel_parser/language/version1/return_types/peptidase_activity.rb +20 -0
  70. data/lib/bel_parser/language/version1/return_types/phosphatase_activity.rb +20 -0
  71. data/lib/bel_parser/language/version1/return_types/products.rb +17 -0
  72. data/lib/bel_parser/language/version1/return_types/protein_abundance.rb +17 -0
  73. data/lib/bel_parser/language/version1/return_types/protein_modification.rb +17 -0
  74. data/lib/bel_parser/language/version1/return_types/reactants.rb +17 -0
  75. data/lib/bel_parser/language/version1/return_types/ribosylation_activity.rb +20 -0
  76. data/lib/bel_parser/language/version1/return_types/rna_abundance.rb +17 -0
  77. data/lib/bel_parser/language/version1/return_types/substitution.rb +17 -0
  78. data/lib/bel_parser/language/version1/return_types/transcriptional_activity.rb +20 -0
  79. data/lib/bel_parser/language/version1/return_types/transport_activity.rb +20 -0
  80. data/lib/bel_parser/language/version1/return_types/truncation.rb +17 -0
  81. data/lib/bel_parser/language/version2.rb +50 -0
  82. data/lib/bel_parser/language/version2/functions/abundance.rb +165 -0
  83. data/lib/bel_parser/language/version2/functions/activity.rb +115 -0
  84. data/lib/bel_parser/language/version2/functions/biological_process.rb +85 -0
  85. data/lib/bel_parser/language/version2/functions/cell_secretion.rb +80 -0
  86. data/lib/bel_parser/language/version2/functions/cell_surface_expression.rb +80 -0
  87. data/lib/bel_parser/language/version2/functions/complex_abundance.rb +190 -0
  88. data/lib/bel_parser/language/version2/functions/composite_abundance.rb +80 -0
  89. data/lib/bel_parser/language/version2/functions/degradation.rb +80 -0
  90. data/lib/bel_parser/language/version2/functions/fragment.rb +119 -0
  91. data/lib/bel_parser/language/version2/functions/from_location.rb +85 -0
  92. data/lib/bel_parser/language/version2/functions/fusion.rb +227 -0
  93. data/lib/bel_parser/language/version2/functions/gene_abundance.rb +195 -0
  94. data/lib/bel_parser/language/version2/functions/list.rb +115 -0
  95. data/lib/bel_parser/language/version2/functions/location.rb +85 -0
  96. data/lib/bel_parser/language/version2/functions/micro_rna_abundance.rb +165 -0
  97. data/lib/bel_parser/language/version2/functions/molecular_activity.rb +83 -0
  98. data/lib/bel_parser/language/version2/functions/pathology.rb +85 -0
  99. data/lib/bel_parser/language/version2/functions/products.rb +80 -0
  100. data/lib/bel_parser/language/version2/functions/protein_abundance.rb +285 -0
  101. data/lib/bel_parser/language/version2/functions/protein_modification.rb +167 -0
  102. data/lib/bel_parser/language/version2/functions/reactants.rb +80 -0
  103. data/lib/bel_parser/language/version2/functions/reaction.rb +85 -0
  104. data/lib/bel_parser/language/version2/functions/rna_abundance.rb +195 -0
  105. data/lib/bel_parser/language/version2/functions/to_location.rb +85 -0
  106. data/lib/bel_parser/language/version2/functions/translocation.rb +90 -0
  107. data/lib/bel_parser/language/version2/functions/variant.rb +83 -0
  108. data/lib/bel_parser/language/version2/return_types/abundance.rb +20 -0
  109. data/lib/bel_parser/language/version2/return_types/activity.rb +20 -0
  110. data/lib/bel_parser/language/version2/return_types/any.rb +74 -0
  111. data/lib/bel_parser/language/version2/return_types/biological_process.rb +17 -0
  112. data/lib/bel_parser/language/version2/return_types/complex_abundance.rb +17 -0
  113. data/lib/bel_parser/language/version2/return_types/fragment.rb +20 -0
  114. data/lib/bel_parser/language/version2/return_types/from_location.rb +20 -0
  115. data/lib/bel_parser/language/version2/return_types/fusion.rb +17 -0
  116. data/lib/bel_parser/language/version2/return_types/gene_abundance.rb +17 -0
  117. data/lib/bel_parser/language/version2/return_types/list.rb +17 -0
  118. data/lib/bel_parser/language/version2/return_types/location.rb +20 -0
  119. data/lib/bel_parser/language/version2/return_types/micro_rna_abundance.rb +17 -0
  120. data/lib/bel_parser/language/version2/return_types/molecular_activity.rb +20 -0
  121. data/lib/bel_parser/language/version2/return_types/pathology.rb +17 -0
  122. data/lib/bel_parser/language/version2/return_types/products.rb +17 -0
  123. data/lib/bel_parser/language/version2/return_types/protein_abundance.rb +17 -0
  124. data/lib/bel_parser/language/version2/return_types/protein_modification.rb +17 -0
  125. data/lib/bel_parser/language/version2/return_types/reactants.rb +17 -0
  126. data/lib/bel_parser/language/version2/return_types/rna_abundance.rb +17 -0
  127. data/lib/bel_parser/language/version2/return_types/to_location.rb +20 -0
  128. data/lib/bel_parser/language/version2/return_types/variant.rb +20 -0
  129. data/lib/bel_parser/mixin/line_continuator.rb +15 -0
  130. data/lib/bel_parser/mixin/line_mapping.rb +14 -0
  131. data/lib/bel_parser/parser.rb +54 -0
  132. data/lib/bel_parser/parsers/ast/mapped_traversal.rb +36 -0
  133. data/lib/bel_parser/parsers/ast/node.rb +705 -0
  134. data/lib/bel_parser/parsers/ast/sexp.rb +8 -0
  135. data/lib/bel_parser/parsers/ast/traversal.rb +21 -0
  136. data/lib/bel_parser/parsers/bel_script.rb +4 -0
  137. data/lib/bel_parser/parsers/bel_script/define_annotation.rb +5476 -0
  138. data/lib/bel_parser/parsers/bel_script/define_annotation.rl +141 -0
  139. data/lib/bel_parser/parsers/bel_script/define_namespace.rb +1780 -0
  140. data/lib/bel_parser/parsers/bel_script/define_namespace.rl +121 -0
  141. data/lib/bel_parser/parsers/bel_script/set.rb +4556 -0
  142. data/lib/bel_parser/parsers/bel_script/set.rl +116 -0
  143. data/lib/bel_parser/parsers/bel_script/unset.rb +706 -0
  144. data/lib/bel_parser/parsers/bel_script/unset.rl +95 -0
  145. data/lib/bel_parser/parsers/common.rb +5 -0
  146. data/lib/bel_parser/parsers/common/blank_line.rb +211 -0
  147. data/lib/bel_parser/parsers/common/blank_line.rl +81 -0
  148. data/lib/bel_parser/parsers/common/comment_line.rb +245 -0
  149. data/lib/bel_parser/parsers/common/comment_line.rl +97 -0
  150. data/lib/bel_parser/parsers/common/common.rb +7 -0
  151. data/lib/bel_parser/parsers/common/common.rl +13 -0
  152. data/lib/bel_parser/parsers/common/identifier.rb +289 -0
  153. data/lib/bel_parser/parsers/common/identifier.rl +106 -0
  154. data/lib/bel_parser/parsers/common/list.rb +2142 -0
  155. data/lib/bel_parser/parsers/common/list.rl +144 -0
  156. data/lib/bel_parser/parsers/common/string.rb +271 -0
  157. data/lib/bel_parser/parsers/common/string.rl +107 -0
  158. data/lib/bel_parser/parsers/expression.rb +7 -0
  159. data/lib/bel_parser/parsers/expression/comment.rb +239 -0
  160. data/lib/bel_parser/parsers/expression/comment.rl +97 -0
  161. data/lib/bel_parser/parsers/expression/parameter.rb +1506 -0
  162. data/lib/bel_parser/parsers/expression/parameter.rl +97 -0
  163. data/lib/bel_parser/parsers/expression/relationship.rb +254 -0
  164. data/lib/bel_parser/parsers/expression/relationship.rl +98 -0
  165. data/lib/bel_parser/parsers/expression/statement_nested.rb +17802 -0
  166. data/lib/bel_parser/parsers/expression/statement_nested.rl +141 -0
  167. data/lib/bel_parser/parsers/expression/statement_observed_term.rb +7291 -0
  168. data/lib/bel_parser/parsers/expression/statement_observed_term.rl +92 -0
  169. data/lib/bel_parser/parsers/expression/statement_simple.rb +10475 -0
  170. data/lib/bel_parser/parsers/expression/statement_simple.rl +112 -0
  171. data/lib/bel_parser/parsers/expression/term.rb +3989 -0
  172. data/lib/bel_parser/parsers/expression/term.rl +157 -0
  173. data/lib/bel_parser/parsers/line_parser.rb +92 -0
  174. data/lib/bel_parser/parsers/mixin/buffer.rb +10 -0
  175. data/lib/bel_parser/parsers/nonblocking_io_wrapper.rb +50 -0
  176. data/lib/bel_parser/script/parser.rb +49 -0
  177. data/lib/bel_parser/vendor/ast.rb +17 -0
  178. data/lib/bel_parser/vendor/ast/node.rb +254 -0
  179. data/lib/bel_parser/vendor/ast/processor.rb +12 -0
  180. data/lib/bel_parser/vendor/ast/processor/mixin.rb +282 -0
  181. data/lib/bel_parser/vendor/ast/sexp.rb +30 -0
  182. metadata +226 -0
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data/.gemspec ADDED
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+ Gem::Specification.new do |spec|
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+ spec.name = 'bel_parser'
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+ spec.version = File.read(
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+ File.join(
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+ File.expand_path(File.dirname(__FILE__)),
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+ 'VERSION'))
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+ spec.summary = %q{Parser for Biolgical Expression Language.}
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+ spec.description = %q{Implements language versions 1.0 and 2.0.}
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+ spec.license = 'Apache-2.0'
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+ spec.authors = [
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+ 'Anthony Bargnesi',
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+ 'Nick Bargnesi',
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+ ]
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+ spec.date = %q{2016-04-05}
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+ spec.email = %q{abargnesi@selventa.com}
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+ spec.files = [
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+ Dir.glob('lib/**/*.{rb,rl}'),
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+ __FILE__,
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+ 'VERSION',
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+ 'CHANGELOG.md',
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+ 'LICENSE',
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+ 'README.md'
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+ ].flatten!
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+ spec.executables = Dir.glob('bin/*').map(&File.method(:basename))
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+ spec.homepage = 'https://github.com/OpenBEL/bel_parser'
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+ spec.require_paths = ['lib']
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+ spec.required_ruby_version = '>= 2.0.0'
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+ end
data/CHANGELOG.md ADDED
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+ # Change Log
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+ All notable changes to bel_parser will be documented in this file. The curated log begins at changes to version 1.0.0.
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+
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+ This project adheres to [Semantic Versioning](http://semver.org/).
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+
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+ ## [1.0.0][1.0.0] - TBD
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+
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+ ### Added
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+
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+ [1.0.0]: https://github.com/OpenBEL/bel_parser/compare/0.0.0...1.0.0
data/LICENSE ADDED
@@ -0,0 +1,191 @@
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+ Apache License
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+ Version 2.0, January 2004
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+ http://www.apache.org/licenses/
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+
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data/README.md ADDED
@@ -0,0 +1,9 @@
1
+ # bel_parser
2
+
3
+ Parser for BEL expressions and the BEL Script document format.
4
+
5
+ ### Installation
6
+
7
+ ### Getting Started
8
+
9
+ ### Design
data/VERSION ADDED
@@ -0,0 +1 @@
1
+ 1.0.0.alpha.1
@@ -0,0 +1,39 @@
1
+ #!/usr/bin/env ruby
2
+ $:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
3
+
4
+ require 'bel_parser'
5
+ require 'bel_parser/language/version2'
6
+ require 'bel_parser/language/semantics/analyzer'
7
+
8
+ module BELParser
9
+ module Expression
10
+ # Parser for BEL Expression.
11
+ class TermSemanticsParser
12
+ include BELParser::Parsers::Common
13
+ include BELParser::Parsers::Expression
14
+
15
+ FILTER = BELParser::ASTFilter.new(:term)
16
+
17
+ def each(io)
18
+ if block_given?
19
+ v2 = BELParser::Language::Version2::Specification.new
20
+ filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
21
+ filtered_ast.each do |results|
22
+ term = results.last.first
23
+ yield BELParser::Language::Semantics.check_term(term, v2)
24
+ end
25
+ else
26
+ enum_for(:each, io)
27
+ end
28
+ end
29
+ end
30
+ end
31
+ end
32
+
33
+ BELParser::Expression::TermSemanticsParser.new.each($stdin) do |signature|
34
+ valid_signatures = signature.compact
35
+ puts 'Signatures:'
36
+ valid_signatures.each do |sig|
37
+ puts " #{sig}"
38
+ end
39
+ end
data/lib/bel_parser.rb ADDED
@@ -0,0 +1,17 @@
1
+ # vendored 'ast' gem
2
+ require 'bel_parser/vendor/ast'
3
+
4
+ # AST model
5
+ require 'bel_parser/parsers/ast/node'
6
+
7
+ # ragel parsers
8
+ require 'bel_parser/parsers/common'
9
+ require 'bel_parser/parsers/expression'
10
+ require 'bel_parser/parsers/bel_script'
11
+
12
+ # AST processors
13
+ require 'bel_parser/ast_generator'
14
+ require 'bel_parser/ast_filter'
15
+
16
+ # Language; version-independent classes
17
+ require 'bel_parser/language'
@@ -0,0 +1,27 @@
1
+ require_relative 'parsers/ast/node'
2
+
3
+ module BELParser
4
+ # ASTFilter filters types of {BELParser::Parsers::AST::Node}.
5
+ class ASTFilter
6
+ def initialize(*types)
7
+ @types = types
8
+ end
9
+
10
+ def each(ast_source)
11
+ if block_given?
12
+ ast_source.each do |(line_number, line, ast_results)|
13
+ selected = filter(ast_results)
14
+ yield([line_number, line, selected]) unless selected.empty?
15
+ end
16
+ else
17
+ enum_for(:each, ast_source)
18
+ end
19
+ end
20
+
21
+ def filter(ast_enum)
22
+ ast_enum.select do |node|
23
+ @types.include?(node.type)
24
+ end
25
+ end
26
+ end
27
+ end
@@ -0,0 +1,86 @@
1
+ require_relative 'parsers/common'
2
+ require_relative 'parsers/expression'
3
+ require_relative 'parsers/bel_script'
4
+ require_relative 'mixin/line_mapping'
5
+ require_relative 'mixin/line_continuator'
6
+
7
+ module BELParser
8
+ # ASTGenerator yields AST results for each line in some {IO}.
9
+ # See #{ASTGenerator#each}.
10
+ class ASTGenerator
11
+ include LineMapping
12
+ include LineContinuator
13
+
14
+ map_const = ->(x) { x.constants.map { |c| x.const_get(c) } }
15
+ PARSERS = [
16
+ map_const.call(BELParser::Parsers::Common),
17
+ map_const.call(BELParser::Parsers::Expression),
18
+ map_const.call(BELParser::Parsers::BELScript)
19
+ ].flatten!
20
+
21
+ # Yields AST results for each line of the IO.
22
+ #
23
+ # @example Receive AST results in given block.
24
+ # # doctest setup
25
+ # require 'bel_parser'
26
+ # self.class.include AST::Sexp
27
+ #
28
+ # # example usage
29
+ # line_io = StringIO.new("\"AKT1\"\n")
30
+ # line = nil
31
+ # ast_res = nil
32
+ # ::BELParser::ASTGenerator.new.each(line_io) { |(line_number, line, results)|
33
+ # # do something
34
+ # }
35
+ #
36
+ # @example Receive AST results as an enumerator.
37
+ # # doctest setup
38
+ # require 'bel_parser'
39
+ # self.class.include AST::Sexp
40
+ #
41
+ # # example usage
42
+ # line_io = StringIO.new("\"AKT1\"\n")
43
+ # line, ast_res = ::BELParser::ASTGenerator.new.each(line_io).first.to_a
44
+ #
45
+ # @param [IO] io the IO-object to read each line from
46
+ # @yield [[Integer, String, Array<AST::Node>]] yields line number, line,
47
+ # and AST results as an {Array}
48
+ # @return [IO, #<Enumerator: #<BELParser::ASTGenerator#each>] the {IO}
49
+ # object is returned if a block is given, otherwise an
50
+ # {Enumerator} object is returned that can be iterated
51
+ # with {Enumerator#each}
52
+ def each(io) # rubocop:disable MethodLength
53
+ if block_given?
54
+ line_enumerator = map_lines(io.each_line.lazy)
55
+
56
+ line_number = 1
57
+ loop do
58
+ begin
59
+ line = expand_line_continuator(line_enumerator)
60
+
61
+ ast_results = []
62
+ PARSERS.map do |parser|
63
+ parser.parse(line) { |ast| ast_results << ast }
64
+ end
65
+ yield([line_number, line, ast_results])
66
+ line_number += 1
67
+ rescue StopIteration
68
+ return
69
+ end
70
+ end
71
+ else
72
+ enum_for(:each, io)
73
+ end
74
+ end
75
+ end
76
+ end
77
+
78
+ if __FILE__ == $PROGRAM_NAME
79
+ BELParser::ASTGenerator.new.each($stdin) do |line_results|
80
+ line_number, line, ast_results = line_results
81
+ puts "#{line_number}: #{line}"
82
+ ast_results.each do |ast|
83
+ puts ast.to_s(1)
84
+ end
85
+ end
86
+ end
@@ -0,0 +1,40 @@
1
+ require_relative 'ast_generator'
2
+ require_relative 'parsers/ast/node'
3
+ require_relative 'parsers/ast/sexp'
4
+ require_relative 'parsers/ast/mapped_traversal'
5
+
6
+ module BELParser
7
+ # ASTValidator applies observers to an AST traversal.
8
+ class ASTValidator
9
+ def initialize(observers: [])
10
+ @observers = observers
11
+ end
12
+
13
+ def each(ast_source, &block)
14
+ if block_given?
15
+ traversal = observable_traversal
16
+ ast_source.each do |(line_number, line, ast_results)|
17
+ traverse(traversal, line_number, line, ast_results, &block)
18
+ end
19
+ else
20
+ enum_for(:each, ast_source)
21
+ end
22
+ end
23
+
24
+ def traverse(traversal, line_number, line, ast_results)
25
+ ast_results.each do |ast|
26
+ traversal.traverse(ast) do |node, results|
27
+ yield([line_number, line, node, (results && results.compact)])
28
+ end
29
+ end
30
+ end
31
+
32
+ def observable_traversal
33
+ traversal = BELParser::Parsers::AST::MappedTraversal.new
34
+ @observers.each do |observer|
35
+ traversal.add_observer(observer)
36
+ end
37
+ traversal
38
+ end
39
+ end
40
+ end