bel_parser 1.0.0.alpha.5 → 1.0.0.alpha.6

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Files changed (24) hide show
  1. checksums.yaml +4 -4
  2. data/VERSION +1 -1
  3. data/bin/bel2_validator +2 -2
  4. data/lib/bel_parser/expression/parser.rb +1 -1
  5. data/lib/bel_parser/expression/{term_validator.rb → validator.rb} +8 -3
  6. data/lib/bel_parser/language/expression_validator.rb +12 -36
  7. data/lib/bel_parser/language/semantics/signature_mapping.rb +10 -14
  8. data/lib/bel_parser/language/syntax/invalid_function.rb +11 -10
  9. data/lib/bel_parser/language/syntax/invalid_relationship.rb +42 -0
  10. data/lib/bel_parser/language/syntax/undefined_namespace.rb +12 -18
  11. data/lib/bel_parser/language/version1_0/return_types/molecular_activity.rb +1 -1
  12. data/lib/bel_parser/language/version2_0/functions/protein_abundance.rb +9 -19
  13. data/lib/bel_parser/parser.rb +1 -1
  14. data/lib/bel_parser/parsers/ast/node.rb +53 -7
  15. data/lib/bel_parser/parsers/expression/{statement_nested.rb → nested_statement.rb} +58 -58
  16. data/lib/bel_parser/parsers/expression/{statement_nested.rl → nested_statement.rl} +6 -6
  17. data/lib/bel_parser/parsers/expression/{statement_observed_term.rb → observed_term.rb} +14 -14
  18. data/lib/bel_parser/parsers/expression/{statement_observed_term.rl → observed_term.rl} +5 -5
  19. data/lib/bel_parser/parsers/expression/{statement_simple.rb → simple_statement.rb} +37 -37
  20. data/lib/bel_parser/parsers/expression/{statement_simple.rl → simple_statement.rl} +6 -6
  21. data/lib/bel_parser/parsers/expression.rb +3 -3
  22. data/lib/bel_parser/parsers/line_parser.rb +3 -3
  23. data/lib/bel_parser/script/parser.rb +1 -1
  24. metadata +9 -8
@@ -869,9 +869,9 @@ class << self
869
869
  end
870
870
  self.bel_en_comment = 77;
871
871
  class << self
872
- attr_accessor :bel_en_statement_simple
872
+ attr_accessor :bel_en_simple_statement
873
873
  end
874
- self.bel_en_statement_simple = 1;
874
+ self.bel_en_simple_statement = 1;
875
875
 
876
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877
877
  begin
@@ -1004,7 +1004,7 @@ begin
1004
1004
  begin
1005
1005
 
1006
1006
  @buffers[:comment] ||= comment(nil)
1007
- yield statement_simple(
1007
+ yield simple_statement(
1008
1008
  statement(
1009
1009
  @buffers[:subject],
1010
1010
  @buffers[:relationship],
@@ -1188,7 +1188,7 @@ begin
1188
1188
  begin
1189
1189
 
1190
1190
  @buffers[:comment] ||= comment(nil)
1191
- yield statement_simple(
1191
+ yield simple_statement(
1192
1192
  statement(
1193
1193
  @buffers[:subject],
1194
1194
  @buffers[:relationship],
@@ -1205,7 +1205,7 @@ begin
1205
1205
  begin
1206
1206
 
1207
1207
  @buffers[:comment] ||= comment(nil)
1208
- yield statement_simple(
1208
+ yield simple_statement(
1209
1209
  statement(
1210
1210
  @buffers[:subject],
1211
1211
  @buffers[:relationship],
@@ -2355,9 +2355,9 @@ class << self
2355
2355
  end
2356
2356
  self.bel_en_comment = 77;
2357
2357
  class << self
2358
- attr_accessor :bel_en_statement_simple
2358
+ attr_accessor :bel_en_simple_statement
2359
2359
  end
2360
- self.bel_en_statement_simple = 1;
2360
+ self.bel_en_simple_statement = 1;
2361
2361
 
2362
2362
 
2363
2363
  begin
@@ -2490,7 +2490,7 @@ begin
2490
2490
  begin
2491
2491
 
2492
2492
  @buffers[:comment] ||= comment(nil)
2493
- yield statement_simple(
2493
+ yield simple_statement(
2494
2494
  statement(
2495
2495
  @buffers[:subject],
2496
2496
  @buffers[:relationship],
@@ -2674,7 +2674,7 @@ begin
2674
2674
  begin
2675
2675
 
2676
2676
  @buffers[:comment] ||= comment(nil)
2677
- yield statement_simple(
2677
+ yield simple_statement(
2678
2678
  statement(
2679
2679
  @buffers[:subject],
2680
2680
  @buffers[:relationship],
@@ -2691,7 +2691,7 @@ begin
2691
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  begin
2692
2692
 
2693
2693
  @buffers[:comment] ||= comment(nil)
2694
- yield statement_simple(
2694
+ yield simple_statement(
2695
2695
  statement(
2696
2696
  @buffers[:subject],
2697
2697
  @buffers[:relationship],
@@ -3841,9 +3841,9 @@ class << self
3841
3841
  end
3842
3842
  self.bel_en_comment = 77;
3843
3843
  class << self
3844
- attr_accessor :bel_en_statement_simple
3844
+ attr_accessor :bel_en_simple_statement
3845
3845
  end
3846
- self.bel_en_statement_simple = 1;
3846
+ self.bel_en_simple_statement = 1;
3847
3847
 
3848
3848
 
3849
3849
  begin
@@ -3976,7 +3976,7 @@ begin
3976
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  begin
3977
3977
 
3978
3978
  @buffers[:comment] ||= comment(nil)
3979
- yield statement_simple(
3979
+ yield simple_statement(
3980
3980
  statement(
3981
3981
  @buffers[:subject],
3982
3982
  @buffers[:relationship],
@@ -4160,7 +4160,7 @@ begin
4160
4160
  begin
4161
4161
 
4162
4162
  @buffers[:comment] ||= comment(nil)
4163
- yield statement_simple(
4163
+ yield simple_statement(
4164
4164
  statement(
4165
4165
  @buffers[:subject],
4166
4166
  @buffers[:relationship],
@@ -4177,7 +4177,7 @@ begin
4177
4177
  begin
4178
4178
 
4179
4179
  @buffers[:comment] ||= comment(nil)
4180
- yield statement_simple(
4180
+ yield simple_statement(
4181
4181
  statement(
4182
4182
  @buffers[:subject],
4183
4183
  @buffers[:relationship],
@@ -5327,9 +5327,9 @@ class << self
5327
5327
  end
5328
5328
  self.bel_en_comment = 77;
5329
5329
  class << self
5330
- attr_accessor :bel_en_statement_simple
5330
+ attr_accessor :bel_en_simple_statement
5331
5331
  end
5332
- self.bel_en_statement_simple = 1;
5332
+ self.bel_en_simple_statement = 1;
5333
5333
 
5334
5334
 
5335
5335
  begin
@@ -5462,7 +5462,7 @@ begin
5462
5462
  begin
5463
5463
 
5464
5464
  @buffers[:comment] ||= comment(nil)
5465
- yield statement_simple(
5465
+ yield simple_statement(
5466
5466
  statement(
5467
5467
  @buffers[:subject],
5468
5468
  @buffers[:relationship],
@@ -5646,7 +5646,7 @@ begin
5646
5646
  begin
5647
5647
 
5648
5648
  @buffers[:comment] ||= comment(nil)
5649
- yield statement_simple(
5649
+ yield simple_statement(
5650
5650
  statement(
5651
5651
  @buffers[:subject],
5652
5652
  @buffers[:relationship],
@@ -5663,7 +5663,7 @@ begin
5663
5663
  begin
5664
5664
 
5665
5665
  @buffers[:comment] ||= comment(nil)
5666
- yield statement_simple(
5666
+ yield simple_statement(
5667
5667
  statement(
5668
5668
  @buffers[:subject],
5669
5669
  @buffers[:relationship],
@@ -6813,9 +6813,9 @@ class << self
6813
6813
  end
6814
6814
  self.bel_en_comment = 77;
6815
6815
  class << self
6816
- attr_accessor :bel_en_statement_simple
6816
+ attr_accessor :bel_en_simple_statement
6817
6817
  end
6818
- self.bel_en_statement_simple = 1;
6818
+ self.bel_en_simple_statement = 1;
6819
6819
 
6820
6820
 
6821
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  begin
@@ -6948,7 +6948,7 @@ begin
6948
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  begin
6949
6949
 
6950
6950
  @buffers[:comment] ||= comment(nil)
6951
- yield statement_simple(
6951
+ yield simple_statement(
6952
6952
  statement(
6953
6953
  @buffers[:subject],
6954
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  @buffers[:relationship],
@@ -7132,7 +7132,7 @@ begin
7132
7132
  begin
7133
7133
 
7134
7134
  @buffers[:comment] ||= comment(nil)
7135
- yield statement_simple(
7135
+ yield simple_statement(
7136
7136
  statement(
7137
7137
  @buffers[:subject],
7138
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  @buffers[:relationship],
@@ -7149,7 +7149,7 @@ begin
7149
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  begin
7150
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7151
7151
  @buffers[:comment] ||= comment(nil)
7152
- yield statement_simple(
7152
+ yield simple_statement(
7153
7153
  statement(
7154
7154
  @buffers[:subject],
7155
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  @buffers[:relationship],
@@ -8299,9 +8299,9 @@ class << self
8299
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  end
8300
8300
  self.bel_en_comment = 77;
8301
8301
  class << self
8302
- attr_accessor :bel_en_statement_simple
8302
+ attr_accessor :bel_en_simple_statement
8303
8303
  end
8304
- self.bel_en_statement_simple = 1;
8304
+ self.bel_en_simple_statement = 1;
8305
8305
 
8306
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8307
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  begin
@@ -8434,7 +8434,7 @@ begin
8434
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  begin
8435
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8436
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  @buffers[:comment] ||= comment(nil)
8437
- yield statement_simple(
8437
+ yield simple_statement(
8438
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  statement(
8439
8439
  @buffers[:subject],
8440
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  @buffers[:relationship],
@@ -8618,7 +8618,7 @@ begin
8618
8618
  begin
8619
8619
 
8620
8620
  @buffers[:comment] ||= comment(nil)
8621
- yield statement_simple(
8621
+ yield simple_statement(
8622
8622
  statement(
8623
8623
  @buffers[:subject],
8624
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  @buffers[:relationship],
@@ -8635,7 +8635,7 @@ begin
8635
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  begin
8636
8636
 
8637
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  @buffers[:comment] ||= comment(nil)
8638
- yield statement_simple(
8638
+ yield simple_statement(
8639
8639
  statement(
8640
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  @buffers[:subject],
8641
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  @buffers[:relationship],
@@ -8929,7 +8929,7 @@ require_relative '../nonblocking_io_wrapper'
8929
8929
  module BELParser
8930
8930
  module Parsers
8931
8931
  module Expression
8932
- module StatementSimple
8932
+ module SimpleStatement
8933
8933
 
8934
8934
  class << self
8935
8935
 
@@ -9822,9 +9822,9 @@ class << self
9822
9822
  end
9823
9823
  self.bel_en_comment = 77;
9824
9824
  class << self
9825
- attr_accessor :bel_en_statement_simple
9825
+ attr_accessor :bel_en_simple_statement
9826
9826
  end
9827
- self.bel_en_statement_simple = 1;
9827
+ self.bel_en_simple_statement = 1;
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9829
9829
 
9830
9830
  # end: ragel
@@ -9971,7 +9971,7 @@ begin
9971
9971
  begin
9972
9972
 
9973
9973
  @buffers[:comment] ||= comment(nil)
9974
- yield statement_simple(
9974
+ yield simple_statement(
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9975
  statement(
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  @buffers[:subject],
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  @buffers[:relationship],
@@ -10155,7 +10155,7 @@ begin
10155
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  begin
10156
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10157
10157
  @buffers[:comment] ||= comment(nil)
10158
- yield statement_simple(
10158
+ yield simple_statement(
10159
10159
  statement(
10160
10160
  @buffers[:subject],
10161
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  @buffers[:relationship],
@@ -10172,7 +10172,7 @@ begin
10172
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  begin
10173
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10174
10174
  @buffers[:comment] ||= comment(nil)
10175
- yield statement_simple(
10175
+ yield simple_statement(
10176
10176
  statement(
10177
10177
  @buffers[:subject],
10178
10178
  @buffers[:relationship],
@@ -10465,7 +10465,7 @@ end
10465
10465
 
10466
10466
  if __FILE__ == $0
10467
10467
  $stdin.each_line do |line|
10468
- BELParser::Parsers::Expression::StatementSimple.parse(line) { |obj|
10468
+ BELParser::Parsers::Expression::SimpleStatement.parse(line) { |obj|
10469
10469
  puts obj.inspect
10470
10470
  }
10471
10471
  end
@@ -19,9 +19,9 @@
19
19
  @buffers[:term_stack] = nil
20
20
  }
21
21
 
22
- action yield_statement_simple {
22
+ action yield_simple_statement {
23
23
  @buffers[:comment] ||= comment(nil)
24
- yield statement_simple(
24
+ yield simple_statement(
25
25
  statement(
26
26
  @buffers[:subject],
27
27
  @buffers[:relationship],
@@ -36,10 +36,10 @@
36
36
  SP+
37
37
  outer_term %statement_object;
38
38
 
39
- statement_simple :=
39
+ simple_statement :=
40
40
  STATEMENT_SIMPLE
41
41
  SP*
42
- COMMENT? %yield_statement_simple
42
+ COMMENT? %yield_simple_statement
43
43
  NL;
44
44
  }%%
45
45
  =end
@@ -52,7 +52,7 @@ require_relative '../nonblocking_io_wrapper'
52
52
  module BELParser
53
53
  module Parsers
54
54
  module Expression
55
- module StatementSimple
55
+ module SimpleStatement
56
56
 
57
57
  class << self
58
58
 
@@ -102,7 +102,7 @@ end
102
102
 
103
103
  if __FILE__ == $0
104
104
  $stdin.each_line do |line|
105
- BELParser::Parsers::Expression::StatementSimple.parse(line) { |obj|
105
+ BELParser::Parsers::Expression::SimpleStatement.parse(line) { |obj|
106
106
  puts obj.inspect
107
107
  }
108
108
  end
@@ -2,6 +2,6 @@ require_relative 'expression/parameter'
2
2
  require_relative 'expression/term'
3
3
  require_relative 'expression/relationship'
4
4
  require_relative 'expression/comment'
5
- require_relative 'expression/statement_observed_term'
6
- require_relative 'expression/statement_simple'
7
- require_relative 'expression/statement_nested'
5
+ 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::StatementObservedTerm,
22
- BELParser::Parsers::Expression::StatementSimple,
23
- BELParser::Parsers::Expression::StatementNested,
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,
@@ -13,7 +13,7 @@ module BELParser
13
13
  include BELParser::Parsers::BELScript
14
14
 
15
15
  FILTER = BELParser::ASTFilter.new(
16
- :statement_simple,
16
+ :simple_statement,
17
17
  :observed_term,
18
18
  :nested_statement,
19
19
  :define_annotation,
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.5
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/term_validator.rb
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/statement_nested.rb
255
- - lib/bel_parser/parsers/expression/statement_nested.rl
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