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
@@ -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