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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
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  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
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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
2691
  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
3976
  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
6821
  begin
@@ -6948,7 +6948,7 @@ begin
6948
6948
  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
6954
  @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
7138
  @buffers[:relationship],
@@ -7149,7 +7149,7 @@ begin
7149
7149
  begin
7150
7150
 
7151
7151
  @buffers[:comment] ||= comment(nil)
7152
- yield statement_simple(
7152
+ yield simple_statement(
7153
7153
  statement(
7154
7154
  @buffers[:subject],
7155
7155
  @buffers[:relationship],
@@ -8299,9 +8299,9 @@ class << self
8299
8299
  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
8306
 
8307
8307
  begin
@@ -8434,7 +8434,7 @@ begin
8434
8434
  begin
8435
8435
 
8436
8436
  @buffers[:comment] ||= comment(nil)
8437
- yield statement_simple(
8437
+ yield simple_statement(
8438
8438
  statement(
8439
8439
  @buffers[:subject],
8440
8440
  @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
8624
  @buffers[:relationship],
@@ -8635,7 +8635,7 @@ begin
8635
8635
  begin
8636
8636
 
8637
8637
  @buffers[:comment] ||= comment(nil)
8638
- yield statement_simple(
8638
+ yield simple_statement(
8639
8639
  statement(
8640
8640
  @buffers[:subject],
8641
8641
  @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;
9828
9828
 
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(
9975
9975
  statement(
9976
9976
  @buffers[:subject],
9977
9977
  @buffers[:relationship],
@@ -10155,7 +10155,7 @@ begin
10155
10155
  begin
10156
10156
 
10157
10157
  @buffers[:comment] ||= comment(nil)
10158
- yield statement_simple(
10158
+ yield simple_statement(
10159
10159
  statement(
10160
10160
  @buffers[:subject],
10161
10161
  @buffers[:relationship],
@@ -10172,7 +10172,7 @@ begin
10172
10172
  begin
10173
10173
 
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