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
@@ -1379,17 +1379,17 @@ class << self
1379
1379
  end
1380
1380
  self.bel_en_comment = 65;
1381
1381
  class << self
1382
- attr_accessor :bel_en_statement_simple
1382
+ attr_accessor :bel_en_simple_statement
1383
1383
  end
1384
- self.bel_en_statement_simple = 69;
1384
+ self.bel_en_simple_statement = 69;
1385
1385
  class << self
1386
1386
  attr_accessor :bel_en_inner_statement
1387
1387
  end
1388
1388
  self.bel_en_inner_statement = 103;
1389
1389
  class << self
1390
- attr_accessor :bel_en_statement_nested
1390
+ attr_accessor :bel_en_nested_statement
1391
1391
  end
1392
- self.bel_en_statement_nested = 1;
1392
+ self.bel_en_nested_statement = 1;
1393
1393
 
1394
1394
 
1395
1395
  begin
@@ -1522,7 +1522,7 @@ begin
1522
1522
  begin
1523
1523
 
1524
1524
  @buffers[:comment] ||= comment(nil)
1525
- yield statement_simple(
1525
+ yield simple_statement(
1526
1526
  statement(
1527
1527
  @buffers[:subject],
1528
1528
  @buffers[:relationship],
@@ -1747,7 +1747,7 @@ begin
1747
1747
  begin
1748
1748
 
1749
1749
  @buffers[:comment] ||= comment(nil)
1750
- yield statement_simple(
1750
+ yield simple_statement(
1751
1751
  statement(
1752
1752
  @buffers[:subject],
1753
1753
  @buffers[:relationship],
@@ -1785,7 +1785,7 @@ begin
1785
1785
  begin
1786
1786
 
1787
1787
  @buffers[:comment] ||= comment(nil)
1788
- yield statement_simple(
1788
+ yield simple_statement(
1789
1789
  statement(
1790
1790
  @buffers[:subject],
1791
1791
  @buffers[:relationship],
@@ -3595,17 +3595,17 @@ class << self
3595
3595
  end
3596
3596
  self.bel_en_comment = 65;
3597
3597
  class << self
3598
- attr_accessor :bel_en_statement_simple
3598
+ attr_accessor :bel_en_simple_statement
3599
3599
  end
3600
- self.bel_en_statement_simple = 69;
3600
+ self.bel_en_simple_statement = 69;
3601
3601
  class << self
3602
3602
  attr_accessor :bel_en_inner_statement
3603
3603
  end
3604
3604
  self.bel_en_inner_statement = 103;
3605
3605
  class << self
3606
- attr_accessor :bel_en_statement_nested
3606
+ attr_accessor :bel_en_nested_statement
3607
3607
  end
3608
- self.bel_en_statement_nested = 1;
3608
+ self.bel_en_nested_statement = 1;
3609
3609
 
3610
3610
 
3611
3611
  begin
@@ -3738,7 +3738,7 @@ begin
3738
3738
  begin
3739
3739
 
3740
3740
  @buffers[:comment] ||= comment(nil)
3741
- yield statement_simple(
3741
+ yield simple_statement(
3742
3742
  statement(
3743
3743
  @buffers[:subject],
3744
3744
  @buffers[:relationship],
@@ -3963,7 +3963,7 @@ begin
3963
3963
  begin
3964
3964
 
3965
3965
  @buffers[:comment] ||= comment(nil)
3966
- yield statement_simple(
3966
+ yield simple_statement(
3967
3967
  statement(
3968
3968
  @buffers[:subject],
3969
3969
  @buffers[:relationship],
@@ -4001,7 +4001,7 @@ begin
4001
4001
  begin
4002
4002
 
4003
4003
  @buffers[:comment] ||= comment(nil)
4004
- yield statement_simple(
4004
+ yield simple_statement(
4005
4005
  statement(
4006
4006
  @buffers[:subject],
4007
4007
  @buffers[:relationship],
@@ -5811,17 +5811,17 @@ class << self
5811
5811
  end
5812
5812
  self.bel_en_comment = 65;
5813
5813
  class << self
5814
- attr_accessor :bel_en_statement_simple
5814
+ attr_accessor :bel_en_simple_statement
5815
5815
  end
5816
- self.bel_en_statement_simple = 69;
5816
+ self.bel_en_simple_statement = 69;
5817
5817
  class << self
5818
5818
  attr_accessor :bel_en_inner_statement
5819
5819
  end
5820
5820
  self.bel_en_inner_statement = 103;
5821
5821
  class << self
5822
- attr_accessor :bel_en_statement_nested
5822
+ attr_accessor :bel_en_nested_statement
5823
5823
  end
5824
- self.bel_en_statement_nested = 1;
5824
+ self.bel_en_nested_statement = 1;
5825
5825
 
5826
5826
 
5827
5827
  begin
@@ -5954,7 +5954,7 @@ begin
5954
5954
  begin
5955
5955
 
5956
5956
  @buffers[:comment] ||= comment(nil)
5957
- yield statement_simple(
5957
+ yield simple_statement(
5958
5958
  statement(
5959
5959
  @buffers[:subject],
5960
5960
  @buffers[:relationship],
@@ -6179,7 +6179,7 @@ begin
6179
6179
  begin
6180
6180
 
6181
6181
  @buffers[:comment] ||= comment(nil)
6182
- yield statement_simple(
6182
+ yield simple_statement(
6183
6183
  statement(
6184
6184
  @buffers[:subject],
6185
6185
  @buffers[:relationship],
@@ -6217,7 +6217,7 @@ begin
6217
6217
  begin
6218
6218
 
6219
6219
  @buffers[:comment] ||= comment(nil)
6220
- yield statement_simple(
6220
+ yield simple_statement(
6221
6221
  statement(
6222
6222
  @buffers[:subject],
6223
6223
  @buffers[:relationship],
@@ -8027,17 +8027,17 @@ class << self
8027
8027
  end
8028
8028
  self.bel_en_comment = 65;
8029
8029
  class << self
8030
- attr_accessor :bel_en_statement_simple
8030
+ attr_accessor :bel_en_simple_statement
8031
8031
  end
8032
- self.bel_en_statement_simple = 69;
8032
+ self.bel_en_simple_statement = 69;
8033
8033
  class << self
8034
8034
  attr_accessor :bel_en_inner_statement
8035
8035
  end
8036
8036
  self.bel_en_inner_statement = 103;
8037
8037
  class << self
8038
- attr_accessor :bel_en_statement_nested
8038
+ attr_accessor :bel_en_nested_statement
8039
8039
  end
8040
- self.bel_en_statement_nested = 1;
8040
+ self.bel_en_nested_statement = 1;
8041
8041
 
8042
8042
 
8043
8043
  begin
@@ -8170,7 +8170,7 @@ begin
8170
8170
  begin
8171
8171
 
8172
8172
  @buffers[:comment] ||= comment(nil)
8173
- yield statement_simple(
8173
+ yield simple_statement(
8174
8174
  statement(
8175
8175
  @buffers[:subject],
8176
8176
  @buffers[:relationship],
@@ -8395,7 +8395,7 @@ begin
8395
8395
  begin
8396
8396
 
8397
8397
  @buffers[:comment] ||= comment(nil)
8398
- yield statement_simple(
8398
+ yield simple_statement(
8399
8399
  statement(
8400
8400
  @buffers[:subject],
8401
8401
  @buffers[:relationship],
@@ -8433,7 +8433,7 @@ begin
8433
8433
  begin
8434
8434
 
8435
8435
  @buffers[:comment] ||= comment(nil)
8436
- yield statement_simple(
8436
+ yield simple_statement(
8437
8437
  statement(
8438
8438
  @buffers[:subject],
8439
8439
  @buffers[:relationship],
@@ -10243,17 +10243,17 @@ class << self
10243
10243
  end
10244
10244
  self.bel_en_comment = 65;
10245
10245
  class << self
10246
- attr_accessor :bel_en_statement_simple
10246
+ attr_accessor :bel_en_simple_statement
10247
10247
  end
10248
- self.bel_en_statement_simple = 69;
10248
+ self.bel_en_simple_statement = 69;
10249
10249
  class << self
10250
10250
  attr_accessor :bel_en_inner_statement
10251
10251
  end
10252
10252
  self.bel_en_inner_statement = 103;
10253
10253
  class << self
10254
- attr_accessor :bel_en_statement_nested
10254
+ attr_accessor :bel_en_nested_statement
10255
10255
  end
10256
- self.bel_en_statement_nested = 1;
10256
+ self.bel_en_nested_statement = 1;
10257
10257
 
10258
10258
 
10259
10259
  begin
@@ -10386,7 +10386,7 @@ begin
10386
10386
  begin
10387
10387
 
10388
10388
  @buffers[:comment] ||= comment(nil)
10389
- yield statement_simple(
10389
+ yield simple_statement(
10390
10390
  statement(
10391
10391
  @buffers[:subject],
10392
10392
  @buffers[:relationship],
@@ -10611,7 +10611,7 @@ begin
10611
10611
  begin
10612
10612
 
10613
10613
  @buffers[:comment] ||= comment(nil)
10614
- yield statement_simple(
10614
+ yield simple_statement(
10615
10615
  statement(
10616
10616
  @buffers[:subject],
10617
10617
  @buffers[:relationship],
@@ -10649,7 +10649,7 @@ begin
10649
10649
  begin
10650
10650
 
10651
10651
  @buffers[:comment] ||= comment(nil)
10652
- yield statement_simple(
10652
+ yield simple_statement(
10653
10653
  statement(
10654
10654
  @buffers[:subject],
10655
10655
  @buffers[:relationship],
@@ -12459,17 +12459,17 @@ class << self
12459
12459
  end
12460
12460
  self.bel_en_comment = 65;
12461
12461
  class << self
12462
- attr_accessor :bel_en_statement_simple
12462
+ attr_accessor :bel_en_simple_statement
12463
12463
  end
12464
- self.bel_en_statement_simple = 69;
12464
+ self.bel_en_simple_statement = 69;
12465
12465
  class << self
12466
12466
  attr_accessor :bel_en_inner_statement
12467
12467
  end
12468
12468
  self.bel_en_inner_statement = 103;
12469
12469
  class << self
12470
- attr_accessor :bel_en_statement_nested
12470
+ attr_accessor :bel_en_nested_statement
12471
12471
  end
12472
- self.bel_en_statement_nested = 1;
12472
+ self.bel_en_nested_statement = 1;
12473
12473
 
12474
12474
 
12475
12475
  begin
@@ -12602,7 +12602,7 @@ begin
12602
12602
  begin
12603
12603
 
12604
12604
  @buffers[:comment] ||= comment(nil)
12605
- yield statement_simple(
12605
+ yield simple_statement(
12606
12606
  statement(
12607
12607
  @buffers[:subject],
12608
12608
  @buffers[:relationship],
@@ -12827,7 +12827,7 @@ begin
12827
12827
  begin
12828
12828
 
12829
12829
  @buffers[:comment] ||= comment(nil)
12830
- yield statement_simple(
12830
+ yield simple_statement(
12831
12831
  statement(
12832
12832
  @buffers[:subject],
12833
12833
  @buffers[:relationship],
@@ -12865,7 +12865,7 @@ begin
12865
12865
  begin
12866
12866
 
12867
12867
  @buffers[:comment] ||= comment(nil)
12868
- yield statement_simple(
12868
+ yield simple_statement(
12869
12869
  statement(
12870
12870
  @buffers[:subject],
12871
12871
  @buffers[:relationship],
@@ -14675,17 +14675,17 @@ class << self
14675
14675
  end
14676
14676
  self.bel_en_comment = 65;
14677
14677
  class << self
14678
- attr_accessor :bel_en_statement_simple
14678
+ attr_accessor :bel_en_simple_statement
14679
14679
  end
14680
- self.bel_en_statement_simple = 69;
14680
+ self.bel_en_simple_statement = 69;
14681
14681
  class << self
14682
14682
  attr_accessor :bel_en_inner_statement
14683
14683
  end
14684
14684
  self.bel_en_inner_statement = 103;
14685
14685
  class << self
14686
- attr_accessor :bel_en_statement_nested
14686
+ attr_accessor :bel_en_nested_statement
14687
14687
  end
14688
- self.bel_en_statement_nested = 1;
14688
+ self.bel_en_nested_statement = 1;
14689
14689
 
14690
14690
 
14691
14691
  begin
@@ -14818,7 +14818,7 @@ begin
14818
14818
  begin
14819
14819
 
14820
14820
  @buffers[:comment] ||= comment(nil)
14821
- yield statement_simple(
14821
+ yield simple_statement(
14822
14822
  statement(
14823
14823
  @buffers[:subject],
14824
14824
  @buffers[:relationship],
@@ -15043,7 +15043,7 @@ begin
15043
15043
  begin
15044
15044
 
15045
15045
  @buffers[:comment] ||= comment(nil)
15046
- yield statement_simple(
15046
+ yield simple_statement(
15047
15047
  statement(
15048
15048
  @buffers[:subject],
15049
15049
  @buffers[:relationship],
@@ -15081,7 +15081,7 @@ begin
15081
15081
  begin
15082
15082
 
15083
15083
  @buffers[:comment] ||= comment(nil)
15084
- yield statement_simple(
15084
+ yield simple_statement(
15085
15085
  statement(
15086
15086
  @buffers[:subject],
15087
15087
  @buffers[:relationship],
@@ -15525,7 +15525,7 @@ require_relative '../nonblocking_io_wrapper'
15525
15525
  module BELParser
15526
15526
  module Parsers
15527
15527
  module Expression
15528
- module StatementNested
15528
+ module NestedStatement
15529
15529
 
15530
15530
  class << self
15531
15531
 
@@ -16928,17 +16928,17 @@ class << self
16928
16928
  end
16929
16929
  self.bel_en_comment = 65;
16930
16930
  class << self
16931
- attr_accessor :bel_en_statement_simple
16931
+ attr_accessor :bel_en_simple_statement
16932
16932
  end
16933
- self.bel_en_statement_simple = 69;
16933
+ self.bel_en_simple_statement = 69;
16934
16934
  class << self
16935
16935
  attr_accessor :bel_en_inner_statement
16936
16936
  end
16937
16937
  self.bel_en_inner_statement = 103;
16938
16938
  class << self
16939
- attr_accessor :bel_en_statement_nested
16939
+ attr_accessor :bel_en_nested_statement
16940
16940
  end
16941
- self.bel_en_statement_nested = 1;
16941
+ self.bel_en_nested_statement = 1;
16942
16942
 
16943
16943
 
16944
16944
  # end: ragel
@@ -17086,7 +17086,7 @@ begin
17086
17086
  begin
17087
17087
 
17088
17088
  @buffers[:comment] ||= comment(nil)
17089
- yield statement_simple(
17089
+ yield simple_statement(
17090
17090
  statement(
17091
17091
  @buffers[:subject],
17092
17092
  @buffers[:relationship],
@@ -17311,7 +17311,7 @@ begin
17311
17311
  begin
17312
17312
 
17313
17313
  @buffers[:comment] ||= comment(nil)
17314
- yield statement_simple(
17314
+ yield simple_statement(
17315
17315
  statement(
17316
17316
  @buffers[:subject],
17317
17317
  @buffers[:relationship],
@@ -17349,7 +17349,7 @@ begin
17349
17349
  begin
17350
17350
 
17351
17351
  @buffers[:comment] ||= comment(nil)
17352
- yield statement_simple(
17352
+ yield simple_statement(
17353
17353
  statement(
17354
17354
  @buffers[:subject],
17355
17355
  @buffers[:relationship],
@@ -17792,7 +17792,7 @@ end
17792
17792
 
17793
17793
  if __FILE__ == $0
17794
17794
  $stdin.each_line do |line|
17795
- BELParser::Parsers::Expression::StatementNested.parse(line) { |obj|
17795
+ BELParser::Parsers::Expression::NestedStatement.parse(line) { |obj|
17796
17796
  puts obj.inspect
17797
17797
  }
17798
17798
  end
@@ -3,7 +3,7 @@
3
3
  %%{
4
4
  machine bel;
5
5
 
6
- include 'statement_simple.rl';
6
+ include 'simple_statement.rl';
7
7
 
8
8
  action statement_init {
9
9
  @buffers[:statement_stack] = [ statement() ]
@@ -40,7 +40,7 @@
40
40
  fret;
41
41
  }
42
42
 
43
- action yield_statement_nested {
43
+ action yield_nested_statement {
44
44
  yield nested_statement(@buffers[:statement_stack][-1])
45
45
  }
46
46
 
@@ -64,10 +64,10 @@
64
64
  # ')' @ast_object
65
65
  ;
66
66
 
67
- statement_nested :=
67
+ nested_statement :=
68
68
  outer_statement
69
69
  SP*
70
- COMMENT? %yield_statement_nested
70
+ COMMENT? %yield_nested_statement
71
71
  NL;
72
72
  }%%
73
73
  =end
@@ -80,7 +80,7 @@ require_relative '../nonblocking_io_wrapper'
80
80
  module BELParser
81
81
  module Parsers
82
82
  module Expression
83
- module StatementNested
83
+ module NestedStatement
84
84
 
85
85
  class << self
86
86
 
@@ -131,7 +131,7 @@ end
131
131
 
132
132
  if __FILE__ == $0
133
133
  $stdin.each_line do |line|
134
- BELParser::Parsers::Expression::StatementNested.parse(line) { |obj|
134
+ BELParser::Parsers::Expression::NestedStatement.parse(line) { |obj|
135
135
  puts obj.inspect
136
136
  }
137
137
  end
@@ -647,9 +647,9 @@ class << self
647
647
  end
648
648
  self.bel_en_comment = 58;
649
649
  class << self
650
- attr_accessor :bel_en_statement_observed_term
650
+ attr_accessor :bel_en_observed_term
651
651
  end
652
- self.bel_en_statement_observed_term = 1;
652
+ self.bel_en_observed_term = 1;
653
653
 
654
654
 
655
655
  begin
@@ -1850,9 +1850,9 @@ class << self
1850
1850
  end
1851
1851
  self.bel_en_comment = 58;
1852
1852
  class << self
1853
- attr_accessor :bel_en_statement_observed_term
1853
+ attr_accessor :bel_en_observed_term
1854
1854
  end
1855
- self.bel_en_statement_observed_term = 1;
1855
+ self.bel_en_observed_term = 1;
1856
1856
 
1857
1857
 
1858
1858
  begin
@@ -3053,9 +3053,9 @@ class << self
3053
3053
  end
3054
3054
  self.bel_en_comment = 58;
3055
3055
  class << self
3056
- attr_accessor :bel_en_statement_observed_term
3056
+ attr_accessor :bel_en_observed_term
3057
3057
  end
3058
- self.bel_en_statement_observed_term = 1;
3058
+ self.bel_en_observed_term = 1;
3059
3059
 
3060
3060
 
3061
3061
  begin
@@ -4256,9 +4256,9 @@ class << self
4256
4256
  end
4257
4257
  self.bel_en_comment = 58;
4258
4258
  class << self
4259
- attr_accessor :bel_en_statement_observed_term
4259
+ attr_accessor :bel_en_observed_term
4260
4260
  end
4261
- self.bel_en_statement_observed_term = 1;
4261
+ self.bel_en_observed_term = 1;
4262
4262
 
4263
4263
 
4264
4264
  begin
@@ -5459,9 +5459,9 @@ class << self
5459
5459
  end
5460
5460
  self.bel_en_comment = 58;
5461
5461
  class << self
5462
- attr_accessor :bel_en_statement_observed_term
5462
+ attr_accessor :bel_en_observed_term
5463
5463
  end
5464
- self.bel_en_statement_observed_term = 1;
5464
+ self.bel_en_observed_term = 1;
5465
5465
 
5466
5466
 
5467
5467
  begin
@@ -6028,7 +6028,7 @@ require_relative '../nonblocking_io_wrapper'
6028
6028
  module BELParser
6029
6029
  module Parsers
6030
6030
  module Expression
6031
- module StatementObservedTerm
6031
+ module ObservedTerm
6032
6032
 
6033
6033
  class << self
6034
6034
 
@@ -6699,9 +6699,9 @@ class << self
6699
6699
  end
6700
6700
  self.bel_en_comment = 58;
6701
6701
  class << self
6702
- attr_accessor :bel_en_statement_observed_term
6702
+ attr_accessor :bel_en_observed_term
6703
6703
  end
6704
- self.bel_en_statement_observed_term = 1;
6704
+ self.bel_en_observed_term = 1;
6705
6705
 
6706
6706
 
6707
6707
  # end: ragel
@@ -7281,7 +7281,7 @@ end
7281
7281
 
7282
7282
  if __FILE__ == $0
7283
7283
  $stdin.each_line do |line|
7284
- BELParser::Parsers::Expression::StatementObservedTerm.parse(line) { |obj|
7284
+ BELParser::Parsers::Expression::ObservedTerm.parse(line) { |obj|
7285
7285
  puts obj.inspect
7286
7286
  }
7287
7287
  end
@@ -6,7 +6,7 @@
6
6
  include 'term.rl';
7
7
  include 'comment.rl';
8
8
 
9
- action yield_statement_observed_term {
9
+ action yield_observed_term {
10
10
  @buffers[:comment] ||= comment(nil)
11
11
  yield observed_term(
12
12
  statement(
@@ -16,10 +16,10 @@
16
16
  @buffers[:comment]))
17
17
  }
18
18
 
19
- statement_observed_term :=
19
+ observed_term :=
20
20
  outer_term
21
21
  SP*
22
- COMMENT? %yield_statement_observed_term
22
+ COMMENT? %yield_observed_term
23
23
  NL;
24
24
  }%%
25
25
  =end
@@ -32,7 +32,7 @@ require_relative '../nonblocking_io_wrapper'
32
32
  module BELParser
33
33
  module Parsers
34
34
  module Expression
35
- module StatementObservedTerm
35
+ module ObservedTerm
36
36
 
37
37
  class << self
38
38
 
@@ -82,7 +82,7 @@ end
82
82
 
83
83
  if __FILE__ == $0
84
84
  $stdin.each_line do |line|
85
- BELParser::Parsers::Expression::StatementObservedTerm.parse(line) { |obj|
85
+ BELParser::Parsers::Expression::ObservedTerm.parse(line) { |obj|
86
86
  puts obj.inspect
87
87
  }
88
88
  end