bel_parser 1.0.0.alpha.5 → 1.0.0.alpha.6
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- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bin/bel2_validator +2 -2
- data/lib/bel_parser/expression/parser.rb +1 -1
- data/lib/bel_parser/expression/{term_validator.rb → validator.rb} +8 -3
- data/lib/bel_parser/language/expression_validator.rb +12 -36
- data/lib/bel_parser/language/semantics/signature_mapping.rb +10 -14
- data/lib/bel_parser/language/syntax/invalid_function.rb +11 -10
- data/lib/bel_parser/language/syntax/invalid_relationship.rb +42 -0
- data/lib/bel_parser/language/syntax/undefined_namespace.rb +12 -18
- data/lib/bel_parser/language/version1_0/return_types/molecular_activity.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/protein_abundance.rb +9 -19
- data/lib/bel_parser/parser.rb +1 -1
- data/lib/bel_parser/parsers/ast/node.rb +53 -7
- data/lib/bel_parser/parsers/expression/{statement_nested.rb → nested_statement.rb} +58 -58
- data/lib/bel_parser/parsers/expression/{statement_nested.rl → nested_statement.rl} +6 -6
- data/lib/bel_parser/parsers/expression/{statement_observed_term.rb → observed_term.rb} +14 -14
- data/lib/bel_parser/parsers/expression/{statement_observed_term.rl → observed_term.rl} +5 -5
- data/lib/bel_parser/parsers/expression/{statement_simple.rb → simple_statement.rb} +37 -37
- data/lib/bel_parser/parsers/expression/{statement_simple.rl → simple_statement.rl} +6 -6
- data/lib/bel_parser/parsers/expression.rb +3 -3
- data/lib/bel_parser/parsers/line_parser.rb +3 -3
- data/lib/bel_parser/script/parser.rb +1 -1
- metadata +9 -8
@@ -869,9 +869,9 @@ class << self
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end
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self.bel_en_comment = 77;
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class << self
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attr_accessor :
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+
attr_accessor :bel_en_simple_statement
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end
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-
self.
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self.bel_en_simple_statement = 1;
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begin
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@@ -1004,7 +1004,7 @@ begin
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begin
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@buffers[:comment] ||= comment(nil)
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-
yield
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+
yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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begin
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@buffers[:comment] ||= comment(nil)
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-
yield
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+
yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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begin
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@buffers[:comment] ||= comment(nil)
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-
yield
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+
yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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@@ -2355,9 +2355,9 @@ class << self
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end
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self.bel_en_comment = 77;
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class << self
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attr_accessor :
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+
attr_accessor :bel_en_simple_statement
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end
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self.
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self.bel_en_simple_statement = 1;
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begin
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begin
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@buffers[:comment] ||= comment(nil)
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yield
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yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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begin
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@buffers[:comment] ||= comment(nil)
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yield
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yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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begin
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@buffers[:comment] ||= comment(nil)
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yield
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yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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end
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self.bel_en_comment = 77;
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class << self
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attr_accessor :
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attr_accessor :bel_en_simple_statement
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end
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self.
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self.bel_en_simple_statement = 1;
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begin
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@@ -3976,7 +3976,7 @@ begin
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begin
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@buffers[:comment] ||= comment(nil)
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yield
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yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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begin
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@buffers[:comment] ||= comment(nil)
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yield
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yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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begin
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@buffers[:comment] ||= comment(nil)
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yield
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yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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@@ -5327,9 +5327,9 @@ class << self
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end
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self.bel_en_comment = 77;
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class << self
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attr_accessor :
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attr_accessor :bel_en_simple_statement
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end
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self.
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self.bel_en_simple_statement = 1;
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begin
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@@ -5462,7 +5462,7 @@ begin
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begin
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@buffers[:comment] ||= comment(nil)
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yield
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yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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begin
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@buffers[:comment] ||= comment(nil)
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-
yield
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+
yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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@@ -5663,7 +5663,7 @@ begin
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begin
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@buffers[:comment] ||= comment(nil)
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-
yield
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+
yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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@@ -6813,9 +6813,9 @@ class << self
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end
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self.bel_en_comment = 77;
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class << self
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-
attr_accessor :
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+
attr_accessor :bel_en_simple_statement
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end
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self.
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self.bel_en_simple_statement = 1;
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begin
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@@ -6948,7 +6948,7 @@ begin
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begin
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@buffers[:comment] ||= comment(nil)
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-
yield
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+
yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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begin
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@buffers[:comment] ||= comment(nil)
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-
yield
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yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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begin
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@buffers[:comment] ||= comment(nil)
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yield
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yield simple_statement(
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statement(
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@buffers[:relationship],
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end
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self.bel_en_comment = 77;
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class << self
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attr_accessor :
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attr_accessor :bel_en_simple_statement
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end
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self.
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self.bel_en_simple_statement = 1;
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begin
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@@ -8434,7 +8434,7 @@ begin
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begin
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@buffers[:comment] ||= comment(nil)
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yield
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yield simple_statement(
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statement(
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@buffers[:relationship],
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begin
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@buffers[:comment] ||= comment(nil)
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yield
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yield simple_statement(
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statement(
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@buffers[:relationship],
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begin
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@buffers[:comment] ||= comment(nil)
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yield
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yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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@@ -8929,7 +8929,7 @@ require_relative '../nonblocking_io_wrapper'
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module BELParser
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module Parsers
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module Expression
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module
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+
module SimpleStatement
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class << self
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end
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self.bel_en_comment = 77;
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class << self
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attr_accessor :
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+
attr_accessor :bel_en_simple_statement
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end
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self.
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self.bel_en_simple_statement = 1;
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# end: ragel
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begin
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@buffers[:comment] ||= comment(nil)
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-
yield
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+
yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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@@ -10155,7 +10155,7 @@ begin
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begin
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@buffers[:comment] ||= comment(nil)
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-
yield
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+
yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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@@ -10172,7 +10172,7 @@ begin
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begin
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@buffers[:comment] ||= comment(nil)
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-
yield
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+
yield simple_statement(
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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@@ -10465,7 +10465,7 @@ end
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if __FILE__ == $0
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$stdin.each_line do |line|
|
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-
BELParser::Parsers::Expression::
|
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+
BELParser::Parsers::Expression::SimpleStatement.parse(line) { |obj|
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puts obj.inspect
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}
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end
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@@ -19,9 +19,9 @@
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@buffers[:term_stack] = nil
|
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}
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-
action
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+
action yield_simple_statement {
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@buffers[:comment] ||= comment(nil)
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-
yield
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+
yield simple_statement(
|
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statement(
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@buffers[:subject],
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@buffers[:relationship],
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@@ -36,10 +36,10 @@
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SP+
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37
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outer_term %statement_object;
|
38
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-
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39
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+
simple_statement :=
|
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STATEMENT_SIMPLE
|
41
41
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SP*
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42
|
-
COMMENT? %
|
42
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+
COMMENT? %yield_simple_statement
|
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NL;
|
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}%%
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=end
|
@@ -52,7 +52,7 @@ require_relative '../nonblocking_io_wrapper'
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|
52
52
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module BELParser
|
53
53
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module Parsers
|
54
54
|
module Expression
|
55
|
-
module
|
55
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+
module SimpleStatement
|
56
56
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|
57
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class << self
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58
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|
@@ -102,7 +102,7 @@ end
|
|
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102
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|
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if __FILE__ == $0
|
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$stdin.each_line do |line|
|
105
|
-
BELParser::Parsers::Expression::
|
105
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+
BELParser::Parsers::Expression::SimpleStatement.parse(line) { |obj|
|
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puts obj.inspect
|
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}
|
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end
|
@@ -2,6 +2,6 @@ require_relative 'expression/parameter'
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|
2
2
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require_relative 'expression/term'
|
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3
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require_relative 'expression/relationship'
|
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4
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require_relative 'expression/comment'
|
5
|
-
require_relative 'expression/
|
6
|
-
require_relative 'expression/
|
7
|
-
require_relative 'expression/
|
5
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+
require_relative 'expression/observed_term'
|
6
|
+
require_relative 'expression/simple_statement'
|
7
|
+
require_relative 'expression/nested_statement'
|
@@ -18,9 +18,9 @@ module LINE
|
|
18
18
|
BELParser::Parsers::Expression::Term,
|
19
19
|
BELParser::Parsers::Expression::Relationship,
|
20
20
|
BELParser::Parsers::Expression::Comment,
|
21
|
-
BELParser::Parsers::Expression::
|
22
|
-
BELParser::Parsers::Expression::
|
23
|
-
BELParser::Parsers::Expression::
|
21
|
+
BELParser::Parsers::Expression::ObservedTerm,
|
22
|
+
BELParser::Parsers::Expression::SimpleStatement,
|
23
|
+
BELParser::Parsers::Expression::NestedStatement,
|
24
24
|
BELParser::Parsers::BELScript::DefineAnnotation,
|
25
25
|
BELParser::Parsers::BELScript::DefineNamespace,
|
26
26
|
BELParser::Parsers::BELScript::Set,
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bel_parser
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.0.0.alpha.
|
4
|
+
version: 1.0.0.alpha.6
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Anthony Bargnesi
|
@@ -29,7 +29,7 @@ files:
|
|
29
29
|
- lib/bel_parser/ast_generator.rb
|
30
30
|
- lib/bel_parser/ast_validator.rb
|
31
31
|
- lib/bel_parser/expression/parser.rb
|
32
|
-
- lib/bel_parser/expression/
|
32
|
+
- lib/bel_parser/expression/validator.rb
|
33
33
|
- lib/bel_parser/language.rb
|
34
34
|
- lib/bel_parser/language/expression_validator.rb
|
35
35
|
- lib/bel_parser/language/function.rb
|
@@ -46,6 +46,7 @@ files:
|
|
46
46
|
- lib/bel_parser/language/specification.rb
|
47
47
|
- lib/bel_parser/language/syntax.rb
|
48
48
|
- lib/bel_parser/language/syntax/invalid_function.rb
|
49
|
+
- lib/bel_parser/language/syntax/invalid_relationship.rb
|
49
50
|
- lib/bel_parser/language/syntax/undefined_namespace.rb
|
50
51
|
- lib/bel_parser/language/syntax_error.rb
|
51
52
|
- lib/bel_parser/language/syntax_function.rb
|
@@ -247,16 +248,16 @@ files:
|
|
247
248
|
- lib/bel_parser/parsers/expression.rb
|
248
249
|
- lib/bel_parser/parsers/expression/comment.rb
|
249
250
|
- lib/bel_parser/parsers/expression/comment.rl
|
251
|
+
- lib/bel_parser/parsers/expression/nested_statement.rb
|
252
|
+
- lib/bel_parser/parsers/expression/nested_statement.rl
|
253
|
+
- lib/bel_parser/parsers/expression/observed_term.rb
|
254
|
+
- lib/bel_parser/parsers/expression/observed_term.rl
|
250
255
|
- lib/bel_parser/parsers/expression/parameter.rb
|
251
256
|
- lib/bel_parser/parsers/expression/parameter.rl
|
252
257
|
- lib/bel_parser/parsers/expression/relationship.rb
|
253
258
|
- lib/bel_parser/parsers/expression/relationship.rl
|
254
|
-
- lib/bel_parser/parsers/expression/
|
255
|
-
- lib/bel_parser/parsers/expression/
|
256
|
-
- lib/bel_parser/parsers/expression/statement_observed_term.rb
|
257
|
-
- lib/bel_parser/parsers/expression/statement_observed_term.rl
|
258
|
-
- lib/bel_parser/parsers/expression/statement_simple.rb
|
259
|
-
- lib/bel_parser/parsers/expression/statement_simple.rl
|
259
|
+
- lib/bel_parser/parsers/expression/simple_statement.rb
|
260
|
+
- lib/bel_parser/parsers/expression/simple_statement.rl
|
260
261
|
- lib/bel_parser/parsers/expression/term.rb
|
261
262
|
- lib/bel_parser/parsers/expression/term.rl
|
262
263
|
- lib/bel_parser/parsers/line_parser.rb
|